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US 11,694,768 B2Granted
Methods and processes for assessment of genetic variations
OwnerJohn A. Tynan, Amin Mazloom +3inventors
InventorsJohn A. Tynan, Amin Mazloom, Yijin Wu, Mark Whidden, Mathias Ehrich
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Abstract
Technology provided herein relates in part to non-invasive classification of one or more genetic copy number variations (CNVs) for a test sample. Technology provided herein is useful for classifying a genetic CNV for a sample as part of non-invasive pre-natal (NIPT) testing and oncology testing, for example.
Claims20
A method for classifying a presence or absence of a copy number variation in a sub-chromosome region of interest for a test sample, comprising:
- (a) obtaining thousands to millions sequence reads for circulating cell free nucleic acid in the test sample;
- (b) mapping the thousands to millions sequence reads to genomic portions of a reference genome;
- (c) determining a classification of a presence or absence of the copy number variation in a predetermined sub-region for the test sample based on a quantification of sequence reads mapped to the sub-region, wherein the sub-region is encompassed by the sub-chromosome region of interest;
- (d) determining a classification of a presence or absence of the copy number variation in a segment of a set of segments based on a quantification of sequence reads mapped to the segment, wherein:
- the determining comprises identifying the set of segments by a segmentation process based on a profile of the thousands to millions sequence reads mapped to each of the genomic portions;
- and
- the segment overlaps with the sub-region;
- and
- (e) determining a classification of the presence or absence of the copy number variation in the sub-chromosome region of interest for the test sample based on:
- (i) the classification in (c), (ii) the classification in (d), and (iii) a fetal fraction determined for the circulating cell free nucleic acid.
7 more elements
A system comprising:
- a memory configured to store computer-executable instructions;
- and
- a processor configured to access the memory and execute the computer-executable instructions to perform operations comprising:
- (a) obtaining thousands to millions sequence reads for circulating cell free nucleic acid in a test sample;
- (b) mapping the thousands to millions sequence reads to genomic portions of a reference genome;
- (c) determining a classification of a presence or absence of a copy number variation in a predetermined sub-region for the test sample based on a quantification of sequence reads mapped to the sub-region, wherein the sub-region is encompassed by a sub-chromosome region of interest;
- (d) determining a classification of a presence or absence of the copy number variation in a segment of a set of segments based on a quantification of sequence reads mapped to the segment, wherein:
- the determining comprises identifying the set of segments by a segmentation process based on a profile of the thousands to millions sequence reads mapped to each of the genomic portions;
- and
- the segment overlaps with the sub-region;
- and
- (e) determining a classification of a presence or absence of the copy number variation in the sub-chromosome region of interest for the test sample based on:
- (i) the classification in (c), (ii) the classification in (d), and (iii) a fetal fraction determined for the circulating cell free nucleic acid.
10 more elements
A non-transitory machine readable storage medium having instructions stored thereon that when executed by one or more processors cause the one or more processors to perform operations comprising:
- (a) obtaining thousands to millions sequence reads for circulating cell free nucleic acid in a test sample;
- (b) mapping the thousands to millions sequence reads to genomic portions of a reference genome;
- (c) determining a classification of a presence or absence of a copy number variation in a predetermined sub-region for the test sample based on a quantification of sequence reads mapped to the sub-region, wherein the sub-region is encompassed by a sub-chromosome region of interest;
- (d) determining a classification of a presence or absence of the copy number variation in a segment of a set of segments based on a quantification of sequence reads mapped to the segment, wherein:
- the determining comprises identifying the set of segments by a segmentation process based on a profile of the thousands to millions sequence reads mapped to each of the genomic portions;
- and
- the segment overlaps with the sub-region;
- and
- (e) determining a classification of a presence or absence of the copy number variation in the sub-chromosome region of interest for the test sample based on:
- (i) the classification in (c), (ii) the classification in (d), and (iii) a fetal fraction determined for the circulating cell free nucleic acid.
7 more elements
Dependencies are inferred from the claim text.