Genetic Variations Resources May 15, 2013 Ansuman Chattopadhyay, PhD, Head Molecular Biology Information Service Health Sciences Library System University of Pittsburgh

Objective  Human genetic variations  Genetic variations databases  Functional analysis of mutations/SNPs

Topics  Databases:  dbSNP  db GAP  GenPheni  DGV  Decipher  OMIM  HGMD  Regulome db  Tools  HugeNavigator  FastSNP  SPOT  GenomeTrax

Human Genetic Variations 1bp 1kb 1Mb >5Mb Duplications Deletions Insertions

Human Genome Variations 321,340,1 bp (0.11 % of the genome) : SNPs 40,568,593 bp (1.35% of the genome) : CNVs Scherer, S.W. (2009), "Copy number variation", in Scherer, S. (ed.), Copy Number Variation:, The Biomedical & Life Sciences Collection, Henry Stewart Talks Ltd, London

SNP Facts

Life Cycle of SNPs and Mutations Mutation/ Private SNP SNPs

Classifications of SNPs Genomic location based

Classifications of SNPs Nucleotide substitution based

Polymorphisms and Disease Markers

International Hap Map Project  Whole-genome genotyping of 10 million SNPs  Technologically daunting  Prohibitively expensive  Researchers tried to downsize the problem of genome-wide genotyping by studying haplotypes.  A haplotype is a contiguous, linear set of SNP alleles along a genome that is inherited as a block.

The Origin of Haplotype

Haplotype Blocks

Haplotype and Tag SNPs

Hap Map Population

Bioinformatics Institutions

dbSNP

dbSNP Stats as of January 25,

Current Status of dbSNP MassGenomics blog by Dan Koboldt

dbSNP Data Types

Ref SNP : rs

Genetic Terminologies

Ref SNP : rs

Submitted SNP: ss

SNPedia and NextBio

Searching dbSNP  Identify  SNPs present in a gene sequence  SNPs reported to be present in a genomic region

Searching dbSNP UCSC Genome Browser UCSC Table Browser NCBI dbSNP page

Searching dbSNP

dbSNP Search result Display

GWAS

GWAS Plot Each SNP is assessed for ‘‘genome-wide’’ significance, after Bonferroni correction.

Publications on HapMap Hap map GWAS

Genome Wide Association Studies

Find SNPs for a Disease/Trait CDC developed HuGENavigator :

GWAS Integrator

What SNPs are associated with “asthma”?

GWAS Integrator : rs rs

GWAS Integrator What SNPs are associated with “asthma”?

GWAS Integrator

GWAS Integrator : rs rs Ref: Moffatt Mf etal. childhood asthma. Nature Jul 26;448(7152): Epub 2007 Jul 4. PubMed PMID:

GWAS Integrator : rs rs

Find associated Genes for a Disease/Trait

Gene Prospector: Asthma

HuGE Navigator An integrated, searchable knowledge base of genetic associations and human genome epidemiology

PheGenI

Clinically Associated Mutations OMIM HGMD

Online Mendelian Inheritance in Man (OMIM)

OMIM

Epigenome and Encyclopedia of DNA Elements Project

Spatiotemporal gene expression TP53 EGFR

A movie on regulated transcription

Epigenetic mechanisms Source: NCBI

Genome in 3D

Chromatin Immuno-Precititation-Seq (ChIP-Seq)

Epigenetic Markers Landmark Paper :

Histone Modifications

Encode Project

Regulome

Regulome db Search rs rs

Hands-on Exercise on Searching dbSNP  Mutations in the human BRCA1 gene are reported to be associated with the early onset of breast cancer.  How many coding nonsynonimous SNPs have been reported to be associated with this gene?  How many of these SNPs shows >40% heterozygosity?  Pick a SNP from the list and find the position of its protein sequence, which shows aa change due to this SNP.  How many in dels are reported to be present in the chromosome chr21: region 33,031,597-33,041,570 ?

Hands –On Exercise Identify genes and SNPs associated with your disease/trait of interest Crohn’s disease, Prostate cancer, LDL cholesterol

Structural Variations ABC ABCBB ABC AC ADCB Normal Duplication Inversion Deletion Insertion CNV

Structural Variations

Structural Variations Databases Database of Genome Variations (DGV) dbVar DECIPHER dbRIP Mitelman Breakpoint Database

DGV

DGV :Genome wide view

DGV

DGV: Chr 1

DGV

Hands-on Exercise Is the CETN1 or Grip1 gene located in a region that is copy number variable? Are there any other genes in this region? Can you find any Inversions or In Dels there as well? What is the frequency of the CNV reported in the study population?

DGV Genome Browser

DGV: Genome Browser

dbVar

DECIPHER

DECIPHER Syndrome Report

Structural Variations Databases Genome Variation Database (DGV) dbVar DECIPHER dbRIP Mitelman Breakpoint Database

dbRIP

Mitelman Breakpoint

Hands-On Exercise Generate an integrated variation map with reference SNPs, Mitelman breakpoints and OMIM diseases for chromosome 17; region 7773, ,000 bp. What gene(s) have you found in this region? Answer key:

Map Viewer Setup

Map Viewer Setup

Genetic Variations Map

Online Mendelian Inheritance in Man (OMIM)

OMIM

UCSC Table Browser

Hands-on Exercise Find all human genes which have only one exon. How many of these also show CNVs? Tips: Use UCSC Table Browser

Biobase Genome Trax and HGMD

Variant File : VCF

GenomeTrax Input

GenomeTrax Result

Functional Analysis of SNPs

SNPs and the Structure of a Gene

Decision Tree for SNP Analysis

Exonic Splicing Enhancer/Silencer

Functional Analysis of SNPs A gene variant primarily found in African Americans, that slightly increases the risk for developing an irregular heartbeat, known as arrhythmia. The variant occurs in the cardiac sodium channel gene SCN5A which results a change of amino acid at the position of 1102 from serine to tyrosine (S To Y). Can you predict the effect of this non-synonymous SNP (rs ). Answer

Functional Analysis of SNPs

 Entrez SNP - Search Entrez SNP by refSNP ID to find SNP information. Entrez SNP  Entrez Protein - Find protein information including its amino acid sequence and the presence of functional domains Entrez Protein  NCBI Amino Acid Explorer - Compare amino acids in terms of physyo-chemical properties NCBI Amino Acid Explorer  NCBI Mutation Analyzer - Predict the effect of amino acid change on the protein structure NCBI Mutation Analyzer  TMHMM Server v Predict the presence of transmembrane helix in a protein sequence TMHMM Server v. 2.0  Russel etal., Amino Acid Properties Table - Predict the effect of amino acid change on the protein structure Russel etal., Amino Acid Properties Table

SNP Gene View for SCN5A

Multiple Sequence Alignment

Amino Acids Comparison NCBI Amino Acid Explorer

Compare Amino Acids Properties Amino Acid Properties Table:

Amino Acids Substitution Preference

Tools for Amino Acid Substitution Effect Prediction SIFT  PolyPhen  SNPs3D  pMUT 

Comparison of AAS prediction tools Pauline C. Ng and Steven Henikoff, Annu. Rev. Genomics Hum. Genet :61–80

Tools on Functional SNP Analysis Search.HSLS MolBio link meta?v%3aproject=BioInfoTools&v%3afile=viv_B7AUre&v%3aframe=list&v%3astate=root%7cN891&id=N891&act ion=list& meta?v%3aproject=BioInfoTools&v%3afile=viv_B7AUre&v%3aframe=list&v%3astate=root%7cN891&id=N891&act ion=list& FASTSNP -- an always up-to-date and extendable service for SNP function analysis and prioritization F-SNP: computationally predicted functional SNPs for disease association studies.

FASTSNP Analysis

FASTSNP Analysis

F-SNP : A Collection of Functional SNPs Specifically Prioritized for Disease Association studies

F-SNP : A Collection of Functional SNPs Specifically Prioritized for Disease Association Studies

Tutorials and References Advanced Course on NCBI Resources (Browser: IE, select.html format) Predictive Functional Analysis of Polymorphisms: An Overview Predictive Functional Analysis of Polymorphisms: An Overview Authors:Michael R. Barnes Book:Bioinformatics for Geneticists Source:Wiley InterScience: Online Books Functional In Silico Analysis of Non-Coding SNPs Authors:Thomas Werner Book:Bioinformatics for Geneticists Source:Wiley InterScience: Online Books Predicting the Effects of Amino Acid Substitutions on Protein Function Predicting the Effects of Amino Acid Substitutions on Protein Function  Pauline C. Ng and Steven Henikoff  Fred Hutchinson Cancer Research Center, Seattle,Washington 98109;

Thank you! Any questions? Carrie IwemaAnsuman Chattopadhyay