Evaluation of a target region capture sequencing platform using monogenic diabetes as a study-model.
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.
Rui
R
Gao
Yanxia
Y
Liu
Anette Prior
AP
Gjesing
Mette
M
Hollensted
Xianzi
X
Wan
Shuwen
S
He
Oluf
O
Pedersen
BGI-Shenzhen, Shenzhen, China. yix@genomics.cn.
Xin
X
Yi
Jun
J
Wang
Torben
T
Hansen
D004252:DNA Mutational Analysis / Q000379:methods*; D003924:Diabetes Mellitus, Type 2 / Q000235:genetics*; D020440:Gene Duplication; D006801:Humans; D054643:INDEL Mutation; D020641:Polymorphism, Single Nucleotide; D017384:Sequence Deletion