@article{d1599558615e47c497e747685213e4a3,
title = "A comparison of genetic imputation methods using Long Life Family Study genotypes and sequence data with the 1000 Genome reference panel",
abstract = "This study compares methods of imputing genetic markers, given a typed GWAS scaffold from the Long Life Family Study (LLFS) and latest reference panel of 1000-Genomes. We examined two programs for pre-phasing haplotypes MACH/SHAPEIT2 and MINIMAC/IMPUTE2 for imputation. SHAPEIT2 is advantageous for haplotype pre-phasing. MINIMAC and IMPUTE2 produced similar imputation quality. We used a 4MB region on chromosome 2 of LLFS and in the Supplement, we compared methods using chromosome 19 data from the Genetic Analysis Workshop-19. IMPUTE2 had the advantage of using two references 1000G and a sequence for a subset of subjects. SHAPEIT2 and IMPUTE2 were used to finalise the full LLFS autosome imputation. In LLFS, 44% of ~80M autosomal imputed variants showed good imputation quality (info ≥ 0.30). Low imputation quality was associated with a predominantly low allele frequency in 1000-Genomes. New emerging large-scale sequences and enhanced imputation methodologies will further improve imputation quality.",
keywords = "1000 Genomes reference, FCGENE software, Genetic imputation, IMPUTE2 software, LLFS, Long life family study, MACH software, MINIMACH software, SHAPEIT2 software, Sequence reference",
author = "Kraja, {Aldi T.} and {Warwick Daw}, E. and Petra Lenzini and Lihua Wang and Lin, {Shiow J.} and Williams, {Christine A.} and Wells, {Alan B.} and Lunetta, {Kathryn L.} and Murabito, {Joanne M.} and Paola Sebastiani and Giuseppe Tosto and Sandra Barral and Minster, {Ryan L.} and Anatoly Yashin and Thomas Perls and Province, {Michael A.}",
note = "Funding Information: Joanne M. Murabito is an Associate Professor, with a medical degree from Mount Sinai School of Medicine in New York, she is Director of the Research Center at the Framingham Heart Study and she is an Associate Professor of Medicine at Boston University School of Medicine. She is the recipient of grant awards from the NIH/NIA. Her research interests include the epidemiology and genetics of longevity, healthy aging, reproductive aging. She continues to practice primary care at Boston Medical Center. Funding Information: The Long Life Family Study is supported by NIH-NIA grant U01AG023746 and DMCC: AG 023746, DK: AG 023712, CU: AG 023749, BU: AG 023755, PT: AG 02374. The GAW19 was supported by NIH grant R01 GM031575. Publisher Copyright: Copyright {\textcopyright} 2020 Inderscience Enterprises Ltd.",
year = "2020",
doi = "10.1504/IJBRA.2020.104855",
language = "English",
volume = "16",
pages = "59--84",
journal = "International Journal of Bioinformatics Research and Applications",
issn = "1744-5485",
number = "1",
}