AgileROH: Rapid identification of autozygous regions using Illumina
short read sequencing data
Abstract
Rare autosomal recessive diseases are a major cause of mortality and
morbidity. They occur more frequently in individuals with consanguineous
parents, in which case the pathogenic variants are often located within
regions of genetic identity by descent. A well-established and effective
way of identifying these “autozygous” genomic regions has been to
search for runs of homozygous genotypes in microarray SNP data. However,
with the widespread use of whole genome and exome sequencing in both
diagnostic and research settings, it has become desirable to be able to
both map autozygous regions and to identify the deleterious variants
using a single data set. We have developed and optimized an algorithm,
implemented as a set of three applications, that identifies autozygous
regions in consanguineous individuals using standard whole exome variant
data. These applications have been successfully used in both research
and diagnostic settings. Availability and implementation: User guides,
compiled programs and sample VCF files are freely available at
http://www.dna-leeds.co.uk/agile/AgileROH/ and
http://www.dna-leeds.co.uk/agile/AgileMultiIdeogram/.