Publications

aCGH

Cheung, V. G., N. Nowak, W. Jang, I. R. Kirsch, S. Zhao, X. N. Chen, T. S. Furey, U. J. Kim, W. L. Kuo, M. Olivier, J. Conroy, A. Kasprzyk, H. Massa, R. Yonescu, S. Sait, C. Thoreen, A. Snijders, E. Lemyre, J. A. Bailey, A. Bruzel, W. D. Burrill, S. M. Clegg, S. Collins, P. Dhami, C. Friedman, C. S. Han, S. Herrick, J. Lee, A. H. Ligon, S. Lowry, M. Morley, S. Narasimhan, K. Osoegawa, Z. Peng, I. Plajzer-Frick, B. J. Quade, D. Scott, K. Sirotkin, A. A. Thorpe, J. W. Gray, J. Hudson, D. Pinkel, T. Ried, L. Rowen, G. L. Shen-Ong, R. L. Strausberg, E. Birney, D. F. Callen, J. F. Cheng, D. R. Cox, N. A. Doggett, N. P. Carter, E. E. Eichler, D. Haussler, J. R. Korenberg, C. C. Morton, D. Albertson, G. Schuler, P. J. de Jong, and B. J. Trask. 2001. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature 409:953-958.

Cowell, J. K., G. H. Barnett, and N. J. Nowak. 2004. Characterization of the 1p/19q chromosomal loss in oligodendrogliomas using comparative genomic hybridization arrays (CGHa). J.Neuropathol.Exp.Neurol. 63:151-158.

Nowak NJ, Gaile D, Conroy JM, McQuaid D, Cowell J, Carter R, Goggins MG, Hruban RH, Maitra A. Genome wide aberrations in pancreatic adenocarcinoma. Cancer, Genetics and Cytogenetics 161:36-50, 2005.

Nowak, N.J., Snijders, A., Conroy, J., and Albertson D.: The BAC Resources. Current Protocols in Human Genetics, 2005.

Cowell, J. K. and N. J. Nowak. 2003. High-resolution analysis of genetic events in cancer cells using bacterial artificial chromosome arrays and comparative genome hybridization. Adv.Cancer Res 90:91-125.

Snijders, A. M., N. J. Nowak, B. Huey, J. Fridlyand, S. Law, J. Conroy, T. Tokuyasu, K. Demir, R. Chiu, J. H. Mao, A. N. Jain, S. J. Jones, A. Balmain, D. Pinkel, and D. G. Albertson. 2005. Mapping segmental and sequence variations among laboratory mice using BAC array CGH. Genome Res 15:302-311.

Cowell, J. K. 2004. High throughput determination of gains and losses of genetic material using high resolution BAC arrays and comparative genomic hybridization. Comb.Chem.High Throughput.Screen. 7:587-596.

Snijders, A. M., N. Nowak, R. Segraves, S. Blackwood, N. Brown, J. Conroy, G. Hamilton, A. K. Hindle, B. Huey, K. Kimura, S. Law, K. Myambo, J. Palmer, B. Ylstra, J. P. Yue, J. W. Gray, A. N. Jain, D. Pinkel, and D. G. Albertson. 2001. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat.Genet. 29:263-264.

Cowell, J. K., S. Matsui, Y. D. Wang, J. LaDuca, J. Conroy, D. McQuaid, and N. J. Nowak. 2004. Application of bacterial artificial chromosome array-based comparative genomic hybridization and spectral karyotyping to the analysis of glioblastoma multiforme. Cancer Genet.Cytogenet. 151:36-51.

Cowell, J. K., Y. D. Wang, K. Head, J. Conroy, D. McQuaid, and N. J. Nowak. 2004. Identification and characterisation of constitutional chromosome abnormalities using arrays of bacterial artificial chromosomes. Br.J.Cancer 90:860-865.

Cowell JK, LaDuca J, Rossi MR, Burkhardt T, Nowak NJ, Matsui S-I. Molecular characterization of the t(3;9) translocation associated with immortalization in the MCF10A cell line. Cancer Genetics and Cytogenetics, 163:223-29, 2005.

Goidts V, Armengol L, Schempp W, Conroy J, Nowak N, Muller S, Cooper DN, Estivill X, Enard W, Szamalek JM, Hameister H, Kehrer-Sawatzki H. Identification of large-scale human-specific copy number differences by inter-species array comparative genomic hybridization. Hum Genet. Mar;119(1-2):185-98., 2006

Hodgson, G., J. H. Hager, S. Volik, S. Hariono, M. Wernick, D. Moore, N. Nowak, D. G. Albertson, D. Pinkel, C. Collins, D. Hanahan, and J. W. Gray. 2001. Genome scanning with array CGH delineates regional alterations in mouse islet carcinomas. Nat.Genet. 29:459-464.

Hackett, C. S., J. G. Hodgson, M. E. Law, J. Fridlyand, K. Osoegawa, P. J. de Jong, N. J. Nowak, D. Pinkel, D. G. Albertson, A. Jain, R. Jenkins, J. W. Gray, and W. A. Weiss. 2003. Genome-wide array CGH analysis of murine neuroblastoma reveals distinct genomic aberrations which parallel those in human tumors. Cancer Res. 63:5266-5273.

Alrawi SJ, Carroll RE, Hill HC, Gibbs JF, Tan D, Brenner BM, Nowak NJ, Swede H, Stoler DL, Anderson GR. Genomic instability of human aberrant crypt foci measured by inter-(simple sequence repeat) PCR and array-CGH. Mutat Res. 2006 Jun 26; [Epub ahead of print].

Deeb G, Baer MR, Gaile DP, Sait SN, Barcos M, Wetzler M, Conroy JM, Nowak NJ, Cowell JK, Cheney RT. Genomic profiling of myeloid sarcoma by array comparative genomic hybridization. Genes Chromosomes Cancer 44(4):373-383, 2005.

DeVries, S., S. Nyante, J. Korkola, R. Segraves, K. Nakao, D. Moore, H. Bae, M. Wilhelm, S. Hwang, and F. Waldman. 2005. Array-based comparative genomic hybridization from formalin-fixed, paraffin-embedded breast tumors. J.Mol.Diagn. 7:65-71.

Lassman AB, Rossi MR, Raizer JJ, Abrey LE, Lieberman FS, Grefe CN, Lamborn K, Pao W, Shih AH, Kuhn JG, Wilson R, Nowak NJ, Cowell JK, DeAngelis LM, Wen P, Gilbert MR, Chang S, Yung WA, Prados M, Holland EC. Molecular study of malignant gliomas treated with epidermal growth factor receptor inhibitors: tissue analysis from North American Brain Tumor Consortium Trials 01-03 and 00-01. Clin Cancer Res. 2005 Nov 1;11(21):7841-50.

Matsui SI, LaDuca J, Rossi MR, Nowak NJ, Cowell JK. Molecular characterization of a consistent 4.5 megabase deletion in 4q28 in prostate cancer cells. Cancer, Genetics and Cytogenetics, 159: 18-26, 2005.

Miliaras D, Grimbizis G, Conroy J, Psarra N, Miliaras S, Nowak N, Bontis J. Novel karyotypic changes detected by comparative genomic hybridization in a case of congenital cervical immature teratoma. Birth Defects Res A Clin Mol Teratol. 73(8):572-576, 2005.

Rossi MR, Gaile D, Laduca J, Matsui SI, Conroy J, McQuaid D, Chervinsky D, Eddy R, Chen HS, Barnett GH, Nowak NJ, Cowell JK. Identification of consistent novel submegabase deletions in low-grade oligodendrogliomas using array-based comparative genomic hybridization. Genes, Chromosomes, Cancer, 44:85-96, 2005.

Rossi MR, La Duca J, Matsui S, Nowak NJ, Hawthorn L, Cowell JK. Novel amplicons on the short arm of chromosome 7 identified using high resolution array CGH contain over expressed genes in addition to EGFR in glioblastoma multiforme. Genes Chromosomes Cancer. 44(4):392-404, 2005.

Rossi MR, Conroy J, McQuaid D Nowak NJ, Rutka JT, Cowell JK. An Array CGH Analysis of Pediatric Medulloblastomas. Genes Chromosomes Cancer. 2006 Mar;45(3):290-303.

Drazinic CM, Ercan-Sencicek AG, Gault LM, Hisama FM, Qumsiyeh MB, Nowak NJ, Cubells JF, State MW. 2005. Rapid array-based genomic characterization of a subtle structural abnormality: a patient with psychosis and der(18)t(5;18)(p14.1;p11.23). Am J Med Genet;134(3):282-9.

Varma G, Varma R, Huang H, Pryshchepava A, Groth J, Fleming D, Nowak NJ, McQuaid D, Conroy J, Mahoney M, Moysich K, Falkner KL, Geradts J. Array comparative genomic hybridisation (aCGH) analysis of premenopausal breast cancers from a nuclear fallout area and matched cases from Western New York. Br J Cancer 93(6):699-708, 2005.

Array analyses

Shankar G, Rossi MR, McQuaid DE, Conroy JM, Gaile DP, Cowell JK, Nowak NJ, Liang P. aCGHViewer: a generic visualization tool for aCGH data. Cancer Informatics 2:36-42, 2006.

Paris, P. L., A. Andaya, J. Fridlyand, A. N. Jain, V. Weinberg, D. Kowbel, J. H. Brebner, J. Simko, J. E. Watson, S. Volik, D. G. Albertson, D. Pinkel, J. C. Alers, T. H. Van Der Kwast, K. J. Vissers, F. H. Schroder, M. F. Wildhagen, P. G. Febbo, A. M. Chinnaiyan, K. J. Pienta, P. R. Carroll, M. A. Rubin, C. Collins, and H. Van Dekken. 2004. Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors. Hum.Mol Genet 13:1303-1313.

Troyanskaya, O., M. Cantor, G. Sherlock, P. Brown, T. Hastie, R. Tibshirani, D. Botstein, and R. B. Altman. 2001. Missing value estimation methods for DNA microarrays. Bioinformatics. 17:520-525.

Snijders, A. M., J. Fridlyand, D. A. Mans, R. Segraves, A. N. Jain, D. Pinkel, and D. G. Albertson. 2003. Shaping of tumor and drug-resistant genomes by instability and selection. Oncogene 22:4370-4379.

Olshen, A. B., E. S. Venkatraman, R. Lucito, and M. Wigler. 2004. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5:557-572.

Pavlidis, P., Q. Li, and W. S. Noble. 2003. The effect of replication on gene expression microarray experiments. Bioinformatics. 19:1620-1627.

Hwang, D., W. A. Schmitt, G. Stephanopoulos, and G. Stephanopoulos. 2002. Determination of minimum sample size and discriminatory expression patterns in microarray data. Bioinformatics. 18:1184-1193.

Nadiminty N, Lou W, Lee SO, Mehraein-Ghomi F, Kirk JS, Conroy JM, Zhang H, Gao AC. Prostate-specific antigen modulates genes involved in bone remodeling and induces osteoblast differentiation of human osteosarcoma cell line SaOS-2. Clin Cancer Res. 2006 Mar 1;12(5):1420-30.

Pan, W., J. Lin, and C. T. Le. 2002. How many replicates of arrays are required to detect gene expression changes in microarray experiments? A mixture model approach. Genome Biol. 3:research0022.

Collins Y, Tan DF, Pejovic T, Mor G, Qian F, Rutherford T, Varma R, McQuaid D, Driscoll D, Jiang M, Deeb G, Lele S, Nowak N, Odunsi K. 2004. Identification of differentially expressed genes in clinically distinct groups of serous ovarian carcinomas using cDNA microarray. Int J Mol Med.;14(1):43-53.

Minderman, H., Conroy, J., O’Loughlin, K.L., McQuaid, D., Quinn, P., Li, S., Pendyala L., Nowak, N., Baer, M.R. In vitro and in vivo irinotecan-induced changes in expression profiles of cell cycle and apoptosis-associated genes in acute myeloid leukemia cells. Mol Cancer Ther 4:885-900, 2005.

Genotyping

Chiu, N. H. and C. R. Cantor. 1999. Mass spectrometry of nucleic acids. Clin.Chem. 45:1578.

Ding, C., R. W. Chiu, T. K. Lau, T. N. Leung, L. C. Chan, A. Y. Chan, P. Charoenkwan, I. S. Ng, H. Y. Law, E. S. Ma, X. Xu, C. Wanapirak, T. Sanguansermsri, C. Liao, M. A. Ai, D. H. Chui, C. R. Cantor, and Y. M. Lo. 2004. MS analysis of single-nucleotide differences in circulating nucleic acids: Application to noninvasive prenatal diagnosis. Proc.Natl.Acad.Sci.U.S.A 101:10762-10767.

Honisch, C., A. Raghunathan, C. R. Cantor, B. O. Palsson, and B. D. van den. 2004. High-throughput mutation detection underlying adaptive evolution of Escherichia coli-K12. Genome Res 14:2495-2502.

Kammerer, S., R. B. Roth, R. Reneland, G. Marnellos, C. R. Hoyal, N. J. Markward, F. Ebner, M. Kiechle, U. Schwarz-Boeger, L. R. Griffiths, C. Ulbrich, K. Chrobok, G. Forster, G. M. Praetorius, P. Meyer, J. Rehbock, C. R. Cantor, M. R. Nelson, and A. Braun. 2004. Large-scale association study identifies ICAM gene region as breast and prostate cancer susceptibility locus. Cancer Res 64:8906-8910.

Kimura MT, Mori T, Conroy J, Nowak NJ, Satomi S, Tamai K, Nagase H. 2005. Two functional coding single nucleotide polymorphisms in STK15 (Aurora-A) coordinately increase esophageal cancer risk. Cancer Res. May 1;65(9):3548-54.

Genomics

McPherson, J. D., M. Marra, L. Hillier, R. H. Waterston, A. Chinwalla, J. Wallis, M. Sekhon, K. Wylie, E. R. Mardis, R. K. Wilson, R. Fulton, T. A. Kucaba, C. Wagner-McPherson, W. B. Barbazuk, S. G. Gregory, S. J. Humphray, L. French, R. S. Evans, G. Bethel, A. Whittaker, J. L. Holden, O. T. McCann, A. Dunham, C. Soderlund, C. E. Scott, D. R. Bentley, G. Schuler, H. C. Chen, W. Jang, E. D. Green, J. R. Idol, V. V. Maduro, K. T. Montgomery, E. Lee, A. Miller, S. Emerling, Kucherlapati, R. Gibbs, S. Scherer, J. H. Gorrell, E. Sodergren, K. Clerc-Blankenburg, P. Tabor, S. Naylor, D. Garcia, P. J. de Jong, J. J. Catanese, N. Nowak, K. Osoegawa, S. Qin, L. Rowen, A. Madan, M. Dors, L. Hood, B. Trask, C. Friedman, H. Massa, V. G. Cheung, I. R. Kirsch, T. Reid, R. Yonescu, J. Weissenbach, T. Bruls, R. Heilig, E. Branscomb, A. Olsen, N. Doggett, J. F. Cheng, T. Hawkins, R. M. Myers, J. Shang, L. Ramirez, J. Schmutz, O. Velasquez, K. Dixon, N. E. Stone, D. R. Cox, D. Haussler, W. J. Kent, T. Furey, S. Rogic, S. Kennedy, S. Jones, A. Rosenthal, G. Wen, M. Schilhabel, G. Gloeckner, G. Nyakatura, R. Siebert, B. Schlegelberger, J. Korenberg, X. N. Chen, A. Fujiyama, M. Hattori, A. Toyoda, T. Yada, H. S. Park, Y. Sakaki, N. Shimizu, S. Asakawa, K. Kawasaki, T. Sasaki, A. Shintani, A. Shimizu, K. Shibuya, J. Kudoh, S. Minoshima, J. Ramser, P. Seranski, C. Hoff, A. Poustka, R. Reinhardt, and H. Lehrach. 2001. A physical map of the human genome. Nature 409:934-941.

Gong, S., C. Zheng, M. L. Doughty, K. Losos, N. Didkovsky, U. B. Schambra, N. J. Nowak, A. Joyner, G. Leblanc, M. E. Hatten, and N. Heintz. 2003. A gene expression atlas of the central nervous system based on bacterial artificial chromosomes. Nature 425:917-925.

Osoegawa, K., A. G. Mammoser, C. Wu, E. Frengen, C. Zeng, J. J. Catanese, and P. J. de Jong. 2001. A bacterial artificial chromosome library for sequencing the complete human genome. Genome Res 11:483-496.

Osoegawa, K., M. Tateno, P. Y. Woon, E. Frengen, A. G. Mammoser, J. J. Catanese, Y. Hayashizaki, and P. J. de Jong. 2000. Bacterial artificial chromosome libraries for mouse sequencing and functional analysis. Genome Res 10:116-128.

Lage, J. M., J. H. Leamon, T. Pejovic, S. Hamann, M. Lacey, D. Dillon, R. Segraves, B. Vossbrinck, A. Gonzalez, D. Pinkel, D. G. Albertson, J. Costa, and P. M. Lizardi. 2003. Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH. Genome Res 13:294-307.