Analysis of pooled DNA samples on high density arrays without prior knowledge of differential hybridization rates.

Nucleic Acids Research
Stuart MacgregorGrant Montgomery

Abstract

Array based DNA pooling techniques facilitate genome-wide scale genotyping of large samples. We describe a structured analysis method for pooled data using internal replication information in large scale genotyping sets. The method takes advantage of information from single nucleotide polymorphisms (SNPs) typed in parallel on a high density array to construct a test statistic with desirable statistical properties. We utilize a general linear model to appropriately account for the structured multiple measurements available with array data. The method does not require the use of additional arrays for the estimation of unequal hybridization rates and hence scales readily to accommodate arrays with several hundred thousand SNPs. Tests for differences between cases and controls can be conducted with very few arrays. We demonstrate the method on 384 endometriosis cases and controls, typed using Affymetrix Genechip(c) HindIII 50 K arrays. For a subset of this data there were accurate measures of hybridization rates available. Assuming equal hybridization rates is shown to have a negligible effect upon the results. With a total of only six arrays, the method extracted one-third of the information (in terms of equivalent sample size) av...Continue Reading

References

Apr 9, 2002·European Journal of Human Genetics : EJHG·Ansar JawaidPak Sham
Jun 20, 2002·Human Genetics·Nadine NortonMichael C O'Donovan
Oct 10, 2002·Fertility and Sterility·Susan TreloarUNKNOWN International Endogene Study Group
Nov 5, 2002·Nature Reviews. Genetics·Pak ShamMichael Owen
Apr 11, 2003·Genetic Epidemiology·Peter M Visscher, Stéphanie Le Hellard
Feb 9, 2005·Genetic Epidemiology·Valentina MoskvinaMichael O'donovan
Feb 11, 2005·Nucleic Acids Research·Claire L SimpsonAmmar Al-Chalabi
Mar 23, 2005·Nature Methods·Hajime MatsuzakiRui Mei
Sep 10, 2005·Molecular and Cellular Probes·Anna RautanenJuha Kere
Sep 24, 2005·Twin Research and Human Genetics : the Official Journal of the International Society for Twin Studies·Zhen Zhen ZhaoGrant W Montgomery
Oct 29, 2005·Nature·UNKNOWN International HapMap Consortium

❮ Previous
Next ❯

Citations

Dec 17, 2009·Behavior Genetics·Stuart Macgregor
Jul 17, 2012·Twin Research and Human Genetics : the Official Journal of the International Society for Twin Studies·Yi LuGeorgia Chenevix-Trench
May 20, 2008·Nature Genetics·Kevin M BrownNicholas K Hayward
Aug 2, 2007·Molecular Psychiatry·S ShifmanJ Flint
Feb 16, 2008·Nucleic Acids Research·Stuart MacgregorPeter M Visscher
Oct 6, 2009·Genome Research·Jamie E CraigStuart MacGregor
Apr 17, 2008·BMC Bioinformatics·Hsin-Chou YangCathy S J Fann
Mar 21, 2007·BMC Genomics·Stefan WilkeningFederico Canzian
Feb 18, 2010·Twin Research and Human Genetics : the Official Journal of the International Society for Twin Studies·Penelope A LindPamela A F Madden
Aug 26, 2014·PloS One·Antònia FlaquerKonstantin Strauch
Nov 14, 2006·American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : the Official Publication of the International Society of Psychiatric Genetics·Qing-Rong LiuGeorge R Uhl
May 26, 2010·Animal Genetics·B L PeirisJ C M Dekkers
Nov 7, 2012·Animal Science Journal = Nihon Chikusan Gakkaihō·Yoshinobu UemotoEiji Kobayashi
Sep 18, 2012·European Neuropsychopharmacology : the Journal of the European College of Neuropsychopharmacology·Lena WeißflogAndreas Reif
Nov 26, 2013·Mitochondrion·Antònia FlaquerRuth Grychtol
Dec 1, 2017·International Journal of Obesity : Journal of the International Association for the Study of Obesity·P KotnikS Horvat
May 2, 2014·Journal of Animal Science·T G McDaneldJ W Keele
Jul 1, 2021·Molecular Ecology Resources·Jefferson F ParilAlexandre Fournier-Level

❮ Previous
Next ❯

Methods Mentioned

BETA
genotyping
chips
PCR

Software Mentioned

Affymetrix GDAS
Affymetrix

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.