Patent Document ID: 9845552
Application ID: 14354528
Patent Status: 1

Claim One:
1. A method, implemented on a computer system comprising one or more processors and system memory, for detecting copy number variations, the method comprising: (a) receiving, by the computer system, a plurality of reads obtained from a sample; (b) providing, on the computer system, a plurality of One Read Bloom filters corresponding to a plurality of regions of a genome and a plurality of Multiple Read Bloom filters corresponding to the plurality of regions of the genome, wherein each Bloom filter comprises a bit array, one or more hash functions, and logic for applying reads to the Bloom filter, each One Read Bloom filter was constructed using approximately read-sized sequences in its corresponding region of the genome, and each Multiple Read Bloom filter was constructed using approximately read-sized sequences found more than once in its corresponding region of the genome; (c) applying, by the one or more processors, each read of the plurality of reads to each One Read Bloom filter to determine a membership of each read in each One Read Bloom filter, wherein applying a read to a Bloom filter comprises: providing the read as an input to each hash function of the one or more hash functions of the Bloom filter, obtaining an output value from each hash function and the read, wherein each output value is associated with a bit position in the bit array of the Bloom filter, and determining that the read is a member of the Bloom filter based on bit values of the bit array at bit positions associated with output values obtained from the one or more hash functions and the read; (d) applying, by the one or more processors, each read of the plurality of reads to each Multiple Read Bloom filter to determine a membership of each read in each Multiple Read Bloom filter; (e) determining, based on the memberships determined in (c) and (d) and by the one or more processors, which one or more regions of the plurality of regions the reads are aligned to; (f) determining, by the one or more processors, from a number of reads aligned to each of the plurality of regions of the genome, read abundance values of the plurality of regions of the genome; (g) comparing, on a region-to-region basis and by the one or more processors, a read abundance value of each region of the plurality of regions of the genome to a threshold number to produce one or more statistical values indicating aberrations of read abundance in one or more regions of the plurality of regions; and (h) making, based on the one or more statistical values, one or more detection calls of copy number variation in one or more of the plurality of regions of the genome.