A novel custom resequencing array for dilated cardiomyopathy

Abstract

Purpose: Genetic tests for the most commonly mutated genes in dilated cardiomyopathy (DCM) can confirm a clinical diagnosis in the proband and inform family management. Presymptomatic family members can be identified, allowing for targeted clinical monitoring to minimize adverse outcomes. However, the marked locus and allelic heterogeneity associated with DCM have made clinical genetic testing challenging. Novel sequencing platforms have now opened up avenues for more comprehensive diagnostic testing while simultaneously decreasing test cost and turn around time.

Methods: By using a custom design based on triplicate resequencing and separate genotyping of known disease-causing variants, we developed the DCM CardioChip for efficient analysis of 19 genes previously implicated in causing DCM.

Results: The chip's analytical sensitivity for known and novel substitution variants is 100% and 98%, respectively. In screening 73 previously tested DCM patients who did not carry clinically significant variants in 10 genes, 7 variants of likely clinical significance were identified in the remaining 9 genes included on the chip. Compared with traditional Sanger-based sequencing, test cost and turn around time were reduced by approximately 50%.

Conclusions: The DCM CardioChip is a highly efficient screening test with a projected clinical sensitivity of 26-29%.

Fig. 1

Design and data output. A, The basic design of a resequencing chip: each base is interrogated by four probes, containing the four possible bases, tiled in a quadrant (four additional probes query the reverse strand and are not shown). Typical hybridization patterns obtained from samples that are homozygous wild type or heterozygous for a variant are shown to the right. B, Triple tiling and minor allele tiling strategy: each probe is tiled in triplicate, with the interrogating position located at the 9th, 13th, and 17th positions on the 25-bp probe (arrows). C, When a known SNP (e.g., C>T) is located near the interrogating position, an additional set of triplicate probes were tiled containing the minor allele. D, Representative data output after the integrated GCOS, GSEQ, and BRLMM analysis. All positions requiring confirmatory analysis are listed in the “follow-up” section (top). For each position, the gene, exon, and wild type base is indicated. In the “call” column, triplicate calls are listed except when the presence of a nearby SNP triggered the use of the three additional minor allele tiling data sets.