<?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%">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><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%">McQuillan, Ruth</style></author><author><style face="normal" font="default" size="100%">Eklund, Niina</style></author><author><style face="normal" font="default" size="100%">Pirastu, Nicola</style></author><author><style face="normal" font="default" size="100%">Kuningas, Maris</style></author><author><style face="normal" font="default" size="100%">McEvoy, Brian P</style></author><author><style face="normal" font="default" size="100%">Esko, Tõnu</style></author><author><style face="normal" font="default" size="100%">Corre, Tanguy</style></author><author><style face="normal" font="default" size="100%">Davies, Gail</style></author><author><style face="normal" font="default" size="100%">Kaakinen, Marika</style></author><author><style face="normal" font="default" size="100%">Lyytikäinen, Leo-Pekka</style></author><author><style face="normal" font="default" size="100%">Kristiansson, Kati</style></author><author><style face="normal" font="default" size="100%">Havulinna, Aki S</style></author><author><style face="normal" font="default" size="100%">Gögele, Martin</style></author><author><style face="normal" font="default" size="100%">Vitart, Veronique</style></author><author><style face="normal" font="default" size="100%">Tenesa, Albert</style></author><author><style face="normal" font="default" size="100%">Aulchenko, Yurii</style></author><author><style face="normal" font="default" size="100%">Hayward, Caroline</style></author><author><style face="normal" font="default" size="100%">Johansson, Åsa</style></author><author><style face="normal" font="default" size="100%">Boban, Mladen</style></author><author><style face="normal" font="default" size="100%">Ulivi, Sheila</style></author><author><style face="normal" font="default" size="100%">Robino, Antonietta</style></author><author><style face="normal" font="default" size="100%">Boraska, Vesna</style></author><author><style face="normal" font="default" size="100%">Igl, Wilmar</style></author><author><style face="normal" font="default" size="100%">Wild, Sarah H</style></author><author><style face="normal" font="default" size="100%">Zgaga, Lina</style></author><author><style face="normal" font="default" size="100%">Amin, Najaf</style></author><author><style face="normal" font="default" size="100%">Theodoratou, Evropi</style></author><author><style face="normal" font="default" size="100%">Polasek, Ozren</style></author><author><style face="normal" font="default" size="100%">Girotto, Giorgia</style></author><author><style face="normal" font="default" size="100%">Lopez, Lorna M</style></author><author><style face="normal" font="default" size="100%">Sala, Cinzia</style></author><author><style face="normal" font="default" size="100%">Lahti, Jari</style></author><author><style face="normal" font="default" size="100%">Laatikainen, Tiina</style></author><author><style face="normal" font="default" size="100%">Prokopenko, Inga</style></author><author><style face="normal" font="default" size="100%">Kals, Mart</style></author><author><style face="normal" font="default" size="100%">Viikari, Jorma</style></author><author><style face="normal" font="default" size="100%">Yang, Jian</style></author><author><style face="normal" font="default" size="100%">Pouta, Anneli</style></author><author><style face="normal" font="default" size="100%">Estrada, Karol</style></author><author><style face="normal" font="default" size="100%">Hofman, Albert</style></author><author><style face="normal" font="default" size="100%">Freimer, Nelson</style></author><author><style face="normal" font="default" size="100%">Martin, Nicholas G</style></author><author><style face="normal" font="default" size="100%">Kähönen, Mika</style></author><author><style face="normal" font="default" size="100%">Milani, Lili</style></author><author><style face="normal" font="default" size="100%">Heliövaara, Markku</style></author><author><style face="normal" font="default" size="100%">Vartiainen, Erkki</style></author><author><style face="normal" font="default" size="100%">Räikkönen, Katri</style></author><author><style face="normal" font="default" size="100%">Masciullo, Corrado</style></author><author><style face="normal" font="default" size="100%">Starr, John M</style></author><author><style face="normal" font="default" size="100%">Hicks, Andrew A</style></author><author><style face="normal" font="default" size="100%">Esposito, Laura</style></author><author><style face="normal" font="default" size="100%">Kolcic, Ivana</style></author><author><style face="normal" font="default" size="100%">Farrington, Susan M</style></author><author><style face="normal" font="default" size="100%">Oostra, Ben</style></author><author><style face="normal" font="default" size="100%">Zemunik, Tatijana</style></author><author><style face="normal" font="default" size="100%">Campbell, Harry</style></author><author><style face="normal" font="default" size="100%">Kirin, Mirna</style></author><author><style face="normal" font="default" size="100%">Pehlic, Marina</style></author><author><style face="normal" font="default" size="100%">Faletra, Flavio</style></author><author><style face="normal" font="default" size="100%">Porteous, David</style></author><author><style face="normal" font="default" size="100%">Pistis, Giorgio</style></author><author><style face="normal" font="default" size="100%">Widen, Elisabeth</style></author><author><style face="normal" font="default" size="100%">Salomaa, Veikko</style></author><author><style face="normal" font="default" size="100%">Koskinen, Seppo</style></author><author><style face="normal" font="default" size="100%">Fischer, Krista</style></author><author><style face="normal" font="default" size="100%">Lehtimäki, Terho</style></author><author><style face="normal" font="default" size="100%">Heath, Andrew</style></author><author><style face="normal" font="default" size="100%">McCarthy, Mark I</style></author><author><style face="normal" font="default" size="100%">Rivadeneira, Fernando</style></author><author><style face="normal" font="default" size="100%">Montgomery, Grant W</style></author><author><style face="normal" font="default" size="100%">Tiemeier, Henning</style></author><author><style face="normal" font="default" size="100%">Hartikainen, Anna-Liisa</style></author><author><style face="normal" font="default" size="100%">Madden, Pamela A F</style></author><author><style face="normal" font="default" size="100%">d'Adamo, Pio</style></author><author><style face="normal" font="default" size="100%">Hastie, Nicholas D</style></author><author><style face="normal" font="default" size="100%">Gyllensten, Ulf</style></author><author><style face="normal" font="default" size="100%">Wright, Alan F</style></author><author><style face="normal" font="default" size="100%">van Duijn, Cornelia M</style></author><author><style face="normal" font="default" size="100%">Dunlop, Malcolm</style></author><author><style face="normal" font="default" size="100%">Rudan, Igor</style></author><author><style face="normal" font="default" size="100%">Gasparini, Paolo</style></author><author><style face="normal" font="default" size="100%">Pramstaller, Peter P</style></author><author><style face="normal" font="default" size="100%">Deary, Ian J</style></author><author><style face="normal" font="default" size="100%">Toniolo, Daniela</style></author><author><style face="normal" font="default" size="100%">Eriksson, Johan G</style></author><author><style face="normal" font="default" size="100%">Jula, Antti</style></author><author><style face="normal" font="default" size="100%">Raitakari, Olli T</style></author><author><style face="normal" font="default" size="100%">Metspalu, Andres</style></author><author><style face="normal" font="default" size="100%">Perola, Markus</style></author><author><style face="normal" font="default" size="100%">Järvelin, Marjo-Riitta</style></author><author><style face="normal" font="default" size="100%">Uitterlinden, André</style></author><author><style face="normal" font="default" size="100%">Visscher, Peter M</style></author><author><style face="normal" font="default" size="100%">Wilson, James F</style></author></authors><translated-authors><author><style face="normal" font="default" size="100%">ROHgen Consortium</style></author></translated-authors></contributors><titles><title><style face="normal" font="default" size="100%">Evidence of inbreeding depression on human height.</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%">Adult</style></keyword><keyword><style  face="normal" font="default" size="100%">Aged</style></keyword><keyword><style  face="normal" font="default" size="100%">Body Height</style></keyword><keyword><style  face="normal" font="default" size="100%">Consanguinity</style></keyword><keyword><style  face="normal" font="default" size="100%">Databases, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Family</style></keyword><keyword><style  face="normal" font="default" size="100%">Female</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes, Recessive</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic Heterogeneity</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome-Wide Association Study</style></keyword><keyword><style  face="normal" font="default" size="100%">Homozygote</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Male</style></keyword><keyword><style  face="normal" font="default" size="100%">Middle Aged</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymorphism, Single Nucleotide</style></keyword><keyword><style  face="normal" font="default" size="100%">Quantitative Trait, Heritable</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">8</style></volume><pages><style face="normal" font="default" size="100%">e1002655</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Stature is a classical and highly heritable complex trait, with 80%-90% of variation explained by genetic factors. In recent years, genome-wide association studies (GWAS) have successfully identified many common additive variants influencing human height; however, little attention has been given to the potential role of recessive genetic effects. Here, we investigated genome-wide recessive effects by an analysis of inbreeding depression on adult height in over 35,000 people from 21 different population samples. We found a highly significant inverse association between height and genome-wide homozygosity, equivalent to a height reduction of up to 3 cm in the offspring of first cousins compared with the offspring of unrelated individuals, an effect which remained after controlling for the effects of socio-economic status, an important confounder (χ(2) = 83.89, df = 1; p = 5.2 × 10(-20)). There was, however, a high degree of heterogeneity among populations: whereas the direction of the effect was consistent across most population samples, the effect size differed significantly among populations. It is likely that this reflects true biological heterogeneity: whether or not an effect can be observed will depend on both the variance in homozygosity in the population and the chance inheritance of individual recessive genotypes. These results predict that multiple, rare, recessive variants influence human height. Although this exploratory work focuses on height alone, the methodology developed is generally applicable to heritable quantitative traits (QT), paving the way for an investigation into inbreeding effects, and therefore genetic architecture, on a range of QT of biomedical importance.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/22829771?dopt=Abstract</style></custom1></record></records></xml>