Array-Based Resequencing Assay for Mutations Causing Hypertrophic Cardiomyopathy

Abstract

Background: Dissecting the complex genetic basis of hypertrophic cardiomyopathy (HCM) may be key to both better understanding and optimally managing this most prevalent genetic cardiovascular disease. An array-based resequencing (ABR) assay was developed to facilitate genetic testing in HCM. Methods: An Affymetrix resequencing array and a single long-range PCR protocol were developed to cover the 3 most commonly affected genes in HCM, MYH7 (myosin, heavy chain 7, cardiac muscle, beta), MYBPC3 (myosin binding protein C, cardiac), and TNNT2 [troponin T type 2 (cardiac)]. Results: The assay detected the underlying point mutation in 23 of 24 reference samples and provided pointers toward identifying a G insertion and a 3-bp deletion. The comparability of array-based assay results to conventional capillary sequencing was ≥99.9%. Both techniques detected 1 heterozygous variant that was missed by the other method. Conclusions: The data provide evidence that ABR can substantially reduce the high workload previously associated with a genetic test for HCM. Therefore, the HCM array could facilitate large-scale studies aimed at broadening the understanding of the genetic and phenotypic diversity of HCM and related cardiomyopathies.

High-throughput resequencing in the diagnosis of BRCA1/2 mutations using oligonucleotide resequencing microarrays

“…In addition to this, we were able to confirm high reproducibility by repeating different experiments. Previous studies showed comparable results concerning accuracy (99.9-100%) and reproducibility [10][11][12][13][14]. These studies also reported call rates ranging from 93.5 to 97.6%.…”

“…In the last few years, the total number of different custom oligonucleotide resequencing microarrays has increased and this technique has been successfully applied in mitochondrial mutation analysis [10], cardiomyopathy [11,12], intrahepatic cholestasis [13], and retinal degeneration [14]. This study focused on two genes, BRCA1 and BRCA2, that are causative for HBOC [5].…”

“…As proof-of-principle, one of the first oligonucleotide microarrays was designed for a single exon (exon 11) of BRCA1 [9]. Over the last 5 years, resequencing oligonucleotide microarrays were established for general mitochondrial mutation analysis [10] and a few diseases like cardiomyopathy [11,12], intrahepatic cholestasis [13], and retinal degeneration [14]. Our Breast Cancer Microarray is the first oligonucleotide resequencing microarray spanning the complete sequence of BRCA1 and BRCA2.…”

Targeted Next-Generation Sequencing for the Molecular Genetic Diagnostics of Cardiomyopathies

“…39 However, insertions and deletions are still more difficult to detect by other novel genetic testing approaches, such as hybridization-based sequencing chips. 40,41 Recent studies identified numerous patients with cardiomyopathy who have more than 1 disease-causing mutation. [42][43][44] These mutations can occur in either the same gene (compound heterozygotes) or in different genes (double heterozygotes) in up to 5% of genetic cardiomyopathies.…”

Next Generation Sequencing for Clinical Diagnostics-Principles and Application to Targeted Resequencing for Hypertrophic Cardiomyopathy

“…59 -62 Genetic testing approaches for HCM have included Sanger sequencing of individual genes and a gene panel approach using resequencing arrays. [62][63][64] Next generation sequencing now offers a new diagnostic approach for HCM.…”