Exome sequencing and genetic testing for MODY.
Exome sequencing and genetic testing for MODY.
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Mody的外显子组测序和基因检测。
DOI：
10.1371/journal.pone.0038050
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Njølstad PR
中科院分区：
文献类型：
--
作者：
Johansson S;Irgens H;Chudasama KK;Molnes J;Aerts J;Roque FS;Jonassen I;Levy S;Lima K;Knappskog PM;Bell GI;Molven A;Njølstad PR
单基因糖尿病的基因检测对患者护理很重要。鉴于糖尿病广泛的遗传和临床异质性，外显子组测序可能提供额外的诊断潜力时，标准的桑格测序为基础的诊断是不确定的。该研究的目的是检查外显子组测序的性能，用于在经历了常规诊断测序的候选基因阴性结果的患者中进行MODY的分子诊断。我们对9例疑似MODY患者进行了外显子组富集，然后进行高通量测序。他们的HNF 1A、HNF 4A、GCK、HNF 1B和INS基因突变均为桑格测序阴性。我们排除了常见的、非编码的和同义的基因变异，并对预先定义的111个与葡萄糖代谢有关的基因中的过滤序列变异进行了深入分析。平均而言，我们获得了整个靶向外显子组的45 X中位数覆盖率，并发现每个个体199个罕见编码变体。我们在111个候选基因的先验列表中确定了每个个体0-4个罕见的非同义和无义变体。其中三种变异被认为是致病性的（分别在ABCC 8，HNF 4A和PPARG中），因此外显子组测序导致了9名患者中至少3名的遗传诊断。在目标外显子组中检测到大约91%的已知杂合SNP，但我们也发现使用我们目前的外显子组测序方法在一些关键糖尿病基因中的覆盖率较低。ARAP 1、GLIS 3、MADD、NOTCH 2和WFS 1基因的新变异需要进一步研究，以揭示它们在糖尿病中的可能作用。我们的研究结果表明，外显子组测序可以提高分子诊断的MODY时，作为一个补充桑格测序。然而，在实现外显子组测序的全部潜力之前，需要改进，特别是关于覆盖率。
Genetic testing for monogenic diabetes is important for patient care. Given the extensive genetic and clinical heterogeneity of diabetes, exome sequencing might provide additional diagnostic potential when standard Sanger sequencing-based diagnostics is inconclusive. The aim of the study was to examine the performance of exome sequencing for a molecular diagnosis of MODY in patients who have undergone conventional diagnostic sequencing of candidate genes with negative results. We performed exome enrichment followed by high-throughput sequencing in nine patients with suspected MODY. They were Sanger sequencing-negative for mutations in the HNF1A, HNF4A, GCK, HNF1B and INS genes. We excluded common, non-coding and synonymous gene variants, and performed in-depth analysis on filtered sequence variants in a pre-defined set of 111 genes implicated in glucose metabolism. On average, we obtained 45 X median coverage of the entire targeted exome and found 199 rare coding variants per individual. We identified 0–4 rare non-synonymous and nonsense variants per individual in our a priori list of 111 candidate genes. Three of the variants were considered pathogenic (in ABCC8, HNF4A and PPARG, respectively), thus exome sequencing led to a genetic diagnosis in at least three of the nine patients. Approximately 91% of known heterozygous SNPs in the target exomes were detected, but we also found low coverage in some key diabetes genes using our current exome sequencing approach. Novel variants in the genes ARAP1, GLIS3, MADD, NOTCH2 and WFS1 need further investigation to reveal their possible role in diabetes. Our results demonstrate that exome sequencing can improve molecular diagnostics of MODY when used as a complement to Sanger sequencing. However, improvements will be needed, especially concerning coverage, before the full potential of exome sequencing can be realized.
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