TY - JOUR
T1 - Accurate and robust prediction of genetic relationship from whole-genome sequences
AU - Li, Hong
AU - Glusman, Gustavo
AU - Huff, Chad
AU - Caballero, Juan
AU - Roach, Jared C.
PY - 2014/2/28
Y1 - 2014/2/28
N2 - Computing the genetic relationship between two humans is important to studies in genetics, genomics, genealogy, and forensics. Relationship algorithms may be sensitive to noise, such as that arising from sequencing errors or imperfect reference genomes. We developed an algorithm for estimation of genetic relationship by averaged blocks (GRAB) that is designed for whole-genome sequencing (WGS) data. GRAB segments the genome into blocks, calculates the fraction of blocks sharing identity, and then uses a classification tree to infer 1st- to 5th- degree relationships and unrelated individuals. We evaluated GRAB on simulated and real sequenced families, and compared it with other software. GRAB achieves similar performance, and does not require knowledge of population background or phasing. GRAB can be used in workflows for identifying unreported relationships, validating reported relationships in family-based studies, and detection of sample-tracking errors or duplicate inclusion. The software is available at familygenomics.systemsbiology.net/grab.
AB - Computing the genetic relationship between two humans is important to studies in genetics, genomics, genealogy, and forensics. Relationship algorithms may be sensitive to noise, such as that arising from sequencing errors or imperfect reference genomes. We developed an algorithm for estimation of genetic relationship by averaged blocks (GRAB) that is designed for whole-genome sequencing (WGS) data. GRAB segments the genome into blocks, calculates the fraction of blocks sharing identity, and then uses a classification tree to infer 1st- to 5th- degree relationships and unrelated individuals. We evaluated GRAB on simulated and real sequenced families, and compared it with other software. GRAB achieves similar performance, and does not require knowledge of population background or phasing. GRAB can be used in workflows for identifying unreported relationships, validating reported relationships in family-based studies, and detection of sample-tracking errors or duplicate inclusion. The software is available at familygenomics.systemsbiology.net/grab.
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U2 - 10.1371/journal.pone.0085437
DO - 10.1371/journal.pone.0085437
M3 - Article
C2 - 24586241
AN - SCOPUS:84896533985
SN - 1932-6203
VL - 9
JO - PloS one
JF - PloS one
IS - 2
M1 - e85437
ER -