Genotype and SNP calling from next-generation sequencing data

R Nielsen, JS Paul, A Albrechtsen, YS Song - Nature Reviews Genetics, 2011 - nature.com
Meaningful analysis of next-generation sequencing (NGS) data, which are produced
extensively by genetics and genomics studies, relies crucially on the accurate calling of …

Genome-wide association studies for common diseases and complex traits

JN Hirschhorn, MJ Daly - Nature reviews genetics, 2005 - nature.com
Genetic factors strongly affect susceptibility to common diseases and also influence disease-
related quantitative traits. Identifying the relevant genes has been difficult, in part because …

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

H Li - Bioinformatics, 2011 - academic.oup.com
Motivation: Most existing methods for DNA sequence analysis rely on accurate sequences
or genotypes. However, in applications of the next-generation sequencing (NGS), accurate …

[HTML][HTML] Complement activation levels are related to disease stage in AMD

TJ Heesterbeek, YTE Lechanteur… - … & visual science, 2020 - iovs.arvojournals.org
Purpose: To study the levels of complement activation in different disease stages of AMD
and the influence of genetic polymorphisms in complement genes. Methods: We included …

Use R!

RGKHG Parmigiani - 2009 - Springer
This book is intended to provide fundamental statistical concepts and tools relevant to the
analysis of genetic data arising from population-based association studies. Elementary …

SNPStats: a web tool for the analysis of association studies

X Solé, E Guinó, J Valls, R Iniesta, V Moreno - Bioinformatics, 2006 - academic.oup.com
A web-based application has been designed from a genetic epidemiology point of view to
analyze association studies. Main capabilities include descriptive analysis, test for Hardy …

GenABEL: an R library for genome-wide association analysis

YS Aulchenko, S Ripke, A Isaacs, CM Van Duijn - Bioinformatics, 2007 - academic.oup.com
Here we describe an R library for genome-wide association (GWA) analysis. It implements
effective storage and handling of GWA data, fast procedures for genetic data quality control …

[PDF][PDF] Preterm birth: causes, consequences, and prevention

RE Behrman, AS Butler - 2007 - cds.psych.ucla.edu
Although individual behaviors have not been proven to have a strong influence on the risk of
preterm birth, consistent evidence suggests that a constellation of favorable lifestyle factors …

Complement factor H polymorphism and age-related macular degeneration

AO Edwards, R Ritter III, KJ Abel, A Manning… - Science, 2005 - science.org
Age-related macular degeneration (AMD) is a common, late-onset, and complex trait with
multiple risk factors. Concentrating on a region harboring a locus for AMD on 1q25-31, the …

Genome-wide association study identifies novel breast cancer susceptibility loci

DF Easton, KA Pooley, AM Dunning, PDP Pharoah… - Nature, 2007 - nature.com
Breast cancer exhibits familial aggregation, consistent with variation in genetic susceptibility
to the disease. Known susceptibility genes account for less than 25% of the familial risk of …