Patent ID: 11929146
Assignee: SEQUENOM, INC.
Field: Computer technology (Electrical engineering)
Classification: CPC G | IPC G

Claim 0:
1. A system comprising memory and one or more microprocessors, which memory comprises instructions and which one or more microprocessors are configured to perform, according to the instructions, a process for determining a presence or absence of one or more chromosome alterations in a test sample of nucleic acids, which process comprises:
(a) identifying discordant read pairs from paired-end sequence reads, wherein the paired-end sequence reads are reads of circulating, cell-free nucleic acid from a test subject sample, thereby identifying discordant read mates;
(b) characterizing a mappability of a plurality of sequence read subsequences of each discordant read mate aligned to a reference genome, each of which sequence read subsequences of each discordant read mate is of a different length;
(c) selecting a subset of the discordant read mates according to a change in the mappability, wherein the subset comprises reads comprising a candidate breakpoint;
(d) comparing (i) the number of discordant read mates from the sample associated with the candidate breakpoints and optionally one or more substantially similar breakpoints, to (ii) the number of discordant read mates from a reference associated with the candidate breakpoint and optionally the one or more substantially similar breakpoints, for the discordant read mates in the subset selected in (c), thereby generating a comparison; and
(e) determining the presence or absence of one or more chromosome alterations for the sample according to the comparison in (d).