Copyright OpenHelix. No use or reproduction without express written consent1
HapMap A resource of Human SNP and haplotype data Materials prepared by: Warren C. Lathe III, Ph.D Updated: Q Version_4.0
Copyright OpenHelix. No use or reproduction without express written consent3 Agenda for HapMap Introduction and Credits Browser Overview Using the Browser & Details Tracks HapMart Search HaploView Software Summary Exercises HapMap:
Copyright OpenHelix. No use or reproduction without express written consent4 HapMap Introduction Started in 2002 Variations in 270 people 4 populations Yoruba in Ibadan, Nigeria (abbreviation: YRI) Japanese in Tokyo, Japan (abbreviation: JPT) Han Chinese in Beijing, China (abbreviation: CHB) CEPH (Utah residents with ancestry from northern and western Europe) (abbreviation: CEU) Over 4 million unique genotyped SNPs
Copyright OpenHelix. No use or reproduction without express written consent5 HapMap Introduction About the project Participant details Participating groups and funding agencies
Copyright OpenHelix. No use or reproduction without express written consent6 HapMap Credits 24 institutions 6 countries 10 funding agencies
Copyright OpenHelix. No use or reproduction without express written consent7 HapMap Publications The International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature 449, Publications The International HapMap Consortium. A haplotype map of the human genome. Nature 437, Original Recent
Copyright OpenHelix. No use or reproduction without express written consent8 HapMap Introduction Project Information Data Useful links Data browser Bulk download
Copyright OpenHelix. No use or reproduction without express written consent9 Agenda for HapMap Introduction and credits Browser Overview Using the Browser & Details Tracks HapMart Search HaploView Software Summary Exercises HapMap:
Copyright OpenHelix. No use or reproduction without express written consent10 HapMap Browser Start Type “clock” Choose data source Click search clock
Copyright OpenHelix. No use or reproduction without express written consent11 HapMap Browser Location LocationExamples
Copyright OpenHelix. No use or reproduction without express written consent12 Browser Search Type search term Select data set View & download Scroll & zoom
Copyright OpenHelix. No use or reproduction without express written consent13 Region Overview Overview of chromosome & statistics Yellow line is location viewed in details section Region of chromosome & statistics
Copyright OpenHelix. No use or reproduction without express written consent14 Details Variation details Gene structure
Copyright OpenHelix. No use or reproduction without express written consent15 Data Tracks Available Data types & annotation tracks to add to details view
Copyright OpenHelix. No use or reproduction without express written consent16 Display Settings Change image width Highlight settings Key and track positions
Copyright OpenHelix. No use or reproduction without express written consent17 Add Your Own Tracks Help
Copyright OpenHelix. No use or reproduction without express written consent18 Agenda for HapMap Introduction and credits Browser Overview Using the Browser & Details Tracks HapMart Search HaploView Software Summary Exercises HapMap:
Copyright OpenHelix. No use or reproduction without express written consent19 Linkage Disequilibrium (LD) Plots, Example LD plots show linkage disequilibrium between two chromosomal segments
Copyright OpenHelix. No use or reproduction without express written consent20 Tag SNPs, Example AACACGCA…TTCGGGGTC…AGTCGACCG AACACGCA…TTCGAGGTC…AGTCAACCG AACATGCA…TTCGGGGTC…AGTCAACCG AACACGCA…TTCGGGGTC…AGTCGACCG Variable positions and alleles from individuals C T C A A A G C A C G G T T C A G G C A T T G A T T G A G C A A C A G T A A T A C C C G A T C T G T G A T A C T G G T G T C G A T T C T G C G G T T G A G A C A haplotype l haplotype 2 haplotype 3 haplotype 4 These variable positions are inherited together or linked: haplotypes A/G C/A/TC/G Some positions can be used to predict haplotype: tag SNPs G, T, C
Copyright OpenHelix. No use or reproduction without express written consent21 Location Help links Type in search term or location Choose data source Click search
Copyright OpenHelix. No use or reproduction without express written consent22 Overview & Details Overview of location & data details
Copyright OpenHelix. No use or reproduction without express written consent23 Adding & Configuring Annotation Reports & Analysis to add data to details Configure
Copyright OpenHelix. No use or reproduction without express written consent24 Adding & Configuring Annotation Click Configure Choose rsquare for LD property
Copyright OpenHelix. No use or reproduction without express written consent25 LD Plot in Details Section Linkage disequilibrium plot
Copyright OpenHelix. No use or reproduction without express written consent26 Zooming In: Add Detail Zooming in allows you to view more detailed data and information
Copyright OpenHelix. No use or reproduction without express written consent27 Zooming In: Add Detail SNPs reference sequences & alleles show up in zoomed view
Copyright OpenHelix. No use or reproduction without express written consent28 Zooming In Further: More Detail Zoom to 20kbp
Copyright OpenHelix. No use or reproduction without express written consent29 Further Zoom & Link Out Click gene Click SNP Zooming further shows more detailed information such as allele frequencies SNP “rs” reference number
Copyright OpenHelix. No use or reproduction without express written consent30 Configuring Tracks Configure tracks
Copyright OpenHelix. No use or reproduction without express written consent31 Adding Data with Tracks LD Plot added Update image Add 3-frames Add tag SNPs
Copyright OpenHelix. No use or reproduction without express written consent32 Added Tracks tag SNPs 3-frames
Copyright OpenHelix. No use or reproduction without express written consent33 Changing Tracks within Browser Window “?” Configuration menu Click track and drag Move track to new position
Copyright OpenHelix. No use or reproduction without express written consent34 Two Places to Add Analysis Add LD plot in tracks section Add tag SNPs in tracks section Add tag SNPs with Reports & Analysis menu Click Configure Add LD plot with Reports & Analysis menu
Copyright OpenHelix. No use or reproduction without express written consent35 Agenda for HapMap Introduction and credits Browser Overview Using the Browser & Details Tracks HapMart Search HaploView Software Summary Exercises HapMap:
Copyright OpenHelix. No use or reproduction without express written consent36 HapMart Access HapMart
Copyright OpenHelix. No use or reproduction without express written consent37 HapMart Searches Three Steps: Start Filter Output
Copyright OpenHelix. No use or reproduction without express written consent38 Click next HapMap Start Choose schema/release Choose population dataset Choose data to search
Copyright OpenHelix. No use or reproduction without express written consent39 HapMart Filters “Start” choices appear on right side Filter data for specific requirements
Copyright OpenHelix. No use or reproduction without express written consent40 Selecting HapMart Filters Choose minor allele frequency Choose SNP type Choose chromosomal location Gene & ENCODE filters
Copyright OpenHelix. No use or reproduction without express written consent41 Selecting HapMart Filters Click next Choose another dataset
Copyright OpenHelix. No use or reproduction without express written consent42 HapMart Output Page “filter” choices appear on right side Choose data attributes
Copyright OpenHelix. No use or reproduction without express written consent43 HapMart Output SNP details Allele frequency Genotype Genotype frequency Genotype count Choose output format, file compression & saved location
Copyright OpenHelix. No use or reproduction without express written consent44 Output Options Output format Download to desktop or show in browser Compress file Click export
Copyright OpenHelix. No use or reproduction without express written consent45 HapMart Export
Copyright OpenHelix. No use or reproduction without express written consent46 Agenda for HapMap Introduction and credits Browser Overview Using the Browser & Details Tracks HapMart Search HaploView Software Summary Exercises HapMap:
Copyright OpenHelix. No use or reproduction without express written consent47 HaploView Software Download Help & download
Copyright OpenHelix. No use or reproduction without express written consent48 HaploView Help & Download Download link
Copyright OpenHelix. No use or reproduction without express written consent49 HaploView Download Data Configure Download genotype data
Copyright OpenHelix. No use or reproduction without express written consent50 HaploView Data Download Click “Go” Choose population Open directly in Haploview or save to disk Choose strand
Copyright OpenHelix. No use or reproduction without express written consent51 Click Choose Format HaploView Data Views Upload file Set parameters Click dumped_region
Copyright OpenHelix. No use or reproduction without express written consent52 Viewing HaploView Uploaded Data Four types of analysis: LD, haplotypes, markers, tag SNPs
Copyright OpenHelix. No use or reproduction without express written consent53 Agenda for HapMap Introduction and credits Browser Overview Using the Browser & Details Tracks HapMart Search HaploView Software Summary Exercises HapMap:
Copyright OpenHelix. No use or reproduction without express written consent54 HapMap Project and Tools
Copyright OpenHelix. No use or reproduction without express written consent55 Other Repositories GVS: SeattleSNPs: Ensembl Genome Browser: UCSC Genome Browser: dbSNP
Copyright OpenHelix. No use or reproduction without express written consent56 Additional Data to View SNPedia: MutaGeneSys: Load and view these data sets on the HapMap GBrowser /12/gbrowse-snpedia.html
Copyright OpenHelix. No use or reproduction without express written consent57 Agenda for HapMap Introduction and credits Browser Overview Using the Browser & Details Tracks HapMart Search HaploView Software Summary Exercises HapMap:
Copyright OpenHelix. No use or reproduction without express written consent58