Genome Biology & Applied Bioinformatics Mehmet Tevfik DORAK, MD PhD SNPs Mehmet Tevfik DORAK, MD PhD

Schedule

Individual SNP Analysis Functionality Scores for the Whole Genome Outline Individual SNP Analysis (SNiPA, rVARbase) Multiple SNP Analysis (PheGenI, SNPnexus) eQTL Resources Browsers Functionality Scores for the Whole Genome

Interpretation of GWAS Findings: Individual SNPs SNiPA: For individual SNP analysis, SNiPA is a very comprehensive tool. Variant Annotation is the section which provides basic information, conservation and functionality scores (CADD included), eQTL results for multiple tissues, chromatin modifications, GWAS associations and regulatory effects summary. Results can be saved as a single PDF file.

Interpretation of GWAS Findings: Individual SNPs Link: http://rv.psych.ac.cn rVARbase compiles information from a variety of sources mainly for regulatory effects of individual SNPs. Results include CCC analysis, miRNA and lncRNA effects, and downloadable.

Interpretation of GWAS Findings: Multiple SNPs SNPnexus: http://www.snp-nexus.org Up to 100 thousand SNPs can be analyzed in one go!

Interpretation of GWAS Findings: Multiple SNPs SNPnexus: http://www.snp-nexus.org Results can be saved as a single Excel file (may be too large for a large number of SNPs).

Interpretation of GWAS Findings: Multiple SNPs PheGenI: http://www.ncbi.nlm.nih.gov/gap/phegeni Multiple SNPs can be analyzed in one go, but no more than around 400. Also provides eQTL results, but only for lymphoblastoid cells. Each component of the results is downloadable.

Results from multiple tissues from the same persons eQTL Resources: GTEx Results from multiple tissues from the same persons GTEx: http://www.gtexportal.org/home Paper: http://science.sciencemag.org/content/348/6235/660.abstract

eQTL Resources: GTEx Link: http://www.gtexportal.org/home/datasets

eQTL Resources: GTEx Link: http://www.gtexportal.org/home/browseEqtls

Address: http://www.gtexportal.org/home/bubbleHeatmapPage/ACTN3 eQTL Resources: GTEx Link: http://www.gtexportal.org/home/bubbleHeatmapPage/ACTN3 Address: http://www.gtexportal.org/home/bubbleHeatmapPage/ACTN3

Address: http://www.gtexportal.org/home/gene/RASSF2 eQTL Resources: GTEx Address: http://www.gtexportal.org/home/gene/RASSF2 Link: http://www.gtexportal.org/home/gene/RASSF2

eQTL Resources Link: http://www.gtexportal.org/home/testyourown

eQTL Resources GTEx is not the only eQTL resource. Many others are available and can be reached via http://www.dorak.info/mtd/bioinf.html.

eQTL and meQTL Expression Quantitative Trait Locus: eQTL Methylation Quantitative Trait Locus: meQTL (most relevant in complex diseases) * * * * Non-synonymous (missense) or non-sense mutations directly affect protein structure or translation (more relevant in Mendelian than complex diseases)

BIOS QTL Browser for eQTL/meQTL analysis Assesses both eQTL and meQTL status of a SNP BIOS QTL Browser: http://genenetwork.nl/biosqtlbrowser Paper: http://biorxiv.org/content/early/2015/12/01/033084.1

mQTLdb for meQTL analysis Results from five life stages Paper: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0926-z

Browsers UCSC: http://genome-euro.ucsc.edu Ensembl: http://www.ensembl.org/Homo_sapiens/Info/Index 1KG: http://browser.1000genomes.org/index.html HapMap: http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/hapmap28_B36 Swiss Regulon: http://swissregulon.unibas.ch/fcgi/sr/annotations

Functionality Scores for the Whole Genome CADD scores: http://cadd.gs.washington.edu/download DANN scores: https://cbcl.ics.uci.edu/public_data/DANN/data EIGEN scores: http://www.columbia.edu/~ii2135/download.html RegulomeDB scores: http://regulomedb.org/downloads dbWGFP Scores: http://bioinfo.au.tsinghua.edu.cn/dbwgfp/downloads.php?page=downlite Pre-computed Structure-PPi scores for COSMIC and 1KG mutations: http://structureppi.bioinfo.cnio.es/Structure

Functionality Scores for the Whole Genome Links: GeneCanyon: http://genocanyon.med.yale.edu:7772 Paper: http://www.nature.com/articles/srep10576 22 different annotations corresponding to either conservation score or biochemical activity, including 2 genomic conservation measures, 2 indicators of open chromatin, 8 histone modifications, and 10 TFBS peaks.

Functionality Scores for the Whole Genome Links: GeneCanyon: http://genocanyon.med.yale.edu:7772 Paper: http://www.nature.com/articles/srep10576 22 different annotations corresponding to either conservation score or biochemical activity, including 2 genomic conservation measures, 2 indicators of open chromatin, 8 histone modifications, and 10 TFBS peaks.

… Looking forward ….. http://www.dorak.info

Course material: http://www.dorak.info/genbiol/course.html