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WO2003056494A2 - Ameliorations apportees a l'analyse - Google Patents

Ameliorations apportees a l'analyse Download PDF

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Publication number
WO2003056494A2
WO2003056494A2 PCT/GB2002/005836 GB0205836W WO03056494A2 WO 2003056494 A2 WO2003056494 A2 WO 2003056494A2 GB 0205836 W GB0205836 W GB 0205836W WO 03056494 A2 WO03056494 A2 WO 03056494A2
Authority
WO
WIPO (PCT)
Prior art keywords
reference sample
test sample
relationship
loci
function
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/GB2002/005836
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English (en)
Other versions
WO2003056494A3 (fr
Inventor
Peter Gill
John Buckleton
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
UK Secretary of State for the Home Department
Original Assignee
UK Secretary of State for the Home Department
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by UK Secretary of State for the Home Department filed Critical UK Secretary of State for the Home Department
Priority to AU2002353189A priority Critical patent/AU2002353189A1/en
Publication of WO2003056494A2 publication Critical patent/WO2003056494A2/fr
Publication of WO2003056494A3 publication Critical patent/WO2003056494A3/fr
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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Classifications

    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection

Definitions

  • This invention concerns improvements in and relating to DNA profile analysis, particularly, in relation to accounting for preferential degradation in DNA profiling.
  • the overall effect is to render mixture consideration expensive in terms of processing and expensive in terms of the time taken to defend findings in court.
  • the present invention has amongst its aims to address issues of subjectivity.
  • the present invention has amongst its aims to render mixture samples suitable for analysis using expert systems and hence suitable to automation.
  • a method for obtaining a test sample relationship between an apparent relative contribution by one or more test sample individuals to a DNA test sample contributed to by two or more test sample individuals and a test sample function involving a loci characteristic the test sample relationship applying to two or more of the loci for which allele identity and allele level in the DNA test sample is determined in analysis, the method including establishing allele identities and allele levels at two or more of the loci for a reference sample contributed to by two or more reference individuals; allocating a pair of the allele identities established for the reference sample at the two or more loci to each of the reference individuals contributing to that reference sample; obtaining an expression of the apparent relative contribution by one or more of the reference individuals at each of the two or more loci, based on the allele levels established for the respective pairs of alleles; providing an initial definition of a reference sample function involving the loci characteristic; considering the relationship between the expression of the apparent relative contribution for the reference sample for each of the two or more loci and the initial definition of the reference
  • the method may include establishing the allele identities and allele levels at two or more of the loci for a reference sample contributed to by two or more reference individuals, allocating a pair of the allele identities established for the reference sample at the two or more loci to each of the reference individuals contributing to that reference sample and obtaining an expression of the apparent relative contribution by one or more of the reference individuals at each of the two or more loci, based on the allele levels established for the respective pairs of alleles for a plurality of different reference samples to establish a plurality of data sets.
  • the relationship between the expression of the apparent relative contribution for the reference sample for each of the two or more loci and the initial definition of the reference sample function is considered for each of the data sets.
  • the definition of the reference sample function is varied to provide a final definition of the reference sample function which provides a form for the relationship between the expression of the apparent relative contribution for the reference sample and the reference sample function to which form a majority of the data sets conform.
  • the first aspect of the invention may include any of the features, options or possibilities set out elsewhere in this document.
  • a test sample relationship between an apparent relative contribution by one or more test sample individuals to a DNA test sample contributed to by two or more test sample individuals and a test sample function involving a loci characteristic, the test sample relationship applying to two or more of the loci for which allele identity and allele level in the DNA test sample is determined in analysis, the method including a) establishing allele identities and allele levels at two or more of the loci for a reference sample contributed to by two or more reference individuals; b) ' allocating a pair of the allele identities established for the reference sample at the two or more loci to each of the reference individuals contributing to that reference sample; c) obtaining an expression of the apparent relative contribution by one or more of the reference individuals at each of the two or more loci, based on the allele levels established for the respective pairs of alleles; d) repeating steps a), b) and c) for a plurality of different reference samples to establish a plurality of data sets; e
  • the form for the relationship is linear.
  • the second aspect of the invention may include any of the features, options or possibilities set out elsewhere in this document.
  • the first and/or second aspects of the invention may particularly include one or more of the following.
  • the test sample relationship is between the apparent mixing ratio for one individual and the test sample function.
  • the loci characteristic involved in the test sample function is the loci molecular weight.
  • the loci characteristic may be the loci weight, for instance the average weight of alleles occurring at that loci and / or the average weight of the allele identities established for that loci.
  • the loci characteristic may be another ordering characteristic for loci or a combination of one or more such characteristics for the loci.
  • test sample relationship preferably applies to each of the loci for which allele identity and allele level are determined in the analysis.
  • test sample relationship applies to at least 5 loci, more preferably at least 8 loci and ideally 10 or more loci.
  • the DNA test sample may be contributed to by two or more persons, one of the persons being a victim and/or one or more of the persons being a suspect.
  • the sample analysis may involve PCR amplification.
  • the test sample allele identities are preferably established using gel electrophoresis or capillary gel electrophoresis.
  • the test sample peak areas are established using gel electrophoresis or capillary gel electrophoresis. Peak heights may be established. Peak heights may be used to establish the allele level for the test samples, but more preferably peak areas are used.
  • the allele identities and/or allele levels are established for the test sample for at least 5 loci, more preferably at least 8 loci and ideally 10 or more loci.
  • the reference sample may be a control sample generated to obtain the reference sample function.
  • the control sample may have a known actual relative contribution from each of the reference individuals.
  • the expression of the apparent relative contributions is preferably obtained by analysis.
  • the control sample may be formed from reference individuals whose genotypes are known.
  • the allocation of the pairs of alleles is preferably based on the alleles known to belong to the respective reference individuals.
  • the reference sample may be a past analysed sample.
  • the reference sample may have been a test sample considered according to another method, for instance by an expert.
  • the allocation of the allele identities to the reference individuals maybe subjective, for instance based on expert analysis.
  • the expression of the apparent relative contributions is preferably obtained by analysis.
  • Preferably at least 20 such reference samples are considered to establish the reference sample function, more preferably at least 50 samples are used.
  • the reference sample may be analysed or have been analysed using PCR amplification.
  • the reference sample allele identities may be or have been established using gel electrophoresis or capillary gel electrophoresis.
  • peak areas identifying the allele identities for the reference sample have been or may be established using gel electrophoresis or capillary gel electrophoresis.
  • Peak heights may be established. Peak heights may have been or may be used to establish the allele level for the reference sample, but more preferably peak areas are used.
  • the allele identities and/or allele levels are or have been established for at least 5 loci, more preferably at least 8 loci and ideally 10 or more loci.
  • the pairs of allele identities allocated at one locus maybe different to the pairs of allele identities allocated at a different locus for that sample.
  • the initial definition of the reference sample function may be that the function is molecular weight.
  • the initial definition may be a theoretically derived function.
  • the initial definition may be an estimate based on expert consideration of the reference sample analysis results.
  • the consideration of the relationship between the expression of the apparent relative contribution for the reference sample for each of the two or more loci and the initial definition of the reference sample function may involve plotting the two against one another.
  • the consideration may involve a determination of the linearity of the relationship.
  • the varying of the definition of the reference sample function seeks to increase the linearity.
  • the varying seeks to obtain an absolutely linear relationship.
  • a relationship which is linear within a threshold may be accepted.
  • the definition of the function maybe varied by introducing or varying scaling factors and/or introducing or varying additive constants and/or introducing or varying subtractive constants and/or by introducing or varying multipliers and/or by introducing or varying dividers and/or by introducing or varying other mathematical features.
  • the relationship for the reference sample may be given by the function incorporated in the formula of a straight line equation.
  • the relationship for the test sample may be given by the function incorporated in the formula of a straight line equation.
  • test sample relationship obtained is used in subsequent methods of evaluating the likelihood that a specified genotype gives rise to the results obtained by analysing the unknown DNA test sample contributed to by two or more sources.
  • test sample relationship obtained is used in subsequent methods to establish the specific genotypes which could have given the results obtained by analysing the unknown DNA test sample from amongst the possible genotypes.
  • test sample relationship accounts for preferential degradation.
  • the results of the method of obtaining a test sample relationship are used in automated analysis of unknown DNA test samples and./or an expert system for the analysis of unknown DNA test samples.
  • a third aspect of the invention we provide a method for identifying one or more specific genotypes which could have given rise to the results obtained by analysing a DNA test sample contributed to by two or more test individuals, the method including :- using a test sample relationship between an apparent relative contribution by one or more test sample individuals to the DNA test sample contributed to by the two or more test sample individuals and a test sample function involving a loci characteristic, the test sample relationship applying to two or more of the loci for which allele identity and allele level in the DNA test sample is determined in analysis, the relationship being obtained by a method including:- establishing allele identities and allele levels at two or more of the loci for a reference sample contributed to by two or more reference individuals; allocating a pair of the allele identities established for the reference sample at the two or more loci to each of the reference individuals contributing to that reference sample; obtaining an expression of the apparent relative contribution by one or more of the reference individuals at each of the two or more loci, based on the allele levels established for the respective pairs of alleles;
  • a fourth aspect of the invention we provide a method for identifying one or more specific genotypes which could have given rise to the results obtained by analysing a DNA test sample contributed to by two or more test individuals, the method including :- using a test sample relationship between an apparent relative contribution by one or more test sample individuals to the DNA test sample contributed to by the two or more test sample individuals and a test sample function involving a loci characteristic, the test sample relationship applying to two or more of the loci for which allele identity and allele level in the DNA test sample is determined in analysis, the relationship being obtained by a method including:- a) establishing allele identities and allele levels at two or more of the loci for a reference sample contributed to by two or more reference individuals; b) allocating a pair of the allele identities established for the reference sample at the two or more loci to each of the reference individuals contributing to that reference sample; c) obtaining an expression of the apparent relative contribution by one or more of the reference individuals at each of the two or more loci, based on the allele levels established
  • the form is a linear form.
  • a method for identifying one or more specific genotypes which could have given rise to the results obtained by analysing a DNA test sample contributed to by two or more test individuals, the method including :- using a test sample relationship between an apparent relative contribution by one or more test sample individuals to the DNA test sample contributed to by the two or more test sample individuals and a test sample function involving a loci characteristic, the test sample relationship applying to two or more of the loci for which allele identity and allele level in the DNA test sample is determined in analysis, the test sample function equating to a reference sample function which gives a linear relationship between the expression of the apparent relative contribution and the reference sample function for a plurality of reference samples; the method for identifying specific genotypes further including:- analysing the DNA test sample to establish the allele identities and the allele levels at two or more of the loci; for the DNA test sample, allocating a pair of the allele identities established at the two or more loci to each of the two or more test sample individuals contributing to that test sample
  • a sixth aspect of the invention we provide a method for identifying one or more specific genotypes which could have given rise to the results obtained by analysing a DNA test sample contributed to by two or more test individuals, the method including :- using a test sample relationship between an apparent relative contribution by one or more test sample individuals to the DNA test sample contributed to by the two or more test sample individuals and a test sample function involving a loci characteristic, the test sample relationship applying to two or more of the loci for which allele identity and allele level in the DNA test sample is determined in analysis, the test sample function equating to a reference sample function which gives a form of relationship between the expression of the apparent relative contribution for the reference sample and the reference sample function to which form the majority the analysis results from a plurality of reference samples conform; the method for identifying specific genotypes further including:- analysing the DNA test sample to establish the allele identities and the allele levels at two or more of the loci; for the DNA test sample, allocating a pair of the allele identities established at the two or more loci to
  • the form is a linear form.
  • the third and/or fourth and/or fifth and/or sixth aspects of the invention may include any features, options or possibilities set out elsewhere in this document including those set out above in relation to the first and/or second and/or third aspects of the invention.
  • the unknown DNA sample is analysed in an equivalent manner to the reference samples analysed in the method of obtaining a test sample relationship.
  • the same number of loci are used.
  • the same loci are used.
  • the allocated pairs of allele identities may be allocated based on user input.
  • User input may include user based interpretation of the allele identity and/or allele level results.
  • a limited number of genotypes are suggested for evaluation where they are allocated by a user.
  • the number may be less than 8 and is ideally 3 or even 2.
  • the allocation may allocate the two allele identities having the highest level at each loci to one source.
  • the allocation of allele identities may involve allocating the pair of allele identities having the lowest level at each loci to a particular source. Preferably the same criteria are used at each locus.
  • the allocation may be made by an expert.
  • the evaluation may made by establishing whether or not the test sample relationship conforms to the reference sample relationship and/or by establishing whether or not the test sample relationship gives a linear relationship.
  • a plot of the expression of the apparent relative contribution against the test sample function is preferably linear where the proposed genotype is a likely candidate for giving the test sample results.
  • the allocated pairs of allele identities may be allocated by considering all possible combinations of allele identities that are possible.
  • the allocation may involve considering all of the possible allele identities that remain after one or more screening criteria are applied.
  • Preferably the allocation is performed by an expert system and/or an automated system.
  • the evaluation may made by establishing whether or not the test sample relationship conforms to a linear relationship.
  • the linear relationship is defined in part by the test sample function, but may be of any gradient or intercept value. In some cases a range of gradients and/or range of intercept values may be specified. In other cases a particular gradient and/or intercept value may be specified.
  • the gradient and/or intercept values, including ranges therefor, which give likely genotypes may be sought using hill climbing algorithms and/or grid searches and/or bisection searches. Preferably those genotypes giving a linear result are considered to be likely genotypes and those giving nonlinear results are considered to be unlikely genotypes.
  • Whether or not a result is linear may be established using a statistical tool, such as least squares analysis.
  • a plot of the expression of the apparent relative contribution against the test sample function is preferably linear where the proposed genotype is a likely candidate for giving the test sample results. Particularly in this embodiment preferably a likelihood that the specified genotype gives rise to the results is provided.
  • the likely genotypes may be separated from the unlikely genotypes using statistical tools.
  • the statistical tools may include hill climbing algorithms and / or grid searches and / or bisection searches.
  • Figure 1 illustrates schematically a series of allele peaks at two separate loci; and Figure 2 illustrates two separate plots of the same weightings using different components sets for the formula.
  • DNA profiling is used in a wide variety of applications, particularly in relation to criminal investigations. There is a frequent need to analyse DNA samples which are mixtures in the sense that they contain DNA from more than one source. Two, three or more persons may contribute to the mixture and the proportion in which a person is represented in the sample is initially unknown in real life situations.
  • genotypes subsequently proposed as giving rise to the results are based on the manner in which preferential degradation was accounted for. Any issue with this adjustment to account for preferential degradation thereby makes the proposals open to debate in law courts or other forums. As with an subjective decision made by an expert it is open to challenge on a case by case basis by other experts. Different experts will reach slightly different conclusions given the same results. Whenever questioned a result needs time consuming and thus expensive expert input in defence of the result.
  • the present invention seeks to provide a non-subjective determination of the actual relative contribution of the persons whilst accounting for preferential degradation.
  • the present invention also seeks to enable the actual relative contribution to be accounted for in an expert system, as opposed to by an expert, thereby rendering mixtures profiling more susceptible to automated handling. By achieving this the invention renders mixtures more applicable to wide scale, automated handling without the need for expert input on a case by case basis. Additionally as the technique is applied consistently between cases it is sufficient to scientifically validate the technique to the court and opposing sides satisfaction on the first few cases in which it is used and not have to undertake that work for each case thereafter. The genotype proposals made when preferential degradation is accounted for in this way, therefore, should be more acceptable.
  • a relationship between the apparent relative contribution at a locus, referred to as a weighting, and a function involving a characteristic of the respective locus is sought which applies throughout the set of loci considered. More preferably a linear relationship between the weightings measured from one or more experimental profiles and the function involving the characteristic, expressed as a function relating to molecular weight of the loci, is sought.
  • the form of the function needs to be established. This in effect forms part of the techniques set up and does not need to performed on a case by case basis once the form of the function has been obtained.
  • the form of the function can be determined using any of at least the two following ways.
  • the degree of fit between the plot and a line can be established using conventional statistical techniques and those within a given threshold will be accepted as fits.
  • the technique It is possible for the technique to be embodied in a modification of the PendulumTM modelling technique described in Gill et al, Forensic Science International 91 (1998) 41-53. The model takes the experimentally determined profile and considers all possible genotype configurations which could have given rise to the result (including those an expert might very quickly discount).
  • a determination is then made as to which of the possible genotypes give rise to linear relationships in keeping with the equation W Li mF Li + c by varying m and c through a range of possible values.
  • W Li mF Li + c by varying m and c through a range of possible values.
  • the intercept and/or gradient of the line is varied and those plots of W Li against F Li which give linear plots are determined so as to indicate genotypes which are possibilities.
  • Least squares analysis can be used to establish whether or not the plot is a sufficiently good linear fit.
  • a number of statistical tools could be used to find the best fit or fits out of the large number of possibilities, including the use of hill climbing algorithms (usually in 2 dimensions), a grid search (usually in 2 dimensions) or a bisection search (usually in 2 dimensions).
  • An expert system embedded form of the invention is thus provided.
  • c in a preferred form of the invention, can range between 0 and 1.
  • m in a preferred form of the invention, m can be centred on 0. In either case the ranges can be considered as uniform a prior or, based on experimental determinations, informed a prior can be employed.
  • W is the weighting at locus Li for a particular person.
  • the formula applies.
  • a plot of the function against weighting could then be made in the appropriate number of dimensions with the values of m and c in the equation then being varied once again to establish which of the possible genotypes give a linear plot in those dimensions and hence represent likely genotypes.
  • the predetermined function could be established, based on the preexisting measurements detailed above or using controlled samples with various known mixing proportions, to give the underlying model.
  • the various likely genotypes or even all possible genotypes could then be considered to establish there degree of match with the relationship established. Good matches would be seen as indicators of likely genotypes which could have given rise to the measured results from the sample under scrutiny whereas poor matches would be seen as indicators of unlikely genotypes.

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  • Bioinformatics & Cheminformatics (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
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  • Proteomics, Peptides & Aminoacids (AREA)
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  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

L'invention concerne un procédé amélioré d'identification d'un ou plusieurs génotypes spécifiques qui peuvent avoir engendrer des résultats obtenus par analyse d'un échantillon test d'ADN auquel deux ou plusieurs individus tests ont été soumis expliquant de façon non subjective les effets de dégradation préférentielle. L'invention concerne également un procédé d'obtention d'une fonction d'échantillon test fondée sur une fonction d'échantillon de référence utilisée par le procédé. La fonction d'échantillon de référence implique une caractéristique loci et produit la relation d'échantillon test entre la contribution relative apparente effectuée par un ou plusieurs individus d'échantillon test et la caractéristique loci. Le procédé de l'invention est particulièrement adapté pour une utilisation dans un système expert.
PCT/GB2002/005836 2001-12-21 2002-12-20 Ameliorations apportees a l'analyse Ceased WO2003056494A2 (fr)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2002353189A AU2002353189A1 (en) 2001-12-21 2002-12-20 Improvements in dna profile analysis

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
GBGB0130675.2A GB0130675D0 (en) 2001-12-21 2001-12-21 Improvements in and relating to analysis
GB0130675.2 2001-12-21

Publications (2)

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WO2003056494A2 true WO2003056494A2 (fr) 2003-07-10
WO2003056494A3 WO2003056494A3 (fr) 2003-12-24

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Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7672789B2 (en) 2002-10-08 2010-03-02 University Of Tennessee Research Foundation Least-Square Deconvolution (LSD): a method to resolve DNA mixtures
US8235903B2 (en) 2007-10-12 2012-08-07 Innoscion, Llc Remotely controlled implantable transducer and associated displays and controls

Family Cites Families (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
GB9930307D0 (en) * 1999-12-22 2000-02-09 Sec Dep Of The Home Department Improvements in or relating to identification
US8898021B2 (en) * 2001-02-02 2014-11-25 Mark W. Perlin Method and system for DNA mixture analysis
GB0130674D0 (en) * 2001-12-21 2002-02-06 Sec Dep Of The Home Department Improvements in and relating to interpreting data

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7672789B2 (en) 2002-10-08 2010-03-02 University Of Tennessee Research Foundation Least-Square Deconvolution (LSD): a method to resolve DNA mixtures
US7860661B2 (en) 2002-10-08 2010-12-28 University Of Tennessee Research Foundation Least-square deconvolution (LSD): a method to resolve DNA mixtures
US8140271B2 (en) 2002-10-08 2012-03-20 University Of Tennessee Research Foundation Least-square deconvolution (LSD): a method to resolve DNA mixtures
US8235903B2 (en) 2007-10-12 2012-08-07 Innoscion, Llc Remotely controlled implantable transducer and associated displays and controls

Also Published As

Publication number Publication date
WO2003056494A3 (fr) 2003-12-24
AU2002353189A1 (en) 2003-07-15
AU2002353189A8 (en) 2003-07-15
GB0130675D0 (en) 2002-02-06

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