The publications below provide a partial list of research citing BioDiscovery software. To add your research to the list, please contact us with the necessary information.

Nexus Copy NumberNexus ExpressionImaGene

Nexus Copy Number

Copy number variation in Fayoumi and Leghorn chickens analyzed using array comparative genomic hybridization.
Abernathy J, Li X, Jia X, Chou W, Lamont SJ, Crooijmans R, Zhou H. Anim Genet. 2014 Jun;45(3):400-11.

PRKAR1B mutation associated with a new neurodegenerative disorder with unique pathology.
Wong TH, Chiu WZ, Breedveld GJ, Li KW, Verkerk AJ, Hondius D, Hukema RK, Seelaar H, Frick P, Severijnen LA, Lammers GJ, Lebbink JH, van Duinen SG, Kamphorst W, Rozemuller AJ; Netherlands Brain Bank, Bakker EB; International Parkinsonism Genetics Network, Neumann M, Willemsen R, Bonifati V, Smit AB, van Swieten J. Brain. 2014 May;137(Pt 5):1361-73.

PARK20 caused by SYNJ1 homozygous Arg258Gln mutation in a new Italian family
Olgiati S, De Rosa A, Quadri M, Criscuolo C, Breedveld GJ, Picillo M, Pappatà S, Quarantelli M, Barone P, De Michele G, Bonifati V. Neurogenetics. 2014 May 10. [Epub ahead of print]

A genomic portrait of resectable hepatocellular carcinomas: Implications of RB1 and FGF19 aberrations for patient stratification.
Ahn SM, Jang SJ, Shim JH, Kim D, Hong SM, Sung CO, Baek D, Haq F, Ansari AA, Lee SY, Chun SM, Choi S, Choi HJ, Kim J, Kim S, Hwang S, Lee YJ, Lee JE, Jung WR, Jang HY, Yang E, Sung WK, Lee NP, Mao M, Lee C, Zucman-Rossi J, Yu E, Lee HC, Kong G. Hepatology. 2014 May 3. [Epub ahead of print]

Development of a conditionally immortalized human pancreatic β cell line.
Scharfmann R, Pechberty S, Hazhouz Y, von Bülow M, Bricout-Neveu E, Grenier-Godard M, Guez F, Rachdi L, Lohmann M, Czernichow P, Ravassard P. J Clin Invest. 2014 May 1;124(5):2087-98.

Reexpression of LSAMP inhibits tumor growth in a preclinical osteosarcoma

Zhang B, Levitt P, Murray M. Molecular Cancer 2014, April 28, 13:93

Mosaic loss of chromosome Y in peripheral blood is associated with shorter survival and higher risk of cancer
Forsberg LA, Rasi C, Malmqvist N, Davies H, Pasupulati S, Pakalapati G, Sandgren J, de Ståhl TD, Zaghlool A, Giedraitis V, Lannfelt L, Score J, Cross NC, Absher D, Janson ET, Lindgren CM, Morris AP, Ingelsson E, Lind L, Dumanski JP. Nat Genet. 2014 Apr 28. [Epub ahead of print]

Can genome array screening replace FISH as a front-line test in multiple myeloma?
Boneva T, Brazma D, Gancheva K, Howard-Reeves J, Raynov J, Grace C, Nacheva EP.
Genes Chromosomes Cancer. 2014 Apr 23. [Epub ahead of print]

DNA copy number changes in tumors within the spectrum of cellular, atypical, and metastasizing fibrous histiocytoma
Charli-Joseph Y, Saggini A, Doyle LA, Fletcher CD, Weier J, Mirza S, Vemula S, Leboit PE.
J Am Acad Dermatol. 2014 Apr 19. Epub ahead of print]

Genome-wide copy number analysis of cerebrospinal fluid tumor cells and their corresponding archival primary tumors
Mark Jesus M. Magbanuaa, Ritu Royb, Eduardo V. Sosaa, Louai Hauranieha, Andrea Kablaniana, Lauren E. Eisenbuda, Artem Ryazantseva, Alfred Aua, Janet H. Scotta, Michelle Meliskoa, John W. Park Genomics Data. 18 April 2014.

Cyclin E involved in early stage carcinogenesis of esophageal adenocarcinoma by SNP DNA microarray and immunohistochemical studies.
Zhou Z, Bandla S, Ye J, Xia Y, Que J, Luketich JD, Pennathur A, Peters JH, Tan D, Godfrey TE. BMC Gastroenterol. 2014 Apr 17;14(1):78. doi: 10.1186/1471-230X-14-78.

Oncogene-like induction of cellular invasion from centrosome amplification.
Godinho SA, Picone R, Burute M, Dagher R, Su Y, Leung CT, Polyak K, Brugge JS, Théry M, Pellman D. Nature. 2014 Apr 13. [Epub ahead of print]

Genomic Aberrations of BRCA1-Mutated Fallopian Tube Carcinomas.
Hunter SM, Ryland GL, Moss P; kConFab Investigators, Gorringe KL, Campbell IG. Am J Pathol. 2014 Apr 13. [Epub ahead of print]

Chromosomal Imbalances in Patients with Congenital Cardiac Defects: A Meta-analysis Reveals Novel Potential Critical Regions Involved in Heart Development.
Thorsson T, Russell WW, El-Kashlan N, Soemedi R, Levine J, Geisler SB, Ackley T, Tomita-Mitchell A, Rosenfeld JA, Töpf A, Tayeh M, Goodship J, Innis JW, Keavney B, Russell MW. Congenit Heart Dis. 2014 Apr 11. [Epub ahead of print]

Characterization of fibroblast growth factor receptor 1 in small-cell lung cancer.
Thomas A, Lee JH, Abdullaev Z, Park KS, Pineda M, Saidkhodjaeva L, Miettinen M, Wang Y, Pack SD, Giaccone G.
J Thorac Oncol. 2014 Apr;9(4):567-71.

Genomic Alterations in Pulmonary Adenocarcinoma In Situ in an Adolescent Patient.
Salomao M, Levy B, Nahum O, Chen J, Mansukhani M, Borczuk AC. Arch Pathol Lab Med. 2014 Apr;138(4):559-63.

Phenotypic, genomic and functional characterization reveals no differences between CD138++ and CD138low subpopulations in multiple myeloma cell lines.
Paíno T, Sarasquete ME, Paiva B, Krzeminski P, San-Segundo L, Corchete LA, Redondo A, Garayoa M, García-Sanz R, Gutiérrez NC, Ocio EM, San-Miguel JF. PLoS One. 2014 Mar 21;9(3):e92378. eCollection 2014.

DNA double-strand breaks cooperate with loss of Ink4 and Arf tumor suppressors to generate glioblastomas with frequent Met amplification.
Camacho CV, Todorova PK, Hardebeck MC, Tomimatsu N, Gil Del Alcazar CR, Ilcheva M, Mukherjee B, McEllin B, Vemireddy V, Hatanpaa K, Story MD, Habib AA, Murty VV, Bachoo R, Burma S. Oncogene. 2014 Mar 17. [Epub ahead of print]

A 1.37-Mb 12p11.22–p11.21 deletion coincident with a 367-kb 22q11.2 duplication detected by array comparative genomic hybridization in an adolescent girl with autism and difficulty in self-care of menstruation.
Chen CP, Lin SP, Chern SR, Wu PS, Su JW, Lee CC, Wang W. Taiwan J Obstet Gynecol. 2014 Mar;53(1):74-8.

Mosaic tetrasomy 9p at amniocentesis: Prenatal diagnosis, molecular cytogenetic characterization, and literature review.
Chen CP, Wang LK, Chern SR, Wu PS, Chen YT, Kuo YL, Chen WL, Lee MS, Wang W. Taiwan J Obstet Gynecol. 2014 Mar;53(1):79-85.

VPREB1 deletions occur independent of lambda light chain rearrangement in childhood acute lymphoblastic leukemia.
Mangum DS, Downie J, Mason CC, Jahromi MS, Joshi D, Rodic V, Müschen M, Meeker N, Trede N, Frazer JK, Zhou Y, Cheng C, Jeha S, Pui CH, Willman CL, Harvey RC, Hunger SP, Yang JJ, Barnette P, Mullighan CG, Miles RR, Schiffman JD. Leukemia. 2014 Jan;28(1):216-20.

Mutation in the SYNJ1 gene associated with autosomal recessive, early-onset parkinsonism
Quadri M, Fang M, Picillo M, Olgiati S, Breedveld GJ, Graafland J, Wu B, Xu F, Erro R, Amboni M, Pappatà S, Quarantelli M, Annesi G, Quattrone A, Chien HF, Barbosa ER; The International Parkinsonism Genetics Network, Oostra BA, Barone P, Wang J, Bonifati Hum Mutat. 2013 Sep. doi: 10.1002/humu.22373. Epub 2013 Aug 6.

Integrated high-resolution array CGH and SKY analysis of homozygous deletions and other genomic alterations present in malignant mesothelioma cell lines
Klorin G, Rozenblum E, Glebov O, Walker RL, Park Y, Meltzer PS, Kirsch IR, Kaye FJ, Roschke AV. Cancer Genet. 2013 Jul 4. pii: S2210-7762(13)00054-9. doi: 10.1016/j.cancergen.2013.04.006. [Epub ahead of print]

Identification of molecular candidates and interaction networks via integrative toxicogenomic analysis in a human cell line following low-dose exposure to the carcinogenic metals cadmium and nickel – See more at:
Kwon JY, Weon JI, Koedrith P, Park KS, Kim IS, Seo YR. Oncol Rep. 2013 Jul 4. doi: 10.3892/or.2013.2587. [Epub ahead of print]

Tumor genetic analyses of patients with metastatic melanoma treated with the BRAF inhibitor Dabrafenib (GSK2118436)
Nathanson KL, Martin AM, Wubbenhorst B, Greshock J, Letrero R, D’Andrea K, O’Day S, Infante JR, Falchook GS, Arkenau HT, Millward M, Brown MP, Pavlick A, Davies MA, Ma B, Gagnon R, Curtis CM, Lebowitz PF, Kefford RF, Long GV. Clin Cancer Res. 2013 Jul 5. [Epub ahead of print]

A dynamic database of microarray-characterized cell lines with various cytogenetic and genomic backgrounds.
Tang Z, Berlin DS, Toji L, Toruner GA, Beiswanger C, Kulkarni S, Martin CL, Emanuel BS, Christman M, Gerry NP. G3 (Bethesda). 2013 Jul 8;3(7):1143-9. doi: 10.1534/g3.113.006577.

Molecular inversion probe array for the genetic evaluation of stillbirth using formalin-fixed, paraffin-embedded tissue.
Rowe LR, Thaker HM, Opitz JM, Schiffman JD, Haddadin ZM, Erickson LK, South ST. J Mol Diagn. 2013 Jul;15(4):466-72. doi: 10.1016/j.jmoldx.2013.03.006. Epub 2013 May 10.

Clinical application of targeted and genome-wide technologies: can we predict treatment responses in chronic lymphocytic leukemia?
Reem Alsolami, Samantha JL Knight & Anna Schuh Personalized Medicine. June 2013, Vol. 10, No. 4, Pages 361-376.

Patient survival in uveal melanoma is not affected by oncogenic mutations in GNAQ and GNA11.
Koopmans AE, Vaarwater J, Paridaens D, Naus NC, Kilic E, de Klein A; Rotterdam Ocular Melanoma Study group. Br J Cancer. 2013 Jul 23;109(2):493-6. doi: 10.1038/bjc.2013.299. Epub 2013 Jun 18.

Genomic Signatures Predict Poor Outcome in Undifferentiated Pleomorphic Sarcomas and Leiomyosarcomas
Silveira SM, Villacis RA, Marchi FA, Barros Filho Mde C, Drigo SA, Neto CS, Lopes A, da Cunha IW, Rogatto SR. PLoS One. 2013 Jun 25;8(6):e67643. doi: 10.1371/journal.pone.0067643. Print 2013.

Single-nucleotide polymorphism-array improves detection rate of genomic alterations in core-binding factor leukemia
Costa AR, Vasudevan A, Krepischi A, Rosenberg C, Chauffaille Mde L. Med Oncol. 2013 Jun;30(2):579. doi: 10.1007/s12032-013-0579-7. Epub 2013 May 1.

Hypodiploid multiple myeloma is characterized by more aggressive molecular markers than non-hyperdiploid multiple myeloma.
Van Wier S, Braggio E, Baker A, Ahmann G, Levy J, Carpten JD, Fonseca R. Haematologica. 2013 Oct;98(10):1586-92. doi: 10.3324/haematol.2012.081083. Epub 2013 May 28.

Loss of dermatan sulfate epimerase (DSE) function results in musculocontractural Ehlers-Danlos syndrome.
Müller T, Mizumoto S, Suresh I, Komatsu Y, Vodopiutz J, Dundar M, Straub V, Lingenhel A, Melmer A, Lechner S, Zschocke J, Sugahara K, Janecke AR. Hum Mol Genet. 2013 Sep 15;22(18):3761-72. doi: 10.1093/hmg/ddt227. Epub 2013 May 23.

High rate of disease-related copy number variations in childhood onset schizophrenia.
Ahn K, Gotay N, Andersen TM, Anvari AA, Gochman P, Lee Y, Sanders S, Guha S, Darvasi A, Glessner JT, Hakonarson H, Lencz T, State MW, Shugart YY, Rapoport JL. Mol Psychiatry. 2013 May 21. doi: 10.1038/mp.2013.59. [Epub ahead of print]

Chromosomal copy number aberrations in colorectal metastases resemble their primary counterparts and differences are typically non-recurrent
Leonie J.M. Mekenkamp, Josien C. Haan, Daniëlle Israeli, Hendrik f. van Essen, Jeroen R. Dijkstra, Patricia van Cleef, Cornelis J.A. Punt, Gerrit A. Meijer, Iris D. Nagtegaal, Bauke Ylstra Dissertation. 2013. Studies in colorectal cancer metastases: implications for clinical practice.

TSC1 involvement in bladder cancer: diverse effects and therapeutic implications.
Guo Y, Chekaluk Y, Zhang J, Du J, Gray NS, Wu CL, Kwiatkowski DJ. J Pathol. 2013 May;230(1):17-27. Epub 2013 Mar 21.

Adenoid Cystic Carcinoma of the Lacrimal Gland: MYB Gene Activation, Genomic Imbalances, and Clinical Characteristics.
von Holstein SL, Fehr A, Persson M, Therkildsen MH, Prause JU, Heegaard S, Stenman G. Ophthalmology. 2013 Oct;120(10):2130-8. doi: 10.1016/j.ophtha.2013.03.030. Epub 2013 May 29

Increased CNV-Region deletions in mild cognitive impairment (MCI) and Alzheimer’s disease (AD) subjects in the ADNI sample
Guffanti G, Torri F, Rasmussen J, Clark AP, Lakatos A, Turner JA, Fallon JH, Saykin AJ, Weiner M; ADNI the Alzheimer’s Disease Neuroimaging Initiative, Vawter MP, Knowles JA, Potkin SG, Macciardi F. Genomics. 2013 Apr 11. pii: S0888-7543(13)00066-9. doi: 10.1016/j.ygeno.2013.04.004. [Epub ahead of print]

Genomic Abnormalities of Waldenström Macroglobulinemia and Related Low-Grade B-Cell Lymphomas
Braggio E, Fonseca R. Clin Lymphoma Myeloma Leuk. 2013 Apr;13(2):198-201. Epub 2013 Mar 9.

High-Resolution Survey in Familial Parkinson Disease Genes Reveals Multiple Independent Copy Number Variation Events in PARK2
Wang L, Nuytemans K, Bademci G, Jauregui C, Martin ER, Scott WK, Vance JM, Zuchner S. Hum Mutat. 2013 Apr 24. doi: 10.1002/humu.22344. [Epub ahead of print]

Combined Dup(7)(q22.1q32.2), Inv(7)(q31.31q31.33), and Ins(7;19)(q22.1;p13.2p13.2) in a 12-year-old boy with Developmental Delay and Various Dysmorphism.
Frühmesser A, Erdel M, Duba HC, Fauth C, Amberger A, Utermann G, Zschocke J, Kotzot D. Eur J Med Genet. 2013 Apr 19. pii: S1769-7212(13)00087-6. doi: 10.1016/j.ejmg.2013.04.003. [Epub ahead of print]

Inversion upstream of FOXF1 in a case of lethal alveolar capillary dysplasia with misalignment of pulmonary veins.
Parris T, Nik AM, Kotecha S, Langston C, Helou K, Platt C, Carlsson P. Am J Med Genet A. 2013 Apr;161(4):764-70. Epub 2013 Feb 26.

Age-specific signatures of glioblastoma at the genomic, genetic, and epigenetic levels.
Bozdag S, Li A, Riddick G, Kotliarov Y, Baysan M, Iwamoto FM, Cam MC, Kotliarova S, Fine HA. PLoS One. 2013 Apr 29;8(4):e62982. doi: 10.1371/journal.pone.0062982. Print 2013.

Age-Specific Signatures of Glioblastoma at the Genomic, Genetic, and Epigenetic Levels
Bozdag S, Li A, Riddick G, Kotliarov Y, Baysan M, et al. PLoS ONE 3013; 8(4): e62982. Epub Apr 31 2013.

DNA copy number profiling reveals extensive genomic loss in hereditary BRCA1 and BRCA2 ovarian carcinomas
Kamieniak MM, Muñoz-Repeto I, Rico D, Osorio A, Urioste M, García-Donas J, Hernando S, Robles-Díaz L, Ramón Y Cajal T, Cazorla A, Sáez R, García-Bueno JM, Domingo S, Borrego S, Palacios J, van de Wiel MA, Ylstra B, Benítez J, García MJ. British Journal of Cancer 108, 1732-1742 (30 April 2013) | doi:10.1038/bjc.2013.141

Post-zygotic Genetic Variation in Health and Disease
HAMID REZA RAZZAGHIAN Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 873

A Familial Deletion of 16q21 Characterized by an SNP Array and Associated With a Normal Phenotype.
Kowalczyk M, Tomaszewska A, Podbiol-Palenta A, Remiszewska B, Galjaard RJ, Zajaczek S, Srebniak MI. Am J Med Genet A. 2013 Apr 30:0. doi: 10.1002/ajmg.a.35912. [Epub ahead of print]

Identification of nine genomic regions of amplification in urothelial carcinoma, correlation with stage, and potential prognostic and therapeutic value
Chekaluk Y, Wu CL, Rosenberg J, Riester M, Dai Q, Lin S, Guo Y, McDougal WS, Kwiatkowski DJ. PLoS One. 2013 Apr 4;8(4):e60927. doi: 10.1371/journal.pone.0060927. Print 2013.

Genome-wide profiling of copy number alterations in triple-negative breast cancer identifies a region at 19p13 associated with lymph node metastasis
Felipe Fidalgo, Amanda Gonçalves, Tatiane Rodrigues, Alex Fiorini, Dirce M Carraro, Carla Rosenberg and Ana CV Krepischi. BMC Proceedings 2013, April 4, 7(Suppl 2):P24.

Copy number alteration signature defines undifferentiated pleomorphic sarcomas and leiomyosarcomas with poor prognosis
Sara M Silveira, Rolando R Andre Rios Villacis, Fabio A Marchi, Mateus de Camargo Barros Filho, Sandra D Linde, Cristovam S Neto, Isabela W da Cunha, Ademar Lopes and Silvia R Rogatto. BMC Proceedings 2013, 7(Suppl 2):P64

Succinate dehydrogenase mutation underlies global epigenomic divergence in gastrointestinal stromal tumor
Killian JK, Kim SY, Miettinen M, Smith C, Merino M, Tsokos M, Quezado M, Smith WI Jr, Jahromi MS, Xekouki P, Szarek E, Walker R, Lasota J, Raffeld M, Klotzle B, Wang Z, Jones L, Zhu YJ, Wang Y, Waterfall J, O’Sullivan M, Bibikova M, Pacak K, Stratakis CA, Janeway KA, Schiffman JD, Fan JB, Helman LJ, Meltzer PS. Cancer Discov. 2013 Apr 2. [Epub ahead of print]

Expanding probe repertoire and improving reproducibility in human genomic hybridization.
Dorman SN, Shirley BC, Knoll JH, Rogan PK. Nucleic Acids Res. 2013 Apr 1;41(7):e81. Epub 2013 Feb 1.

The molecular profile of adult T-cell acute lymphoblastic leukemia: mutations in RUNX1 and DNMT3A are associated with poor prognosis in T-ALL.
Grossmann V, Haferlach C, Weissmann S, Roller A, Schindela S, Poetzinger F, Stadler K, Bellos F, Kern W, Haferlach T, Schnittger S, Kohlmann A. Genes Chromosomes Cancer. 2013 Apr;52(4):410-22. Epub 2013 Jan 23.

Identification of Chromosomal Errors in Human Preimplantation Embryos with Oligonucleotide DNA Microarray
Liang L, Wang CT, Sun X, Liu L, Li M, Witz C, Williams D, Griffith J, Skorupski J, Haddad G, Gill J, Wang WH. PLoS One. 2013 Apr 16;8(4):e61838. doi: 10.1371/journal.pone.0061838. Print 2013.

Criteria for inference of chromothripsis in cancer genomes.
Korbel JO, Campbell PJ. Cell. 2013 Mar 14;152(6):1226-36.

Chromothripsis and Focal Copy Number Alterations Determine Poor Outcome in Malignant Melanoma
Hirsch D, Kemmerling R, Davis S, Camps J, Meltzer PS, Ried T, Gaiser T. Cancer Res. 2013 Mar 1;73(5):1454-60. Epub 2012 Dec 27.

Large duplication in MTM1 associated with myotubular myopathy.
Amburgey K, Lawlor MW, Del Gaudio D, Cheng YW, Fitzpatrick C, Minor A, Li X, Aughton D, Das S, Beggs AH, Dowling JJ. Neuromuscul Disord. 2013 Mar;23(3):214-8. Epub 2012 Dec 28.

Identification of prognostic gene signatures of glioblastoma: a study based on TCGA data analysis.
Kim YW, Koul D, Kim SH, Lucio-Eterovic AK, Freire PR, Yao J, Wang J, Almeida JS, Aldape K, Yung WK. Neuro Oncol. 2013 Mar 15. [Epub ahead of print]

Deficiency of FRAS1-related extracellular matrix 1 (FREM1) causes congenital diaphragmatic hernia in humans and mice.
Beck TF, Veenma D, Shchelochkov OA, Yu Z, Kim BJ, Zaveri HP, van Bever Y, Choi S, Douben H, Bertin TK, Patel PI, Lee B, Tibboel D, de Klein A, Stockton DW, Justice MJ, Scott DA. Hum Mol Genet. 2013 Mar 1;22(5):1026-38. Epub 2012 Dec 5.

263.4 kb deletion within the TCF4 gene consistent with Pitt-Hopkins syndrome, inherited from a mosaic parent with normal phenotype.
Kousoulidou L, Tanteles G, Moutafi M, Sismani C, Patsalis PC, Anastasiadou V. Eur J Med Genet. 2013 Mar 23. [Epub ahead of print]

Mitotically active proliferative nodule arising in a giant congenital melanocytic nevus: a diagnostic pitfall.
Nguyen TL, Theos A, Kelly DR, Busam K, Andea AA. Am J Dermatopathol. 2013 Feb;35(1):e16-21.

Recurrent loss of heterozygosity in 1p36 associated with TNFRSF14 mutations in IRF4 translocation negative pediatric follicular lymphomas.
Martin-Guerrero I, Salaverria I, Burkhardt B, Szczepanowski M, Baudis M, Bens S, de Leval L, Garcia-Orad A, Horn H, Lisfeld J, Pellissery S, Klapper W, Oschlies I, Siebert R. Haematologica. 2013 Feb 26. [Epub ahead of print]

CCND2 rearrangements are the most frequent genetic events in cyclin D1(-) mantle cell lymphoma.
Salaverria I, Royo C, Carvajal-Cuenca A, Clot G, Navarro A, Valera A, Song JY, Woroniecka R, Rymkiewicz G, Klapper W, Hartmann EM, Sujobert P, Wlodarska I, Ferry JA, Gaulard P, Ott G, Rosenwald A, Lopez-Guillermo A, Quintanilla-Martinez L, Harris NL, Jaffe ES, Siebert R, Campo E, Beà S. Blood. 2013 Feb 21;121(8):1394-402. Epub 2012 Dec 18.

Terminal Deletion 2q37.3 in a Patient with Klippel-Trenaunay-Weber Syndrome.
Puiu I, Stoica A, Sosoi S, Puiu A, Ioana M, Burada F. Fetal Pediatr Pathol. 2013 Feb 25. [Epub ahead of print]

Exonic deletions in AUTS2 cause a syndromic form of intellectual disability and suggest a critical role for the C terminus.
Beunders G, Voorhoeve E, Golzio C, Pardo LM, Rosenfeld JA, Talkowski ME, Simonic I, Lionel AC, Vergult S, Pyatt RE, van de Kamp J, Nieuwint A, Weiss MM, Rizzu P, Verwer LE, van Spaendonk RM, Shen Y, Wu BL, Yu T, Yu Y, Chiang C, Gusella JF, Lindgren AM, Morton CC, van Binsbergen E, Bulk S, van Rossem E, Vanakker O, Armstrong R, Park SM, Greenhalgh L, Maye U, Neill NJ, Abbott KM, Sell S, Ladda R, Farber DM, Bader PI, Cushing T, Drautz JM, Konczal L, Nash P, de Los Reyes E, Carter MT, Hopkins E, Marshall CR, Osborne LR, Gripp KW, Thrush DL, Hashimoto S, Gastier-Foster JM, Astbury C, Ylstra B, Meijers-Heijboer H, Posthuma D, Menten B, Mortier G, Scherer SW, Eichler EE, Girirajan S, Katsanis N, Groffen AJ, Sistermans EA. Am J Hum Genet. 2013 Feb 7;92(2):210-20. Epub 2013 Jan 17.

Complex craniosynostosis is associated with the 2p15p16.1 microdeletion syndrome.
Florisson JM, Mathijssen IM, Dumee B, Hoogeboom JA, Poddighe PJ, Oostra BA, Frijns JP, Koster L, de Klein A, Eussen B, de Vries BB, Swagemakers S, van der Spek PJ, Verkerk AJ. Am J Med Genet A. 2013 Feb;161A(2):244-53. Epub 2013 Jan 9.

Cerebellar and posterior fossa malformations in patients with autism-associated chromosome 22q13 terminal deletion
Aldinger KA, Kogan J, Kimonis V, Fernandez B, Horn D, Klopocki E, Chung B, Toutain A, Weksberg R, Millen KJ, Barkovich AJ, Dobyns WB. Am J Med Genet A. 2013 Jan;161A(1):131-6. Epub 2012 Dec 7.

Germline DNA Copy Number Aberrations Identified as Potential Prognostic Factors for Breast Cancer Recurrence
Sapkota Y, Ghosh S, Lai R, Coe BP, Cass CE, Yasui Y, Mackey JR, Damaraju S. PLoS One. 2013;8(1):e53850. Epub 2013 Jan 16.

Small Intestinal Neuroendocrine Tumor: A Rare Malignancy with Favorable Outcome
Norlén, O Acta Universitatis Upsaliensis. Digital Comprehensive Summaries of Uppsala
Dissertations from the Faculty of Medicine 844. 88 pp. Uppsala. ISBN 978-91-554-8548-1.

Post-zygotic Genetic Variation in Health and Disease
HAMID REZA RAZZAGHIAN Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 873

Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells.
Abyzov A, Mariani J, Palejev D, Zhang Y, Haney MS, Tomasini L, Ferrandino AF, Rosenberg Belmaker LA, Szekely A, Wilson M, Kocabas A, Calixto NE, Grigorenko EL, Huttner A, Chawarska K, Weissman S, Urban AE, Gerstein M, Vaccarino FM. Nature. 2012 Nov 18. doi: 10.1038/nature11629. [Epub ahead of print]

Copy number variation in pediatric multiple sclerosis.
McElroy J, Krupp L, Johnson B, McCauley J, Qi Z, Caillier S, Gourraud P, Yu J, Nathanson L, Belman A, Hauser S, Waubant E, Hedges D, Oksenberg J. Mult Scler. 2012 Dec 13. [Epub ahead of print]

Genomic profiling of isolated circulating tumor cells from metastatic breast cancer patients.
Magbanua MJ, Sosa EV, Roy R, Eisenbud LE, Scott JH, Olshen A, Pinkel D, Rugo H, Park JW. Cancer Res. 2012 Nov 7. [Epub ahead of print]

Novel tumor subgroups of urothelial carcinoma of the bladder defined by integrated genomic analysis
Hurst CD, Platt F, Taylor CF, Knowles MA. Clin Cancer Res. 2012 Aug 29. [Epub ahead of print]

A novel nonsense CDK5RAP2 mutation in a Somali child with primary microcephaly and sensorineural hearing loss
Pagnamenta, A. T., Murray, J. E., Yoon, G., Akha, E. S., Harrison, V., Bicknell, L. S., Ajilogba, K., Stewart, H., Kini, U., Taylor, J. C., Keays, D. A., Jackson, A. P. and Knight, S. J.L. Am J Med Genet A. 2012 Aug 10. doi: 10.1002/ajmg.a.35558. [Epub ahead of print]

Differentiation of malignant melanoma from benign nevus using a novel genomic microarray with low specimen requirements.
Chandler WM, Rowe LR, Florell SR, Jahromi MS, Schiffman JD, South ST. Arch Pathol Lab Med. 2012 Aug;136(8):947-55.

Clinically significant copy number alterations and complex rearrangements of MYB and NFIB in head and neck adenoid cystic carcinoma.
Persson M, Andrén Y, Moskaluk CA, Frierson HF Jr, Cooke SL, Futreal PA, Kling T, Nelander S, Nordkvist A, Persson F, Stenman G. Genes Chromosomes Cancer. 2012 Aug;51(8):805-17. Epub 2012 Apr 16.

Genomic characterization of testis cancer: association of alterations with outcome of clinical stage 1 mixed germ cell nonseminomatous germ cell tumor of the testis.
Mohamed GH, Gelfond JA, Nicolas MM, Brand TC, Sarvis JA, Leach RJ, Johnson-Pais TL. Urology. 2012 Aug;80(2):485.e1-5. Epub 2012 Apr 13.

A Comprehensive Characterization of Genome-Wide Copy Number Aberrations in Colorectal Cancer Reveals Novel Oncogenes and Patterns of Alterations
Xie T, D’ Ario G, Lamb JR, Martin E, Wang K, Tejpar S, Delorenzi M, Bosman FT, Roth AD, Yan P, Bougel S, Di Narzo AF, Popovici V, Budinská E, Mao M, Weinrich SL, Rejto PA, Hodgson JG. PLoS One. 2012;7(7):e42001. Epub 2012 Jul 31.

Recurrent mutations of MYD88 and TBL1XR1 in primary central nervous system lymphomas
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Benign hereditary chorea: phenotype, prognosis, therapeutic outcome and long term follow-up in a large series with new mutations in the TITF1/NKX2-1 gene
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Beyond KRAS mutation status: influence of KRAS copy number status and microRNAs on clinical outcome to cetuximab in metastatic colorectal cancer patients
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A tumour suppressor network relying on the polyamine-hypusine axis.
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Oncology In Vivo Data Integration for Hypothesis Generation
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Copy number aberrations of BCL2 and CDKN2A/B identified by array-CGH in thymic epithelial tumors
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Molecular inversion probes: a novel microarray technology and its application in cancer research
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Molecular inversion probe analysis detects novel copy number alterations in Ewing sarcoma.
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From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer.
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Identification of osteosarcoma driver genes by integrative analysis of copy number and gene expression data.
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Frequency of mesenchymal-epithelial transition factor gene (MET) and the catalytic subunit of phosphoinositide-3-kinase (PIK3CA) copy number elevation and correlation with outcome in patients with early stage breast cancer
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MicroRNA-24 regulates XIAP to reduce the apoptosis threshold in cancer cells
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Candidate locus analysis for PHACE syndrome.
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Genetic Prognostic Factors and Follow-up in Uveal Melanoma
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Mesenchymal stem cells derived from adipose tissue are not affected by renal disease
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Agenesis of the corpus callosum and gray matter heterotopia in three patients with constitutional mismatch repair deficiency syndrome
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Rare Copy Number Variants Observed in Hereditary Breast Cancer Cases Disrupt Genes in Estrogen Signaling and TP53 Tumor Suppression Network
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A Prominin-1-Rich Pediatric Glioblastoma: Biologic Behavior Is Determined by Oxygen Tension-Modulated CD133 Expression but Not Accompanied by Underlying Molecular Profiles
Laura K Donovan,* Nicola E Potter,† Tracy Warr,‡ and Geoffrey J Pilkington* Transl Oncol. 2012 June; 5(3): 141–154.

Chromosomal copy number alterations are associated with persistent lymph node metastasis after chemoradiation in locally advanced rectal cancer.
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A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions.
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A novel unbalanced de novo translocation der(5)t(4;5)(q26;q21.1) in adult T-cell precursor lymphoblastic leukemia
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Mitotic recombination of chromosome arm 17q as a cause of loss of heterozygosity of NF1 in neurofibromatosis type 1-associated glomus tumors
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Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes
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Down-regulation of ANAPC13 and CLTCL1: Early Events in the Progression of Preinvasive Ductal Carcinoma of the Breast
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Evidence of novel fine-scale structural variation at autism spectrum disorder candidate loci.
Hedges DJ, Hamilton-Nelson KL, Sacharow SJ, Nations L, Beecham GW, Kozhekbaeva ZM, Butler BL, Cukier HN, Whitehead PL, Ma D, Jaworski JM, Nathanson L, Lee JM, Hauser SL, Oksenberg JR, Cuccaro ML, Haines JL, Gilbert JR, Pericak-Vance MA. Mol Autism. 2012 Apr 2;3:2.

Down-regulation of ANAPC13 and CLTCL1: Early Events in the Progression of Preinvasive Ductal Carcinoma of the Breast.
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High-Resolution Genomic Profiling of Chromosomal Abnormalities in Human Stem Cells Using the 135 K StemArray.
Elliott AM, Hohenstein Elliott KA, Kammesheidt A. Stem Cells Int. 2012;2012:431534. Epub 2012 Apr 5.

Comparative genomics of esophageal adenocarcinoma and squamous cell carcinoma.
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Bilateral dysgerminoma associated with gonadoblastoma and sex-cord stromal tumour with annular tubules in a 28-year-old fertile woman with normal karyotype.
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Sequential array comparative genomic hybridization analysis identifies copy number changes during blastic transformation of chronic myeloid leukemia
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Characterization of Gene Amplification-Driven SKP2 Overexpression in Myxofibrosarcoma: Potential implications in tumor progression and therapeutics
Li CF, Wang JM, Kang HY, Huang CK, Wang JW, Fang FM, Wang YH, Wu WR, Li SH, Yu SC, Lee JC, Lan J, Shiue YL, Wu LC, Huang HY. Clin Cancer Res. 2012 Mar 15;18(6):1598-610. Epub 2012 Feb 9.

Genomic SNP array as a gold standard for prenatal diagnosis of foetal ultrasound abnormalities
Srebniak MI, Boter M, Oudesluijs GO, Cohen-Overbeek T, Govaerts LC, Diderich KE, Oegema R, Knapen MF, van de Laar IM, Joosten M, Van Opstal D, Galjaard RJ.

PTP1B is an androgen receptor-regulated phosphatase that promotes the progression of prostate cancer.
Lessard L, Labbé DP, Deblois G, Bégin LR, Hardy S, Mes-Masson AM, Saad F, Trotman LC, Giguère V, Tremblay ML. Cancer Res. 2012 Mar 15;72(6):1529-37. Epub 2012 Jan 26.

Duplication of CXC chemokine genes on chromosome 4q13 in a melanoma-prone family
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Multiplex ligation-dependent probe amplification equals fluorescence in-situ hybridization for the identification of patients at risk for metastatic disease in uveal melanoma.
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PTEN genomic deletions that characterize aggressive prostate cancer originate close to segmental duplications.
Yoshimoto M, Ludkovski O, DeGrace D, Williams JL, Evans A, Sircar K, Bismar TA, Nuin P, Squire JA. Genes Chromosomes Cancer. 2012 Feb;51(2):149-60. Epub 2011 Nov 1.

Age-related somatic structural changes in the nuclear genome of human blood cells.
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Diagnostic interpretation of array data using public databases and internet sources.
de Leeuw N, Dijkhuizen T, Hehir-Kwa JY, Carter NP, Feuk L, Firth HV, Kuhn RM, Ledbetter DH, Martin CL, van Ravenswaaij-Arts CM, Scherer SW, Shams S, Van Vooren S, Sijmons R, Swertz M, Hastings R. Hum Mutat. 2012 Feb 14. doi: 10.1002/humu.22049. [Epub ahead of print]

Deletion or epigenetic silencing of AJAP1 on 1p36 in glioblastoma
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Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis
Brown KH, Dobrinski KP, Lee AS, Gokcumen O, Mills RE, Shi X, Chong WW, Chen JY, Yoo P, David S, Peterson SM, Raj T, Choy KW, Stranger BE, Williamson RE, Zon LI, Freeman JL, Lee C. Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):529-34. Epub 2011 Dec 27.

A t(17;22)(q21;q12) with partial ETV4 deletion in a soft tissue Ewing sarcoma.
Rougemont AL, Bouron-Dal Soglio D, Patey-Mariaud de Serre N, Fetni R, Fan L, Barrette S, Fournet JC. Cancer Genet. 2012 Jan-Feb;205(1-2):55-60.

Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations
Rausch T, Jones DT, Zapatka M, Stütz AM, Zichner T, Weischenfeldt J, Jäger N, Remke M, Shih D, Northcott PA, Pfaff E, Tica J, Wang Q, Massimi L, Witt H, Bender S, Pleier S, Cin H, Hawkins C, Beck C, von Deimling A, Hans V, Brors B, Eils R, Scheurlen W, Blake J, Benes V, Kulozik AE, Witt O, Martin D, Zhang C, Porat R, Merino DM, Wasserman J, Jabado N, Fontebasso A, Bullinger L, Rücker FG, Döhner K, Döhner H, Koster J, Molenaar JJ, Versteeg R, Kool M, Tabori U, Malkin D, Korshunov A, Taylor MD, Lichter P, Pfister SM, Korbel JO. Cell. 2012 Jan 20;148(1-2):59-71.

Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer
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Thymic malignancies: from clinical management to targeted therapies.
Kelly RJ, Petrini I, Rajan A, Wang Y, Giaccone G. J Clin Oncol. 2011 Dec 20;29(36):4820-7. Epub 2011 Nov 21.

Genome-wide association of copy-number variation reveals an association between short stature and the presence of low-frequency genomic deletions.
Dauber A, Yu Y, Turchin MC, Chiang CW, Meng YA, Demerath EW, Patel SR, Rich SS, Rotter JI, Schreiner PJ, Wilson JG, Shen Y, Wu BL, Hirschhorn JN. Am J Hum Genet. 2011 Dec 9;89(6):751-9. Epub 2011 Nov 23.

Clonal diversity analysis using SNP microarray: a new prognostic tool for chronic lymphocytic leukemia
Zhang L, Znoyko I, Costa LJ, Conlin LK, Daber RD, Self SE, Wolff DJ. Cancer Genet. 2011 Dec;204(12):654-65.

Duplication of the ZIC2 gene is not associated with holoprosencephaly.
Jobanputra V, Burke A, Kwame AY, Shanmugham A, Shirazi M, Brown S, Warburton PE, Levy B, Warburton D. Am J Med Genet A. 2011 Nov 21.

Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity
Rasmussen M, Sundström M, Göransson Kultima H, Botling J, Micke P, Birgisson H, Glimelius B, Isaksson A. Genome Biol. 2011 Oct 24;12(10):R108.

Array-based genomic screening at diagnosis and during follow-up in chronic lymphocytic leukemia
Gunnarsson R, Mansouri L, Isaksson A, Göransson H, Cahill N, Jansson M, Rasmussen M, Lundin J, Norin S, Buhl AM, Smedby KE, Hjalgrim H, Karlsson K, Jurlander J, Geisler C, Juliusson G, Rosenquist R. Haematologica. 2011 Aug;96(8):1161-9. Epub 2011 May 5.

Cyclin Dependent Kinase 5 is amplified and over-expressed in pancreatic cancer and activated by mutant K-Ras
Eggers JP, Grandgenett PM, Collisson EC, Lewallen ME, Tremayne J, Singh PK, Swanson BJ, Andersen JM, Caffrey TC, High RR, Ouellette M, Hollingsworth MA. Clin Cancer Res. 2011 Oct 1;17(19):6140-50. Epub 2011 Aug 8.

Genome wide copy number analysis of paediatric Burkitt lymphoma using formalin-fixed tissues reveals a subset with gain of chromosome 13q and corresponding miRNA over expression
Schiffman JD, Lorimer PD, Rodic V, Jahromi MS, Downie JM, Bayerl MG, Sanmann JN, Althof PA, Sanger WG, Barnette P, Perkins SL, Miles RR. Br J Haematol. 2011 Nov;155(4):477-486.

Practical guidelines for interpreting copy number gains detected by high-resolution array in routine diagnostics.
Hanemaaijer NM, Sikkema-Raddatz B, van der Vries G, Dijkhuizen T, Hordijk R, van Essen AJ, Veenstra-Knol HE, Kerstjens-Frederikse WS, Herkert JC, Gerkes EH, Leegte LK, Kok K, Sinke RJ, van Ravenswaaij-Arts CM. Eur J Hum Genet. 2011 Sep 21.

Age- and gender-dependent obesity in individuals with 16p11.2 deletion
Yongguo Yua, Haitao Zhua, David T. Millera, James F. Gusellab, Orah S. Platta, Bai-Lin Wu. Journal of Genetics and Genomics, 2011 September;38(9):403-409.

Identification of PHLPP1 as a Tumor Suppressor Reveals the Role of Feedback Activation in PTEN-Mutant Prostate Cancer Progression
Muhan Chen, Christopher P. Pratt, Martha E. Zeeman, Nikolaus Schultz, Barry S. Taylor, Audrey O’Neill, Mireia Castillo-Martin, Dawid G. Nowak, Adam Naguib, Danielle M. Grace, Jernej Murn, Nick Navin, Gurinder S. Atwal, Chris Sander, William L. Gerald, Carlos Cordon-Cardo, Alexandra C. Newton, Brett S. Carver, Lloyd C. Trotman. Cancer Cell; 16 August 2011;20(2):173-186.

A stress response pathway regulates DNA damage through ß2-adrenoreceptors and ß-arrestin-1
Hara MR, Kovacs JJ, Whalen EJ, Rajagopal S, Strachan RT, Grant W, Towers AJ, Williams B, Lam CM, Xiao K, Shenoy SK, Gregory SG, Ahn S, Duckett DR, Lefkowitz RJ. Nature. 2011 Aug 21;477(7364):349-53.

Isolation of a new cell population in the glioblastoma microenvironment
Anne Clavreul, Amandine Etcheverry, Agnès Chassevent, Véronique Quillien, Tony Avril, Marie-Lise Jourdan, Sophie Michalak, Patrick François, Jean-Luc Carré and Jean Mosser, et al. Journal of Neuro-Oncology, 2011 August, online.

The 3q29 microdeletion syndrome: report of three new unrelated patients and in silico “RNA binding” analysis of the 3q29 region
Dasouki MJ, Lushington GH, Hovanes K, Casey J, Gorre M. July 2011. Am J Med Genet Part A 155:1654–1660.

Prostasomal DNA characterization and transfer into human sperm
Ronquist GK, Larsson A, Ronquist G, Isaksson A, Hreinsson J, Carlsson L, Stavreus-Evers A. Mol Reprod Dev. 2011 Jul;78(7):467-76.

Primary central nervous system lymphomas: a validation study of array-based comparative genomic hybridization in formalin-fixed paraffin-embedded tumor specimens
Braggio E, McPhail ER, Macon W, Lopes MB, Schiff D, Law M, Fink S, Sprau D, Giannini C, Dogan A, Fonseca R, O’Neill BP. Clin Cancer Res. 2011 Jul 1;17(13):4245-53.

7 Mb de novo deletion within 8q21 in a patient with distal arthrogryposis type 2B (DA2B)
Hofmann K, Becker J, Heller R, Boute O, Andrieux J, Hoyer J, Ekici AB, Reis A, Rauch A. Eur J Med Genet. 2011 Jun 21..

Structural Chromosome Abnormalities Associated with Obesity: Report of Four New Subjects and Review of Literature
J. Dasouki, Majed; L. Youngs, Erin; Hovanes, Karine. Current Genomics, Volume 12, Number 3, May 2011 , pp. 190-203(14).

Manitoba-oculo-tricho-anal (MOTA) syndrome is caused by mutations in FREM1
Slavotinek AM, Baranzini SE, Schanze D, Labelle-Dumais C, Short KM, Chao R, Yahyavi M, Bijlsma EK, Chu C, Musone S, Wheatley A, Kwok PY, Marles S, Fryns JP, Maga AM, Hassan MG, Gould DB, Madireddy L, Li C, Cox TC, Smyth I, Chudley AE, Zenker M. J Med Genet. 2011 Jun;48(6):375-82. Epub 2011 Apr 20.

High-resolution array CGH identifies common mechanisms that drive embryonal rhabdomyosarcoma pathogenesis
Paulson V, Chandler G, Rakheja D, Galindo RL, Wilson K, Amatruda JF, Cameron S. Genes Chromosomes Cancer. 2011 Jun;50(6):397-408. doi: 10.1002/gcc.20864. Epub 2011 Mar 15.

BCL6 enables Ph+ acute lymphoblastic leukaemia cells to survive BCR-ABL1 kinase inhibition
Duy C, Hurtz C, Shojaee S, Cerchietti L, Geng H, Swaminathan S, Klemm L, Kweon SM, Nahar R, Braig M, Park E, Kim YM, Hofmann WK, Herzog S, Jumaa H, Koeffler HP, Yu JJ, Heisterkamp N, Graeber TG, Wu H, Ye BH, Melnick A, Müschen M. Nature. 2011 May 19;473(7347):384-8.

Early G1 cyclin-dependent kinases as prognostic markers and potential therapeutic targets in esophageal adenocarcinoma
Amin Ismail*, Santhoshi Bandla, Marie Reveiller, Liana Toia, Zhongren Zhou, William E Gooding, Irina Kalatskaya, Lincoln Stein, Mary D’Souza, Virginia R Litle, Jeffrey H Peters, Arjun Pennathur, James D. Luketich, and Tony E Godfrey. Clin Cancer Res. 2011 May 18. [Epub ahead of print]

Maffucci syndrome: A genome-wide analysis using high resolution single nucleotide polymorphism and expression arrays on four cases.
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Molecular Karyotypes of Hodgkin and Reed-Sternberg Cells at Disease Onset Reveal Distinct Copy Number Alterations in Chemosensitive versus Refractory Hodgkin Lymphoma
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Chromosomal copy number alterations are associated with tumor response to chemoradiation in locally advanced rectal cancer.
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Unknown partner for USP6 and unusual SS18 rearrangement detected by fluorescence in situ hybridization in a solid aneurysmal bone cyst.
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Alternative lengthening of telomeres-An enhanced chromosomal instability in aggressive non-MYCN amplified and telomere elongated neuroblastomas
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Molecular characterization of acquired tolerance of tumor cells to picropodophyllin (PPP)
Hashemi J, Worrall C, Vasilcanu D, Fryknäs M, Sulaiman L, Karimi M, Weng WH, Lui WO, Rudduck C, Axelson M, Jernberg-Wiklund H, Girnita L, Larsson O, Larsson C. PLoS One. 2011 Mar 14;6(3):e14757.

Recognition of potential predictive markers for diagnosis in Korean serous ovarian cancer patients at stage IIIc using array comparative genomic hybridization with high resolution
Jee Young Kwon, Young Rok Seo and Woong Shick Ahn. Molecular & Cellular Toxicology. 2011 Mar; 7(1):77-86.

Genome-wide studies of copy number variation and exome sequencing identify rare variants in BAG3 as a cause of dilated cardiomyopathy.
Norton N, Li D, Rieder MJ, Siegfried JD, Rampersaud E, Züchner S, Mangos S, Gonzalez-Quintana J, Wang L, McGee S, Reiser J, Martin E, Nickerson DA, Hershberger RE. Am J Hum Genet. 2011 Mar 11;88(3):273-82. Epub 2011 Feb 25.

High-resolution genomic screening in mantle cell lymphoma–specific changes correlate with genomic complexity, the proliferation signature and survival
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Genome-wide analysis of Ollier disease: Is it all in the genes?
Pansuriya TC, Oosting J, Krenács T, Taminiau AH, Verdegaal SH, Sangiorgi L, Sciot R, Hogendoorn PC, Szuhai K, Bovée JV. Orphanet J Rare Dis. 2011 Jan 14;6(1):2.

Accuracy of CNV Detection from GWAS Data
Zhang D, Qian Y, Akula N, Alliey-Rodriguez N, Tang J; Bipolar Genome Study, Gershon ES, Liu C. PLoS One. 2011 Jan 13;6(1):e14511.

Evidence-based genomic diagnosis characterized chromosomal and cryptic imbalances in 30 elderly patients with myelodysplastic syndrome and acute myeloid leukemia
Renu Bajaj, Fang Xu, Bixia Xiang, Katherine Wilcox, Autumn J DiAdamo, Rachana Kumar, Alexandra Pietraszkiewicz, Stephanie Halene, Peining Li. Molecular Cytogenetics, 2011 Jan; 4:3.

A new 17p13.3 microduplication including the PAFAH1B1 and YWHAE genes resulting from an unbalanced X;17 translocation
Hyon C, Marlin S, Chantot-Bastaraud S, Mabboux P, Beaujard MP, Al Ageeli E, Vazquez MP, Picard A, Siffroi JP, Portnoï MF. Eur J Med Genet. 2010 Dec 31. [Epub ahead of print]

Small Molecule Inhibition of GDC-0449 Refractory Smoothened Mutants and Downstream Mechanisms of Drug Resistance
Dijkgraaf GJ, Alicke B, Weinmann L, Januario T, West K, Modrusan Z, Burdick D, Goldsmith R, Robarge K, Sutherlin D, Scales SJ, Gould SE, Yauch RL, de Sauvage FJ. Cancer Res. 2011 Jan 15;71(2):435-44. Epub 2010 Dec 1

Molecular characterization of putative chordoma cell lines
Brüderlein S, Sommer JB, Meltzer PS, Li S, Osada T, Ng D, Möller P, Alcorta DA, Kelley MJ. Sarcoma. 2010; Epub 2010 Dec 30.

Comparable low-level mosaicism in affected and non affected tissue of a complex CDH patient
Veenma D, Beurskens N, Douben H, Eussen B, Noomen P, Govaerts L, Grijseels E, Lequin M, de Krijger R, Tibboel D, de Klein A, Van Opstal D. PLoS One. 2010 Dec 21;5(12).

Common pathogenetic mechanism involving human chromosome 18 in familial and sporadic ileal carcinoid tumors
Janet L. Cunningham, Teresita Díaz de Ståhl, Tobias Sjöblom, Gunnar Westin, Jan P. Dumanski, Eva T. Janson. 2010 Nov. Genes, Chromosomes and Cancer.

Targeted resequencing of candidate genes using selector probes
H. Johansson, M. Isaksson, E. Falk Sörqvist, F. Roos, J. Stenberg, T. Sjöblom, J. Botling, P. Micke, K. Edlund, S. Fredriksson, H. Göransson Kultima, Olle Ericsson, and Mats Nilsson. 2010 Nov. Nucleic Acids Research.

Gene copy number variation in male breast cancer by aCGH
Stefania Tommasi, Anita Mangia, Giuseppina Iannelli, Patrizia Chiarappa, Elena Rossi, Laura Ottini, Marcella Mottolese, Wainer Zoli, Orsetta Zuffardi, Angelo Paradiso. 2010 Nov. Analytical Cellular Pathology / Cellular Oncology.

Archival Fine-Needle Aspiration Cytopathology (FNAC) Samples
Untapped Resource for Clinical Molecular Profiling

J. Keith Killian, Robert L. Walker, Miia Suuriniemi, Laura Jones, Stephanie Scurci, Parvati Singh, Robert Cornelison, Shannon Harmon, Nichole Boisvert, Jack Zhu, Yonghong Wang, Sven Bilke, Sean Davis, Giuseppe Giaccone , William I. Smith, Jr and Paul S. Meltzer. J Mol Diagn. Nov 2010; 12: 739-745

Genomic, immunophenotypic, and NPM1/FLT3 mutational studies on 17 patients with normal karyotype acute myeloid leukemia (AML) followed by aberrant karyotype AML at relapse.
Wang ES, Sait SN, Gold D, Mashtare T, Starostik P, Ford LA, Wetzler M, Nowak NJ, Deeb G. Cancer Genet Cytogenet. 2010 Oct 15;202(2):101-7.

No Haploinsufficiency but Loss of Heterozygosity for EXT in Multiple Osteochondromas
Reijnders CM, Waaijer CJ, Hamilton A, Buddingh EP, Dijkstra SP, Ham J, Bakker E, Szuhai K, Karperien M, Hogendoorn PC, Stringer SE, Bovée JV. Am J Pathol. 2010 Oct;177(4):1946-57. Epub 2010 Sep 2.

Distinctive Phenotypic Abnormalities Associated with Submicroscopic 21q22 Deletion Including DYRK1A
R. Oegemaa, A. de Kleina, A.J. Verkerkb, R. Schota, B. Dumeeb, H. Doubena, B. Eussena, L. Dubbela, P.J. Poddighea, I. van der Laara, W.B. Dobynsc, P.J. van der Spekb, M.H. Lequind, I.F.M. de Cooe, M.-C.Y. de Wite, M.W. Wesselsa, G.M.S. Mancinia. Mol Syndromol 2010 Sept; 1:113-120.

Molecular diversity in ductal carcinoma in situ (DCIS) and early invasive breast cancer
Muggerud AA, Hallett M, Johnsen H, Kleivi K, Zhou W, Tahmasebpoor S, Amini RM, Botling J, Børresen-Dale AL, Sørlie T, Wärnberg F. Mol Oncol. 2010 Aug;4(4):357-68.

Evaluation of high-resolution microarray platforms for genomic profiling of bone tumours
Kresse SH, Szuhai K, Barragan-Polania AH, Rydbeck H, Cleton-Jansen AM, Myklebost O, Meza-Zepeda LA. BMC Res Notes. 2010 Aug 8;3:223.

A de novo duplication of Xp11.22-p11.4 in a girl with intellectual disability, structural brain anomalies, and preferential inactivation of the normal X chromosome.
Holden ST, Clarkson A, Thomas NS, Abbott K, James MR, Willatt L. Am J Med Genet A. 2010 Jul;152A(7):1735-40.

Loss of p15/Ink4b accompanies tumorigenesis triggered by complex DNA double-strand breaks
Camacho CV, Mukherjee B, McEllin B, Ding LH, Hu B, Habib A, Xie XJ, Nirodi C, Saha D, Story M, Balajee A, Bachoo RM, Boothman DA, Burma S. Carcinogenesis. 2010 Jul 26. [Epub ahead of print]

Application of Nexus Copy Number Software for CNV Detection and Analysis.
Bert Eussen and Annelies de Klein. European Cytogeneticists Association Newsletter. July 2010.

A novel mutation of GATA4 in a familial atrial septal defect
Chen Y, Mao J, Sun Y, Zhang Q, Cheng HB, Yan WH, Choy KW, Li H. Clin Chim Acta. 2010 Jul 24. [Epub ahead of print]
NF1 Is a Tumor Suppressor in Neuroblastoma that Determines Retinoic Acid Response and Disease Outcome

Michael Hölzel, Sidong Huang, Jan Koster, Ingrid Øra, Arjan Lakeman, Huib Caron, Wouter Nijkamp, Jing Xie, Tom Callens, Shahab Asgharzadeh, Robert C. Seeger, Ludwine Messiaen, Rogier Versteeg, René Bernards. Cell – 23 July 2010

Array comparative genomic hybridization-based characterization of genetic alterations in pulmonary neuroendocrine tumors
Voortman J, Lee JH, Killian JK, Suuriniemi M, Wang Y, Lucchi M, Smith WI Jr, Meltzer P, Wang Y, Giaccone G. Proc Natl Acad Sci U S A. 2010 Jul 20;107(29):13040-5.

Genetic profiles of gastroesophageal cancer: combined analysis using expression array and tiling array–comparative genomic hybridization
Isinger-Ekstrand A, Johansson J, Ohlsson M, Francis P, Staaf J, Jönsson M, Borg A, Nilbert M. Cancer Genet Cytogenet. 2010 Jul 15;200(2):120-6.

Patterns and incidence of chromosomal instability and their prognostic relevance in breast cancer subtypes
Smid M, Hoes M, Sieuwerts AM, Sleijfer S, Zhang Y, Wang Y, Foekens JA, Martens JW. Breast Cancer Res Treat. 2010 Jul 15. [Epub ahead of print]

Low grade mosaic for a complex supernumerary ring chromosome 18 in an adult patient with multiple congenital anomalies
van der Veken LT, Dieleman MM, Douben H, van de Brug JC, van de Graaf R, Hoogeboom AJ, Poddighe PJ, de Klein A. Mol Cytogenet. 2010 Jul 9;3:13.

Clinical Implications of Gene Dosage and Gene Expression Patterns in Diploid Breast Carcinoma.
Parris TZ, Danielsson A, Nemes S, Kovács A, Delle U, Fallenius G, Möllerström E, Karlsson P, Helou K. Clin Cancer Res. 2010 Jun 15.

HDMX regulates p53 activity and confers chemoresistance to 3-Bis (2-chloroethyl)-1-nitrosoureaG
Jin G, Cook S, Cui B, Chen WC, Keir ST, Killela P, Di C, Payne CA, Gregory SG, McLendon R, Bigner DD, Yan H. Neuro Oncol. 2010 May 14. [Epub ahead of print]

Tourette disorder spectrum maps to chromosome 14q31. 1 in an Italian kindred
Breedveld GJ, Fabbrini G, Oostra BA, Berardelli A, Bonifati V. Neurogenetics. 2010 May 2. [Epub ahead of print]

High-density screening reveals a different spectrum of genomic aberrations in chronic lymphocytic leukemia patients with “stereotyped” IGHV3-21 and IGHV4-34 B cell receptors
Marincevic M, Cahill N, Gunnarsson R, Isaksson A, Mansouri M, Göransson H, Rasmusson M, Jansson M, Ryan F, Karlsson K, Adami HO, Davi F, Jurlander J, Juliusson G, Stamatopoulus K, Rosenquist R. Haematologica. 2010 Apr 26. [Epub ahead of print]

Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis.
Baranzini SE, Mudge J, van Velkinburgh JC, Khankhanian P, Khrebtukova I, Miller NA, Zhang L, Farmer AD, Bell CJ, Kim RW, May GD, Woodward JE, Caillier SJ, McElroy JP, Gomez R, Pando MJ, Clendenen LE, Ganusova EE, Schilkey FD, Ramaraj T, Khan OA, Huntley JJ, Luo S, Kwok PY, Wu TD, Schroth GP, Oksenberg JR, Hauser SL, Kingsmore SF. Nature. 2010 Apr 29;464(7293):1351-6.

A pathway-based classification of human breast cancer.
Gatza ML, Lucas JE, Barry WT, Kim JW, Wang Q, Crawford MD, Datto MB, Kelley M, Mathey-Prevot B, Potti A, Nevins JR. Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):6994-9. Epub 2010 Mar 24.

Analysis of Segmental Duplications, Mouse Genome Synteny and Recurrent Cancer-Associated Amplicons in Human Chromosome 6p21–p12
J.W. Martin, M. Yoshimoto, O. Ludkovski, P.S. Thorner, M. Zielenska, J.A. Squire, P.A.S. Nuin. Cytogenet Genome Res 2010;128:199-213

Oligonucleotide-based array CGH analysis of diffuse large B-cell lymphomas identifies gain of 7q22 as the most common genomic alteration
Edward A. Medina, Aswani R Bolla, Rajya L Bandi and Ryan S Robetorye. FASEB J. 2010 24:954.11.

Application of Nexus Copy Number Software for CNV Detection and Analysis.
Darvishi K. Curr Protoc Hum Genet. 2010 Apr;Chapter 4:Unit4.14.

In-depth investigation of the molecular pathogenesis of bladder cancer in a unique 26-year old patient with extensive multifocal disease: a case report.
Zuiverloon TC, Abas CS, van der Keur KA, Vermeij M, Tjin SS, van Tilborg AG, Busstra M, Zwarthoff EC.BMC Urol. 2010 Feb 26;10:5.

Unfavorable prognosis of CRTC1-MAML2 positive mucoepidermoid tumors with CDKN2A deletions.
Anzick SL, Chen WD, Park Y, Meltzer P, Bell D, El-Naggar AK, Kaye FJ. Genes Chromosomes Cancer. 2010 Jan;49(1):59-69.

Genomic alterations in histopathologically normal breast tissue from BRCA1 mutation carriers may be caused by BRCA1 haploinsufficiency.
Rennstam K, Ringberg A, Cunliffe HE, Olsson H, Landberg G, Hedenfalk I.Genes Chromosomes Cancer. 2010 Jan;49(1):78-90.

Frequent genetic differences between matched primary and metastatic breast cancer provide an approach to identification of biomarkers for disease progression.
Andrzej B Poplawski, Michal Jankowski, Stephen W Erickson, Teresita Díaz de Ståhl, E Christopher Partridge, Chiquito Crasto, Jingyu Guo, John Gibson, Uwe Menzel, Carl EG Bruder, et al. European Journal of Human Genetics (6 January 2010).

Genetics of uveal melanoma
Hanneke W Mensink, Dion Paridaens, Annelies de Klein Expert Review of Ophthalmology, December 2009, Vol. 4, No. 6, Pages 607-616.

Copy number variations are a rare cause of non-CMT1A Charcot-Marie-Tooth disease.
Huang J, Wu X, Montenegro G, Price J, Wang G, Vance JM, Shy ME, Züchner S. J Neurol. 2009 Dec 1. [Epub ahead of print]

Detailed cytogenetic and array analysis of pediatric primitive sarcomas reveals a recurrent CIC-DUX4 fusion gene event.
Yoshimoto M, Graham C, Chilton-MacNeill S, Lee E, Shago M, Squire J, Zielenska M, Somers GR. Cancer Genet Cytogenet. 2009 Nov;195(1):1-11.

Genomic Landscape of Meningiomas.
Lee Y, Liu J, Patel S, Cloughesy T, Lai A, Farooqi H, Seligson D, Dong J, Liau L, Becker D, Mischel P, Shams S, Nelson S.Brain Pathol. 2009 Nov 20. [Epub ahead of print]

Glioblastoma Proto-oncogene SEC61-gamma Is Required for Tumor Cell Survival and Response to Endoplasmic Reticulum Stress.
Lu Z, Zhou L, Killela P, Rasheed AB, Di C, Poe WE, McLendon RE, Bigner DD, Nicchitta C, Yan H. Cancer Res. 2009 Nov 17. [Epub ahead of print]

High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians
Hajime Matsuzaki , Pei-Hua Wang , Jing Hu , Rich Rava and Glenn K Fu, Genome Biology 2009, 9 Nov., 10:R125

Integrative genomics reveals mechanisms of copy number alterations responsible for transcriptional deregulation in colorectal cancer
Camps J, Nguyen QT, Padilla-Nash HM, Knutsen T, McNeil NE, Wangsa D, Hummon AB, Grade M, Ried T, Difilippantonio MJ. Genes Chromosomes Cancer. 2009 Nov;48(11):1002-17.

CNTNAP2 and NRXN1 are mutated in autosomal-recessive Pitt-Hopkins-like mental retardation and determine the level of a common synaptic protein in Drosophila.

Zweier C, de Jong EK, Zweier M, Orrico A, Ousager LB, Collins AL, Bijlsma EK, Oortveld MA, Ekici AB, Reis A, Schenck A, Rauch A. Am J Hum Genet. 2009 Nov;85(5):655-66. Epub 2009 Nov 5.

Microarray based analysis of 3p25-p26 deletions (3p- syndrome).
Shuib S, McMullan D, Rattenberry E, Barber RM, Rahman F, Zatyka M, Chapman C, Macdonald F, Latif F, Davison V, Maher ER. Am J Med Genet A. 2009 Oct;149A(10):2099-105.

Genomic and epigenetic evidence for oxytocin receptor deficiency in autism.
Gregory SG, Connelly JJ, Towers AJ, Johnson J, Biscocho D, Markunas CA, Lintas C, Abramson RK, Wright HH, Ellis P, Langford CF, Worley G, Delong GR, Murphy SK, Cuccaro ML, Persico A, Pericak-Vance MA.
BMC Med. 2009 Oct 22;7:62.

Disruption of ST5 is associated with mental-retardation and multiple congenital anomalies.
Göhring I, Tagariello A, Endele S, Stolt CC, Ghassibé M, Fisher M, Thiel CT, Trautmann U, Vikkula M, Winterpacht A, Fitzpatrick DR, Rauch A. J Med Genet. 2009 Oct 19. [Epub ahead of print]

Identification of chromosome 7 inversion breakpoints in an autistic family narrows candidate region for autism susceptibility.
Cukier HN, Skaar DA, Rayner-Evans MY, Konidari I, Whitehead PL, Jaworski JM, Cuccaro ML, Pericak-Vance MA, Gilbert JR. Autism Res. 2009 Oct;2(5):258-66.

Large but not small copy-number alterations correlate to high-risk genomic aberrations and survival in chronic lymphocytic leukemia: a high-resolution genomic screening of newly diagnosed patients.
Gunnarsson R, Isaksson A, Mansouri M, Göransson H, Jansson M, Cahill N, Rasmussen M, Staaf J, Lundin J, Norin S, Buhl AM, Smedby KE, Hjalgrim H, Karlsson K, Jurlander J, Juliusson G, Rosenquist R. Leukemia. 2009 Sep 10.

Array-CGH analysis indicates a high prevalence of genomic rearrangements in holoprosencephaly: an updated map of candidate loci.
Bendavid C, Rochard L, Dubourg C, Seguin J, Gicquel I, Pasquier L, Vigneron J, Laquerrière A, Marcorelles P, Jeanne-Pasquier C, Rouleau C, Jaillard S, Mosser J, Odent S, David V. Hum Mutat. 2009 Aug;30(8):1175-82.

A highly annotated whole-genome sequence of a Korean individual.
Kim JI, Ju YS, Park H, Kim S, Lee S, Yi JH, Mudge J, Miller NA, Hong D, Bell CJ, Kim HS, Chung IS, Lee WC, Lee JS, Seo SH, Yun JY, Woo HN, Lee H, Suh D, Lee S, Kim HJ, Yavartanoo M, Kwak M, Zheng Y, Lee MK, Park H, Kim JY, Gokcumen O, Mills RE, Zaranek AW, Thakuria J, Wu X, Kim RW, Huntley JJ, Luo S, Schroth GP, Wu TD, Kim H, Yang KS, Park WY, Kim H, Church GM, Lee C, Kingsmore SF, Seo JS. Nature. 2009 Jul 8.

Gene copy number and malaria biology.
Anderson TJ, Patel J, Ferdig MT. Trends Parasitol. 2009 Jul;25(7):336-43. Epub 2009 Jun 24.

DNA copy number variation and gene expression analyses reveal the implication of specific oncogenes and genes in GBM.
Margareto J, Leis O, Larrarte E, Pomposo IC, Garibi JM, Lafuente JV. Cancer Invest. 2009 Jun;27(5):541-8.

High resolution array analysis: diagnosing pregnancies with abnormal ultrasound findings.
Tyreman M, Abbott KM, Willatt LR, Nash R, Lees C, Whittaker J, Simonic I. J Med Genet. 2009 Aug;46(8):531-41. Epub 2009 May 17.

Copy Number Variation in African Americans.
Joseph P. McElroy, Matthew R. Nelson, Stacy J. Caillier, Jorge, R. Oksenberg. BMC Genetics 2009, 10:15.

Genomic aberrations in squamous cell lung carcinoma related to lymph node or distant metastasis.
Boelens MC, Kok K, van der Vlies P, van der Vries G, Sietsma H, Timens W, Postma DS, Groen HJ, van den Berg A. Lung Cancer. 2009 Mar 24. [Epub ahead of print].

Customized oligonucleotide array-based comparative genomic hybridization as a clinical assay for genomic profiling of chronic lymphocytic leukemia
Sargent R, Jones D, Abruzzo LV, Yao H, Bonderover J, Cisneros M, Wierda WG, Keating MJ, Luthra R. J Mol Diagn. 2009 Jan;11(1):25-34. Epub 2008 Dec 12.

6.7 Mb interstitial duplication in chromosome band 11q24.2q25 associated with infertility, minor dysmorphic features and normal psychomotor development
Göhring Ina; Blümlein Hans-Martin; Hoyer Juliane; Ekici Arif B; Trautmann Udo; Rauch Anita. Eur J Med Genet. 2008 Nov-Dec;51(6):666-71. Epub 2008 Aug 12. [PubMed]

Multiple sub-microscopic genomic lesions are a universal feature of chronic myeloid leukaemia at diagnosis
Khorashad JS, De Melo VA, Fiegler H, Gerrard G, Marin D, Apperley JF, Goldman JM, Foroni L, Reid AG. Leukemia. 2008 Sep;22(9):1806-7. Epub 2008 Jul 31. [Abstract] [PubMed]

3.8 MB Deletion of Chromosome 5q in a Newborn Tracheal Agenesis Patient
Elisabeth de Jong, Hannie Douben, Bert Eussen, Dick Tibboel and Annelies de Klein. Poster presentation at ASHG 2008, Philadelphia, PA [Poster]

DNA Copy Number Stratification of Breast Cancer Samples Identifies Distinct Biological Mechanisms
S. Shams, R. Davis, B. Poirier, J. Gregg. Poster presentation at AACR Translational Cancer Medicine Conference, July 2008, San Diego, CA. [Poster]

Detection of copy number alterations in metastatic melanoma by a DNA fluorescence in situ hybridization probe panel and array comparative genomic hybridization: a southwest oncology group study (S9431)
Moore SR, Persons DL, Sosman JA, Bobadilla D, Bedell V, Smith DD, Wolman SR, Tuthill RJ, Moon J, Sondak VK, Slovak ML. Detection of copy number alterations in metastatic melanoma by a DNA fluorescence in situ hybridization probe panel and array comparative genomic hybridization: a southwest oncology group study (S9431). Clin Cancer Res. 2008 May 15;14(10):2927-35. [PubMed]
A de-novo 7.6 Mb tandem duplication of 14q32.2-qter associated with primordial short stature with neurosecretory growth hormone dysfunction, distinct facial anomalies and mild developmental delay

Thiel CT, Dörr HG, Trautmann U, Hoyer J, Hofmann K, Kraus C, Ekici AB, Reis A, Rauch A. A de novo 7.6Mb tandem duplication of 14q32.2-qter associated with primordial short stature with neurosecretory growth hormone dysfunction, distinct facial anomalies and mild developmental delay. Eur J Med Genet. 2008 Jul-Aug; 51(4):362-7. Epub 2008 Mar 20. [PubMed]

Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia
Tom Walsh, Jon M. McClellan, Shane E. McCarthy, Anjene M. Addington, Sarah B. Pierce, Greg M. Cooper, Alex S. Nord, Mary Kusenda, Dheeraj Malhotra, Abishek Bhandari, Sunday M. Stray, Caitlin F. Rippey, Patricia Roccanova, Vlad Makarov, B. Lakshmi, Robert L. Findling, Linmarie Sikich, Thomas Stromberg , Barry Merriman, Nitin Gogtay, Philip Butler, Kristen Eckstrand, Laila Noory, Peter Gochman, Robert Long, Zugen Chen, Sean Davis, Carl Baker, Evan E. Eichler, Paul S. Meltzer, Stanley F. Nelson, Andrew B. Singleton, Ming K. Lee, Judith L. Rapoport, Mary-Claire King, Jonathan Sebat. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science, 27 March 2008. (10.1126/science.1155174). [Abstract]

Challenges In Array CGH For the Analysis Of Cancer Samples

Nowak NJ, Miecznikowski J, Moore SR, Gaile D, Bobadilla D, Smith DD, Kernstine K, Forman SJ, Mwahech-Fauceglia P, Reid M, Stoler D, Loree T, Rigual N, Sullivan M, Weiss LM, Hicks D, Slovak ML. Challenges In Array CGH For the Analysis Of Cancer Samples. Genetics in Medicine, 9(9): 585-595, 2007. [PubMed]

Nexus Expression

Overexpression of ANXA1 confers independent negative prognostic impact in rectal cancers receiving concurrent chemoradiotherapy.
Sheu MJ, Li CF, Lin CY, Lee SW, Lin LC, Chen TJ, Ma LJ. Tumour Biol. 2014 May 9. [Epub ahead of print]

Clinical relevance of breast cancer-related genes as potential biomarkers for oral squamous cell carcinoma.
Toshima Z Parris, Luaay Aziz, Anikó Kovács, Shahin Hajizadeh, Szilárd Nemes, May Semaan, Chang Chen, Per Karlsson, Khalil Helou BMC Cancer 2014, 14:324 (7 May 2014)

Cyclin-dependent kinase 4 overexpression is mostly independent of gene amplification and constitutes an independent prognosticator for nasopharyngeal carcinoma.
Chen TJ, Lee SW, Lin LC, Lin CY, Chang KY, Li CF. Tumour Biol. 2014 Apr 27. [Epub ahead of print]

Deficiency in asparagine synthetase expression in rectal cancers receiving concurrent chemoradiotherapy: negative prognostic impact and therapeutic relevance.
Lin CY, Sheu MJ, Li CF, Lee SW, Lin LC, Wang YF, Chen SH. Tumour Biol. 2014 Apr 13. [Epub ahead of print]

Whole blood transcriptomics and urinary metabolomics to define adaptive biochemical pathways of high-intensity exercise in 50-60 year old masters athletes.

Mukherjee K, Edgett BA, Burrows HW, Castro C, Griffin JL, Schwertani AG, Gurd BJ, Funk CD. PLoS One. 2014 Mar 18;9(3):e92031. doi: 10.1371/journal.pone.0092031. eCollection 2014.

cDNA microarray profiling of rat cholangiocarcinoma induced by thioacetamide.
Yeh CN, Weng WH, Lenka G, Tsao LC, Chiang KC, Pang ST, Chen TW, Jan YY, Chen MF. Mol Med Rep. 2013 Aug;8(2):350-60. doi: 10.3892/mmr.2013.1516. Epub 2013 Jun 10.

A dynamic and complex monochloramine stress response in Escherichia coli revealed by transcriptome analysis.
Holder D, Berry D, Dai D, Raskin L, Xi C. Water Res. 2013 Sep 15;47(14):4978-85. doi: 10.1016/j.watres.2013.05.041. Epub 2013 May 31.

Comparative analysis of transcriptional gene regulation indicates similar physiologic response in mouse tissues at low absorbed doses from intravenously administered 211At.
Langen B, Rudqvist N, Parris TZ, Schüler E, Helou K, Forssell-Aronsson E. J Nucl Med. 2013 Jun;54(6):990-8. doi: 10.2967/jnumed.112.114462. Epub 2013 May 8.

DNA Damage-Mediated c-Myc Degradation Requires 14-3-3 Sigma
Wen, Yu-Ye; Chou, Ping-Chieh; Phan, Liem; Su, Chun-Hui; Chen, Jian; Hsieh, Yun-Chi; Xue, Yu-Wen; Qu, Chang-Ju; Gully, Chris; Parreno, Ken; Teng, Chiehlin; Hsu, Shih-Lan; Yeung, Sai-Ching; Wang, Huamin; Lee, Mong-Hong Cancer Hallmarks, Volume 1, Number 1, March 2013 , pp. 3-17(15).

Overexpression of thymidylate synthetase confers an independent prognostic indicator in nasopharyngeal carcinoma.
Lee SW, Chen TJ, Lin LC, Li CF, Chen LT, Hsing CH, Hsu HP, Tsai CJ, Huang HY, Shiue YL. Exp Mol Pathol. 2013 Aug;95(1):83-90. doi: 10.1016/j.yexmp.2013.05.006. Epub 2013 May 28.

ASS1 as a Novel Tumor Suppressor Gene in Myxofibrosarcoma: Aberrant loss via epigenetic DNA methylation confers aggressive phenotypes, negative prognostic impact, and therapeutic relevance.
Huang HY, Wu WR, Wang YH, Wang JW, Fang FM, Tsai JW, Li SH, Hung HC, Yu SC, Lan J, Shiue YL, Hsing CH, Chen LT, Li CF. Clin Cancer Res. 2013 Apr 2. [Epub ahead of print]

IGFBP-5 overexpression as a poor prognostic factor in patients with urothelial carcinomas of upper urinary tracts and urinary bladder
Liang PI, Wang YH, Wu TF, Wu WR, Liao AC, Shen KH, Hsing CH, Shiue YL, Huang HY, Hsu HP, Chen LT, Lin CY, Tai C, Wu JY, Li CF. J Clin Pathol. 2013 Mar 28. [Epub ahead of print]

Clinical Implications of Gene Dosage and Gene Expression Patterns in Diploid Breast Carcinoma.
Parris TZ, Danielsson A, Nemes S, Kovács A, Delle U, Fallenius G, Möllerström E, Karlsson P, Helou K. Clin Cancer Res. 2010 Jun 15.

Human TCR-alpha beta+ CD4- CD8- T cells can derive from CD8+ T cells and display an inflammatory effector phenotype.
Crispín JC, Tsokos GC. J Immunol. 2009 Oct 1;183(7):4675-81. Epub 2009 Sep 4. [PubMed]


New methods to analyse microarray data that partially lack a reference signal.
Carpaij N, Fluit AC, Lindsay JA, Bonten MJ, Willems RJ. BMC Genomics. 2009 Nov 13;10:522. [PubMed]

Identification of a novel microRNA cluster miR-193b-365 in multiple myeloma.
Unno K, Zhou Y, Zimmerman T, Platanias LC, Wickrema A. Leuk Lymphoma. 2009 Nov;50(11):1865-71. [PubMed]

Loading-related regulation of gene expression in bone in the contexts of estrogen deficiency, lack of estrogen receptor alpha and disuse.
Zaman G, Saxon LK, Sunters A, Hilton H, Underhill P, Williams D, Price JS, Lanyon LE. Bone. 2009 Oct 24. [Epub ahead of print] [PubMed]

Anti-carbohydrate antibodies of normal sera: findings, surprises and challenges.
Huflejt ME, Vuskovic M, Vasiliu D, Xu H, Obukhova P, Shilova N, Tuzikov A, Galanina O, Arun B, Lu K, Bovin N. Mol Immunol. 2009 Sep;46(15):3037-49. Epub 2009 Jul 15. [PubMed]

Dicer-dependent microRNA pathway controls invariant NKT cell development.
Fedeli M, Napolitano A, Wong MP, Marcais A, de Lalla C, Colucci F, Merkenschlager M, Dellabona P, Casorati G. J Immunol. 2009 Aug 15;183(4):2506-12. Epub 2009 Jul 22. [PubMed]

FOXP3 inhibits activation-induced NFAT2 expression in T cells thereby limiting effector cytokine expression.
Torgerson TR, Genin A, Chen C, Zhang M, Zhou B, Añover-Sombke S, Frank MB, Dozmorov I, Ocheltree E, Kulmala P, Centola M, Ochs HD, Wells AD, Cron RQ. J Immunol. 2009 Jul 15;183(2):907-15. Epub 2009 Jun 29. [PubMed]

Use of spermatozoal mRNA profiles to study gene-environment interactions in human germ cells.
Linschooten JO, Van Schooten FJ, Baumgartner A, Cemeli E, Van Delft J, Anderson D, Godschalk RW. Mutat Res. 2009 Jul 10;667(1-2):70-6. [PubMed]

Consequences of perinatal treatment with L-arginine and antioxidants for the renal transcriptome in spontaneously hypertensive rats.
Wesseling S, Koeners MP, Kantouh F, Joles JA, Braam B. Pflugers Arch. 2009 Jul;458(3):513-24. Epub 2009 Feb 3. [PubMed]

Genome-wide identification of long noncoding RNAs in CD8+ T cells.
Pang KC, Dinger ME, Mercer TR, Malquori L, Grimmond SM, Chen W, Mattick JS. J Immunol. 2009 Jun 15;182(12):7738-48. [PubMed]

Transcriptomic analysis of aorta from a short-term high-fat diet fed mouse reveals changes in the expression of vessel structure genes.
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Hoff B., Kuklin, A., Shams, A. Gene Expression Pattern Analysis with Clustering in the Data Mining System GeneSight. BIOforum, International Life Sciences and Technology, February, 2001, Advanced Publication.

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