Abstract
Studies of complex genetic diseases have revealed many risk factors of small effect, but the combined amount of heritability explained is still low. Genome-wide association studies are often underpowered to identify true effects because of the very large number of parallel tests. There is, therefore, a great need to generate data sets that are enriched for those markers that have an increased a priori chance of being functional, such as markers in genomic regions involved in gene regulation. ReMo-SNPs is a computational program developed to aid researchers in the process of selecting functional SNPs for association analyses in user-specified regions and/or motifs genome-wide. The useful feature of automatic selection of genotyped markers in the user-provided material makes the output data ready to be used in a following association study. In this article we describe the program and its functions. We also validate the program by including an example study on three different transcription factors and results from an association study on two psychiatric phenotypes. The flexibility of the ReMo-SNPs program enables the user to study any region or sequence of interest, without limitation to transcription factor binding regions and motifs. The program is freely available at: http://www.neuro.ki.se/ReMo-SNPs/.
Highlights
Recent advances in high-throughput sequencing and genotyping techniques have enabled researchers to generate unprecedented amounts of genomic data. These efforts have led to the identification of more than 60 million single nucleotide polymorphisms (SNPs) (Frazer et al, 2007). Information about these markers has been gathered in the National Center for Biotechnology Information (NCBI) Database of Single Nucleotide Polymorphisms, which holds information about their location, alleles and frequencies (Sherry et al, 2001)
Mutations in these regulatory sequences that are introduced by SNPs occurring within the motif may have a major impact on gene function and could in many cases contribute to disease risk, onset and/or severity
For the SNP Function Annotation Portal and SNP Function Prediction tools, vitamin D receptor (VDR) motif-SNPs within verified regions generated significantly higher scores, the rest showed a tendency for higher scores except for peroxisome proliferator-activated receptor (PPAR) in the SNP Function Annotation Portal, where the motif-SNPs placed outside the transcription factor binding regions generated higher scores
Summary
Studies of complex genetic diseases have revealed many risk factors of small effect, but the combined amount of heritability explained is still low. Genome-wide association studies are often underpowered to identify true effects because of the very large number of parallel tests. There is, a great need to generate data sets that are enriched for those markers that have an increased a priori chance of being functional, such as markers in genomic regions involved in gene regulation. ReMo-SNPs is a computational program developed to aid researchers in the process of selecting functional SNPs for association analyses in user-specified regions and/or motifs genome-wide. The useful feature of automatic selection of genotyped markers in the user-provided material makes the output data ready to be used in a following association study. The flexibility of the ReMo-SNPs program enables the user to study any region or sequence of interest, without limitation to transcription factor binding regions and motifs. The program is freely available at: http://www. neuro.ki.se/ReMo-SNPs/
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