{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,25]],"date-time":"2024-07-25T23:06:14Z","timestamp":1721948774187},"reference-count":42,"publisher":"Springer Science and Business Media LLC","issue":"S1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Recent technology advances have enabled sequencing of individual genomes, promising to revolutionize biomedical research. However, deep sequencing remains more expensive than microarrays for performing whole-genome SNP genotyping.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>In this paper we introduce a new multi-locus statistical model and computationally efficient genotype calling algorithms that integrate shotgun sequencing data with linkage disequilibrium (LD) information extracted from reference population panels such as Hapmap or the 1000 genomes project. Experiments on publicly available 454, Illumina, and ABI SOLiD sequencing datasets suggest that integration of LD information results in genotype calling accuracy comparable to that of microarray platforms from sequencing data of low-coverage. A software package implementing our algorithm, released under the GNU General Public License, is available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/dna.engr.uconn.edu\/software\/GeneSeq\/\" ext-link-type=\"uri\">http:\/\/dna.engr.uconn.edu\/software\/GeneSeq\/<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Integration of LD information leads to significant improvements in genotype calling accuracy compared to prior LD-oblivious methods, rendering low-coverage sequencing as a viable alternative to microarrays for conducting large-scale genome-wide association studies.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-s1-s53","type":"journal-article","created":{"date-parts":[[2011,2,18]],"date-time":"2011-02-18T20:04:40Z","timestamp":1298059480000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads"],"prefix":"10.1186","volume":"12","author":[{"given":"Jorge","family":"Duitama","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Justin","family":"Kennedy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sanjiv","family":"Dinakar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Y\u00f6zen","family":"Hern\u00e1ndez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yufeng","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ion I","family":"M\u0103ndoiu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2011,2,15]]},"reference":[{"key":"4411_CR1","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1038\/nature07517","volume":"456","author":"D Bentley","year":"2008","unstructured":"Bentley D, et al.: Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry. Nature 2008, 456: 53\u201359. 10.1038\/nature07517","journal-title":"Nature"},{"issue":"78","key":"4411_CR2","first-page":"78","volume":"327","author":"R Drmanac","year":"2009","unstructured":"Drmanac R, et al.: Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays. Science 2009, 327(78):78\u201381.","journal-title":"Science"},{"issue":"10","key":"4411_CR3","doi-asserted-by":"publisher","first-page":"e254+","DOI":"10.1371\/journal.pbio.0050254","volume":"5","author":"S Levy","year":"2007","unstructured":"Levy S, et al.: The Diploid Genome Sequence of an Individual Human. PLoS Biology 2007, 5(10):e254+. 10.1371\/journal.pbio.0050254","journal-title":"PLoS Biology"},{"key":"4411_CR4","doi-asserted-by":"publisher","first-page":"1527","DOI":"10.1101\/gr.091868.109","volume":"19","author":"K McKernan","year":"2009","unstructured":"McKernan K, et al.: Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Research 2009, 19: 1527\u20131541. 10.1101\/gr.091868.109","journal-title":"Genome Research"},{"issue":"9","key":"4411_CR5","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1038\/nbt.1561","volume":"27","author":"D Pushkarev","year":"2009","unstructured":"Pushkarev D, Neff N, Quake S: Single-molecule sequencing of an individual human genome. Nature Biotechnology 2009, 27(9):847\u2013850. 10.1038\/nbt.1561","journal-title":"Nature Biotechnology"},{"issue":"18","key":"4411_CR6","doi-asserted-by":"publisher","first-page":"943","DOI":"10.1038\/nature08795","volume":"463","author":"S Schuster","year":"2010","unstructured":"Schuster S, et al.: Complete Khoisan and Bantu genomes from southern Africa. Nature 2010, 463(18):943\u2013947. 10.1038\/nature08795","journal-title":"Nature"},{"key":"4411_CR7","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1038\/nature07484","volume":"456","author":"J Wang","year":"2008","unstructured":"Wang J, et al.: The diploid genome sequence of an Asian individual. Nature 2008, 456: 60\u201365. 10.1038\/nature07484","journal-title":"Nature"},{"key":"4411_CR8","doi-asserted-by":"publisher","first-page":"872","DOI":"10.1038\/nature06884","volume":"452","author":"D Wheeler","year":"2008","unstructured":"Wheeler D, et al.: The complete genome of an individual by massively parallel DNA sequencing. Nature 2008, 452: 872\u2013876. 10.1038\/nature06884","journal-title":"Nature"},{"key":"4411_CR9","unstructured":"The 1000 Genomes Project Consortium: The 1000 Genomes Project Consortium.[http:\/\/www.1000genomes.org\/]"},{"key":"4411_CR10","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1101\/gad.1864110","volume":"24","author":"M Snyder","year":"2010","unstructured":"Snyder M, Du J, Gerstein M: Personal genome sequencing: current approaches and challenges. Genes & Development 2010, 24: 423\u2013431. 10.1101\/gad.1864110","journal-title":"Genes & Development"},{"key":"4411_CR11","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1186\/1471-2164-11-385","volume":"11","author":"A Bashir","year":"2010","unstructured":"Bashir A, Bansal V, Bafna V: Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance. BMC Genomics 2010, 11: 385. 10.1186\/1471-2164-11-385","journal-title":"BMC Genomics"},{"key":"4411_CR12","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1186\/1471-2105-9-239","volume":"9","author":"M Wendl","year":"2008","unstructured":"Wendl M, Wilson R: Aspects of coverage in medical DNA sequencing. BMC Bioinformatics 2008, 9: 239. 10.1186\/1471-2105-9-239","journal-title":"BMC Bioinformatics"},{"key":"4411_CR13","doi-asserted-by":"publisher","first-page":"851","DOI":"10.1038\/nature06258","volume":"449","author":"The International HapMap Consortium","year":"2007","unstructured":"The International HapMap Consortium: A second generation human haplotype map of over 3.1 million SNPs. Nature 2007, 449: 851\u2013861. 10.1038\/nature06258","journal-title":"Nature"},{"issue":"6","key":"4411_CR14","doi-asserted-by":"publisher","first-page":"e1000529","DOI":"10.1371\/journal.pgen.1000529","volume":"5","author":"BN Howie","year":"2009","unstructured":"Howie BN, Donnelly P, Marchini J: A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies. PLoS Genet 2009, 5(6):e1000529. 10.1371\/journal.pgen.1000529","journal-title":"PLoS Genet"},{"issue":"9","key":"4411_CR15","doi-asserted-by":"publisher","first-page":"1155","DOI":"10.1089\/cmb.2007.0133","volume":"15","author":"J Kennedy","year":"2008","unstructured":"Kennedy J, M\u0103ndoiu I, Pa\u015faniuc B: Genotype Error Detection and Imputation using Hidden Markov Models of Haplotype Diversity. Journal of Computational Biology 2008, 15(9):1155\u20131171. 10.1089\/cmb.2007.0133","journal-title":"Journal of Computational Biology"},{"key":"4411_CR16","first-page":"2290","volume":"79","author":"Y Li","year":"2006","unstructured":"Li Y, Abecasis GR: Mach 1.0: Rapid Haplotype Reconstruction and Missing Genotype Inference. American Journal of Human Genetics 2006, 79: 2290.","journal-title":"American Journal of Human Genetics"},{"key":"4411_CR17","doi-asserted-by":"publisher","first-page":"906","DOI":"10.1038\/ng2088","volume":"39","author":"J Marchini","year":"2007","unstructured":"Marchini J, Howie B, Myers S, McVean G, Donnelly P: A new multipoint method for genome-wide association studies by imputation of genotypes. Nature Genetics 2007, 39: 906\u2013913. 10.1038\/ng2088","journal-title":"Nature Genetics"},{"key":"4411_CR18","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1086\/428594","volume":"76","author":"M Stephens","year":"2005","unstructured":"Stephens M, Scheet P: Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. American Journal of Human Genetics 2005, 76: 449\u2013462. 10.1086\/428594","journal-title":"American Journal of Human Genetics"},{"key":"4411_CR19","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1093\/bioinformatics\/btm603","volume":"24","author":"X Wen","year":"2008","unstructured":"Wen X, Nicolae DL: Association studies for untyped markers with TUNA. Bioinformatics 2008, 24: 435\u2013437. 10.1093\/bioinformatics\/btm603","journal-title":"Bioinformatics"},{"issue":"7","key":"4411_CR20","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1038\/nrg2796","volume":"11","author":"J Marchini","year":"2010","unstructured":"Marchini J, Howie B: Genotype imputation for genome-wide association studies. Nature reviews. Genetics 2010, 11(7):499\u2013511. 10.1038\/nrg2796","journal-title":"Nature reviews. Genetics"},{"issue":"18","key":"4411_CR21","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1016\/j.ajhg.2009.11.004","volume":"85","author":"B Browning","year":"2009","unstructured":"Browning B, Yu Z: Simultaneous Genotype Calling and Haplotype Phasing Improves Genotype Accuracy and Reduces False-Positive Associations for Genome-wide Association Studies. The American Journal of Human Genetics 2009, 85(18):847\u2013861. 10.1016\/j.ajhg.2009.11.004","journal-title":"The American Journal of Human Genetics"},{"issue":"2","key":"4411_CR22","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1038\/ejhg.2008.198","volume":"17","author":"DR Nyholt","year":"2008","unstructured":"Nyholt DR, Yu CE, Visscher PM: On Jim Watson\u2019s APOE status: genetic information is hard to hide. European Journal of Human Genetics 2008, 17(2):147\u2013149. 10.1038\/ejhg.2008.198","journal-title":"European Journal of Human Genetics"},{"key":"4411_CR23","unstructured":"Applied Biosystems: SOLiD 4 System product description.[https:\/\/products.appliedbiosystems.com\/]"},{"key":"4411_CR24","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1093\/ije\/dyn147","volume":"38","author":"PR Burton","year":"2009","unstructured":"Burton PR, Hansell AL, Fortier I, Manolio TA, Khoury MJ, Little J, Elliott P: Size matters: just how big is BIG?: Quantifying realistic sample size requirements for human genome epidemiology. Int. J. Epidemiol. 2009, 38: 263\u2013273. 10.1093\/ije\/dyn147","journal-title":"Int. J. Epidemiol"},{"issue":"3","key":"4411_CR25","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1101\/gr.8.3.186","volume":"8","author":"B Ewing","year":"1998","unstructured":"Ewing B, Green P: Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Research 1998, 8(3):186\u2013194.","journal-title":"Genome Research"},{"issue":"2-3","key":"4411_CR26","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1023\/A:1007425814087","volume":"29","author":"Z Ghahramani","year":"1997","unstructured":"Ghahramani Z, Jordan M: Factorial Hidden Markov Models. Mach. Learn. 1997, 29(2\u20133):245\u2013273. 10.1023\/A:1007425814087","journal-title":"Mach. Learn"},{"key":"4411_CR27","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1023\/A:1007469218079","volume":"32","author":"S Fine","year":"1998","unstructured":"Fine S, Singer Y, Tishby N: The Hierarchical Hidden Markov Model: Analysis and Applications. Mach. Learn. 1998, 32: 41\u201362. 10.1023\/A:1007469218079","journal-title":"Mach. Learn"},{"key":"4411_CR28","doi-asserted-by":"publisher","first-page":"1243","DOI":"10.1089\/cmb.2005.12.1243","volume":"12","author":"G Kimmel","year":"2005","unstructured":"Kimmel G, Shamir R: A block-free hidden Markov model for genotypes and its application to disease association. Journal of Computational Biology 2005, 12: 1243\u20131260. 10.1089\/cmb.2005.12.1243","journal-title":"Journal of Computational Biology"},{"key":"4411_CR29","first-page":"355","volume-title":"Bioinformatics Algorithms: Techniques and Applications, preliminary version Proc. WABI 2005","author":"P Rastas","year":"2008","unstructured":"Rastas P, Koivisto M, Mannila H, Ukkonen E: Phasing genotypes using a Hidden Markov model. In Bioinformatics Algorithms: Techniques and Applications, preliminary version Proc. WABI 2005. Wiley; 2008:355\u2013373."},{"key":"4411_CR30","first-page":"90","volume-title":"Proc. CSB","author":"R Schwartz","year":"2004","unstructured":"Schwartz R: Algorithms for Association Study Design Using a Generalized Model of Haplotype Conservation. Proc. CSB 2004, 90\u201397."},{"key":"4411_CR31","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1214\/aoms\/1177697196","volume":"41","author":"L Baum","year":"1970","unstructured":"Baum L, Petrie T, Soules G, Weiss N: A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains. Annals of Mathematical Statistics 1970, 41: 164\u2013171. 10.1214\/aoms\/1177697196","journal-title":"Annals of Mathematical Statistics"},{"issue":"3","key":"4411_CR32","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1016\/S0022-0000(02)00009-0","volume":"65","author":"R Lyngs\u00f8","year":"2002","unstructured":"Lyngs\u00f8 R, Pedersen C: The consensus string problem and the complexity of comparing hidden Markov models. Journal of Computer Systems Science 2002, 65(3):545\u2013569. 10.1016\/S0022-0000(02)00009-0","journal-title":"Journal of Computer Systems Science"},{"issue":"2","key":"4411_CR33","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1109\/TCBB.2007.70223","volume":"5","author":"A Gusev","year":"2008","unstructured":"Gusev A, Mandoiu I, Pasaniuc B: Highly Scalable Genotype Phasing by Entropy Minimization. IEEE\/ACM Trans. on Computational Biology and Bioinformatics 2008, 5(2):252\u2013261. 10.1109\/TCBB.2007.70223","journal-title":"IEEE\/ACM Trans. on Computational Biology and Bioinformatics"},{"issue":"2","key":"4411_CR34","doi-asserted-by":"publisher","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","volume":"5","author":"S Kurtz","year":"2004","unstructured":"Kurtz S, et al.: Versatile and open software for comparing large genomes. Genome Biology 2004, 5(2):R12. 10.1186\/gb-2004-5-2-r12","journal-title":"Genome Biology"},{"key":"4411_CR35","doi-asserted-by":"publisher","first-page":"1851","DOI":"10.1101\/gr.078212.108","volume":"18","author":"H Li","year":"2008","unstructured":"Li H, Ruan J, Durbin R: Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research 2008, 18: 1851\u20131858. 10.1101\/gr.078212.108","journal-title":"Genome Research"},{"key":"4411_CR36","doi-asserted-by":"publisher","first-page":"1124","DOI":"10.1101\/gr.088013.108","volume":"19","author":"R Li","year":"2009","unstructured":"Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J: SNP detection for massively parallel whole-genome resequencing. Genome Research 2009, 19: 1124\u20131132. 10.1101\/gr.088013.108","journal-title":"Genome Research"},{"issue":"16","key":"4411_CR37","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al.: The Sequence Alignment\/Map format and SAMtools. Bioinformatics 2009, 25(16):2078\u20132079. 10.1093\/bioinformatics\/btp352","journal-title":"Bioinformatics"},{"key":"4411_CR38","volume-title":"Thunder (beta version)","author":"Y Li","year":"2010","unstructured":"Li Y, Abecasis G: Thunder (beta version).2010. [http:\/\/genome.sph.umich.edu\/wiki\/Thunder]"},{"key":"4411_CR39","volume-title":"Genome research","author":"SQQ Le","year":"2010","unstructured":"Le SQQ, Durbin R: SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples. Genome research 2010."},{"key":"4411_CR40","volume-title":"Tech. Rep. 0911.1765,","author":"J Kennedy","year":"2009","unstructured":"Kennedy J, Mandoiu I, Pasaniuc B: GEDI: Scalable Algorithms for Genotype Error Detection and Imputation. Tech. Rep. 0911.1765, Cornell University arXiv e-print; 2009. [http:\/\/arxiv.org\/abs\/0911.1765]"},{"issue":"Suppl 9","key":"4411_CR41","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 J, Han T, Kaput J, Fuscoe J, Tong W: 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"},{"key":"4411_CR42","unstructured":"Illumina: Empowering GWAS for a new era of discovery.[http:\/\/www.illumina.com\/documents\/products\/technotes\/technote_empower_gwas.pdf]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-S1-S53.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T13:46:35Z","timestamp":1630503995000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-S1-S53"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,2,15]]},"references-count":42,"journal-issue":{"issue":"S1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4411"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-s1-s53","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,2,15]]},"assertion":[{"value":"15 February 2011","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S53"}}