Methods of detecting somatic and germline variants in impure tumors
US11978535B2 · kind B2 · utility
Assignee
Inventors
Key dates
| Filing date | Feb 1, 2018 |
| Grant date | May 7, 2024 |
| Priority date | — |
| Expiry date | Jan 29, 2041 |
Classification
- Technology area (CPC C)Chemistry; Metallurgy
- CPC primaryC12Q2600/156
- WIPO fieldMeasurement
- WIPO sectorInstruments
Abstract
A system is provided that considers allele fraction shifts as a function of copy number and clonal heterogeneity. The system leverages differences between allele frequencies to differentiate between somatic and normal variants in impure tumor samples. In solid tumors, stromal cells and infiltrating lymphocytes are typically interspersed among the tumor cells. The normal cell contamination in tumors can be leveraged to differentiate somatic from germline variants. We explicitly model allelic copy number and clonal sample fractions so that we can examine how these factors impact the power to detect somatic variants. The system models the copy number alterations, which can also affect the allele frequencies of both somatic and germline variants. The expected allele frequencies can be calculated. The expected allele frequencies for somatic and germline differ with tumor content for different copy number alterations.
Source: USPTO / EPO open patent data. Objective bibliographic and citation counts.