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The practicing statistician must also choose whether to conduct parametric or nonparametric tests. Because of the complexities involved, Mendel offers users several analysis options. The different options are tied together by shared input and output conventions and a shared language for defining models. Mendel also features new statistics and theory found in no other genetics software. The most important innovations include: association testing by penetrance estimation, expansion of matched\u2010pair designs to permutation unit designs, and a rigorous implementation of the measured genotype approach for quantitative trait loci. This report explains how Mendel imputes allele counts and conducts both asymptotic and permutation tests in the measured genotype framework. <jats:italic>Genet. Epidemiol<\/jats:italic>. \u00a9 2005 Wiley\u2010Liss, Inc.<\/jats:p>","DOI":"10.1002\/gepi.20073","type":"journal-article","created":{"date-parts":[[2005,4,15]],"date-time":"2005-04-15T22:49:38Z","timestamp":1113605378000},"page":"36-50","source":"Crossref","is-referenced-by-count":50,"title":["Association testing with Mendel"],"prefix":"10.1002","volume":"29","author":[{"given":"Kenneth","family":"Lange","sequence":"first","affiliation":[]},{"given":"Janet S.","family":"Sinsheimer","sequence":"additional","affiliation":[]},{"given":"Eric","family":"Sobel","sequence":"additional","affiliation":[]}],"member":"311","published-online":{"date-parts":[[2005,4,15]]},"reference":[{"key":"e_1_2_1_2_1","first-page":"22","article-title":"Allele frequency estimation from data on relatives","volume":"48","author":"Boehnke M","year":"1991","journal-title":"Amer J Hum Genet"},{"key":"e_1_2_1_3_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-1809.1986.tb01037.x"},{"key":"e_1_2_1_4_1","first-page":"324","article-title":"Rank analysis of incomplete block designs","volume":"39","author":"Bradley RA","year":"1952","journal-title":"Biometrika"},{"key":"e_1_2_1_5_1","doi-asserted-by":"publisher","DOI":"10.1086\/428628"},{"key":"e_1_2_1_6_1","doi-asserted-by":"publisher","DOI":"10.1136\/bmj.1.5122.603"},{"key":"e_1_2_1_7_1","first-page":"811","article-title":"A note on the application of the transmission disequilibrium test when a parent is missing","volume":"56","author":"Curtis D","year":"1995","journal-title":"Am J Hum Genet"},{"key":"e_1_2_1_8_1","first-page":"663","article-title":"Heritability of quantitative variation at the group\u2010specific component (Gc) locus","volume":"36","author":"Daiger SP","year":"1984","journal-title":"Am J Hum Genet"},{"key":"e_1_2_1_9_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-46808-7_28"},{"key":"e_1_2_1_10_1","doi-asserted-by":"publisher","DOI":"10.1159\/000152448"},{"key":"e_1_2_1_11_1","doi-asserted-by":"publisher","DOI":"10.1002\/ajmg.1320570319"},{"key":"e_1_2_1_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/sj.ejhg.5201301"},{"key":"e_1_2_1_13_1","doi-asserted-by":"publisher","DOI":"10.1002\/gepi.1370040304"},{"key":"e_1_2_1_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/0010-4809(82)90064-7"},{"key":"e_1_2_1_15_1","doi-asserted-by":"publisher","DOI":"10.1002\/gepi.20000"},{"key":"e_1_2_1_16_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-1809.1982.tb01588.x"},{"key":"e_1_2_1_17_1","first-page":"264","volume-title":"Biostatistical Genetics and genetic epidemiology","author":"Horvath S","year":"2002"},{"key":"e_1_2_1_18_1","doi-asserted-by":"publisher","DOI":"10.1590\/S0004-282X2001000100004"},{"key":"e_1_2_1_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/7.11.1745"},{"key":"e_1_2_1_20_1","doi-asserted-by":"publisher","DOI":"10.1137\/1035004"},{"key":"e_1_2_1_21_1","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.1998.5.1"},{"key":"e_1_2_1_22_1","first-page":"1347","article-title":"Parametric and nonparametric linkage analysis: a unified multipoint approach","volume":"58","author":"Kruglyak L","year":"1996","journal-title":"Am J Hum Genet"},{"key":"e_1_2_1_23_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.84.8.2363"},{"key":"e_1_2_1_24_1","first-page":"A1886","article-title":"Mendel version 4.0: A complete package for the exact genetic analysis of discrete traits in pedigree and population data sets","volume":"69","author":"Lange K","year":"2001","journal-title":"Am J Hum Genet"},{"key":"e_1_2_1_25_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-0-387-21750-5"},{"key":"e_1_2_1_26_1","doi-asserted-by":"publisher","DOI":"10.1159\/000152714"},{"key":"e_1_2_1_27_1","doi-asserted-by":"publisher","DOI":"10.1002\/gepi.1370050611"},{"key":"e_1_2_1_28_1","first-page":"881","article-title":"Robust statistical modeling using the t distribution","volume":"84","author":"Lange K","year":"1989","journal-title":"JASA"},{"key":"e_1_2_1_29_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-1809.1980.tb00956.x"},{"key":"e_1_2_1_30_1","first-page":"588","article-title":"Estimation of the recombination fraction in human pedigrees: efficient computation of the likelihood for human linkage studies","volume":"26","author":"Ott J","year":"1974","journal-title":"Am J Hum Genet"},{"key":"e_1_2_1_31_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.273.5281.1516"},{"key":"e_1_2_1_32_1","doi-asserted-by":"publisher","DOI":"10.1016\/0198-8859(81)90148-8"},{"key":"e_1_2_1_33_1","unstructured":"S.A.G.E.2001.Statistical Analysis for Genetic Epidemiology S.A.G.E. 4.1. 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