Background: Hypertrophic cardiomyopathy (HCM) is a common heritable cardiovascular disorder. Previous studies have shown phenotype-guided genetic testing can predict the likelihood of a positive HCM genetic test allowing for the confirmation of disease etiology and screening of appropriate family members.
Objective: To assess next generation sequencing (NGS) for HCM in genetically elusive cases from prior research-based genetic testing.
Methods: NGS (exome or genome) was performed on 36 unrelated HCM patients (19 female) previously denoted genotype-negative by DHPLC-based genetic analysis of the most common HCM-associated myofilament genes. Despite a current genotype-negative status, all patients had high pre-test clinical probability of being sarcomere gene-positive. Following NGS, a gene-specific target analysis was performed on the 10 most common HCM-associated myofilament genes (MYBPC3, MYH7, TNNT2, TNNI3, MYL2, MYL3, ACTC1, TPM1, TNNC1, MYH6) as well as an expanded gene panel analysis including 50 additional HCM-associated genes. Only rare (minor allele frequency < 0.0005 in gnomAD) non-synonymous (NS) variants that satisfied ACMG guideline criteria for pathogenic (P) or likely pathogenic (LP) were considered.
Results: Overall, 21/36 (58%) unrelated patients had at least 1 rare nonsynonymous variant in the top 10 HCM-associated genes. Of these, 16/36 (44%) had at least 1 LP or P variant in MYBPC3 (3 missense, 3 nonsense, 7 splice-error, 4 deletion/insertion), 2 in MYH7 (missense), 2 in MYL2 (missense), and 1 in MYL3 (missense). Of the 6 unique MYBPC3 splice-error variants, 4 would be considered novel as they resided outside the canonical (first 2 nucleotides before or after an exon) splice-site (3190+5G>A, 3491-3C>G, 1624+4A>T, 3330+5G>A). Our expanded gene panel analysis identified 4 LP or P variants in 2 additional patients: FLNC (K1671E), HRAS (G12V), GAA (E176fs*45), and CSRP3 (L44P).
Conclusion: NGS identified genetic causes for 23 of 36 previously gene-elusive HCM cases allowing for a more accurate diagnosis and treatment for HCM patients and families. Any HCM patient with high clinical probability for sarcomeric HCM, deemed genotype negative based on pre-NGS research grade mutational analysis, should undergo repeat genetic testing.