Patent ID: 11961591
Assignee: LIFE TECHNOLOGIES CORPORATION
Field: Biotechnology (Chemistry)
Classification: CPC G  C | IPC C  G

Claim 0:
1. A method for detecting an internal tandem duplication in an FLT3 gene of a sample, comprising:
amplifying a nucleic acid sample in a presence of a primer pool to produce a plurality of template polynucleotide strands, the primer pool including a plurality of target specific primers targeting regions of exons of the FLT3 gene;
disposing the plurality of template polynucleotide strands in a plurality of reaction confinement regions on a sensor array, wherein the sensor array comprises at least 105 sensors in electrical communication with the reaction confinement regions;
exposing a plurality of the template polynucleotide strands disposed in the reaction confinement regions on the sensor array to a series of flows of sequencing reagents including nucleotide species and polymerase to obtain raw sequencing data reads for the template polynucleotide strands;
determining base sequences of the raw sequencing data reads by base calling to generate a plurality of reads, wherein the plurality of reads includes a plurality of forward reads and a plurality of reverse reads;
mapping the forward reads and the reverse reads to a reference genome, wherein the reference genome includes the targeted regions of exons of the FLT3 gene, wherein the mapping produces a pileup comprising a plurality of alignments of the forward reads and the reverse reads with the reference genome and a plurality of columns corresponding to positions along the reference genome, wherein a portion of the plurality of forward reads and the plurality of reverse reads are partially mapped to the reference genome for a plurality of partially mapped reads, wherein a partially mapped read includes a mapped portion, a soft-clipped portion and a breakpoint;
analyzing the partially mapped reads intersecting a column of the pileup for tandem duplications, including:
detecting a duplication in the soft-clipped portion by comparing a sequence of the soft-clipped portion to a sequence of the mapped portion of the partially mapped read adjacent to the breakpoint;
determining an insert size of the duplication in the soft-clipped portion;
filtering the detected duplications based on properties of duplicated copies to form filtered partially mapped reads;
assigning the filtered partially mapped read to a category based on the insert size to generate a plurality of categories corresponding to a plurality of insert sizes, each category having a number of members corresponding to the filtered partially mapped reads having the corresponding insert size;
converting the categories into features corresponding to the column, wherein a feature includes the insert size and a sequence of an insert at an insert position; and
merging the features corresponding to one or more columns representing a same insert to determine a location and a size of a tandem duplication.