{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,2]],"date-time":"2025-11-02T15:45:30Z","timestamp":1762098330630},"reference-count":21,"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":[[2009,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>During this recent decade, microarray-based single nucleotide polymorphism (SNP) data are becoming more widely used as markers for linkage analysis in the identification of loci for disease-associated genes. Although microarray-based SNP analyses have markedly reduced genotyping time and cost compared with microsatellite-based analyses, applying these enormous data to linkage analysis programs is a time-consuming step, thus, necessitating a high-throughput platform.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We have developed SNP HiTLink (<jats:underline>SNP<\/jats:underline>\n              <jats:underline>Hi<\/jats:underline> gh <jats:underline>T<\/jats:underline> hroughput <jats:underline>Link<\/jats:underline> age analysis system). In this system, SNP chip data of the Affymetrix Mapping 100 k\/500 k array set and Genome-Wide Human SNP array 5.0\/6.0 can be directly imported and passed to parametric or model-free linkage analysis programs; MLINK, Superlink, Merlin and Allegro. Various marker-selecting functions are implemented to avoid the effect of typing-error data, markers in linkage equilibrium or to select informative data.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>The results using the 100 k SNP dataset were comparable or even superior to those obtained from analyses using microsatellite markers in terms of LOD scores obtained. General personal computers are sufficient to execute the process, as runtime for whole-genome analysis was less than a few hours. This system can be widely applied to linkage analysis using microarray-based SNP data and with which one can expect high-throughput and reliable linkage analysis.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-10-121","type":"journal-article","created":{"date-parts":[[2009,4,24]],"date-time":"2009-04-24T18:28:04Z","timestamp":1240597684000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data"],"prefix":"10.1186","volume":"10","author":[{"given":"Yoko","family":"Fukuda","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yasuo","family":"Nakahara","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hidetoshi","family":"Date","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuji","family":"Takahashi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun","family":"Goto","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Akinori","family":"Miyashita","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ryozo","family":"Kuwano","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hiroki","family":"Adachi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eiji","family":"Nakamura","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shoji","family":"Tsuji","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2009,4,24]]},"reference":[{"issue":"4","key":"2851_CR1","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1086\/424696","volume":"75","author":"DM Evans","year":"2004","unstructured":"Evans DM, Cardon LR: Guidelines for genotyping in genomewide linkage studies: single-nucleotide-polymorphism maps versus microsatellite maps. Am J Hum Genet 2004, 75(4):687\u2013692. 10.1086\/424696","journal-title":"Am J Hum Genet"},{"issue":"2","key":"2851_CR2","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1086\/377137","volume":"73","author":"TC Matise","year":"2003","unstructured":"Matise TC, Sachidanandam R, Clark AG, Kruglyak L, Wijsman E, Kakol J, Buyske S, Chui B, Cohen P, de Toma C, et al.: A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set. Am J Hum Genet 2003, 73(2):271\u2013284. 10.1086\/377137","journal-title":"Am J Hum Genet"},{"issue":"1","key":"2851_CR3","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1086\/422195","volume":"75","author":"S John","year":"2004","unstructured":"John S, Shephard N, Liu G, Zeggini E, Cao M, Chen W, Vasavda N, Mills T, Barton A, Hinks A, et al.: Whole-genome scan, in a complex disease, using 11,245 single-nucleotide polymorphisms: comparison with microsatellites. Am J Hum Genet 2004, 75(1):54\u201364. 10.1086\/422195","journal-title":"Am J Hum Genet"},{"issue":"1","key":"2851_CR4","first-page":"252","volume":"53","author":"RW Cottingham Jr","year":"1993","unstructured":"Cottingham RW Jr, Idury RM, Schaffer AA: Faster sequential genetic linkage computations. Am J Hum Genet 1993, 53(1):252\u2013263.","journal-title":"Am J Hum Genet"},{"issue":"11","key":"2851_CR5","doi-asserted-by":"publisher","first-page":"3443","DOI":"10.1073\/pnas.81.11.3443","volume":"81","author":"GM Lathrop","year":"1984","unstructured":"Lathrop GM, Lalouel JM, Julier C, Ott J: Strategies for multilocus linkage analysis in humans. Proc Natl Acad Sci USA 1984, 81(11):3443\u20133446. 10.1073\/pnas.81.11.3443","journal-title":"Proc Natl Acad Sci USA"},{"issue":"4","key":"2851_CR6","doi-asserted-by":"publisher","first-page":"346","DOI":"10.1375\/twin.8.4.346","volume":"8","author":"GW Montgomery","year":"2005","unstructured":"Montgomery GW, Campbell MJ, Dickson P, Herbert S, Siemering K, Ewen-White KR, Visscher PM, Martin NG: Estimation of the rate of SNP genotyping errors from DNA extracted from different tissues. Twin Res Hum Genet 2005, 8(4):346\u2013352. 10.1375\/twin.8.4.346","journal-title":"Twin Res Hum Genet"},{"issue":"Suppl 9","key":"2851_CR7","doi-asserted-by":"publisher","first-page":"S17","DOI":"10.1186\/1471-2105-9-S9-S17","volume":"9","author":"H Hong","year":"2008","unstructured":"Hong H, Su Z, Ge W, Shi L, Perkins R, Fang H, Xu J, Chen JJ, Han T, Kaput J, et al.: Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples. BMC Bioinformatics 2008, 9(Suppl 9):S17. 10.1186\/1471-2105-9-S9-S17","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"2851_CR8","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1016\/j.ygeno.2007.05.011","volume":"90","author":"IW Saunders","year":"2007","unstructured":"Saunders IW, Brohede J, Hannan GN: Estimating genotyping error rates from Mendelian errors in SNP array genotypes and their impact on inference. Genomics 2007, 90(3):291\u2013296. 10.1016\/j.ygeno.2007.05.011","journal-title":"Genomics"},{"issue":"2","key":"2851_CR9","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1159\/000022846","volume":"49","author":"D Gordon","year":"1999","unstructured":"Gordon D, Heath SC, Ott J: True pedigree errors more frequent than apparent errors for single nucleotide polymorphisms. Hum Hered 1999, 49(2):65\u201370. 10.1159\/000022846","journal-title":"Hum Hered"},{"issue":"6","key":"2851_CR10","doi-asserted-by":"publisher","first-page":"1106","DOI":"10.1086\/426000","volume":"75","author":"Q Huang","year":"2004","unstructured":"Huang Q, Shete S, Amos CI: Ignoring linkage disequilibrium among tightly linked markers induces false-positive evidence of linkage for affected sib pair analysis. Am J Hum Genet 2004, 75(6):1106\u20131112. 10.1086\/426000","journal-title":"Am J Hum Genet"},{"issue":"4","key":"2851_CR11","doi-asserted-by":"publisher","first-page":"992","DOI":"10.1086\/342666","volume":"71","author":"DJ Schaid","year":"2002","unstructured":"Schaid DJ, McDonnell SK, Wang L, Cunningham JM, Thibodeau SN: Caution on pedigree haplotype inference with software that assumes linkage equilibrium. Am J Hum Genet 2002, 71(4):992\u2013995. 10.1086\/342666","journal-title":"Am J Hum Genet"},{"issue":"Suppl 1","key":"2851_CR12","doi-asserted-by":"publisher","first-page":"S189","DOI":"10.1093\/bioinformatics\/18.suppl_1.S189","volume":"18","author":"M Fishelson","year":"2002","unstructured":"Fishelson M, Geiger D: Exact genetic linkage computations for general pedigrees. Bioinformatics 2002, 18(Suppl 1):S189\u2013198.","journal-title":"Bioinformatics"},{"issue":"1","key":"2851_CR13","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1038\/ng786","volume":"30","author":"GR Abecasis","year":"2002","unstructured":"Abecasis GR, Cherny SS, Cookson WO, Cardon LR: Merlin \u2013 rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 2002, 30(1):97\u2013101. 10.1038\/ng786","journal-title":"Nat Genet"},{"issue":"1","key":"2851_CR14","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1038\/75514","volume":"25","author":"DF Gudbjartsson","year":"2000","unstructured":"Gudbjartsson DF, Jonasson K, Frigge ML, Kong A: Allegro, a new computer program for multipoint linkage analysis. Nat Genet 2000, 25(1):12\u201313. 10.1038\/75514","journal-title":"Nat Genet"},{"issue":"10","key":"2851_CR15","doi-asserted-by":"publisher","first-page":"1015","DOI":"10.1038\/ng1005-1015","volume":"37","author":"DF Gudbjartsson","year":"2005","unstructured":"Gudbjartsson DF, Thorvaldsson T, Kong A, Gunnarsson G, Ingolfsdottir A: Allegro version 2. Nat Genet 2005, 37(10):1015\u20131016. 10.1038\/ng1005-1015","journal-title":"Nat Genet"},{"key":"2851_CR16","volume-title":"BRLMM: an Improved Genotype Calling Method for the GeneChip\u00ae Human Mapping 500 K Array Set","author":"Affymetrix I","year":"2006","unstructured":"Affymetrix I: BRLMM: an Improved Genotype Calling Method for the GeneChip\u00aeHuman Mapping 500 K Array Set.2006. [http:\/\/www.affymetrix.com\/support\/technical\/whitepapers\/brlmm_whitepaper.pdf]"},{"issue":"6968","key":"2851_CR17","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1038\/nature02168","volume":"426","author":"The International HapMap Consortium","year":"2003","unstructured":"The International HapMap Consortium: The International HapMap Project. Nature 2003, 426(6968):789\u2013796. 10.1038\/nature02168","journal-title":"Nature"},{"issue":"17","key":"2851_CR18","doi-asserted-by":"publisher","first-page":"3565","DOI":"10.1093\/bioinformatics\/bti571","volume":"21","author":"K Hoffmann","year":"2005","unstructured":"Hoffmann K, Lindner TH: easyLINKAGE-Plus \u2013 automated linkage analyses using large-scale SNP data. Bioinformatics 2005, 21(17):3565\u20133567. 10.1093\/bioinformatics\/bti571","journal-title":"Bioinformatics"},{"issue":"4","key":"2851_CR19","first-page":"A254","volume":"65","author":"T Hiekkalinna","year":"1999","unstructured":"Hiekkalinna T, Peltonen L: New program: AUTOSCAN 1.0 automated use of linkage analysis programs. American Journal of Human Genetics 1999, 65(4):A254-A254.","journal-title":"American Journal of Human Genetics"},{"issue":"13","key":"2851_CR20","doi-asserted-by":"publisher","first-page":"3060","DOI":"10.1093\/bioinformatics\/bti449","volume":"21","author":"EL Webb","year":"2005","unstructured":"Webb EL, Sellick GS, Houlston RS: SNPLINK: multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal. Bioinformatics 2005, 21(13):3060\u20133061. 10.1093\/bioinformatics\/bti449","journal-title":"Bioinformatics"},{"key":"2851_CR21","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1186\/1471-2105-7-227","volume":"7","author":"TR Gaunt","year":"2006","unstructured":"Gaunt TR, Rodriguez S, Zapata C, Day IN: MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers. BMC Bioinformatics 2006, 7: 227. 10.1186\/1471-2105-7-227","journal-title":"BMC Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-121.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,31]],"date-time":"2021-08-31T21:36:03Z","timestamp":1630445763000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-121"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,4,24]]},"references-count":21,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["2851"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-121","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,4,24]]},"assertion":[{"value":"24 December 2008","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 April 2009","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 April 2009","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"121"}}