Pattern of sequence variation across 213 environmental response genes

Genome Research
Robert J LivingstonDeborah A Nickerson

Abstract

To promote the clinical and epidemiological studies that improve our understanding of human genetic susceptibility to environmental exposure, the Environmental Genome Project (EGP) has scanned 213 environmental response genes involved in DNA repair, cell cycle regulation, apoptosis, and metabolism for single nucleotide polymorphisms (SNPs). Many of these genes have been implicated by loss-of-function mutations associated with severe diseases attributable to decreased protection of genomic integrity. Therefore, the hypothesis for these studies is that individuals with functionally significant polymorphisms within these genes may be particularly susceptible to genotoxic environmental agents. On average, 20.4 kb of baseline genomic sequence or 86% of each gene, including a substantial amount of introns, all exons, and 1.3 kb upstream and downstream, were scanned for variations in the 90 samples of the Polymorphism Discovery Resource panel. The average nucleotide diversity across the 4.2 MB of these 213 genes is 6.7 x 10(-4), or one SNP every 1500 bp, when two random chromosomes are compared. The average candidate environmental response gene contains 26 PHASE inferred haplotypes, 34 common SNPs, 6.2 coding SNPs (cSNPs), and 2.5 non...Continue Reading

References

Dec 15, 1969·JAMA : the Journal of the American Medical Association·J LiebermanA S Schneider
Dec 31, 1997·Science·F S CollinsA Charkravarti
Jul 14, 1998·Nature Genetics·D A NickersonC F Sing
Jan 23, 1999·Nature Genetics·A Chakravarti
Nov 5, 1999·Human Heredity·L B JordeA W Eriksson
Dec 11, 1999·Nucleic Acids Research·E WingenderF Schacherer
Jun 3, 2000·Nature Genetics·B Ewing, P Green
Sep 13, 2000·Nucleic Acids Research·S AoufouchiC A Reynaud
Mar 7, 2001·Human Molecular Genetics·S SunyaevP Bork
Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
Mar 10, 2001·Nature·R SachidanandamUNKNOWN International SNP Map Working Group
Mar 10, 2001·Nature Genetics·L Kruglyak, D A Nickerson
Mar 20, 2001·Nature Reviews. Genetics·K Olden, S Wilson
May 11, 2001·Nature·D E ReichE S Lander
Jul 14, 2001·Science·J C StephensG F Vovis
Oct 5, 2001·Nature Genetics·G C JohnsonJ A Todd
Aug 31, 2002·Nucleic Acids Research·Vasily RamenskyShamil Sunyaev
May 20, 2003·Human Mutation·Peter D StensonDavid N Cooper
Jun 26, 2003·Nucleic Acids Research·Pauline C Ng, Steven Henikoff
Aug 5, 2003·Nature Reviews. Genetics·Jeffrey D Wall, Jonathan K Pritchard
May 1, 1964·The American Journal of Digestive Diseases·A P KLOTZ
Sep 27, 2003·British Journal of Haematology·Géraldine MathonnetDaniel Sinnett
Oct 24, 2003·American Journal of Human Genetics·Matthew Stephens, Peter Donnelly
Dec 19, 2003·Nucleic Acids Research·Alex BatemanSean R Eddy
Dec 19, 2003·American Journal of Human Genetics·Christopher S CarlsonDeborah A Nickerson
Dec 20, 2003·Nature·UNKNOWN International HapMap Consortium
Dec 31, 2003·Mutation Research·W LadigesJ Velazquez
May 22, 2004·Nature Reviews. Genetics·UNKNOWN International HapMap Consortium

❮ Previous
Next ❯

Citations

Jul 30, 2008·Genetica·Peter D Keightley, Daniel L Halligan
Jul 20, 2010·Interdisciplinary Sciences, Computational Life Sciences·C George Priya Doss, Rao Sethumadhavan
Jun 1, 2005·The Medical Clinics of North America·Kenneth Olden, Sandra L White
Apr 15, 2005·Mutation Research·Yousin Suh, Jan Vijg
May 28, 2010·Journal of Human Genetics·Yongbiao ZhangDuen-Mei Wang
Oct 19, 2006·Nature Reviews. Genetics·Eric Jorgenson, John S Witte
Dec 14, 2006·European Journal of Human Genetics : EJHG·Keyue Ding, Iftikhar J Kullo
Jun 15, 2007·European Journal of Human Genetics : EJHG·Zongli XuJack A Taylor
Jun 5, 2008·Proceedings of the National Academy of Sciences of the United States of America·Nicholas J MariniJasper Rine
Oct 23, 2012·The Journal of Biological Chemistry·Selena S SchattauerCharles Chavkin
Sep 20, 2012·Human Molecular Genetics·Shamil R Sunyaev
Mar 18, 2009·Molecular Biology and Evolution·Bret A Payseur, Peicheng Jing
May 8, 2009·Molecular Biology and Evolution·Jeffrey D WallVincent Plagnol
Jun 8, 2010·Molecular Biology and Evolution·Kazuhiko Ohshima, Kumiko Igarashi
Jun 19, 2010·Molecular Biology and Evolution·Anders AlbrechtsenRasmus Nielsen
Nov 10, 2010·Molecular Biology and Evolution·Athanasios KousathanasPeter D Keightley
Mar 4, 2011·Molecular Biology and Evolution·Jeffrey D WallPaul Marjoram
May 22, 2008·Genome Research·Jeffrey D WallMichael F Hammer
Nov 26, 2008·Genome Research·Gary K ChenJeffrey D Wall
Dec 25, 2009·Genome Research·David LomelinNeil Risch
Oct 28, 2005·Genome Research·Andrew G ClarkRasmus Nielsen
Oct 28, 2005·Genome Research·Christopher S CarlsonDeborah A Nickerson
Dec 22, 2005·Genome Research·Marta SoldevilaJaume Bertranpetit
Jun 3, 2011·Journal of Medical Genetics·Wei-Yu LinAngela Cox
Mar 30, 2007·Annual Review of Biomedical Engineering·Sobin Kim, Ashish Misra
Aug 30, 2005·Annual Review of Genomics and Human Genetics·Dana C CrawfordDeborah A Nickerson
Jul 11, 2006·Annual Review of Genomics and Human Genetics·Pauline C Ng, Steven Henikoff
Jan 14, 2009·Cancer Prevention Research·David J CastroDavid E Williams
Apr 25, 2009·Journal of Biomedical Science·C George Priya Doss, Rao Sethumadhavan
Feb 8, 2008·BMC Genetics·Shehnaz K HussainStephen M Schwartz
Nov 6, 2009·BMC Genomics·Alexander ChurbanovChindo Hicks
Sep 20, 2006·BMC Genomics·Erwin TantosoKuo-Bin Li
Jun 29, 2007·Pediatric Research·Aaron HamvasF Sessions Cole

❮ Previous
Next ❯

Related Concepts

Related Feeds

Apoptosis

Apoptosis is a specific process that leads to programmed cell death through the activation of an evolutionary conserved intracellular pathway leading to pathognomic cellular changes distinct from cellular necrosis

Related Papers

Annual Review of Genomics and Human Genetics
Dana C CrawfordDeborah A Nickerson
Mechanisms of Ageing and Development
Julie A SchneiderJ Claiborne Stephens
Nature
International HapMap Consortium
© 2021 Meta ULC. All rights reserved