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. 2014 Sep 30;16(5):447.
doi: 10.1186/s13075-014-0447-7.

Targeted exon sequencing fails to identify rare coding variants with large effect in rheumatoid arthritis

So-Young Bang, Young-Ji Na, Kwangwoo Kim, Young Bin Joo, Youngho Park, Jaemoon Lee, Sun-Young Lee, Adnan A Ansari, Junghee Jung, Hwanseok Rhee, Jong-Young Lee, Bok-Ghee Han, Sung-Min Ahn, Sungho Won, Hye-Soon Lee, Sang-Cheol Bae

Targeted exon sequencing fails to identify rare coding variants with large effect in rheumatoid arthritis

So-Young Bang et al. Arthritis Res Ther. .

Abstract

Introduction: Although it has been suggested that rare coding variants could explain the substantial missing heritability, very few sequencing studies have been performed in rheumatoid arthritis (RA). We aimed to identify novel functional variants with rare to low frequency using targeted exon sequencing of RA in Korea.

Methods: We analyzed targeted exon sequencing data of 398 genes selected from a multifaceted approach in Korean RA patients (n = 1,217) and controls (n = 717). We conducted a single-marker association test and a gene-based analysis of rare variants. For meta-analysis or enrichment tests, we also used ethnically matched independent samples of Korean genome-wide association studies (GWAS) (n = 4,799) or immunochip data (n = 4,722).

Results: After stringent quality control, we analyzed 10,588 variants of 398 genes from 1,934 Korean RA case controls. We identified 13 nonsynonymous variants with nominal association in single-variant association tests. In a meta-analysis, we did not find any novel variant with genome-wide significance for RA risk. Using a gene-based approach, we identified 17 genes with nominal burden signals. Among them, VSTM1 showed the greatest association with RA (P = 7.80 × 10-4). In the enrichment test using Korean GWAS, although the significant signal appeared to be driven by total genic variants, we found no evidence for enriched association of coding variants only with RA.

Conclusions: We were unable to identify rare coding variants with large effect to explain the missing heritability for RA in the current targeted resequencing study. Our study raises skepticism about exon sequencing of targeted genes for complex diseases like RA.

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Figures

Figure 1
Figure 1
Description of the study design. We analyzed data from protein-coding variants within targeted genes using three different strategies for analysis.
Figure 2
Figure 2
Enrichment analysis of 77 novel genes with nominal signal on exon sequencing in the GWAS dataset. (A) We performed logistic regressions including 10 principal components using 1,000-times permuted phenotypes. The numbers of (B) genic, (C) exonic, (D) nonsynonymous (NonSyn), and (E) synonymous (Syn) variants reaching the P <0.05 threshold following 1,000 permutations are shown. Significant enrichment of SNVs using the P <0.05 threshold was assessed using Fisher’s exact tests (** P <0.01). These enrichment signals were driven by each group (P enrichment (genic) = 1.04 × 10−32, P enrichment (exon) = 0.41, P enrichment (NonSyn) = 0.18, and P enrichment (Syn) = 0.98 at P threshold = 0.05).
Figure 3
Figure 3
Rare variants of VSTM1 identified by exon sequencing. The seven nonsynonymous variants of VSTM1 that were validated by the Sanger sequencing method were primarily singletons driven from controls except for A33T (RA (n = 3), control (n = 5)). The four nonsynonymous variants of VSTM1 lie within the coding regions of the immunoglobulin-like domain.
See this image and copyright information in PMC

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