Methods and processes for non-invasive assessment of genetic variations
AssigneeSequenom, Inc.
InventorsZeljko Dzakula, Cosmin Deciu, Chen Zhao
Life of this patent
Estimating the term…
Abstract
A method and system for analyzing circulating cell-free nucleic acids from a pregnant female with reduced bias. Counts of sequence reads mapped to portions of a reference genome are obtained. A regression model is generated that models the relationship between the counts and the GC content. The read counts are normalized according to the regression model to remove the GC bias. The normalized counts are used for further analysis, such as the detection of fetal aneuploidy.
Claims19
A computer-implemented method for calculating with reduced bias genomic section levels for a test sample, comprising:
- (I) sequencing circulating cell-free nucleic acid from a test sample by a non-targeted massively parallel sequencing process, thereby generating sequence reads for the test sample;
- (II) mapping, using a processor, the sequence reads to a reference genome;
- (III) obtaining, using a processor, counts of sequence reads mapped to portions of the reference genome;
- (IV) normalizing, using a processor, the counts of the sequence reads according to a process comprising:
- (a) determining one or more estimates of curvature for the test sample from a fitted relation between (i) the counts of the sequence reads mapped to the portions of the reference genome obtained in (III) for the test sample, and (ii) GC content of the respective portions of the reference genome;
- (b) providing, for the respective portions, one or more portion-specific estimates of curvature for multiple portions of the reference genome from a fitted relation between (i) one or more sample-specific estimates of curvature for a plurality of euploid samples, and (ii) counts of sequence reads mapped to the respective portions of the reference genome for the plurality of euploid samples;
- and
- (c) calculating a normalized genomic section level of each of the respective portions of the reference genome for the test sample according to
- (1) the counts of the sequence reads obtained in (III) for the test sample,
- (2) the one or more estimates of curvature determined in (IV) (a) for the test sample, and
- (3) the one or more portion-specific estimates of curvature provided in (IV) (b),
- thereby providing normalized genomic section levels, whereby bias in the counts of the sequence reads mapped to each of the portions of the reference genome is reduced in the normalized genomic section levels.
A system comprising a sequencer configured to generate sequence reads from a circulating cell-free nucleic acid test sample by a non-targeted massively parallel sequencing process, one or more processors, and memory, which memory comprises instructions executable by the one or more processors, and which instructions executable by the one or more processors are configured to:
- (I) map the sequence reads generated by the sequencer to a reference genome;
- (II) count the sequence reads mapped to portions of the reference genome;
- (III) normalize the counts of the sequence reads according to a process comprising:
- (a) determining one or more estimates of curvature for the test sample from a fitted relation between (i) the counts of the sequence reads mapped to the portions of the reference genome in (II) for the test sample, and (ii) GC content of the respective portions of the reference genome;
- (b) providing, for the respective portions, one or more portion-specific estimates of curvature for multiple portions of the reference genome from a fitted relation between (i) one or more sample-specific estimates of curvature for a plurality of euploid samples, and (ii) counts of sequence reads mapped to the respective portions of the reference genome for the plurality of euploid samples;
- and
- (c) calculating a normalized genomic section level of the respective portions of the reference genome for the test sample according to
- (1) the counts of the sequence reads in (II) for the test sample,
- (2) the one or more estimates of curvature determined in (III) (a) for the test sample, and
- (3) the one or more portion-specific estimates of curvature provided in (III) (b),
- thereby providing normalized genomic section levels, whereby bias in the counts of the sequence reads mapped to the portions of the reference genome is reduced in the normalized genomic section levels.
Dependencies are inferred from the claim text.