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US20060088871A1 - Dynamic genomic deletion expansion and formulation of molecular marker panels for integrated molecular pathology diagnosis and characterization of tissue, cellular fluid, and pure fluid specimens - Google Patents

Dynamic genomic deletion expansion and formulation of molecular marker panels for integrated molecular pathology diagnosis and characterization of tissue, cellular fluid, and pure fluid specimens Download PDF

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US20060088871A1
US20060088871A1 US11/256,152 US25615205A US2006088871A1 US 20060088871 A1 US20060088871 A1 US 20060088871A1 US 25615205 A US25615205 A US 25615205A US 2006088871 A1 US2006088871 A1 US 2006088871A1
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dna
tumor
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Sydney Finkelstein
Patricia Swalsky
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
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Definitions

  • the application relates to methods, materials, kits and devices for achieving a diagnosis, prognosis, and/or determination of the biological aggressiveness of a tumor based on the temporal profile (time course) of genomic deletion expansion.
  • the materials, methods, kits and devices disclosed herein can also be used for pre-cancerous growths and diagnosis and prognosis of non-malignant tissues and cells.
  • Cancer is characterized by the stepwise accumulation of genetic damage.
  • Such genetic damage includes mutations and aberrant expression of oncogenes and tumor suppressor genes that are causally related to phenotypic expression of malignant characteristics such as rapid uncontrolled growth, local invasion, and metastasis (Weir et al., 2004 Cancer Cell. 6(5): 433-8; and Osborne et al., 2004 Oncologist 9(4): 361-77).
  • individual mutations are acquired by affected cells, clonal expansion of biologically more aggressive tumor cells ensues (Braakhuis et al., 2005 Semin. Cancer Biol. 15(2): 113-20; Breivik et al., 2005 Semin Cancer Biol. 15(1): 51-60).
  • cancer cells with increasing mutational change come to replace precursor cells with fewer mutations, which is the driving force for clonal expansion.
  • the process is dynamic one occurring across the entire tumor, with the creation of distinct tumor cell clones in topographic regions that undergo neoplastic progression at different rates. To a large extent, the process is irreversible, with the most biologically aggressive cellular elements of a particular cancer overgrowing the relatively less aggressive cellular components.
  • the majority of human cancers are eventually dominated by clonal expanding malignant cells possessing specific, detectable mutational alterations directly responsible for tumor growth and biological behavior.
  • genomic deletion (Bishop A J, et al., 2003 Exp. Mol. Pathol. 74(2): 94-105;ffy, 2003 Cancer Lett. 192(1): 1-17).
  • This form of damage is commonly associated with tumor suppressor gene inactivation which follows a two-step process (Baker et al., 2003 Genes Chromosomes Cancer. 38(4): 329 and Knudson, 2001 Lancet Oncol. 2(10): 642-5).
  • First, one normal copy of the tumor suppressor is inactivated, typically by means of point mutational damage.
  • the second step is genomic deletion of the remaining normal copy, often with adjacent non-coding DNA being included in the deletional region (Baker et al., 2003 and Knudson, 2001).
  • a primary objective in the management of cancer is predicting the intrinsic biological aggressiveness of an individual neoplasm, so that it may be treated in an appropriate manner. Cancers that are intrinsically indolent should be treated in a conservative manner to avoid the unnecessary morbidity associated with the side effects of therapy. In contrast, cancers that can be predicted to behave in a more aggressive fashion justifiably demand a more aggressive therapy to avoid under the under-treatment of the patient. Thus, it is essential to effectively prognosticate the biological aggressiveness of each cancer on an individual patient basis.
  • the prediction of cancer aggressiveness involves searching for specific microscopic features such as high mitotic rate, cellular anaplasia, nuclear pleomorphism, etc.
  • Conventional teaching does not require that the prediction of cancer aggressive require criteria other than those encompassed by microscopic observation. At the extremes (i.e. near normal cellular appearance with no evidence of high mitotic rate, cellular anaplasia, nuclear pleomorphism versus extensive high mitotic rate, cellular anaplasia, nuclear pleomorphism), these criteria are generally reliable.
  • the majority of clinical cases fall in between the polar ends of this spectrum with some but not all microscopic features of biological aggressiveness present. Under these circumstances, the prediction of tumor biological aggressiveness cannot be carried out microscopically with certainty.
  • the use of additional technique to derive correlative mutational information can serve as a powerful means to add discriminating information leading to greater certainty.
  • compositions, kits, and devices for assessing dynamic genomic deletional expansion that can be determined using small amounts of tissue, fixative-treated tissue, cellular specimens, and/or fluid specimens that directly and effectively prognosticate cancer biological aggressiveness and combinations thereof.
  • This observation has heretofore not been described, yet its application in everyday clinical practice can be highly effective and easy to perform.
  • the result is a new modality with which to characterize a tumor in a patient on an individual basis.
  • the patient is preferably human, such diagnosis can also be performed on other animals for veterinary diagnosis. It may be expected to have profound consequences for future diagnosis of cancer and pre-cancer states and, by consequence, therapeutic management.
  • the materials, methods, and kits provided herein can be utilized to diagnose and characterize the biological aggressiveness of a tissue or cells, such as a neoplastic tissue, thereby improving patient diagnosis and treatment of the patient with the tissue abnormality.
  • a method of determining tumor aggressiveness in a patient comprising the steps of: (a) amplifying DNA from a microdissection section of the biological sample; (b) analyzing two or more genes for the presence of a nucleotide deletion wherein a deletion is the acquisition of genetic mutation; (c) analyzing each gene with an array of markers to determine the extent of nucleotide deletion; (d) determining the order of acquisition of each nucleotide deletion in the patient; and (e) collating the data from steps (a) to (d) to determine tumor aggressiveness of the patient.
  • the reagents used to amplify DNA from the biological sample of the patient when admixed for amplification, comprises about 1 to about 15 mM magnesium chloride (other valency ions such as manganese can be substituted in the form of MnCl 2 ), more preferably from about 6.0 to about 10.0 mM (and every 0.1 mM value in between), and most preferably about 8.0 mM magnesium chloride.
  • the solution preferably also comprises when admixed about 5 to about 20 g/100 mL sucrose (and any 0.1 g/100 mL value there between), more preferably the solution contains about 12.0 g/100 mL sucrose.
  • the biological sample can be pretreated with a proteinase from about 2 hours to overnight.
  • the proteinase treatment occurs at about 37° C. and halted by boiling the sample for about 5 minutes.
  • Suitable proteinases include but are not limited to proteinase K, pronase, subtilisin, thermolysin, papain, or a combination of proteinases. Proteinases are present in an amount of about 0.5% to about 2.0% final volume of lysis buffer (and every 0.1% value there between), and preferably about 1.0%.
  • the lysis buffer further includes a nonionic detergent.
  • Nonionic detergents can include but are not limited to nonidet P40, Tween (e.g., Tween 20), Triton X, or Nikkol. The nonionic detergents are present in the amount of about 0.5% to about 2.0% (and any 0.1% value in between).
  • the biological sample may be a cell-free fluid sample, a blood sample, a cytology sample, a urine sample, a tissue swab, or resected tissue.
  • the cell-free fluid sample contains non-nuclear DNA.
  • the resected tissue may be frozen, fresh, stained, or fixative-treated, or a combination thereof. More than one type of biological sample can be utilized for each patient. For example, a fluid sample and a resected tissue sample can be analyzed and the data from each combined. Additionally, biological samples can be derived from more than one point of origin in a patient.
  • a biological sample can be obtained from a putative primary tumor as well as a biological sample from a putative second unrelated tumor or from a putative metastatic lesion, or combination thereof.
  • samples of each nodule may be analyzed alone or the data combined.
  • Step (c) of the method may be repeated to obtain replicate data.
  • the method may further comprise the step of identifying a treatment plan to treat the tumor of said patient which best treats the tumor based on the determination of tumor aggression.
  • the biological sample may be microdissected tissue, and the steps of (b) and/or (c) may be performed on DNA obtained from two or more microdissected sections of the tissue sample. Step (c) may be repeated to obtain replicate data.
  • the patient may also have a fluid sample, and the fluid sample may undergo analysis comprising: (a) amplifying DNA from the fluid sample of the patient; (b) analyzing two or more genes for the presence of nucleotide deletion from the amplified DNA; (c) analyzing each nucleotide deletion with an array of markers to determine the extent of nucleotide deletion; (d) determining the order of acquisition of each nucleotide deletion in the patient; and (e) validating the collated data with the data from the fluid sample. Markers can be used to determine whether the mutation was environmentally induced, such as by exposure to trichloroethylene or other chemical, a germ line mutation, or a spontaneous mutation.
  • kits for determining tumor aggressiveness comprising (i) a device for amplifying DNA; and (ii) sets of cancer specific markers for assessing nucleotide deletion and extent of nucleotide deletion.
  • the markers can include markers for environmentally-induced mutations, spontaneous mutations, and/or germ line mutations.
  • the kit may also provide for reagents for amplifying DNA as discussed above.
  • the device for amplifying and determining genomic deletion may also comprise a data storage component for storing patient information regarding sex, age, weight, medical history, family medical history, prior cancer history and genetic analysis of a prior cancer, and genomic deletion acquisition data. This information may further be stored in a relational database, wherein factors are weighted in order to best determine treatment strategy.
  • Another aspect provided is a method of creating a panel of molecular markers for detecting a condition in a patient comprising the steps of: (a) determining gene targets for detection of a mutation to include in a molecular marker analysis for a marker panel; (b) delineating genomic regions for each gene target; (c) identifying a 4 to 1500 nucleotide repeat microsatellite and/or a minisatellite in the genomic region that will constitute the marker panel; (d) identifying at least two 4 to 1500 nucleotide microsatellites and/or minisatellites positioned a certain distance from each other and performing genomic deletional expansion; (e) determining the amount of DNA in the biological sample; (f) determining the quality of DNA in the biological sample by quantitative PCR; (g) determining the quality of DNA in the biological sample by means on competitive template PCR (CT-PCR); (h) determining the amplifiability of DNA for each 4 to 1500 repeat microsatellite and/or minisatellite; (i
  • markers or marker panels identified by the above method are also contemplated.
  • FIG. 1 Phenomena of Genomic Deletion Expansion.
  • FIG. 1 depicts a representative ideogram of one of two copies of a chromosome (chromosome 1). The arrow demarcates the position of a tumor suppressor gene on the chromosome.
  • the second normal copy of the gene is deleted leading to clonal expansion of phenotypically more aggressive cancer cells. Over time and through successive replications of the tumor cells, the deleted region undergoes progressive expansion of the deleted region (left to right). The rate of this expansion is proportional to the tumor's biological aggressiveness.
  • the two ends of the deletion regions are attached resulting in an intact chromosome that lacks an expanding segment of its genome.
  • FIG. 2 Determination of the Timeline of Mutation Acquisition.
  • Timeline determination of the temporal sequence of acquired mutations occurs in two independent ways both reliant upon the fundamental concept of clonal expansion. The first is to compare the presence or absence of mutations at topographically separate locations within a tumor. Mutations that are present over a wider topographic distribution were acquired earlier in time those mutations that are focally distributed occurred later in time. The second is to measure the proportion of tumor cells bearing specific mutations. Mutations present in a high proportion of tumor cells occurred earlier in temporal sequence that other mutations affecting a smaller percentage of tumor cells at a specific location.
  • FIG. 3 Quality Control Analytic Validation. Quality control measures to monitor analytic precision are presented in this schematic. Analytic validation operates at two levels. The first is with respect to the sample which is replicated in a fashion leading that allows a determination of variation between separate samples. The second operates at the individual marker level with replication allowing a determination of the variation for specific markers within individual samples. The variability between individual results that are replicated can be used as a means to understand the significance of results.
  • FIG. 4 Electropherograms depicting an example of marker replication. In this replicate analysis for two different markers, the ratio of the allele peak heights is very similar providing validation of the analytical precision of the technique.
  • the x-axis reflects the base pair length of the amplicon, and the y-axis is the relative fluorescence units detected.
  • FIG. 5 Allelic imbalance due to inadequate amounts of amplifiable DNA producing false-positive imbalance is depicted.
  • Allelic dropout the ratio of the allele peak heights is highly variable, yet these are replicate analysis of the identical specific marker from the identical specific microdissected specimen or source of DNA. Quality control measures are essential to guard against the occurrence of allelic dropout that will result in false positive results.
  • the x-axis reflects the base pair length of the amplicon, and the y-axis is the relative fluorescence units detected.
  • FIG. 6 Procedure for comparative analysis of tumor-specific mutational profiles, as performed on tissue samples from esophagus and lung.
  • FIG. 7 Tumor-specific mutational profiling, as performed on tissue, from right upper lobe and right lower lobe of lung from the same patient.
  • FIG. 8 Tumor-specific mutational profiling, as performed on tissue from patient with squamous cell carcinoma of the tongue and gingival cancer.
  • FIG. 9 Tumor-specific mutational profiling, as performed on liver tissue from two different patients with cirrhosis.
  • FIG. 10 Tumor-specific mutational profiling, as performed on renal tissue and lip tissue from the same patient.
  • FIG. 11 Summary of mutational profiling for discrimination of cancer recurrence versus new primary cancer formation, as performed on samples from 278 patients.
  • FIG. 12 Bar graphs illustrating discordance, showing tumor recurrent and concordance, showing new primary cancers.
  • FIG. 13 Summary of results, showing 100% definitive diagnosis using mutational marker panels.
  • FIG. 14 Stutter band analysis using tetranucleotide or greater microsatellites as polymorphic markers. Use of a dinucleotide renders a series of shorter stutter band peaks, which reduces the exactness of quantitative determination of the amount of fluorescence for the true PCR product.
  • FIG. 15 Temporal sequence analysis of acquired mutational damage as used to create a molecular classification of gliomas.
  • FIG. 16 Endoscopic ultrasound images of a pancreatic cancer (left panels) and molecular analysis of the biological sample obtained by fine need aspiration.
  • FIG. 17 Microdissection of the biopsy fragments of duodenal mucosa showing adenomatous change (upper left panels).
  • the biopsied fragments were paraffin-embedded, fixative treated biopsy samples, which were analyzed for a molecular analysis (lower left panel).
  • the markers constituting the panel used to search for evidence for or against the APC gene germ line mutation are shown.
  • the marker panel consists of three intragenic single nucleotide polymorphisms (SNPs) in exons 10, 15, and the 3′ non-translated region of the APC gene.
  • the marker panel also includes three tetranucleotide or large microsatellites situated in proximity, but outside the APC gene.
  • the top right panel shows a representative example of one of the tetranucleotide microsatellites (i.e., D5S592), which shows a concordant pattern of allelic loss in two separate sites of neoplasia formation in this patient.
  • all the tumor deposits showed the same concordant microsatellite band loss, which supports a germ line mutation in the APC gene.
  • the x-axis reflects the base pair length of the amplicon, and the y-axis is the relative fluorescence units detected.
  • the normal samples show that the two polymorphic bases are of equal intensity, while the two tumor samples show a relative loss of the thymidine bearing allele.
  • FIG. 18 Dysplasia of the esophagus of a patient is shown in the left panel. The molecular analysis of the patient is shown in the right hand panel.
  • Novel methods, reagents, kits, and devices that improve the analysis of microdissected tissue, microdissected cytology, and fluid specimens are presented herein.
  • the methods can be applied to DNA extracted from any source, including fresh specimens.
  • the methods are especially well suited for those types of small biopsies and minute specimens encountered in clinical practice. Described herein are more effective means of predicting tumor biological aggressiveness, which is essential to planning appropriate therapy.
  • the methods and devices herein can be used on fresh specimens (e.g., biopsied tissue and frozen sections) as well as on minute, fixative-treated, and/or stained specimens.
  • the aspects described allow molecular pathologic examination of fixative-treated or fresh tissue specimens (or frozen), stained or unstained cytology preparations, and cell-free fluid samples obtained from biopsy and/or needle aspiration of solid tissue or fluid specimens. These biological samples can be very small in size (i.e., measuring less than about 1 mm in greatest dimension for resected tissue).
  • the methods advance the sensitivity and specificity of prediction of the biological aggressiveness of a tumor that currently is based on specific microscopic and selected molecular features.
  • the methods can be combined with existing pathology practice to provide a more detailed view of a particular patient's condition.
  • the methods also describe characterization of a new parameter, dynamic genomic deletional expansion. This parameter is specifically designed to be highly integrated with microscopic analysis.
  • the analytical platform includes:
  • a preferred analytical platform is designed to correlate with and significantly improve histopathologic and cytologic observation, thereby complementing and improving existing pathology practice.
  • qPCR quantitative polymerase chain reaction
  • tumor suppressor genes most often undergo a two-step process of gene inactivation (Baker et al., 2003 and Knudson, 2001).
  • the first step is often point mutational damage in a critical region of a gene leading to activation or inactivation of that copy.
  • the second step is the loss of the second “normal” copy of the gene. This can occur by an interstitial genomic deletion encompassing part or all of the gene and the adjacent non-coding DNA (Baker et al., 2003 and Knudson, 2001).
  • the materials and methods described herein assist to characterize this process.
  • the genomic interstitial deletion can be a dynamic process that progresses leading to a greater widening of the deleted genomic segment.
  • the deletion can undergo further expansion over time in cells clonally derived from precursor tumor cells.
  • the pattern and rate of the expansion provides highly useful information with which to characterize a particular neoplasm. Given the reality of clinical practice that one can only look at a subset of the entire set of accumulated mutational change, it becomes highly efficient to more carefully examine the individual detectable deletions rather than attempt to seek new mutational damage in order to better predict tumor biological aggressiveness.
  • Materials and methods are provide in order to formulate panels of markers based on tetranucleotide (or pentanucleotide, hexanucleotide or greater in length of repeat nucleic acid sequences including minisatellite) repeats targeting genomic regions associated with, but not necessarily associated with, the location of common tumor suppressor genes and not strictly limited to any particular gene. These repeated domains can be any length from 4 nucleotides to 50 nucleotides (and any integer value in between). Methods describe how markers are to be paired for each genomic region but separated by distance to each other in order to provide information concerning the directionality of deletion expansion (genomic deletion expansion).
  • instructions are provided whereby normal samples are carefully analyzed in sufficient number to enable a thorough understanding of their behavior under conditions of lower amounts of DNA quantity and under conditions when the DNA is degraded.
  • Methods such as comparative template polymerase chain reaction (CT-PCT) and evaluation of fluorescence generation (or other detectable means) are used to quantify marker function under these conditions.
  • CT-PCT comparative template polymerase chain reaction
  • fluorescence generation or other detectable means
  • patient is meant to include any mammal including, but not limited to, bovines, primates, equines, porcines, caprines, ovines, felines, canines, and any rodent (e.g., rats, mice, hamsters, and guinea pigs).
  • a preferred primate is a human. Patients thus can include agricultural animals and domesticated animals under veterinary care.
  • the genes provided herein are generally referring to the human gene or disease, it is evident that this can be applied to the cognate animal gene or cognate animal disease.
  • tissue is meant to include resected tissue (fixed, stained, or treated), cytology specimens, blood and blood fractions from a patient or from a tissue bank.
  • biological sample is meant to include “tissue” and “cells” as well as “fluid samples” which contains free floating DNA. Free floating DNA is non-nuclear DNA that is in fluid or that adheres to the walls of cells or cysts.
  • the biological samples can be any sample containing DNA or cells from a patient.
  • Such samples include but are not limited to fine needle aspirates, a cytology sample, a blood sample, a spinal tap, resected tissue, frozen tissue, blood sample, fixed tissue, a urine sample, a tissue swab (e.g., buccal swab or pap smear), and the like.
  • genomic deletional expansion is meant a defined region of the chromosome often containing all or part of a known or putative tumor suppressor gene that undergoes deletion during cancer development and progression. Expansion pertains to the progressive enlargement of the deletional segments of gene during progressive cycles of tumor cell replication. While this definition applies to tumor suppressor genes it may also apply to other genes that function to control cell growth and/or which have not as yet been formally recognized as tumor suppressor genes.
  • genomic amplification expansion is meant a defined region of a chromosome which contains a gene that undergoes amplification of a segment of the gene during cancer development and/or progression.
  • Her2/neu is a gene wherein a segment of the genome containing the gene is amplified during breast cancer.
  • tumor is meant to include any malignant or non-malignant tissue or cellular containing material or cells.
  • non-malignant tissue is meant to include any abnormal tissue or cell phenotype and/or genotype associated with metaplasia, hyperplasia, a polyp, or pre-cancerous conditions (e.g., leukoplakia, colon polyps), regenerative change, physiologic adaption to stress or injury and cellular change in response to stress of injury.
  • Tumor is meant to include both solid tumors as well as leukemias and lymphomas. “Neoplasm”, “malignancy”, and “cancer” are used interchangeably.
  • tumor aggressiveness or “tumor aggression” is meant the phenotypic expression of a malignancy that is associated with increased adverse biological behavior. This includes phenomenon such as capacity for early metastatic seeding, capacity for wide visceral organ dissemination, rapid growth and invasion, lack of treatment responsiveness, short treated disease free interval and short overall patient survival.
  • genetic acquisition due to familial inheritance is meant a genomic deletion that is part of the patient's germ line. Such mutations occur in all the cells and are not caused by environmental factors nor do they arise spontaneously.
  • genetic acquisition due to an environmental factor is meant exposure to a carcinogen or mutagen which causes a change in the patient's genome. This can be caused by viruses, food-borne carcinogens, exposure to chemicals (e.g., occupational hazards), or unknown environmental agents.
  • Environmental factors can include but are not limited to trichloroethylene, tobacco smoke (tobacco use or as second hand smoke), arsenic, asbestos, crystalline silica, benzenes, penzo[a]pyrene, beryllium, bis(chloro)methyl ether, 1,3-butadiene, chromium V1 compounds, coal tar, pitch, nickel compounds, soots, mustard gas, erionite, nickel compounds, heterocyclic amines, aflatoxin, vinyl chloride, thorium dioxide, phenacetin, 4-aminobiophenyl, benzidine, 2-naphthylamine, phenacetin, cadmium, cyclosporine A, ethylene oxide, N-nitroso compounds, nitric oxide, antineoplastic agents, and compounds that cause free oxygen radicals.
  • RNA viruses e.g., retroviruses such as human T-lymphotropic virus type 1 and type 2, human immunodeficiency virus, and hepatitis C virus
  • DNA viruses such as hepadnaviruses, papillomaviruses, Epstein-Barr virus, Kaposi's sarcoma-associated herpesvirus, simian vacuolating virus 40 and other polyomaviruses.
  • Environmental factors can also include treatment for cancer by radiation or chemotherapy. Radiation exposure is also meant to be included in environmental factors, such as that which is an occupational hazard, sun exposure, and the like.
  • spontaneous mutation is meant a mutation that occurs during the development of a cancer or a growth that is progressing towards cancer that is not a germ-line mutation. Such mutations can include environmentally induced mutations.
  • the malignancies and precancerous conditions that can be diagnosed using the materials and methods described herein include solid tumors as well as leukemias and lymphomas.
  • the cancers include but are not limited to cancers of the head and neck (e.g., nasal cavity, paranasal sinuses, nasopharynx, oral cavity, oropharynx, larynx, hypopharynx, salivary glands, and paragangliomas), lung tumors (e.g., non-small cell and small cell lung tumors), neoplasms of the mediastinum, cancers of the gastrointestinal tract (e.g., colon, esophageal carinoma, pancreatic carcinoma, gastric carcinoma hepatobiliary cancers, cancers of the small intestine, cancer of the rectum, and cancer of the anal region), genitourinary cancers (e.g., kidney cancer, bladder cancer, prostate cancer, cancers of the urethra and penis, and cancer of
  • cancer or neoplasm is also meant to include metastatic disease and reoccurrence or relapse of a cancer(s).
  • virally induced neoplasms such as adenovirus, HIV-1, or human papilloma virus induced neoplasms such as cervical cancer and Kaposi's sarcoma, and primary CNS lymphoma.
  • Conditions that create a germline deletion alteration can be included as having the capacity for dynamic genomic deletion expansion. This would encompass inherited genetic alterations, translocations and inherited or somatically acquired DNA damage.
  • Lymphomas include but are not limited to Hodgkin's lymphoma, non-Hodgkin's lymphoma (B-cell non-Hodgkin's lymphoma and T-cell non-Hodgkin's lymphoma), cutaneous T-cell lymphomas (CTCL), lymphoplasmacytoid lymphoma (LPL), mantle cell lymphoma (MCL), follicular lymphoma (FL), diffuse large cell lymphoma (DLCL), Burkitt's lymphoma (BL), Lennert's lymphoma (lymphoepithelioid lymphoma), Sezary syndrome, anaplastic large cell lymphoma (ALCL), and primary central nervous system lymphomas.
  • CTCL cutaneous T-cell lymphomas
  • LPL lymphoplasmacytoid lymphoma
  • MCL mantle cell lymphoma
  • FL follicular lymphoma
  • DLCL diffuse large cell lymphoma
  • Leukemias include chronic myelogenous leukemia (CML), acute myelogenous leukemia (AML), acute promyelocytic leukemia, acute lymphoblastic leukemia (ALL), prolymphocytic leukemia, hairy cell leukemia, T-cell chronic lymphocytic leukemia, plasma cell neoplasms, chronic lymphocytic leukemia (CLL), and myelodysplastic syndromes (e.g., chronic myelomonocytic leukemia).
  • Preferred cancers are those that can be readily screened or found either by visual inspection of the patient's skin (skin cancer), mammography (biopsy of lumps), gynecologic cancers (PAP smears and gynecologic examination), or colorectal examination (identification and removal of polyps).
  • skin cancer skin cancer
  • mammography biopsy of lumps
  • gynecologic cancers PAP smears and gynecologic examination
  • colorectal examination identification and removal of polyps.
  • the methods and materials provided herein can also be used on tissue samples that have been surgically resected from the patient (resected bowel, removed lung and liver, or other organs).
  • the methods and materials described herein can also be utilized in diagnosing non-malignant conditions and rendering a diagnosis of cancer from cell aspirates.
  • the methods described herein are those needed to perform the analysis that will culminate in a more accurate assessment of tumor biological aggressiveness. These methods can be performed on any tissue sample, i.e., resected tissue, drawn blood, cytologic specimen, or fluid specimen (e.g., fluid from a cyst). While there are overall common considerations for all these types of specimens, in fact the specific performance of the analysis will differ. These differences will be described in a subsection for each type of specimen. Preferably, these methods can be used on a combination of specimens such that the data from each specimen can be collated for further validation of the diagnosis and prognosis achieved by the genetic determination. Additionally, if using a microdissected sample, multiple microdissection representing different sections of tumor from the tissue block can be used as controls, and as validation of tumor aggressiveness.
  • tissue sample i.e., resected tissue, drawn blood, cytologic specimen, or fluid specimen (e.g., fluid from a cyst). While there are overall common considerations for all these types of specimens,
  • the specimen source be it tissue sections, cytology preparation, and/or fluid containing DNA
  • the specimen source is treated in such a fashion that DNA becomes available for nucleic acid amplification. This can involve extraction of DNA or treatment of a rude lysate in such as manner as to render the DNA accessible for amplification. This will vary according to the specimen's type and is described below. Any system that renders DNA into a state suitable for nucleic acid amplification will prove sufficient. Those techniques that accomplish this with minimal effort and rapid time, in general, will be preferred. For example, DNA can be analyzed directly using the technique of Topographic Genotyping, which is designed for clinical use with fixative treated, stained cellular specimens. See U.S. Pat. No. 6,340,563 which is incorporated by reference herein in its entirety for all purposes.
  • the extracted pure DNA or the crude lysate DNA is treated proteinase K at a concentration of 10 mg/mL at 37° C. for 2 hours.
  • the aliquot of sample containing DNA is added to PCR reaction mixture containing Taq polymerase (or suitable substitute enzyme), deoxyribonucleotides and buffer.
  • Taq polymerase or suitable substitute enzyme
  • deoxyribonucleotides and buffer.
  • additional magnesium chloride to a level of 5 mM and sucrose to a concentration of 30%.
  • Oligonucleotide primers are used in nucleic acid amplification reactions to generate DNA from polymorphic regions of the genomes in proximity to sites of potential deletion. If the sites of deletion are unknown, a broad panel of amplification reactions can be used to search for the existence of such deletion.
  • a useful approach in this regard is to target tumor supporessor genes that have been shown to be associated with deletion in neoplastic lesions of the type being evaluated. Other approaches are not excluded such as the used of random markers to detected unexpected sites of genomic deletion.
  • Genomic sites of deletion may already be shown to exist in which case the analysis can focus on these regions.
  • a site of genomic deletion can be identified using a variety of methods, such as fluorescent in-situ hybridization with suitable molecular probes or comparative genomic hybridization. Other techniques can also be used such as classical cytogenetic analysis of viable tumor cells. With the site of deletion known, one can consult any one of a large number of public or private molecular biology databases that describe the presence of polymorphic DNA markers for specific genomic regions. A series of such markers can then be used to evaluate the extent of genomic deletion at two or more sites within a given neoplasm.
  • microdissection targets are selected on the basis of correlative microscopic features. Serial unstained standard four micron thick histologic recut sections are prepared along with a stained slide for determination of precise tissue targets. The tissue blocks that are selected for sectioning are those that contain the most representative tissue targets for microdissection based analysis. The size and configuration of each microdissection target is guided by histopathologic features to provide maximum representativeness and purity of cellular constituents.
  • Each microdissection target is manually removed using a pointed scalpel under stereomicroscopic observation.
  • tissue target removal such as equipment assisted tissue sampling (i.e., laser capture microdissection and other methods) or manual tissue removal can be substituted with varying degrees of effectiveness.
  • microdissected tissue is placed into a tube containing 25 microliters of lysis buffer composed of 1% NP-40 in dilute, 10 mM Tris, pH 7. After treatment with proteinase K as describe above, the sample is pelleted at 10,000 rpm in a table top centrifuge. The aliquot for nucleic acid amplification is taken from just above the pellet.
  • the methodology is very similar to that described for tissues. Instead of unstained slides as is used for tissue sections, the pap smear stained cytology smear of liquid cytology slide is used for microdissection. Prior to removing the coverslip by immersion in xylene or other solvent, the precise cellular collections are marked with ink on the reverse surface of the glass slides. This will enable the targets of cells to be identified after the coverslip has been removed in order to allow access to the cells of interest.
  • the cells are removed by manual microdissection in exactly the same manner as for tissue sections.
  • the microdissected cells are then placed into tubes and prepared as for tissue microdissection.
  • the amount of cytology microdissection should be large enough to produce a pellet after centrifugation that is barely visible in size by naked eye examination.
  • Fluid specimens undergo direct DNA extraction by filter collection or other suitable isolation methodology such as DNA precipitation, glass bead separation or other technique.
  • the collected DNA is resuspending in a small volume after which it may be quantified by optical density measurement.
  • the DNA is now ready for nucleic acid amplification.
  • Nonfixed tissue specimens could exist in several forms.
  • One common form is that of frozen sections of fresh tissue which are handled in an identical fashion to that for fixed tissue sections.
  • Another form is that of pieces of fresh/frozen tissue that require mincing followed by homogenization in order to render the DNA amenable to further isolation. Any standard protocol to extract DNA from a tissue specimen would be suitable.
  • a series of polymorphic markers are selected which may be in the form of microsatellites or single nucleotide polymorphisms or any other polymorphism that enables the status of each individual allele of genomic DNA to be selectively recognized.
  • the concept here is to utilize a series of genomic markers that vary in their specific localization at a gene or genomic site of deletion. The presence of absence of the amount of each polymorphic marker will be used to define the length of genomic deletion. The more serially placed markers the show loss, the greater in length will be the linear length of the genomic deletion.
  • markers are designed to cover the location of the deletion and adjacent DNA both on the centromeric and telomeric side.
  • Table 2 A representative example is shown in Table 2 for APC.
  • a similar approach can be applied to any gene of interest across all chromosomes.
  • the source of specific markers can be obtained from molecular biology databases in the public domain (Internet: ⁇ URL:www.nih.gov>).
  • the size of the deletion can be as short as a single base deletion which is the resolution capacity of most automated capillary electrophoresis units.
  • the size of genomic deletion will vary according to the position of the polymorphic markers used. Markers that are close to each other in genomic distance will provide quantitative information on small genomic deletions. More widely spaced markers can be used when the deletional areas are larger in size. Thus, any number of markers may be used. In Table 2, four markers are shown for simplicity, 2 on either side of the deleted gene. However, any number of markers can be used.
  • the distance relationship between individual deletion markers is generally available in most databases in the public domain (Internet: ⁇ URL:www.nih.gov>).
  • genomic deletion expansion Operating in parallel as a means to define genomic deletion expansion are quantitative values for the degree of deletion according to individual topographic targets. Deletions that affect a larger number of microdissected cells or DNA at a given site indicate that the deletion has expanded to involve that increased proportion of cells. Thus both the topographic distribution and the quantitative degree of LOH deletion are used to define the rate of genomic deletional expansion.
  • Allelic imbalance analysis (also commonly referred to as loss of heterozygosity analysis) is then performed for each of the polymorphic markers. This involves PCR followed by electrophoresis to determine the balance status for polymorphic alleles. Manufacture's instructions with respect to fragment analysis should be consulted and followed for optimal performance of the deletional analysis (i.e., ABI 3100 Genetic Analyzer, Applied Biosystems, Foster City, Calif.). The cumulative information for all of the topographic targets with respect to each of the polymorphic markers used to assess deletion is then performed. By comparing the results for each marker at the various topographic sites it is possible to define a process of deletion expansion associated with topographic distribution of microdissection targets. Fluid and cytology samples are handled in a similar way with separate targets obtained from different cytology slides and separate fluid specimens.
  • Allelic imbalance refers to the degree of LOH present for a given microdissection target and for a specific individual mutational marker. Allelic imbalance is preferred over either deletion or amplification since either of the latter two processes could produce an identical value for imbalance.
  • the threshold for significant imbalance is defined as a degree of imbalance that exceeds the range of variation in normal sample allele peak height ratios with 95% confidence. This must be determined for each individual marker and for each combination of alleles since the ratios are specific to each pairing. This requires a sufficiently large patient cohort that encompasses all known allele combinations in adequate numbers of subjects to derive 95% confidence intervals for the variation in peak height ratios. Any system of allelic imbalance analysis can be substituted and will yield the same results.
  • the analysis is then carried out quantitatively to determine the proportion of cells and/or DNA affected by imbalance.
  • the following description can be used for microdissected tissue samples.
  • An equivalent method can be used on cytology cells and DNA extracted from free-fluid.
  • amplification is performed as follows. An aliquot of the extracted DNA is removed for PCR amplification of individual polymorphic microsatellite markers. Preferably, only about 1 ⁇ L is utilized but other sized aliquots of DNA can also serve equally well. Nucleic acid amplification can be carried out according to methods known in the art, e.g., GeneAmp kit, Applied Biosystems, Foster City, Calif. Other variations on the PCR reaction can be substituted. Fluorescent labeled oligonucleotide primers can be employed for quantitative determination of allelic imbalance based on the peak height ratio of polymorphic microsatellite alleles.
  • Each peak height ratio will be generated for all specific markers from each of the different microdissection targets. In normal samples without deletional damage, these ratios will vary around a mean value. When ratios are derived from test samples that fall beyond two standard deviations about the means, allelic imbalance or LOH is said to be present. It is also possible to use the value of the imbalance to derive the proportion of cells affected by deletion. When compared between two or more topographic targets it is then a simple matter to detect genomic deletion expansion. Other labeled primers can also be substituted as can other quantitative systems for PCR and/or qualitative approaches.
  • Post-amplification products from Section 2.2.1 are electrophoresed and relative fluorescence determined for individual allele peak height (using for example a GeneScan ABI3100, Applied Biosystems, Foster City, Calif.). The ratio of peaks are calculated by dividing the value for the shorter-sized allele by that of the longer sized allele. Thresholds for significant allelic imbalance have been determined beforehand in extensive studies using normal (non-tumor) specimens representing each unique pairing of individual alleles for every marker used in the panel. Peak height ratios falling outside of two standard deviations beyond the mean for each polymorphic allele pairing are assessed as showing significant allelic imbalance.
  • the non-tumor (normal) tissue targets are used to establish an informativeness status, and then to determine the individual pattern of polymorphic marker alleles.
  • allelic imbalance is established, it is then possible to calculate the proportion of cellular DNA that is subject to hemizygous loss.
  • a polymorphic marker pairing whose peak height ratio is ideally 1.00 in normal tissue with a standard deviation in non-neoplastic tissue of 0.23, could be inferred to have approximately 50% of its cellular content affected by hemizygous loss, if the peak height ratio was 0.5 or 2.0. This requires that a minimum of 50% of the DNA in a given sample be derived from cells possessing deletion of the specific microsatellite marker.
  • allelic imbalance The deviation from the ideal normal ratio of 1.0 indicates which specific allele is affected.
  • allele ratios below 0.5 or above 2.0 can be mathematically correlated with the proportion of cells affected by genomic loss.
  • Other algorithms for quantitative determination of allelic imbalance can be used with equal effectiveness.
  • the proportion of cells or DNA accounting for the imbalance can be determined for each marker.
  • This information is used with the information derived from microscopic analysis of the tissue section or cytology cells from where the samples originated. Particular attention here is paid to the extent of non-neoplastic cell inclusion, as these cells can provide normal DNA to the analysis.
  • the inclusion of normal cellular elements is not limited and is only mentioned in order to provide greater understanding for the quantitation of allelic imbalance. This provides a baseline value for the maximal degree of allelic imbalance since normal cells and their normal DNA will contribute to the ultimate result for allelic. The inclusion of some degree of normal (non-tumor) cellular elements will not interfere with the final characterization of genomic deletion expansion.
  • the proportion of cells or DNA affected by an imbalance can then be determined for markers pertaining to a specific genomic deletion (Table 3).
  • a gradient of reduced mutation involvement indicates that a proportion of tumor cells with an expanded deletion is present in the area from which the sample was derived. This analysis is sensitive for detected genomic deletion expansions up to the threshold representing two standard deviations above the mean for normal allele peak ratios.
  • the exemplified APC gene region contains deletion damage.
  • Polymorphic microsatellites are varying distances away from the deleted region and show progressively small proportions of affected cells.
  • the deletion is shown to be expanding, and the rate of expansion is quantitatively expressed by the diminishing proportion of cells manifesting this change in the topographic sites from where the source of DNA has been obtained.
  • the use of additional markers for allelic balance representing genomic sites at different distance from the gene of interest will provide the user with a clearer understanding on how rapidly the genomic deletion is expanding.
  • topographic regions refers to separate targets for molecular analysis that can be referred to specific distance measurements away from each other or in relationship to certain landmarks. For example, microdissection targets that are separated by a distance of 2 cm are topographically related to each by this distance. The greater the topographic distance between two targets, the greater will be the genomic deletion if it is to be detected as different from each other. Since deletion expansion is unidirectional towards progressively greater expansion, cells towards the periphery or margins of a particular solid tumor will show correspondingly greater deleted regions.
  • the topographic distribution of deleted segments over distance from the center of a tumor provides the diagnosing physician/veterinarian with a quantitative measure of how rapidly the deleted segment is expanding.
  • Table 4 evidence is provided demonstrating that a higher grade neoplasm possesses a high rate of deletion expansion.
  • a variety of mathematical formulae can be created to quantify the rate of expansion taking into account the distance away for the tumor suppressor gene or other gene of interest and the proportion of cells or DNA affected by imbalance.
  • the sidedness (centromeric versus telomeric) of the deletional expansion can also be calculated as described above (Table 4).
  • the pattern of deletional expansion can also be used to test whether a particular gene is in fact the center of genomic deletion as described above (Table 4). For example if an expanding deletion if found to be present in a particular tumor, the smallest size of the deletion will provide the most circumscribed localization for the position of the mutated tumor suppressor gene that is responsible for the initiation of the process.
  • the topographic target that shows this minimal deleted region will contain the initial focus of neoplastic cells that were subject to mutational change for this tumor suppressor gene alteration.
  • the pattern of the genomic expansion will then inform the user on the three dimensional directionality of clonal expansion emanating from that altered mutated collection of cells.
  • genomic deletions Table 5
  • information for the APC gene on 5q is combined with data for the TP53 gene on 17p.
  • the first boxed region relates to the APC deletional analysis
  • the bottom 5 rows of Table 5 relate to the TP53 deletional analysis.
  • the rate of genomic deletion expansion may not necessarily be the same for all deletions in a given tumor, in general, the more malignant neoplasms show similar degrees of deletion expansions for multiple separate genomic deletions. When a large number of extensive genomic deletions are present, this provides strong support that the neoplasm is intrinsically aggressive, whereas the converse supports indolent biological behavior.
  • Rate of genomic expansion over distance Adetectable genomic expansion(Mb)/ ⁇ distance between two specific microdissection targets (mM),
  • the rate of genomic expansion over distance is directly related to biological aggressiveness.
  • the sidedness (centromeric versus telomeric) of the deletional expansion can also be calculated as described in the previous section (Table 5). This is accomplished using the same formula but applied to markers providing information either in the direction towards the centrimere or towards the telomeric end of the chromosome on which the marker is located. The information can be used to determine the extent of genomic instability or imbalance that exists for a tumor in a given patient specimen.
  • deletion expansion Having established the presence and rate of deletion expansion, it is very useful to incorporate microscopic cellular analyses in order to derive the greatest understanding of the significance of the deletion expansion. For example, one common use is to distinguish between a low-grade component of cancer that served as the precursor to the subsequent development of a high-grade malignancy versus the infiltrating edge of a high-grade neoplasm that can appear relatively sparse. This can be explained in more detail as follows.
  • a true low grade precursor component of a high-grade neoplasm would manifest little or no deletional genomic expansion as evaluated using multiple microdissection targets. Thus if one sought the presence of a determined the rate of deletional expansion in sparse and more cellular regions of a tumor, the low grade precursor component would show a lower or absence value compared to the high-grade component.
  • both regions would show a high rate of genomic deletional expansion which may in fact be greater in the sparsely cellular infiltrating edge than in the cellular high-grade areas of cancer. This would establish that the sparsely cellular area is in fact more aggressive in keeping with the infiltrating edge of a malignancy.
  • the time course of mutation acquisition can be derived by defining the topographic distribution of each mutation with earlier mutations manifesting their presence over a wider distance. Later mutations tend to be more focally confined ( FIG. 2 ).
  • Another means for deriving the timeline of mutation accumulation is based on the proportion of tumor cells with specific mutational damage at a particular location. Mutations present in a higher proportion of tumor cells that are in a particular location were acquired earlier, than different mutations that are present in a lesser proportion.
  • This analysis is then combined with the data from analysis of the expansion of genomic deletions to provide a dynamic understanding of aggregating genomic damage in particular neoplasms. Then the rate of genomic deletion expansion is determined for the various microdissection targets providing quantitative data on the rate of clonal expansion and deletional expansion.
  • RATE GENOMIC DELETION EXPANSION MUTATION 1 ⁇ proportion of cells affected by deletion MUTATION 1/ ⁇ genomic distance separating the markers being used.
  • RATE CLONAL EXPANSION MUTATION 1 ⁇ percentage of microdissected cells bearin MUTATION 1 / ⁇ distance between two specific microdissection targets (mM) BIOLOGICAL AGGRESSIVITY INDEX is a function of RATE OVERALL MUTATION ACCUMULATION +RATE CLONAL EXPANSION +RATE GENOMIC DELETIONAL EXPANSION These are all parameters which quantify the instability of the deleted genomic segment in relationship with tumor growth.
  • a cancer with rapidly widening genomic deletion that deletes a largers genomic segment and does so over a shorter topographic distance and also shows rapid acquisition of abundant mutational damage will be predictably more aggressive.
  • the cumulative information is organized in a suitable display form so that it may be reviewed and conclusions drawn concerning the significance of the findings by the diagnosing physician.
  • the data can be coupled with various treatment options associated with the patient's diagnosis to permit the attending physician to discuss with the patient.
  • An example of such as display is shown in the examples below.
  • the second level of quality control is replication of individual marker analyses ( FIG. 3 ).
  • the same marker performed in triplicate and should yield equivalent quantitative results.
  • the degree of variation may be used as a means to assess analytic precision with respect to marker replication.
  • deletion expansion the availability of additional polymorphic markers within the observed segment of expansion is a useful means to independently corroborate the results.
  • FIG. 4 The electropherograms shown in FIG. 4 demonstrate that replicate analyses yield virtually identical results ( FIG. 4 ).
  • allelic imbalance is demonstrated due to inadequate amounts of amplifiable DNA. The issue of inadequate DNA should be minimized otherwise it can lead to false positive values for allelic imbalance. False positives will in turn affect the determination of the dynamic mutational profile. Replicate analysis is the most direct way to identify this problem.
  • a preferred analytical validation method can be achieved by comparing the molecular analysis from biopsy a sampling of a particular tissue or organ to that obtained from analysis of microdissected samples from the resected specimen. A high degree of concordance should be evident using this methodology.
  • the genomic expansion technology can be used to determine whether a cancer or benign growth is a germ line growth or somatic cell related mutation. Additionally, the methods and materials described herein can be used to determine whether a mutation is induced by an environmental factor (i.e., chemical exposure, radiation exposure, exposure to food-borne toxin, viral, and the like).
  • an environmental factor i.e., chemical exposure, radiation exposure, exposure to food-borne toxin, viral, and the like.
  • TCE trichloroethylene
  • VHL gene damage is common in sporadic RCC, however the precise location of genetic alteration has been described as being unique and distinct in subjects exposed to TCE. More specifically, point mutation is more common and tends to affect exons 1 and 2 of the gene compared to sporadic RCC, where VHL point mutation is relatively less common and if present, is observed affecting exon 3 and the distal part of the gene sequence. Also, in TCE exposed patients with RCC, multiple hits of the VHL have been noted, which is very uncommon in sporadic RCC. Finally, damage to other genes situated on chromosome 3p have been reported as unique to TCE exposure.
  • Table 7 outlines a unique marker panel which assesses the issue in patients exposed to TCE. Seven polymorphic microsatellites were used that are distributed across the 3p chromosomal arm from 3p12.3 to 3p26.3. Between the polymorphic microsatellites, specific potential TCE-associated genes with growth regulatory properties are listed in their natural order along the 3p arm. In turn, single nucleotide polymorphisms (SNPs) within each gene are listed when such information is available.
  • SNPs single nucleotide polymorphisms
  • the assessment of mutations arising from TCE exposure can be utilized with any environmental causative.
  • the technique can be utilized to determine whether diseases are caused, for example, by occupational hazards or by some other causative.
  • the results applied to the patient pool with TCE exposure can be utilized for any of the environmental factors listed herein.
  • LOH loss of heterozygosity
  • NI noninformative
  • BLU BLU gene
  • TOP2B topoisomerase 2 beta
  • RARB retinoic acid receptor beta
  • XPC XPC gene
  • Prox proximal
  • Dist distal
  • nt nucleotide
  • seq sequence
  • CDN 115 C HIST-GLUT codon 115 histidine-glutamine
  • VHL gene deletion and unique point mutation is present in certain patients (i.e., patients #1, #4 and #5 of Table 8), all the patients were observed to manifest an allelic imbalance at 3p24.2.
  • genomic deletional expansion to define the origin of temporally early gene deletion, two genes at 3p24.2 were observed to be responsible. These consist of retinoic acid receptor beta and topoisomerase 2 beta. These two genes can be seen to play a critical role in early TCE-associated gene damage and cancer development.
  • deletional expansion into the region occupied by VHL may be responsible for analytic evidence of VHL deletion without the finding of point mutational change. By microdissecting lesions at multiple locations and then quantifying the proportion of cells affected by deletion mutation, valuable information can be gathered to assist in defining the molecular pathogenesis of certain forms of human cancer.
  • Genomic deletion expansion is well suited to resolving this issue. If the tumor is metastatic to the site where it is detected, the advanced nature of tumor progression will declare itself by the presence of abundant concordant detectable mutational change each of which will show evidence of deletional expansion. On the other hand, if the cancer is primary at that site of formation, then multiple microdissection targets of the tumor will show a spectrum of accumulated mutational change with some sites showing few mutations and others showing progressively increasing amounts of mutations. Additionally, there will be only mild degrees of deletional expansion in one or more sites in keeping with the fact that tumor present at those sites are early and therefore the primary site in formation.
  • a patient presented with a tumor mass of the lip.
  • the lip is an uncommon site of cancer formation. Therefore, a metastasis to the lip from an occult primary was suspected, yet no other primary tumor was identified.
  • the tumor displayed microscopic features that suggested possible metastatic origin in lung or gastrointestinal tract. Immunohistochemical staining was inconclusive for determination of the primary site of formation.
  • LOH loss of heterozygosity
  • Tetranucleotide microsatellites are far less numerous than dinucleotide repeat microsatellites and thus one cannot, in general, obtain a marker closest to a particular gene of interest. This approach is entirely opposite to the approaches described in the literature for the purpose of assembling marker panels. The literature teaches that the markers closest to the gene of interest should be used. The literatures teaches away from the use of markers that are more distant to the gene of interest.
  • tetranucleotide, and longer, microsatellites produce less artifact stutter bands when DNA containing microsatellites are amplified by the polymerase chain (PCR) reaction ( FIG. 14 ).
  • Stutter band formation reduces the ability to perform quantitative analysis of DNA content based on peak height content. While specific algorithms can be applied to estimate the effect of stutter band formation on DNA content, this correction factor can produce significant errors, which in turn reduces the ability to achieve quantitative DNA content analysis.
  • the minimal stutter bands associated with tetranucleotide formation are more reproducible and can be accommodated much easier by mathematical correction factors (Perlin et al., 1995 Am. J. Hum. Genet. 57(5): 1199-210).
  • dinucleotide repeat microsatellites and SNPs when searching for specific gene imbalance is that they are closer and often time situated within specific genes of interest. This is not the case with tetranucleotide polymorphisms (or larger), which tend to be found outside specific genes. However, carcinogenesis induced genomic loss or gains cannot be so effectively predicted and genes other than the ones being targeting may be in fact responsible for allelic imbalance. Thus, the apparent advantages attributed to dinucleotide microsatellites and SNPs are greatly outweighed by the advantage of more exact quantitative analysis of tetranucleotide repeats.
  • tetranucleotide (or greater) polymorphisms as the marker of choice
  • the conventional teaching is to select such regions based on the existence of cancer specific associated gene mutations linked to a particular cancer of interest which is being studied. While this recommendation has merit, the novel approach provided herein emphasizes the use of markers that have already been developed and employed to study genomic regions in other forms of cancer. The reason for this is that quantitative data will already be in place to more thoroughly evaluate the significance of threshold levels of allelic imbalance, whereas with the introduction of totally new markers, the process of accruing sufficient quantitative information to be thoroughly familiar with the behavior of a particular marker will be delayed. If complete different markers are used for each and every form of human cancer, then it may never be possible in a reasonable amount of time to accumulate detailed experience with any one marker. As stated before, this is contrary to conventional teaching, which places great emphasis on the uniqueness of individual markers.
  • tetranucleotide (or larger) microsatellite markers are selected so that they are not immediately next to each other, but rather separated by a distance of 10-20 megabases (Mb) although other distances can function equally well.
  • Mb megabases
  • This approach is entirely counterintuitive to conventional thought and practice in the selection of markers, where it is strongly recommended that markers that target a particular regions should be as close to each other as possible, preferably next to each other.
  • the reasoning behind conventional practice is that close proximity of both markers can be expected to produce exactly the same allelic imbalance information. In the case of dinucleotide microsatellites and SNPs, this objective can be met due to the greater number of such markers distributed along the human genome, which in turn makes it simple to follow this recommendation.
  • the methods disclosed herein provide spaced markers in order that genomic deletional expansion (GDE) can be determined in those patients found to be informative for both markers to a certain region. Recognition and quantitative of GDE is extremely valuable when searching for and characterizing allelic imbalance in pathology specimens. In addition to providing evidence for allelic imbalance, the methods provide information on tumor biological aggressiveness, because more aggressive cancer show greater degrees of GDE. Also GDE provides directionality information on the genome. Thus, GDE provides information on where the particular gene is situation that is actually responsible for mutation and not merely assumed to be responsible.
  • the next step of the method is to evaluate each marker on a large number of normal samples prepared in the same manner as those biologic samples that are to be evaluated in the context of disease states.
  • Conventional teaching would proceed directly with the analysis of pathologic samples, but in the method described here the analysis of a sufficiently large sample of normal specimens is needed in order to evaluate each marker for their ability to provide quantitative information. Because there is effort involved in accumulating this information on every new marker, one can appreciate the value in using the same markers for different organ panels, as it makes best use of the accumulated data. While each marker must be capable of detecting mutational damage and addresses the clinical needs for which the analysis is being performed, the use of the same marker whenever possible is highly advantageous. Conventional guidelines teach away from this, because conventional guidelines emphasize the fact that each marker panel must be different for each tissue, each organ, and/or clinical situation.
  • Data is collected on each marker as shown in a representative table below for a single marker.
  • the distribution of specific alleles (columns A1 and A2 representing the two alleles, i.e., allele 1 and allele 2, in individual subjects) is determined for the general population.
  • This information is not available in molecular biology database repositories such as GenBank.
  • the data presented in Table 10 can be compared to that from the human genome project (Internet: ⁇ URL:http://www.gdb.org>). In fact, the data present in those sources is based on far a smaller number, which invariably is not as complete as the information provided herein.
  • the ratio of peak heights is determined on each specimen (column labeled AVE in Table 10). These average values form a distribution which can be evaluated mathematically to define ranges of normal values within certain degrees of confidence. Many different forms of statistical analysis can be applied and we have chosen to regard the overall values as having a typical bell curve distribution. This then allows 95% confidence intervals to be defined as two standard deviation around the mean (columns labeled SD, low, and high [2 standard deviations above and below the average value] in Table 10). Values within the range are considered “normal”, because small populations of mutated cells cannot be detected above the background of normal peak height ratio variation. Values beyond the range for normal variation are considered as bearing mutational change in a significant proportion of cells that exceed the minimum threshold for peak height ratio variation.
  • the ratio of peak heights for polymorphic microsatellite alleles can be converted into a percentage of mutated cells for the individual sample that has been taken. This turns a value that is difficult to visualize (ratio of peak heights) into a value that has real meaning, i.e. percentage of mutated cells in a given area of a specimen.
  • the conversion is based on a model of allelic deletion as it applies to tumor suppressor genes in which one copy of the target region contains a point mutation or other cause for functional inactivation.
  • the second event is genomic deletion of the remaining normal gene copy to create a total functional deficit of tumor suppressor gene activity. This has been known as the Knudsen hypothesis and is now well established in our understanding of human carcinogenesis.
  • the ability to detect mutational change in a population of analyzed cells will depend upon the expected variability in the peak height ratios. Using the example described above with 95% confidence limits, values falling outside 2 standard deviations may be considered as bearing mutated cells.
  • the critical threshold value is determined by the distribution of normal values (N AVERAGE ) and the statistical algorithm (i.e. 2 standard deviations) that is applied to the distribution to determine what is within the normal range of variation. This approach is not designed to detect one mutated cell amongst hundreds or more of non-mutated cells. Rather the method detects significant clonal expansion of acquired mutations that confer a favorable growth advantage as determined by the ability to exceed values that will fall outside of the normal range of variation of normal values.
  • the distribution of normal average values may be greatly influenced by the amount of amplifiable DNA present in the sample.
  • Lower absolute amounts of DNA can often create a wider distribution of normal average values, and so requires that suitable adjustments be made in the definition of threshold levels for significant allelic imbalance.
  • standard deviations may be expected to be greater; thus, the thresholds for mutation detection must be correspondingly widened.
  • Quantity of DNA is not the only factor. Quality of DNA is equally critical since degraded DNA, while present when measured by OD, may actually be totally incapable of being effectively amplified in the extreme cases of DNA degradation.
  • An appreciation of DNA degradation is important to detecting mutational change, because samples typically are exposed to chemical fixatives and treatment during histologic preparation of tissue section of cytology slides that act to increase DNA degradation. Unlike samples in the laboratory which have the luxury of being immediately acted upon in the fresh state, clinical samples do not share this advantage and in fact must be assumed to have some degree of DNA degradation. Conventional teaching fails to recognize this reality and offers no useful recommendations in this regard.
  • the recommendation to simply divide the lesional value by the normal value is valueless, because the “normal” value may be obtained under conditions of low amount and quality of DNA and so may itself show significant variability. This variability will then be introduced into all subsequent determinations of lesional values.
  • the DNA may be extracted in a conventional manner, and the quantity of extracted DNA measured by means of optical density (OD).
  • OD optical density
  • qPCR quantitative nucleic acid amplification
  • the DNA cannot simply be extracted.
  • the amount of DNA can be easily measured in small biopsy samples, because the usual methods for DNA extraction suffer from low yield when the specimen has been subject to chemical fixation. In such circumstances, it is better not to attempt to extract pure DNA and make it amplifiable DNA from a crude lysate of the specimen.
  • Topographic GenotypingTM TG is strongly recommended (Topographic GenotypingTM, U.S. Pat. No. 6,340,563) as well as the techniques discussed in the U.S.
  • CT-PCR competitive template polymerase chain reaction
  • a gene/pseudogene pair is required that share close homology in genomic sequence but differ by the presence of a deletion of varying size in one of the sequences. This is usually encountered in gene/pseudogene pairing. However, it may be seen in other situations as well, such as between genes that are members of a large gene family. Such a situation can also be constructed in vitro by manipulating genomic sequences to possess deletions of predetermined size.
  • glucocerebrosidase gene (GenBank D13286) and its pseudogene (GenBank D13287), and the human carboxyl ester lipase (CEL) gene (GenBank M94579) and its pseudogene (GenBank M94580).
  • CEL carboxyl ester lipase
  • Other similar examples can also be employed.
  • the glucocerebrosidase gene and its pseudogene is sufficient, as it affords specific deletional regions of 19 bases and 55 bases in the exon 1 and 9 respectively.
  • the competitive template PCR (CT-PCR) reaction for the glucocerebrosidase gene/pseudogene pairing provide a novel and sensitive means to quantitate the degree of DNA degradation.
  • the CT-PCR reaction which is performed in triplicate (or more) at varying concentrations, provides quantitative information on the quality of DNA with respect to degradation, and quantitative information on the representative amplifiability of the DNA.
  • the CT-PCR reaction provides a sensitive means to quantitatively characterize DNA degradation in a fashion that is essentially independent of the various phases of nucleic acid amplification (exponential phase, plateau phase) and is effective on minute specimen samples.
  • a second method is used to quantify both the amount and degradation of DNA and is based on an analysis of the fluorescence distribution generated by nucleic acid amplification.
  • the primers used for amplification possess fluorescent labels on their 5′ end as a means for detection and quantification by capillary electrophoresis.
  • the amount of fluorescence produced for each peak height is related to the amplifiability of the DNA, which in turn is greatly influenced by the amount of starting DNA effective for amplification and its quality. The greater in amount that each amplicon is produced, the greater will be the fluorescence values that are generated for each polymorphic allele. Other factors influence total fluorescence in addition to template amount and quality and relate to the kinetics of the individual PCR reaction such as efficiency of primer hybridization and polymerization.
  • Table 11 may be applied first to normal samples and then to lesional specimens. This example is for a microdissected tissue specimen and so the amount of extracted DNA is not available as described above. It would be apparent that this can also be applied to a fluid cytology sample or other biological sample. Table 11 serves as a general template that must be refined for each marker and corresponding primer pair. Levels of CT-PCR and fluorescence that define states of reduced DNA content and increased DNA degradation can be derived for each marker. Markers that are sensitive to low amounts of DNA or degradation should not be used, because they are likely to give spurious values in clinical specimens that are less than optimal.
  • a panel is then formulated of markers based on tetranucleotide (or greater) repeats targeting genomic regions associated with the location of common tumor suppressor genes but not strictly limited to any particular one. Markers are paired for each genomic region but spatially separated to provide information concerning the directionality of deletion expansion (genomic deletion expansion). Having defined a set of markers, normal samples are then carefully analyzed in sufficient number to enable a thorough understanding of their behavior under conditions of lower amounts of DNA quantity and under conditions when the DNA is degraded. Methods such as CT-PCT and evaluation of fluorescence generation are used to quantify marker function under these conditions. Using normal specimens, thresholds for significant allelic imbalance are defined using statistical methods recognizing the critical attributes of DNA quantity and quality. At this point the marker panel is ready to application to lesional samples.
  • the materials and methods described herein are those needed to perform the analysis that will used on the constructed panels to evaluate their effectiveness to address needs for their use. These methods can be performed on any tissue sample, ie resected tissue, drawn blood, cytologic specimen, or fluid specimen (e.g., fluid from a cyst). While there are overall common considerations for all these types of specimens, in fact the specific performance of the analysis will differ. These differences will be described in a subsection for each type of specimen. Preferably, these methods can be used on a combination of specimens such that the data from each specimen can be collated for further validation of the diagnosis and prognosis achieved by the genetic determination. Additionally, if using a microdissected sample, multiple microdissection representing different sections of tumor from the tissue block can be used as controls, and as validation of tumor aggressiveness.
  • Table 12 lists primers that can be used to amplify tetranucleotide microsatellites with a high degree of robustness and accuracy. The stutter band formation with each is minimal and precise quantification is easily performed. These primers are used in combination with each other to produce highly efficient panels for molecular pathology evaluation of precancer, cancer and related conditions. Also included in the panel are specific non-microsatellite targets such as k-ras-2 exon 1 point mutation detection. These additional sets can be combined with tetranucleotide panels for further optimization. The list below is just a sample as other primer sets and tetranucleotide or longer targets can be added. All primers in Table 12 are listed in a 5′ to 3′ direction.
  • Panels may be constructed as follows for specific applications:
  • Glioma molecular analysis D1S1193, D1S407, D1S1172, LMYC, D9S254, D9S251, D10S1173, D10S520, D17S974, D17S1289, D17S1161, D19S400, and/or D19S559.
  • This panel is based upon the use of four tetranucleotide/pentanucleotide microsatellites on 1p to differentiate interstitial from telomeric 1p deletion.
  • the markers for 9p, 10q and 17p are in proximity to the DKN2A, PTEN, and TP53 genes which are very commonly mutated in gliomas. 19q markers are included as they are lost in close correlation with loss of 1p markers.
  • the 17q marker is included, because it has been found to be frequently imbalanced in gliomas.
  • markers correspond to 1p36, 3p25, 5q23, 9p21, 10q23, 17p13, 17q21, 21q22, and 22q12 which are situated in proximity to important tumor suppressor genes.
  • markers correspond to 1p36, 3p25, 5q23, 9p21, 10q23, 17p13, 17q21, 21q22, and 22q12, which are situated in proximity to important tumor suppressor genes.
  • Discrimination between low versus high grade glioma D1S1193, D1S407, D1S1172, LMYC, D3S2303, D3S1539, D5S592, D5S615, D9S254, D9S251, D10S1173, D10S520, D17S974, D17S1289, D17S1161, D19S400, and/or D19S559.
  • This panel is based upon the use of four tetranucleotide/pentanucleotide microsatellites on 1p to differentiate interstitial from telomeric 1p deletion.
  • markers for 9p, 10q and 17p are in proximity to the DKN2A, PTEN and TP53 genes which are very commonly mutated in gliomas. 19q markers are included as they are lost in close correlation with loss of 1p markers. 3p, 5q, and 17q marker is included because it has been found to be frequently imbalanced in gliomas.
  • Trichlorethylene (TCE) associated mutational damage D1S1193, D1S407, D3S2303, D3S2327, D3S1745, D3S1540, D3S1542, D3S1539, D5S592, D5S615, D9S254, D9S251, D10S1173, D10S520, D17S974, D17S1289, D17S1161, D21S1244, and/or D22S532+/ ⁇ K-RAS-2 point mutation when lung, pancreatic and colon cancer are being evaluated.
  • the emphasis on 3p markers reflects the sensitivity of the region for mutational change. The remaining markers are used as a general survey for acquired mutational damage.
  • Discrimination between benign versus malignant Discrimination between reactive versus neoplastic proliferation: D1S1193, D1S407, D3S2303, D3S1539, D5S592, D5S615, D9S254, D9S251, D10S1173, D10S520, D17S974, D17S1289, D17S1161, D21S1244, and/or D22S532+/ ⁇ K-RAS-2 point mutation when lung, pancreatic and colon cancer are being evaluated. These markers correspond to 1p36, 3p25, 5q23, 9p21, 10q23, 17p13, 17q21, 21q22, and 22q12, which are situated in proximity to important tumor suppressor genes.
  • Discrimination between reactive gliosis versus glioma Discrimination between low versus high grade glioma: D1S1193, D1S407, D1S1172, LMYC, D3S2303, D3S1539, D5S592, D5S615, D9S254, D9S251, D10S1173, D10S520, D17S974, D17S1289, D17S1161, D19S400, and/or D19S559.
  • This panel is based upon the use of four tetranucleotide/pentanucleotide microsatellites on 1p to differentiate interstitial from telomeric 1p deletion.
  • markers for 9p, 10q, and 17p are in proximity to the DKN2A, PTEN, and TP53 genes which are very commonly mutated in gliomas. 19q markers are included, as they are lost in close correlation with loss of 1p markers. Markers for 3p, 5q, and 17q are included, because it has been found to be frequently imbalanced in gliomas. In this case, a patient with brain cancer (with a glioma) is being distinguished from an individual with reactive gliosis (caused by multiple sclerosis, an infarction, an infection, and the like).
  • a lysis buffer (Buffer B) was made by adding 2 mL 5M NaCl (Sodium Chloride, Fisher Scientific Cat. # AC32730-0010), 5 mL 0.5M EDTA pH 8.6 (ethylenediaminetetraacetic acid disodium salt, Fisher Scientific Cat. # BP120-500 with sodium hydroxide, Fisher Cat. # BP359-500 to pH the EDTA to 8.6), 1 mL 1M Tris (Tris Ultra Pure ICN, Fisher Scientific Cat. # 819638), and 500 ⁇ L 0.5% NP-40 Surfact-Amps 20 solution in water (Surfact-Amps 20, Pierce Cat.
  • PCR Grade Distilled Water PCR Grade Distilled Water DNAse, RNAse Free 1 micron filtered, Fisher Scientific Cat. # BP2470
  • This buffer was stored in the refrigerator, but it is also stable and can remain at room temperature for a least 1 year or longer. Storing in the refrigerator reduces the tendency for bubbles to form and increases accuracy in pipeting of the buffer.
  • lysis buffer Buffer B
  • PCR polypropylene tubes which were RNase- and DNase-free, as well as DNA-free.
  • the tubes were then tightly capped and then stored at room temperature for at least 1 year or longer.
  • These tubes were used to process and store DNA microdissected off tissue on glass slides (histology or cytology) or cells from cytology brushes, buccal brushes or cells from cell lines.
  • concentrations of these reagents may be varied both upwards and downwards with similar or reduced effectiveness.
  • Other nonionic detergents besides NP-40 or Tween may be substituted for breaking up fixative-treated tissue in the crude lysate.
  • Tissue sections may be sectioned thicker or thinner with equivalent effect; however 4-5 microns is recommended as it is the standard thickness for sectioning fixative treated tissue.
  • a pointed tipped scalpel No. 11 Feather scalpel was used for microdissection. The tip of the scalpel was dipped into the lysis buffer (Buffer B) to wet the tip.
  • the wetted tip was used to remove the tissue of interest under stereomicroscopic observation (Olympus SZ-PT stereomicroscope).
  • the reverse (unsharpened) side of the pointed tip was the most advantageous orientation for microdissected tissue or cytology slides.
  • Other aspects of the scalpel can be used with varying effectiveness.
  • the tissue, as it is scrapped off the slide, will adhere to the wetted tip.
  • the wetted tip and tissue thereon were lifted off the glass slide and the tip dipped gently back into the tube with lysis buffer (Buffer B), where the tissue was released from the tip and put into the buffer solution.
  • Buffer B lysis buffer
  • the tip was wet when removed. With the wetted tip more tissue was collected and placed in the tube, and the blade was carefully and thoroughly wiped and set aside for the next target. Tissue may be added until the tissue begins to appear to be opaque when viewed through the tube. The tube then was capped tightly.
  • the volume of lysis buffer (Buffer B) was adjusted based on the visible estimation of the amount of tissue in the tube. If no cellular material was present, no additional buffer was added. If a small amount was seen at the bottom of the tube, another 25 ⁇ L of buffer was added. When the amount of cellular material was seen to fill approximately half the volume of fluid in the tube, 50 ⁇ L of buffer was added. When the amount of cellular material appears to almost fill or fill the total volume in the tube, 75 ⁇ L of buffer was added. The range of this volume adjustment to match the amount of lysis buffer to the amount of microdissected tissue can vary with equal effectiveness, as long as the microdissected tissue is not excessively diluted or heavily concentrated.
  • Proteinase K up to a concentration of 2 mg/mL, was added and the lysate incubated at 37° C. for two hours. The duration of digestion may be greater than 2 hours; convenient overnight digestion may work effectively. Proteinase digestion was then stopped by boiling the sample for 5 minutes. Once brought down to room temperature, the processed sample tubes were centrifuged at 5,000-10,000 rpms for 5-10 minutes. The duration of centrifugation may vary considerably beyond five minutes; however greatly excessive pelleting is not useful. At this point the sample had been processed into a crude lysate which was ready to proceed to PCR.
  • a qPCR reaction for the first exon of the k-ras-2 gene was performed in duplicate to assess the amplifiability of the DNA (see PCR procedure described below). Two microliters of DNA were used in each of these duplicate reactions (Icycler, BioRad, Hercules, Calif.). The Ct values for the duplicate reactions, representing the quantity of amplifiable starting DNA, were averaged and used as a measure of DNA amplifiability.
  • PCR mix was prepared using reagents from the AmpliTaq Gold DNA Polymerase with Gold Buffer kit (Applied Biosystems, Foster City, Calif.) with some modifications.
  • a 12.5 ⁇ L volume PCR was performed in 96-well PCR plates (Fisher Plate, 96-Well, semi-skirted Cat. # 12 566 134). Following manufacturer's kit instructions, 1.25 ⁇ L Gold Buffer and 1.25 ⁇ L magnesium chloride were added.
  • Incubations range from 15 seconds to 15 minutes.
  • One microliter of crude lysate was used in each singleplex reaction with primers designed to amplify a specific genomic segment within or outside of a genes or genomic regions of interest.
  • Oligonucleotide primers were added as desired.
  • a stock mixture buffer was then used to add Taq polymerase, deoxyribonucleotides, and salts to the final amplification mix.
  • the magnesium concentration was significantly increased to a level of 8 mM in order to improve hybridization of the probe to the template DNA. Also important was the addition of sucrose to a final concentration 12 g/100 mL (12 gram percent). The addition of sucrose at this level may assist in the relaxation of double strands in turn encouraging primer annealing. Other substitutions using similar reagents may be used with equivalent effects expected. Other equivalent sugars may be substituted for sucrose. Further, other ions of equivalent valency, such as manganese, may be substituted for magnesium. Also, the concentration of the reagents provided herein can be adjusted with correlative beneficial effects.
  • the 1 ⁇ L of amplified DNA was mixed with 10-18 ⁇ L of deionized Formamide and 1 ⁇ L of a 40%-50% Rox Calibrator Solution.
  • Samples were loaded onto the capillary electrophoresis (ABI 3100 Genetic Analyzer, Applied Biosystems, Foster City, Calif.) and electrophoresed through POP4 polymer.
  • POP6 polymer from ABI is suitable, as well as any polymer which can discriminate the size of base pairs.
  • Samples were run through a 36 cm capillary array, although the 50 cm capillary array could be substituted.
  • GeneScan software may be used, with the settings Dye set D and GS400HD Analysis Module. Injection times varied between 22-27 seconds and run times varied between 1020 and 1500 seconds. Other software that allows the user to identify and measure peak height may be substituted, such as 3730xl DNA Analyzer software.
  • Other capillary equipment from, for example, Beckman and Agilent may be used as well.
  • Amplification primers were designed with fluorescent labels attached to their 5′ end so that they may be detected and quantified.
  • Fluorescent labels include 5-HEX, TAMRA, 5,6-FAM (Integrated DNA Technologies, Inc.; Coralville, Iowa) or (Synthegen, LLC; Houston, Tex.), and NED (ABI 3100 Genetic Analyzer, Applied Biosystems, Foster City, Calif.).
  • the fluorescently labeled DNA flows through the capillary electrophoresis, it is sorted by size and as it passes a window, the laser fires to cause the labels to fluoresce.
  • the fluorescent is captured by a camera as it passes the window.
  • the time in which the fluorescent is captured determined the length of the patient's alleles, and the amount determines the peak height which indicates the amount of PCR product that was amplified in the PCR reaction.
  • the ratio of polymorphic peak heights or specific peak heights representing defined amplification products was then used to detect and quantify mutational change that may be present.
  • the software allows the user to chose peaks, and once a peak is chosen, it generates a row of data including the allele lengths and peak heights.
  • the data was copied into an Microsoft Excel® table.
  • the Excel®table was then imported into a database, which merges the capillary electrophoresis data with the sample information, so that results may be searched by patient's name or other identifiers, as well as used to generate a report of molecular results linked to each patient's target.
  • the first exon of the k-ras-2 oncogene was PCR amplified.
  • the PCR product underwent a PCR clean-up step using Microcon YM50 (Millipore Corp., Bedford, Mass.) and following manufacturer instructions to remove amplification primers.
  • Cycle sequencing BigDye Terminator Cycle Sequencing Kit V1.1, Applied Biosystems, Foster City, Calif.
  • DyeEx 2.0 Spin Kit was used for post-cycle sequencing, to remove excess unincorporated fluorescent dye and primers following manufacturer's instructions. There are many kits on the market that can be substituted.
  • a 96-well standard PCR plate was used to load samples on the capillary electrophoresis equipment. Each well held 15 ⁇ L of distilled or PCR Grade Distilled Water (PCR Grade Distilled Water DNAse, RNAse Free 1 micron filtered, Fisher Scientific Cat. # BP2470) and 5 ⁇ L of the post cycle sequencing cleaned up sample. Samples were then entered into the Sequencing software program and electrophoresed by capillary electrophoresis on the 3100 Genetic Analyzer (ABI 3100 Genetic Analyzer, Applied Biosystems, Foster City, Calif.
  • Dye set E mobility file DT3100POP4LR(BD)V1.mod, using the Run Module UltraSeq36_POP4DefaultModule and analyzed with BC-3100POP4UR_SeqOfftOff.saz module.
  • Fluorescent labeling was used and the sequence was read by fluorescent capillary electrophoresis.
  • the iQ SYBR Green Supermix (Bio-Rad Cat #170-8880, Hercules, Calif.) was used to make a 25 ⁇ L volume reaction mix. Following manufacturer's instructions, 12.5 ⁇ L of 2 ⁇ SYBR Green Supermix was added, as well as 0.25 ⁇ L of the upstream primer and 0.25 ⁇ L of the downstream primer. The primers were at a concentration of 0.5 to 1.0 ⁇ M. In addition, 2.5 ⁇ L of a 60% sucrose in PCR grade water (i.e., the same water used for the other PCR reactions mixes) was added.
  • the concentration of magnesium chloride was increased by adding 2 ⁇ L of 25 mM magnesium chloride (Applied Biosystems, Foster City, Calif.). 5.75 ⁇ L PCR grade water was added, to bring to the volume up to 23 ⁇ L. 2 ⁇ L of the DNA lysate (prepared from cytology or histology microdissected tissue or cells or buccal brush or other solid tissue as appropriate) or 2 ⁇ L of DNA extracted (from fluid specimens) was added to the mix, using the Qiagen or equivalent kit or other DNA method of extracting DNA from cells.
  • the iQ SYBR Green Supermix contains fluorescein which was used by a real-time PCR thermal cycler “iCycler” as a “well factor” background check.
  • the mix may be prepared using the PCR mix described above with the addition of background fluorescence and the SYBR Green.
  • detection methods such as TaqMan Probes.
  • 2.5 ⁇ L of a 60% sucrose in PCR grade water should be added and the concentration of magnesium chloride doubled, regardless of the detection method used.
  • the thermal cycling used is identical to that of PCR, except it is performed on a real-time thermal cycler such as the iCycler (Bio-Rad Cat. #170-8880, Hercules, Calif.).
  • This real-time thermal cycler allows the immediate viewing of the increase in fluorescence, indicating an increase in PCR product.
  • the real-time thermal cycler allows for the analysis of the amount of fluorescence detected (here, the detection of SYBR green).
  • the software sets a threshold above background which indicates when the PCR reaction is in the exponential rate of growth phase. When each sample's fluorescence passes that threshold, the software assigns a “Ct” or Cycle Threshold value.
  • the Ct is calculated as the point in the PCR cycle when the curve passes the threshold. The lower the Ct value, the more effective and more PCR product is being made. The higher the CT value, then the less effective and less PCR product is made. If the sample does not pass the threshold, it is read as “NA” or “not applicable”, indicating that very little to no PCR product was made.
  • the Ct infers how much and/or quality of the DNA was present at the starting point. DNA of poor quality (broken into small sections, cross-linked to proteins etc) or DNA present in very small amounts has a high to “NA” Ct value. DNA of good quality and/or present in larger amounts has lower Ct values.
  • Genome Database Internet: ⁇ URL:http://www.gdb.org>. Previously amplified DNA was labeled with radioactivity ( 35 S, 33 P, 32 P) and electrophoresed through 6-8% polyacrylamide bis-acrylamide gel.
  • the ratio of peaks was calculated by dividing the value for the shorter sized allele by that of the longer sized allele.
  • Thresholds for significant allelic imbalance were determined beforehand in extensive studies using normal (non-neoplastic) specimens representing each unique pairing of individual alleles for every marker used in the panel. Peak height ratios falling outside of two standard deviations beyond the mean for each polymorphic allele pairing were assessed as showing significant allelic imbalance.
  • non-neoplastic tissue served as a source of DNA to establish informativeness status and then to determine the exact pattern of polymorphic marker alleles. Having established significant allelic imbalance, it was then possible to calculate the proportion of cellular DNA that was subject to hemizygous loss.
  • a polymorphic marker pairing whose peak height ratio was ideally 1.00 in normal tissue with a 95% confidence intervals from 0.78 to 1.62, could be inferred to have 50% of its cellular content affected by hemizygous loss if the peak height ratio was 0.5 or 2.0. This requires that a minimum of 50% of the DNA in a given sample be derived from cells possessing deletion of the specific microsatellite marker. The deviation from ideal normal ratio of 1.0 indicated which specific allele was affected. In a similar fashion, allele ratios below 0.5 or above 2.0 could be mathematically correlated with the proportion of cells affected by genomic loss.
  • Table 13 shows the various genomic targets that are being interrogated by oligonucleotide primer sets. Of importance is the delineation of the specific thermocycler profiles that are to be used to most effectively amplify these individual genomic targets using the primers detailed in the accompanying table.
  • the denaturing temperature in all cases was 95° C.
  • the polymerization temperature in all cases was 72° C.
  • the annealing temperature is shown by the first number and the total number of cycles needed is indicated by the second number.
  • D17S974 is amplified with an annealing temperature of 55° C. for 35 cycles. This provides the exact conditions by which each PCR is to be performed.
  • the first number is the profile
  • the second number is the annealing temperature
  • the third is the # of cycles Panels/ Tests ICYCLER Sep. 14, 2004 3 M 55 30 1 55 40 2 55 35 5 53 35 6 53 30 1 55 40 Major D1s.407 D9s.254 D17S.1161 D9s.251*** D3s.2303* Analysis D10s.1173 D5s.592*** D1s.1193*** D5s.615** D22s532* GAUCHER D10s.520*** D17s.974*** D3s.1539* E9 FAM D21S.1244*** D17s.1289*** Fluid D1s.407* D9s.254* D17S.1161* D9s.251 D3s.2303* Kras2 E1 Analysis Pancreatic D10s.1173* D5s.592*** D1s.1193*** D5s.615** D22s532* Fluid GAUCHER D10s.520
  • Two sets of markers were used for each of the genes studied for the patient sample.
  • the first set of markers used was D5S2027 and D5S1965
  • the second set of markers used was D5S346 and D5S1170. See Table 17 for the primers utilized.
  • the proximal and distal markers respectively flank the APC gene and assist in determining the extent of the gene's deletion. Additional markers may be utilized to further validate and determine the deletional extent for the APC gene.
  • Table 14 shows the two sets of proximal and distal markers used to assess the gene deletions for the particular patient same for APC, CDKN2A, PTEN, and TP53.
  • Colorectal cancer exhibits prominent genomic deletional expansion affecting the APC gene region located at 5q23.
  • Tumor cells show a dynamic expansion in going from the center of the tumor to the periphery, which supports determination that this neoplasm was biologically aggressive.
  • the results for the CDKN2A gene indicated that there was a dynamic genomic deletional expansion of the gene, but the expansion was not centered on this gene. Rather, the geneomic deletion was seen to expand into the territory of the gene. From the CDKN2A data it was concluded that genomic deletion does in fact exist.
  • the analysis also indicated that an alternative target gene that is centromeric to the CDKN2A gene may be part of the developing aggressiveness of the cancer.
  • This technology allows the diagnosing physician to more precisely define the most likely target gene or genomic area representing the center for expanding deletional damage. Moreover, by performing the analysis at multiple sites, the affected tissue sites for the origin of cellular clones with specific deletions can be determined with greater precision.
  • the results for TP53 analysis showed no imbalance, and thus no evidence for genomic deletion expansion.
  • the molecular features of this patient's are those of an aggressive form of colorectal cancer capable of generating multiple independent and overlapping clones of tumor cells. Three of four (75%) target genomic regions showed mutational damage. This level of mutation acquisition is highly predictive (over 95% confidence) of aggressive colon cancer biological behavior.
  • Example 1 four genes (i.e., APC, CDKN2A, PTEN, and TP53) were analyzed in the patient sample for the extent of deletion using two sets for each gene of distal and proximal markers. Additional markers can be used to further validate and describe the extent of the genetic deletion. Additionally, different genes and/or more genes can be analyzed using this method to further describe the aggressive character of the disease. Additionally, this data can be coupled with data from different microdissected portions (e.g., normal cells, cells located on the margin of the putative tumor). It would be evident that the genes analyzed would vary depending on the type of cancer and the involvement of a particular gene in that cancer (see Table 1), as well was the combination of number of genes analyzed.
  • APC i.e., APC, CDKN2A, PTEN, and TP53
  • Genomic deletional expansion analysis can be applied to a single genomic target are any number of separate genes or genomic markers. The larger the number of markers analyzed, the greater detail will be generated for assessment of tumor biological aggressiveness.
  • Example 2 in contrast to Example 1, the same here was determined to have a lower rate of deletion expansion compared to the sample from the patient in Example 1.
  • the patient with the tumor here was shown to have a tumor that is less biological aggressive than the tumor of the patient in Example 1 based on the fact that there is less acquired detectable mutational change.
  • the tumor was shown to have fewer allelic imbalances and those imbalances were expanding at a slower rate.
  • the hepatocellular carcinoma was determined to have two detectable allelic imbalance mutations affecting the CDKN2A and PTEN genes.
  • the results of the markers for each gene analyzed are presented in Table 16
  • a 59 year old man with longstanding heartburn underwent upper gastrointestinal endoscopy, which included a biopsy of the esophagus ( FIG. 6 ). This revealed invasive adenocarcinoma that was treated by an esophagectomy.
  • the 9p imbalance, affecting alternative alleles, can thus be seen to have been acquired later in time in the lung cancer but earlier in time in the esophageal cancer.
  • the information derived by microdissection genotyping provides unequivocal evidence that the two cancers are independent primary tumors enabling lung surgery to proceed for curative intent.
  • the lung tumor sections were reviewed by microscopy, and the most representative microscopic sites of cancer were identified for the upper and lower lobe cancers ( FIG. 7 ). Multiple sites were selected for microdissection and mutational analysis ( FIG. 7 ). The materials and methods used to make the molecular diagnosis are detailed in Example 1, supra.
  • a 70 year male was found to have an anterior gingival ulcerated mass discovered at the time of dental work.
  • a biopsy revealed invasive squamous cell carcinoma ( FIG. 8 ).
  • an enlarged lymph node was detected in the submandibular region and considered to represent metastasis from the anterior gingival cancer.
  • a base of tongue squamous cell carcinoma was discovered at the time of lymph node enlargement.
  • Microscopic appearance and immunohistochemical staining were not of value in the discrimination.
  • the lymph node metastatic cancer matched the anterior gingival squamous cell carcinomaalmost precisely, whereas it was discordant with respect to the base of tongue malignancy. Not only was the concordance seen at the level of specific affected markers, but also in terms of specific alleles affected and furthermore in the time course of mutation acquisition. This provides powerful support for the conclusion regarding the origin for metastatic cancer spread.
  • liver cancer Two patients were awaiting liver transplantation for advanced cirrhosis ( FIG. 9 ). Both patients were identical with respect to clinical features, cause of cirrhosis and biochemical dysfunction. Both patients were found to have two nodules appear in the cirrhotic liver, in right and left lobes. Metastatic liver cancer is a contraindication for autologous liver transplantation, and therefore both patients might have been excluded from this therapeutic option at this point. However, liver cancer can arise in a multicentric fashion in this context and may not preclude the use of autologous liver transplantation for early stage cancer without spread. Biopsies were taken of both nodules in each patient with the purpose to differentiate liver cancer metastasis versus de novo multicentric cancer formation ( FIG. 9 ).
  • the tumor was confined to the kidney without evidence of spread beyond Gerota's fascia or metastasis. Five years later a solitary lip nodule was noticed and biopsied.
  • the histology was consistent with metastatic clear cell carcinoma of the kidney however a benign tumor of skin adnexal origin or minor salivary gland origin could not be excluded.
  • the relationship between the prior kidney cancer the current lip tumor was sought using microdissection and comparative mutational analysis. See FIG. 10 .
  • VHL von-Hippel Lindau
  • RRC renal cell carcinoma
  • Metastatic tumors were fully concordant in most cases with only slight differences in mutational profile accounting for the remaining cases ( FIG. 12 ).
  • discordant cancers were fully discordant to a degree that enabled the distinction to take place in a highly objective fashion. Concordance extended to the level of specific alleles affected and time course of mutation accumulation rendered the analysis highly sensitive, specific and objective.
  • the present example illustrates how the determination of the timing of sequential mutation acquisition in colorectal cancer can provide discriminating information regarding tumor aggressiveness.
  • Current microscopic evaluation of colorectal cancer is designed primarily to confirm the presence of tumor, classify the degree of cellular differentiation and define pathology stage. Morphologic analysis cannot define inherent variability in tumor biological aggressiveness or treatment responsiveness on an individual patient basis, essential for optimizing oncologic therapy.
  • Each microdissected sample was quantitatively genotyped for a broad panel of mutational damage, including k-ras-2 point mutation and LOH at 1p36, 3p26, 5q23, 9p21, 10q23, 17p13, 17q21, 18q25, 21q23 and 22q12 (16 markers).
  • the detailed mutational profile at multiple sites was used to define each tumors unique timeline of mutation acquisition.
  • microdissection based mutational profiling at multiple sites in primary and metastatic colorectal cancer using clinical fixed tissue specimens in routine pathology can delineate the time course of mutation acquisition. More aggressive forms of colorectal cancer possess a higher mutational load early in tumorigenesis and are characterized by greater discordance in newly acquired mutations between primary and metastatic sites. In turn, this provides the basis for a new integrated molecular pathology approach to classify colorectal cancer in clinical practice.
  • the present example illustrates the discrimination of cancer recurrence/metastasis versus de novo cancer formation. Distinguishing recurrent cancer from independent formation of a new cancer can be problematic, especially when the neoplasms share similar histologic features. Discriminating multicentric de novo cancer from intraorgan spread of malignancy can be difficult using staining techniques. Major treatment decisions may depend upon the certainty of this differentiation.
  • a middle aged woman was being evaluated for pancreatic cancer using endoscopic ultrasound imaging and fine needle aspiration ( FIG. 16 ).
  • Two cystic lesions were found, next to each other in the head of the pancreas.
  • Fine needle aspiration biopsy was performed of each cyst (cysts #1 and #2), and the fluid sent for cytology evaluation and molecular analysis.
  • a buccal brush was also obtained to serve as a source of non-neoplastic DNA.
  • the materials and methods used to obtain the molecular diagnosis are as set forth in Example 1, supra.
  • cyst #2 could be performed in assurance that values would be representative of the true status of the cyst fluid DNA. Three allelic imbalance mutations were detected and accurate quantification enabled their unique temporal profile of mutation accumulation to be determined. Cyst #2 could be shown to be malignant from a molecular perspective and the patient then sent for suitable treatment. In this case pancreatic cancer was discovered at an early and highly treatable stage.
  • the marker panel contains tetranucleotide microsatellite markers with well known beyond and abundant statistical information using normal samples. Only the markers for 18q22 and k-ras-2 point mutation could be considered as associated with genes known to be linked to pancreatic ductal cancer formation. Conventional teaching would view this panel as inferior and unsuitable for use. However, the advantages of the panel as described in this application as well as the results which clearly benefited the patient validate is efficacy.
  • a 75 year old male with a long history of severe heartburn and Barrett's esophagus underwent biopsy surveillance of the Barrett's mucosa ( FIG. 18 ).
  • the histologic diagnosis based on microscopy was “low grade dysplasia with focal areas suspicious for high grade dysplasia”.
  • Molecular analysis was required to arrive at a definitive diagnosis given that low grade dysplasia is treated conservatively, while high grade dysplasia requires ablation of the mucosa or surgical excision of the esophagus.
  • the materials and methods used to obtain the molecular diagnosis are as set forth in Example 1, supra.
  • the marker panel used in this example was based on tetranucleotide repeat microsatellites. None of the tetranucleotide repeats used are uniquely associated with specific cancer genes linked to esophageal cancer. The markers are situated close to well known tumor suppressor genes such as APC, CDKN2A, PTEN, and TP53. While mutations in these genes have been described in esophageal cancer they are not unique to that tumor type and can be seen in many different forms of human cancer. Rather, these primers sets are well characterized for molecular analysis and were successfully applied to the problem of Barrett's dysplasia.

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WO2006047482A3 (fr) 2006-06-29
US20060115844A1 (en) 2006-06-01
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US20060141497A1 (en) 2006-06-29
US20140296103A1 (en) 2014-10-02
US20190049452A1 (en) 2019-02-14
WO2006047481A3 (fr) 2006-11-23
EP1809769A2 (fr) 2007-07-25
WO2006047483A3 (fr) 2007-01-04
WO2006047484A3 (fr) 2006-10-26
WO2006047484A2 (fr) 2006-05-04
WO2006047482A2 (fr) 2006-05-04
US20060088870A1 (en) 2006-04-27
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