RaPID-Query for fast identity by descent search and genealogical analysis

Area of Science:

• Genetics
• Bioinformatics
• Computational Biology

Background:

• Genealogical search, inferring familial relatedness via DNA matches, is crucial for finding missing persons and identifying suspects.
• The increasing size of genetic databases necessitates faster and more accurate search methods for individuals outside existing panels.
• Current methods often lack efficiency or error tolerance for large-scale, one-versus-all genealogical queries.

Purpose of the Study:

• To introduce RaPID-Query, a novel method for rapid identity-by-descent (IBD) detection.
• To enable fast and accurate genealogical searches against large genetic databases.
• To provide a tool that tolerates errors and allows for one-versus-all queries.

Main Methods:

• RaPID-Query utilizes random projection for identity-by-descent (IBD) detection.
• It integrates matches across multiple PBWT indexes to locate IBD segments efficiently.
• The method allows for mismatched sites and specifies a minimum cutoff length for detected segments.

Main Results:

• A single query against the UK biobank autosomal chromosomes averaged 2.76 seconds.
• Achieved low false negative (0.016) and false positive (0.012) rates on a large sequencing panel.
• Demonstrated high accuracy in distinguishing familial relatedness up to the fourth degree (AUC ≥ 97.28%).

Conclusions:

• RaPID-Query offers a fast and accurate solution for genealogical search against large genetic databases.
• The method's performance is comparable to state-of-the-art IBD detection techniques.
• High-quality IBD segments identified by RaPID-Query effectively determine familial relationships.