PATHOGENIC VARIANTS WITHIN ACMG SECONDARY FINDINGS GENES IN 24,591 HEALTHY INDIVIDUALS USING CLINICAL EXOME SEQUENCING FOR CARRIER SCREENING

Expanded carrier screening (ECS) aims to reduce the burden of recessive single-gene disorders by identifying the genetic risk for the offspring of individuals in reproductive age. ECS using exome sequencing could also reveal information that may influence on individual’s health. A significant group of clinically actionable genes are the secondary findings (SF) list defined by the ACMG. Our objective was to assess the frequency of SF pathogenic variants in individuals undergoing ECS. Retrospective analysis of clinical exome data from an ECS program to assess the frequency of pathogenic variants for the 59 SF gene list defined by the ACMG. A database was built using anonymized sequencing data of 24,591 clinical exomes (TruSight One sequencing panel; Illumina) intended for ECS before Assisted Reproductive Techniques, from September 2015 to June 2019. Females represented the 50.9% (12,525) of tested individuals and males the remainder 49.1% (12,066). Distribution between patients and gamete donors was 59.3% (14,588) vs 40.7% (10,003), respectively. All patients self-reported European ancestry except a subset of 475 Emirati individuals. Sequencing data were processed using a proprietary bioinformatic pipeline for the 59 genes included in the ACMG recommendations for reporting of secondary findings (ACMG SFv2.0) (Kalia et al., 2016). Variant pathogenicity was performed in compliance with ACMG-AMP guidelines (Richards et al., 2015) using an in-house algorithm, private and public databases, and updated literature, only (likely) pathogenic variants were considered as a SF. The overall frequency of individuals with pathogenic variants was 2.6% (n=636). No differences in the frequency of SF was found between genders neither between patients and donors. At least one (likely) pathogenic variant was identified in 39 of 59 ACMG genes. In total, 344 unique variants were detected in 652 alleles. The most frequent pathogenic variant was the X-linked NM_000169.2:c.427G>A in GLA gene (n=19). BRCA1 and BRCA2 were the most frequently positive called genes, with 95 unique pathogenic variants detected in 131 individuals (20.6%). When dividing by ancestry, same frequency of SF was found in Emiratis (2.5%) and European (2.6%). In contrast, differences were found for the most frequently positive genes. Top-three positive genes among Emiratis were SCN5A, KCNQ1 and RYR1; while for Europeans were BRCA2, MYBPC3 and LDLR. Remarkably, the variant most frequently detected in European-ancestry individuals (NM_000169.2:c.427G>A in GLA) was not detected in Arabs. Conversely, 6 out of 10 unique variants found in Arabs were not detected in the large European database. The analysis of the ACMG SF genes provided evidence of pathogenicity in 2.6% of the tested individuals. Same frequency was found among genders and patient-donor status, as well as for European and Emirati populations. However, genetic heterogeneity was found among the two populations both at the gene and at the variant level.