US 2026/0031185 A1Published application

Genomic sequencing selection system

AssigneeQuest Diagnostics Investments Incorporated

InventorsAnindya Bhattacharya, Anna Gerasimova, Quoclinh Nguyen, Christopher Elzinga, Edward Moler

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Abstract

The systems and methods discussed herein can calculate sequencing statistics such as coverage depth for sequencing data. The present solution can determine variant frequencies and identify clinically relevant variants. The present solution can read BAM and VCF input files and Phred scaled quality scores. The present solution can select relatively high quality reads based on the quality scores and can calculate reference and alternative allele counts for SNPs, insertions and deletions (INDELs), and structural variants.

Claims20

Dependent claims

A system for managing data in data buffers, comprising:

a data processing system having one or more processors coupled with memory, the data processing system configured to:
retrieve, from a data repository, a file comprising data identifying a plurality of gene sequence reads, wherein the data for each of the plurality of gene sequence reads comprises a respective indication of a position, a base value, and a quality score;
load, onto a data buffer, the data identifying the plurality of gene sequence reads from the file;
select a first portion of the data corresponding to a first subset of the plurality of gene sequence reads, wherein each of the first subset of the plurality of gene sequence reads are associated with a chromosome;
filter the first portion of the data corresponding to the first subset of the plurality of gene sequence reads, to select a second portion of the data corresponding to a second subset of the plurality of gene sequence reads comprising base values having an associated quality score above a threshold;
store, on the data buffer, the second portion of the data by discarding a remaining portion of the data corresponding to a third subset of the plurality of gene sequence reads;
determine, using the second portion of the data, (i) an alternative base count identifying a number of deletions, insertions, reference skips, soft clips, or hard clips and (ii) an aggregate count for nucleotides at each base pair position corresponding to the second subset of the plurality of gene sequence reads;
generate an identification of a gene sequence variant in the second subset of the plurality of gene sequence reads based on a ratio between the alternative base count and the aggregate count;
and
provide, for display, the identification of the gene sequence variant in the second subset of the plurality of gene sequence reads.

7 more elements

A method of managing data in data buffers, comprising:

retrieving, by a data processing system, from a data repository, a file comprising data identifying a plurality of gene sequence reads, wherein the data for each of the plurality of gene sequence reads comprises an indication of a position, a base value, and a quality score;
loading, by the data processing system, onto a data buffer, the data identifying the plurality of gene sequence reads from the file;
selecting, by the data processing system, a first portion of the data corresponding to a first subset of the plurality of gene sequence reads, wherein each of the first subset of the plurality of gene sequence reads are associated with a chromosome;
filtering, by the data processing system, the first portion of the data corresponding to the first subset of the plurality of gene sequence reads to select a second portion of the data corresponding to a second subset of the plurality of gene sequence reads comprising base values having an associated quality score above a first threshold;
storing, by the data processing system, on the data buffer, the second portion of the data by discarding a remaining portion of the data corresponding to a third subset of the plurality of gene sequence reads;
determining, by the data processing system, using the second portion of the data, (i) an alternative base count identifying a number of deletions, insertions, reference skips, soft clips, or hard clip and (ii) an aggregate count for nucleotides at each base pair position corresponding to the second subset of the plurality of gene sequence reads;
generating, by the data processing system, an identification of a gene sequence variant in the second subset of the plurality of gene sequence reads based on a ratio between the alternative base count and the aggregate count;
and
providing, by the data processing system, for display, the identification of the gene sequence variant in the second subset of the plurality of gene sequence reads.

6 more elements

Dependencies are inferred from the claim text.