GM06990

GM06990 LCL from B-Lymphocyte

Description:

CEPH/UTAH PEDIGREE 1331
CYTOCHROME P450, SUBFAMILY IIC, POLYPEPTIDE 9; CYP2C9
HUMAN VARIATION PANEL - EUROPEAN WHITE PANEL OF 8
HUMAN VARIATION PANEL - EUROPEAN WHITE PANEL OF 16
HUMAN VARIATION PANEL - EUROPEAN WHITE PANEL OF 24
SNP500 PANEL

Affected:

No Data

Sex:

Female

Age:

No Data

Overview

Repository

NIGMS Human Genetic Cell Repository

Subcollection

CEPH
Repository Linkage Families
Pharmacogenetics

Biopsy Source

Peripheral vein

Cell Type

B-Lymphocyte

Tissue Type

Blood

Transformant

Epstein-Barr Virus

Sample Source

LCL from B-Lymphocyte

Race

White

Ethnicity

UTAH/MORMON

Family Member

Relation to Proband

mother

Confirmation

Clinical summary/Case history

Species

Homo sapiens

Common Name

Human

Remarks

Mother; 46,XX; donor subject is heterozygous for a C>T change at nucleotide 416 (416C>T) in exon 3 of the CYP2C9 gene (CYP2C9*2) which results in a substitution of cysteine for arginine at codon 144 [Arg144Cys (R144C)]

Characterizations

IDENTIFICATION OF SPECIES OF ORIGIN

Species of Origin Confirmed by Nucleoside Phosphorylase, Glucose-6-Phosphate Dehydrogenase, and Lactate Dehydrogenase Isoenzyme Electrophoresis and by Chromosome Analysis

GENE MAPPING & DOSAGE STUDIES - Y CHROMOSOME

PCR analysis of DNA from this cell culture gave a negative result with a primer for Yq11, DYS227.

Phenotypic Data

Remarks

Publications

Joshi I, DeRycke J, Palmowski M, LeSuer R, Feng W, Genome-wide mapping of DNA double-strand breaks from eukaryotic cell cultures using Break-seq STAR protocols2:100554 2021

PubMed ID: 34189468

Chakraborty A, Jenjaroenpun P, Li J, El Hilali S, McCulley A, Haarer B, Hoffman EA, Belak A, Thorland A, Hehnly H, Schildkraut C, Chen CL, Kuznetsov VA, Feng W, Replication Stress Induces Global Chromosome Breakage in the Fragile X Genome Cell reports32:108179 2020

PubMed ID: 32966779

Gao GF, Parker JS, Reynolds SM, Silva TC, Wang LB, Zhou W, Akbani R, Bailey M, Balu S, Berman BP, Brooks D, Chen H, Cherniack AD, Demchok JA, Ding L, Felau I, Gaheen S, Gerhard DS, Heiman DI, Hernandez KM, Hoadley KA, Jayasinghe R, Kemal A, Knijnenburg TA, Laird PW, Mensah MKA, Mungall AJ, Robertson AG, Shen H, Tarnuzzer R, Wang Z, Wyczalkowski M, Yang L, Zenklusen JC, Zhang Z, Genomic Data Analysis Network Z, Liang H, Noble MS, Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data Cell systems9:24-34.e10 2019

PubMed ID: 31344359

Schaefer N, Li X, Seibold MA, Jarjour NN, Denlinger LC, Castro M, Coverstone AM, Teague WG, Boomer J, Bleecker ER, Meyers DA, Moore WC, Hawkins GA, Fahy J, Phillips BR, Mauger DT, Dakhama A, Gellatly S, Pavelka N, Berman R, Di YP, Wenzel SE, Chu HW, The effect of BPIFA1/SPLUNC1 genetic variation on its expression and function in asthmatic airway epithelium JCI insight4:24-34.e10 2019

PubMed ID: 30996135

Zajac GJM, Fritsche LG, Weinstock JS, Dagenais SL, Lyons RH, Brummett CM, Abecasis GR, Estimation of DNA contamination and its sources in genotyped samples Genetic epidemiology4:24-34.e10 2019

PubMed ID: 31452258

Zhou W1, Triche TJ Jr1, Laird PW1, Shen H1., SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions Nucleic Acids Research4:24-34.e10 2018

PubMed ID: 30085201

Fairbanks DJ, Fairbanks AD, Ogden TH, Parker GJ, Maughan PJ, NANOGP8: evolution of a human-specific retro-oncogene G3 (Bethesda, Md)2:1447-57 2012

PubMed ID: 23173096

ENCODE Project Consortium , Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J, Kaul R, Khatun J, Lajoie BR, Landt SG, Lee BK, Pauli F, Rosenbloom KR, Sabo P, Safi A, Sanyal A, Shoresh N, Simon JM, Song L, Trinklein ND, Altshuler RC, Birney E, Brown JB, Cheng C, Djebali S, Dong X, Dunham I, Ernst J, Furey TS, Gerstein M, Giardine B, Greven M, Hardison RC, Harris RS, Herrero J, Hoffman MM, Iyer S, Kelllis M, Khatun J, Kheradpour P, Kundaje A, Lassman T, Li Q, Lin X, Marinov GK, Merkel A, Mortazavi A, Parker SC, Reddy TE, Rozowsky J, Schlesinger F, Thurman RE, Wang J, Ward LD, Whitfield TW, Wilder SP, Wu W, Xi HS, Yip KY, Zhuang J, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M, Pazin MJ, Lowdon RF, Dillon LA, Adams LB, Kelly CJ, Zhang J, Wexler JR, Green ED, Good PJ, Feingold EA, Bernstein BE, Birney E, Crawford GE, Dekker J, Elinitski L, Farnham PJ, Gerstein M, Giddings MC, Gingeras TR, Green ED, Guigó R, Hardison RC, Hubbard TJ, Kellis M, Kent WJ, Lieb JD, Margulies EH, Myers RM, Snyder M, Starnatoyannopoulos JA, Tennebaum SA, Weng Z, White KP, Wold B, Khatun J, Yu Y, Wrobel J, Risk BA, Gunawardena HP, Kuiper HC, Maier CW, Xie L, Chen X, Giddings MC, Bernstein BE, Epstein CB, Shoresh N, Ernst J, Kheradpour P, Mikkelsen TS, Gillespie S, Goren A, Ram O, Zhang X, Wang L, Issner R, Coyne MJ, Durham T, Ku M, Truong T, Ward LD, Altshuler RC, Eaton ML, Kellis M, Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Batut P, Bell I, Bell K, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena HP, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Li G, Luo OJ, Park E, Preall JB, Presaud K, Ribeca P, Risk BA, Robyr D, Ruan X, Sammeth M, Sandu KS, Schaeffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Hayashizaki Y, Harrow J, Gerstein M, Hubbard TJ, Reymond A, Antonarakis SE, Hannon GJ, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR, Rosenbloom KR, Sloan CA, Learned K, Malladi VS, Wong MC, Barber GP, Cline MS, Dreszer TR, Heitner SG, Karolchik D, Kent WJ, Kirkup VM, Meyer LR, Long JC, Maddren M, Raney BJ, Furey TS, Song L, Grasfeder LL, Giresi PG, Lee BK, Battenhouse A, Sheffield NC, Simon JM, Showers KA, Safi A, London D, Bhinge AA, Shestak C, Schaner MR, Kim SK, Zhang ZZ, Mieczkowski PA, Mieczkowska JO, Liu Z, McDaniell RM, Ni Y, Rashid NU, Kim MJ, Adar S, Zhang Z, Wang T, Winter D, Keefe D, Birney E, Iyer VR, Lieb JD, Crawford GE, Li G, Sandhu KS, Zheng M, Wang P, Luo OJ, Shahab A, Fullwood MJ, Ruan X, Ruan Y, Myers RM, Pauli F, Williams BA, Gertz J, Marinov GK, Reddy TE, Vielmetter J, Partridge EC, Trout D, Varley KE, Gasper C, Bansal A, Pepke S, Jain P, Amrhein H, Bowling KM, Anaya M, Cross MK, King B, Muratet MA, Antoshechkin I, Newberry KM, McCue K, Nesmith AS, Fisher-Aylor KI, Pusey B, DeSalvo G, Parker SL, Balasubramanian S, Davis NS, Meadows SK, Eggleston T, Gunter C, Newberry JS, Levy SE, Absher DM, Mortazavi A, Wong WH, Wold B, Blow MJ, Visel A, Pennachio LA, Elnitski L, Margulies EH, Parker SC, Petrykowska HM, Abyzov A, Aken B, Barrell D, Barson G, Berry A, Bignell A, Boychenko V, Bussotti G, Chrast J, Davidson C, Derrien T, Despacio-Reyes G, Diekhans M, Ezkurdia I, Frankish A, Gilbert J, Gonzalez JM, Griffiths E, Harte R, Hendrix DA, Howald C, Hunt T, Jungreis I, Kay M, Khurana E, Kokocinski F, Leng J, Lin MF, Loveland J, Lu Z, Manthravadi D, Mariotti M, Mudge J, Mukherjee G, Notredame C, Pei B, Rodriguez JM, Saunders G, Sboner A, Searle S, Sisu C, Snow C, Steward C, Tanzer A, Tapanan E, Tress ML, van Baren MJ, Walters N, Washieti S, Wilming L, Zadissa A, Zhengdong Z, Brent M, Haussler D, Kellis M, Valencia A, Gerstein M, Raymond A, Guigó R, Harrow J, Hubbard TJ, Landt SG, Frietze S, Abyzov A, Addleman N, Alexander RP, Auerbach RK, Balasubramanian S, Bettinger K, Bhardwaj N, Boyle AP, Cao AR, Cayting P, Charos A, Cheng Y, Cheng C, Eastman C, Euskirchen G, Fleming JD, Grubert F, Habegger L, Hariharan M, Harmanci A, Iyenger S, Jin VX, Karczewski KJ, Kasowski M, Lacroute P, Lam H, Larnarre-Vincent N, Leng J, Lian J, Lindahl-Allen M, Min R, Miotto B, Monahan H, Moqtaderi Z, Mu XJ, O'Geen H, Ouyang Z, Patacsil D, Pei B, Raha D, Ramirez L, Reed B, Rozowsky J, Sboner A, Shi M, Sisu C, Slifer T, Witt H, Wu L, Xu X, Yan KK, Yang X, Yip KY, Zhang Z, Struhl K, Weissman SM, Gerstein M, Farnham PJ, Snyder M, Tenebaum SA, Penalva LO, Doyle F, Karmakar S, Landt SG, Bhanvadia RR, Choudhury A, Domanus M, Ma L, Moran J, Patacsil D, Slifer T, Victorsen A, Yang X, Snyder M, White KP, Auer T, Centarin L, Eichenlaub M, Gruhl F, Heerman S, Hoeckendorf B, Inoue D, Kellner T, Kirchmaier S, Mueller C, Reinhardt R, Schertel L, Schneider S, Sinn R, Wittbrodt B, Wittbrodt J, Weng Z, Whitfield TW, Wang J, Collins PJ, Aldred SF, Trinklein ND, Partridge EC, Myers RM, Dekker J, Jain G, Lajoie BR, Sanyal A, Balasundaram G, Bates DL, Byron R, Canfield TK, Diegel MJ, Dunn D, Ebersol AK, Ebersol AK, Frum T, Garg K, Gist E, Hansen RS, Boatman L, Haugen E, Humbert R, Jain G, Johnson AK, Johnson EM, Kutyavin TM, Lajoie BR, Lee K, Lotakis D, Maurano MT, Neph SJ, Neri FV, Nguyen ED, Qu H, Reynolds AP, Roach V, Rynes E, Sabo P, Sanchez ME, Sandstrom RS, Sanyal A, Shafer AO, Stergachis AB, Thomas S, Thurman RE, Vernot B, Vierstra J, Vong S, Wang H, Weaver MA, Yan Y, Zhang M, Akey JA, Bender M, Dorschner MO, Groudine M, MacCoss MJ, Navas P, Stamatoyannopoulos G, Kaul R, Dekker J, Stamatoyannopoulos JA, Dunham I, Beal K, Brazma A, Flicek P, Herrero J, Johnson N, Keefe D, Lukk M, Luscombe NM, Sobral D, Vaquerizas JM, Wilder SP, Batzoglou S, Sidow A, Hussami N, Kyriazopoulou-Panagiotopoulou S, Libbrecht MW, Schaub MA, Kundaje A, Hardison RC, Miller W, Giardine B, Harris RS, Wu W, Bickel PJ, Banfai B, Boley NP, Brown JB, Huang H, Li Q, Li JJ, Noble WS, Bilmes JA, Buske OJ, Hoffman MM, Sahu AO, Kharchenko PV, Park PJ, Baker D, Taylor J, Weng Z, Iyer S, Dong X, Greven M, Lin X, Wang J, Xi HS, Zhuang J, Gerstein M, Alexander RP, Balasubramanian S, Cheng C, Harmanci A, Lochovsky L, Min R, Mu XJ, Rozowsky J, Yan KK, Yip KY, Birney E, An integrated encyclopedia of DNA elements in the human genome Nature489:57-74 2011

PubMed ID: 22955616

Lee BK, Bhinge AA, Iyer VR, Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis Nucleic acids research489:57-74 2011

PubMed ID: 21247883

Wang X, Abudu A, Son S, Dang Y, Venta PJ, Zheng YH, Analysis of Human APOBEC3H Haplotypes and Anti-Human Immunodeficiency Virus Type-1 Activity Journal of virology85(7):3142-52 2011

PubMed ID: 21270145

Docherty SJ, Davis OS, Haworth CM, Plomin R, Mill J, DNA methylation profiling using bisulfite-based epityping of pooled genomic DNA Methods (San Diego, Calif)52:255-8 2010

PubMed ID: 20599507

Gheldof N, Smith EM, Tabuchi TM, Koch CM, Dunham I, Stamatoyannopoulos JA, Dekker J, Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene Nucleic acids research38:4325-36 2010

PubMed ID: 20360044

Robyr D, Friedli M, Gehrig C, Arcangeli M, Marin M, Guipponi M, Farinelli L, Barde I, Verp S, Trono D, Antonarakis SE, Chromosome conformation capture uncovers potential genome-wide interactions between human conserved non-coding sequences PloS one6:e17634 2010

PubMed ID: 21408183

Watson RG, Muhale F, Thorne LB, Yu J, O'Neil BH, Hoskins JM, Meyers MO, Deal AM, Ibrahim JG, Hudson ML, Walko CM, McLeod HL, Auman JT, Amplification of thymidylate synthetase in metastatic colorectal cancer patients pretreated with 5-fluorouracil-based chemotherapy European journal of cancer (Oxford, England : 1990)46:3358-64 2010

PubMed ID: 20727737

Brunson T, Wang Q, Chambers I, Song Q, A copy number variation in human NCF1 and its pseudogenes BMC genetics11:13 2009

PubMed ID: 20178640

Lambert CA, Connelly CF, Madeoy J, Qiu R, Olson MV, Akey JM, Highly punctuated patterns of population structure on the X chromosome and implications for African evolutionary history American journal of human genetics86:34-44 2009

PubMed ID: 20085712

Shaw, D.M., Sutherland, A.M., Russell, J.A., Lichtenstein, S.V., and Walley, K.R., Novel polymorphism of interleukin-18 associated with greater inflammation after cardiac surgery Critical Care13:R9 2009

PubMed ID: 19178691

Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B, Histone modifications at human enhancers reflect global cell-type-specific gene expression Nature13:R9 2008

PubMed ID: 19295514

Li L, Fridley B, Kalari K, Jenkins G, Batzler A, Safgren S, Hildebrandt M, Ames M, Schaid D, Wang L, Gemcitabine and Cytosine Arabinoside Cytotoxicity: Association with Lymphoblastoid Cell Expression Cancer research68:7050-7058 2008

PubMed ID: 18757419

Lian Z, Karpikov A, Lian J, Mahajan MC, Hartman S, Gerstein M, Snyder M, Weissman SM, A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation Genome research18:1224-37 2008

PubMed ID: 18487515

Bergen AW, Baccarelli A, McDaniel TK, Kuhn K, Pfeiffer R, Kakol J, Bender P, Jacobs K, Packer B, Chanock SJ, Yeager M, Cis sequence effects on gene expression BMC genomics8:296 2007

PubMed ID: 17727713

Boyko AR, Williamson SH, Indap AR, Degenhardt JD, Hernandez RD, Lohmueller KE, Adams MD, Schmidt S, Sninsky JJ, Sunyaev SR, White TJ, Nielsen R, Clark AG, Bustamante CD, Assessing the evolutionary impact of amino acid mutations in the human genome PLoS genetics4:e1000083 2007

PubMed ID: 18516229

Crawford DC, Ritchie MD, Rieder MJ, Identifying the genotype behind the phenotype: a role model found in VKORC1 and its association with warfarin dosing Pharmacogenomics8:487-96 2007

PubMed ID: 17465713

Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J, Dike S, Wyss C, Henrichsen CN, Holroyd N, Dickson MC, Taylor R, Hance Z, Foissac S, Myers RM, Rogers J, Hubbard T, Harrow J, Guigó R, Gingeras TR, Antonarakis SE, Reymond A, Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions Genome research17:746-59 2007

PubMed ID: 17567994

ENCODE Project Consortium , Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, NISC Comparative Sequencing Program EA, Baylor College of Medicine Human Genome Sequencing Center EA, Washington University Genome Sequencing Center EA, Broad Institute EA, Children's Hospital Oakland Research Institute EA, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ, Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature447:799-816 2007

PubMed ID: 17571346

Greenbaum JA, Parker SC, Tullius TD, Detection of DNA structural motifs in functional genomic elements Genome research17:940-6 2007

PubMed ID: 17568009

Koch CM, Andrews RM, Flicek P, Dillon SC, Karaöz U, Clelland GK, Wilcox S, Beare DM, Fowler JC, Couttet P, James KD, Lefebvre GC, Bruce AW, Dovey OM, Ellis PD, Dhami P, Langford CF, Weng Z, Birney E, Carter NP, Vetrie D, Dunham I, The landscape of histone modifications across 1% of the human genome in five human cell lines Genome research17:691-707 2007

PubMed ID: 17567990

Lin JM, Collins PJ, Trinklein ND, Fu Y, Xi H, Myers RM, Weng Z, Transcription factor binding and modified histones in human bidirectional promoters Genome research17:818-27 2007

PubMed ID: 17568000

rieder, M.J., Reiner, A.P. and Rettie, A.E., Gamma-glutamyl carboxylase (GGCX) tagSNPs have limited utility for predicting warfarin maintenance dose. J Thrombosis and Haemostasis5(11):2227-2234 2007

PubMed ID: 17764537

Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng D, Guigó R, Gingeras TR, Weissman S, Miller P, Snyder M, Gerstein MB, The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci Genome research17:732-45 2007

PubMed ID: 17567993

Thurman RE, Day N, Noble WS, Stamatoyannopoulos JA, Identification of higher-order functional domains in the human ENCODE regions Genome research17:917-27 2007

PubMed ID: 17568007

Xu X, Bieda M, Jin VX, Rabinovich A, Oberley MJ, Green R, Farnham PJ, A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members Genome research17:1550-61 2007

PubMed ID: 17908821

Zhang ZD, Paccanaro A, Fu Y, Weissman S, Weng Z, Chang J, Snyder M, Gerstein MB, Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions Genome research17:787-97 2007

PubMed ID: 17567997

Kadota M, Yang HH, Hu N, Wang C, Hu Y, Taylor PR, Buetow KH, Lee MP, Allele-specific chromatin immunoprecipitation studies show genetic influence on chromatin state in human genome PLoS genetics3:e81 2006

PubMed ID: 17511522

Bhangale TR, Rieder MJ, Livingston RJ, Nickerson DA, Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes. Hum Mol Genet14(1):59-69 2005

PubMed ID: 15525656

Bustamante CD, Fledel-Alon A, Williamson S, Nielsen R, Hubisz MT, Glanowski S, Tanenbaum DM, White TJ, Sninsky JJ, Hernandez RD, Civello D, Adams MD, Cargill M, Clark AG, Natural selection on protein-coding genes in the human genome Nature437:1153-7 2005

PubMed ID: 16237444

Carlson CS, Aldred SF, Lee PK, Tracy RP, Schwartz SM, Rieder M, Liu K, Williams OD, Iribarren C, Lewis EC, Fornage M, Boerwinkle E, Gross M, Jaquish C, Nickerson DA, Myers RM, Siscovick DS, Reiner AP, Polymorphisms within the C-Reactive Protein (CRP) Promoter Region Are Associated with Plasma CRP Levels. Am J Hum Genet77(1):64-77 2005

PubMed ID: 15897982

Carlson CS, Thomas DJ, Eberle MA, Swanson JE, Livingston RJ, Rieder MJ, Nickerson DA, Genomic regions exhibiting positive selection identified from dense genotype data Genome research15:1553-65 2005

PubMed ID: 16251465

Feuk L, Macdonald JR, Tang T, Carson AR, Li M, Rao G, Khaja R, Scherer SW, Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies. PLoS Genet1(4):e56 2005

PubMed ID: 16254605

Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, Ballinger DG, Frazer KA, Cox DR, Whole-genome patterns of common DNA variation in three human populations. Science307(5712):1072-9 2005

PubMed ID: 15718463

Meza MM, Yu L, Rodriguez YY, Guild M, Thompson D, Gandolfi AJ, Klimecki WT, Developmentally restricted genetic determinants of human arsenic metabolism: association between urinary methylated arsenic and CYT19 polymorphisms in children Environmental health perspectives113:775-81 2005

PubMed ID: 15929903

Miretti MM, Walsh EC, Ke X, Delgado M, Griffiths M, Hunt S, Morrison J, Whittaker P, Lander ES, Cardon LR, Bentley DR, Rioux JD, Beck S, Deloukas P, A high-resolution linkage-disequilibrium map of the human major histocompatibility complex and first generation of tag single-nucleotide polymorphisms. Am J Hum Genet76(4):634-46 2005

PubMed ID: 15747258

Ramsey CD, Lazarus R, Camargo CA, Weiss ST, Celedón JC, Polymorphisms in the interleukin 17F gene (IL17F) and asthma Genes and immunity6:236-41 2005

PubMed ID: 15703761

Smith KM, Bauer L, Fischer M, Barkley R, Navia BA, Identification and characterization of human NR4A2 polymorphisms in attention deficit hyperactivity disorder American journal of medical genetics Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics133:57-63 2005

PubMed ID: 15635701

Akey JM, Eberle MA, Rieder MJ, Carlson CS, Shriver MD, Nickerson DA, Kruglyak L, Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol2(10):e286 2004

PubMed ID: 15361935

Bersaglieri T, Sabeti PC, Patterson N, Vanderploeg T, Schaffner SF, Drake JA, Rhodes M, Reich DE, Hirschhorn JN, Genetic signatures of strong recent positive selection at the lactase gene. Am J Hum Genet74(6):1111-20 2004

PubMed ID: 15114531

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