Disease-associated variants in different categories of disease located in distinct regulatory elements.

BACKGROUND: The invention of high throughput sequencing technologies has led to the discoveries of hundreds of thousands of genetic variants associated with thousands of human diseases. Many of these genetic variants are located outside the protein coding regions, and as such, it is challenging to interpret the function of these genetic variants by traditional genetic approaches. Recent genome-wide functional genomics studies, such as FANTOM5 and ENCODE have uncovered a large number of regulatory elements across hundreds of different tissues or cell lines in the human genome. These findings provide an opportunity to study the interaction between regulatory elements and disease-associated genetic variants. Identifying these diseased-related regulatory elements will shed light on understanding the mechanisms of how these variants regulate gene expression and ultimately result in disease formation and progression. RESULTS: In this study, we curated and categorized 27,558 Mendelian disease variants, 20,964 complex disease variants, 5,809 cancer predisposing germline variants, and 43,364 recurrent cancer somatic mutations. Compared against nine different types of regulatory regions from FANTOM5 and ENCODE projects, we found that different types of disease variants show distinctive propensity for particular regulatory elements. Mendelian disease variants and recurrent cancer somatic mutations are 22-fold and 10- fold significantly enriched in promoter regions respectively (q<0.001), compared with allele-frequency-matched genomic background. Separate from these two categories, cancer predisposing germline variants are 27-fold enriched in histone modification regions (q<0.001), 10-fold enriched in chromatin physical interaction regions (q<0.001), and 6-fold enriched in transcription promoters (q<0.001). Furthermore, Mendelian disease variants and recurrent cancer somatic mutations share very similar distribution across types of functional effects. We further found that regulatory regions are located within over 50% coding exon regions. Transcription promoters, methylation regions, and transcription insulators have the highest density of disease variants, with 472, 239, and 72 disease variants per one million base pairs, respectively. CONCLUSIONS: Disease-associated variants in different disease categories are preferentially located in particular regulatory elements. These results will be useful for an overall understanding about the differences among the pathogenic mechanisms of various disease-associated variants.

[Genomewide association study: advances, challenges and deliberation].

Genomewide association study (GWAS) is a novel strategy for discovering genetic basis of human complex disease or trait. It utilizes millions of single nucleotide polymorphisms (SNPs) , which cover the whole genome, to conduct case-control association studies. In recent years, following the newly established Human Genome Project (HGP) and International Human HapMap project, large number of human complex disease/trait associated genetic variants have been identified through GWAS method, which provides important clues for understanding the mechanisms of related disorders. Due to the complexity of these multi-factorial diseases/traits and the complication of GWAS system itself, the GWAS remains many problems. In this review, we will discuss the potential issues in the following aspects as research methods, study subjects, genetic markers and statistical analysis.

A missense mutation in the gammaD-crystallin gene CRYGD associated with autosomal dominant congenital cataract in a Chinese family.

PURPOSE: To identify the genetic defect in autosomal dominant congenital cataracts in a six generation Chinese family. METHODS: Clinical and ophthalmological examinations were performed on the affected and unaffected family members. All the members were genotyped with microsatellite markers at loci which were considered to be associated with cataracts. A two-point LOD score was calculated using the Linkage package after genotyping. A mutation was detected by direct sequencing using gene specific primers. RESULTS: Clinical heterogeneity was observed within this family, three affected individuals showed nuclear cataract and others had coralliform cataracts. Significant evidence of linkage was obtained at markers D2S325 (LOD score [Z]=3.10, recombination fraction [theta]=0.0) and D2S1782 (Z=5.97, theta=0.0), respectively. Haplotype analysis indicated that the cataract gene was close to those two markers. Sequencing of the gammaD-crystallin gene (CRYGD) revealed a C>T transition in exon 2, that causes a conservative substitution of Arg to Cys at codon 14 (R14C). This mutation co-segregated with all affected individuals and was not observed in unaffected or 100 normal unrelated individuals. Bioinformatic analyses also showed that a highly conserved region was located at Arg14. CONCLUSIONS: This study is the first reported case with phenotype of coralliform/nuclear cataract that associated with the mutation of Arg14Cys (R14C) CRYGD.

Identification of novel mutations of IRF6 gene in Chinese families with Van der Woude syndrome.

Van der Woude syndrome (VWS) is an autosomal dominant disorder of syndromic clefts clinically characterized by lower lip pits, cleft lip and/or palate, hypodontia. Mutations in the IRF6 gene have recently been found to cause VWS and more than 70 mutations have been reported. However, genotype distribution and prevalence of IRF6 mutations underlying Chinese are largely unknown. In the present study, we report on four Chinese families with VWS. Considerably variable clinical phenotypes were observed between and within each family. By direct sequencing, three novel mutations (Y111H, S407fsX436, F165fsX166) as well as a recurrent mutation (R400W) were identified. In contrast to the IRF6 mutations reported in Caucasians, the majority of these mutations occurred at a run of 1- or 2-base repetitive sequence unit, and localized neither in the conserved DNA-binding domain nor in the Smad-interferon regulatory factor-binding domain (SMIR). Therefore, our results indicate the existence of other putative IRF6 regions that are predisposed to mutations. Repeated nucleotides in the IRF6 coding regions may increase the instability and chance of DNA replication errors, and are prone to be potential mutation hot-spots.