title: When Does Choice of Accuracy Measure Alter Imputation Accuracy Assessments?
abstract: Imputation, the process of inferring genotypes for untyped variants, is used to identify and refine genetic association findings. Inaccuracies in imputed data can distort the observed association between variants and a disease. Many statistics are used to assess accuracy; some compare imputed to genotyped data and others are calculated without reference to true genotypes. Prior work has shown that the Imputation Quality Score (IQS), which is based on Cohen's kappa statistic and compares imputed genotype probabilities to true genotypes, appropriately adjusts for chance agreement; however, it is not commonly used. To identify differences in accuracy assessment, we compared IQS with concordance rate, squared correlation, and accuracy measures built into imputation programs. Genotypes from the 1000 Genomes reference populations (AFR N = 246 and EUR N = 379) were masked to match the typed single nucleotide polymorphism (SNP) coverage of several SNP arrays and were imputed with BEAGLE 3.3.2 and IMPUTE2 in regions associated with smoking behaviors. Additional masking and imputation was conducted for sequenced subjects from the Collaborative Genetic Study of Nicotine Dependence and the Genetic Study of Nicotine Dependence in African Americans (N = 1,481 African Americans and N = 1,480 European Americans). Our results offer further evidence that concordance rate inflates accuracy estimates, particularly for rare and low frequency variants. For common variants, squared correlation, BEAGLE R2, IMPUTE2 INFO, and IQS produce similar assessments of imputation accuracy. However, for rare and low frequency variants, compared to IQS, the other statistics tend to be more liberal in their assessment of accuracy. IQS is important to consider when evaluating imputation accuracy, particularly for rare and low frequency variants.
authors.affiliation: Department of Genetics, Washington University, St. Louis, Missouri, United States of America.
authors.forename: Shelina
authors.initials: S
authors.lastname: Ramnarine
authors.affiliation: Chinese Academy of Sciences, Key Laboratory of Brain Function and Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
authors.forename: Juan
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Department of Psychiatry, Washington University, St. Louis, Missouri, United States of America.
authors.forename: Li-Shiun
authors.initials: LS
authors.lastname: Chen
authors.affiliation: Department of Medicine, Washington University, St. Louis, Missouri, United States of America.
authors.forename: Robert
authors.initials: R
authors.lastname: Culverhouse
authors.affiliation: Department of Genetics, Washington University, St. Louis, Missouri, United States of America.
authors.forename: Weimin
authors.initials: W
authors.lastname: Duan
authors.affiliation: Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division, Research Triangle Institute (RTI) International, Research Triangle Park, North Carolina, United States of America.
authors.forename: Dana B
authors.initials: DB
authors.lastname: Hancock
authors.affiliation: Department of Psychiatry, Washington University, St. Louis, Missouri, United States of America.
authors.forename: Sarah M
authors.initials: SM
authors.lastname: Hartz
authors.affiliation: Fellow Program and Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, North Carolina, United States of America.
authors.forename: Eric O
authors.initials: EO
authors.lastname: Johnson
authors.affiliation: Department of Psychiatry, Washington University, St. Louis, Missouri, United States of America.
authors.forename: Emily
authors.initials: E
authors.lastname: Olfson
authors.affiliation: Genometrics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States of America.
authors.forename: Tae-Hwi
authors.initials: TH
authors.lastname: Schwantes-An
authors.affiliation: Department of Genetics, Washington University, St. Louis, Missouri, United States of America.
authors.forename: Nancy L
authors.initials: NL
authors.lastname: Saccone
mesh_terms: D000328:Adult; D002755:Choice Behavior; D005787:Gene Frequency; D023281:Genomics / Q000379:methods*; D005838:Genotype; D006801:Humans; D015810:Linkage Disequilibrium; D011336:Probability; D011786:Quality Control; D014029:Tobacco Use Disorder / Q000235:genetics