Diagnosing fetal chromosomal aneuploidy using paired end

• US 8,442,774 B2
• Filed: 03/28/2012
• Issued: 05/14/2013
• Est. Priority Date: 07/23/2007
• Status: Active Grant

• Current Assignee: Chinese University of Hong Kong
• Original Assignee: Chinese University of Hong Kong
• Inventors: Lo, Yuk-Ming Dennis, Chiu, Rossa Wai Kwun, Chan, Kwan Chee
• Primary Examiner(s): SIMS, JASON M
• Application Number:
  US13/433,110
• Publication Number:
  US 20120190559A1
• Time in Patent Office: 412 Days
• Field of Search: None
• US Class Current: 702/19
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2537/16 Assays for determining copy number or wherein the copy number is of special importance
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/10 Ploidy or copy number detection
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search

Abstract

Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. The determination of the relative amounts may count sequences of only certain length. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists. Prior to sequencing, the biological sample may be enriched for DNA fragments of a particular sizes.

Claims

1. A method for performing prenatal diagnosis of a fetal chromosomal aneuploidy in a fetus by analyzing a biological sample obtained from a female subject pregnant with the fetus, wherein the biological sample includes nucleic acid molecules from the female subject and from the fetus, the method comprising:

sequencing a plurality of the nucleic acid molecules contained in the biological sample to obtain paired-end sequence reads for each of the plurality of nucleic acid molecule;

aligning the paired-end sequenced reads of the plurality of nucleic acid molecules to identify from which chromosomes the nucleic acid molecules originate;

determining a length for each of the plurality of nucleic acid molecules based on the paired-end sequence reads;

determining a first amount of nucleic acid molecules identified as originating from a first chromosome;

determining a second amount of nucleic acid molecules identified as originating from one or more second chromosomes, wherein the determination of the first amount and the second amount is based on the determined lengths of the corresponding nucleic acid molecules;

determining a parameter from the first amount and the second amount;

comparing the parameter to one or more cutoff values; and

based on the comparison, determining a classification of whether a fetal chromosomal aneuploidy exists for the first chromosome.

2. The method of claim 1, wherein determining a length for each of the nucleic acid molecules includes:

identifying a location of each sequenced end of a nucleic acid molecule on a reference sequence; and

determining the length between the two locations on the reference sequence.

3. The method of claim 1, wherein the parameter is includes a ratio of the first amount and the second amount.

4. The method of claim 1, wherein the nucleic acid molecules of the one or more second chromosomes have an expected average length that is within two nucleotides of the expected average length for the nucleic acid molecules of the first chromosome.

5. The method of claim 1, wherein the nucleic acid molecules of the one or more second chromosomes have an expected maximum and minimum length that are both within two nucleotides of the expected maximum and minimum length for the nucleic acid molecules of the first chromosome.

6. The method of claim 1, wherein the nucleic acid molecules used to determine the first amount are selected to be less than a first specified number of nucleotides.

7. The method of claim 6, wherein the nucleic acid molecules used to determine the second amount are selected to be less than another specified number of nucleotides, wherein the another specified number is different than the first specified number.

8. The method of claim 7, wherein the another specified number is selected based on an expected size distribution for the nucleic acid molecules of the least one of the second chromosomes that are in the biological sample.

9. The method of claim 6, wherein the first specified number is selected to provide at least a specific total amount for the first amount and the second amount.

10. The method of claim 9, wherein the total amount is a count of two million nucleic acid molecules.

11. The method of claim 9, wherein the total amount is a count of 250,000 nucleic acid molecules.

12. The method of claim 6, wherein the first specified number of nucleotides is between about 125 nucleotides and about 175 nucleotides.

13. The method of claim 6, wherein the nucleic acid molecules used to determine the first amount are selected to be greater than a second specified number of nucleotides.

14. The method of claim 13, wherein the second specified number is between about 100 and about 125 nucleotides.

15. The method of claim 13, wherein the nucleic acid molecules used to determine the second amount are selected to be greater than another specified number of nucleotides, wherein the another specified number is different than the second specified number.

16. The method of claim 1, wherein prior to sequencing, the biological sample has been enriched for nucleic acid molecules less than a predetermined number of nucleotides.

17. The method of claim 1, wherein the paired-end sequence reads of each nucleic acid molecule include all of the respective nucleic acid molecule.

18. The method of claim 1, wherein the biological sample is blood, plasma, serum, urine or saliva.

19. The method of claim 1, wherein the first chromosome is chromosome 21, chromosome 18, chromosome 13, chromosome X, or chromosome Y.

21. The method of claim 1, wherein the first amount is the accumulated lengths of the nucleic acid molecules identified as originating from the first chromosome, and the second amount is the accumulated lengths of the nucleic acid molecules identified as originating from the one or more second chromosomes.

20. A computer program product comprising a computer readable medium encoded with a plurality of instructions for controlling a computing system to perform an operation for performing prenatal diagnosis of a fetal chromosomal aneuploidy in a fetus by analyzing a biological sample obtained from a female subject pregnant with the fetus, wherein the biological sample includes nucleic acid molecules from the female subject and from the fetus, the operation comprising:

receiving paired-end sequence reads for each of a plurality of the nucleic acid molecules contained in the biological sample;

aligning the paired-end sequenced reads of the plurality of nucleic acid molecules to identify from which chromosomes the nucleic acid molecules originate;

determining a length for each of the plurality of nucleic acid molecules based on the paired-end sequence reads;

determining a first amount of nucleic acid molecules identified as originating from a first chromosome;

determining a second amount of nucleic acid molecules identified as originating from one or more of the second chromosomes, wherein the determination of the first amount and the second amount is based on the determined lengths of the corresponding nucleic acid molecules;

determining a parameter from the first amount and the second amount;

comparing the parameter to one or more cutoff values; and

based on the comparison, determining a classification of whether a fetal chromosomal aneuploidy exists for the first chromosome.