{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,2]],"date-time":"2026-01-02T17:17:34Z","timestamp":1767374254615},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2846,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Gene expression Quantitative Trait Locus (eQTL) mapping measures the association between transcript expression and genotype in order to find genomic locations likely to regulate transcript expression. The availability of both gene expression and high-density genotype data has improved our ability to perform eQTL mapping in inbred mouse and other homozygous populations. However, existing eQTL mapping software does not scale well when the number of transcripts and markers are on the order of 105 and 105\u2013106, respectively.<\/jats:p>\n               <jats:p>Results: We propose a new method, FastMap, for fast and efficient eQTL mapping in homozygous inbred populations with binary allele calls. FastMap exploits the discrete nature and structure of the measured single nucleotide polymorphisms (SNPs). In particular, SNPs are organized into a Hamming distance-based tree that minimizes the number of arithmetic operations required to calculate the association of a SNP by making use of the association of its parent SNP in the tree. FastMap's tree can be used to perform both single marker mapping and haplotype association mapping over an m-SNP window. These performance enhancements also permit permutation-based significance testing.<\/jats:p>\n               <jats:p>Availability: The FastMap program and source code are available at the website: http:\/\/cebc.unc.edu\/fastmap86.html<\/jats:p>\n               <jats:p>Contact: \u00a0iir@unc.edu; nobel@email.unc.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn648","type":"journal-article","created":{"date-parts":[[2008,12,18]],"date-time":"2008-12-18T01:25:09Z","timestamp":1229563509000},"page":"482-489","source":"Crossref","is-referenced-by-count":30,"title":["FastMap: Fast eQTL mapping in homozygous populations"],"prefix":"10.1093","volume":"25","author":[{"given":"Daniel M.","family":"Gatti","sequence":"first","affiliation":[{"name":"1 Department of Environmental Sciences and Engineering, 2Department of Statistics and Operations Research and 3Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina 27599, USA"}]},{"given":"Andrey A.","family":"Shabalin","sequence":"additional","affiliation":[{"name":"1 Department of Environmental Sciences and Engineering, 2Department of Statistics and Operations Research and 3Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina 27599, USA"}]},{"given":"Tieu-Chong","family":"Lam","sequence":"additional","affiliation":[{"name":"1 Department of Environmental Sciences and Engineering, 2Department of Statistics and Operations Research and 3Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina 27599, USA"}]},{"given":"Fred A.","family":"Wright","sequence":"additional","affiliation":[{"name":"1 Department of Environmental Sciences and Engineering, 2Department of Statistics and Operations Research and 3Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina 27599, USA"}]},{"given":"Ivan","family":"Rusyn","sequence":"additional","affiliation":[{"name":"1 Department of Environmental Sciences and Engineering, 2Department of Statistics and Operations Research and 3Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina 27599, USA"}]},{"given":"Andrew B.","family":"Nobel","sequence":"additional","affiliation":[{"name":"1 Department of Environmental Sciences and Engineering, 2Department of Statistics and Operations Research and 3Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina 27599, USA"},{"name":"1 Department of Environmental Sciences and Engineering, 2Department of Statistics and Operations Research and 3Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina 27599, USA"}]}],"member":"286","published-online":{"date-parts":[[2008,12,17]]},"reference":[{"key":"2023013110102572100_B1","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1038\/71641","article-title":"Genealogies of mouse inbred strains","volume":"24","author":"Beck","year":"2000","journal-title":"Nat. Genet."},{"key":"2023013110102572100_B2","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1093\/bioinformatics\/btg112","article-title":"R\/qtl: QTL mapping in experimental crosses","volume":"19","author":"Broman","year":"2003","journal-title":"Bioinformatics"},{"key":"2023013110102572100_B3","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1038\/ng1497","article-title":"Uncovering regulatory pathways that affect hematopoietic stem cell function using \u2018genetical genomics\u2019","volume":"37","author":"Bystrykh","year":"2005","journal-title":"Nat. Genet."},{"key":"2023013110102572100_B4","doi-asserted-by":"crossref","first-page":"2383","DOI":"10.1093\/bioinformatics\/bti241","article-title":"Methodological aspects of the genetic dissection of gene expression","volume":"21","author":"Carlborg","year":"2005","journal-title":"Bioinformatics"},{"key":"2023013110102572100_B5","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1016\/j.ygeno.2005.07.010","article-title":"Integrating QTL and high-density SNP analyses in mice to identify Insig2 as a susceptibility gene for plasma cholesterol levels","volume":"86","author":"Cervino","year":"2005","journal-title":"Genomics"},{"key":"2023013110102572100_B6","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1038\/ng1518","article-title":"Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function","volume":"37","author":"Chesler","year":"2005","journal-title":"Nat. Genet."},{"key":"2023013110102572100_B7","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1093\/genetics\/138.3.963","article-title":"Empirical threshold values for quantitative triat mapping","volume":"138","author":"Churchill","year":"1994","journal-title":"Genetics"},{"key":"2023013110102572100_B8","doi-asserted-by":"crossref","first-page":"1133","DOI":"10.1038\/ng1104-1133","article-title":"The Collaborative Cross, a community resource for the genetic analysis of complex traits","volume":"36","author":"Churchill","year":"2004","journal-title":"Nat. Genet."},{"key":"2023013110102572100_B9","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1093\/genetics\/142.1.285","article-title":"Permutation tests for multiple loci affecting a quantitative character","volume":"142","author":"Doerge","year":"1996","journal-title":"Genetics"},{"key":"2023013110102572100_B10","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1093\/genetics\/151.1.373","article-title":"Statistical methods for mapping quantitative trait loci from a dense set of markers","volume":"151","author":"Dupuis","year":"1999","journal-title":"Genetics"},{"key":"2023013110102572100_B11","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1038\/nature06258","article-title":"A second generation human haplotype map of over 3.1 million SNPs","volume":"449","author":"Frazer","year":"2007","journal-title":"Nature"},{"key":"2023013110102572100_B12","doi-asserted-by":"crossref","first-page":"1050","DOI":"10.1038\/nature06067","article-title":"A sequence-based variation map of 8.27 million SNPs in inbred mouse strains","volume":"448","author":"Frazer","year":"2007","journal-title":"Nature"},{"key":"2023013110102572100_B13","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1002\/hep.21682","article-title":"Genome-level analysis of genetic regulation of liver gene expression networks","volume":"46","author":"Gatti","year":"2007","journal-title":"Hepatology"},{"key":"2023013110102572100_B14","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1038\/hdy.1992.131","article-title":"A simple regression method for mapping quantitative trait loci in line crosses using flanking markers","volume":"69","author":"Haley","year":"1992","journal-title":"Heredity"},{"key":"2023013110102572100_B15","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1038\/ng1599","article-title":"Complement factor 5 is a quantitative trait gene that modifies liver fibrogenesis in mice and humans","volume":"37","author":"Hillebrandt","year":"2005","journal-title":"Nat. Genet."},{"key":"2023013110102572100_B16","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1007\/s00335-005-0169-x","article-title":"From genetical genomics to systems genetics: potential applications in quantitative genomics and animal breeding","volume":"17","author":"Kadarmideen","year":"2006","journal-title":"Mamm. Genome"},{"key":"2023013110102572100_B17","doi-asserted-by":"crossref","first-page":"1709","DOI":"10.1534\/genetics.107.080101","article-title":"Efficient control of population structure in model organism association mapping","volume":"178","author":"Kang","year":"2008","journal-title":"Genetics"},{"key":"2023013110102572100_B18","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1093\/genetics\/156.2.855","article-title":"On the differences between maximum likelihood and regression interval mapping in the analysis of quantitative trait loci","volume":"156","author":"Kao","year":"2000","journal-title":"Genetics"},{"key":"2023013110102572100_B19","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1111\/j.1541-0420.2005.00437.x","article-title":"Statistical methods for expression quantitative trait loci (eQTL) mapping","volume":"62","author":"Kendziorski","year":"2006","journal-title":"Biometrics"},{"key":"2023013110102572100_B20","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The human genome browser at UCSC","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"2023013110102572100_B21","doi-asserted-by":"crossref","first-page":"9705","DOI":"10.1073\/pnas.91.21.9705","article-title":"Asymptotic theory for gene mapping","volume":"91","author":"Kong","year":"1994","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023013110102572100_B22","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1093\/genetics\/121.1.185","article-title":"Mapping mendelian factors underlying quantitative traits using RFLP linkage maps","volume":"121","author":"Lander","year":"1989","journal-title":"Genetics"},{"key":"2023013110102572100_B23","doi-asserted-by":"crossref","first-page":"930","DOI":"10.1007\/s00335-001-1016-3","article-title":"Map Manager QTX, cross-platform software for genetic mapping","volume":"12","author":"Manly","year":"2001","journal-title":"Mamm. Genome"},{"key":"2023013110102572100_B24","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1186\/1471-2105-7-61","article-title":"Comparative analysis of haplotype association mapping algorithms","volume":"7","author":"McClurg","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023013110102572100_B25","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1534\/genetics.106.066241","article-title":"Genomewide association analysis in diverse inbred mice: power and population structure","volume":"176","author":"McClurg","year":"2007","journal-title":"Genetics"},{"key":"2023013110102572100_B26","doi-asserted-by":"crossref","first-page":"1224","DOI":"10.1038\/ng1619","article-title":"Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits","volume":"37","author":"Mehrabian","year":"2005","journal-title":"Nat. Genet."},{"key":"2023013110102572100_B27","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1007\/s00335-005-0187-8","article-title":"How replicable are mRNA expression QTL?","volume":"17","author":"Peirce","year":"2006","journal-title":"Mamm. Genome"},{"key":"2023013110102572100_B28","doi-asserted-by":"crossref","first-page":"e393","DOI":"10.1371\/journal.pbio.0020393","article-title":"Use of a dense single nucleotide polymorphism map for in silico mapping in the mouse","volume":"2","author":"Pletcher","year":"2004","journal-title":"PLoS Biol."},{"key":"2023013110102572100_B29","doi-asserted-by":"crossref","first-page":"1675","DOI":"10.1101\/gr.6380007","article-title":"Initial sequence and comparative analysis of the cat genome","volume":"17","author":"Pontius","year":"2007","journal-title":"Genome Res."},{"key":"2023013110102572100_B30","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1093\/genetics\/155.2.945","article-title":"Inference of population structure using multilocus genotype data","volume":"155","author":"Pritchard","year":"2000","journal-title":"Genetics"},{"key":"2023013110102572100_B31","doi-asserted-by":"crossref","first-page":"i401","DOI":"10.1093\/bioinformatics\/btm220","article-title":"Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows","volume":"23","author":"Roberts","year":"2007","journal-title":"Bioinformatics"},{"key":"2023013110102572100_B32","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1007\/s00335-007-9045-1","article-title":"The polymorphism architecture of mouse genetic resources elucidated using genome-wide resequencing data: implications for QTL discovery and systems genetics","volume":"18","author":"Roberts","year":"2007","journal-title":"Mamm. Genome"},{"key":"2023013110102572100_B33","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1038\/nature01434","article-title":"Genetics of gene expression surveyed in maize, mouse and man","volume":"422","author":"Schadt","year":"2003","journal-title":"Nature"},{"key":"2023013110102572100_B34","doi-asserted-by":"crossref","first-page":"9440","DOI":"10.1073\/pnas.1530509100","article-title":"Statistical significance for genomewide studies","volume":"100","author":"Storey","year":"2003","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023013110102572100_B35","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1007\/s00335-008-9098-9","article-title":"An imputed genotype resource for the laboratory mouse","volume":"19","author":"Szatkiewicz","year":"2008","journal-title":"Mamm. Genome"},{"key":"2023013110102572100_B36","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1385\/NI:1:4:299","article-title":"WebQTL web-based complex trait analysis","volume":"1","author":"Wang","year":"2003","journal-title":"NeuroInformatics"},{"key":"2023013110102572100_B37","doi-asserted-by":"crossref","first-page":"1767","DOI":"10.1101\/gr.2668204","article-title":"Haplotype analysis in multiple crosses to identify a QTL gene","volume":"14","author":"Wang","year":"2004","journal-title":"Genome Res."},{"key":"2023013110102572100_B38","doi-asserted-by":"crossref","first-page":"1100","DOI":"10.1038\/ng2087","article-title":"On the subspecific origin of the laboratory mouse","volume":"39","author":"Yang","year":"2007","journal-title":"Nat. Genet."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/4\/482\/48985603\/bioinformatics_25_4_482.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/4\/482\/48985603\/bioinformatics_25_4_482.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T19:44:17Z","timestamp":1675194257000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/4\/482\/249278"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,12,17]]},"references-count":38,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2009,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn648","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,2,15]]},"published":{"date-parts":[[2008,12,17]]}}}