公开(公告)号：US20200075122A1

公开(公告)日：2020-03-05

申请号：US16550672

申请日：2019-08-26

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Ruchi Chaudhary ,  Fiona HYLAND

IPC: G16B20/20

Abstract: A targeted panel with low sample input requirements from a tumor only sample may be processed to estimate mutation load in a tumor sample. The method may include: detecting variants in nucleic acid sequence reads corresponding to targeted locations in the tumor sample genome; annotating detected variants with an annotation information from a population database; filtering the detected variants, wherein the filtering retains the somatic variants and removes germline variants; calculating an initial TMB; and applying a calibration to the initial TMB level to produce a final TMB level for the mutation load of the tumor sample genome. The filtering may also include retaining nonsynonymous SNVs and indels for the analysis.

公开(公告)号：US20210343367A1

公开(公告)日：2021-11-04

申请号：US17371378

申请日：2021-07-09

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Ruchi Chaudhary ,  Fiona HYLAND

IPC: G16B20/20 ,  G16B20/00 ,  G16B30/00 ,  G16B30/10

Abstract: A targeted panel with low sample input requirements from a tumor only sample may be processed to estimate mutation load in a tumor sample. The method may include detecting variants in nucleic acid sequence reads corresponding to targeted locations in the tumor sample genome; annotating detected variants with an annotation information from a population database; filtering the detected variants, wherein the filtering rule set retains the somatic variants and removes germ-line variants; counting the identified somatic variants to give a number of somatic variants; determining a number of bases in covered regions of the targeted locations in the tumor sample genome; and calculating a number of somatic variants per megabase, provides an estimate of the mutation load per megabase in the tumor sample genome.

公开(公告)号：US11101019B2

公开(公告)日：2021-08-24

申请号：US15834520

申请日：2017-12-07

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Ruchi Chaudhary ,  Fiona Hyland

IPC: G16B20/00 ,  G16B30/00

Abstract: A targeted panel with low sample input requirements from a tumor only sample may be processed to estimate mutation load in a tumor sample. The method may include: detecting variants in nucleic acid sequence reads corresponding to targeted locations in the tumor sample genome; annotating detected variants with an annotation information from a population database; filtering the detected variants, wherein the filtering rule set retains the somatic variants and removes germ-line variants; counting the identified somatic variants to give a number of somatic variants; determining a number of bases in covered regions of the targeted locations in the tumor sample genome; and calculating a number of somatic variants per megabase, provides an estimate of the mutation load per megabase in the tumor sample genome.

公开(公告)号：US20180165410A1

公开(公告)日：2018-06-14

申请号：US15834520

申请日：2017-12-07

Applicant: Life Technologies Corporation

Inventor： Ruchi Chaudhary ,  Fiona Hyland

IPC: G06F19/18

Abstract: A targeted panel with low sample input requirements from a tumor only sample may be processed to estimate mutation load in a tumor sample. The method, including detecting variants in nucleic acid sequence reads corresponding to targeted locations in the tumor sample genome; annotating detected variants with an annotation information from a population database; filtering the detected variants, wherein the filtering rule set retains the somatic variants and removes germ-line variants; counting the identified somatic variants to give a number of somatic variants; determining a number of bases in covered regions of the targeted locations in the tumor sample genome; and calculating a number of somatic variants per megabase, provides an estimate of the mutation load per megabase in the tumor sample genome.