Using cell-free DNA fragment size to determine copy number variations

Patent metadata

Field	Value
Publication number	US-11430541-B2
Application number	US-201816119993-A
Country	US
Kind code	B2
Filing date	Aug 31, 2018
Priority date	Feb 3, 2016
Publication date	Aug 30, 2022
Grant date	Aug 30, 2022

Abstract

Disclosed are methods for determining copy number variation (CNV) known or suspected to be associated with a variety of medical conditions. In some embodiments, methods are provided for determining copy number variation of fetuses using maternal samples comprising maternal and fetal cell free DNA. In some embodiments, methods are provided for determining CNVs known or suspected to be associated with a variety of medical conditions. Some embodiments disclosed herein provide methods to improve the sensitivity and/or specificity of sequence data analysis by deriving a fragment size parameter. In some implementations, information from fragments of different sizes are used to evaluate copy number variations. In some implementations, one or more t-statistics obtained from coverage information of the sequence of interest is used to evaluate copy number variations. In some implementations, one or more fetal fraction estimates are combined with one or more t-statistics to determine copy number variations.

First claim

What is claimed is:

1. A method, implemented using a computer comprising one or more processors and system memory, for determining a copy number variation (CNV) of a nucleic acid sequence of interest in a test sample comprising cell-free nucleic acid fragments originating from two or more genomes, the method comprising:
(a) receiving sequence reads obtained by sequencing the cell-free nucleic acid fragments in the test sample;
(b) aligning the sequence reads of the cell-free nucleic acid fragments or aligning fragments containing the sequence reads to bins of a reference genome comprising a sequence of interest, thereby providing test sequence tags, wherein the reference genome is divided into a plurality of bins;
(c) determining fragment sizes of at least some of the cell-free nucleic acid fragments present in the test sample;
(d) determining first coverages of the sequence tags for the bins of the reference genome using sequence tags for the cell-free nucleic acid fragments having sizes in a first size domain;
(e) determining second coverages of the sequence tags for the bins of the reference genome using sequence tags for the cell-free nucleic acid fragments having sizes in a second size domain, wherein the second size domain is different from the first size domain; and
(f) determining a copy number variation in the sequence of interest using the first coverages and the second coverages.

2. The method of claim 1 , wherein (f) comprises determining the copy number variation in the sequence of interest using size characteristics of bins in the sequence of interest in addition to the first coverages and the second coverages, wherein the size characteristics of the bins were determined using fragment sizes of reads aligned to the bins.

3. The method of claim 1 , wherein the first size domain comprises cell-free nucleic acid fragments of substantially all sizes in the sample, and the second size domain comprises only cell-free nucleic acid fragments smaller than a defined size.

4. The method of claim 1 , wherein the second size domain comprises only the cell-free nucleic acid fragments smaller than about 150 bp.

5. The method of claim 1 , wherein (f) comprises determining the copy number variation based on a likelihood ratio obtained from the first coverages and the second coverages.

6. The method of claim 5 , wherein the likelihood ratio comprises a first likelihood that the test sample is an aneuploid sample over a second likelihood that the test sample is a euploid sample.

7. The method of claim 1 , wherein (f) comprises determining the copy number variation in the sequence of interest based on a likelihood ratio obtained using one or more values of fetal fraction, the first coverages, and the second coverages.

8. The method of claim 7 , wherein the one or more values of fetal fraction comprise a value of fetal fraction calculated using the fragment sizes of at least some of the cell-free nucleic acid fragments.

9. The method of claim 8 , wherein the value of fetal fraction is calculated by:
obtaining a frequency distribution of the fragment sizes; and
applying the frequency distribution to a model relating fetal fraction to frequency of fragment size to obtain the fetal fraction value.

10. The method of claim 7 , wherein the likelihood ratio is calculated from a fetal fraction, a t-statistic of short fragments, and a t statistics of all fragments, wherein the short fragments are cell-free nucleic acid fragments in the first size domain, which is a first size range smaller than a criterion size, and the all fragments are cell-free nucleic acid fragments in the second size domain, which includes the short fragments and fragments longer than the criterion size.

11. The method of claim 10 , wherein the likelihood ratio is calculated:

LR
=

Σ

ff
total

⁢

q
⁡

(

ff
total

)

*

p
1

⁡

(

T
short

,

T
all

|

ff
est

)

p
0

⁡

(

T
short

,

T
all

)

where p 1 represents a likelihood that data come from a multivariate normal distribution representing a 3-copy or 1-copy model, p 0 represents a likelihood that data come from a multivariate normal distribution representing a 2-copy model, T short , T all are T scores calculated from chromosomal coverage generated from short fragments and all fragments, and q(ff total ) is a density distribution of the fetal fraction.

12. The method of claim 1 , wherein the copy number variation comprises monosomy X, trisomy X, trisomy 13, trisomy 18, or trisomy 21.

13. The method of claim 1 , wherein (f) comprises obtaining a first t-statistic using the first coverages and a second t-statistic using the second coverages.

14. The method of claim 2 , wherein the size characteristic for a bin comprises a ratio of fragments of size smaller than a defined value to total fragments in the bin.

15. The method of claim 14 , wherein (f) comprises obtaining a third t-statistic using the size characteristics of bins.

16. The method of claim 15 , wherein (f) comprises calculating a likelihood ratio from a first t-statistic for the sequence of interest using the first coverages, a second t-statistic for the sequence of interest using the second coverages, and third t-statistic for the sequence of interest using the size characteristics.

17. The method of claim 1 , wherein (d) and/or (e) comprises:
(i) determining a number of sequence tags aligning to the bin, and
(ii) normalizing the number of sequence tags aligning to the bin by accounting for bin-to-bin variations due to factors other than copy number variation.

18. The method of claim 17 , wherein normalizing the number of sequence tags comprises: normalizing for GC content of the sample, normalizing for a global wave profile of variation of a trainin

Assignees

• Verinata Health Inc

Inventors

• Duenwald Sven
• Comstock David A
• Barbacioru Catalin
• Chudova Darya I
• Rava Richard P
• Jones Keith W
• Chen Gengxin
• Skvortsov Dimitri

Classifications

• G06F18/24323

  Tree-organised classifiers · CPC title

• G06F18/23

  Clustering techniques · CPC title

• G16B20/10 Primary

  Ploidy or copy number detection · CPC title

• C12Q2537/16

  Assays for determining copy number or wherein the copy number is of special importance · CPC title

• G16B30/00

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