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Study Index

Click the links, you will be directed to the corresponding tables below.

Head and neck cancer

Head and Neck Cancer

Cancer of digestive organs

Colorectal Cancer
Liver Cancer
Stomach Cancer

Cancer of respiratory organs

Lung Cancer

Skin cancer

Skin Cancer

Malignant neoplasm of mesothelial and soft tissue

Mesothelial and Soft Tissue Cancer

Breast cancer

Breast Cancer

Cancer of female genital organs

Ovary Cancer
Placental Cancer
Uterus Cancer

Cancer of male genital organs

Prostate Cancer

Cancer of urinary tract

Kidney Cancer

Malignant neoplasm of eye, brain and other parts of central nervous system

Glioma
Medulloblastoma
Neuroblastoma

Malignant neoplasm of lymphoid,haematopoietic and related tissue

Acute Lymphoblastic Leukemia (ALL)
Peripheral B-cell Neoplasm
Peripheral T-cell Neoplasm
Myeloid Neoplasm

Studies containing multiple types of cancer

Multiple Types


Study Tables

Head and Neck Cancer

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GSE11782 FOXM1 in Early Human Squamous Cell Carcinoma Oncogenesis and it is Enhanced by Nicotine during Malignant Transformation Gemenetzidis E, Bose A, Riaz AM, Chaplin T et al
FOXM1 upregulation is an early event in human squamous cell carcinoma and it is enhanced by nicotine during malignant transformation.
PLoS One 2009;4(3):e4849
GSE15051 Nasopharyngeal carcinoma(NPC) cell lines (copy number analysis)

GSE15526 Analysis of genomic instability in esophageal squamous cell carcinoma (ESCC) Hu N, Wang C, Ng D, Clifford R et al.
Genomic characterization of esophageal squamous cell carcinoma from a high-risk population in China.
Cancer Res 2009 Jul 15;69(14):5908-17.
GSE20939 Genetic and Epigenetic Somatic Alterations in Head and Neck Squamous Cell Carcinomas Are Globally Coordinated but Not Locally Targeted Poage GM, Christensen BC, Houseman EA, McClean MD et al.
Genetic and epigenetic somatic alterations in head and neck squamous cell carcinomas are globally coordinated but not locally targeted.
PLoS One 2010 Mar 11;5(3):e9651.

Colorectal Cancer

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GSE5347 High Resolution Copy Number Analysis of Paraffin Embedded Archival Tissue Using SNP Arrays Oosting J, Lips EH, van Eijk R, Eilers PH et al.
High-resolution copy number analysis of paraffin-embedded archival tissue using SNP BeadArrays
Genome Res 2007 Mar;17(3):368-76
GSE7946 SNP array analysis of chromosomal instability patterns discriminates rectal adenomas from carcinomas Lips EH, van Eijk R, de Graaf EJ, Oosting J et al.
Integrating chromosomal aberrations and gene expression profiles to dissect rectal tumorigenesis
BMC Cancer 2008 Oct 29;8:314
GSE11417 Chromosome copy number and LOH analysis of colorectal carcinoma specimens Kurashina K, Yamashita Y, Ueno T, Koinuma K et al.
Chromosome copy number analysis in screening for prognosis-related genomic regions in colorectal carcinoma
Cancer Sci 2008 Sep;99(9):1835-40
GSE16125 Integrative approach for prioritizing cancer genes in sporadic colon cancer Reid JF, Gariboldi M, Sokolova V, Capobianco P et al.
Integrative approach for prioritizing cancer genes in sporadic colon cancer.
Genes Chromosomes Cancer 2009 Nov;48(11):953-62.

Liver Cancer

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GSE9845 Copy number alterations of 103 hepatocellular carcinomas with hepatitis C virus etiology Chiang DY, Villanueva A, Hoshida Y, Peix J et al.
Focal gains of VEGFA and molecular classification of hepatocellular carcinoma
Cancer Res 2008 Aug 15;68(16):6779-88

Stomach Cancer

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GSE10611 Gastric Cancer Cell Lines Hou Q, Wu YH, Grabsch H, Zhu Y et al.
Integrative genomics identifies RAB23 as an invasion mediator gene in diffuse-type gastric cancer
Cancer Res 2008 Jun 15;68(12):4623-30

Pancreas Cancer

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GSE7130 Pancreatic cancer_Affymetrix 100K SNP arrays Harada T, Chelala C, Bhakta V, Chaplin T et al.
Genome-wide DNA copy number analysis in pancreatic cancer using high-density single nucleotide polymorphism arrays
Oncogene 2008 Mar 20;27(13):1951-60
GSE14579 FACS-sorted Pancreatic Adenocarcinoma for Molecular Profiling Boyd ZS, Raja R, Johnson S, Eberhard DA et al
A tumor sorting protocol that enables enrichment of pancreatic adenocarcinoma cells and facilitation of genetic analyses.
J Mol Diagn 2009 Jul;11(4):290-7

Lung Cancer

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ZHAO05 Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis Zhao X, Weir BA, LaFramboise T, Lin M et al.
Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis
Cancer Res. 2005 Jul 1;65(13):5561-70
GSE7068 Small Cell Lung Carcinoma(SCLC) cell line profiling on 100K arrays Guo J, Anderson MG, Tapang P, Palma JP et al.
Identification of genes that confer tumor cell resistance to the aurora B kinase inhibitor, AZD1152
Pharmacogenomics J 2009 Apr;9(2):90-102
GSE16092 Quantification of Normal Cell Fraction and Copy Number Neutral LOH in Clinical Lung Cancer Samples Using SNP Array Data G?ransson H, Edlund K, Ryd?ker M, Rasmussen M et al.
Quantification of normal cell fraction and copy number neutral LOH in clinical lung cancer samples using SNP array data.
PLoS One 2009 Jun 26;4(6):e6057.
GSE17247 Predicting drug activity in non-small cell lung cancer based on genetic lesions Sos ML, Michel K, Zander T, Weiss J et al.
Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions.
J Clin Invest 2009 Jun;119(6):1727-40.
GSE17429 Affymetrix SNP array data for 30 NSCLC samples Ramos AH, Dutt A, Mermel C, Perner S et al.
Amplification of chromosomal segment 4q12 in non-small cell lung cancer.
Cancer Biol Ther 2009 Nov;8(21):2042-50.
GSE18797 Affymetrix SNP array data for non-small cell lung cancer cell line samples

GSE19388 Affymetrix SNP array data for non-small cell lung cancer cell line samples, PC-9 Ercan D, Zejnullahu K, Yonesaka K, Xiao Y et al.
Amplification of EGFR T790M causes resistance to an irreversible EGFR inhibitor.
Oncogene 2010 Apr 22;29(16):2346-56.

Skin Cancer

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GSE2520 Affymetrix 100K SNP array data of Melanoma Garraway LA, Widlund HR, Rubin MA, Getz G et al.
Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma
Nature 2005 Jul 7;436(7047):117-22
GSE7822 A comparison of DNA copy number profiling platforms using a panel of melanoma cell lines Greshock J, Feng B, Nogueira C, Ivanova E et al.
A comparison of DNA copy number profiling platforms
Cancer Res 2007 Nov 1;67(21):10173-80
GSE8164 Imatinib targeting of KIT-mutant oncoprotein in melanoma Jiang X, Zhou J, Yuen NK, Corless CL et al.
Imatinib targeting of KIT-mutant oncoprotein in melanoma
Clin Cancer Res 2008 Dec 1;14(23):7726-32
GSE17359 Affymetrix SNP array data for melanoma short-term cultures and cell lines Berger MF, Levin JZ, Vijayendran K, Sivachenko A et al.
Integrative analysis of the melanoma transcriptome.
Genome Res 2010 Apr;20(4):413-27.
GSE17595 Affymetrix SNP array data for Sezary Syndrome (SS) samples

GSE17534 Affymetrix 250K StyI SNP array data from PBMCs and cell lines of metastatic melanoma patients


Mesothelial and Soft Tissue Cancer

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GSE8046 Whole-Genome Profiling in Liposarcomas Reveals Genetic Alterations Common to Specific Telomere Maintenance Mechanisms Johnson JE, Gettings EJ, Schwalm J, Pei J et al.
Whole-genome profiling in liposarcomas reveals genetic alterations common to specific telomere maintenance mechanisms
Cancer Res 2007 Oct 1;67(19):9221-8
GSE8798 Genomic profiling of TP53 and non-TP53 Li-Fraumeni syndrome tumors reveals hits in the p53 and overlapping pathways

GSE15696 SNP chip data of EWS


Breast Cancer

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GSE3743 Human Breast Tumor SNPs Richardson AL, Wang ZC, De Nicolo A, Lu X et al.
X chromosomal abnormalities in basal-like human breast cancer
Cancer Cell 2006 Feb;9(2):121-32
GSE7545 Affymetrix 500K Mapping Array data from breast tumors Haverty PM, Fridlyand J, Li L, Getz G et al.
High-resolution genomic and expression analyses of copy number alterations in breast tumors
Genes Chromosomes Cancer 2008 Jun;47(6):530-42
GSE9154 Optimizations of DNA isolation and copy number analysis identifies regions of genomic gain/loss in early breast cancer

GSE10099 Multi-dimensional genomic analysis in breast cancer patients Zhang Y, Martens JW, Yu JX, Jiang J et al.
Copy number alterations that predict metastatic capability of human breast cancer
Cancer Res 2009 May 1;69(9):3795-801
GSE10747 Analysis of genetic changes in MCF10A series cells and MCFDCIS derived xenografts Hu M, Yao J, Carroll DK, Weremowicz S et al.
Regulation of in situ to invasive breast carcinoma transition
Cancer Cell 2008 May;13(5):394-406
GSE13696 Copy number profiling of 45 human breast cancer cell lines on Affymetrix 100K SNP arrays Hu X, Stern HM, Ge L, O'Brien C et al.
Genetic alterations and oncogenic pathways associated with breast cancer subtypes
Mol Cancer Res 2009 Apr;7(4):511-22
GSE16619 Identification of novel gene amplification events in breast cancer Kadota M, Sato M, Duncan B, Ooshima A et al.
Identification of novel gene amplifications in breast cancer and coexistence of gene amplification with an activating mutation of PIK3CA.
Cancer Res 2009 Sep 15;69(18):7357-65.
GSE19594 SNP array data of breast cancer Li Y, Zou L, Li Q, Haibe-Kains B et al
Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer.
Nat Med 2010 Feb;16(2):214-8.

Ovary Cancer

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GSE11960 Affymetrix 500K Mapping Array data from ovary tumors Haverty PM, Hon LS, Kaminker JS, Chant J et al.
High-resolution analysis of copy number alterations and associated expression changes in ovarian tumors
BMC Med Genomics 2009 May 6;2:21
GSE13813 50K SNP Copy Number Analysis of Ovarian Carcinomas Etemadmoghadam D, deFazio A, Beroukhim R, Mermel C et al.
Integrated genome-wide DNA copy number and expression analysis identifies distinct mechanisms of primary chemoresistance in ovarian carcinomas
Clin Cancer Res 2009 Feb 15;15(4):1417-27
GSE20565 Primary and secondary ovarian tumors


Placental Cancer

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GSE12713 Definitive haplotypes from a collection of complete hydatidiform moles (CHMs) Higasa K, Kukita Y, Kato K, Wake N et al.
Evaluation of haplotype inference using definitive haplotype data obtained from complete hydatidiform moles, and its significance for the analyses of positively selected regions
PLoS Genet 2009 May;5(5):e1000468

Uterus Cancer

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GSE8605 Combined arrayCGH and SNP-loss of heterozygosity analysis in cervical cancer Kloth JN, Oosting J, van Wezel T, Szuhai K et al.
Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex genetic alterations in cervical cancer
BMC Genomics 2007 Feb 20;8:53
GSE10092 Genome-wide SNP Array Identification of Genetic Alterations in Cervical Cancer Scotto L, Narayan G, Nandula SV, Arias-Pulido H et al.
Identification of copy number gain and overexpressed genes on chromosome arm 20q by an integrative genomic approach in cervical cancer: potential role in progression
Genes Chromosomes Cancer 2008 Sep;47(9):755-65
GSE14860 Integrated genomic profiling of endometrial carcinoma Salvesen HB, Carter SL, Mannelqvist M, Dutt A et al.
Integrated genomic profiling of endometrial carcinoma associates aggressive tumors with indicators of PI3 kinase activation
Proc Natl Acad Sci U S A 2009 Mar 24;106(12):4834-9

Prostate Cancer

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GSE12702 Genomic profiling of prostate cancer in African-American patients Castro P, Creighton CJ, Ozen M, Berel D et al.
Genomic profiling of prostate cancers from African American men
Neoplasia 2009 Mar;11(3):305-12
GSE13439 Virtual Karyotyping of Androgen Insensitive Prostate Cancer Sircar K, Yoshimoto M, Monzon FA, Koumakpayi IH et al.
PTEN genomic deletion is associated with p-Akt and AR signalling in poorer outcome, hormone refractory prostate cancer
J Pathol 2009 Aug;218(4):505-13
GSE18333 Distinct genomic differences in prostate cancer between Western countries and China


Kidney Cancer

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GSE8271 Chromophobe and Oncocytoma Renal Cell Carcinomas: gene expression and SNP analysis Koeman JM, Russell RC, Tan MH, Petillo D et al.
Somatic pairing of chromosome 19 in renal oncocytoma is associated with deregulated EGLN2-mediated [corrected] oxygen-sensing response
PLoS Genet 2008 Sep 5;4(9):e1000176
GSE9469 Copy Number Analysis of Renal Epithelial Neoplasms Monzon FA, Hagenkord JM, Lyons-Weiler MA, Balani JP et al.
Whole genome SNP arrays as a potential diagnostic tool for the detection of characteristic chromosomal aberrations in renal epithelial tumors
Mod Pathol 2008 May;21(5):599-608
GSE11447 Diagnosis of Morphologically Challenging Cases of Renal Epithelial Neoplasms by Virtual Karyotypes with SNP Arrays Hagenkord JM, Parwani AV, Lyons-Weiler MA, Alvarez K et al.
Virtual karyotyping with SNP microarrays reduces uncertainty in the diagnosis of renal epithelial tumors
Diagn Pathol 2008 Nov 6;3:44
GSE14670 Virtual-Karyotyping with SNP microarrays in morphologically challenging renal cell neoplasms

GSE14994 Patterns of gene expression and copy-number alterations in VHL disease-associated and sporadic ccRCC Beroukhim R, Brunet JP, Di Napoli A, Mertz KD et al.
Patterns of gene expression and copy-number alterations in von-hippel lindau disease-associated and sporadic clear cell carcinoma of the kidney.
Cancer Res 2009 Jun 1;69(11):4674-81.

Glioma

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GSE9635 Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma Beroukhim R, Getz G, Nghiemphu L, Barretina J et al.
Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma
Proc Natl Acad Sci U S A 2007 Dec 11;104(50):20007-12
GSE10007 Epigenetic-Mediated Dysfunction of the BMP Pathway Inhibits Differentiation of Human Glioblastoma Initiating Cells Lee J, Son MJ, Woolard K, Donin NM et al.
Epigenetic-mediated dysfunction of the bone morphogenetic protein pathway inhibits differentiation of glioblastoma-initiating cells
Cancer Cell 2008 Jan;13(1):69-80
GSE10922 Prevalence of Copy-number neutral LOH in glioblastomas revealed by analysis of laser-microdissected tissues

GSE13021 Copy number analysis of human glioblastoma multiforme Solomon DA, Kim JS, Cronin JC, Sibenaller Z et al.
Mutational inactivation of PTPRD in glioblastoma multiforme and malignant melanoma
Cancer Res 2008 Dec 15;68(24):10300-6
GSE14296 Genotype and expression profiling of primitive neuroectodermal tumours Li M, Lee KF, Lu Y, Clarke I et al.
Frequent amplification of a chr19q13.41 microRNA polycistron in aggressive primitive neuroectodermal brain tumors.
Cancer Cell 2009 Dec 8;16(6):533-46. PMID:
GSE14804 SNP copy number data from glioblastoma subcutaneous xenografts Hodgson JG, Yeh RF, Ray A, Wang NJ et al.
Comparative analyses of gene copy number and mRNA expression in GBM tumors and GBM xenografts
Neuro Oncol 2009 Jan 12
GSE14806 Comparative analyses of gene copy number and mRNA expression in GBM tumors and GBM xenografts Hodgson JG, Yeh RF, Ray A, Wang NJ et al
Comparative analyses of gene copy number and mRNA expression in glioblastoma multiforme tumors and xenografts
Neuro Oncol 2009 Oct;11(5):477-87.
GSE14960 Affymetrix SNP array data for low-grade astrocytoma samples Forshew T, Tatevossian RG, Lawson AR, Ma J et al.
Activation of the ERK/MAPK pathway: a signature genetic defect in posterior fossa pilocytic astrocytomas
J Pathol 2009 Jun;218(2):172-81
GSE18828 Affymetrix SNP array data for Diffuse Intrinsic Pontine Glioma Zarghooni M, Bartels U, Lee E, Buczkowicz P et al.
Whole-genome profiling of pediatric diffuse intrinsic pontine gliomas highlights platelet-derived growth factor receptor alpha and poly (ADP-ribose) polymerase as potential therapeutic targets.
J Clin Oncol 2010 Mar 10;28(8):1337-44.
GSE19612 A Hierarchy of Self-Renewing Tumor-Initiating Cell Types in Glioblastoma Chen R, Nishimura MC, Bumbaca SM, Kharbanda S et al.
A hierarchy of self-renewing tumor-initiating cell types in glioblastoma.
Cancer Cell 2010 Apr 13;17(4):362-75.

Medulloblastoma

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GSE14437 High-resolution copy number analysis of medulloblastoma Northcott PA, Nakahara Y, Wu X, Feuk L et al.
Multiple recurrent genetic events converge on control of histone lysine methylation in medulloblastoma
Nat Genet 2009 Apr;41(4):465-72

Neuroblastoma

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GSE8333 SNP array analysis of neuroblastoma tumors George RE, Attiyeh EF, Li S, Moreau LA et al.
Genome-wide analysis of neuroblastomas using high-density single nucleotide polymorphism arrays
PLoS One 2007 Feb 28;2(2):e255
GSE12494 SNP data from Neuroblastoma samples Chen Y, Takita J, Choi YL, Kato M et al.
Oncogenic mutations of ALK kinase in neuroblastoma
Nature 2008 Oct 16;455(7215):971-4
GSE13137 Identification of candidate neuroblastoma genes by combining genomic and expression microarrays: SNP data Lastowska M, Viprey V, Santibanez-Koref M, Wappler I et al.
Identification of candidate genes involved in neuroblastoma progression by combining genomic and expression microarrays with survival data
Oncogene 2007 Nov 22;26(53):7432-44
GSE14656 Comparison of primary neuroblastoma tumors and derivative early-passage cell lines using genome-wide SNP array analysis Volchenboum SL, Li C, Li S, Attiyeh EF et al.
Comparison of primary neuroblastoma tumors and derivative early-passage cell lines using genome-wide single nucleotide polymorphism array analysis
Cancer Res 2009 May 15;69(10):4143-9

Acute Lymphoblastic Leukemia (ALL)

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GSE7255 Genomic profiling data of 40 childhood leukemia patients Kuiper RP, Schoenmakers EF, van Reijmersdal SV, Hehir-Kwa JY et al.
High-resolution genomic profiling of childhood ALL reveals novel recurrent genetic lesions affecting pathways involved in lymphocyte differentiation and cell cycle progression
Leukemia 2007 Jun;21(6):1258-66
GSE9611 Adult and adolescent acute lymphoblastic leukemia Paulsson K, Cazier JB, Macdougall F, Stevens J et al.
Microdeletions are a general feature of adult and adolescent acute lymphoblastic leukemia: Unexpected similarities with pediatric disease
Proc Natl Acad Sci U S A 2008 May 6;105(18):6708-13
GSE10792 Genome wide genotyping and gene expression data of childhood B-cell precursor Acute lymphoblastic leukemia(ALL) without known genetic aberrations Bungaro S, Dell'Orto MC, Zangrando A, Basso D et al.
Integration of genomic and gene expression data of childhood ALL without known aberrations identifies subgroups with specific genetic hallmarks
Genes Chromosomes Cancer 2009 Jan;48(1):22-38
GSE12660 Genomic profiling data of 19 pediatric lympohoblastic lymphoma patients

GSE20353 IKZF1 deletions predict relapse in uniformly treated pediatric precursor B-ALL Kuiper RP, Waanders E, van der Velden VH, van Reijmersdal SV et al.
IKZF1 deletions predict relapse in uniformly treated pediatric precursor B-ALL.
Leukemia 2010 May 6.

Peripheral B-cell Neoplasm

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GSE7425 Genome-wide detection of recurring sites of uniparental disomy in folicular and transformed follicular lymphoma Fitzgibbon J, Iqbal S, Davies A, O'shea D et al.
Genome-wide detection of recurring sites of uniparental disomy in follicular and transformed follicular lymphoma
Leukemia 2007 Jul;21(7):1514-20
GSE8567 SNPchip analysis of single cell products Iwamoto K, Bundo M, Ueda J, Nakano Y et al.
Detection of chromosomal structural alterations in single cells by SNP arrays: a systematic survey of amplification bias and optimized workflow
PLoS One 2007 Dec 12;2(12):e1306
GSE11036 Molecular and transcriptional characterization of chromosome 17p loss in chronic lymphocytic leukemia, experiment B Fabris S, Mosca L, Todoerti K, Cutrona G et al.
Molecular and transcriptional characterization of 17p loss in B-cell chronic lymphocytic leukemia
Genes Chromosomes Cancer 2008 Sep;47(9):781-93
GSE11038 Molecular and transcriptional characterization of chromosome 17p loss in chronic lymphocytic leukemia Fabris S, Mosca L, Todoerti K, Cutrona G et al
Molecular and transcriptional characterization of 17p loss in B-cell chronic lymphocytic leukemia.
Genes Chromosomes Cancer 2008 Sep;47(9):781-93
GSE12906 SNP data from lymphoma samples Kato M, Sanada M, Kato I, Sato Y et al.
Frequent inactivation of A20 in B-cell lymphomas
Nature 2009 Jun 4;459(7247):712-6
GSE13557 Screening for copy-number alterations and LOH in chronic lymphocytic leukemia(CLL) - a comparative study of four microarray platforms Gunnarsson R, Staaf J, Jansson M, Ottesen AM et al.
Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia--a comparative study of four differently designed, high resolution microarray platforms
Genes Chromosomes Cancer 2008 Aug;47(8):697-711
GSE13989 A20 IN MARGINAL ZONE LYMPHOMAS(MZL) Novak U, Rinaldi A, Kwee I, Nandula SV et al.
The NF-{kappa}B negative regulator TNFAIP3 (A20) is inactivated by somatic mutations and genomic deletions in marginal zone lymphomas
Blood 2009 May 14;113(20):4918-21
GSE15127 Genomic profiles of diffuse large B-cell lymphomas Compagno M, Lim WK, Grunn A, Nandula SV et al.
Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma
Nature 2009 Jun 4;459(7247):717-21
GSE16406 Copy-number alterations correlate to high-risk genomic aberrations and survival in chronic lymphocytic leukemia Gunnarsson R, Isaksson A, Mansouri M, G?ransson H et al.
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.
Leukemia 2010 Jan;24(1):211-5.

Peripheral T-cell Neoplasm

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GSE10387 SNP-based mapping and gene expression profiling identifies novel chromosomal imbalances and candidate genes in T-cell prolymphocytic leukemia(T-PLL) Durig J, Bug S, Klein-Hitpass L, Boes T et al.
Combined single nucleotide polymorphism-based genomic mapping and global gene expression profiling identifies novel chromosomal imbalances, mechanisms and candidate genes important in the pathogenesis of T-cell prolymphocytic leukemia with inv(14)(q11q32)
Leukemia 2007 Oct;21(10):2153-63
GSE15842 SNP array genomic profiling of PTCL NOS Hartmann S, Gesk S, Scholtysik R, Kreuz M et al.
High resolution SNP array genomic profiling of peripheral T cell lymphomas, not otherwise specified, identifies a subgroup with chromosomal aberrations affecting the REL locus.
Br J Haematol 2010 Feb;148(3):402-12.

Myeloid Neoplasm

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GSE7210 Relapse versus diagnostic acute myeloid leukaemia(AML) samples analysed using Affymetrix 10K SNP array Raghavan M, Smith LL, Lillington DM, Chaplin T et al.
Segmental uniparental disomy is a commonly acquired genetic event in relapsed acute myeloid leukemia
Blood 2008 Aug 1;112(3):814-21
GSE7490 Frequent Partial Uniparental Disomy Due to Somatic Recombination in Acute Myeloid Leukemia Raghavan M, Lillington DM, Skoulakis S, Debernardi S et al
Genome-wide single nucleotide polymorphism analysis reveals frequent partial uniparental disomy due to somatic recombination in acute myeloid leukemias.
Cancer Res 2005 Jan 15;65(2):375-8
GSE11522 Integrative genomic approach reveals expression of intronic miR-335, miR-342, and miR-561 in multiple myeloma Ronchetti D, Lionetti M, Mosca L, Agnelli L et al.
An integrative genomic approach reveals coordinated expression of intronic miR-335, miR-342, and miR-561 with deregulated host genes in multiple myeloma
BMC Med Genomics 2008 Aug 13;1:37
GSE12896 Prognostic significance of copy-number alterations in multiple myeloma Avet-Loiseau H, Li C, Magrangeas F, Gouraud W et al.
Prognostic significance of copy-number alterations in multiple myeloma.
J Clin Oncol 2009 Sep 20;27(27):4585-90.
GSE14016 SNP data of acute promyelocytic leukemia(APL) samples Akagi T, Shih LY, Kato M, Kawamata N et al.
Hidden abnormalities and novel classification of t(15;17) acute promyelocytic leukemia (APL) based on genomic alterations
Blood 2009 Feb 19;113(8):1741-8
GSE15187 SNP chip data of MDS Sanada M, Suzuki T, Shih LY, Otsu M et al
Gain-of-function of mutated C-CBL tumour suppressor in myeloid neoplasms.
Nature 2009 Aug 13;460(7257):904-8
GSE15688 Acquired mutations in TET2 are common in myelodysplastic syndromes Langemeijer SM, Kuiper RP, Berends M, Knops R et al.
Acquired mutations in TET2 are common in myelodysplastic syndromes.
Nat Genet 2009 Jul;41(7):838-42.
GSE15714 Affymetrix SNP array data for pediatric acute myeloid leukemia (AML) samples at diagnosis: Hind SNP array Radtke I, Mullighan CG, Ishii M, Su X et al
Genomic analysis reveals few genetic alterations in pediatric acute myeloid leukemia.
Proc Natl Acad Sci U S A 2009 Aug 4
GSE16121 Integrated genomics approach to detect allelic imbalances in multiple myeloma, SNP data Agnelli L, Mosca L, Fabris S, Lionetti M et al.
A SNP microarray and FISH-based procedure to detect allelic imbalances in multiple myeloma: an integrated genomics approach reveals a wide gene dosage effect
Genes Chromosomes Cancer 2009 Jul;48(7):603-14
GSE16122 A SNP microarray and FISH-based procedure to detect allelic imbalances in multiple myeloma A SNP microarray and FISH-based procedure to detect allelic imbalances in multiple myeloma: an integrated genomics approach reveals a wide gene dosage effect.
Genes Chromosomes Cancer 2009 Jul;48(7):603-14
Genes Chromosomes Cancer 2009 Jul;48(7):603-14
GSE17498 Identification of MicroRNA Expression Patterns and a MicroRNAs/mRNA Regulatory Network in Multiple Myeloma Lionetti M, Biasiolo M, Agnelli L, Todoerti K et al
Identification of microRNA expression patterns and definition of a microRNA/mRNA regulatory network in distinct molecular groups of multiple myeloma.
Blood 2009 Dec 10;114(25):e20-6
GSE18197 High-resolution SNP-array profiling in myeloproliferative neoplasms Stegelmann F, Bullinger L, Griesshammer M, Holzmann K et al.
High-resolution single-nucleotide polymorphism array-profiling in myeloproliferative neoplasms identifies novel genomic aberrations.
Haematologica 2010 Apr;95(4):666-9.
GSE18964 SNP chip data of CML, resistant with tyrosine kinase inhibitor Nowak D, Ogawa S, Muschen M, Kato M et al.
SNP array analysis of tyrosine kinase inhibitor-resistant chronic myeloid leukemia identifies heterogeneous secondary genomic alterations.
Blood 2010 Feb 4;115(5):1049-53.
GSE19101 Identification of Acquired Copy Number Alterations and Uniparental Disomies in Cytogenetically Normal AML Bullinger L, Kr?nke J, Sch?n C, Radtke I et al
Identification of acquired copy number alterations and uniparental disomies in cytogenetically normal acute myeloid leukemia using high-resolution single-nucleotide polymorphism analysis
Leukemia 2010 Feb;24(2):438-49
GSE19647 SNP data of MPD/MPN samples Thoennissen NH, Krug UO, Lee DH, Kawamata N et al
Prevalence and prognostic impact of allelic imbalances associated with leukemic transformation of Philadelphia chromosome-negative myeloproliferative neoplasms.
Blood 2010 Apr 8;115(14):2882-90.
GSE19523 Affymetrix SNP array data for Genomic Instability and Myelodysplasia with Monosomy 7 Stein S, Ott MG, Schultze-Strasser S, Jauch A et al
Genomic instability and myelodysplasia with monosomy 7 consequent to EVI1 activation after gene therapy for chronic granulomatous disease.
Nat Med 2010 Feb;16(2):198-204

Multiple Types

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ZHAO04 An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays Zhao X, Li C, Paez JG, Chin K et al.
An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays
Cancer Res. 2004 May 1;64(9):3060-71
GSE8649 High-resolution genetic analysis of cancer cell lines with near normal karyotypes Mao X, Young BD, Chaplin T, Shipley J et al.
Subtle genomic alterations and genomic instability revealed in diploid cancer cell lines
Cancer Lett 2008 Aug 18;267(1):49-54
GSE9585 Genome-wide DNA copy number predictors of lapatinib sensitivity in tumour-derived cell lines Greshock J, Cheng J, Rusnak D, Martin AM et al.
Genome-wide DNA copy number predictors of lapatinib sensitivity in tumor-derived cell lines
Mol Cancer Ther 2008 Apr;7(4):935-43
GSE12019 Fine-scale mapping of copy-number alterations with massively parallel sequencing Chiang DY, Getz G, Jaffe DB, O'Kelly MJ et al.
High-resolution mapping of copy-number alterations with massively parallel sequencing
Nat Methods 2009 Jan;6(1):99-103
GSE13372 High-resolution mapping of copy-number alterations with massively parallel sequencing Chiang DY, Getz G, Jaffe DB, O'Kelly MJ et al.
High-resolution mapping of copy-number alterations with massively parallel sequencing
Nat Methods 2009 Jan;6(1):99-103
GSE15126 A gene expression signature associated with K-Ras addiction reveals regulators of EMT and tumor cell survival Singh A, Greninger P, Rhodes D, Koopman L et al.
A gene expression signature associated with K-Ras addiction reveals regulators of EMT and tumor cell survival
Cancer Cell 2009 Jun 2;15(6):489-500
GSE17958 Affymetrix SNP array data for 47 lung squamous cell carcinoma and 40 esophageal squamous cell carcinoma samples. Bass AJ, Watanabe H, Mermel CH, Yu S et al.
SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas.
Nat Genet 2009 Nov;41(11):1238-42.
GSE18252 Somatic mutations in p85alfa promote tumorigenesis through p110alfa activation Jaiswal BS, Janakiraman V, Kljavin NM, Chaudhuri S et al
Somatic mutations in p85alpha promote tumorigenesis through class IA PI3K activation.
Cancer Cell 2009 Dec 8;16(6):463-74
GSE19399 Affymetrix 250K StyI SNP array data across multiple human cancer types Beroukhim R, Mermel CH, Porter D, Wei G et al.
The landscape of somatic copy-number alteration across human cancers.
Nature 2010 Feb 18;463(7283):899-905.
GSK GSK Cancer Cell Line Genomic Profiling Data,provided by GlaxoSmithKline


Genomic position: (gene name, refSeq ID, coordinate range or miRNA ID)

Genomic position:   

Examples: BRCA1, NM_017414, chr3:1-1000000, mir-137


Caculate the frequency of copy number aberrations which are: (optional)

Greater Than:     and/or    Less Than:   

Examples: GT 2.2 (one-sided region), GT 2.2 and LT 1.8 (two-sided region), GT 1.8 and LT 2.2 (close region)