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DK2904111T3 - Immunkompetence evaluering af adaptiv immunreceptor diversitet og klonalitet karakterisering - Google Patents

Immunkompetence evaluering af adaptiv immunreceptor diversitet og klonalitet karakterisering Download PDF

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DK2904111T3
DK2904111T3 DK13779666.0T DK13779666T DK2904111T3 DK 2904111 T3 DK2904111 T3 DK 2904111T3 DK 13779666 T DK13779666 T DK 13779666T DK 2904111 T3 DK2904111 T3 DK 2904111T3
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air
immunotherapy
polypeptide
tcr
sequences
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DK13779666.0T
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Harlan Robins
Julie Rubinstein
Ryan Emerson
Jianda Yuan
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Adaptive Biotechnologies Corp
Memorial Sloan Kettering Cancer Center
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
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    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/16—Primer sets for multiplex assays
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search

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Claims (13)

1. Fremgangsmåde til at forudsige et immunologisk respons hos et forsøgsindivid af en immunterapi omfattende: at amplificere nukleinsyresekvenser fra en eller flere faste tumorprøver, der omfatter lymfoide celler, hvori prøverne er tilvejebragt fra forsøgsindividet ved et eller flere tidspunkter forud for og efter behandling med nævnte immunterapi, og hvor nukleinsyresekvenserne er amplificeret i et multipleks PCR-assay ved anvendelse af et stort antal adaptive immunreceptor (AIR) V-segment oligonukleotidprimere og enten et stort antal AIR J-segment oligonukleotidprimere eller et eller flere AIR C-segment oligonukleotidprimere; at tilvejebringe nukleinsyresekvensinformation fra de amplificerede nukleinsyresekvenser, hvori nævnte nukleinsyresekvensinformationen omfatter sekvenser for et stort antal unikke omarrangerede nukleinsyresekvenser, der hver koder for et adaptivt immunreceptor (AIR) polypeptid; at kvantificere en AIR sekvensdiversitetsscore for nævnte ene eller flere faste tumorprøver baseret på det samlede antal unikke omarrangerede DNA-sekvenser i nævnte ene eller flere faste tumorprøver, hvor nævnte AIR sekvensdiversitetsscore kvantificeres under anvendelse af nukleinsyresekvensinformationen ; at kvantificere en AIR sekvensfordelingsscore for nævnte ene eller flere faste tumorprøver ved at beregne en hyppighed af forekomsten af et stort antal unikke omarrangerede DNA-sekvenser i nævnte ene eller flere faste tumorprøver, hvor nævnte AIR sekvensfordelingsscore kvantificeres under anvendelse af nævnte nukleinsyresekvensinformation; at bestemme en forsøgsindividvurderingsscore for nævnte ene eller flere faste tumorprøver baseret på nævnte AIR sekvensdiversitetsscore og nævnte AIR sekvensfordelingsscore; at sammenligne nævnte forsøgsindividvurderingsscore med en kontrolemnevurderingsscore, der er opnået fra en prøve fra et kontroleme med et kendt respons på nævnte immunterapi; og at forudsige et immunologisk respons for nævnte forsøgsindivid for nævnte immunterapi baseret på nævnte sammenligning.
2. Fremgangsmåde ifølge krav 1, hvor nævnte nukleinsyrer omfatter genomisk DNA, cDNA eller mRNA.
3. Fremgangsmåde ifølge krav 1 eller krav 2, hvor bestemmelse af en forsøgsindividvurderingsscore omfatter at kvantificere en AIR sekvensfordelingsscore for nævnte forsøgsindivid ved: at bestemme et antal unikke omarrangerede AIR sekvenser, der tegner sig for en kombineret hyppighed af forekomsten på op til 50%, 40%, 30%, 20% eller 10% af det samlede antal observerede omarrangerede sekvenser i nævnte prøve; og at karakterisere nævnte AIR sekvensfordelingsscore som en lav score, hvis antallet af unikke omarrangerede AIR sekvenser, der har nævnte kombinerede hyppighed af forekomsten af det samlede antal observerede omarrangerede sekvenser i nævnte prøve, er mindre end eller lig med en forudbestemt tærskelværdi.
4. Fremgangsmåde ifølge krav 1, hvor nævnte forsøgsindivid (i) forudsiges at have det samme responsresultat af immunterapi sammenlignet med kontrolemnet eller (ii) forudsiges at have et andet responsresultat af immunterapi sammenlignet med nævnte kontrolemne.
5. Fremgangsmåde ifølge krav 1, hvor nævnte immunterapi omfatter: (i) et immunterapeutisk antistof, et cytokin, et immunsuppressivt middel eller en vaccine; (ii) en inhibitor af en negativ regulator af immunsystemet, valgfrit hvori enten (a) nævnte negative regulator er valgt fra en gruppe bestående af CTLA-4, LAG3 og PD-1 eller (b) nævnte inhibitor er et anti-PD-1 antistof eller et anti-CTLA-4 antistof valgt fra gruppen bestående af ipilimumab og tremelimumab; eller (iii) et middel, rettet mod en immunresponsforstærker, valgfrit hvori nævnte immunresponsforstærker er valgt blandt 41BB/CD137, OX40/CD134 og CD40.
6. Fremgangsmåde ifølge krav 1, der yderligere omfatter at bestemme en tilstedeværelse af en klonekspansion af mindst en klon i en prøve, der er tilvejebragt fra nævnte forsøgsindivid efter nævnte immunterapibehandling, hvori nævnte mindst ene klon har en hyppighed af forekomst, der er statistisk signifikant forskellig fra en gennemsnitlig hyppighed af forekomst af et sæt resterende kloner i nævnte prøve og tidligere ikke havde en hyppighed af forekomst, som var statistisk signifikant forskellig fra en gennemsnitlig hyppighed af forekomst af et sæt resterende kloner i en prøve tilvejebragt fra nævnte forsøgsindivid forud for nævnte immunterapi.
7. Fremgangsmåde ifølge krav 6, hvor nævnte sæt af resterende kloner omfatter kloner, som hver har en hyppighed af forekomst, der er i top 50%, 40%, 30%, 20% eller 10% af de samlede kloner i prøven.
8. Fremgangsmåde ifølge krav 6, hvor nævnte klonekspansion af nævnte mindst ene klon er indicerende for et dårlig respons af nævnte forsøgsindivid for nævnte immunterapibehandling.
9. Fremgangsmåde ifølge krav 1, hvor bestemmelse af en forsøgsindividvurderingsscore omfatter bestemmelse af en AIR sekvensfordelingsscore for nævnte ene eller flere prøver ved at vælge et sæt af unikke omarrangerede sekvenser i en af nævnte prøver med en hyppighed af forekomst, der er statistisk signifikant højere sammenlignet med en tærskelhyppighed af forekomsten, der er fastsat af andre unikke omarrangerede sekvenser i nævnte ene eller flere prøver.
10. Fremgangsmåde ifølge krav 1, der yderligere omfatter: at kategorisere nævnte forsøgsindivid baseret på nævnte forsøgsindividvurderingsscore i nævnte ene eller flere prøver som en ikke-responder eller responder til immunterapi i sammenligning med kontrolemnet og at stratificere en patientpopulation af forsøgsindivider ifølge den relative sandsynlighed for at reagere på immunterapi.
11. Fremgangsmåde ifølge krav 1, hvor: (i) at bestemme nævnte forsøgsindividvurderingsscore omfatter ekstrapolering baseret på en matematisk model af en samlet AIR repertoire diversitet af nævnte forsøgsindivid ved sekventering af nukleinsyresekvenserne fra en af nævnte prøver og bestemmelse af et forsøgsindividvurderingsscore fra nævnte samlede AIR repertoire diversitet, optimalt hvor nævnte matematiske model er en uset artsmodel; eller (i i) at bestemme den nævnte forsøgsindividvurderingsscore hvilket omfatter kvantificering af en AIR sekvensfordelingsscore, hvor nævnte kvantificering af nævnte AIR fordelingsscore omfatter at beregne en Shannon entropiscore ved anvendelse af nævnte nukleinsyresekvensinformation fra nævnte ene eller flere prøver.
12. Fremgangsmåde ifølge krav 1, hvor nævnte adaptive immunreceptor (AIR) polypeptid er et pattedyr AIR polypeptid og er valgt fra et T-celle receptor-gamma (TCRG) polypeptid, et T-celle receptor-beta (TCRB) polypeptid, en T-celle receptor alpha (TCRA) polypeptid, et T-celle receptor-delta (TCRD) polypeptid, et immunoglobulin tungkædet (IGH) polypeptid og et immunoglobulin letkædet (IGL) polypeptid, eventuelt hvori: (i) nævnte IGH polypeptid er valgt fra et IgM, et IgA polypeptid, et IgG polypeptid, et IgD polypeptid og et IgE polypeptid; (ii) nævnte IGL polypeptid er valgt fra et IGL-lambda polypeptid og et IGL-kappa polypeptid; eller (iii) nævnte pattedyr AIR polypeptid er valgt fra et humant AIR polypeptid, et ikke-humant primat AIR polypeptid, et gnaver AIR polypeptid, et hunde AIR polypeptid, et katte AIR polypeptid og et ungulat AIR polypeptid.
13. Fremgangsmåde ifølge krav 1, hvor nævnte forsøgsindivid er et individ, der har eller mistænkes for at have en ondartet lidelse, eventuelt hvor: (i) den ondartede lidelse er valgt blandt en hæmatologisk malignitet, et melanom, en sarcom og et carcinom; eller (ii) den ondartede lidelse er valgt blandt ondartet melanom, småcellet lungekræft, ikke-småcellet lungekræft, nyrecellekarcinom, bugspytkirtelcancer, brystkræft, ovariecancer og prostatacancer.
DK13779666.0T 2012-10-01 2013-10-01 Immunkompetence evaluering af adaptiv immunreceptor diversitet og klonalitet karakterisering DK2904111T3 (da)

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US201261708534P 2012-10-01 2012-10-01
PCT/US2013/062925 WO2014055561A1 (en) 2012-10-01 2013-10-01 Immunocompetence assessment by adaptive immune receptor diversity and clonality characterization

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