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Sequencing of specific genomic regions has been successfully applied to the investigation of genetic diseases and large-scale validation of candidate genes responsible for complex diseases. It can be also used in the field of plant and animal breeding. However, focusing only on coding exons is insufficient and expensive for large-scale, deep exome sequencing of thousands of samples. To facilitate your research, BGI provides target region sequencing in combination with other NGS integrated solutions. BGI has extensive experience in target region sequencing, with over 65,000 samples sequenced.

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A large-scale screen for coding variants predisposing to psoriasis. Nature Genetics 46, 45-50 (2014).

Research Background

Psoriasis is a complex, chronic, lifelong skin disease. It typically first strikes people between the ages of 15 to 35, but can affect anyone at any age, including children. This disease is considered to be caused by the combinations of multiple factors, such as environment, genetics, and immunology. To explore the contribution of functional coding variants to psoriasis, we employed two-stage genome-wide association studies to identify risk coding variants.

Phase I Discovery stage

We analyzed nonsynonymous single-nucleotide variants (SNVs) across the genome by exome sequencing in781 psoriasis cases and 676 controls. The whole exome sequencing efforts yielded 518,308 SNVs. Of these variants, 20.62% were nonsynonymous, and 68.13% were rare. Single variant and gene-based association analyses identified 133 nonsynonymous SNVs and 742 candidate genes with suggestive evidence of associations.

Phase II Validation stage

We conducted follow-up validation in 1,326 candidate genes by targeted sequencing in 9,946 psoriasis cases and 9,906 controls from the Chinese population. A total of 3.2 Mb of coding DNA surrounding the targeted regions of 1,326 genes (covering 133 SNVs, 622 immune disease–related genes, and some top genes) was captured. This validation targeted sequencing stage totally identified 82,387 nonsynonymous SNVs, of which 97.07% were rare. Association analyses of the combined data from exome and targeted sequencing identified six common and low-frequency nonsynonymous SNVs at genome-wide significance.

In Summary

We carried out a comprehensive analysis of coding SNVs in a large sample and discovered two independent low-frequency variants with moderate effect on disease risk. Single-variant and gene-based association analyses of nonsynonymous SNVs did not identify newly associated genes for psoriasis in the regions subjected to targeted resequencing. This suggests that the contribution of rare coding variants in the targeted genes to psoriasis is much smaller than previously thought.

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