Methods for detecting variants in next-generation sequencing genomic data
US11990206B2 · kind B2 · utility
Assignee
Inventors
Key dates
| Filing date | Dec 7, 2017 |
| Grant date | May 21, 2024 |
| Priority date | — |
| Expiry date | May 23, 2041 |
Classification
- Technology area (CPC G)Physics
- CPC primaryG16B30/10
- WIPO fieldComputer technology
- WIPO sectorElectrical engineering
Abstract
A genomic data analyzer may be configured to detect and characterize, with a variant calling module, genomic variant scenarios in sequencing reads from an enriched patient genomic sample comprising a combination of a first repeat pattern and a second repeat pattern, such as repeats of homopolymer (single nucleotide) and/or heteropolymer (multiple nucleotide) basic motifs. The variant calling module may estimate the probability distribution of the length of the first repeat pattern and the probability distribution of the length of the second repeat pattern by comparing the distribution of the repeat pattern length measurements in patient data to the distribution of the repeat pattern length measurements in control data, in order to remove biases possibly induced by the next generation sequencing laboratory setup both in control and patient data. The variant calling module may further measure, read by read, the joint probability distribution for the first and the second repeat patterns lengths, and compare it with the expected joint probability distribution for various genomic variant scenarios for the patient, each variant scenario being characterized by a first length of the first …
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