P238 Good concordance between predicted HLA typing from whole exome sequencing and actual HLA type

Aim HLA typing is performed for optimal donor selection in transplant, but also can be performed for other diverse purposes including pharmacogenomics, autoimmune diseases, and research purposes. Decreasing costs have resulted in increasing use of whole exome sequencing, both in research and clinical settings. The ability to obtain accurate HLA types from whole exome sequencing could result in decreased costs of clinical HLA typing as well as expanded research opportunities. Methods Exome sequencing was performed on blood samples from women with invasive breast cancer referred for neoadjuvant chemotherapy and enrolled in the Breast Cancer Genome-Guided Therapy Study (BEAUTY) at our institution. Whole exome data for a subset of 59 participants was filtered to include reads mapping to the HLA region and typed using the commercial software HLA Target (Omixon, Budapest, Hungary). Due to the limited availability of DNA, low to medium resolution SSO typing for HLA-A,B,C,DRB1, DQA1 and DQB1 was performed on the blood samples. Results of the presumed alleles were compared with those predicted by the software. Results Of the 59 samples tested, 14 were unable to be analyzed in Omixon Target. Of the remaining 45 samples, 27 demonstrated concordance at the second field and seven at the first field. The remaining eleven samples were heterozygous at HLA-DQB1 or DQA1 by SSO but were reported to be homozygous by Target. Conclusions This pilot study demonstrated that reasonably concordant HLA typing results can be obtained from whole exome data after analyzing reads in the MHC region.