公开(公告)号：WO2019005877A1

公开(公告)日：2019-01-03

申请号：PCT/US2018/039609

申请日：2018-06-26

Applicant: GRAIL, INC.

Inventor： SAKARYA, Onur ,  LAMPING, John

IPC: G06F19/22 ,  G06F19/24 ,  G06F19/18 ,  C12Q1/6806

CPC classification number: G16B5/00 ,  C12Q1/6806 ,  G06N20/00 ,  G16B30/00 ,  G16B30/10 ,  G16B30/20 ,  G16B40/10 ,  C12Q2535/122 ,  C12Q2537/165

Abstract: Detecting cross-contamination between test samples used for determining cancer in a subject is beneficial. To detect cross-contamination, test sequences including at least one single nucleotide polymorphism are prepared using genome sequencing techniques. Some of the test sequences can be filtered to improve accuracy and precision. A prior contamination probability for each test sequence is determined based on a minor allele frequency. A contamination model including a likelihood test is applied to a test sequence. The likelihood test obtains a current contamination probability representing the likelihood that the test sample is contaminated. The contamination model can also determine a likelihood that the sample includes loss of heterozygosity representing the likelihood that the test sequence is contaminated. Test samples that are contaminated are removed. A source for the contaminated test sample can be found by comparing contaminated test sequences to other test sequences.