A comparison between similarity matrices for principal component analysis to assess population stratification in sequenced genetic data sets
Genetic similarity matrices are commonly used to assess population substructure (PS) in
genetic studies. Through simulation studies and by the application to whole-genome …
genetic studies. Through simulation studies and by the application to whole-genome …
Genome‐wide association analysis of COVID‐19 mortality risk in SARS‐CoV‐2 genomes identifies mutation in the SARS‐CoV‐2 spike protein that colocalizes with P …
SARS‐CoV‐2 mortality has been extensively studied in relation to host susceptibility. How
sequence variations in the SARS‐CoV‐2 genome affect pathogenicity is poorly understood …
sequence variations in the SARS‐CoV‐2 genome affect pathogenicity is poorly understood …
Unsupervised cluster analysis of SARS‐CoV‐2 genomes reflects its geographic progression and identifies distinct genetic subgroups of SARS‐CoV‐2 virus
Over 10,000 viral genome sequences of the SARS‐CoV‐2virus have been made readily
available during the ongoing coronavirus pandemic since the initial genome sequence of …
available during the ongoing coronavirus pandemic since the initial genome sequence of …
Limitations of principal components in quantitative genetic association models for human studies
Y Yao, A Ochoa - Elife, 2023 - elifesciences.org
Abstract Principal Component Analysis (PCA) and the Linear Mixed-effects Model (LMM),
sometimes in combination, are the most common genetic association models. Previous PCA …
sometimes in combination, are the most common genetic association models. Previous PCA …
Fast computation of the eigensystem of genomic similarity matrices
The computation of a similarity measure for genomic data is a standard tool in computational
genetics. The principal components of such matrices are routinely used to correct for biases …
genetics. The principal components of such matrices are routinely used to correct for biases …
locStra: Fast analysis of regional/global stratification in whole‐genome sequencing studies
Abstract locStra is an‐package for the analysis of regional and global population
stratification in whole‐genome sequencing (WGS) studies, where regional stratification …
stratification in whole‐genome sequencing (WGS) studies, where regional stratification …
Unsupervised outlier detection applied to SARS-CoV-2 nucleotide sequences can identify sequences of common variants and other variants of interest
As of June 2022, the GISAID database contains more than 11 million SARS-CoV-2
genomes, including several thousand nucleotide sequences for the most common variants …
genomes, including several thousand nucleotide sequences for the most common variants …
Two mutations in the SARS-CoV-2 spike protein and RNA polymerase complex are associated with COVID-19 mortality risk
Background SARS-CoV-2 mortality has been extensively studied in relation to host
susceptibility. How sequence variations in the SARS-CoV-2 genome affect pathogenicity is …
susceptibility. How sequence variations in the SARS-CoV-2 genome affect pathogenicity is …
Effect of population stratification on SNP‐by‐environment interaction
Proportions of false‐positive rates in genome‐wide association analysis are affected by
population stratification, and if it is not correctly adjusted, the statistical analysis can produce …
population stratification, and if it is not correctly adjusted, the statistical analysis can produce …
Unsupervised cluster analysis of SARS-CoV-2 genomes indicates that recent (June 2020) cases in Beijing are from a genetic subgroup that consists of mostly …
Research efforts of the ongoing SARS-CoV-2 pandemic have focused on viral genome
sequence analysis to understand how the virus spread across the globe. Here, we assess …
sequence analysis to understand how the virus spread across the globe. Here, we assess …