PT  - JOURNAL ARTICLE
AU  - Mahmoud Koko
AU  - Mohammed O. E. Abdallah
AU  - Mutaz Amin
AU  - Muntaser Ibrahim
TI  - A bioinformatic panel to interrogate thousands of ExAC variants with minor reference allele that are missed by conventional variant calling
AID  - 10.1101/093450
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 093450
4099  - http://biorxiv.org/content/early/2016/12/12/093450.short
4100  - http://biorxiv.org/content/early/2016/12/12/093450.full
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.