公开(公告)号：US10937522B2

公开(公告)日：2021-03-02

申请号：US16211609

申请日：2018-12-06

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Brijesh Krishnaswami ,  Yuandan Lou ,  Asim Siddiqui ,  Heinz Breu ,  Amitabh Shukla ,  Karl Kuhlmann

IPC: G16B20/00 ,  G06F16/9038 ,  G16B50/00

Abstract: Systems and method for annotating variants within a genome can call variants from reads or receive called variants directly and associate the called variants with functional annotations and interpretive annotations. A summary report of the called variants, the associated functional annotations, and the associated interpretive annotations can be generated.

公开(公告)号：US20180276338A1

公开(公告)日：2018-09-27

申请号：US15928202

申请日：2018-03-22

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Paolo Vatta ,  Onur Sakarya ,  Heinz Breu ,  Liviu Popescu ,  Asim Siddiqui ,  Fiona Hyland

IPC: G06F19/22

CPC classification number: G16B30/00

Abstract: Systems and methods are used to identify an exon junction from a single read of a transcript. A transcript sample is interrogated and a read sequence is produced using a nucleic acid sequencer. A first exon sequence and a second exon sequence are obtained using the processor. The first exon sequence is mapped to a prefix of the read sequence using the processor. The second exon sequence is mapped to a suffix of the read sequence using the processor. A sum of a number of sequence elements of the first exon sequence that overlap the prefix of the read sequence, of a number of sequence elements of the second exon sequence that overlap the suffix of the read sequence, and of a constant is calculated using the processor. If the sum equals a length of the read sequence, a junction is identified in the read using the processor.

公开(公告)号：US11817180B2

公开(公告)日：2023-11-14

申请号：US16279315

申请日：2019-02-19

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Zheng Zhang ,  Danwei Guo ,  Yuandan Lou ,  Asim Siddiqui ,  Dumitru Brinza

IPC: G16B30/10 ,  G16B30/00 ,  G16B30/20

CPC classification number: G16B30/10 ,  G16B30/00 ,  G16B30/20

Abstract: Nucleic acid sequence mapping/assembly methods are disclosed. The methods initially map only a contiguous portion of each read to a reference sequence and then extends the mapping of the read at both ends of the mapped contiguous portion until the entire read is mapped (aligned). In various embodiments, a mapping score can be calculated for the read alignment using a scoring function, score (i, j)=M+mx, where M can be the number of matches in the extended alignment, x can be the number of mismatches in the alignment, and m can be a negative penalty for each mismatch. The mapping score can be utilized to rank or choose the best alignment for each read.

公开(公告)号：US20220284986A1

公开(公告)日：2022-09-08

申请号：US17699439

申请日：2022-03-21

Applicant: Life Technologies Corporation

Inventor： Paolo Vatta ,  Onur Sakarya ,  Heinz Breu ,  Liviu Popescu ,  Asim Siddiqui ,  Fiona Hyland

IPC: G16B30/10 ,  G16B30/00

Abstract: Identification of exon junctions includes obtaining a first read sequence based on a detected plurality of signals of a first sequence. A list of exon prefix and suffix sequences are generated by identifying exons of the human genome with a prefix sequence mapping to a suffix sequence of the first read sequence and by identifying exons with a suffix sequence mapping to a prefix sequence of the first read sequence. A pair of exon sequences is selected, with a first exon sequence being one of the exon suffix sequences and a second exon sequence being one of the exon prefix sequences. Summing a number of sequence elements of the first exon sequence that overlap the prefix of the first read sequence, a number of sequence elements of the second exon sequence that overlap the suffix of the first read sequence, and a constant is used to identify a fusion junction.