Abstract - Text

Abstract-Text

Introduction:

Implementation of exome and genome sequencing (ES/GS) into routine diagnostics implicates the possibility of identifying secondary findings (SF). The American College of Medical Genetics and Genomics (ACMG) has recommended that clinical sequencing laboratories return SFs associated with medically actionable conditions. In our routine diagnostics, patients have had the option to receive SF since 2017. In this study our goal was to retrospectively analyze all SF in our ES/GS cohort to better estimate the prevalence of SFs in Germany.

Material and Methods:

ES was performed in 10,771 and GS in 2,017 probands between 01/2017 and 01/2021 for different clinical indications. NGS libraries were prepared from genomic DNA using standard protocols (Agilent SureSelect XT Human All Exon V5/V7 enrichment kits, Illumina TruSeq DNA PCR-Free Kits) and sequenced on an Illumina NovaSeq6000. The cohort was searched for likely pathogenic or pathogenic, clinically relevant DNA variants (LPV/PV) in the 59 genes of ACMG59 SF list and in additional 8 HBOC genes (ATM, BARD1, BRIP1, CDH1, CHEK2, PALB2, RAD51C and RAD51D) using an in-house bioinformatics pipeline (megSAP,https://github.com/imgag/megSAP). Heterozygous carriers in genes associated with autosomal-recessive conditions were excluded. Variants were classified according to the ACMG guidelines. As a next step all variants that confirmed the clinical diagnosis were excluded. The number of follow-up segregations of family members performed at our institute was assessed.

Results:

In total 5.1% (n=652) LPV/PVs were detected in the ACMG59 and HBOC genes in the cohort of 12,788 exomes/genomes independent of the clinical indication. SFs were identified in 3.2% of patients (n=403), and 6 patients had two SFs each (MYH7+RAD51D, PKP2+TNNI3, CHEK2+KCNH2, MYH7+RAD51D, BARD1+BRCA1, ATM+MYBPC3). SFs were mainly detected in CHEK2 (n = 71), BRCA2 (n=36), ATM (n = 31), BRCA1 (n = 23), RAD51D (n=23), APOB (n=22) and RYR1 (n=22). No SFs were found in 24 genes of the ACMG59 list as well as in one of the HBOC genes (CDH1). Genetic counseling was performed at our institute in 83 cases upon completion of the SF-report. In 45% (n=37) of the cases, follow-up appointments with other family members were made to perform segregation studies. In 55% (n=46) of the cases, we have not heard back from the families so far.

Conclusion:

Our study indicates that medically actionable secondary findings can be identified in about 3.2% of individuals in our cohort. This approach has the potential to enable patients and their relatives to optimize individual prevention strategies. Detailed counseling on SFs pre- and post-genetic testing is crucial. More follow-up studies will be needed to understand how patients and their families cope with SFs in the long run and whether they truly take action upon receiving the result of SFs.