VEGAS2: Gene-based test software using 1000 Genomes reference sets. User Manual

Transcription

1 VEGAS2: Gene-based test software using 1000 Genomes reference sets. User Manual Version: 16:09:002 Date: 16 th September 2014 By Aniket Mishra, Stuart Macgregor Statistical Genetics Group QIMR Berghofer Medical Research Institute Brisbane, Australia

2 1. Introduction 2. Web-Interface 3. Offline Interface a. Installation b. Input files c. Options d. Example 4. References Content

3 Introduction VEGAS2 is an upgrade of gene-based association testing package VEGAS[1]. It performs gene based test using simulation approach. It consider all SNPs with maf>0.01 provided by 1000 genome project [2]. SNPs are assigned to genes of which co-ordinates are based on hg19 assembly (For full description of how genelist file been made refer the Methods section of VEGAS2 paper). The webbased version and offline version are provided. Both these versions are easy to use and only require two column input text file with 1 st column of SNP ids and other with p-values. One significant application of VEGAS2 is to perform gene-based test on X-chromosome GWAS summary data by accounting for linkage disequilibrium between SNPs. Allele frequency may vary in between male and female samples. In VEGAS2 we provide sex option, which allows user to specify either Males or Females from 1000G populations to consider while calculating ld matrix. Stratifying on sexes may lead to loss of power. The variation in allele frequency could be because of sampling error. By default, VEGAS2 assumes no allele frequency difference between males and females and perform analysis using all individuals irrespective of sex (Example A). To give flexibility to incorporate regulatory SNPs in gene testing five different gene-definitions are provided (see in options). The statistics of number of SNPs assigned through different gene definitions for 1000 Genomes phase 1 populations are provided in table 1. Gene Definition 0kbloc 10kbloc 20kbloc 50kbloc 0kbldbin Population 1000GEURO GASN GAFR GAMR *These are number of unique SNPs assigned to one or more hg19 genes. These SNPs are filtered with maf>0.01 and hwe p-value> Web-Based Interface Web-based version of VEGAS2 can be accessed through Offline interface VEGAS2 offline version is developed in perl scripting language for unix/linux based operating system. It can downloaded from Installation Download the Unzip and untar it using following command tar zxvf zvegas2offline.tgz cd VEGAS2offline

4 In this directory, you will find two executable files 1. VEGAS2.pl 2. VEGAS2.config And two directories a. VEGAS2database b. VEGAS2scripts You can move the two directories wherever you would like to and then provide path of these directories as arguments while running VEGAS2.config as follows $ sh vegas2.config /path/of/vegas2database /path/of/vegas2scripts For example $ sh vegas2.config /scratch/aniketm/vegas2database /home/aniketm/bin/vegas2scripts It will edit required paths in vegas2.pl present in working directory. Now you can move VEGAS2 executable file wherever you would like and delete VEGAS2 folder and VEGAS2.config file etc. Input files a. SNP id and p-values: It is as a two-column whitespace separated text file. The first column lists 1000G SNP ids and other column lists respective GWAS p-values. This file should be without header and should not have NAs. e.g. rs rs rs rs rs rs rs rs rs rs b. Genelist file: It is the one column text file with list of gene symbol. e.g. PIK3R1 SEMA3E PTCHD1-AS

5 Options -pop -subpop -genesize To specify which 1000G phase1 population to use out of 1000GEURO (european), 1000GASN (asian), 1000GAMR (american) and 1000GAFR (african). Options to use 1000 Genomes phase 3 populations data are 1000GEUROPhase3 (european), 1000GASNPhase3 (asian), 1000GAMRPhase3 (american) and 1000GAFRPhase3 (african) Provide the sub reference population out of EURO (default) or CEU, GBR, IBS, FIN, TSI for 1000GEURO reference population or ASN, CHB, CHS, JPT for 1000GASN reference population or AFR, ASW, LWK, YRI for 1000GAFR reference population or AMR, CLM, MXL, PUR To specify which gene definition to use. There are five options available viz. 0kbloc (default), 10kbloc, 20kbloc, 50kbloc and 0kbldbin -chr To run vegas2 on specific chromosome. It could be in between 1 to 23. -genelist -top -bestsnp -sex -max -adjust -out To run vegas2 on specific list of genes. It tell vegas2 to perform top percentage test where it consider specified percentage of top SNPs It tell vegas2 to perform best SNP test. This option is provided for X-chromosome analysis. It tells vegas2 to consider either male (Default) of female 1000G individuals to make ld matrix for simulations. It tells VEGAS2 the maximum number of simulation to perform. It must be above 1e6. To get genomic inflation corrected p-values. It will create one more file <outfile>.corrected It tells VEGAS2 the output file name. Note: Do not provide chr and genelist option together. Similarly top and bestsnp will not work together. Example VEGAS2offline directory contains two example (test) files as follows: 1. test_vegas2input.txt two-column vegas2 input file. 2. genelist.txt genelist input file for genelist parameter in vegas2. (A) Default usage: $/path/of/vegas2 <SNPPvaluefile> -pop 1000GEURO subpop EURO genesize 0kbloc top 100 sex BothMnF max out genebased.v2out

6 ./vegas2 test_vegas2input.txt -pop 1000GEURO -subpop EURO -genesize 0kbloc -top 100 sex BothMnF max out genebased.v2out Chr Gene nsnps nsims Start Stop Test Pvalue TopSNP TopSNP-pvalue 15 "FSIP1" "rs " "NF1" "rs " "RAB11FIP4" "rs " "NF2" "rs " "ZMAT5" "rs105311" "DMD" "rs " "PTCHD1-AS" "rs " "LOC " "rs " "LOC " "rs " (B) Use of bestsnp option on chromosome 22, on Finish (FIN) population with 10 kb upstream/downstream gene definition: $ perl /path/of/vegas2.pl <SNPPvaluefile> -pop 1000GEURO -subpop FIN -genesize 10kbloc -chr 22 -bestsnp./vegas2 test_vegas2input.txt -pop 1000GEURO -subpop FIN -genesize 10kbloc -chr 22 -bestsnp Chr Gene nsnps nsims Start Stop Test Pvalue TopSNP TopSNP-pvalue 22 "CABP7" "rs105311" "NF2" "rs " "ZMAT5" "rs105311" (C) Use of top test to consider top 5% of SNPs on genelist, on TSI European population with 0kbldbin gene definition: $ perl /path/of/vegas2.pl <SNPPvaluefile> genelist <Genelist file> -pop 1000GEURO subpop TSI genesize 0kbldbin top 5./vegas2 test_vegas2input.txt -genelist genelist.txt -pop 1000GEURO -subpop TSI -genesize 0kbldbin -top 5

7 Chr Gene nsnps nsims Start Stop Test Pvalue TopSNP TopSNP-pvalue 23 "PTCHD1-AS" "rs " "PIK3R1" "rs " "SEMA3E" "rs " (D) Use of top test to consider 20% of top SNPs on chromosome 23 (X-chromosome), All European population with 20kbloc gene definition on Males: $ perl /path/of/vegas2.pl <SNPPvaluefile> top 20 genesize 20kbloc chr 23 sex Males./vegas2 test_vegas2input.txt -top 20 -genesize 20kbloc -chr 23 -sex Males Chr Gene nsnps nsims Start Stop Test Pvalue TopSNP TopSNP-pvalue 23 "DMD" "rs " "PTCHD1-AS" "rs " (E) Use of best test on chromosome 23 (X-chromosome), European CEU population with 50kbloc gene definition on Females: $ perl /path/of/vegas2.pl <SNPPvaluefile> -bestsnp -pop 1000GEURO -subpop CEU -genesize 50kbloc -chr 23 -sex Females./vegas2 test_vegas2input.txt -bestsnp -pop 1000GEURO -subpop CEU -genesize 50kbloc -chr 23 -sex Females Chr Gene nsnps nsims Start Stop Test Pvalue TopSNP TopSNP-pvalue 23 "BGN" "rs " "DMD" "rs " "HAUS7" "rs " "PTCHD1-AS" "rs " "ZFP92" "rs "

8 References 1. Liu JZ, McRae AF, Nyholt DR, Medland SE, Wray NR, Brown KM, Investigators A, Hayward NK, Montgomery GW, Visscher PM, et al: A versatile gene-based test for genome-wide association studies. Am J Hum Genet 2010, 87: Genomes Project C, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA: An integrated map of genetic variation from 1,092 human genomes. Nature 2012, 491:56-65.