Publications from the Waldman Laboratory

2009

• Crane CA, Panner A, Murray JC, Wilson SP, Xu H, Chen L, Simko JP, Waldman FM, Pieper RO, and Parsa AT, PI(3) kinase is associated with a mechanism of immunoresistance in breast and prostate cancer. Oncogene, 28(2): p. 306-12.2009.   Link to PDF.     Link to journal article    

2008

• Choueiri TK, Vaziri SA, Jaeger E, Elson P, Wood L, Bhalla IP, Small EJ, Weinberg V, Sein N, Simko J, Golshayan AR, Sercia L, Zhou M, Waldman FM, Rini BI, Bukowski RM, and Ganapathi R, von Hippel-Lindau gene status and response to vascular endothelial growth factor targeted therapy for metastatic clear cell renal cell carcinoma. J Urol, 180(3): p. 860-5.2008.   Link to PDF.     Link to journal article    

• Nickerson ML, Jaeger E, Shi Y, Durocher JA, Mahurkar S, Zaridze D, Matveev V, Janout V, Kollarova H, Bencko V, Navratilova M, Szeszenia-Dabrowska N, Mates D, Mukeria A, Holcatova I, Schmidt LS, Toro JR, Karami S, Hung R, Gerard GF, Linehan WM, Merino M, Zbar B, Boffetta P, Brennan P, Rothman N, Chow WH, Waldman FM, and Moore LE, Improved identification of von Hippel-Lindau gene alterations in clear cell renal tumors. Clin Cancer Res, 14(15): p. 4726-34.2008.   Link to PDF.     Link to journal article    

• Raphael BJ, Volik S, Yu P, Wu C, Huang G, Linardopoulou EV, Trask BJ, Waldman FM, Costello J, Pienta KJ, Mills GB, Bajsarowicz K, Kobayashi Y, Shivaranjani S, Paris P, Tao Q, Aerni SJ, Brown RP, Bashir A, Gray JW, Cheng JF, de Jong P, Nefedov M, Ried T, Padilla-Nash HM, and Collins CC, A sequence-based survey of the complex structural organization of tumor genomes. Genome Biol, 9(3): p. R59.2008. Link to PDF. Link to journal article

• Signoretti S, Bratslavsky G, Waldman FM, Reuter VE, Haaga J, Merino M, Thomas GV, Pins MR, Libermann T, Gillespie J, Tomaszewski JE, Compton CC, Hruszkewycz A, Linehan WM, and Atkins MB, Tissue-based research in kidney cancer: current challenges and future directions. Clin Cancer Res, 14(12): p. 3699-705.2008. Link to PDF. Link to journal article

• Tutt A, Wang A, Rowland C, Gillett C, Lau K, Chew K, Dai H, Kwok S, Ryder K, Shu H, Springall R, Cane P, McCallie B, Kam-Morgan L, Anderson S, Buerger H, Gray J, Bennington J, Esserman L, Hastie T, Broder S, Sninsky J, Brandt B, and Waldman F, Risk estimation of distant metastasis in node-negative, estrogen receptor-positive breast cancer patients using an RT-PCR based prognostic expression signature. BMC Cancer, 8: p. 339.2008. Link to PDF. Link to journal article

2007

• Adduci KM, Annis CE, DeVries S, Chew KL, Boutin J, Magrane G, Ljung BM, Waldman FM, and Esserman LJ, Fluorescence in situ hybridization of ductal lavage samples identifies malignant phenotypes from cytologically normal cells in women with breast cancer. Cancer, 111(3): p. 185-91.2007. Link to PDF. Link to journal article

• Korkola JE, Blaveri E, DeVries S, Moore DH, 2nd, Hwang ES, Chen YY, Estep AL, Chew KL, Jensen RH, and Waldman FM, Identification of a robust gene signature that predicts breast cancer outcome in independent data sets. BMC Cancer, 7: p. 61.2007. Link to PDF. Link to journal article

2006

• Chin K, Devries S, Fridlyand J, Spellman PT, Roydasgupta R, Kuo WL, Lapuk A, Neve RM, Qian Z, Ryder T, Chen F, Feiler H, Tokuyasu T, Kingsley C, Dairkee S, Meng Z, Chew K, Pinkel D, Jain A, Ljung BM, Esserman L, Albertson DG, Waldman FM, Gray JW. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 10(6):529-41, 2006.   Link to PDF.     Link to journal article    

• Fridlyand J, Snijders AM, Ylstra B, Li H, Olshen A, Segraves R, Dairkee S, Tokuyasu T, Ljung BM, Jain AN, McLennan J, Ziegler J, Chin K, Devries S, Feiler H, Gray JW, Waldman F, Pinkel D, Albertson DG. Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer 6:96, 2006.   Link to PDF.     Link to journal article    

• Neve RM, Chin K, Fridlyand J, Yeh J, Baehner FL, Fevr T, Clark L, Bayani N, Coppe JP, Tong F, Speed T, Spellman PT, Devries S, Lapuk A, Wang NJ, Kuo WL, Stilwell JL, Pinkel D, Albertson DG, Waldman FM, McCormick F, Dickson RB, Johnson MD, Lippman M, Ethier S, Gazdar A, Gray JW. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell 10(6):515-27, 2006.   Link to PDF.     Link to journal article    

• Rini BI, Jaeger E, Weinberg V, Sein N, Chew K, Fong K, Simko J, Small EJ, Waldman FM. Clinical response to therapy targeted at vascular endothelial growth factor in metastatic renal cell carcinoma: impact of patient characteristics and Von Hippel-Lindau gene status. BJU Int 98(4):756-62, 2006.   Link to PDF.     Link to journal article     Primary Data Available Here

• Sternlicht MD, Dunning AM, Moore DH, Pharoah PD, Ginzinger DG, Chin K, Gray JW, Waldman FM, Ponder BA, Werb Z. Prognostic value of PAI1 in invasive breast cancer: evidence that tumor-specific factors are more important than genetic variation in regulating PAI1 expression. Cancer Epidemiol Biomarkers Prev 15(11):2107-14, 2006.   Link to PDF.     Link to journal article    

• Trautmann K, Terdiman JP, French AJ, Roydasgupta R, Sein N, Kakar S, Fridlyand J, Snijders AM, Albertson DG, Thibodeau SN, Waldman FM. Chromosomal instability in microsatellite-unstable and stable colon cancer. Clin Cancer Res 12(21):6379-85, 2006.   Link to PDF.     Link to journal article    

2005

• Blaveri, E., Brewer, J. L., Roydasgupta, R., Fridlyand, J., Devries, S., Koppie, T., Pejavar, S., Mehta, K., Carroll, P., Simko, J. P., and Waldman, F. M. Bladder cancer stage and outcome by array-based comparative genomic hybridization. Clin Cancer Res, 11:7012-7022, 2005.   Link to PDF.     Link to journal article   Primary Data Available Here

• Blaveri E, Simko JP, Korkola JE, Brewer JL, Baehner F, Mehta K DeVries S, Koppie T, Pejavar S, Carroll P, and Waldman FM. Bladder cancer outcome and subtype classification by gene expression. Clinical Cancer Research, 11:4044-55, 2005.   Link to journal article.     Or Link to PDF.     Primary Data Available Here

• DeVries S, Nyante S, Korkola J, Segraves R, Nakao N, Moore D, Bae H, Wilhelm M, Hwang S, Waldman FM. Array based comparative genomic hybridization from formalin fixed paraffin embedded breast tumors. Journal of Molecular Diagnostics 7:65-71, 2005.  Link to journal article.     Or Link to PDF.    

• Goebell PJ, Groshen S, Schmitz-Drager BJ, Sylvester R, Kogevinas M, Malats N, Sauter G, Grossman HB, Dinney CN, Waldman F and Cote RJ. Concepts for Banking Tissue in Urologic Oncology—The International Bladder Cancer Bank. Clin Can Res 11:413-415, 2005.  Link to journal article.     Or Link to PDF.    

• Mehta KR, Nakao K, Zuraek MB, Ruan DT, Bergsland EK, Venook AP, Fridlyand J, Moore DH, Tokuyasu TA, Jain AN, Warren RS, Terdiman JP and Waldman FM. Fractional genomic alteration detected by array-based comparative genomic hybridization independently predicts survival after hepatic resection for metastatic colorectal cancer. Clinical Cancer Research, 11:1791-1797, 2005.  Link to journal article.     Or Link to PDF.     Primary Data Available Here

2004

• Goebell PJ, Groshen S, Schmitz-Drager BJ, Sylvester R, Kogevinas M, Malats N, Sauter G, Barton Grossman H, Waldman F and Cote RJ. The International Bladder Cancer Bank: Proposal for a new study concept. Urol Oncol 22(4):277-84, 2004.  Link to journal article.     Or Link to PDF.    

• Hwang ES, DeVries S, Chew KL, Moore DH, 2nd, Kerlikowske K, Thor A, Ljung BM and Waldman FM. Patterns of chromosomal alterations in breast ductal carcinoma in situ. Clin Cancer Res 10(15):5160-7, 2004.  Link to journal article.     Or Link to PDF.    

• Hwang ES, Nyante SF, Chen YY, Moore D, DeVries S, Korkola JE, Esserman LJ, and Waldman FM. Clonality of lobular carcinoma in situ and synchronous invasive lobular cancer. Cancer 100(12):2562-72, 2004.   Link to journal article.     Or Link to PDF.     Primary Data Available Here

• Liu D, Liu C, DeVries S, Waldman F, Cote RJ, and Datar RH. Lm-pcr permits highly representative whole genome amplification of DNA isolated from small number of cells and paraffin-embedded tumor tissue sections. Diagn Mol Pathol 13(2):105-15, 2004.   Link to journal article.     Or Link to PDF

• Nakao K, Mehta KR, Fridlyand J, Moore DH, Jain AN, Lafuente A, Wiencke JW, Terdiman JP, and Waldman FM. High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization. Carcinogenesis 25(8):1345-1357, 2004.   Link to journal article.     Or Link to PDF.     Primary Data Available Here

2003

• Cheng J, Huang H, Pak J, Shapiro E, Sun TT, Cordon-Cardo C, Waldman FM and Wu XR. Allelic loss of p53 gene is associated with genesis and maintenance, but not invasion, of mouse carcinoma in situ of the bladder. Cancer Res 63(1):179-85, 2003.   Link to journal article.     Or Link to PDF.

• Jeruss JS, Liu NX, Chung Y, Magrane G, Waldman F, Edgerton S, Yang X and Thor AD. Characterization and chromosomal instability of novel derived cell lines from a wt-erbB-2 transgenic mouse model. Carcinogenesis 24(4):659-64, 2003.   Link to journal article.     Or Link to PDF.

• Kerlikowske K, Molinaro A, Cha I, Ljung BM, Ernster VL, Stewart K, Chew K, Moore DH, 2nd and Waldman F. Characteristics associated with recurrence among women with ductal carcinoma in situ treated by lumpectomy. J Natl Cancer Inst 95(22):1692-702, 2003.   Link to journal article.     Or Link to PDF.

• Korkola JE, DeVries S, Fridlyand J, Hwang ES, Estep AL, Chen YY, Chew KL, Dairkee SH, Jensen RM and Waldman FM. Differentiation of lobular versus ductal breast carcinomas by expression microarray analysis. Cancer Res 63(21):7167-75, 2003.   Link to journal article.     Or Link to PDF.     Primary Data Available Here

• Korkola JE, Estep AL, Pejavar S, DeVries S, Jensen R and Waldman FM. Optimizing stringency for expression microarrays. Biotechniques 35(4):828-35, 2003.   Link to PDF.

• Moore LE, Smith AH, Eng C, DeVries S, Kalman D, Bhargava V, Chew K, Ferreccio C, Rey OA, Hopenhayn C, Biggs ML, Bates MN and Waldman FM. P53 alterations in bladder tumors from arsenic and tobacco exposed patients. Carcinogenesis 24(11):1785-91, 2003.   Link to journal article.     Or Link to PDF.

• Veltman JA, Fridlyand J, Pejavar S, Olshen AB, Korkola JE, DeVries S, Carroll P, Kuo WL, Pinkel D, Albertson D, Cordon-Cardo C, Jain AN and Waldman FM. Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors. Cancer Res 63(11):2872-80, 2003.   Link to journal article.     Or Link to PDF.

2002

• Aust DE, Terdiman JP, Willenbucher RF, Chang CG, Molinaro-Clark A, Baretton GB, Loehrs U, and Waldman FM. The apc/beta-catenin pathway in ulcerative colitis-related colorectal carcinomas: A mutational analysis. Cancer 94(5):1421-7., 2002.   Link to manuscript. Or Link to PDF.

• Moore LE, Smith AH, Eng C, Kalman D, DeVries S, Bhargava V, Chew K, Moore D, 2nd, Ferreccio C, Rey OA, and Waldman FM. Arsenic-related chromosomal alterations in bladder cancer. J Natl Cancer Inst 94(22):1688-96., 2002.   Link to manuscript.

• Orntoft TF, Thykjaer T, Waldman FM, Wolf H, and Celis JE. Genome-wide study of gene copy numbers, transcripts, and protein levels in pairs of non-invasive and invasive human transitional cell carcinomas. Mol Cell Proteomics 1(1):37-45., 2002. Link to manuscript.

• Presti JC, Jr., Wilhelm M, Reuter V, Russo P, Motzer R, and Waldman F. Allelic loss on chromosomes 8 and 9 correlates with clinical outcome in locally advanced clear cell carcinoma of the kidney. J Urol 167(3):1464-8., 2002. Link to PDF.

• Terdiman JP, Aust DE, Chang CG, Willenbucher RF, Baretton GB, and Waldman FM. High resolution analysis of chromosome 18 alterations in ulcerative colitis-related colorectal cancer. Cancer Genet Cytogenet 136(2):129-37., 2002. Link to manuscript.

• Thor AD, Eng C, Devries S, Paterakos M, Watkin WG, Edgerton S, Moore DH, 2nd, Etzell J, and Waldman FM. Invasive micropapillary carcinoma of the breast is associated with chromosome 8 abnormalities detected by comparative genomic hybridization. Hum Pathol 33(6):628-31., 2002.   Link to manuscript.

• Wilhelm M, Veltman JA, Olshen AB, Jain AN, Moore DH, Presti JC, Jr., Kovacs G, and Waldman FM. Array-based comparative genomic hybridization for the differential diagnosis of renal cell cancer. Cancer Res 62(4):957-60., 2002.   Link to manuscript.

2001

• Aust DE, Terdiman JP, Willenbucher RF, Chew K, Ferrell L, Florendo C, Molinaro-Clark A, Baretton GB, Löhrs U, and Waldman FM. Altered distribution of ß-catenin, and its binding proteins E-cadherin and APC, in ulcerative colitis-related colorectal cancers. Modern Pathology 14(1):29-39, 2001.  Link to manuscript.     Or Link to PDF.

• Etzell JE, Devries S, Chew K, Florendo C, Molinaro A, Ljung BM, and Waldman FM. Loss of chromosome 16q in lobular carcinoma in situ. Human Pathology 32(3):292-296, 2001. Link to manuscript.

• Gong G, DeVries S, Chew KL, Cha I, Ljung BM, and Waldman  FM. Genetic changes in paired atypical and usual ductal hyperplasia of the breast by comparative genomic hybridization. Clin. Cancer Res. 2001 7: 2410-2414.  Link to manuscript.

• Waldman FM, Hwang ES, Etzell J, Eng C, DeVries S, Bennington J, and Thor A. Genomic alterations in tubular breast carcinomas. Human Pathology 32(2):222-226, 2001.   Link to manuscript.

2000

• Aust DE, Willenbucher RF, Terdiman JP, Ferrell LD, Chang CG, Moore DH, 2nd, Molinaro-Clark A, Baretton GB, Loehrs U, and Waldman FM. Chromosomal alterations in ulcerative colitis-related and sporadic colorectal cancers by comparative genomic hybridization. Human Pathology 31(1):109-114, 2000.  Link to PDF.

• Baehner R, Magrane G, Balassanian R, Chang C, Millward C, Wakil AE, Osorio RW, and Waldman FM. Donor origin of neuroendocrine carcinoma in 2 transplant patients determined by molecular cytogenetics. Human Pathology 31(11):1425-1429, 2000.   Link to manuscript .

• Goodson WH, III, Moore DH, Ljung BM, Chew K, Mayall B, Smith HS, and Waldman FM. The prognostic value of proliferation indices: A study with in vivo bromodeoxyuridine and KI-67. Breast Cancer Research and Treatment 59(2):113-123, 2000.  Link to PDF.

• McShane LM, Aamodt R, Cordon-Cardo C, Cote R, Faraggi D, Fradet Y, Grossman HB, Peng A, Taube SE, and Waldman FM. Reproducibility of p53 immunohistochemistry in bladder tumors. Clinical Cancer Research 6(5):1854-1864, 2000.   Link to PDF.

• Moore L, Godfrey T, Eng C, Smith A, Ho R, and Waldman FM. Validation of fluorescent SSCP analysis for sensitive detection of p53 mutations. Biotechniques 28(5):986-992, 2000.   Link to manuscript.   Link to PDF.

• Muscheck M, Abol-Enein H, Chew K, Moore D, 2nd, Bhargava V, Ghoneim MA, Carroll PR, and Waldman FM. Comparison of genetic changes in schistosome-related transitional and squamous bladder cancers using comparative genomic hybridization. Carcinogenesis 21(9):1721-1726, 2000.   Link to manuscript.  Link to PDF.

• Waldman FM, DeVries S, Chew KL, Moore DH, Kerlikowske K, and Ljung BM. Chromosomal alterations in ductal carcinomas in situ and their in situ recurrences. Journal of the National Cancer Institute 92(4):313-320, 2000.   Link to manuscript.  Link to PDF.

Earlier Publications

• Isola J, Chu L, DeVries S, Matsumura K, Chew K, Ljung BM and Waldman FM. Genetic alterations in ERBB2-amplified breast carcinomas. Clin Cancer Res 5(12):4140-5, 1999. Link to manuscript. Link to PDF.

• Jarrard DF, Sarkar S, Shi Y, Yeager TR, Magrane G, Kinoshita H, Nassif N, Meisner L, Newton MA, Waldman FM and Reznikoff CA. p16/pRb pathway alterations are required for bypassing senescence in human prostate epithelial cells. Cancer Res 59(12):2957-64, 1999. Link to manuscript. Link to PDF.

• Willenbucher RF, Aust DE, Chang CG, Zelman SJ, Ferrell LD, Moore DH, 2nd and Waldman FM. Genomic instability is an early event during the progression pathway of ulcerative-colitis-related neoplasia. Am J Pathol 154(6):1825-30, 1999. Link to manuscript. Link to PDF.

• Korn WM, Yasutake T, Kuo WL, Warren RS, Collins C, Tomita M, Gray J and Waldman FM. Chromosome arm 20q gains and other genomic alterations in colorectal cancer metastatic to liver, as analyzed by comparative genomic hybridization and fluorescence in situ hybridization. Genes Chromosomes Cancer 25(2):82-90, 1999. Link to abstract.

• Hovey RM, Chu L, Balazs M, DeVries S, Moore D, Sauter G, Carroll PR, and Waldman FM. Genetic alterations in primary bladder cancers and their metastases. Cancer Research 58(16):3555-3560, 1998. Link to Abstract.
  

• Nishizaki T, DeVries S, Chew K, Goodson WH, 3rd, Ljung BM, Thor A, and Waldman FM. Genetic alterations in primary breast cancers and their metastases: Direct comparison using modified comparative genomic hybridization. Genes, Chromosomes and Cancer 19(4):267-272, 1997.  Link to PDF.

• Nishizaki T, Chew K, Chu L, Isola J, Kallioniemi A, Weidner N, and Waldman FM. Genetic alterations in lobular breast cancer by comparative genomic hybridization. International Journal of Cancer 74(5):513-517, 1997. Link to PDF.

• Moch H, Presti JC, Jr., Sauter G, Buchholz N, Jordan P, Mihatsch MJ, and Waldman FM. Genetic aberrations detected by comparative genomic hybridization are associated with clinical outcome in renal cell carcinoma. Cancer Research 56(1):27-30, 1996. Link to Abstract.

• Kallioniemi A, Kallioniemi OP, Citro G, Sauter G, Devries S, Kerschmann R, Caroll P, and Waldman F. Identification of gains and losses of DNA sequences in primary bladder cancer by comparative genomic hybridization. Genes Chromosomes & Cancer 12(3):213-219, 1995. Link to Abstract.

• Isola JJ, Kallioniemi OP, Chu LW, Fuqua SA, Hilsenbeck SG, Osborne CK, and Waldman FM. Genetic aberrations detected by comparative genomic hybridization predict outcome in node-negative breast cancer. American Journal of Pathology 147(4):905-911, 1995. Link to Abstract.

• Kallioniemi A, Kallioniemi OP, Piper J, Tanner M, Stokke T, Chen L, Smith HS, Pinkel D, Gray JW, and Waldman FM. Detection and mapping of amplified DNA sequences in breast cancer by comparative genomic hybridization. Proceedings of the National Academy of Sciences USA (6):2156-2160, 1994.  Link to Manuscript.

• Kallioniemi OP, Kallioniemi A, Kurisu W, Thor A, Chen LC, Smith HS, Waldman FM, Pinkel D, and Gray JW. Erbb2 amplification in breast cancer analyzed by fluorescence in situ hybridization. Proceedings of the National Academy of Sciences USA 89(12):5321-5325, 1992. Link to Manuscript.

• Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, and Pinkel D. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258(5083):818-821, 1992. Link to Manuscript.