公开(公告)号：US20230340585A1

公开(公告)日：2023-10-26

申请号：US18152813

申请日：2023-01-11

Applicant: Life Technologies Corporation

Inventor： Sameh El-Difrawy

IPC: C12Q1/6869 ,  C12Q1/6809 ,  C12Q1/6886 ,  G16B50/00 ,  G16B40/20 ,  G16B20/00

CPC classification number: C12Q1/6869 ,  C12Q1/6809 ,  C12Q1/6886 ,  G16B50/00 ,  G16B40/20 ,  G16B20/00 ,  C12Q2600/156

Abstract: Methods for evaluating microsatellite instability (MSI) analyze nucleic acid sequence reads corresponding to a plurality of marker regions for MSI. The marker regions may include long homopolymers and/or short tandem repeats (STRs). For a target homopolymer, a histogram of homopolymer signal values is calculated based on flow space signal measurements for the homopolymer region in the sequence reads. A score per marker based on features of the histogram of homopolymer signal values is determined for each marker region corresponding to the target homopolymers. For a target STR, the method includes calculating a histogram of repeat lengths for sequence reads corresponding to the marker region of the target STR. A score per STR marker is calculated based on features of the histogram of repeat lengths. A plurality of per marker scores may be combined to form a total MSI score for the sample.

公开(公告)号：US20180181707A1

公开(公告)日：2018-06-28

申请号：US15807695

申请日：2017-11-09

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Sameh El-Difrawy

IPC: G06F19/22 ,  G06F19/24

CPC classification number: G16B30/00 ,  C12Q1/6869 ,  G16B5/00 ,  G16B40/00 ,  C12Q2535/122 ,  C12Q2537/165

Abstract: Methods, systems and non-transitory machine-readable storage medium are provided to mitigate insertion errors and deletion errors in STR sequences and improve accuracy in determination of the number of repeats. A method includes determining one or more optimum clusters for a set of flow space signal measurements, wherein at least one of the optimum clusters is associated with a homopolymer length, modifying a base call at the position in the repeat region sequence to the homopolymer length associated with the optimum cluster to produce a corrected repeat region sequence, thereby correcting an insertion error or a deletion error. The method may further include detecting variations in the flanks associating those variations with the length of the STR.

公开(公告)号：US20240175084A1

公开(公告)日：2024-05-30

申请号：US18529188

申请日：2023-12-05

Applicant: Life Technologies Corporation

Inventor： Sameh El-Difrawy

IPC: C12Q1/6869 ,  C12Q1/6809 ,  C12Q1/6886 ,  G16B20/00 ,  G16B40/20 ,  G16B50/00

CPC classification number: C12Q1/6869 ,  C12Q1/6809 ,  C12Q1/6886 ,  G16B20/00 ,  G16B40/20 ,  G16B50/00 ,  C12Q2600/156

Abstract: Methods for evaluating microsatellite instability (MSI) analyze nucleic acid sequence reads corresponding to a plurality of marker regions for MSI. The marker regions may include long homopolymers and/or short tandem repeats (STRs). For a target homopolymer, a histogram of homopolymer signal values is calculated based on flow space signal measurements for the homopolymer region in the sequence reads. A score per marker based on features of the histogram of homopolymer signal values is determined for each marker region corresponding to the target homopolymers. For a target STR, the method includes calculating a histogram of repeat lengths for sequence reads corresponding to the marker region of the target STR. A score per STR marker is calculated based on features of the histogram of repeat lengths. A plurality of per marker scores may be combined to form a total MSI score for the sample.

公开(公告)号：US12168800B2

公开(公告)日：2024-12-17

申请号：US18529188

申请日：2023-12-05

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Sameh El-Difrawy

IPC: G16B40/20 ,  C12Q1/6809 ,  C12Q1/6869 ,  C12Q1/6886 ,  G16B20/00 ,  G16B50/00

Abstract: Methods for evaluating microsatellite instability (MSI) analyze nucleic acid sequence reads corresponding to a plurality of marker regions for MSI. The marker regions may include long homopolymers and/or short tandem repeats (STRs). For a target homopolymer, a histogram of homopolymer signal values is calculated based on flow space signal measurements for the homopolymer region in the sequence reads. A score per marker based on features of the histogram of homopolymer signal values is determined for each marker region corresponding to the target homopolymers. For a target STR, the method includes calculating a histogram of repeat lengths for sequence reads corresponding to the marker region of the target STR. A score per STR marker is calculated based on features of the histogram of repeat lengths. A plurality of per marker scores may be combined to form a total MSI score for the sample.

公开(公告)号：US11866778B2

公开(公告)日：2024-01-09

申请号：US18152813

申请日：2023-01-11

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Sameh El-Difrawy

IPC: G16B40/20 ,  C12Q1/6869 ,  C12Q1/6809 ,  C12Q1/6886 ,  G16B50/00 ,  G16B20/00

CPC classification number: C12Q1/6869 ,  C12Q1/6809 ,  C12Q1/6886 ,  G16B20/00 ,  G16B40/20 ,  G16B50/00 ,  C12Q2600/156

Abstract: Methods for evaluating microsatellite instability (MSI) analyze nucleic acid sequence reads corresponding to a plurality of marker regions for MSI. The marker regions may include long homopolymers and/or short tandem repeats (STRs). For a target homopolymer, a histogram of homopolymer signal values is calculated based on flow space signal measurements for the homopolymer region in the sequence reads. A score per marker based on features of the histogram of homopolymer signal values is determined for each marker region corresponding to the target homopolymers. For a target STR, the method includes calculating a histogram of repeat lengths for sequence reads corresponding to the marker region of the target STR. A score per STR marker is calculated based on features of the histogram of repeat lengths. A plurality of per marker scores may be combined to form a total MSI score for the sample.

公开(公告)号：US11572586B2

公开(公告)日：2023-02-07

申请号：US16595681

申请日：2019-10-08

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Sameh El-Difrawy

IPC: G16B40/20 ,  C12Q1/6869 ,  C12Q1/6809 ,  C12Q1/6886 ,  G16B50/00 ,  G16B20/00

Abstract: Methods for evaluating microsatellite instability (MSI) analyze nucleic acid sequence reads corresponding to a plurality of marker regions for MSI. The marker regions may include long homopolymers and/or short tandem repeats (STRs). For a target homopolymer, a histogram of homopolymer signal values is calculated based on flow space signal measurements for the homopolymer region in the sequence reads. A score per marker based on features of the histogram of homopolymer signal values is determined for each marker region corresponding to the target homopolymers. For a target STR, the method includes calculating a histogram of repeat lengths for sequence reads corresponding to the marker region of the target STR. A score per STR marker is calculated based on features of the histogram of repeat lengths. A plurality of per marker scores may be combined to form a total MSI score for the sample.