| Title: | RaPID-Query for fast identity by descent search and genealogical analysis |
| Journal: | Bioinformatics |
| Published: | 11 May 2023 |
| Pubmed: | https://pubmed.ncbi.nlm.nih.gov/37166451/ |
| DOI: | https://doi.org/10.1093/bioinformatics/btad312 |
| URL: | https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad312/50278158/btad312.pdf |
Publication 11438
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Abstract
MOTIVATION: Due to the rapid growth of the genetic database size, genealogical search, a process of inferring familial relatedness by identifying DNA matches, has become a viable approach to help individuals finding missing family members or law enforcement agencies locating suspects. A fast and accurate method is needed to search an out-of-database individual against millions of individuals. Most existing approaches only offer all-versus-all within panel match. Some prototype algorithms offer one-versus-all query from out-of-panel individual, but they do not tolerate errors.</p>
RESULTS: A new method, random projection-based identity-by-descent (IBD) detection (RaPID) query, is introduced to make fast genealogical search possible. RaPID-Query identifies IBD segments between a query haplotype and a panel of haplotypes. By integrating matches over multiple PBWT indexes, RaPID-Query manages to locate IBD segments quickly with a given cutoff length while allowing mismatched sites. A single query against all UK biobank autosomal chromosomes was completed within 2.76 seconds on average, with the minimum length 7 cM and 700 markers. RaPID-Query achieved a 0.016 false negative rate and a 0.012 false positive rate simultaneously on a chromosome 20 sequencing panel having 86 265 sites. This is comparable to the state-of-the-art IBD detection method TPBWT(out-of-sample) and Hap-IBD. The high-quality IBD segments yielded by RaPID-Query were able to distinguish up to fourth degree of the familial relatedness for a given individual pair, and the area under the receiver operating characteristic curve values are at least 97.28%.</p>
AVAILABILITY AND IMPLEMENTATION: The RaPID-Query program is available at https://github.com/ucfcbb/RaPID-Query.</p>
4 Authors
- Yuan Wei
- Ardalan Naseri
- Degui Zhi
- Shaojie Zhang
1 Application
| Application ID | Title |
|---|---|
| 24247 | Searching Identity-by-descent segments in biobank-scale cohorts |
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