Copy number variation data in malignant mouse mammary cell lines
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Maxwell Lee
PROVIDER: E-GEOD-69902 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Many preclinical therapy studies have focused on a small number of well-described mouse allograft or human xenograft models that poorly represent the heterogeneity of human disease. Here we have assembled a panel of mouse mammary cell lines derived from spontaneously-arising mouse mammary tumors or from mammary tumors arising in genetically engineered mouse models. We used the Affymetrix Mouse Diversity Genotyping Array to address DNA copy number variation in the genomes of the cell lines of this panel. The resulting information about regions of amplification and deletion should help inform biological analyses as well as provide a reference for cell line authentication/identification.
2016-06-15 | GSE69902 | GEO
Project description:Human pluripotent stem cells commonly undergo adaptive changes during prolonged passaging in vitro. We have developed a new laminin-521 based method for self-renewal of human pluripotent stem cells. SNP6.0 array was used to assess genetic stability of several human ES cell lines cultured in the new system with two lines (H1 and HS401) cultured on feeders (standard conditions) Two main objectives in this study: To compare the number of the CNVs in human ES cells at early and late passages; for example, samples HS980 p6 and HS980 p31 represent HS980 cells at passages 6 and 31, respectively. The overall conclusion is that the observed number of CNVs is similar in the cells at early and late passages. This analysis can be remade without the reference samples. To compare the number of CNVs in control human ES cells (H1 and HS401) grown under standard protocol with that in cells (HS980, HS983a, HS999, HS916, and HS1001) grown under a new, developed by us, protocol. Because the cells were from different individuals, we could not compare them directly. Instead, we compared them to a set of samples from 75 healthy individuals, and then with each other. For the Reference These samples had been hybridized in the same lab as our samples, but for a different project; and the data were kindly provided by Prof. Kere. However, the same overall conclusion would result from an other sufficiently large dataset of healthy human individuals. Please note that 75 healthy individual samples had been hybridized in the same lab as our samples and the data were kindly provided by Prof. Kere, which is linked as a Series supplementary file ('75_samples_ref.REF'). It is a Reference Model File that Affymetrix Genotyping Console software has created based on data from 75 healthy individuals (i.e. processed file based on the CEL files of the 75 healthy individuals). The file derives from the "CN/LOH Reference Model File Creation and Analysis (Batch Sample Mode)" process according to the Genotyping Console manual. It contains SNP-wise information on the observed distribution of hybridization intensities of a set of samples that are assumed to be diploid in copy number (for most part of their genomes at least). This file is then used to compare the intensities observed in the CEL files of interest to infer deviations from the reference as CNVs. Thus, in combination with the CEL files (from each ES cell line), this file enables the exact replication of the CNV analyses done for the various human ES cell lines study. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted cultured human ES cells. Several lines were analysed at different time points of the experiment. The analysis was done using default parameters and comparing each sample against a reference set of 75 healthy individuals provided by Juha Kere.
2013-12-19 | E-GEOD-53436 | biostudies-arrayexpress
Project description:Methods of comprehensive microarray based analyses of single cell DNA are rapidly emerging. Whole genome amplification (WGA) remains a critical component for these methods to be successful. A number of commercially available WGA kits have been independently utilized in previous single cell microarray studies. However, direct comparison of their performance on single cells has not been conducted. The present study demonstrates that among previously published methods, a single cell GenomePlex WGA protocol provides the best combination of speed and accuracy for SNP microarray based copy number analysis when compared to a REPLI-g or GenomiPhi based protocol. Alternatively, for applications that do not have constraints on turn-around time and that are directed at accurate genotyping rather than copy number assignments, a REPLI-g based protocol may provide the best solution. Affymetrix SNP arrays were processed according to the manufacturer's directions on DNA extracted from human fibroblast cell lines and single fibroblast cells. Afflymetrix SNP array analysis was successfully completed on 46 lymphocyte single cell samples, 8 gDNA extracted from cell lines, 11 reference gDNA extracted from cell lines and 3 reference gDNA samples from the RMA of New Jersey DNA bank. GSM617116 to GSM617129: CEL files were processed using GTYPE version 4 (Affymetrix Inc., Genotyping Console 4.0 Manual) using the DM algorithm for genotype calls. Copy number and loss of heterozygosity were calculated from CHP files using CNAT version 4.1 (Affymetrix Inc., Genotyping Console 4.0 Manual) analysis against a reference set consisting of three normal females from in house gDNA bank, 11 normal females from Coriel cell lines and 16 normal females from the HapMap database (www.hapmap.org). The 16 normal females are NA10855, NA10863, NA11832, NA12057, NA12234, NA12717, NA12813, NA18505, NA18508, NA18517, NA19137, NA19152, NE00088, NE00091, NE00403, and NE01119.
2010-12-20 | E-GEOD-24690 | biostudies-arrayexpress
Project description:To identify novel mechanisms regulating allogeneic hematopoietic cell engraftment, we previously used a forward genetic approach and described identification, in mice, of the Bmgr5 bone marrow (BM) engraftment quantitative trait locus (QTL). This QTL confers dominant and large allele effects for engraftment susceptibility. It was localized to chromosome 16 by classical quantitative genetic techniques in a segregating backcross bred from susceptible BALB.K and resistant B10.BR mice. We now report verification of the Bmgr5 QTL using reciprocal chromosome 16 consomic strains. The BM engraftment phenotype in these consomic mice shows that Bmgr5 susceptibility alleles are not only sufficient but also indispensable for conferring permissiveness for allogeneic BM engraftment. Using panels of congenic mice, we resolved the Bmgr5 QTL into two separate subloci, termed Bmgr5a and Bmgr5b, each conferring permissiveness for the engraftment phenotype and both fine mapped to an interval amenable to positional cloning. Candidate Bmgr5 genes were then prioritized using whole exome DNA sequencing and microarray gene expression profiling. Further studies are needed to elucidate the genetic interaction between Bmgr5a and Bmgr5b and identify causative genes and underlying gene variants. This may lead to new approaches for overcoming the problem of graft rejection in clinical hematopoietic cell transplantation. B10.BALBChr16 and BALB.B10Chr16 consomic strain mice were constructed in our laboratory for validation of bone marrow engraftment and graft-vs-host diseaes QTLs. The parental strains for consomic line construction were B10.BR (B10.BR-H2k H2-T18a/SgSnJJrep) and BALB.K (C.C3-H2k/LilMcdJ). The JAX Mouse Diveristy 620K SNP Array was used to verify adequate removal of residual background heterozygosity. Liver DNA was delivered to JAX Mouse Diversity Genotyping Array Service (Jackson Laboratory) for the SNP Array genotyping.
2013-01-10 | E-GEOD-43377 | biostudies-arrayexpress
Project description:Generating sufficient DNA for high-throughput genetic analysis has always been a challenge for clinical settings where the amount of source DNA is limited. Multiple displacement amplification (MDA) has been proposed as a promising candidate for such situations. Previous work with lower-resolution arrays confirmed the utility of single-cell MDA products for large-size (~30 Mb) genome variation screening. We tested the performance of single-cell MDA products on the SNP 6.0 arrays to examine the performance of single-cell MDA in SNP genotyping, copy number polymorphism, de novo copy number variation (CNV) and loss of heterozygosity (LOH) analysis. Our data show that for SNP genotyping, single-cell MDA did not obtain complete genome coverage or high sequence fidelity. For CNV calling, single-cell MDA introduced stochastic amplification artifacts in log2 ratio profiles, reducing the robustness of CNV calling; however, by adjusting smooth window size, it is still possible to analyze large chromosomal aberrations, and homozygous deletions as small as 500 kb can still be identified from the noisy log2 ratio profiles. Our results also suggest that even with a modified protocol (reduction of reaction volume, addition of a molecular crowding reagent, minimization of reaction time), single-cell MDA presented little improvement over the unmodified protocol, but by increasing the number of cells as template to 5M-bM-^@M-^S10 cells, SNP 6.0 array results comparable to those of 10 ng genomic DNA MDA could be obtained. Algorithms like PICNIC improved the CNV calling, suggesting that better algorithms can better utilize single-cell MDA array results. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cell line samples, and multiple displacement samples. Genotyping, Copy number and LOH analysis of Affymetrix SNP 6.0 arrays was performed for 3 samples of unamplified cell line genomic DNA, 2 samples of DNA obtained by multiple displacement amplification from 10ng genomic DNA, 3 single-cell multiple displacement amplification (MDA) products, single cell modified MDA amplification product, 5-cell modified MDA amplification product, 10-cell modified MDA amplification product.
2011-03-25 | E-GEOD-28132 | biostudies-arrayexpress
Project description:The biology of small cell ovarian carcinoma of the hypercalcemic type (SCCOHT), which is a rare and aggressive form of ovarian cancer, is poorly understood. Tumourigenicity, in vitro growth characteristics, genetic and genomic anomalies, and sensitivity to standard and novel chemotherapeutic treatments were investigated in the unique SCCOHT cell line, BIN-67, to provide further insight in the biology of this rare type of ovarian cancer. Chromosomal anomalies in BIN-67 cells were inferred using the Infinium? genotyping technology with the HumanHap300-Duo Genotyping BeadChip (Illumina, San Diego, CA, USA). This BeadChip contains about 318,000 genetic markers within approximately a 5 kb median SNP spacing. Genotyping and imaging using BeadStudio Data Analysis software (Illumina, San Diego, CA, USA) were performed at the McGill University and Genome Quebec Innovation Centre (Montreal, QC).
2013-09-24 | E-MTAB-1584 | biostudies-arrayexpress
Project description:Development of a new carcinoma cell line (HC-AFW1) derived from a pediatric liver tumor The cell line HC-AFW1 was derived from a 4 year old boy suffering from HCC through culturing and passage into immuno-deficient mice. The cell line is stable now for over 8 months of culture with a doubling time of 40 h. The tumor cells show an epithelial histology and express hepatoma proteins such as Alpha-fetoprotein (AFP), Glypican 3, E-cadherin, CD10, CD326, HepPar1, Vimentin and Desmin. Catenin beta shows a deletion of 49 amino acids in the exon 3 involving the phosphorylation sites of GSK3 and is detectable in the cell nuclei. Cytogenetic analysis revealed large anomalies in the chromosomal map including chromosomal aberrations found in hepatoblastoma as well as in adult HCC. Copy number analysis of two different passages of HC-AFW1 cells Two tumor specimens were used for tissue culture and xenotransplantation into NSG mice. Tumor cells derived from xenografts were cultured and designated as HC-AFW1. DNA was analyzed from the passage 2 (2P2). HC-AFW2 was derived from tissue culture without transfer in to mice. Primary tissue samples were minced into pieces of 3x3 mm and cultured on 6 well plates (Becton Dickenson, Frankfurt, Germany) in DMEM (GIBCO BRL, Carlsbad, CA) supplemented with 10% FCS (growth medium). Cell cultures were maintained in a humidified atmosphere containing 5% CO2 at 37°C. For subculturing cells were detached from the culture surface using accutase in Dulbecco´s PBS containing 0.5mM EDTA (PAA Laboratories GmbH, Cölbe, Germany) for 2-3 minutes at 37°C. A sub-cultivation ratio of 1:4 and 1:6 was performed twice per week. Cells were stored in liquid nitrogen as a suspension in complete growth medium with 10% DMSO. DNA from patient blood and tumor samples was isolated with the QiaAmp DNA mini Kit according to manufacturer's instructions (Qiagen, Hilden, Germany). Single nucleotide polymorphism (SNP) and copy number polymorphism (CNP) genotyping were performed using the Genome-Wide Human SNP Array 6.0 and Genotyping Console (GTC) software (Affymetrix, Santa Clara, CA).
2011-12-01 | E-GEOD-29283 | biostudies-arrayexpress
Project description:We used high-resolution SNP genotyping to identify regions of genomic gain and loss in the genome of 212 medulloblastomas, a malignant pediatric brain tumor. Focal amplifications of fifteen known oncogenes and focal deletions of twenty known tumor suppressor genes (TSG) were revealed, most not previously implicated in medulloblastoma. Importantly, we identified novel amplifications and homozygous deletions, including recurrent, mutually exclusive, highly focal genetic events in genes targeting histone lysine methylation, particularly histone 3, lysine 9 (H3K9). Post-translational modification of histone proteins is critical for regulation of gene expression, can participate in determining stem cell fates, and has been implicated in carcinogenesis. Consistent with our genetic data, restoration of expression of genes controlling H3K9 methylation greatly diminishes proliferation of medulloblastoma in vitro. Copy number aberrations of genes with critical roles in writing, reading, removing, and blocking the state of histone lysine methylation, particularly H3K9, suggest that defective control of the histone code contributes to the pathogenesis of medulloblastoma. Keywords: Affymetrix SNP array Genomic DNA isolated from fresh frozen primary human medulloblastomas and medulloblastoma cell lines were subjected to SNP genotyping using either Affymetrix 100K or 500K GeneChip Mapping array sets for the purpose of obtaining genome-wide copy number and LOH profiles.
2010-04-06 | E-GEOD-14437 | biostudies-arrayexpress
Project description:This study presents exon array expression data for multiple mammary tumor cell lines derived from various genetically-engineered mouse models of mammary cancer as well as from cell lines derived from spontaneously arising mouse mammary tumors.
2016-05-27 | GSE69541 | GEO
Project description:Five NPC cell lines (HONE1, CNE1, CNE2, 5-8F, and 6-10B) and an immortalized nasopharyngeal epithelial cell line NP69 were evaluated with 250K SNP arrays (Affymetrix) to detect the genome-wide DNA copy number alterations. The same type of data of 45 Chinese samples from the HapMap project was used as normal control. Data was analyzed using GCOS (GeneChip operating software, Ver.1.4), GTYPE (GeneChip Genotyping Analysis Software, Ver.4.1), and CNAT (chromosome copy number analysis tool, Ver.4.0, BRLMM algorithm).
2009-03-04 | E-GEOD-15051 | biostudies-arrayexpress