Testing for Hardy-Weinberg equilibrium in samples with related individuals

Genetics
Catherine BourgainM S McPeek

Abstract

When the classical chi(2) goodness-of-fit test for Hardy-Weinberg (HW) equilibrium is used on samples with related individuals, the type I error can be greatly inflated. In particular the test is inappropriate in population isolates where the individuals are related through multiple lines of descent. In this article, we propose a new test for HW (the QL-HW test) suitable for any sample with related individuals, including large inbred pedigrees, provided that their genealogy is known. Performed conditional on the pedigree structure, the QL-HW test detects departures from HW that are not due to the genealogy. Because the computation of the QL-HW test becomes intractable for very polymorphic loci in large inbred pedigrees, a simpler alternative, the GCC-HW test, is also proposed. The statistical properties of the QL-HW and GCC-HW tests are studied through simulations considering a sample of independent nuclear families, a sample of extended outbred genealogies, and samples from the Hutterite population, a North American highly inbred isolate. Finally, the method is used to test a set of 143 biallelic markers spanning 82 genes in this latter population.

References

Aug 1, 1995·Genetics·F Rousset, M Raymond
Jun 5, 1995·American Journal of Medical Genetics·M L Katz, A N Siakotos
Jun 23, 1998·American Journal of Human Genetics·J R O'Connell, D E Weeks
Dec 29, 1998·American Journal of Human Genetics·D M NielsenB S Weir
Sep 14, 1999·Molecular Psychiatry·D GonenE H Cook
Mar 21, 2000·American Journal of Human Genetics·M AbneyC Ober
Jan 16, 2002·American Journal of Human Genetics·Julie A DouglasMichael Boehnke
Jan 16, 2002·American Journal of Human Genetics·Eric SobelKenneth Lange
Jan 17, 2002·Genetic Epidemiology·L AlmasyJ Blangero
Oct 29, 2002·Diabetes·Daniel B MirelJanelle A Noble
Aug 21, 2003·American Journal of Human Genetics·Catherine BourgainMary Sara McPeek
Jun 8, 2004·Biometrics·Mary Sara McPeekCarole Ober

❮ Previous
Next ❯

Citations

Sep 29, 2007·Human Genetics·Irene Gallego Romero, Carole Ober
Apr 16, 2009·European Journal of Human Genetics : EJHG·Jin J ZhouJanet S Sinsheimer
May 26, 2011·European Journal of Human Genetics : EJHG·Jessica X ChongCarole Ober
Apr 12, 2008·The New England Journal of Medicine·Carole OberGeoffrey L Chupp
Jun 6, 2009·Annals of Human Genetics·Dewei SheZhaohai Li
May 4, 2007·Human Heredity·Vincenza ColonnaM Graziella Persico
Jan 19, 2013·Human Heredity·Daniel J SchaidGregory D Jenkins
Mar 20, 2010·American Journal of Epidemiology·Ramal MoonesingheUNKNOWN CDC/NCI NHANES III Genomics Working Group
Jan 16, 2016·Scientific Reports·Yi-Shin ChenWei Pan
Sep 9, 2008·Schizophrenia Research·Jiajun ShiJames B Potash
Aug 3, 2013·American Journal of Human Biology : the Official Journal of the Human Biology Council·Stella AslibekyanHemant K Tiwari
Feb 6, 2007·Journal of Fluency Disorders·Jacqueline K Wittke-ThompsonNancy J Cox
Feb 6, 2009·Genetic Epidemiology·Jinbo ChenPeter Kraft
Mar 28, 2008·European Journal of Haematology·K Sigvard OlssonRuma R Chowdhury
Jul 31, 2010·Molecular Ecology·Ivana JankovicNoah A Rosenberg
Aug 22, 2008·Schizophrenia Research·Jiajun ShiChunyu Liu
Jan 1, 2015·Calcified Tissue International·Allison L KuipersJoseph M Zmuda
Aug 13, 2013·The Journal of Allergy and Clinical Immunology·Tsung-Chieh YaoCarole Ober
Sep 18, 2012·American Journal of Human Genetics·Jessica X ChongCarole Ober
May 29, 2012·American Journal of Human Genetics·Gülüm KosovaCarole Ober
Mar 18, 2021·Biometrics·Lin Zhang, Lei Sun

❮ 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.