Method for improving the sensitivity of detection in determining copy number variations

A method, implemented at a computer system that includes one or more processors and system memory, for creating a sequence mask for evaluation of copy number of a nucleic acid sequence of interest, the method comprising:

• (a) providing, at the computer system, a training set comprising sequence reads from a plurality of unaffected training samples;
• (b) aligning, by the computer system, the sequence reads of the training set to a reference genome comprising the nucleic acid sequence of interest, thereby providing training sequence tags for the training samples;
• (c) dividing, by the computer system, the reference genome into a plurality of bins;
• (d) determining for each unaffected training sample, by the computer system, a coverage of training sequence tags in each bin for each training sample, wherein the coverage indicates an abundance of sequence tags in a bin;
• (e) determining, for each bin, an expected coverage of the training sequence tags across all training samples;
• (f) adjusting, by the computer system, the coverage of the training sequence tags in each bin for each training sample according to the expected coverage in each bin, thereby obtaining global-profile-corrected coverages of the training sequence tags in the bins for each training sample;

A system for evaluation of copy number of a nucleic acid sequence of interest in a test sample, the system comprising:

• a sequencer for receiving nucleic acids from the test sample providing nucleic acid sequence information from the sample;
• one or more processors;
• and
• one or more computer-readable storage media having stored thereon instructions for execution on said processor to evaluate copy number in the test sample using a method comprising:
• (a) providing, at the system, sequence reads of the test sample;
• (b) aligning, by the one or more processors, the sequence reads of the test sample to a reference genome comprising the nucleic acid sequence of interest, thereby providing test sequence tags;
• (c) determining, by the one or more processors, a coverage of the test sequence tags located in each bin, wherein the reference genome is divided into a plurality of bins;
• (d) providing, by the one or more processors, a global profile for the nucleic acid sequence of interest, wherein the global profile comprises an expected coverage in each bin, and wherein the expected coverage is obtained from a training set of unaffected training samples sequenced and aligned in substantially the same manner as the test sample, the expected coverage exhibiting variation from bin to bin;
• (e) adjusting, by the one or more processors, the coverage of the test sequence tags according to the expected coverage in each bin, thereby obtaining a global-profile-corrected coverage in each bin of the test sequence tags;
• (f) adjusting, by the one or more processors, the global-profile-corrected coverages based on the a relation between GC content level and the global-profile-corrected coverage for the bins of the test sequence tags, thereby obtaining a sample-GC-corrected coverage of the test sequence tags on the nucleic acid sequence of interest;
• and
• (g) evaluating, by the one or more processors, copy number of the nucleic acid sequence of interest in the test sample based on the sample-GC-corrected coverage.

A computer program product comprising one or more computer-readable non-transitory storage media having stored thereon computer-executable instructions that, when executed by one or more processors of a computer system, cause the computer system to implement a method for evaluation of copy number of a chromosome or a nucleic acid sequence of interest in a test sample comprising fetal and maternal cell-free nucleic acids, the method comprising:

• (a) providing, at the computer system, sequence reads obtained by a nucleic acid sequencer from the test sample, which test sample comprises nucleic acid molecules from one or more genomes;
• (b) aligning, by the computer system, the sequence reads of the test sample to a reference genome comprising the nucleic acid sequence of interest, thereby providing test sequence tags;
• (c) determining, by the computer system, a coverage of the test sequence tags located in each bin, wherein the reference genome is divided into a plurality of bins, and wherein the coverage indicates an abundance of sequence tags in a bin;
• (d) providing, by the computer system, a global profile for the nucleic acid sequence of interest, wherein the global profile comprises an expected coverage in each bin, and wherein the expected coverage is obtained from a training set of unaffected training samples comprising nucleic acid molecules sequenced and aligned in substantially the same manner as the test sample, the expected coverage exhibiting variation from bin to bin;
• (e) adjusting, by the computer system, the coverage of the test sequence tags using the expected coverage in each bin of at least the nucleic acid sequence of interest, thereby obtaining global-profile-corrected coverages for the nucleic acid sequence of interest;
• (f) adjusting, by the computer system, global-profile-corrected coverages based on a relation between GC content levels and the global-profile-corrected coverages, thereby obtaining sample-GC-corrected coverages for the nucleic acid sequence of interest;
• and
• (g) evaluating, by the computer system, a copy number of the nucleic acid sequence of interest in the test sample based on the sample-GC-corrected coverages, wherein the sample-GC-corrected coverages improve a signal level and/or reduce a noise level for determining the copy number of the nucleic acid sequence of interest.