Combined size- and count-based analysis of maternal plasma for detection of fetal subchromosomal aberrations

Patent metadata

Field	Value
Publication number	US-10319463-B2
Application number	US-201614994023-A
Country	US
Kind code	B2
Filing date	Jan 12, 2016
Priority date	Jan 23, 2015
Publication date	Jun 11, 2019
Grant date	Jun 11, 2019

Abstract

An aberration in a fetal genome can be identified by analyzing a sample of fetal and maternal DNA. Classifications of whether an aberration (amplification or deletion) exists in a subchromosomal region are determined using count-based and size-based methods. The count classification and the size classification can be used in combination to determine whether only the fetus or only the mother, or both, have the aberration in the subchromosomal region, thereby avoiding false positives when the mother has the aberration and the fetus does not.

First claim

What is claimed is:

1. A method of identifying a subchromosomal aberration in a fetal genome of a fetus by analyzing a biological sample from a female subject pregnant with the fetus, the biological sample including cell-free DNA molecules from the female subject and the fetus, the method comprising:
for each of a plurality of DNA molecules in the biological sample:
measuring a size of the DNA molecule;
identifying a location of the DNA molecule in a reference genome, thereby obtaining locations of the plurality of DNA molecules;

detecting, by a computer system, an aberration in the biological sample of a first subchromosomal region by:
determining a first amount of the plurality of DNA molecules located in the first subchromosomal region using the locations of the plurality of DNA molecules;
determining a second amount of the plurality of DNA molecules located in a second region using the locations of the plurality of DNA molecules;
computing a count parameter from the first amount and the second amount; and
comparing the count parameter to one or more count threshold to determine a count classification of a type of aberration existing in the biological sample for the first subchromosomal region;

determining, by the computer system, a size classification for the first subchromosomal region by:
calculating a first statistical value of sizes of the plurality of DNA molecules located in the first subchromosomal region;
calculating a reference statistical value of sizes of DNA molecules located in a reference region;
determining a separation value between the first statistical value and the reference statistical value; and
comparing the separation value to one or more size thresholds to obtain the size classification; and

determining whether the fetus has the aberration in the first subchromosomal region based on the size classification and the count classification.

2. The method of claim 1 , further comprising:
identifying the first subchromosomal region by:
determining a respective bin count parameter for each of a plurality of non-overlapping bins in the reference genome, each respective bin count parameter determined from a respective amount of DNA molecules location in a respective bin; and
performing a segmentation process that merges consecutive bins into a merged segment based on the consecutive bins having a same count classification, wherein the first subchromosomal region corresponds to a first merged segment.

3. The method of claim 2 , wherein the segmentation process includes at least one of: a binary circular segmentation and a Hidden Markov model.

4. The method of claim 1 , further comprising:
detecting a plurality of aberrations in the biological sample for a plurality of other subchromosomal regions by comparing other count parameters to the one or more count thresholds to determine other count classifications; and
determining whether the fetus has the plurality of aberrations in the plurality of other subchromosomal regions based on the other count classifications and other size classifications for the plurality of other subchromosomal regions.

5. The method of claim 1 , wherein the count classification is over-represented or under-represented.

6. The method of claim 1 , wherein the aberration is a deletion or a duplication.

7. The method of claim 1 , wherein the size classification is one of longer, shorter, or equal.

8. The method of claim 1 , wherein the fetus is determined to have an amplification in the first subchromosomal region when:
the count classification indicates the amplification and the size classification indicates the aberration does not exist in the first subchromosomal region, or
the count classification indicates the amplification and the size classification indicates the amplification.

9. The method of claim 8 , further comprising:
determining the female subject to also have the amplification in the first subchromosomal region when the count classification indicates the amplification and the size classification indicates the aberration does not exist in the first subchromosomal region.

10. The method of claim 8 , further comprising:
determining the female subject not to have the amplification in the first subchromosomal region when the count classification indicates the amplification and the size classification indicates the amplification.

11. The method of claim 1 , wherein the fetus is determined to have a deletion in the first subchromosomal region when:
the count classification indicates the deletion and the size classification indicates the aberration does not exist in the first subchromosomal region, or
the count classification indicates the deletion and the size classification indicates the deletion.

12. The method of claim 11 , further comprising:
determining the female subject to also have the deletion in the first subchromosomal region when the count classification indicates the deletion and the size classification indicates the aberration does not exist in the first subchromosomal region.

13. The method of claim 11 , further comprising:
determining the female subject not to have the deletion in the first subchromosomal region when the count classification indicates the deletion and the size classification indicates the deletion.

14. The method of claim 1 , wherein the fetus is determined not to have the aberration when:
the count classification indicates an amplification and the size classification indicates a deletion, or
the count classification indicates the deletion and the size classification indicates the amplification.

15. The method of claim 14 , further comprising:
determining the female subject to have the amplification when the count classification indicates the amplification and the size classification indicates the deletion.

16. The method of claim 14 , further comprising:
determining the female subject to have the deletion when the count classification indicates the deletion and the size classification indicates the amplification.

17. The method of claim 1 , further comprising:
determining a first bin count parameter for a first bin of the first subchromosomal region, the first subchromosomal region including one or more bins, the first bin count parameter determined from a third amount of DNA molecules located in a third region and a fourth amount of DNA molecules located in the first bin;
computing a mean of control bin count parameters for the first bin using control samples;
computing a first score for the first bin by subtracting the mean of control bin count parameters from the first bin count parameter; and
determining whether the first score is greater than a cutoff value to identify whether the female subject has the aberration for the first subchromosomal region.

18. The method of claim 17 , further comprising:
measuring a fetal DNA concentration in the biological sample;
computing a difference between the first score and the fetal DNA concentration, and wherein the determining whether the first score is greater than the cutoff value includes determining whether the difference is greater than a high threshold value.

19. The method of claim 18 , further comprising:
comparing the difference to a low threshold; and
determining that only the fetus has the aberration for the first subchromosomal region when the difference is below a low threshold value.

20. The method of claim 17 , wherein subtracting the mean of control bin count parameters from the first bin count parameter provide

Assignees

• Univ Hong Kong Chinese

Inventors

• Lo Yuk-Ming Dennis
• Chiu Rossa Wai Kwun
• Chan Kwan Chee
• Jiang Peiyong
• Yu Cheuk Yin Jandy

Classifications

• C12Q1/6883

  for diseases caused by alterations of genetic material · CPC title

• 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 · CPC title

• G16B20/10 Primary

  Ploidy or copy number detection · CPC title

• G16B30/00 Primary

  ICT specially adapted for sequence analysis involving nucleotides or amino acids · CPC title

• G16B20/20

  Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection · CPC title