GEO DataSets

(Submitter supplied) We applied DNA content based flow cytometry methods to interrogate the genomes of clinical samples from 21 patients with early onset colorectal carcinoma (EOCRC). These included a fresh frozen sample obtained from a surgical resection and 20 archived formalin fixed paraffin embedded (FFPE) samples from a Mayo Clinic tissue bank. Our flow sorting methods are compatible with analyses of biopsies of interest including FFPE samples and frozen biopsies. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL19387

7 Samples

Download data: TXT

(Submitter supplied) We applied DNA content flow cytometry to pancreatic ductal adenocarcinoma (PDAC) biopsies. We interrogated purified sorted tumor fractions with whole genome copy number variant (CNV) and next generation sequencing (NGS) analyses. These identified a variety of somatic genomic lesions targeting genes and cellular pathways in PDAC. Of significant interest are lesions that may affect responses to therapies.

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL19387

2 Samples

Download data: TXT

(Submitter supplied) We applied DNA content flow cytometry to a series of prostate cancer (PC) patient derived tumor xenografts (PDTXs). We interrogated purified sorted tumor fractions from each sample with whole genome copy number variant (CNV) analyses. These identified a variety of somatic genomic lesions targeting genes and cellular pathways in PC. Of significant interest are lesions that may affect responses to therapies. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL19387

3 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL4091 GPL19387

63 Samples

Download data: TXT

(Submitter supplied) Chromosomal imbalances are implicated in the etiology of developmental delay (DD) and congenital malformation (CM). We therefore conducted high resolution array comparative genomic hybridization (array CGH) of sixty three Saudi patients [11 by Agilent-001850/CGH1x244A and 52 by Agilent-014693/CGH2x400k] for investigating and understanding the genetic heterogeneity underlying DD/CM. A total of 76 disease associated copy number variants (CNVs) were detected in twenty four patients including 1p36, 1q21, 3p23, 6p24, 7q11, 8q24, 9q33, 10p14, 11p15, 11q12, 11q24, 13q21, 15q13, 16p13, 18q23, trisomy 18, 20q11, 21q22, 22q11.21, 47,XXY and 45,X0. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL19387

52 Samples

Download data: TXT

(Submitter supplied) To define the sources and the extent of heterogeneity, we performed an in-depth analysis of the genomic architecture of three chemoradiation-naïve breast cancers with well-defined clinical features including variable ER, PR, Her2 receptor expression and distinct pathogenic BRCA2mut genotypes. The latter included a germ line carrier and a patient with a somatic variant. In each case we combined DNA content-based flow cytometry with whole exome sequencing and genome wide copy number variant (CNV) analysis of distinct populations sorted from multiple (4-18) mapped biopsies within the tumors and involved lymph nodes. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL19387

40 Samples

Download data: TXT, XLSX

(Submitter supplied) We applied DNA content flow cytometry to ten patient derived triple negative breast cancer (TNBC) xenografts (PDXs) from the Baylor College of Medicine (BCM). We interrogated purified sorted tumor fractions from each sample with whole genome copy number variant (CNV) analyses. These identified a variety of somatic genomic lesions that are common in TNBC including three cases with 9p24.1 amplification targeting PD-L1-PDL2 and JAK2 (PDJ amplicon) and recurring focal amplicons of oncogenic drivers found commonly in the TNBC PDXs including MYC and EGFR. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL19387

10 Samples

Download data: TXT

(Submitter supplied) To investigate the longitudinal mutational patterns arising in Lynch Syndrome associated tumors we interrogated the genomes of five different cancers that arose over a period of 10 years in a patient who underwent resection in the absence of chemotherapy and radiation for each cancer. These included a papillary transitional cell carcinoma (PTCC) in the renal pelvis, a duodenal carcinoma, two separate CRCs that arose 3 years apart, and multiple regions of a triple negative breast cancer (TNBC). more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL19387

5 Samples

Download data: TXT, XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19387 GPL20301

25 Samples

Download data: BED, TXT

(Submitter supplied) We applied DNA content flow cytometry to a series of adenosquamous cancer of the pancreas (ASCP) tumor samples and patient derived xenografts (PDXs). We interrogated purified sorted tumor fractions from each sample with whole genome copy number variant (CNV) and whole exome sequencing (WES) analyses. These identified a variety of somatic genomic lesions targeting chromatin regulators in ASCP genomes that were superimposed on well characterized genomic lesions including mutations in KRAS and TP53, homozygous deletion of CDKN2A, and amplification of c-MYC, that are common in PDACs. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL19387

19 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Other; Genome variation profiling by array

Platforms:

GPL19387 GPL25534

79 Samples

Download data: RCC, TXT

(Submitter supplied) Transcriptional and genomic profiling study of HIV positive and HIV negative Diffuse Large B-Cell Lymphoma (DLBCL). Tumors were subtyped using the Lymph2Cx assay. Only GCB (germinal center like B-cell) subtypes were then subjected to digitial gene expression profiling and array comparative genomic hybridization (aCGH). The study used DNA extracted from FFPE DLBCL tumors derived from HIV(+) and HIV(-) patients to assess copy number variation differences between the HIV(+) and HIV(-) cohorts. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL19387

39 Samples

Download data: TXT

(Submitter supplied) We used DNA content-based flow cytometry to distinguish and isolate nuclei of clonal tumor populations from primary and metastatic refractory testicular germ cell tumors (TGCTs) tissues. We then interrogated each sorted tumor populationwith whole genome aCGH and next generation sequencing (NGS). we have explored the clonal basis of refractory TGCT by investigating distinct tumor populations that were present in each tumor. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL19387

11 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platforms:

GPL19387 GPL24575

2 Samples

Download data: TXT

(Submitter supplied) Double minutes (DMs), a major form of gene amplification, commonly carry oncogenes or chemoresistance-related genes that are associated with the occurrence, development and prognosis of tumors. Thus, probing molecular structures of DMs allows us to further understand molecular mechanisms underlying tumorigenesis. In this study, we identified four amplification regions by high-density array CGH in a human colorectal adenocarcinoma cell line NCI-H716. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL19387

1 Sample

Download data: TXT

(Submitter supplied) We used DNA content-based flow cytometry to distinguish and isolate nuclei of clonal tumor populations from resected triple negative breast cancer tissues. We then interrogated each sorted tumor population with whole genome aCGH and next generation sequencing (NGS). The genomic data was correlated with IHC staining for PD-1 and PD-L1.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL19387

48 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by genome tiling array

Platforms:

GPL19387 GPL17077

15 Samples

Download data: TXT

(Submitter supplied) IVLBCL is a rare distinct disease entity of extranodal large B-cell lymphoma . The disease is characterized by selective growth of tumor cells in the lumina of small vessels and by the absence of remarkable lymphadenopathy. We have developed patient derived xenograft IVLBCL mouse models from primary patient bone marrow samples. This dataset includes the array CGH analysis of IVLBCL tumor cells from the mouse xenograft models.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL19387

7 Samples

Download data: TXT

(Submitter supplied) This experiment investigates In Vitro and In Vivo Activity of AMG 337, a Potent and Selective MET Kinase Inhibitor, in MET-Dependent Cancer Models. The goal of this study was to examine the effects of AMG337 on proliferation in cancer cell lines with varying MET copy number, the hypothesis being that high-level focal MET amplification is required to confer MET oncogene addiction and AMG337 sensitivity.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL19387

21 Samples

Download data: TXT

(Submitter supplied) Runt-related transcription factor 3 (RUNX3) has been described as a tumor suppressor for gastric cancer and other solid malignancies. Despite its key role in physiological T-cell differentiation, there is rare information on its relevance for the development of human T-cell lymphoma or leukemia. Here we show that alterations of RUNX3 by either heterozygous deletion or methylation of its distal promoter can be observed in the tumor cells of 15/21 (71%) patients suffering from Sézary Syndrome (SS), an aggressive variant of cutaneous T-cell lymphoma. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL19387 GPL5114

23 Samples

Download data: GPR, TXT