The impact of genotyping error on family-based analysis of quantitative traits

European Journal of Human Genetics : EJHG
Gonçalo R AbecasisLon R Cardon

Abstract

Errors in genotyping can substantially influence the power to detect linkage using affected sib-pairs, but it is not clear what effect such errors have on quantitative trait analyses. Here we use Monte Carlo simulation to examine the influence of genotyping error on multipoint vs two-point analysis, variable map density, locus effect size and allele frequency in quantitative trait linkage and association studies of sib-pairs. The analyses are conducted using variance components methods. We contrast the effects of error on quantitative trait analyses with those on the affected sib-pair design. The results indicate that genotyping error influences linkage studies of affected sib pairs more severely than studies of quantitative traits in unselected sibs. In situations of modest effect size, 5% genotyping error eliminates all supporting evidence for linkage to a true susceptibility locus in affected pairs, but may only result in a loss of 15% of linkage information in random pairs. Multipoint analysis does not suffer substantially more than two-point analysis; for moderate error rates (< 5%), multipoint analysis with error is more powerful than two-point with no error. Map density does not appear to be an important factor for linka...Continue Reading

References

Nov 1, 1992·Genomics·S E Lincoln, E S Lander
Aug 1, 1991·Proceedings of the National Academy of Sciences of the United States of America·D C ShieldsN E Morton
Apr 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·E S Lander, P Green
Sep 13, 1996·Science·N Risch, K Merikangas
Nov 5, 1997·American Journal of Human Genetics·A Kong, N J Cox
Jan 23, 1999·American Journal of Human Genetics·D W FulkerJ K Hewitt
Jan 13, 2000·American Journal of Human Genetics·G R AbecasisW O Cookson
Mar 31, 2000·American Journal of Human Genetics·J A DouglasK Lange
Jul 26, 2000·European Journal of Human Genetics : EJHG·G R AbecasisL R Cardon

❮ Previous
Next ❯

Citations

May 31, 2007·Osteoporosis International : a Journal Established As Result of Cooperation Between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA·S-F LeiH-W Deng
May 9, 2007·Cardiovascular Drugs and Therapy·James P Tsikouris, Michael J Peeters
Feb 24, 2006·European Journal of Human Genetics : EJHG·Yen-Pei Christy ChangAravinda Chakravarti
Nov 1, 2008·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Justin KennedyBogdan Paşaniuc
Aug 25, 2011·Bioinformatics·Barak MarkusDan Geiger
Dec 21, 2004·Nucleic Acids Research·Ya-Hui ChangYuh-Shan Jou
Mar 5, 2002·Genome Research·Daniel E WeeksMichael B Gorin
Sep 21, 2006·Annals of Human Genetics·K F Cheng
Nov 14, 2006·Annals of Human Genetics·K Van SteenG Molenberghs
Jun 3, 2005·The Journal of Clinical Investigation·Derek Gordon, Stephen J Finch
Apr 21, 2006·BMC Bioinformatics·Simon FiddyRichard Mott
Aug 30, 2008·BMC Genetics·Jérémie J P LebrecHans C van Houwelingen
Mar 17, 2009·BMC Genomics·Wenqing FuLi Jin
Aug 2, 2008·PLoS Genetics·Paul Scheet, Matthew Stephens
Feb 16, 2006·PLoS Medicine·Stuart H RalstonUNKNOWN GENOMOS Investigators
Apr 26, 2002·Pharmacogenomics·Roy Pettipher, Lon R Cardon
Jul 24, 2010·Yi chuan = Hereditas·Tong-Ming Yin
Apr 11, 2014·Genetic Epidemiology·Charles Y K CheungEllen M Wijsman
Mar 5, 2005·Journal of Bone and Mineral Research : the Official Journal of the American Society for Bone and Mineral Research·Hui ShenHong-Wen Deng
Apr 16, 2014·Statistics in Medicine·Chunling LiuSusan Halabi
Mar 31, 2016·Genetic Epidemiology·Olga A VsevolozhskayaQing Lu
Jan 16, 2002·American Journal of Human Genetics·Eric SobelKenneth Lange
Dec 29, 2005·American Journal of Human Genetics·Tadao ArinamiUNKNOWN Japanese Schizophrenia Sib-Pair Linkage Group
Mar 6, 2015·Genetic Epidemiology·Shuang FengGonçalo R Abecasis
Sep 12, 2007·American Journal of Human Genetics·Jared R Kohler, David J Cutler
Aug 5, 2005·American Journal of Human Genetics·Stephen SawcerUNKNOWN International Multiple Sclerosis Genetics Consortium

❮ Previous
Next ❯

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.