<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">McCarthy, Shane</style></author><author><style face="normal" font="default" size="100%">Das, Sayantan</style></author><author><style face="normal" font="default" size="100%">Kretzschmar, Warren</style></author><author><style face="normal" font="default" size="100%">Delaneau, Olivier</style></author><author><style face="normal" font="default" size="100%">Wood, Andrew R</style></author><author><style face="normal" font="default" size="100%">Teumer, Alexander</style></author><author><style face="normal" font="default" size="100%">Kang, Hyun Min</style></author><author><style face="normal" font="default" size="100%">Fuchsberger, Christian</style></author><author><style face="normal" font="default" size="100%">Danecek, Petr</style></author><author><style face="normal" font="default" size="100%">Sharp, Kevin</style></author><author><style face="normal" font="default" size="100%">Luo, Yang</style></author><author><style face="normal" font="default" size="100%">Sidore, Carlo</style></author><author><style face="normal" font="default" size="100%">Kwong, Alan</style></author><author><style face="normal" font="default" size="100%">Timpson, Nicholas</style></author><author><style face="normal" font="default" size="100%">Koskinen, Seppo</style></author><author><style face="normal" font="default" size="100%">Vrieze, Scott</style></author><author><style face="normal" font="default" size="100%">Scott, Laura J</style></author><author><style face="normal" font="default" size="100%">Zhang, He</style></author><author><style face="normal" font="default" size="100%">Mahajan, Anubha</style></author><author><style face="normal" font="default" size="100%">Veldink, Jan</style></author><author><style face="normal" font="default" size="100%">Peters, Ulrike</style></author><author><style face="normal" font="default" size="100%">Pato, Carlos</style></author><author><style face="normal" font="default" size="100%">van Duijn, Cornelia M</style></author><author><style face="normal" font="default" size="100%">Gillies, Christopher E</style></author><author><style face="normal" font="default" size="100%">Gandin, Ilaria</style></author><author><style face="normal" font="default" size="100%">Mezzavilla, Massimo</style></author><author><style face="normal" font="default" size="100%">Gilly, Arthur</style></author><author><style face="normal" font="default" size="100%">Cocca, Massimiliano</style></author><author><style face="normal" font="default" size="100%">Traglia, Michela</style></author><author><style face="normal" font="default" size="100%">Angius, Andrea</style></author><author><style face="normal" font="default" size="100%">Barrett, Jeffrey C</style></author><author><style face="normal" font="default" size="100%">Boomsma, 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face="normal" font="default" size="100%">Dedoussis, George</style></author><author><style face="normal" font="default" size="100%">Dörr, Marcus</style></author><author><style face="normal" font="default" size="100%">Farmaki, Aliki-Eleni</style></author><author><style face="normal" font="default" size="100%">Ferrucci, Luigi</style></author><author><style face="normal" font="default" size="100%">Forer, Lukas</style></author><author><style face="normal" font="default" size="100%">Fraser, Ross M</style></author><author><style face="normal" font="default" size="100%">Gabriel, Stacey</style></author><author><style face="normal" font="default" size="100%">Levy, Shawn</style></author><author><style face="normal" font="default" size="100%">Groop, Leif</style></author><author><style face="normal" font="default" size="100%">Harrison, Tabitha</style></author><author><style face="normal" font="default" size="100%">Hattersley, Andrew</style></author><author><style face="normal" font="default" size="100%">Holmen, Oddgeir L</style></author><author><style face="normal" font="default" size="100%">Hveem, Kristian</style></author><author><style face="normal" font="default" size="100%">Kretzler, Matthias</style></author><author><style face="normal" font="default" size="100%">Lee, James C</style></author><author><style face="normal" font="default" size="100%">McGue, Matt</style></author><author><style face="normal" font="default" size="100%">Meitinger, Thomas</style></author><author><style face="normal" font="default" size="100%">Melzer, David</style></author><author><style face="normal" font="default" size="100%">Min, Josine L</style></author><author><style face="normal" font="default" size="100%">Mohlke, Karen L</style></author><author><style face="normal" font="default" size="100%">Vincent, John B</style></author><author><style face="normal" font="default" size="100%">Nauck, Matthias</style></author><author><style face="normal" font="default" size="100%">Nickerson, 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Kerrin</style></author><author><style face="normal" font="default" size="100%">Spector, Timothy</style></author><author><style face="normal" font="default" size="100%">Stambolian, Dwight</style></author><author><style face="normal" font="default" size="100%">Tuke, Marcus</style></author><author><style face="normal" font="default" size="100%">Tuomilehto, Jaakko</style></author><author><style face="normal" font="default" size="100%">Van den Berg, Leonard H</style></author><author><style face="normal" font="default" size="100%">van Rheenen, Wouter</style></author><author><style face="normal" font="default" size="100%">Völker, Uwe</style></author><author><style face="normal" font="default" size="100%">Wijmenga, Cisca</style></author><author><style face="normal" font="default" size="100%">Toniolo, Daniela</style></author><author><style face="normal" font="default" size="100%">Zeggini, Eleftheria</style></author><author><style face="normal" font="default" size="100%">Gasparini, Paolo</style></author><author><style face="normal" font="default" size="100%">Sampson, Matthew G</style></author><author><style face="normal" font="default" size="100%">Wilson, James F</style></author><author><style face="normal" font="default" size="100%">Frayling, Timothy</style></author><author><style face="normal" font="default" size="100%">de Bakker, Paul I W</style></author><author><style face="normal" font="default" size="100%">Swertz, Morris A</style></author><author><style face="normal" font="default" size="100%">McCarroll, Steven</style></author><author><style face="normal" font="default" size="100%">Kooperberg, Charles</style></author><author><style face="normal" font="default" size="100%">Dekker, Annelot</style></author><author><style face="normal" font="default" size="100%">Altshuler, David</style></author><author><style face="normal" font="default" size="100%">Willer, Cristen</style></author><author><style face="normal" font="default" size="100%">Iacono, William</style></author><author><style face="normal" font="default" size="100%">Ripatti, Samuli</style></author><author><style face="normal" font="default" size="100%">Soranzo, Nicole</style></author><author><style face="normal" font="default" size="100%">Walter, Klaudia</style></author><author><style face="normal" font="default" size="100%">Swaroop, Anand</style></author><author><style face="normal" font="default" size="100%">Cucca, Francesco</style></author><author><style face="normal" font="default" size="100%">Anderson, Carl A</style></author><author><style face="normal" font="default" size="100%">Myers, Richard M</style></author><author><style face="normal" font="default" size="100%">Boehnke, Michael</style></author><author><style face="normal" font="default" size="100%">McCarthy, Mark I</style></author><author><style face="normal" font="default" size="100%">Durbin, Richard</style></author></authors><translated-authors><author><style face="normal" font="default" size="100%">Haplotype Reference Consortium</style></author></translated-authors></contributors><titles><title><style face="normal" font="default" size="100%">A reference panel of 64,976 haplotypes for genotype imputation.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Genet</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat. Genet.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2016 Aug 22</style></date></pub-dates></dates><language><style face="normal" font="default" size="100%">ENG</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;We describe a reference panel of 64,976 human haplotypes at 39,235,157 SNPs constructed using whole-genome sequence data from 20 studies of predominantly European ancestry. Using this resource leads to accurate genotype imputation at minor allele frequencies as low as 0.1% and a large increase in the number of SNPs tested in association studies, and it can help to discover and refine causal loci. We describe remote server resources that allow researchers to carry out imputation and phasing consistently and efficiently.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/27548312?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">O'Connell, Jared</style></author><author><style face="normal" font="default" size="100%">Gurdasani, Deepti</style></author><author><style face="normal" font="default" size="100%">Delaneau, Olivier</style></author><author><style face="normal" font="default" size="100%">Pirastu, Nicola</style></author><author><style face="normal" font="default" size="100%">Ulivi, Sheila</style></author><author><style face="normal" font="default" size="100%">Cocca, Massimiliano</style></author><author><style face="normal" font="default" size="100%">Traglia, Michela</style></author><author><style face="normal" font="default" size="100%">Huang, Jie</style></author><author><style face="normal" font="default" size="100%">Huffman, Jennifer E</style></author><author><style face="normal" font="default" size="100%">Rudan, Igor</style></author><author><style face="normal" font="default" size="100%">McQuillan, Ruth</style></author><author><style face="normal" font="default" size="100%">Fraser, Ross M</style></author><author><style face="normal" font="default" size="100%">Campbell, Harry</style></author><author><style face="normal" font="default" size="100%">Polasek, Ozren</style></author><author><style face="normal" font="default" size="100%">Asiki, Gershim</style></author><author><style face="normal" font="default" size="100%">Ekoru, Kenneth</style></author><author><style face="normal" font="default" size="100%">Hayward, Caroline</style></author><author><style face="normal" font="default" size="100%">Wright, Alan F</style></author><author><style face="normal" font="default" size="100%">Vitart, Veronique</style></author><author><style face="normal" font="default" size="100%">Navarro, Pau</style></author><author><style face="normal" font="default" size="100%">Zagury, Jean-Francois</style></author><author><style face="normal" font="default" size="100%">Wilson, James F</style></author><author><style face="normal" font="default" size="100%">Toniolo, Daniela</style></author><author><style face="normal" font="default" size="100%">Gasparini, Paolo</style></author><author><style face="normal" font="default" size="100%">Soranzo, Nicole</style></author><author><style face="normal" font="default" size="100%">Sandhu, Manjinder S</style></author><author><style face="normal" font="default" size="100%">Marchini, Jonathan</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A general approach for haplotype phasing across the full spectrum of relatedness.</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS Genet</style></secondary-title><alt-title><style face="normal" font="default" size="100%">PLoS Genet.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Chromosome Mapping</style></keyword><keyword><style  face="normal" font="default" size="100%">Cohort Effect</style></keyword><keyword><style  face="normal" font="default" size="100%">Family</style></keyword><keyword><style  face="normal" font="default" size="100%">Genotype</style></keyword><keyword><style  face="normal" font="default" size="100%">Haplotypes</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Pedigree</style></keyword><keyword><style  face="normal" font="default" size="100%">Phenotype</style></keyword><keyword><style  face="normal" font="default" size="100%">Recombination, Genetic</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2014</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2014 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">e1004234</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Many existing cohorts contain a range of relatedness between genotyped individuals, either by design or by chance. Haplotype estimation in such cohorts is a central step in many downstream analyses. Using genotypes from six cohorts from isolated populations and two cohorts from non-isolated populations, we have investigated the performance of different phasing methods designed for nominally 'unrelated' individuals. We find that SHAPEIT2 produces much lower switch error rates in all cohorts compared to other methods, including those designed specifically for isolated populations. In particular, when large amounts of IBD sharing is present, SHAPEIT2 infers close to perfect haplotypes. Based on these results we have developed a general strategy for phasing cohorts with any level of implicit or explicit relatedness between individuals. First SHAPEIT2 is run ignoring all explicit family information. We then apply a novel HMM method (duoHMM) to combine the SHAPEIT2 haplotypes with any family information to infer the inheritance pattern of each meiosis at all sites across each chromosome. This allows the correction of switch errors, detection of recombination events and genotyping errors. We show that the method detects numbers of recombination events that align very well with expectations based on genetic maps, and that it infers far fewer spurious recombination events than Merlin. The method can also detect genotyping errors and infer recombination events in otherwise uninformative families, such as trios and duos. The detected recombination events can be used in association scans for recombination phenotypes. The method provides a simple and unified approach to haplotype estimation, that will be of interest to researchers in the fields of human, animal and plant genetics.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/24743097?dopt=Abstract</style></custom1></record></records></xml>