Methods of fetal abnormality detection

• US 8,318,430 B2
• Filed: 02/07/2012
• Issued: 11/27/2012
• Est. Priority Date: 01/23/2010
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Verinata Health Incorporated (Illumina Incorporated)
• Inventors: Chuu, Yue-Jen, Rava, Richard P.
• Primary Examiner(s): Dunston, Jennifer
• Assistant Examiner(s): Mahatan, Channing S
• Application Number:
  US13/368,035
• Publication Number:
  US 20120135872A1
• Time in Patent Office: 294 Days
• Field of Search: None
• US Class Current: 435/6.1
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

Methods and kits for selectively enriching non-random polynucleotide sequences are provided. Methods and kits for generating libraries of sequences are provided. Methods of using selectively enriched non-random polynucleotide sequences for detection of fetal aneuploidy are provided.

Claims

1. A method for determining a presence or absence of a fetal aneuploidy in a fetus for each of a plurality of maternal blood samples obtained from a plurality of different pregnant women, said maternal blood samples comprising fetal and maternal cell-free genomic DNA, said method comprising:

(a) obtaining a fetal and maternal cell-free genomic DNA sample from each of the plurality of maternal blood samples;

(b) selectively enriching a plurality of non-random polynucleotide sequences of each fetal and maternal cell-free genomic DNA sample of (a) to generate a library derived from each fetal and maternal cell-free genomic DNA sample of enriched and indexed fetal and maternal non-random polynucleotide sequences, wherein each library of enriched and indexed fetal and maternal non-random polynucleotide sequences includes an indexing nucleotide sequence which identifies a maternal blood sample of the plurality of maternal blood samples,

wherein said plurality of non-random polynucleotide sequences comprises at least 100 different non-random polynucleotide sequences selected from a first chromosome tested for being aneuploid and at least 100 different non-random polynucleotide sequences selected from a reference chromosome, wherein the first chromosome tested for being aneuploid and the reference chromosome are different, and wherein each of said plurality of non-random polynucleotide sequences is from 10 to 1000 nucleotide bases in length,

(c) pooling the libraries generated in (b) to produce a pool of enriched and indexed fetal and maternal non-random polynucleotide sequences;

(d) performing massively parallel sequencing of the pool of enriched and indexed fetal and maternal non-random polynucleotide sequences of (c) to produce sequence reads corresponding to enriched and indexed fetal and maternal non-random polynucleotide sequences of each of the at least 100 different non-random polynucleotide sequences selected from the first chromosome tested for being aneuploid and sequence reads corresponding to enriched and indexed fetal and maternal non-random polynucleotide sequences of each of the at least 100 different non-random polynucleotide sequences selected from the reference chromosome;

(e) based on the indexing nucleotide sequence, for each of the plurality of maternal blood samples, enumerating sequence reads corresponding to enriched and indexed fetal and maternal non-random polynucleotide sequences selected from the first chromosome tested for being aneuploid and sequence reads corresponding to enriched and indexed fetal and maternal non-random polynucleotide sequences selected from the reference chromosome; and

(f) for each of the plurality of maternal blood samples, determining the presence or absence of a fetal aneuploidy comprising using a number of enumerated sequence reads corresponding to the first chromosome and a number of enumerated sequence reads corresponding to the reference chromosome of (e).

2. The method of claim 1, wherein for each of the plurality of maternal blood samples determining the presence or absence of a fetal aneuploidy comprises comparing the number of enumerated sequence reads corresponding to the first chromosome tested for being aneuploid with the number of enumerated sequence reads corresponding to the reference chromosome.

3. The method of claim 1, wherein said plurality of non-random polynucleotide sequences comprises at least 300 different non-random polynucleotide sequences selected from the first chromosome tested for being aneuploid and at least 300 different non-random polynucleotide sequences selected from the reference chromosome.

4. The method of claim 3, wherein said plurality of non-random polynucleotide sequences comprises at least 500 different non-random polynucleotide sequences selected from the first chromosome tested for being aneuploid and at least 500 different non-random polynucleotide sequences selected from the reference chromosome.

5. The method of claim 1, wherein each of said plurality of non-random polynucleotide sequences is from 10 to 500 nucleotide bases in length.

6. The method of claim 1, wherein each of said plurality of non-random polynucleotide sequences is from 50 to 150 nucleotide bases in length.

7. The method of claim 1, wherein said first chromosome tested for being aneuploid is selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, chromosome X, and chromosome Y.

8. The method of claim 7, wherein said fetal aneuploidy comprises fetal aneuploidy of a chromosome selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, chromosome X, and chromosome Y.

9. The method of claim 8, wherein said fetal aneuploidy is selected from the group consisting of trisomy 21, trisomy 18, trisomy 13, and monosomy X.

10. The method of claim 1, wherein said reference chromosome is selected from the group consisting of chromosome 1, chromosome 2, chromosome 3, chromosome 13, chromosome 18, and chromosome 21.

11. The method of claim 1, wherein said fetal aneuploidy comprises monosomy, trisomy, tetrasomy, or pentasomy of the first chromosome.

12. The method of claim 1, wherein said selectively enriching of (b) comprises performing polymerase chain reaction (PCR) amplification.

13. The method of claim 12, wherein for each fetal and maternal cell-free genomic DNA sample PCR amplification comprises hybridizing at least two oligonucleotides to each of the at least 100 different non-random polynucleotide sequences selected from the first chromosome tested for being aneuploid and each of the at least 100 different non-random polynucleotide sequences selected from the reference chromosome.

14. The method of claim 13, wherein said oligonucleotides do not hybridize to non-random polynucleotide sequences comprising one or more polymorphisms.

15. The method of claim 13, wherein each of said oligonucleotides has a substantially similar melting temperature.

16. The method of claim 1, wherein said massively parallel sequencing generates at least 30 nucleotide bases per sequence read.

17. The method of claim 1, wherein said fetal aneuploidy comprises partial monosomy or partial trisomy.

18. The method of claim 1, wherein said plurality of non-random polynucleotide sequences comprises no more than 1000 different non-random polynucleotide sequences selected from the first chromosome tested for being aneuploid and no more than 1000 different non-random polynucleotide sequences selected from the reference chromosome.

19. A method for determining a presence or absence of a fetal aneuploidy in a fetus for each of a plurality of maternal blood samples obtained from a plurality of different pregnant women, said maternal blood samples comprising fetal and maternal cell-free genomic DNA, said method comprising:

(a) obtaining a fetal and maternal cell-free genomic DNA sample from each of the plurality of maternal blood samples;

(b) selectively enriching a plurality of non-random polynucleotide sequences of each fetal and maternal cell-free genomic DNA sample of (a) to generate a library derived from each fetal and maternal cell-free genomic DNA sample of enriched and indexed fetal and maternal non-random polynucleotide sequences, wherein each library of enriched and indexed fetal and maternal non-random polynucleotide sequences includes an indexing nucleotide sequence which identifies a maternal blood sample of the plurality of maternal blood samples,

wherein said plurality of non-random polynucleotide sequences comprises at least 100 different non-random polynucleotide sequences selected from at least one chromosome region tested for being aneuploid and at least 100 different non-random polynucleotide sequences selected from at least one chromosome control region, wherein the at least one chromosome region tested for being aneuploid and the at least one chromosome control region are different, and wherein each of said plurality of non-random polynucleotide sequences is from 10 to 1000 nucleotide bases in length;

(c) pooling the libraries generated in (b) to produce a pool of enriched and indexed fetal and maternal non-random polynucleotide sequences;

(d) performing massively parallel sequencing of the pool of enriched and indexed fetal and maternal non-random polynucleotide sequences of (c) to produce sequence reads corresponding to enriched and indexed fetal and maternal non-random polynucleotide sequences of each of the at least 100 different non-random polynucleotide sequences selected from the at least one chromosome region tested for being aneuploid and sequence reads corresponding to enriched and indexed fetal and maternal non-random polynucleotide sequences of each of the at least 100 different non-random polynucleotide sequences selected from the at least one chromosome control region;

(e) based on the indexing nucleotide sequence, for each of the plurality of maternal blood samples, enumerating sequence reads corresponding to enriched and indexed fetal and maternal non-random polynucleotide sequences selected from the at least one chromosome region tested for being aneuploid and sequence reads corresponding to enriched and indexed fetal and maternal non-random polynucleotide sequences selected from the at least one chromosome control region; and

(f) for each of the plurality of maternal blood samples, determining the presence or absence of a fetal aneuploidy comprising using a number of enumerated sequence reads corresponding to the at least one chromosome region tested for being aneuploid and a number of enumerated sequence reads corresponding to the at least one chromosome control region of (e).

20. The method of claim 19, wherein for each of the plurality of maternal blood samples determining the presence or absence of a fetal aneuploidy comprises comparing the number of enumerated sequence reads corresponding to the at least one chromosome region tested for being aneuploid with the number of enumerated sequence reads corresponding to the at least one chromosome control region.

21. The method of claim 19, wherein said plurality of non-random polynucleotide sequences comprises at least 300 different non-random polynucleotide sequences selected from the at least one chromosome region tested for being aneuploid and at least 300 different non-random polynucleotide sequences selected from the at least one chromosome control region.

22. The method of claim 19, wherein each of said plurality of non-random polynucleotide sequences is from 10 to 500 nucleotide bases in length.

23. The method of claim 19, wherein the at least one chromosome region tested for being aneuploid is selected from at least one chromosome selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, chromosome X, and chromosome Y.

24. The method of claim 23, wherein said fetal aneuploidy comprises fetal aneuploidy of a chromosome selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, chromosome X, and chromosome Y.

25. The method of claim 24, wherein said fetal aneuploidy is selected from the group consisting of trisomy 21, trisomy 18, trisomy 13, and monosomy X.

26. The method of claim 19, wherein the at least one chromosome control region is selected from at least one chromosome selected from the group consisting of chromosome 1, chromosome 2, chromosome 3, chromosome 13, chromosome 18, and chromosome 21.

27. The method of claim 19, wherein said fetal aneuploidy comprises monosomy, trisomy, tetrasomy, or pentasomy of at least one chromosome.

28. The method of claim 19, wherein said selectively enriching of (b) comprises performing polymerase chain reaction (PCR) amplification.

29. The method of claim 28, wherein for each fetal and maternal cell-free genomic DNA sample PCR amplification comprises hybridizing at least two oligonucleotides to each of the at least 100 different non-random polynucleotide sequences selected from the at least one chromosome region tested for being aneuploid and each of the 100 different non-random polynucleotide sequences selected from the at least one chromosome control region.

30. The method of claim 19, wherein said plurality of non-random polynucleotide sequences comprises no more than 1000 different non-random polynucleotide sequences selected from the at least one chromosome region tested for being aneuploid and no more than 1000 different non-random polynucleotide sequences selected from the at least one chromosome control region.