hapmap如何寻找SNP位点.ppt

1、Using HapMap.Org,A Tutorial Lincoln Stein, Cold Spring Harbor Laboratory,Goal of This Tutorial,This tutorial will show you how to: Find HapMap SNPs near a gene or region of interest (ROI). View patterns of LD in the ROI. Select tag SNPs in the ROI. Download information on the SNPs in ROI for use in

2、Haploview. Generate customized extracts of the entire data set. Download the entire data set in bulk.,Finding HapMap SNPs in a Region of Interest,Find the region of the genome containing the DTNBP1 gene. Identify the characterized SNPs in the region. View the patterns of LD in the region. Pick tag S

3、NPs. Download the region in Haploview format.,1: Surf to the HapMap Browser,1a. Go to ,1b. Select “Browse Project Data”,2: Search for DTNBP1,2. Type search term “DTNBP1”,Use data source menu to select a different data release. Current release is the default.,Search for a gene name, a c

4、hromosome band, or a phrase like “insulin receptor”,3: Examine Region,Chromosome-wide summary data is shown in overview,Default tracks show HapMap genotyped SNPs, named genes from Entrez, and alternative mRNA splicing patterns,3: Examine Region (cont),Use the Scroll/Zoom buttons and menu to change p

5、osition & magnification,As you zoom in, the display changes to indicate more detail.,4: Turn on LD & Haplotype Tracks,These sections allow you to adjust the display and to superimpose your own data on the HapMap.,4a. Scroll to “Tracks” section and turn on the LD Plot and Haplotype Display tracks,4b.

6、 Press “Update Image”,5: View variation patterns,Triangle plot shows LD values using r2 or D in one or more HapMap population,Phased haplotype track shows all 180 chromosomes with alleles colored yellow and blue.,6: Adjust Track Settings,6a. Select the analysis track to adjust,6b. Press “Configure”,

7、6: Adjust Track Settings (cont),6c. Adjust populations and display settings.,6d. Press “Configure”,7: Turn on Tag SNP Track,7a. Activate the “tag SNP Picker” and press “Update Image”,8: Adjust Tagger,8a. Select “Annotate tag SNP Picker” and press “Configure”,The tag SNPs are selected on the fly as y

8、ou navigate around the genome.,8: Adjust Tagger (cont),Select population,Select tagging algorithm and parameters.,optional upload list of SNPs to be included, excluded, or design scores.,8b. Press “Configure” to save changes.,9: Generate Reports,9. Select the desired “Download” option and press “Go”

9、 or “Configure”,Available Downloads: Pairwise LD values Allele & Genotype frequencies Raw genotypes Tag SNPs,9: Generate Reports (cont),The Genotype download format can be saved to disk and loaded into Haploview.,9: Generate Reports (cont),The tag SNP download is the same as you get from TAGGER,Gene

10、rating Extracts of the HapMap Dataset,Find all HapMap characterized SNPs that: 1. Have a MAF 0.20. 2. Cause a nonsynonymous amino acid change.,1. Surf to ,1. From , click on “HapMart”,2. Select the population of interest,2a. Choose the population or “All Populations”,

11、2b. Press “Next”,3. Select the desired filters,3a. Check “Allele Frequency Filter” and select MAF = 0.2,2b. Select “SNPs found in Exons synonymous coding SNPs”,2c. Press “Next”,4. Select output fields,4a. Choose among several pages of fields.,4b. Select the fields to include in the report.,2c. Press

12、 “Export”,The summary shows active filters and # SNPs to be output.,Options at the bottom let you select text or Excel format.,5. Download report,Download the Complete Data,Download the entire HapMap data set to your own computer,Surf to ,1. From , click on “Bulk Data Dow

13、nlooad”,2. Choose the Data Type,Raw genotypes,Analytic results,Allele & genotype frequencies,Assays,Your own copy of the HapMap Browser,2. Select “Genotypes”,3. Choose the Desired Release,3. Select “latest”,4. Choose the Dataset,QC Filtered with duplicate data removed.,QC filtered, duplicate data not removed.,Not filtered, reudundant data not removed.,4. Select “non-redundant”,5. Downloa