RT Journal Article
SR Electronic
T1 A bioinformatic panel to interrogate thousands of ExAC variants with minor reference allele that are missed by conventional variant calling
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 093450
DO 10.1101/093450
A1 Mahmoud Koko
A1 Mohammed O. E. Abdallah
A1 Mutaz Amin
A1 Muntaser Ibrahim
YR 2016
UL http://biorxiv.org/content/early/2016/12/12/093450.abstract
AB In variation sites with minor reference alleles, overlooking the detection of homozygous reference genotypes results in inadequate identification of potential disease variants. Current variant calling practices miss these clinically relevant alleles warranting new approaches. More than 26,000 Eome Aggregation Consortium (ExAC) variants have a minor reference allele including 44 variants with known ClinVar disease alleles. We demonstrated how the current variant calling standards miss homozygous reference disease variants in these sites. We developed a bioinformatic panel that can be used to screen these variants using commonly available variant callers. We provide here a simple strategy to screen potential disease-causing variants when present in homozygous reference state.