GLIDERS

Genome-wide LInkage DisEquilibrium Repository and Search Engine

GLIDERS (Genome-wide LInkage DisEquilibrium Repository and Search engine) is a simple web-based tool constructed to enable researchers to check if SNPs have long-range LD (i.e. <200kb) with other SNPs genotyped in HapMap phase 2 and 3 (The International HapMap Consortium 2007). Associations between any pair-wise HapMap SNPs over any distance can be retrieved.

[Genome Research Limited]

Overview

The LD statistics stored in GLIDERS were obtained by calculating r2 and D' between every possible HapMap phase 2 and 3 SNP pairing (as long as both SNPs had MAF≥ 5% and they passed quality control). Quality control thresholds included genotyping success rate greater than 95%; greater than zero and less than 75% heterozygosity; and HWE p<5.7x10-7 (for build 35), or p<0.0001 (for build 36: central HapMap QC). Unphased HapMap SNPs positioned on builds 35 (HapMap phase 2 release 21) and 36 (HapMap phase 2 release 23 and phase 3 draft 2) were used to calculate genome-wide LD.

It is possible to specify filters for the information returned by GLIDERS. These include: distance (lower and upper limits), r2, MAF and population sample (CEU, YRI, JPT+CHB). There is a choice of builds 35 (phase 2 only) or 36 (phase 2 and 3) for HapMap SNP locations on the human genome.

The SNP search returns all those associations occurring between the listed SNP(s) and HapMap SNPs that pass the search criteria set by the user. These are returned in the form of a web-page table with links to downloadable files containing the same information as the table. In addition to D' and r2 values, GLIDERS also returns a chi-squared statistic for the SNP associations along with the respective raw and Bonferroni corrected (BFC) p-values. The Bonferroni correction is based on the total number of inter-SNP comparisons carried out genome-wide. The p-values are specific to this chi-squared statistic and not to r2 or D'.

If any of the array check boxes (located below the selection criteria drop-down menus) are selected, the returned information will include membership of the SNPs on the arrays selected. To select all arrays simply click the "All listed arrays" check box.

Search

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Instructions

Inputting SNPs

Inputting SNPs

Inputting SNPs

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It is possible to either enter a single SNP (use only rs IDs, the "rs" prefix must be used, otherwise the SNP ID will not be recognized) or paste in a list of SNP rs IDs (as long as there are spaces between the SNP names they do not have to be entered on separate lines). When pasting SNP names it is OK to include other text or characters, as these will be ignored. A maximum of 20 SNP names can be entered in a single request.

Selecting parameters

Selecting parameters

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Selecting parameters

It is possible to search for associations that occur only over certain distances (using minimum and maximum limits), have r2 greater than a defined limit and/or occur only between SNPs with a minimal MAF. It is also possible to only retrieve those associations occurring in particular HapMap population samples. Click on the "Selecting search parameters" header for a descriptive example.

Output

Results from Genome-Wide LD search

Results from Genome-Wide LD search

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Example of output results table including download options

Example of output results table including download options

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The output can be viewed on the resulting web page or can be viewed and downloaded as a text file. Click on the "Output" header for a description of the output page. The output can get very large if many SNPs are entered on the input page. We would recommend using less than 1,000 SNPs especially if using a low (<0.5) r2 threshold. The output text file is named after the first or only SNP entered in GLIDERS.

Example results for Genome-Wide LD search

Example results for Genome-Wide LD search

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Any SNPs in the submission list that were not included in the genome-wide LD analysis are listed in the output along with the reason why they were excluded. For example, some SNPs fail QC, are not in HapMap (or that particular sample/build of HapMap) or do not have any associations within the criteria set. Some examples can be viewed by clicking on the "Output" header. The abbreviations used for listing QC failure are: "gen:" which lists the genotype success rate; "het:" lists information on SNP heterozygosity in the respective HapMap sample set; "MAF" indicates minor allele frequency; and HWE: the Hardy-Weinberg chi-squared statistic. SNPs with no LD associations within the selected criteria may have associations at less strict thresholds. SNPs not listed in the HapMap sample may be present in other populations or in alternate builds.

Publications

  • GLIDERS--a web-based search engine for genome-wide linkage disequilibrium between HapMap SNPs.

    Lawrence R, Day-Williams AG, Mott R, Broxholme J, Cardon LR and Zeggini E

    BMC bioinformatics 2009;10;367

  • A second generation human haplotype map of over 3.1 million SNPs.

    International HapMap Consortium, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C, Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, Zhao H, Zhao H, Zhou J, Gabriel SB, Barry R, Blumenstiel B, Camargo A, Defelice M, Faggart M, Goyette M, Gupta S, Moore J, Nguyen H, Onofrio RC, Parkin M, Roy J, Stahl E, Winchester E, Ziaugra L, Altshuler D, Shen Y, Yao Z, Huang W, Chu X, He Y, Jin L, Liu Y, Shen Y, Sun W, Wang H, Wang Y, Wang Y, Xiong X, Xu L, Waye MM, Tsui SK, Xue H, Wong JT, Galver LM, Fan JB, Gunderson K, Murray SS, Oliphant AR, Chee MS, Montpetit A, Chagnon F, Ferretti V, Leboeuf M, Olivier JF, Phillips MS, Roumy S, Sallée C, Verner A, Hudson TJ, Kwok PY, Cai D, Koboldt DC, Miller RD, Pawlikowska L, Taillon-Miller P, Xiao M, Tsui LC, Mak W, Song YQ, Tam PK, Nakamura Y, Kawaguchi T, Kitamoto T, Morizono T, Nagashima A, Ohnishi Y, Sekine A, Tanaka T, Tsunoda T, Deloukas P, Bird CP, Delgado M, Dermitzakis ET, Gwilliam R, Hunt S, Morrison J, Powell D, Stranger BE, Whittaker P, Bentley DR, Daly MJ, de Bakker PI, Barrett J, Chretien YR, Maller J, McCarroll S, Patterson N, Pe'er I, Price A, Purcell S, Richter DJ, Sabeti P, Saxena R, Schaffner SF, Sham PC, Varilly P, Altshuler D, Stein LD, Krishnan L, Smith AV, Tello-Ruiz MK, Thorisson GA, Chakravarti A, Chen PE, Cutler DJ, Kashuk CS, Lin S, Abecasis GR, Guan W, Li Y, Munro HM, Qin ZS, Thomas DJ, McVean G, Auton A, Bottolo L, Cardin N, Eyheramendy S, Freeman C, Marchini J, Myers S, Spencer C, Stephens M, Donnelly P, Cardon LR, Clarke G, Evans DM, Morris AP, Weir BS, Tsunoda T, Mullikin JC, Sherry ST, Feolo M, Skol A, Zhang H, Zeng C, Zhao H, Matsuda I, Fukushima Y, Macer DR, Suda E, Rotimi CN, Adebamowo CA, Ajayi I, Aniagwu T, Marshall PA, Nkwodimmah C, Royal CD, Leppert MF, Dixon M, Peiffer A, Qiu R, Kent A, Kato K, Niikawa N, Adewole IF, Knoppers BM, Foster MW, Clayton EW, Watkin J, Gibbs RA, Belmont JW, Muzny D, Nazareth L, Sodergren E, Weinstock GM, Wheeler DA, Yakub I, Gabriel SB, Onofrio RC, Richter DJ, Ziaugra L, Birren BW, Daly MJ, Altshuler D, Wilson RK, Fulton LL, Rogers J, Burton J, Carter NP, Clee CM, Griffiths M, Jones MC, McLay K, Plumb RW, Ross MT, Sims SK, Willey DL, Chen Z, Han H, Kang L, Godbout M, Wallenburg JC, L'Archevêque P, Bellemare G, Saeki K, Wang H, An D, Fu H, Li Q, Wang Z, Wang R, Holden AL, Brooks LD, McEwen JE, Guyer MS, Wang VO, Peterson JL, Shi M, Spiegel J, Sung LM, Zacharia LF, Collins FS, Kennedy K, Jamieson R and Stewart J

    Nature 2007;449;7164;851-61

Funding

  • University of Oxford
  • Wellcome Trust Sanger Institute
  • International HapMap Project

Contact

If you have any questions about GLIDERS please contact Robert Lawrence (Zeggini Group). (Feel free to mail me about any bugs/improvements!)

* quick link - http://q.sanger.ac.uk/g5jn0inj