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. 2014 Jan 29:15:13.
doi: 10.1186/1471-2156-15-13.

Evaluation of a target region capture sequencing platform using monogenic diabetes as a study-model

Rui Gao, Yanxia Liu, Anette Prior Gjesing, Mette Hollensted, Xianzi Wan, Shuwen He, Oluf Pedersen, Xin Yi  1 , Jun Wang, Torben Hansen
Affiliations

Evaluation of a target region capture sequencing platform using monogenic diabetes as a study-model

Rui Gao et al. BMC Genet. .

Abstract

Background: Monogenic diabetes is a genetic disease often caused by mutations in genes involved in beta-cell function. Correct sub-categorization of the disease is a prerequisite for appropriate treatment and genetic counseling. Target-region capture sequencing is a combination of genomic region enrichment and next generation sequencing which might be used as an efficient way to diagnose various genetic disorders. We aimed to develop a target-region capture sequencing platform to screen 117 selected candidate genes involved in metabolism for mutations and to evaluate its performance using monogenic diabetes as a study-model.

Results: The performance of the assay was evaluated in 70 patients carrying known disease causing mutations previously identified in HNF4A, GCK, HNF1A, HNF1B, INS, or KCNJ11. Target regions with a less than 20-fold sequencing depth were either introns or UTRs. When only considering translated regions, the coverage was 100% with a 50-fold minimum depth. Among the 70 analyzed samples, 63 small size single nucleotide polymorphisms and indels as well as 7 large deletions and duplications were identified as being the pathogenic variants. The mutations identified by the present technique were identical with those previously identified through Sanger sequencing and Multiplex Ligation-dependent Probe Amplification.

Conclusions: We hereby demonstrated that the established platform as an accurate and high-throughput gene testing method which might be useful in the clinical diagnosis of monogenic diabetes.

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Figures

Figure 1
Figure 1
Depth and coverage of all pre-screened samples. For each screened sample (X-axis), the sequencing depth and the coverage of at least 1-fold depth are depicted as square (■) and diamond (♦), respectively. The Y-axis are Mean Depth (left) and coverage (right) respectively.
Figure 2
Figure 2
The distribution of pathogenic (suspected pathogenic) variants of disease-causing genes among 70 pre-screened samples. The mutation type (large exon deletion/duplication, splice, nonsense, missense, small indel) are present by gradually changing color in blue.
See this image and copyright information in PMC

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