Fast genome-wide pedigree quantitative trait loci analysis using MENDEL

Hua Zhou, Jin Zhou, Eric M. Sobel, Kenneth Lange

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

The linkage era left a rich legacy of pedigree samples that can be used for modern genome-wide association sequencing (GWAS) or next-generation sequencing (NGS) studies. Family designs are naturally equipped to detect rare variants, control for population stratification, and facilitate the study of parent-of-origin effects. Unfortunately, pedigree likelihoods are notoriously hard to compute, and current software for association mapping in pedigrees is prohibitively slow in processing dense marker maps. In a recent release of the comprehensive genetic analysis software MENDEL, we implemented an ultra-fast score test for association mapping with pedigree-based GWAS or NGS study data. Our implementation (a) works for random sample data, pedigree data, or a mix of both;(b) allows for covariate adjustment, including correction for population stratification;(c) accommodates both univariate and multivariate quantitative traits; and (d) allows missing values in multivariate traits. In this paper, we assess the capabilities of MENDEL on the Genetic Analysis Workshop 18 sequencing data. For instance, when jointly testing the 4 longitudinally measured diastolic blood pressure traits, it takes MENDEL less than 51 minutes on a standard laptop computer to read, quality check, and analyze a data set with 959 individuals and 8.3 million single-nucleotide polymorphisms (SNPs). Our analysis reveals association of one SNP in the q32.2 region of chromosome 1. MENDEL is freely available on http://www.genetics.ucla.edu/software.

Original languageEnglish (US)
Article numberS93
JournalBMC Proceedings
Volume8
DOIs
StatePublished - Jun 17 2014
Externally publishedYes

Fingerprint

Quantitative Trait Loci
Pedigree
Polymorphism
Nucleotides
Genes
Genome
Laptop computers
Blood pressure
Chromosomes
Software
Single Nucleotide Polymorphism
Blood Pressure
Testing
Processing
Chromosomes, Human, Pair 1
Population
Education
Genetics

ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Fast genome-wide pedigree quantitative trait loci analysis using MENDEL. / Zhou, Hua; Zhou, Jin; Sobel, Eric M.; Lange, Kenneth.

In: BMC Proceedings, Vol. 8, S93, 17.06.2014.

Research output: Contribution to journalArticle

Zhou, Hua ; Zhou, Jin ; Sobel, Eric M. ; Lange, Kenneth. / Fast genome-wide pedigree quantitative trait loci analysis using MENDEL. In: BMC Proceedings. 2014 ; Vol. 8.
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