Diagnostic yield of targeted next generation sequencing in 2002 Dutch cardiomyopathy patients

Abstract

Background: Next-generation sequencing (NGS) is increasingly used for clinical evaluation of cardiomyopathy patients as it allows for simultaneous screening of multiple cardiomyopathy-associated genes. Adding copy number variant (CNV) analysis of NGS data is not routine yet and may contribute to the diagnostic yield. Objectives: Determine the diagnostic yield of our targeted NGS gene panel in routine clinical diagnostics of Dutch cardiomyopathy patients and explore the impact of exon CNVs on diagnostic yield. Methods: Patients (N = 2002) referred for clinical genetic analysis underwent diagnostic testing of 55-61 genes associated with cardiomyopathies. Samples were analyzed and evaluated for single nucleotide variants (SNVs), indels and CNVs. CNVs identified in the NGS data and suspected of being pathogenic based on type, size and location were confirmed by additional molecular tests. Results: A (likely) pathogenic (L)P variant was detected in 22.7% of patients, including 3 with CNVs and 25 where a variant was identified in a gene currently not associated with the patient's cardiomyopathy subtype. Only 15 out of 2002 patients (0.8%) were found to carry two (L)P variants. Conclusion:The yield of routine clinical diagnostics of cardiomyopathies was relatively low when compared to literature. This is likely due to the fact that our study reports the outcome of patients in daily routine diagnostics, therefore also including patients not fully fulfilling (subtype specific) cardiomyopathy criteria. This may also explain why (L)P variants were identified in genes not associated with the reported subtype. The added value of CNV analysis was shown to be limited but not negligible.

Validation of New Gene Variant Classification Methods: a Field-Test in Diagnostic Cardiogenetics

“…Variants detected in our cohort are routinely submitted to ClinVar ( https://www.ncbi.nlm.nih.gov/clinvar ). A comprehensive description of the cohort, genetic analysis, variant interpretation, and classification protocols are described in our previous study ( Alimohamed et al, 2021 ).…”

“…We initially validated the potential of using constraint scores for prioritizing and (re)classifying variants by determining the number of variants from our cohort classified as LP or P using our routine diagnostic criteria (RDC) ( Alimohamed et al, 2021 ) and the number of these variants that would have been predicted to have increased risk of pathogenicity using the recommendation from the scores from the CE/EF based approach and therefore may be classified (L)P. Next, the concordance between these groups was calculated.…”

“…Although promising, the outcomes of these statistical methods have not been generally applied in routine clinical diagnostics, and therefore its value in reducing the number of VUSs in such a setting has not been evaluated yet. Our objective was to validate the use of constraint metrics data for variant pathogenicity assessment of cardiomyopathy genes in a diagnostic cardiomyopathy cohort ( Alimohamed et al, 2021 ). We first validated the use of these data for variant classification in a Dutch cohort of 2,002 patients by comparing its outcome to that of variants classified as (L)P applying our routine diagnostic criteria (RDC).…”

Genetic risk factors for dilated cardiomyopathy

“…Наряду с TTNtv, мутации в других саркомерных генах, кодирующих белки толстых филаментов (тяжелые цепи альфа и бета миозина -MYH6 и MYH7; миозин-связывающий протеин -MYBPC3) определяются в разных популяциях от 1-4% (MYH6) до 4-10% (MYH7) у пациентов с ДКМП, а у пациентов с ГКМП мутации в саркомерных генах встречаются от 30% до 50% (30-40% в гене MYBPC3 и 20-30% в MYH7) [25]. Литературные источники сегодня представляют весьма противоречивые данные о распространенности мутаций в гене MYBPC3 у пациентов с ДКМП -от низкой (1-2%) до парадоксально высокой (15-27% в отдельных популяциях, например, в Швеции) [2,4].…”

“…Принято считать, что в 10% случаев мутации в этих генах являются причиной ДКМП [3][4][5]. В представленной нами когорте частота выявления мутаций в генах MYBPC3 (n=3), MYH6 (n=1) и MYH7 (n=4) составила 13,1% (8 из 61) генпозитивных случаев; эти данные сопоставимы с результатами генетического исследования популяции ДКМП в Дании, где распространённость генотипов MYBPC3 и MYH7 составила 12,2% [25] К настоящему времени получены убедительные доказательства, подтверждающие связь мутаций в гене SCN5A, кодирующем α-субъединицу натриевого канала Nav1.5, с нарушением проводимости, аритмией и ДКМП. Частота патогенных вариантов SCN5A достигает 2-4% всех случаев ДКМП [25].…”