DK2496717T3 - Analyse af føtalt genom ud fra en maternel biologisk prøve - Google Patents
Analyse af føtalt genom ud fra en maternel biologisk prøve Download PDFInfo
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- DK2496717T3 DK2496717T3 DK10782468.2T DK10782468T DK2496717T3 DK 2496717 T3 DK2496717 T3 DK 2496717T3 DK 10782468 T DK10782468 T DK 10782468T DK 2496717 T3 DK2496717 T3 DK 2496717T3
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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
- 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
- C12Q1/6813—Hybridisation assays
- C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
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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
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- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- 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
- 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
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- 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
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- 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
- G16B20/10—Ploidy or copy number detection
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- 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
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- 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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- 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
- G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- 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
- C12Q2600/154—Methylation markers
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- 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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- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
- Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
- Y10T436/00—Chemistry: analytical and immunological testing
- Y10T436/14—Heterocyclic carbon compound [i.e., O, S, N, Se, Te, as only ring hetero atom]
- Y10T436/142222—Hetero-O [e.g., ascorbic acid, etc.]
- Y10T436/143333—Saccharide [e.g., DNA, etc.]
Claims (15)
1. Fremgangsmåde til bestemmelse af mindst en del af genomet for et ufødt foster hos en gravid kvinde, hvilket foster har en far samt en mor, der er den gravide kvinde, og hvor faren haret paternelt genom med paterneile haplotyper, og moren har et maternelt genom med materneile haplotyper, hvilken fremgangsmåde omfatter: (a) at analysere en flerhed af nukleinsyremolekylerfra en biologisk prøve, der er opnået fra den gravide kvinde, hvor den biologiske prøve indeholder en blanding af materneile og føtale nukleinsyrer, og hvor analyse af et nukleinsyremolekyle indbefatter: (i) at identificere en placering af nukleinsyremolekylet i det humane genom; og (ii) at bestemme en respektiv allel af nukleinsyremolekylet; (b) at bestemme en paternel allel, der er arvet af fosteret fra faren, på hvert locus i en første flerhed af loci, idet de identificerede placeringer af nukleinsyrerne fra den biologiske prøve, som er bestemt i (a)(i), indbefatter den første flerhed af loci, hvor den første flerhed af lod findes på det samme kromosom, og hvor det materneile genom er heterozygot på loci i den første flerhed af loci; (c) at bestemme hver af to materneile haplotyper for den første flerhed af loci; (d) at bestemme mængder af respektive alleler på hvert locus i den første flerhed af loci med et computersystem baseret på de bestemte alleler af nukleinsyremolekylerne på loci i den første flerhed af loci; (e) at sammenligne relative mængder af de respektive alleler af nukleinsyremolekylerne på mere end ét locus i den første flerhed af loci og (f) at bestemme, hvilken af de to materneile haplotyper der er arvet af det ufødte foster fra moren på den del af genomet, som er omfattet af den første flerhed af lod, baseret på sammenligningen.
2. Fremgangsmåde ifølge krav 1, hvor bestemmelse af allelen, der er arvet fra faren, på hvert locus i den første flerhed af loci, indbefatter: at bestemme en anden flerhed af loci i det paterneile genom, der er heterozygote, og hvor det materneile genom er homozygot på loci i den anden flerhed af loci; at identificere alleler, der er til stede i det paternelle genom på respektive loci i den anden flerhed af loci og fraværende i det materneile genom, i flerheden af nukleinsyremolekyler; at identificere den arvede paterneile haplotype som haplotypen med de identificerede alleler og at anvende den arvede paterneile haplotype til at bestemme allelen, der er arvet fra faren, på hvert locus i den første flerhed af loci.
3. Fremgangsmåde ifølge krav 1, hvor bestemmelse af hver af de to materneile haplotyper for den første flerhed af loci indbefatter: at identificere allelerne i det materneile genom på en eller flere loci i den første flerhed af loci baseret på mængderne af de bestemte respektive alleler af nukleinsyremolekylerne på et respektivt locus; at identificere en flerhed af referencehaplotyper og at sammenligne de identificerede alleler i det materneile genom med allelerne på de tilsvarende loci for flerheden af referencehaplotyper for at identificere de to materneile haplotyper.
4. Fremgangsmåde ifølge krav 3, hvor bestemmelse af hver af de to materneile haplotyper for den første flerhed af loci yderligere indbefatter: at sammenligne en identificeret allel fra det materneile genom gentagne gange med flerheden af referencehaplotyper, indtil hver af de to materneile haplotyper er unikt identificeret.
5. Fremgangsmåde ifølge krav 1, hvor bestemmelse af allelen, der er arvet fra faren, på hvert locus i den første flerhed af lod, er baseret på analysen af flerheden af nukleinsyremolekyler fra en biologisk prøve, og hvor bestemmelse af allelen, der er arvet fra faren, på hvert locus i den første flerhed af loci, indbefatter: at bestemme en anden flerhed af loci, på hvilke det føtale genom er heterozygot, og det maternelle genom er homozygot; at bestemme allelen, der er arvet fra faren, på hvert locus i den anden flerhed af loci ved: at bestemme relative mængder af de bestemte respektive alleler af nukleinsyremolekylerne på det respektive locus i den anden flerhed; og at identificere allelen med den mindste relative mængde som værende den arvede allel på det respektive locus; at identificere en flerhed af referencehaplotyper; at anvende allelerne, der er arvet fra faren, på hvert locus i den anden flerhed af loci til at bestemme, hvilken af referencehaplotyperne der er arvet fra faren, idet den bestemte haplotype indbefatter den første flerhed af loci; og at bestemme allelerne, der er arvet fra faren, på den første flerhed af loci ud fra haplotypen, der er bestemt som værende arvet fra faren.
6. Fremgangsmåde ifølge krav 5, hvor bestemmelse af, hvilken af referencehaplotyperne der er arvet fra faren, indbefatter: at sammenligne allelerne, der er bestemt som værende arvet fra faren, på hvert locus i den anden flerhed af loci, gentagne gange med allelerne på de tilsvarende loci for flerheden af referencehaplotyper, indtil de referencehaplotyper, der er arvet fra faren, er unikt identificeret.
7. Fremgangsmåde ifølge krav 5, hvor bestemmelse af et specifikt locus som værende et locus i den anden flerhed af loci, på hvilke det føtale genom er heterozygot, og det materneile genom er homozygot, indbefatter: at bestemme en afskæringsværdi for et antal forudsagte tællinger afen allel på det specifikke locus, hvilken afskæringsværdi forudsiger, hvorvidt det maternelle genom er homozygot, og det føtale genom er heterozygot, hvor afskæringsværdien bestemmes baseret på en statistisk fordeling af antal tællinger for forskellige kombinationer af homozygoti og heterozygoti på det specifikke locus; at påvise en første allel og en anden allel på det specifikke locus baseret på analysen af nukleinsyremolekylerne fra den biologiske prøve; at bestemme et antal faktiske tællinger af den første allel baseret på analysen af flerheden af nukleinsyremolekylerfra den biologiske prøve og at bestemme, at det føtale genom er heterozygot for den første allel og en anden allel, og at det materneile genom er homozygot for den anden allel, når antallet af faktiske tællinger er mindre end afskæringsværdien.
8. Fremgangsmåde ifølge krav 7, hvor den statistiske fordeling er afhængig af en fraktionskoncentration af nukleinsyremolekyler fra den biologiske prøve, der stammer fra fosteret.
9. Fremgangsmåde ifølge krav 8, hvor den statistiske fordeling yderligere er afhængig af antallet af flerheden af nukleinsyremolekyler, der svarer til det specifikke locus.
10. Fremgangsmåde ifølge krav 1, hvor bestemmelse af allelen, der er arvet fra faren, på hvert locus i den første flerhed af lod, indbefatter: at bestemme en anden flerhed af loci i det paterneile genom, der er homozygote, ved at analysere det paternelle genom, hvor den første flerhed af loci er den anden flerhed af loci; at bestemme allelen fra det paternelle genom på hvert locus i den første flerhed af loci og at udpege de respektive alleler på loci i den første flerhed af loci som værende allelerne, der er arvet fra faren.
11. Fremgangsmåde ifølge krav 1, der yderligere omfatter: at bestemme, hvilken haplotype der er arvet af det ufødte foster fra moren for et første genomafsnit, som indbefatter den første undergruppe af nærliggende loci, for hvert locus i en første undergruppe af nærliggende loci, hvor bestemmelse af haplotypen indbefatter: (a) at bestemme en første mængde af bestemte respektive alleler af nukleinsyremolekylerne, der matcher én af de to materneile haplotyper for den første undergruppe af på hinanden følgende loci; (b) at bestemme en anden mængde af bestemte respektive alleler af nukleinsyremolekylerne, der matcher den anden af de to materneile haplotyper for den første undergruppe af på hinanden følgende loci; og (c) at bestemme den arvede haplotype for det første genomafsnit baseret på en sammenligning af den første mængde med den anden mængde.
12. Fremgangsmåde ifølge krav 11, hvor den første undergruppe af nærliggende loci er yderligere inddelt i to delgrupper, hvor den første delgruppe består af loci, for hvilke genotyperne hos faren matcher de genotyper, der udgør en første haplotype hos moren, og den anden delgruppe består af loci, for hvilke genotyperne hos faren matcher de genotyper, der udgør en anden haplotype hos moren; og hvor (a)-(c) udføres individuelt for de to delgrupper, hvilken fremgangsmåde yderligere omfatter: at bestemme den arvede haplotype for det første genomafsnit baseret på resultaterne fra (c) for disse to delgrupper.
13. Fremgangsmåde ifølge krav 1, der yderligere omfatter: at bestemme, at fosteret har arvet en mutation fra moren, ved: at analysere den haplotype hos moren, der er arvet af fosteret; og at identificere mutationen i den arvede haplotype.
14. Fremgangsmåde ifølge krav 1, hvor analyse af en flerhed af nukleinsyremolekylerfra den biologiske prøve indbefatter: at berige den biologiske prøve med nukleinsyrer i en målregion i et genom og/eller, fortrinsvis, at sekventere nukleinsyrer i målregionen, og hvor en første flerhed af loci findes i målregionen.
15. Maskinlæsbart medie, der lagrer softwarekode, som er i stand til at blive udført af et computersystem, idet softwarekoden er udformet til ved udførelse at bevirke, at computersystemet gennemfører en fremgangsmåde ifølge et hvilket som helst af de foregående krav.
Applications Claiming Priority (4)
Application Number | Priority Date | Filing Date | Title |
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US25856709P | 2009-11-05 | 2009-11-05 | |
US25907509P | 2009-11-06 | 2009-11-06 | |
US38185410P | 2010-09-10 | 2010-09-10 | |
PCT/US2010/055655 WO2011057094A1 (en) | 2009-11-05 | 2010-11-05 | Fetal genomic analysis from a maternal biological sample |
Publications (1)
Publication Number | Publication Date |
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DK2496717T3 true DK2496717T3 (da) | 2017-07-24 |
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Family Applications (3)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
DK17168527.4T DK3241914T3 (da) | 2009-11-05 | 2010-11-05 | Føtal genomanalyse af en maternel biologisk prøve |
DK20200970.0T DK3783110T3 (da) | 2009-11-05 | 2010-11-05 | Føtal genomisk analyse fra en maternel biologisk prøve |
DK10782468.2T DK2496717T3 (da) | 2009-11-05 | 2010-11-05 | Analyse af føtalt genom ud fra en maternel biologisk prøve |
Family Applications Before (2)
Application Number | Title | Priority Date | Filing Date |
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DK17168527.4T DK3241914T3 (da) | 2009-11-05 | 2010-11-05 | Føtal genomanalyse af en maternel biologisk prøve |
DK20200970.0T DK3783110T3 (da) | 2009-11-05 | 2010-11-05 | Føtal genomisk analyse fra en maternel biologisk prøve |
Country Status (24)
Country | Link |
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US (5) | US8467976B2 (da) |
EP (5) | EP3241914B1 (da) |
JP (3) | JP5540105B2 (da) |
CN (2) | CN105779280B (da) |
AU (1) | AU2010315037B9 (da) |
BR (1) | BR112012010694B8 (da) |
CA (1) | CA2779695C (da) |
CY (1) | CY1122003T1 (da) |
DK (3) | DK3241914T3 (da) |
EA (1) | EA033752B1 (da) |
ES (3) | ES2628874T3 (da) |
FI (1) | FI3783110T3 (da) |
HK (1) | HK1222413A1 (da) |
HR (2) | HRP20230134T1 (da) |
HU (3) | HUE034854T2 (da) |
IL (3) | IL219521A (da) |
LT (2) | LT3783110T (da) |
MX (3) | MX355132B (da) |
PL (3) | PL3241914T3 (da) |
PT (3) | PT2496717T (da) |
RS (2) | RS63944B1 (da) |
SI (2) | SI3783110T1 (da) |
TW (1) | TWI458976B (da) |
WO (1) | WO2011057094A1 (da) |
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