Linkage disequilibrium between STRPs and SNPs across the human genome.

American Journal of Human Genetics
Bret A PayseurJames L Weber

Abstract

Patterns of linkage disequilibrium (LD) reveal the action of evolutionary processes and provide crucial information for association mapping of disease genes. Although recent studies have described the landscape of LD among single nucleotide polymorphisms (SNPs) from across the human genome, associations involving other classes of molecular variation remain poorly understood. In addition to recombination and population history, mutation rate and process are expected to shape LD. To test this idea, we measured associations between short-tandem-repeat polymorphisms (STRPs), which can mutate rapidly and recurrently, and SNPs in 721 regions across the human genome. We directly compared STRP-SNP LD with SNP-SNP LD from the same genomic regions in the human HapMap populations. The intensity of STRP-SNP LD, measured by the average of D', was reduced, consistent with the action of recurrent mutation. Nevertheless, a higher fraction of STRP-SNP pairs than SNP-SNP pairs showed significant LD, on both short (up to 50 kb) and long (cM) scales. These results reveal the substantial effects of mutational processes on LD at STRPs and provide important measures of the potential of STRPs for association mapping of disease genes.

References

Apr 12, 1994·Proceedings of the National Academy of Sciences of the United States of America·A Di RienzoN B Freimer
Aug 1, 1993·Human Molecular Genetics·J L Weber, C Wong
Jan 1, 1996·Nature Genetics·W Amos, D C Rubinstzein
Sep 13, 1996·Science·N Risch, K Merikangas
Feb 4, 1997·Proceedings of the National Academy of Sciences of the United States of America·R ChakrabortyR Deka
Jun 19, 1998·American Journal of Human Genetics·B BrinkmannB Rolf
Aug 3, 1999·Genetics·G A HuttleyS J O'Brien
Oct 16, 1999·Proceedings of the National Academy of Sciences of the United States of America·G CooperW Amos
Jun 8, 2000·Bioinformatics·G R Abecasis, W O Cookson
Sep 9, 2000·Genetics·M W Nachman, S L Crowell
Oct 19, 2000·Advances in Genetics·J L Weber, K W Broman
Nov 21, 2000·American Journal of Human Genetics·G R AbecasisW O Cookson
Dec 7, 2000·Evolution; International Journal of Organic Evolution·C Zapata
Mar 7, 2001·Human Molecular Genetics·U HoltkemperB Brinkmann
Mar 20, 2001·American Journal of Human Genetics·M StephensP Donnelly
May 11, 2001·Nature·D E ReichE S Lander
Jun 19, 2001·American Journal of Human Genetics·J K Pritchard
Jun 19, 2001·American Journal of Human Genetics·J K Pritchard, M Przeworski
Oct 5, 2001·Nature Genetics·M J DalyE S Lander
Jan 17, 2002·American Journal of Human Genetics·Qing-Yang HuangHong-Wen Deng
Jan 31, 2002·Trends in Genetics : TIG·Magnus Nordborg, Simon Tavaré
May 25, 2002·Human Molecular Genetics·Thomas G SchulzeFrancis J McMahon
May 25, 2002·Science·Stacey B GabrielDavid Altshuler
Jun 8, 2002·Nature Genetics·Augustine KongKari Stefansson
Dec 21, 2002·Science·Noah A RosenbergMarcus W Feldman
Feb 26, 2003·BMC Genomics·Nader GhebraniousJames L Weber
Jul 29, 2003·Proceedings of the National Academy of Sciences of the United States of America·John D Storey, Robert Tibshirani
Aug 26, 2003·Journal of Human Genetics·Jun Ohashi, Katsushi Tokunaga
Nov 25, 2003·American Journal of Human Genetics·Noah A RosenbergJonathan K Pritchard
Jan 22, 2004·Nature Reviews. Genetics·Krina T Zondervan, Lon R Cardon
Apr 24, 2004·Science·Gilean A T McVeanPeter Donnelly
May 22, 2004·Nature Reviews. Genetics·Hans Ellegren

❮ Previous
Next ❯

Citations

Jan 20, 2009·Human Genetics·Unda TodtChristian Kubisch
Nov 11, 2008·Human Molecular Genetics·Claire L SimpsonAmmar Al-Chalabi
Mar 18, 2009·Molecular Biology and Evolution·Bret A Payseur, Peicheng Jing
Feb 19, 2013·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Richard C DavisAldons J Lusis
Dec 8, 2015·Nature Genetics·Melissa GymrekYaniv Erlich
Jan 7, 2010·Haemophilia : the Official Journal of the World Federation of Hemophilia·E Medina-Acosta
Aug 20, 2014·Genome Research·Thomas WillemsYaniv Erlich
Nov 2, 2018·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Danilo Hottis LyraRoberto Fritsche-Neto
May 17, 2017·Proceedings of the National Academy of Sciences of the United States of America·Michael D EdgeNoah A Rosenberg
May 20, 2020·Molecular Psychiatry·Chen ZhangMing Li
Oct 26, 2018·Nature Communications·Shubham SainiMelissa Gymrek
Apr 23, 2021·Journal of Forensic Sciences·Ran LiJianye Ge

❮ 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.

Related Papers

Molecular Biology and Evolution
Gergely J Szöllosi, Imre Derényi
Proceedings of the National Academy of Sciences of the United States of America
Elhanan Borenstein, Eytan Ruppin
Proceedings of the National Academy of Sciences of the United States of America
H L Carson, R Lande
© 2022 Meta ULC. All rights reserved