Genetic Variations ResourcesMay 15, 2013

Ansuman Chattopadhyay, PhD, Head Molecular Biology Information ServiceHealth Sciences Library SystemUniversity of Pittsburghansuman@pitt.edu

http://www.hsls.pitt.edu/guides/genetics

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

1bp1kb1Mb>5Mb

SNPs

In/DelMicro- and Mini-satellites

Copy Number Variations(CNVs)

Chromosomal rearrangements

Deletions / Inversions/ Translocations

DuplicationsDeletionsInsertions

100 % Population

100 % Population0.4-0.6 % Population

Human Genome Variations

321,340,1 bp (0.11 % of the genome) : SNPs40,568,593 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

Single Nucleotide Polymorphisms

SNPs

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 Projecthttp://www.hapmap.org/

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

http://www.1000genomes.org/about

Bioinformatics Institutionshttp://www.ebi.ac.uk/http://www.ncbi.nlm.nih.gov/

dbSNP

dbSNP Statsas of January 25, 2010

http://www.ncbi.nlm.nih.gov/SNP/snp_summary.cgi

Current Status of dbSNP

MassGenomics blog by Dan Koboldthttp://goo.gl/TwltA

dbSNP Data Types

Ref SNP : rs4244285

Ref SNP : rs4244285

Genetic Terminologies

Ref SNP : rs4244285

Submitted SNP: ss5586415

SNPedia and NextBio

http://goo.gl/aOsoX

http://goo.gl/Lqqd4

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

http://www.ncbi.nlm.nih.gov/snp

Searching dbSNP

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 Studieshttp://www.genome.gov/gwastudies/

Find SNPs for a Disease/Trait

CDC developed HuGENavigator : http://hugenavigator.net/

GWAS Integrator

GWAS Integrator

What SNPs are associated with “asthma”?

GWAS Integrator : rs7216389

GWAS Integrator

What SNPs are associated with “asthma”?

GWAS Integrator

GWAS Integrator : rs7216389

Ref: Moffatt Mf etal.childhood asthma. Nature. 2007 Jul 26;448(7152):470-3. Epub 2007 Jul 4. PubMed PMID: 17611496.

GWAS Integrator : rs7216389

Find associated Genes for a Disease/Trait

Gene Prospector: Asthma

Gene Prospector: Asthma

HuGE NavigatorAn 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 andEncyclopedia of DNA

Elements Project

Spatiotemporal gene expression

TP53

EGFR

A movie on regulated transcription

http://vcell.ndsu.edu/animations/regulatedtranscription/index.htm

Epigenetic mechanisms

Source: NCBIhttp://www.ncbi.nlm.nih.gov/books/NBK45788/#epi_sci_bkgrd.About_Epigenetics

Genome in 3D

http://www.nature.com/nature/journal/v470/n7333/pdf/470289a.pdf

Chromatin Immuno-Precititation-Seq(ChIP-Seq)

Epigenetic MarkersLandmark Paper:

http://www.nature.com/ng/journal/v39/n3/full/ng1966.html

Histone Modifications

http://goo.gl/GQ9V8

http://www.hsls.pitt.edu/guides/genetics

Encode Project

http://www.genome.gov/10005107

http://goo.gl/QeIbQ

Regulome

Regulome db Search

rs7216389 rs2853669

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

Copy Number

Variations (CNVs)

Structural Variations

A B C

A B CB B

ABC

A C

A D CB

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

DECIPHERhttps://decipher.sanger.ac.uk/application/dashboard

DECIPHER Syndrome Report

DECIPHER Syndrome Report

Structural Variations Databases Genome Variation Database

(DGV) dbVar DECIPHER dbRIP Mitelman Breakpoint Database

dbRIPhttp://dbrip.brocku.ca/searchRIP.html

Mitelman Breakpoint

Hands-On Exercise

Generate an integrated variation map with reference SNPs, Mitelman breakpoints and OMIM diseases for chromosome 17; region 7773,000-7792,000 bp. What gene(s) have you found in this region?

Answer key: http://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Variation/Exercises/var_qa3.html

Map Viewer Setuphttp://www.ncbi.nlm.nih.gov/projects/mapview

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 http://goo.gl/pUhQ4

Variant File : VCF

GenomeTrax Input

GenomeTrax Result

FUNCTIONAL ANALYSIS OF

MUTATIONS

Functional Analysis of SNPs

http://www.hsls.pitt.edu/guides/genetics

SNPs and the Structure of a Gene

http://www.hsls.pitt.edu/guides/genetics

Decision Tree for SNP Analysis

http://www.hsls.pitt.edu/guides/genetics

Exonic Splicing Enhancer/Silencer

http://www.hsls.pitt.edu/guides/genetics

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 (rs7626962).

Answer

http://www.hsls.pitt.edu/guides/genetics

Functional Analysis of SNPs

Functional Analysis of SNPs

Entrez SNP - Search Entrez SNP by refSNP ID to find SNP information.

Entrez Protein - Find protein information including its amino acid sequence and the presence of functional domains 

NCBI Amino Acid Explorer - Compare amino acids in terms of physyo-chemical properties

NCBI Mutation Analyzer - Predict the effect of amino acid change on the protein structure

TMHMM Server v. 2.0 - Predict the presence of transmembrane helix in a protein sequence

Russel etal., Amino Acid Properties Table - Predict the effect of amino acid change on the protein structure

SNP Gene View for SCN5A

Multiple Sequence Alignment

http://www.hsls.pitt.edu/guides/genetics

Amino Acids ComparisonNCBI Amino Acid Explorer

http://www.hsls.pitt.edu/guides/genetics

Compare Amino Acids Properties Amino Acid Properties Table:

http://www.russell.embl.de/aas/

http://www.hsls.pitt.edu/guides/genetics

Amino Acids Substitution Preference

http://www.hsls.pitt.edu/guides/genetics

Tools for Amino Acid Substitution Effect Prediction SIFT

http://sift.jcvi.org/ PolyPhen

http://genetics.bwh.harvard.edu/pph/ SNPs3D

http://www.snps3d.org/ pMUT

http://mmb2.pcb.ub.es:8080/PMut/

http://www.hsls.pitt.edu/guides/genetics

Comparison of AAS prediction tools

Pauline C. Ng and Steven Henikoff, Annu. Rev. Genomics Hum. Genet. 2006. 7:61–80

Tools on Functional SNP Analysis Search.HSLS MolBio link http://search.hsls.pitt.edu/vivisimo/cgi-bin/query-meta?v%3aproject=BioInfoTools&v%3afile=viv_B7AUre&v%3afra

me=list&v%3astate=root%7cN891&id=N891&action=list&

FASTSNP -- an always up-to-date and extendable service for SNP function analysis and prioritization

http://fastsnp.ibms.sinica.edu.tw/

F-SNP: computationally predicted functional SNPs for disease association studies.

http://compbio.cs.queensu.ca/F-SNP/

http://www.hsls.pitt.edu/guides/genetics

FASTSNP Analysis

http://www.hsls.pitt.edu/guides/genetics

FASTSNP Analysis

http://www.hsls.pitt.edu/guides/genetics

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

http://www.hsls.pitt.edu/guides/genetics

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

http://www.hsls.pitt.edu/guides/genetics

Tutorials and References Advanced Course on NCBI Resources

(Browser: IE, select .html format)

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 WernerBook:Bioinformatics for GeneticistsSource:Wiley InterScience: Online Books

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 Iwema Ansuman Chattopadhyayiwema@pitt.edu ansuman@pitt.edu 412-383-6887 412-648-1297

http://www.hsls.pitt.edu/guides/genetics