Wei V. Chen, M.S., B.S.
Department of Epidemiology
University of Texas M. D. Anderson Cancer Center
Houston, TX 77030
Tel: (713) 745-1080 (o)
Email: weichen@mdanderson.org
Education:
1990 B. S., Biology, Nanjing University, Nanjing, P. R. China.
1995 M. S., Molecular Genetics, University of Houston, Houston, Texas.
1997-2001 M. S. Candidate, Computer Science, University of Houston, Houston, Texas.
Experience:
06/1999 – 05/2002 Assistant Epidemiologist I/II
05/2002 – present
Programmer Analyst II/III
Department of Epidemiology, UT M.D. Anderson Cancer Center, Houston, Texas
Conduct advanced genetic analyses for large amounts of complex genetic disease data
(Rheumatoid Arthritis, LFS, Carney, DZ Twins, Glioma, Lung Cancer, Wilms Tumor, Crohn’s
Disease, etc.) and simulation studies (GAW15, Microdeletion, RA Canada), implementing
software packages and tools of programming, database, and web page. Develop, improve and
maintain the programs used in data processing as needed. Test and develop new analysis
methods. Facilitate cross-training of genetic software and help with manuscript preparation.
Linkage/Association software used: SAGE, LINKAGE,
Genehunter/GenehunterPlus/Genehunter MODSCORE, ASPEX, RELATIVE, PEDCHECK,
IBD, IBDN, PDT, FBAT, Simwalk2, Mendel, Mega2, Merlin, GOLD, Transmit, EMLD, LOKI,
Haplore, Allegro, SNPLINK, PHASE, PEDSTAT, HAPSTAT, LAMP, Haploview, Structure,
Eigenstrat, PLINK, TUNA.
09/1995 - 05/1999
Research Assistant II
Division of Hematology, Department of Internal Medicine, University of Texas-Houston Health
Science Center, Houston, Texas
Conducted research on structures of enzymes involved in cardiovascular diseases and
research on developing non-steroid anti-inflammation drugs (NSAIDS, eg. to inflammatory
arthritis).
01/1993 - 08/1995
Teaching Assistant
Department of biology, University of Houston, Houston, Texas
Conducted genome mapping research focusing on the development of a detailed,
integrated physical map of human chromosome 8 and searching for genes of several genetic
diseases (Langer-Giedion Syndrome, Trichorhinophalangeal Syndrome and Multiple Exostoses).
08/1990 - 12/1992
Pharmacist in Chinese Herbal Medicine
Institute of Medicinal Control, Jiangyin, Jiangsu, P.R. China
Conducted quality control and inspection of Chinese herbal medicines, using biological
and biochemical methods.
Computer Skills:
Languages: Perl, C, PL/SQL, HTML, C++, Java, Visual Basic.
Platforms: SUN, PC, VAX/VMS, SGI, and Apple Macintosh.
Operating Systems: Windows 9x/NT/XP, UNIX, LINUX, VMS, MacOS.
Software Tools: Microsoft Access, SQL*Plus, PL/SQL, SQL*Forms, Oracle Developer/2000
(Oracle Forms, Reports, and Graphics), CGI, CVIPtools, CVIPlab.
Courses Taken: Data Base Management Systems, Internet Computing, Computer Networks,
Software Engineering, Computer Vision, Structured Programming and Analysis, C Language
Programming, Object-Oriented Analysis and Design, Introduction to Logic and Computing,
Fundamentals of Operating Systems, Advanced Computer Methods in Biochemistry.
Molecular Genetics Background/Skills:
Background: Recombinant DNA, Molecular genetics, Tools in molecular biology, Cell
signaling, Seminars and journal clubs in Genetics, Human Genetics, Developmental Biology,
and Biology.
Techniques: cell culture, immunofluorescence microscopy, immunochemistry assay, enzyme
activity assay, Western blotting, protein purification, PCR and Alu PCR, cloning, sequencing,
Southern hybridization, DNA preparations (YAC, cosmid, and plasmid), RNA preparation,
agarose and polyacrylamide gel electrophoresis, YAC and cosmid library screening, contig
construction, primer designing, gene searching, solid and liquid chromatography, basic
techniques in cytogenetics, biochemistry, and microbiology.
Publications and Papers Presented at Meetings:
1. Robert M. Plenge, M.D., Ph.D.*, et al. Whole Genome Association Study in Rheumatoid
Arthritis Identifies TRAF1-C5 as a New Susceptibility Locus. Paper submitted to the
New England Journal of Medicine, June 2007.
2. Elaine F. Remmers, Ph.D.*, Robert M. Plenge, M.D., Ph.D.*, Annette T. Lee, Ph.D.,
Robert R. Graham, Ph.D., Geoffrey Hom, Ph.D., Timothy W. Behrens, M.D., Paul I. W.
de Bakker, Ph.D., Julie M. Le, B.S., Hye-Soon Lee, M.D., Ph.D., Franak Batliwalla,
Ph.D., Wentian Li, Ph.D., Seth L. Masters, Ph.D., Matthew G. Booty, B.S., John P.
Carulli, Ph.D., Leonid Padyukov, M.D., Ph.D., Lars Alfredsson, Ph.D., Lars Klareskog,
M.D., Ph.D., Wei V. Chen, M.S., Christopher I. Amos, Ph.D., Lindsey A. Criswell,
M.D., M.P.H., Michael F. Seldin, M.D., Ph.D., Daniel L. Kastner, M.D., Ph.D., Peter K.
Gregersen, M.D. STAT4 and Risk of Rheumatoid Arthritis and Systemic Lupus
Erythematosus. Paper accepted by The New England Journal of Medicine, May 2007.
E.F. Remmers1, R.M. Plenge2, A.T. Lee3, R.R. Graham2, G. Hom4, T.W. Behrens4,
P.I.W. de Bakker2, J.M. Le1, H.-S. Lee3, J.P. Carulli5, L. Padyukov6, L. Alfredsson6, L.
Klareskog6, W.V. Chen7, C.I. Amos7, L.A. Criswell8, M.F. Seldin9, D.L. Kastner1, P.K.
Gregersen3. A variant form of the signal transducer and activator of transcription gene
(STAT4) increases genetic susceptibility to rheumatoid arthritis and systemic lupus
erythematosus. Abstrat submitted to AGHG 2007.
3. Wei V. Chen1, Christopher I. Amos1, Carol J. Etzel1, Sanjay Shete, Peter K. Gregersen2.
Comparison of Genome-wide SNP Linkage Analyses in Caucasian and Hispanic
NARAC Families. Paper accepted by 15th Genetic Analysis Workshop (GAW15), 2006.
4. Chih-Chieh Wu, Wei V. Chen. Christopher I. Amos, and Sanjay Shete. Two-Locus SNP
Genome-Wide Scan in Caucasian Families with Rheumatoid Arthritis. Manuscript
submitted to 15th Genetic Analysis Workshop (GAW15), 2006.
5. Xiaojun Zhou, Wei Chen, Michael Swartz, Yue Lu, Robert Yu, Chris Amos, Chih-Chieh
Wu, Sanjay Shete§. Joint linkage and Imprinting analyses of GAW15 Rheumatoid
Arthritis and Gene Expression Data. Paper accepted to 15th Genetic Analysis Workshop
(GAW15), 2006.
6. Kim Taylor, Wei V. Chen, Chris Amos, Lindsey Criswell. Genome-wide SNP Linkage
Analyses of Quantitative Rheumatoid Arthritis Phenotypes in Caucasian NARAC
Families. Paper accepted to 15th Genetic Analysis Workshop (GAW15), 2006.
7. Carol J. Etzel, Tracy J. Costello, Sumesh Kachroo, Wei V. Chen, Christopher I. Amos.
Meta-analysis of chromosome X for linkage to rheumatoid arthritis. Manuscript
submitted to 15th Genetic Analysis Workshop (GAW15), 2006.
8. C.I. Amos1, W.V. Chen1, X. Liu2, D. Mosher3, W. Maksymowych4, E. Keystone2,D.
Zhu1, S. Shete1, K. Siminovitch2 . Dense SNP marker analysis identifies regions of
linkage for rheumatoid arthritis. Paper in preparation.
9. 1Lindsey A. Criswell, M.D., M.P.H., 2Wei V. Chen, M.S., 3Naila B. Ahmad, M.D.,
4
Damini Jawaheer, Ph.D., 1Raymond F. Lum, M.P.H., 3Mark H. Wener, M.D., 5Peter K.
Gregersen, M.D., 2Christopher I. Amos, Ph.D. Dissecting the Heterogeneity of
Rheumatoid Arthritis Through Linkage Analysis of Quantitative Traits. Accepted for an
oral presentation at the Annual Scientific Meeting of ACR and ARHP in San Antonio,
Texas, October 16 - 21, 2004. Poster presented at 2004 IGES meeting and 2004 NARAC
SAB meeting. Paper Arthritis and Rheumatism ar-06-0061.R2
10. Christopher I Amos1, Wei Vivien Chen1, Annette Lee2, Wentian Li2, Marlena Kern2,
Robert Lundsten2, Franak Batliwalla2, Elaine Remmers3 , Daniel A. Kastner3, Lindsey A.
Criswell4, , Mike F. Seldin5, and Peter K. Gregersen2. High-density SNP analysis of 642
Caucasian families with rheumatoid arthritis identifies two new linkage regions on 11p12
and 2q33. Talk presented at IGES 2005 and AJHG annual meeting October 2005, Utah.
Paper on Genes Immun 2006;7:277-86.
11. EF Remmers1, J Le1, W Li2, AT Lee2, W Chen3, MF Seldin4, LA Criswell5, C Amos3,
PK Gregersen2, DL Kastner1. ASSOCIATION ANALYSIS OF THE CHROMOSOME
18q RHEUMATOID ARTHRITIS SUSCEPTIBILITY REGION IDENTIFIED BY
LINKAGE IN THE NORTH AMERICAN RHEUMATOID ARTHRITIS
CONSORTIUM COHORT. Abstract for meeting: Beyond HapMap 2006.
12. John S, Amos C, Shephard N, Chen W, Butterworth A, Etzel C, Jawaheer D, Seldin M,
Silman A, Gregersen P, Worthington J. Linkage analysis of rheumatoid arthritis in US
and UK families reveals interactions between HLA-DRB1 and loci on chromosomes 6q
and 16p. Paper on Arthritis Rheum. 2006 May;54(5):1482-90.
13. Carol J. Etzel1, Damini Jawaheer2, Michael F. Seldin3, Wei V. Chen1, Peter
Gregersen2, Christopher I. Amos1 for NARAC4. Genome-wide Meta-analytic Methods
Applied to Rheumatoid Arthritis. Presentation at annual IGES meeting, Noordwijkerhout,
the Netherlands, Sep. 11-12, 2004. Paper on Hum Genet. 2006 Jul;119(6):634-41.
14. Catherine Derom1, Damini Jawaheer 2, Wei V. Chen 3, Chris Amos3, Peter K. Gregersen
2
, Robert Vlietinck1. Genome-wide linkage scan for spontaneous DZ twinning. Paper on
Eur J Hum Genet. 2006 Jan;14(1):117-22.
15. Tom W. J. Huizinga1, Christopher I. Amos2, Annette H.M. van der Helm-van Mil1, Wei
Chen2, Floris A. van Gaalen1, Damini Jawaheer3, Geziena M.T. Schreuder4, Mark
Wener5, Ferdinand C. Breedveld1, Naila Ahmad5, Raymond F. Lum6 , Rene R.P. de
Vries4, Peter K. Gregersen3 , Rene E.M. Toes1, Lindsey A. Criswell. Refining the
complex rheumatoid arthritis phenotype based on specificity of the HLA-DRB1 shared
epitope for antibodies to citrullinated proteins. Paper on Arthritis Rheum 52, 3433-3438
(2005).
16. E. Remmers, J. Balow, Jr., W. Li, I. Aksentijevich, A. Lee, A. Damle, W. Chen, C.
Amos, P. Gregersen, D. Kastner. Linkage sidequilibrium structure and association
analysis of candidate genes located within the rheumatoid arthritis susceptibility region
on chromosome 18q. The Keystone symposium "Human Genome Sequence Variation
and the Inherited Basis of Common Disease", Jan 8-13, 2004, Breckenridge, CO.
17. E. Remmers1, J. Balow, Jr.1, W. Li2, I. Aksentijevich1, A. Lee2, A. Damle2, W. Chen3, C.
Amos3, P. Gregersen2, D. Kastner1. Possible association of a 14 kb haplotype block from
the receptor activator of NF-kappa B (RANK) gene with susceptibility to rheumatoid
arthritis. ASHG 2003 annual meeting, poster accepted, published.
18. Jawaheer D, Seldin MF, Amos CI, Chen WV, Shigeta R, Etzel C, Damle A, Xiao X,
Chen D, Lum RF, Monteiro J, Kern M, Criswell LA, Albani S, Nelson JL, Clegg DO,
Pope R, Schroeder HW Jr, Bridges SL Jr, Pisetsky DS, Ward R, Kastner DL, Wilder RL,
Pincus T, Callahan LF, Flemming D, Wener MH, Gregersen PK; North American
Rheumatoid Arthritis Consortium. Screening the genome for rheumatoid arthritis
susceptibility genes: a replication study and combined analysis of 512 multicase families.
Paper on Arthritis Rheum. 2003 Apr; 48(4): 906-16.
19. Jawaheer D, Li WT, Graham RR, Chen W, Damle A, Xiao XL, Monteiro J, Khalili H,
Lee A, Lundsten R, Begovich A, Bugawan T, Erlich H, Elder JT, Criswell LA, Seldin
MF, Amos CI, Behrens TW, Gregersen PK. Dissecting the genetic complexity of the
association between human leukocyte antigens and rheumatoid arthritis. Paper on
AMERICAN JOURNAL OF HUMAN GENETICS 71 (3): 585-594 SEP 2002.
20. C. Etzel, D. Jawaheer, M. Seldin, W. Chen, P. K. Gregersen, C. I. Amos. Use of
regression trees to detect linkage of Rheumatoid Arthritis to chromosome 1. Abstract
accepted at ASHG annual meeting, 2002.
21. Damini Jawaheer, Michael F. Seldin, Christopher I. Amos, Wei V. Chen, Russell
Shigeta, Joanita Monteiro, Marlene Kern, Lindsey Criswell, Salvatore Albani, Lee
Nelson, Daniel O. Clegg, Richard Pope, Harry W Schroeder, Jr., S. Louis Bridges, Jr.,
David S. Pisetsky, Daniel L. Kastner, Ronal L. Wilder, Theodore Pincus, Leigh F.
Callahan, Donald Flemming, Mark H. Wener & Peter K. Gregersen and North American
Rheumatoid Arthritis Consortium (2001). A genome-wide screen in multiplex
rheumatoid arthritis families suggests genetic overlap with other autoimmune diseases.
Paper on The American Journal of Human Genetics 68:927-936, 2001.
22. Damini Jawaheer, Robert Graham, Wei Chen, Aarti Damle, Nina Kohn, Timothy W
Behrens, Joanita Monteiro, Ann B Begovich, Michael F Seldin, Lindsey A Criswell,
James T Elder, Krishnan Pillaipakkamnatt, Christopher I Amos and Peter K Gregersen.
Dense mapping within the MHC suggests a complex pattern of haplotype associations
with Rheumatoid Arthritis. Abstract accepted by 65th Annual Scientific Meeting of the
American College of Rheumatology (ACR). San Francisco, November 11-15, 2001.
23. Amos, C. I., Jawaheer D., Behrens T. W., Elder J. T., Chen W., Seldin M. F., Gregersen
P. K. Joint effects of HLA loci in causing rheumatoid arthritis. Oral presentation
accepted by 10th Conference of the International Genetic Epidemiology Society.
September 2 - 4, 2001 - Garmisch-Partenkirchen, Germany.
24. Damini Jawaheer, Michael F. Seldin, Christopher I. Amos, Wei Chen, Joanita Monteiro,
Lindsey Criswell, Salvo Albani, Lee Nelson, Daniel O. Clegg, Richard Pope, Harry W
Schroeder, S. Louis Bridges, David S. Pisetsky, Daniel Kastner, Ronals Wilder, Theodore
Pincus, Leigh Callahan, Peter K. Gregersen and North American Rheumatoid Arthritis
Consortium (2000). A genome wide screen for allele sharing in the first 300 rheumatoid
arthritis sibling pairs of the NARAC collection. Abstract and talk presented at 64th
Annual Scientific Meeting of the American College of Rheumatology (ACR) and 35th
Annual Scientific Meeting of the Association of Rheumatology Health Professionals
(ARHP), Philadelphia, October-November 2000. Abstract on Arthritis & Rheumatism 43
(9): S390, 1943. Abstract presented by 50th Annual Meeting of American Society of
Human Genetics, Philadelphia, October 2000. Abstract on The American Journal of
Human Genetics 67: (4) 323.
25. D. Jawaheer, W. Chen, T. Costello, J. Monteiro, C. Amos, M. Seldin, L. Criswell, S.
Bridges, H. Schroeder, D. Pisetsky, D. Kastner, R. Wilder, R. Pope, D. Clegg, R. Ward,
S. Albani, JL. Nelson, M. Wener, L. Callahan, T. Pincus and PK. Gregersen (1999).
Analysis of affected sibling pairs with rheumatoid arthritis: the North American
Rheumatoid Arthritis Consortium. Poster presented at 49th Annual Meeting of American
Society of Human Genetics, San Francisco. Abstract on The American Journal of
Human Genetics 65: (4) 1544.
26. Wei Chen, Timothy R. Pawelek and Richard J. Kulmacz (1999). Hydroperoxide
dependence and cooperative cyclooxygenase kinetics in Prostaglandin H Synthase-1 and
2. The Journal of Biological Chemistry 274: 20301-20306.
27. Richard J. Kulmacz , Timothy R. Pawelek and Wei Chen (1999). Interplay between fatty
acid and peroxide in cyclooxygenase kinetics of PGH synthase-1 and -2. Poster presented
on 1999 Keystone Meeting, Denver, USA.
28. Guishan Xiao, Wei Chen, Richard J. Kulmacz (1999). Comparison of prostaglandin H
synthase-1 and -2 structural stabilities, a chapter in book: Eicosanoids and Other
Bioactive Lipids in Cancer, Inflammation and Radiation Injury, 4 (Kenneth V. Honn et
al., ed.). Series: Advances in Experimental Medicine & Biology 469: pp115-118, Kluwer
Academic / Plenum Publishers, New York.
29. Qiupeng Guo, Wei Chen, and Richard J. Kulmacz (1998). Effects of Sangstat Peptides
on PGHS-1 and -2 Cyclooxygenase Kinetics.
30. Guishan Xiao, Wei Chen, and Richard J. Kulmacz (1998). Comparison of structural
stabilities of prostaglandin H synthase-1 and -2. The Journal of Biological Chemistry
273: 6801-6811.
31. Richard J. Kulmacz, Wei Chen, and Guishan Xiao (1998). Comparison of the folding
stabilities of the two prostaglandin H synthase isoforms. Poster presented at Annual
Meeting of American Society for Biochemistry and Molecular Biology, Washington,
D.C. Abstract on FASEB 12: A1386.
32. Wei Chen, Y. Lin, K.-H. Ruan, and Richard J. Kulmacz. Determination of the membrane
topology of thromboxane A synthase. (supported by NIH grant NS-23327).
33. W. Chen, Y. Lin, K.-H. Ruan, and R. J. Kulmacz (1998). Intracellular topology of
thromboxane A synthase. Poster presented at Annual Meeting of American Society for
Biochemistry and Molecular Biology, Washington, D.C. Abstract on FASEB 12: A1387.
34. Guishan Xiao, Wei Chen, and Richard J. Kulmacz (1997). Comparison of prostaglandin
H synthase-1 and -2 structural stabilities. Talk presented at Eicosanoids & Other
Bioactive Lipids in Cancer, Inflammation and Related Diseases 5th International
Conference, La Jolla, California, USA. Also appeared as a book chapter.
35. R. J., Kulmacz, W. Chen, and L.-H. Wang (1996). Differential control of
cyclooxygenase catalysis in PGH synthase isoforms: role of hydroperoxide initiator. Talk
presented at Frontiers in Bioactive Lipids '96 XVIth Washington International Spring
Symposium, Washington, DC, USA.
Also published as a chapter in book (J.Y. Vanderhoek, ed.), pp. 101-104, Plenum Press,
New York.
36. Richard J., Kulmacz, Wei Chen, and Lee-Ho Wang (1996). Differential control of
cyclooxygenase catalysis in PGH synthase isoforms: role of hydroperoxide initiator. A
book chapter in Frontiers in Bioactive Lipids (J.Y. Vanderhoek, ed.): pp. 101-104,
Plenum Press, New York.
37. Chen, W., Hou, J., Wagner, M. J., and Wells, D. E. (1996). An integrated physical map
covering 25cM of human chromosome 8. Genomics 32: 117-120.
38. Wei Chen, M.S. thesis, University of Houston. Construction of a 25MB integrated YAC
contig spanning deletion regions of Langer-Giedion syndrome patients in 8q23-8q24.1.
July, 1995.
39. Hou, J., Parrish, J., Lüdecke, H.-J., Sapru, M., Wang, Y., Chen, W., Hill, A., SiegelBartelt, J., Northrup, H., Elder, F.F.B, Chinault, C., Horsthemke, B., Wagner, M. J., and
Wells, D. E. (1995). A 4-megabase YAC contig that spans the Langer-Giedion Syndrome
region on human chromosome 8q24.1: use in refining the location of the
Trichorhinophalangeal Syndrome and Multiple Exostoses genes. Genomics 29: 87-97.
40. M. Wagner, W. Chen, J. Hou, J. Parrish, H.-J. Lüdecke, B. Horsthemke, and D. Wells
(1994). A physical map covering 25 cM of human chromosome 8 and including the
Langer-Giedion syndrome region. Poster presented at 44th Annual Meeting of American
Society of Human Genetics, Montreal, Canada. Abstract on The American Journal of
Human Genetics 55: 1598.
41. Michael Wagner, Wei Chen, Jessie Gu, Xiang Gu, Jianzhong Hou, Hua Li, HermannJosef Lüdeke, and Dan Wells (1994). Integrated physical maps of chromosome 8. Poster
presented at Human Genome Mapping Workshop 94, Oxford, England. Abstract on
Cytogenetics and Cell Genetics 68:162.