Chromosome aberrations in solid tumors

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Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications

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Mutations of the BRAF gene in human cancer

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Gene expression profiling predicts clinical outcome of breast cancer

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Studies of the HER-2/ neu Proto-Oncogene in Human Breast and Ovarian Cancer

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A Gene-Expression Signature as a Predictor of Survival in Breast Cancer

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Real time quantitative PCR.Preprint

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The fundamental role of epigenetic events in cancer

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PTEN , a Putative Protein Tyrosine Phosphatase Gene Mutated in Human Brain, Breast, and Prostate Cancer

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Comparative Genomic Hybridization for Molecular Cytogenetic Analysis of Solid Tumors

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Ploidy status rarely changes in myeloma patients at disease progression

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Reconstructing tumor amplisomes

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In vivo modeling of metastatic human high-grade serous ovarian cancer in mice

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Genomic Instability and Telomere Fusion of Canine Osteosarcoma Cells

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Genome Wide Analysis of Chromosomal Alterations in Oral Squamous Cell Carcinomas Revealed over Expression of MGAM and ADAM9

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Chromosomal Instability, Aneuploidy, and Gene Mutations in Human Sporadic Colorectal Adenomas

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Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysis

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An integrated genomic analysis of Tudor domain–containing proteins identifies PHD finger protein 20‐like 1 (PHF20L1) as a candidate oncogene in breast cancer

Jiang, Y., Liu, L., Shan, W., & Yang, Z.-Q. (2015) · Molecular Oncology · doi:10.1016/j.molonc.2015.10.013 · Cited by 32

Impaired nonhomologous end-joining in mismatch repair-deficient colon carcinomas

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DeAnnCNV: a tool for online detection and annotation of copy number variations from whole-exome sequencing data

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Correlation Between Histologic Assessment and Fluorescence In Situ Hybridization Using MelanoSITE in Evaluation of Histologically Ambiguous Melanocytic Lesions

Zembowicz, A., Yang, S.-E., Kafanas, A., & Lyle, S. R. (2012) · Archives of Pathology & Laboratory Medicine · doi:10.5858/arpa.2011-0673-oa · Cited by 31

An Improved Bayesian Information Criterion for Multiple Change-Point Models

Hannart, A., & Naveau, P. (2012) · Technometrics · doi:10.1080/00401706.2012.694780 · Cited by 31

Comparative analysis of algorithms for integration of copy number and expression data

Louhimo, R., Lepikhova, T., Monni, O., & Hautaniemi, S. (2012) · Nature Methods · doi:10.1038/nmeth.1893 · Cited by 30

A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets †

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Transcription Factors BARX1 and DLX4 Contribute to Progression of Clear Cell Renal Cell Carcinoma via Promoting Proliferation and Epithelial–Mesenchymal Transition

Sun, G., Ge, Y., Zhang, Y., Yan, L., Wu, X., Ouyang, W., Wang, Z., Ding, B., Zhang, Y., Long, G., et al. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.626328 · Cited by 30

Spontaneous transformation of murine epithelial cells requires the early acquisition of specific chromosomal aneuploidies and genomic imbalances

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Inhibition of Aurora-B function increases formation of multinucleated cells in p53 gene deficient cells and enhances anti-tumor effect of temozolomide in human glioma cells

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Integrated Analysis of Genetic Abnormalities of the Histone Lysine Methyltransferases in Prostate Cancer

Zhang, Y., Yan, L., Yao, W., Chen, K., Xu, H., & Ye, Z. (2019) · Medical Science Monitor · doi:10.12659/msm.912294 · Cited by 30

Global Survey of Chromatin Accessibility Using DNA MicroarraysPreprint

Weil, M. R., Widłak, P., Minna, J. D., & Garner, H. R. (2004) · Genome Research · doi:10.1101/gr.1396104 · Cited by 30

Chapter 6: Structural Variation and Medical Genomics

Raphael, B. J. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002821 · Cited by 32

Localization of sporadic neuroendocrine tumors by gene expression analysis of their metastases

Posorski, N., Kaemmerer, D., Ernst, G., Grabowski, P., Hoersch, D., Hommann, M., & von Eggeling, F. (2011) · Clinical & Experimental Metastasis · doi:10.1007/s10585-011-9397-5 · Cited by 29

A streamlined workflow for single-cells genome-wide copy-number profiling by low-pass sequencing of LM-PCR whole-genome amplification products

Ferrarini, A., Forcato, C., Buson, G., Tononi, P., Monaco, V. D., Terracciano, M., Bolognesi, C., Fontana, F., Medoro, G., Neves, R. P., et al. (2018) · PLoS ONE · doi:10.1371/journal.pone.0193689 · Cited by 30

Micronucleus formation in human cancer cells is biased by chromosome size

Bochtler, T., Kartal‐Kaess, M., Granzow, M., Hielscher, T., Cosenza, M. R., Herold‐Mende, C. C., Jauch, A. S., & Krämer, A. (2018) · Genes Chromosomes and Cancer · doi:10.1002/gcc.22707 · Cited by 29

The Progenetix oncogenomic resource in 2021

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Mitochondrial RNA methyltransferase TRMT61B is a new, potential biomarker and therapeutic target for highly aneuploid cancers

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Chapter 9 A Single Molecule System for Whole Genome Analysis

Zhou, S., Herschleb, J., & Schwartz, D. C. (2007) · Perspectives in bioanalysis · doi:10.1016/s1871-0069(06)02009-x · Cited by 29

Genomic aberrations in normal appearing mucosa fields distal from oral potentially malignant lesions

Giaretti, W., Maffei, M. E., Pentenero, M., Scaruffi, P., Donadini, A., Nallo, E. D., Malacarne, D., Marino, R., Familiari, U., Coco, S., et al. (2011) · Cellular Oncology · doi:10.1007/s13402-011-0064-2 · Cited by 29

Array comparative genomic hybridization analysis revealed four genomic prognostic biomarkers for primary gastric cancers

Tomioka, N., Morita, K., Kobayashi, N., Tada, M., Itoh, T., Saitoh, S., Kondo, M., Takahashi, N., Kataoka, A., Nakanishi, K., et al. (2010) · Cancer Genetics and Cytogenetics · doi:10.1016/j.cancergencyto.2010.04.017 · Cited by 29

Finding recurrent copy number alterations preserving within-sample homogeneity

Morganella, S., Pagnotta, S. M., & Ceccarelli, M. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr488 · Cited by 28

Genomic instability in radiation-induced mouse lymphoma from p53 heterozygous mice

Mao, J., Li, J., Jiang, T., Li, Q., Wu, D., Pérez‐Losada, J., Delrosario, R., Peterson, L. E., Balmain, A., & Cai, W. (2005) · Oncogene · doi:10.1038/sj.onc.1208926 · Cited by 28

p57KIP2 immunohistochemical staining of gestational trophoblastic tumours does not identify the type of the causative pregnancy

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Fusion of the Dhfr/Mtx and IR/MAR Gene Amplification Methods Produces a Rapid and Efficient Method for Stable Recombinant Protein Production

Noguchi, C., Araki, Y., Miki, D., & Shimizu, N. (2012) · PLoS ONE · doi:10.1371/journal.pone.0052990 · Cited by 28

Expression of the kinetochore protein Hec1 during the cell cycle in normal and cancer cells and its regulation by the pRb pathway

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Cytogenomics of cancers: From chromosome to sequence

Bernheim, A. (2010) · Molecular Oncology · doi:10.1016/j.molonc.2010.06.003 · Cited by 28

Chromosomal instability and APC gene mutations in human sporadic colorectal adenomas

Giaretti, W., Venesio, T., Prevosto, C., Lombardo, F., Ceccarelli, J., Molinu, S., & Risio, M. (2004) · The Journal of Pathology · doi:10.1002/path.1623 · Cited by 28

Wavelet Transformations of Tumor Expression Profiles Reveals a Pervasive Genome-Wide Imprinting of Aneuploidy on the Cancer Transcriptome

Aggarwal, A., Leong, S. H., Lee, C. Q. E., Kon, O. L., & Tan, P. B. O. (2005) · Cancer Research · doi:10.1158/0008-5472.186.65.1 · Cited by 28

Significance of estrogen receptor 1 (ESR-1) gene imbalances in colon and hepatocellular carcinomas based on tissue microarrays analysis

Tsiambas, E., Georgiannos, S. N., Salemis, N. S., Alexopoulou, D., Lambropoulou, S., Dimo, B., Ioannidis, I., Kravvaritis, C., Karameris, A., Patsouris, E., et al. (2010) · Medical Oncology · doi:10.1007/s12032-010-9554-8 · Cited by 27

Analytical platform evaluation for quantification of ERG in prostate cancer using protein and mRNA detection methods

He, J., Schepmoes, A., Shi, T., Wu, C., Fillmore, T., Gao, Y., Smith, R. D., Qian, W., Rodland, K., Liu, T., et al. (2015) · Journal of Translational Medicine · doi:10.1186/s12967-015-0418-z · Cited by 28

Analysis of the role of mutations in the KMT 2D histone lysine methyltransferase in bladder cancer

Ding, B., Yan, L., Zhang, Y., Wang, Z., Zhang, Y., Ding, X., Ye, Z., & Xu, H. (2019) · FEBS Open Bio · doi:10.1002/2211-5463.12600 · Cited by 27

Detailed Genome-Wide SNP Analysis of Major Salivary Carcinomas Localizes Subtype-Specific Chromosome Sites and Oncogenes of Potential Clinical Significance

Zhang, L., Mitani, Y., Caulı́n, C., Rao, P. H., Kies, M. S., Saintigny, P., Zhang, N., Weber, R. S., Lippman, S. M., & El‐Naggar, A. K. (2013) · American Journal Of Pathology · doi:10.1016/j.ajpath.2013.02.020 · Cited by 26

Chromosome integrity at a double-strand break requires exonuclease 1 and MRX

Nakai, W., Westmoreland, J., Yeh, E., Bloom, K., & Resnick, M. A. (2010) · DNA repair · doi:10.1016/j.dnarep.2010.10.004 · Cited by 28

Systematic Review of Genetic Variation in Chromosome 5p15.33 and Telomere Length as Predictive and Prognostic Biomarkers for Lung Cancer

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NDRG4 hypermethylation is a potential biomarker for diagnosis and prognosis of gastric cancer in Chinese population

Chen, X., Yang, Y., Liu, J., Li, B., Xu, Y., Li, C., Xu, Q., Liu, G., Chen, Y., Ying, J., et al. (2016) · Oncotarget · doi:10.18632/oncotarget.14099 · Cited by 27

HetRCNA: A Novel Method to Identify Recurrent Copy Number Alternations from Heterogeneous Tumor Samples Based on Matrix Decomposition Framework

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Genetic variation in DNA-repair pathways and response to radiochemotherapy in esophageal adenocarcinoma: a retrospective cohort study of the Eastern Cooperative Oncology Group

Yoon, H. H., Catalano, P. J., Murphy, K. M., Skaar, T. C., Philips, S., Powell, M. E., Montgomery, E. A., Hafez, M. J., Offer, S. M., Liu, G., et al. (2011) · BMC Cancer · doi:10.1186/1471-2407-11-176 · Cited by 26

Omics‐based profiling of carcinoma of the breast and matched regional lymph node metastasis

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Oncogene Expression and Genetic Background Influence the Frequency of DNA Copy Number Abnormalities in Mouse Pancreatic Islet Cell Carcinomas

Hager, J. H., Hodgson, J., Fridlyand, J., Hariono, S., Gray, J. W., & Hanahan, D. (2004) · Cancer Research · doi:10.1158/0008-5472.can-03-3522 · Cited by 25

Immune and genomic signatures in oral (head and neck) cancer

Chakraborty, P., Karmakar, T., Arora, N., & Mukherjee, G. (2018) · Heliyon · doi:10.1016/j.heliyon.2018.e00880 · Cited by 25

Cancer plasticity: Investigating the causes for this agility

Saha, S., Pradhan, N., Neha, B., Mahadevappa, R., Minocha, S., & Kumar, S. (2022) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2022.12.005 · Cited by 27

High level of chromosomal aberration in ovarian cancer genome correlates with poor clinical outcome

Cope, L., Wu, R., Shih, I., & Wang, T. (2012) · Gynecologic Oncology · doi:10.1016/j.ygyno.2012.11.031 · Cited by 24

High definition cytogenetics and oligonucleotide aCGH analyses of cisplatin‐resistant ovarian cancer cells

Prasad, M., Bernardini, M. Q., Tsalenko, A., Marrano, P. M., Paděrová, J., Lee, C., Ben‐Dor, A., Barrett, M. T., & Squire, J. A. (2008) · Genes Chromosomes and Cancer · doi:10.1002/gcc.20547 · Cited by 25

Serine hydroxymethyltransferase 2 expression promotes tumorigenesis in rhabdomyosarcoma with 12q13-q14 amplification

Nguyen, T., Vemu, P. L., Hoy, G. E., Boudjadi, S., Chatterjee, B., Shern, J. F., Khan, J. I., Sun, W., & Barr, F. G. (2021) · Journal of Clinical Investigation · doi:10.1172/jci138022 · Cited by 24

MET alterations in advanced non-small cell lung cancer

Sakamoto, M., & Patil, T. (2023) · Lung Cancer · doi:10.1016/j.lungcan.2023.02.018 · Cited by 24

Telomere-Centromere-Driven Genomic Instability Contributes to Karyotype Evolution in a Mouse Model of Melanoma

Silva, A. G. D. S., Graves, H. A., Guffei, A., Ricca, T. I., Mortara, R. A., Jasiulionis, M. G., & Mai, S. (2010) · Neoplasia · doi:10.1593/neo.91004 · Cited by 25

Ovarian Cancer: In Search of Better Marker Systems Based on DNA Repair Defects

Varga, D., Deniz, M., Schwentner, L., & Wiesmüller, L. (2013) · International Journal of Molecular Sciences · doi:10.3390/ijms14010640 · Cited by 23

p53 modulates homologous recombination at I-SceI-induced double-strand breaks through cell-cycle regulation

Rieckmann, T., Kriegs, M., Nitsch, L., Hoffer, K., Rohaly, G., Köcher, S., Petersen, C., Dikomey, E., Dornreiter, I., & Dahm‐Daphi, J. (2012) · Oncogene · doi:10.1038/onc.2012.123 · Cited by 27

Increased centrosome amplification in aged stem cells of the Drosophila midgut

Park, J., Pyo, J.-H., Na, H.-J., Jeon, H.-J., Kim, Y.-S., Arking, R., & Yoo, M. (2014) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2014.06.085 · Cited by 24

A Streamlined Method for Detecting Structural Variants in Cancer Genomes by Short Read Paired-End Sequencing

Mijušković, M., Brown, S. M., Tang, Z., Lindsay, C., Efstathiadis, E., Deriano, L., & Roth, D. B. (2012) · PLoS ONE · doi:10.1371/journal.pone.0048314 · Cited by 24

Cytomorphologic features of thyroid disease in patients with DICER1 mutations: A report of cytology–histopathology correlation in 7 patients

Darbinyan, A., Morotti, R. A., Cai, G., Prasad, M. L., Christison-Lagay, E. R., Dinauer, C., & Adeniran, A. (2020) · Cancer Cytopathology · doi:10.1002/cncy.22329 · Cited by 24

Aneuploidy in mitosis of PtK1 cells is generated by random loss and nondisjunction of individual chromosomes

Torosantucci, L., Puzzonia, M. D. S., Cenciarelli, C., Rens, W., & Degrassi, F. (2009) · Journal of Cell Science · doi:10.1242/jcs.047944 · Cited by 24

Measurements of metaphase and interphase chromosome aberrations transmitted through early cell replication rounds in human lymphocytes exposed to low-LET protons and high-LET 12C ions

Manti, L., Durante, M., Grossi, G., Ortenzia, O., Pugliese, M., Scampoli, P., & Gialanella, G. (2006) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/j.mrfmmm.2005.12.010 · Cited by 24

A Mechanism of Gene Amplification Driven by Small DNA Fragments

Mukherjee, K., & Storici, F. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1003119 · Cited by 27

Molecular therapeutics: promise and challenges

Kohn, E. C., Lu, Y., Wang, H., Yu, Q., Yu, S., Hall, H. S., Smith, D. L., Meric‐Bernstam, F., Hortobágyi, G. N., & Mills, G. B. (2004) · Seminars in Oncology · doi:10.1053/j.seminoncol.2004.01.009 · Cited by 24

Mechanisms of Topoisomerase I (TOP1) Gene Copy Number Increase in a Stage III Colorectal Cancer Patient Cohort

Smith, D. H., Christensen, I. J., Jensen, N. F., Markussen, B., Rømer, M. U., Nygård, S. B., Müller, S., Nielsen, H. J., Brünner, N., & Nielsen, K. V. (2013) · PLoS ONE · doi:10.1371/journal.pone.0060613 · Cited by 23

Evaluation of Topoisomerase IIa Expression in Pancreatic Ductal Adenocarcinoma: A Pilot Study Using Chromogenic in situ Hybridization and Immunohistochemistry on Tissue Microarrays

Tsiambas, E., Karameris, A., TINIAKOS, D. G., & Karakitsos, P. (2007) · Pancreatology · doi:10.1159/000101877 · Cited by 23

A transgenic system for generation of transposon Ac/Ds-induced chromosome rearrangements in rice

Yu, C., Han, F., Zhang, P., Birchler, J. A., & Peterson, T. (2012) · Theoretical and Applied Genetics · doi:10.1007/s00122-012-1925-4 · Cited by 23

Application of SNP Microarrays to the Genome-Wide Analysis of Chromosomal Instability in Premalignant Airway Lesions

Nakachi, I., Rice, J. L., Coldren, C. D., Edwards, M. G., Stearman, R. S., Glidewell, S. C., Varella‐Garcia, M., Franklin, W. A., Keith, R. L., Lewis, M. T., et al. (2013) · Cancer Prevention Research · doi:10.1158/1940-6207.capr-12-0485 · Cited by 23

Mechanisms of Sarcomagenesis

Matushansky, I., & Maki, R. G. (2005) · Hematology/Oncology Clinics of North America · doi:10.1016/j.hoc.2005.03.006 · Cited by 23

Selecting biomedical data sources according to user preferences

Cohen‐Boulakia, S., Lair, S., Stransky, N., Graziani, S., Radvanyi, F., Barillot, E., & Froidevaux, C. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth949 · Cited by 23

Chromosomal aberrations in squamous cell carcinomas of the upper aerodigestive tract: biologic insights and clinical opportunities

Wreesmann, V. B., & Singh, B. (2005) · Journal of Oral Pathology and Medicine · doi:10.1111/j.1600-0714.2005.00343.x · Cited by 24

Influence of methylenetetrahydrofolate reductase polymorphisms in oral cancer patients

Sailasree, R., Nalinakumari, K. R., Sebastian, P., & Kannan, S. (2010) · Journal of Oral Pathology and Medicine · doi:10.1111/j.1600-0714.2010.00943.x · Cited by 22

Chromosome instability in neuroblastoma (Review)

Fusco, P., Esposito, M. R., & Tonini, G. P. (2018) · Oncology Letters · doi:10.3892/ol.2018.9545 · Cited by 23

Signatures of Selection in Fusion Transcripts Resulting From Chromosomal Translocations in Human Cancer

de Mendíbil, I. O., Vizmanos, J. L., & Novo, F. J. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004805 · Cited by 21

Stromal control of oncogenic traits expressed in response to the overexpression of GLI2, a pleiotropic oncogene

Snijders, A. M., Huey, B., Connelly, S., Roy, R., Jordan, R. C., Schmidt, B. L., & Albertson, D. G. (2008) · Oncogene · doi:10.1038/onc.2008.421 · Cited by 22

Fusion between tumor cells enhances melanoma metastatic potential

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Clinical Characteristics and Outcome of Patients with Neuroblastoma Presenting Genomic Amplification of Loci Other than MYCN

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