ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
The ANNOVAR tool to annotate single nucleotide variants and insertions/deletions, such as examining their functional consequence on genes, inferring cytogenetic bands, reporting functional importance scores, finding variants in conserved regions, or identifying variants reported in the 1000 Genomes Project and dbSNP is developed.
PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data.
PennCNV, a hidden Markov model (HMM) based approach, is presented for kilobase-resolution detection of CNVs from Illumina high-density SNP genotyping data, demonstrating the feasibility of whole-genome fine-mapping ofCNVs via high- density SNP genotypesing.
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci
A meta-analysis of six Crohn's disease genome-wide association studies and a series of in silico analyses highlighted particular genes within these loci implicated functionally interesting candidate genes including SMAD3, ERAP2, IL10, IL2RA, TYK2, FUT2, DNMT3A, DENND1B, BACH2 and TAGAP.
Functional impact of global rare copy number variation in autism spectrum disorders
The genome-wide characteristics of rare (<1% frequency) copy number variation in ASD are analysed using dense genotyping arrays to reveal many new genetic and functional targets in ASD that may lead to final connected pathways.
Pathway-based approaches for analysis of genomewide association studies.
It is demonstrated that pathway-based approaches, which jointly consider multiple contributing factors in the same pathway, might complement the most-significant SNPs/genes approach and provide additional insights into interpretation of GWA data on complex diseases.
Autism genome-wide copy number variation reveals ubiquitin and neuronal genes
Several new susceptibility genes encoding neuronal cell-adhesion molecules, including NLGN1 and ASTN2, were enriched with CNVs in ASD cases compared to controls, and duplications 55 kilobases upstream of complementary DNA AK123120 indicate that these two important gene networks expressed within the central nervous system may contribute to the genetic susceptibility of ASD.
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis
Moderate powered genome-wide association studies (GWAS) have enabled more than 20 additional risk loci to be identified and have shown that multiple variants exerting modest individual effects have a key role in disease susceptibility.
Common genetic variants on 5p14.1 associate with autism spectrum disorders
The results implicate neuronal cell-adhesion molecules in the pathogenesis of ASDs, and represent, to the authors' knowledge, the first demonstration of genome-wide significant association of common variants with susceptibility to ASDs.
Genotype, haplotype and copy-number variation in worldwide human populations
The analysis of high-quality genotypes at 525,910 single-nucleotide polymorphisms (SNPs) and 396 copy-number-variable loci in a worldwide sample of 29 populations produces new inferences about inter-population variation, support the utility of CNVs in human population-genetic research, and serve as a genomic resource for human- genetic studies in diverse worldwide populations.
Analysing biological pathways in genome-wide association studies
The development of pathway-based approaches for GWA studies are reviewed, their practical use and caveats are discussed, and it is suggested that pathway- based approaches may also be useful for future GWA study data sets with sequencing data.