User:Dbeatty/Sandbox

Association Mapping (or LD Mapping )

Background
Population structure can lead to false positives. GC - Gas Chromotography

Software

 * Affeymetrix LD (C/C++)
 * FASTLINK (C - last updated 1999?)
 * Software for Linkage and Mapping
 * PyPop (Python/C)
 * Haploview (Java)
 * Software from Broad Institute (that may or may not be helpful)
 * MERLIN (Linkage, Parametric Linkage, IBD Estimation, Regression, LD, Association Analysis) (C++)
 * LAMP (Linkage and Association Modeling in Pedigrees - uses maximum likelihood model) (C++)
 * All Software from BIO 666
 * Association Mapping Software (including MCMC, HapCluster, and Block-Association Mapping)
 * SPAGeDi (Spatial Pattern Analysis of Genetic Diversity - primarily designed to characterize the spatial genetic structure of mapped individuals and/or mapped populations using genotype data of any ploidy level.)
 * TASSEL (is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.)
 * Structure (is a free software package for using multi-locus genotype data to investigate population structure.)
 * STRAT (is a companion program to structure. It is written for use in association mapping, enabling valid case-control studies even in the presence of population structure.)
 * Links to software from STATISTICAL GENETICS: Gene Mapping Through Linkage and Association textbook

Linkage Disequilibrium Measures

 * correlation coefficient delta (Hill and Robertson 1968)
 * Lewontin's D' (range constrained by allele frequencies 1964)
 * robust formulation of the population attributable risk delta
 * Yule's Q
 * Kaplan and Weir's proportional difference d under the assumption of complete disequalibrium between disease and marker loci

Maize Websites

 * Edward Buckler's Maize Lab
 * Molecular and Functional Diversity of the Maize Genome
 * MaizeGDB - Maize Genetics and Genomics Database
 * Maize Mapping Project
 * The TIGR Maize Database

Maize Markers

 * MaizeGDB - 2018 SSR

Lecture Notes

 * Hardy Weinberg Equilibrium
 * Linkage Disequalibrium
 * Haplotyping
 * Haplotype Based Association Tests
 * IBS Methods for Affected Pairs Linkage

Terms and Phrases

 * SNP (Single Nucleotide Polymorphism)
 * Linkage
 * Linkage Disequalibrium
 * Association Mapping
 * Association Mapping slides (129 pages)
 * Coalescent theory for LD mapping
 * Markov Chain Monte Carlo (MCMC)
 * Recombination
 * Haplotype
 * Hardy Weinberg principle