title: ALDsuite: Dense marker MALD using principal components of ancestral linkage disequilibrium.
abstract: BACKGROUND
  Mapping by admixture linkage disequilibrium (MALD) is a whole genome gene mapping method that uses LD from extended blocks of ancestry inherited from parental populations among admixed individuals to map associations for diseases, that vary in prevalence among human populations. The extended LD queried for marker association with ancestry results in a greatly reduced number of comparisons compared to standard genome wide association studies. As ancestral population LD tends to confound the analysis of admixture LD, the earliest algorithms for MALD required marker sets sufficiently sparse to lack significant ancestral LD between markers. However current genotyping technologies routinely provide dense SNP data, which convey more information than sparse sets, if this information can be efficiently used. There are currently no software solutions that offer both local ancestry inference using dense marker data and disease association statistics.
  
  
  RESULTS
  We present here an R package, ALDsuite, which accounts for local LD using principal components of haplotypes from surrogate ancestral population data, and includes tools for quality control of data, MALD, downstream analysis of results and visualization graphics.
  
  
  CONCLUSIONS
  ALDsuite offers a fast, accurate estimation of global and local ancestry and comes bundled with the tools needed for MALD, from data quality control through mapping of and visualization of disease genes.
authors.affiliation: BSP CCR Genetics Core, Leidos Biomedical Research, Inc, Frederick National Laboratory, Frederick, MD, 21702, USA. johnsonra@mail.nih.gov.|Chaire de Bioinformatique, Conservatiore National des Arts et Metieèrs, Paris, 75003, France. johnsonra@mail.nih.gov.
authors.forename: Randall C
authors.initials: RC
authors.lastname: Johnson
authors.affiliation: BSP CCR Genetics Core, Leidos Biomedical Research, Inc, Frederick National Laboratory, Frederick, MD, 21702, USA. nelsong@mail.nih.gov.
authors.forename: George W
authors.initials: GW
authors.lastname: Nelson
authors.affiliation: Chaire de Bioinformatique, Conservatiore National des Arts et Metieèrs, Paris, 75003, France. jean-francois.zagury@cnam.fr.
authors.forename: Jean-Francois
authors.initials: JF
authors.lastname: Zagury
authors.affiliation: Basic Research Laboratory, Leidos Biomedical Research, Inc, Frederick National Laboratory, Frederick, MD, 21702, USA. winklerc@mail.nih.gov.
authors.forename: Cheryl A
authors.initials: CA
authors.lastname: Winkler
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods*; D008040:Genetic Linkage; D005828:Genetics, Population; D006801:Humans; D015810:Linkage Disequilibrium; D008390:Markov Chains; D008957:Models, Genetic; D012984:Software