{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T20:57:51Z","timestamp":1675285071317},"reference-count":23,"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":[[2013,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>DNA pooling constitutes a cost effective alternative in genome wide association studies. In DNA pooling, equimolar amounts of DNA from different individuals are mixed into one sample and the frequency of each allele in each position is observed in a single genotype experiment. The identification of haplotype frequencies from pooled data in addition to single locus analysis is of separate interest within these studies as haplotypes could increase statistical power and provide additional insight.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We developed a method for maximum-parsimony haplotype frequency estimation from pooled DNA data based on the sparse representation of the DNA pools in a dictionary of haplotypes. Extensions to scenarios where data is noisy or even missing are also presented. The resulting method is first applied to simulated data based on the haplotypes and their associated frequencies of the AGT gene. We further evaluate our methodology on datasets consisting of SNPs from the first 7Mb of the HapMap CEU population. Noise and missing data were further introduced in the datasets in order to test the extensions of the proposed method. Both HIPPO and HAPLOPOOL were also applied to these datasets to compare performances.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>We evaluate our methodology on scenarios where pooling is more efficient relative to individual genotyping; that is, in datasets that contain pools with a small number of individuals. We show that in such scenarios our methodology outperforms state-of-the-art methods such as HIPPO and HAPLOPOOL.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-14-270","type":"journal-article","created":{"date-parts":[[2013,9,8]],"date-time":"2013-09-08T06:16:31Z","timestamp":1378620991000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Maximum-parsimony haplotype frequencies inference based on a joint constrained sparse representation of pooled DNA"],"prefix":"10.1186","volume":"14","author":[{"given":"Guido H","family":"Jajamovich","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexandros","family":"Iliadis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dimitris","family":"Anastassiou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaodong","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2013,9,8]]},"reference":[{"issue":"26","key":"6053_CR1","doi-asserted-by":"publisher","first-page":"16871","DOI":"10.1073\/pnas.262671399","volume":"99","author":"A Bansal","year":"2002","unstructured":"Bansal A, van den Boom D, Kammerer S, Honisch C, Adam G, Cantor CR, Kleyn P, Braun A: Association testing by DNA pooling: an effective initial screen. Proc Nat Acad Sci. 2002, 99 (26): 16871-16874. 10.1073\/pnas.262671399.","journal-title":"Proc Nat Acad Sci"},{"issue":"3","key":"6053_CR2","doi-asserted-by":"publisher","first-page":"734","DOI":"10.1086\/515512","volume":"61","author":"LF Barcellos","year":"1997","unstructured":"Barcellos LF, Klitz W, Field LL, Tobias R, Bowcock AM, Wilson R, Nelson MP, Nagatomi J, Thomson G: Association mapping of disease loci, by use of a pooled DNA genomic screen. Am J Hum Genet. 1997, 61 (3): 734-747. 10.1086\/515512.","journal-title":"Am J Hum Genet"},{"issue":"2","key":"6053_CR3","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1080\/07853890310021724","volume":"36","author":"N Norton","year":"2004","unstructured":"Norton N, Williams M, O\u2019Donovan C, Owen J: DNA pooling as a tool for large-scale association studies in complex traits. Annals Med. 2004, 36 (2): 146-152. 10.1080\/07853890310021724.","journal-title":"Annals Med"},{"key":"6053_CR4","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1086\/510686","volume":"80","author":"JV Pearson","year":"2007","unstructured":"Pearson JV, Huentelman MJ, Halperin RF, Tembe WD, Melquist S, Homer N, Brun M, Szelinger S, Coon KD, Zismann VL, et al: Identification of the genetic basis for complex disorders by use of pooling-based genomewide single-nucleotide-polymorphism association studies. Am J Human Genet. 2007, 80: 126-139. 10.1086\/510686.","journal-title":"Am J Human Genet"},{"issue":"11","key":"6053_CR5","doi-asserted-by":"publisher","first-page":"862","DOI":"10.1038\/nrg930","volume":"3","author":"P Sham","year":"2002","unstructured":"Sham P, Bader JS, Craig I, O\u2019Donovan M, Owen M: DNA pooling: a tool for large-scale association studies. Nat Rev Genet. 2002, 3 (11): 862-871.","journal-title":"Nat Rev Genet"},{"issue":"3","key":"6053_CR6","doi-asserted-by":"publisher","first-page":"1747","DOI":"10.1534\/genetics.105.042648","volume":"173","author":"Y Zuo","year":"2006","unstructured":"Zuo Y, Zou G, Zhao H: Two-stage designs in case-control association analysis. Genetics. 2006, 173 (3): 1747-1760. 10.1534\/genetics.105.042648.","journal-title":"Genetics"},{"issue":"22","key":"6053_CR7","doi-asserted-by":"publisher","first-page":"3048","DOI":"10.1093\/bioinformatics\/btm435","volume":"23","author":"B Kirkpatrick","year":"2007","unstructured":"Kirkpatrick B, Armendariz CS, Karp RM, Halperin E: HAPLOPOOL: improving haplotype frequency estimation through DNA pools and phylogenetic modeling. Bioinformatics. 2007, 23 (22): 3048-3055. 10.1093\/bioinformatics\/btm435.","journal-title":"Bioinformatics"},{"issue":"20","key":"6053_CR8","doi-asserted-by":"publisher","first-page":"2556","DOI":"10.1093\/bioinformatics\/btq492","volume":"26","author":"AY Kuk","year":"2010","unstructured":"Kuk AY, Xu J, Yang Y: A study of the efficiency of pooling in haplotype estimation. Bioinformatics. 2010, 26 (20): 2556-2563. 10.1093\/bioinformatics\/btq492.","journal-title":"Bioinformatics"},{"issue":"5-6","key":"6053_CR9","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1046\/j.1469-1809.2002.00125.x","volume":"66","author":"B Barratt","year":"2002","unstructured":"Barratt B, Payne F, Rance H, Nutland S, Todd J, Clayton D: Identification of the sources of error in allele frequency estimations from pooled DNA indicates an optimal experimental design. Annals Hum Genet. 2002, 66 (5-6): 393-405.","journal-title":"Annals Hum Genet"},{"issue":"2","key":"6053_CR10","doi-asserted-by":"publisher","first-page":"384","DOI":"10.1086\/346116","volume":"72","author":"T Ito","year":"2003","unstructured":"Ito T, Chiku S, Inoue E, Tomita M, Morisaki T, Morisaki H, Kamatani N: Estimation of haplotype frequencies, linkage-disequilibrium measures, and combination of haplotype copies in each pool by use of pooled DNA data. Am J Hum Genet. 2003, 72 (2): 384-10.1086\/346116.","journal-title":"Am J Hum Genet"},{"key":"6053_CR11","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1002\/gepi.10195","volume":"24","author":"S Wang","year":"2003","unstructured":"Wang S, Kidd KK, Zhao H: On the use of DNA pooling to estimate haplotype frequencies. Genet Epidemiol. 2003, 24: 74-82. 10.1002\/gepi.10195.","journal-title":"Genet Epidemiol"},{"issue":"12","key":"6053_CR12","doi-asserted-by":"publisher","first-page":"7225","DOI":"10.1073\/pnas.1237858100","volume":"100","author":"Y Yang","year":"2003","unstructured":"Yang Y, Zhang J, Hoh J, Matsuda F, Xu P, Lathrop M, Ott J: Efficiency of single-nucleotide polymorphism haplotype estimation from pooled DNA. Proc Nat Acad Sci. 2003, 100 (12): 7225-7230. 10.1073\/pnas.1237858100.","journal-title":"Proc Nat Acad Sci"},{"issue":"17","key":"6053_CR13","doi-asserted-by":"publisher","first-page":"1942","DOI":"10.1093\/bioinformatics\/btn324","volume":"24","author":"H Zhang","year":"2008","unstructured":"Zhang H, Yang HC, Yang Y: PoooL: an efficient method for estimating haplotype frequencies from large DNA pools. Bioinformatics. 2008, 24 (17): 1942-1948. 10.1093\/bioinformatics\/btn324.","journal-title":"Bioinformatics"},{"issue":"3","key":"6053_CR14","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1093\/bioinformatics\/btn623","volume":"25","author":"AY Kuk","year":"2009","unstructured":"Kuk AY, Zhang H, Yang Y: Computationally feasible estimation of haplotype frequencies from pooled DNA with and without Hardy-Weinberg equilibrium. Bioinformatics. 2009, 25 (3): 379-386. 10.1093\/bioinformatics\/btn623.","journal-title":"Bioinformatics"},{"issue":"8","key":"6053_CR15","doi-asserted-by":"publisher","first-page":"1343","DOI":"10.1002\/sim.5540","volume":"32","author":"AY Kuk","year":"2012","unstructured":"Kuk AY, Li X, Xu J: A fast collapsed data method for estimating haplotype frequencies from pooled genotype data with applications to the study of rare variants. Stat Med. 2012, 32 (8): 1343-1360.","journal-title":"Stat Med"},{"key":"6053_CR16","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1109\/TCBB.2009.71","volume":"8","author":"D Gasbarra","year":"2011","unstructured":"Gasbarra D, Kulathinal S, Pirinen M, Sillanpaa MJ: Estimating haplotype frequencies by combining data from large DNA pools with database information. Comput Biol Bioinform IEEE\/ACM Trans. 2011, 8: 36-44.","journal-title":"Comput Biol Bioinform IEEE\/ACM Trans"},{"issue":"24","key":"6053_CR17","doi-asserted-by":"publisher","first-page":"3296","DOI":"10.1093\/bioinformatics\/btp584","volume":"25","author":"M Pirinen","year":"2009","unstructured":"Pirinen M: Estimating population haplotype frequencies from pooled SNP data using incomplete database information. Bioinformatics. 2009, 25 (24): 3296-3302. 10.1093\/bioinformatics\/btp584.","journal-title":"Bioinformatics"},{"issue":"5","key":"6053_CR18","doi-asserted-by":"publisher","first-page":"1145","DOI":"10.1093\/molbev\/mst016","volume":"30","author":"D Kessner","year":"2013","unstructured":"Kessner D, Turner TL, Novembre J: Maximum Likelihood Estimation of Frequencies of Known Haplotypes from Pooled Sequence Data. Mol Biol Evol. 2013, 30 (5): 1145-1158. 10.1093\/molbev\/mst016.","journal-title":"Mol Biol Evol"},{"key":"6053_CR19","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1007\/978-3-642-37195-0_4","volume-title":"Research in Computational Molecular Biology","author":"I Eskin","year":"2013","unstructured":"Eskin I, Hormozdiari F, Conde L, Riby J, Skibola C, Eskin E, Halperin E: eALPS: estimating abundance levels in pooled sequencing using available genotyping data. Research in Computational Molecular Biology. 2013, Berlin, Germany: Springer Berlin Heidelberg, 32-44."},{"issue":"11","key":"6053_CR20","doi-asserted-by":"publisher","first-page":"1723","DOI":"10.1089\/cmb.2011.0189","volume":"18","author":"A Amir","year":"2011","unstructured":"Amir A, Zuk O: Bacterial community reconstruction using compressed sensing. J Comput Biol. 2011, 18 (11): 1723-1741. 10.1089\/cmb.2011.0189.","journal-title":"J Comput Biol"},{"issue":"14","key":"6053_CR21","doi-asserted-by":"publisher","first-page":"1773","DOI":"10.1093\/bioinformatics\/btg239","volume":"19","author":"L Wang","year":"2003","unstructured":"Wang L, Xu Y: Haplotype inference by maximum parsimony. Bioinformatics. 2003, 19 (14): 1773-1780. 10.1093\/bioinformatics\/btg239.","journal-title":"Bioinformatics"},{"key":"6053_CR22","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1561\/2200000016","volume":"3","author":"S Boyd","year":"2011","unstructured":"Boyd S, Parikh N, Chu E, Peleato B, Eckstein J: Distributed optimization and statistical learning via the alternating direction method of multipliers. Foundations Trends\u00ae; Mach Learn. 2011, 3: 1-122.","journal-title":"Foundations Trends\u00ae; Mach Learn"},{"key":"6053_CR23","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1086\/338446","volume":"70","author":"T Niu","year":"2002","unstructured":"Niu T, Qin ZS, Xu X, Liu JS: Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am J Hum Genet. 2002, 70: 157-10.1086\/338446.","journal-title":"Am J Hum Genet"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-270.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T01:24:52Z","timestamp":1630545892000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-270"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,9,8]]},"references-count":23,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2013,12]]}},"alternative-id":["6053"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-270","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,9,8]]},"assertion":[{"value":"12 April 2013","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 August 2013","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 September 2013","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"270"}}