{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,25]],"date-time":"2025-10-25T18:55:28Z","timestamp":1761418528639},"reference-count":28,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2008,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>There has been considerable effort focused on developing efficient programs for tagging single-nucleotide polymorphisms (SNPs). Many of these programs do not account for potential reduced genomic coverage resulting from genotyping failures nor do they preferentially select SNPs based on functionality, which may be more likely to be biologically important.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We have developed a user-friendly and efficient software program, Snagger, as an extension to the existing open-source software, Haploview, which uses pairwise <jats:italic>r<\/jats:italic>\n              <jats:sup>2<\/jats:sup> linkage disequilibrium between single nucleotide polymorphisms (SNPs) to select tagSNPs. Snagger distinguishes itself from existing SNP selection algorithms, including Tagger, by providing user options that allow for: (1) prioritization of tagSNPs based on certain characteristics, including platform-specific design scores, functionality (i.e., coding status), and chromosomal position, (2) efficient selection of SNPs across multiple populations, (3) selection of tagSNPs outside defined genomic regions to improve coverage and genotyping success, and (4) picking of surrogate tagSNPs that serve as backups for tagSNPs whose failure would result in a significant loss of data. Using HapMap genotype data from ten ENCODE regions and design scores for the Illumina platform, we show similar coverage and design score distribution and fewer total tagSNPs selected by Snagger compared to the web server Tagger.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>Snagger improves upon current available tagSNP software packages by providing a means for researchers to select tagSNPs that reliably capture genetic variation across multiple populations while accounting for significant genotyping failure risk and prioritizing on SNP-specific characteristics.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-9-174","type":"journal-article","created":{"date-parts":[[2008,3,27]],"date-time":"2008-03-27T19:14:23Z","timestamp":1206645263000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":36,"title":["Snagger: A user-friendly program for incorporating additional information for tagSNP selection"],"prefix":"10.1186","volume":"9","author":[{"given":"Christopher K","family":"Edlund","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Won H","family":"Lee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dalin","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David J","family":"Van Den Berg","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David V","family":"Conti","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,3,27]]},"reference":[{"key":"2159_CR1","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1186\/1471-2105-6-60","volume":"6","author":"L Wang","year":"2005","unstructured":"Wang L, Liu S, Niu T, Xu X: SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management. BMC Bioinformatics. 2005, 6: 60-","journal-title":"BMC Bioinformatics"},{"key":"2159_CR2","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1186\/1471-2105-6-38","volume":"6","author":"K Ding","year":"2005","unstructured":"Ding K, Zhang J, Zhou K, Shen Y, Zhang X: htSNPer1.0: software for haplotype block partition and htSNPs selection. BMC Bioinformatics. 2005, 6: 38-","journal-title":"BMC Bioinformatics"},{"issue":"20","key":"2159_CR3","doi-asserted-by":"publisher","first-page":"2679","DOI":"10.1093\/hmg\/ddg294","volume":"12","author":"CA Haiman","year":"2003","unstructured":"Haiman CA, Stram DO, Pike MC, Kolonel LN, Burtt NP, Altshuler D, Hirschhorn J, Henderson BE: A comprehensive haplotype analysis of CYP19 and breast cancer risk: the Multiethnic Cohort. Hum Mol Genet. 2003, 12 (20): 2679-2692.","journal-title":"Hum Mol Genet"},{"issue":"6822","key":"2159_CR4","doi-asserted-by":"publisher","first-page":"860","DOI":"10.1038\/35057062","volume":"409","author":"International Human Genome Sequencing Consortium","year":"2001","unstructured":"International Human Genome Sequencing Consortium: Initial sequencing and analysis of the human genome. Nature. 2001, 409 (6822): 860-921.","journal-title":"Nature"},{"issue":"7063","key":"2159_CR5","doi-asserted-by":"publisher","first-page":"1299","DOI":"10.1038\/nature04226","volume":"437","author":"International HapMap Consortium","year":"2005","unstructured":"International HapMap Consortium: A Haplotype Map of the Human Genome. Nature. 2005, 437 (7063): 1299-1320.","journal-title":"Nature"},{"issue":"11","key":"2159_CR6","doi-asserted-by":"publisher","first-page":"1298","DOI":"10.1038\/ng1899","volume":"38","author":"PI de Bakker","year":"2006","unstructured":"de Bakker PI, Burtt NP, Graham RR, Guiducci C, Yelensky R, Drake JA, Bersaglieri T, Penney KL, Butler J, Young S, Onofrio RC, Lyon HN, Stram DO, Haiman CA, Freedman ML, Zhu X, Cooper R, Groop L, Kolonel LN, Henderson BE, Daly MJ, Hirschhorn JN, Altshuler D: Transferability of tag SNPs in genetic association studies in multiple populations. Nat Genet. 2006, 38 (11): 1298-1303.","journal-title":"Nat Genet"},{"issue":"2","key":"2159_CR7","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1186\/1479-7364-2-2-144","volume":"2","author":"DO Stram","year":"2005","unstructured":"Stram DO: Software for tag single nucleotide polymorphism selection. Human Genomics. 2005, 2 (2): 144-151.","journal-title":"Human Genomics"},{"issue":"3","key":"2159_CR8","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1016\/S0168-9525(03)00022-2","volume":"19","author":"LR Cardon","year":"2003","unstructured":"Cardon LR, Abecasis GR: Using haplotype blocks to map human complex trait loci. TRENDS in Genetics. 2003, 19 (3): 135-140.","journal-title":"TRENDS in Genetics"},{"issue":"2","key":"2159_CR9","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1038\/ng1001-233","volume":"29","author":"GCL Johnson","year":"2001","unstructured":"Johnson GCL, Esposito L, Barratt BJ, Smith AN, Heward J, Di Genova G, Ueda H, Cordell HJ, Eaves IA, Dudbridge F, Twells RCJ, Payne F, Hughes W, Nutland S, Stevens H, Carr P, Tuomilehto-Wolf E, Tuomilehto J, Gough SCL, Clayton DG, Todd JA: Haplotype tagging for the identification of common disease genes. Nature Genetics. 2001, 29 (2): 233-237.","journal-title":"Nature Genetics"},{"issue":"1","key":"2159_CR10","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1086\/381000","volume":"74","author":"CS Carlson","year":"2004","unstructured":"Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA: Selecting a Maximally Informative Set of Single-Nucleotide Polymorphisms for Association Analyses Using Linkage Disequilibrium. American Journal of Human Genetics. 2004, 74 (1): 106-120.","journal-title":"American Journal of Human Genetics"},{"issue":"11","key":"2159_CR11","doi-asserted-by":"publisher","first-page":"1217","DOI":"10.1038\/ng1669","volume":"37","author":"PI de Bakker","year":"2005","unstructured":"de Bakker PI, Yelensky R, Pe'er I, Gabriel SB, Daly MJ, Altshuler D: Efficiency and power in genetic association studies. Nature Genetics. 2005, 37 (11): 1217-1223.","journal-title":"Nature Genetics"},{"issue":"2","key":"2159_CR12","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1093\/bioinformatics\/bth457","volume":"21","author":"JC Barrett","year":"2005","unstructured":"Barrett JC, Fry B, Maller J, Daly MJ: Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2005, 21 (2): 263-265.","journal-title":"Bioinformatics"},{"issue":"3-4","key":"2159_CR13","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1159\/000083546","volume":"58","author":"BV Halldorsson","year":"2004","unstructured":"Halldorsson BV, Istrail S, De La Vega FM: Optimal Selection of SNP Markers for Disease Association Studies. Human Heredity. 2004, 58 (3-4): 190-202.","journal-title":"Human Heredity"},{"issue":"2","key":"2159_CR14","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1093\/bioinformatics\/bti762","volume":"22","author":"ZS Qin","year":"2006","unstructured":"Qin ZS, Gopalakrishnan S, Abecasis GR: An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria. Bioinformatics. 2006, 22 (2): 220-225.","journal-title":"Bioinformatics"},{"issue":"1","key":"2159_CR15","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1093\/bioinformatics\/bth482","volume":"21","author":"K Zhang","year":"2005","unstructured":"Zhang K, Qin ZS, Chen T, Liu JS, Waterman MS, Sun F: HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. Bioinformatics. 2005, 21 (1): 131-134.","journal-title":"Bioinformatics"},{"issue":"1","key":"2159_CR16","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1086\/321275","volume":"69","author":"J Pritchard","year":"2001","unstructured":"Pritchard J, Przeworski M: Linkage Disequilibrium in Humans: Models and Data. American Journal of Human Genetics. 2001, 69 (1): 1-14.","journal-title":"American Journal of Human Genetics"},{"issue":"1","key":"2159_CR17","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1007\/s00439-006-0182-5","volume":"120","author":"BN Howie","year":"2006","unstructured":"Howie BN, Carlson CS, Rieder MJ, Nickerson DA: Efficient selection of tagging single-nucleotide polymorphisms in multiple populations. Hum Genet. 2006, 120 (1): 58-68.","journal-title":"Hum Genet"},{"key":"2159_CR18","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1142\/9781860948732_0011","volume":"6","author":"L Liu","year":"2007","unstructured":"Liu L, Wu Y, Lonardi S, Jiang T: Efficient Algorithms for Genome-Wide tagSNP Selection Across Populations via the Linkage Disequilibrium Criterion. Comput Syst Bioinformatics Conf. 2007, 6: 67-78.","journal-title":"Comput Syst Bioinformatics Conf"},{"key":"2159_CR19","volume-title":"Bioinformatics","author":"Z Xu","year":"2007","unstructured":"Xu Z, Kaplan NL, Taylor JA: TAGster: Efficient Selection of LD tag SNPs in Single or Multiple Populations. Bioinformatics. 2007"},{"key":"2159_CR20","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1186\/1471-2105-6-263","volume":"6","author":"YT Huang","year":"2005","unstructured":"Huang YT, Zhang K, Chen T, Chao KM: Selecting additional tag SNPs for tolerating missing data in genotyping. BMC Bioinformatics. 2005, 6: 263-","journal-title":"BMC Bioinformatics"},{"issue":"7164","key":"2159_CR21","doi-asserted-by":"publisher","first-page":"851","DOI":"10.1038\/nature06258","volume":"449","author":"KA Frazer","year":"2007","unstructured":"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, Sallee 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'Archeveque 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, Stewart J: A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007, 449 (7164): 851-861.","journal-title":"Nature"},{"key":"2159_CR22","unstructured":"Mapping 500K HapMap Genotype Data Set. [http:\/\/www.affymetrix.com\/support\/technical\/sample_data\/500k_hapmap_genotype_data.affx]"},{"issue":"3","key":"2159_CR23","doi-asserted-by":"publisher","first-page":"436","DOI":"10.1101\/gr.212802","volume":"12","author":"PC Ng","year":"2002","unstructured":"Ng PC, Henikoff S: Accounting for human polymorphisms predicted to affect protein function. Genome Res. 2002, 12 (3): 436-446.","journal-title":"Genome Res"},{"issue":"6788","key":"2159_CR24","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1038\/35015718","volume":"405","author":"NJ Risch","year":"2000","unstructured":"Risch NJ: Searching for genetic determinants in the new millennium. Nature. 2000, 405 (6788): 847-856.","journal-title":"Nature"},{"key":"2159_CR25","unstructured":"Java. [http:\/\/www.java.com]"},{"key":"2159_CR26","unstructured":"WinZip. [http:\/\/www.winzip.com]"},{"key":"2159_CR27","unstructured":"GNU zip. [http:\/\/www.gzip.org]"},{"key":"2159_CR28","unstructured":"GNU Tar. [http:\/\/www.gnu.org\/software\/tar]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-174.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T03:20:22Z","timestamp":1630466422000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-174"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,3,27]]},"references-count":28,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["2159"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-174","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,3,27]]},"assertion":[{"value":"27 November 2007","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 March 2008","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 March 2008","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"174"}}