公开(公告)号：US11894105B2

公开(公告)日：2024-02-06

申请号：US16136463

申请日：2018-09-20

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Rajesh Gottimukkala ,  Cheng-Zong Bai ,  Dumitru Brinza ,  Jeoffrey Schageman ,  Varun Bagai

IPC: G16B30/00 ,  C12Q1/6853 ,  G16B30/10 ,  G16B20/20 ,  G16B50/50

CPC classification number: G16B30/00 ,  C12Q1/6853 ,  G16B20/20 ,  G16B30/10 ,  G16B50/50

Abstract: A method for compressing nucleic acid sequence data wherein each sequence read is associated with a molecular tag sequence, wherein a portion of the sequence reads alignments correspond to sequence reads mapped to a targeted fusion reference sequence includes determining a consensus sequence read for each family of sequence reads based on flow space signal measurements corresponding to the family of sequence reads, determining a consensus sequence alignment for each family of sequence reads, wherein a portion of the consensus sequence alignments correspond to the consensus sequence reads aligned with the targeted fusion reference sequence, generating a compressed data structure comprising consensus compressed data, the consensus compressed data including the consensus sequence read and the consensus sequence alignment for each family, and detecting a fusion using the consensus sequence reads and the consensus sequence alignments from the compressed data structure.

公开(公告)号：US20210217491A1

公开(公告)日：2021-07-15

申请号：US17248083

申请日：2021-01-08

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Sowmi Utiramerur ,  Dumitru Brinza ,  Marcin Sikora ,  Christian Koller ,  Earl Hubbell ,  Chantal Roth ,  Rajesh Gottimukkala

IPC: G16B30/00 ,  G16B20/20

Abstract: Systems and method for determining variants can receive mapped reads and determine a distribution of matched-filter residuals distribution from a plurality of reads at a homopolymer region. The distribution of matched-filter residuals can be fit to uni-modal and bi-modal models. Based on the model that best fits the distribution of matched-filter residuals, the heterozygosity of the sample and the absence or presence of an insertion/deletion in the homopolymer can be determined.

公开(公告)号：US11021734B2

公开(公告)日：2021-06-01

申请号：US15952463

申请日：2018-04-13

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Dumitru Brinza ,  Fiona Hyland

IPC: C12Q1/6869 ,  C12Q1/6858 ,  C12Q1/6806 ,  G16B30/00

Abstract: Systems and method for validation of sequencing results can amplify a target region of a nucleic acid sample in the presence of a primer pool including target specific and variant specific primers. The variant specific primers can include variant specific barcodes and variant specific sequences. An amplicon can be sequenced to determine the sequence of the variant specific barcode. The variant can be identified based on the sequence of the variant specific barcode, and the location of the variant can be determined by mapping the amplicon to a reference sequence.

公开(公告)号：US20180340234A1

公开(公告)日：2018-11-29

申请号：US15989359

申请日：2018-05-25

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Charles Scafe ,  Dumitru Brinza ,  James Veitch ,  Rongsu Qi ,  Fiona Hyland

IPC: C12Q1/6886 ,  C12Q1/6851 ,  C12Q1/6869 ,  G06F19/22 ,  G06F19/24

Abstract: A method for detecting large rearrangements in BRCA1 and BRCA2 genes includes amplifying a nucleic acid sample in the presence of a primer pool to produce amplicons, where the primer pool includes target specific primers targeting regions of exons of the BRCA1 and BRCA2 genes. The method further includes sequencing the amplicons to generate a plurality of reads, mapping the reads to a reference sequence, determining a number of reads per amplicon for the amplicons associated with the exons of the BRCA and the BRCA2 genes, determining exon copy numbers for the exons of the BRCA1 and BRCA2 genes based on the number of reads per amplicon, detecting an exon deletion or duplication based on the exon copy numbers, and detecting a whole gene deletion of the BRCA1 or BRCA2 gene based on the number of reads per amplicon associated with the exons of the BRCA1 and BRCA2 genes.

公开(公告)号：US20180068061A1

公开(公告)日：2018-03-08

申请号：US15672865

申请日：2017-08-09

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Sowmi Utiramerur ,  Dumitru Brinza ,  Marcin Sikora ,  Christian Koller ,  Earl Hubbell ,  Chantal Roth ,  Rajesh Gottimukkala

IPC: G06F19/22

CPC classification number: G16B30/00

Abstract: Systems and method for determining variants can receive mapped reads and determine a distribution of matched-filter residuals distribution from a plurality of reads at a homopolymer region. The distribution of matched-filter residuals can be fit to uni-modal and bi-modal models. Based on the model that best fits the distribution of matched-filter residuals, the heterozygosity of the sample and the absence or presence of an insertion/deletion in the homopolymer can be determined.