Method of determining clonotypes and clonotype profiles
US9043160B1 · kind B1 · utility
Assignee
Inventors
Key dates
| Filing date | Aug 2, 2011 |
| Grant date | May 26, 2015 |
| Priority date | — |
| Expiry date | Sep 29, 2032 |
Classification
- Technology area (CPC C)Chemistry; Metallurgy
- CPC primaryC12Q2600/16
- WIPO fieldComputer technology
- WIPO sectorElectrical engineering
Abstract
The invention is directed to methods for determining clonotypes and clonotype profiles in assays for analyzing immune repertoires by high throughput nucleic acid sequencing of somatically recombined immune molecules. In one aspect, the invention comprises generating a clonotype profile from an individual by generating sequence reads from a sample of recombined immune molecules; forming from the sequence reads a sequence tree representing candidate clonotypes each having a frequency; coalescing with a highest frequency candidate clonotype any lesser frequency candidate clonotypes whenever such lesser frequency is below a predetermined value and whenever a sequence difference therebetween is below a predetermined value to form a clonotype. After such coalescence, the candidate clonotypes is removed from the sequence tree and the process is repeated. This approach permits rapid and efficient differentiation of candidate clonotypes with genuine sequence differences from those with experimental or measurement errors, such as sequencing errors.
Source: USPTO / EPO open patent data. Objective bibliographic and citation counts.