NDLI: ALDsuite: Dense marker MALD using principal components of ancestral linkage disequilibrium

Content Provider	Springer Nature : BioMed Central
Author	Johnson, Randall C Nelson, George W Zagury, Jean-Francois Winkler, Cheryl A
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.
Related Links	https://bmcgenomdata.biomedcentral.com/counter/pdf/10.1186/s12863-015-0179-y.pdf
Ending Page	11
Page Count	11
Starting Page	1
File Format	HTM / HTML
ISSN	27306844
DOI	10.1186/s12863-015-0179-y
Journal	BMC Genomic Data
Issue Number	1
Volume Number	16
Language	English
Publisher	BioMed Central
Publisher Date	2015-03-07
Access Restriction	Open
Subject Keyword	Life Sciences Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Genetics and Population Dynamics Admixture linkage disequilibrium MALD Admixture inference
Content Type	Text
Resource Type	Article
Subject	Health Informatics Genetics
Journal Impact Factor	1.9/2023
5-Year Journal Impact Factor	1.9/2023

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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ALDsuite: Dense marker MALD using principal components of ancestral linkage disequilibrium