scholarly journals Approximately independent linkage disequilibrium blocks in human populations

2015 ◽  
Author(s):  
Tomaz Berisa ◽  
Joseph K. Pickrell
Keyword(s):  
Linkage Disequilibrium ◽  
Human Genome ◽  
Association Studies ◽  
Automated Analysis ◽  
Genome Wide Association ◽  
Human Populations ◽  
Genome Wide Association Studies ◽  
Multiple Genome ◽  
Genome Wide

We present a method to identify approximately independent blocks of linkage disequilibrium (LD) in the human genome. These blocks enable automated analysis of multiple genome-wide association studies.

scholarly journals A New Diversity Panel for Winter Rapeseed (Brassica napus L.) Genome-Wide Association Studies

Agronomy ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 2006
Author(s):  
David P. Horvath ◽  
Michael Stamm ◽  
Zahirul I. Talukder ◽  
Jason Fiedler ◽  
Aidan P. Horvath ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Brassica Napus ◽  
Association Studies ◽  
Decay Rates ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
High Quality ◽  
Brassica Napus L ◽  
Genome Wide ◽  
Quality Markers

A diverse population (429 member) of canola (Brassica napus L.) consisting primarily of winter biotypes was assembled and used in genome-wide association studies. Genotype by sequencing analysis of the population identified and mapped 290,972 high-quality markers ranging from 18.5 to 82.4% missing markers per line and an average of 36.8%. After interpolation, 251,575 high-quality markers remained. After filtering for markers with low minor allele counts (count > 5), we were left with 190,375 markers. The average distance between these markers is 4463 bases with a median of 69 and a range from 1 to 281,248 bases. The heterozygosity among the imputed population ranges from 0.9 to 11.0% with an average of 5.4%. The filtered and imputed dataset was used to determine population structure and kinship, which indicated that the population had minimal structure with the best K value of 2–3. These results also indicated that the majority of the population has substantial sequence from a single population with sub-clusters of, and admixtures with, a very small number of other populations. Analysis of chromosomal linkage disequilibrium decay ranged from ~7 Kb for chromosome A01 to ~68 Kb for chromosome C01. Local linkage decay rates determined for all 500 kb windows with a 10kb sliding step indicated a wide range of linkage disequilibrium decay rates, indicating numerous crossover hotspots within this population, and provide a resource for determining the likely limits of linkage disequilibrium from any given marker in which to identify candidate genes. This population and the resources provided here should serve as helpful tools for investigating genetics in winter canola.

scholarly journals The mouse QTL map helps interpret human genome-wide association studies for HDL cholesterol

2011 ◽  
Vol 52 (6) ◽  
pp. 1139-1149 ◽  
Author(s):  
Magalie S. Leduc ◽  
Malcolm Lyons ◽  
Katayoon Darvishi ◽  
Kenneth Walsh ◽  
Susan Sheehan ◽  
...  
Keyword(s):  
Human Genome ◽  
Association Studies ◽  
Hdl Cholesterol ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Qtl Map
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