Posts Tagged ‘bb’

Genome-wide association studies | Nature Reviews Methods Primers

January 25, 2025

g accounts for the cumulative effect of all other variants on the phenotype besides the effect of the specific variant being tested (SNP s).

Although theoretically we should consider the effect of g when testing for GWAS associations, in practice don’t think this happens in standard GWAS tools, such as PLINK and REGENIE (see below).

PLINK: https://www.cog-genomics.org/plink/2.0/assoc

REGENIE: https://www.nature.com/articles/s41588-021-00870-7#Sec10

https://www.nature.com/articles/s43586-021-00056-9

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Bioart

November 7, 2024

https://bioart.niaid.nih.gov/discover

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Quantitative GWAS & QTL studies

February 25, 2023

Primer
Published: 25 January 2023

Molecular quantitative trait loci

François Aguet, Kaur Alasoo, Yang I. Li, Alexis Battle, Hae Kyung Im, Stephen B. Montgomery & Tuuli Lappalainen

Nature Reviews Methods Primers volume 3, Article number: 4 (2023)

Related to the discussion about quantitative GWAS and QTL, this primer review (and in particular box 1) is helpful in clarifying the (non) difference between the two types of studies:

https://www.nature.com/articles/s43586-022-00188-6

The statistics behind quantitative GWAS and QTL studies is the same, the only main difference might be the multiple testing correction procedure.
In general, it’s more a nomenclature distinction, as the term “QTL” is often used specifically for molecular traits.

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