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Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics [meDIP-seq]

ABSTRACT: Validation of methylation data for 9 osteosarcoma Patient tumours and PDXs by MeDIP followed by next generation sequencing

ORGANISM(S): Homo sapiens

PROVIDER: GSE59351 | GEO | 2014/11/26

SECONDARY ACCESSION(S): PRJNA255126

REPOSITORIES: GEO

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Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics [meDIP-seq]

Project description:Validation of methylation data for 9 osteosarcoma Patient tumours and PDXs by MeDIP followed by next generation sequencing 9 samples, MeDIP done with Diagenode kit and libraries prepped using NEB kit, sequenced on HiSeq 2000

2014-11-26 | E-GEOD-59351 | biostudies-arrayexpress

Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics [methylation profiling by array]

Project description:Illumina Infinium 450k Human DNA Methylation BeadChip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in Osteosarcoma and Colon Cancer PDXs Bisulphite converted DNA from each sample was hybridised to the Illumina Infinium 450k Human Methylation BeadChip.

2014-11-26 | E-GEOD-59134 | biostudies-arrayexpress

Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics [methylation profiling by array]

Project description:Illumina Infinium 450k Human DNA Methylation BeadChip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in Osteosarcoma and Colon Cancer PDXs

2014-11-26 | GSE59134 | GEO

Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics.

Project description:BackgroundThe use of tumour xenografts is a well-established research tool in cancer genomics but has not yet been comprehensively evaluated for cancer epigenomics.MethodsIn this study, we assessed the suitability of patient-derived tumour xenografts (PDXs) for methylome analysis using Infinium 450 K Beadchips and MeDIP-seq.ResultsControlled for confounding host (mouse) sequences, comparison of primary PDXs and matching patient tumours in a rare (osteosarcoma) and common (colon) cancer revealed that an average 2.7% of the assayed CpG sites undergo major (Δβ ≥ 0.51) methylation changes in a cancer-specific manner as a result of the xenografting procedure. No significant subsequent methylation changes were observed after a second round of xenografting between primary and secondary PDXs. Based on computational simulation using publically available methylation data, we additionally show that future studies comparing two groups of PDXs should use 15 or more samples in each group to minimise the impact of xenografting-associated changes in methylation on comparison results.ConclusionsOur results from rare and common cancers indicate that PDXs are a suitable discovery tool for cancer epigenomics and we provide guidance on how to overcome the observed limitations.

| S-EPMC4292812 | biostudies-literature

Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-11-26 | E-GEOD-59352 | biostudies-arrayexpress

Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics

Project description:This SuperSeries is composed of the SubSeries listed below.

2014-11-26 | GSE59352 | GEO

Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics

Project description:Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics

| PRJNA255123 | ENA

Methylome analysis of colorectal cancer cell line DNA (HCT116) and colorectal cancer patient derived xenografts (PDXs) using MeDIP-seq and cfMeDIP-seq

Project description:Three separate experiments were carried out using MeDIP-seq and cfMeDIP-seq for methylome analysis. For the first experiment, different starting amounts of HCT116 cell line DNA, sheared to mimic cell-free DNA, were analyzed using MeDIP-seq and cfMeDIP-seq. In the second experiment the limit of detection of cfMeDIP-seq was tested using varying dilutions of colorectal cancer cell line DNA (HCT116) with multiple myeloma cell line DNA (MM1.S). For both cell line DNA samples, the DNA was sheared to mimic cell-free DNA. In the final experiment, we tested the enrichment of human ctDNA using cfMeDIP-seq performed on plasma collected from patient-derived xenografts (PDXs) generated in mice from two colorectal cancer patients.

2018-04-01 | GSE79838 | GEO

Methylome analysis of colorectal cancer cell line DNA (HCT116) and colorectal cancer patient derived xenografts (PDXs) using MeDIP-seq and cfMeDIP-seq

Project description:Methylome analysis of colorectal cancer cell line DNA (HCT116) and colorectal cancer patient derived xenografts (PDXs) using MeDIP-seq and cfMeDIP-seq

| PRJNA317165 | ENA

MeDIP chip from ZOS and ZOSM osteosarcoma cell lines

Project description:Epigenetic change of genes expression, including hypomethylation-linked activation of oncogenes and hypermethylation-associated inactivation of tumor suppressor genes, can affect almost all the cellular signaling pathways that participate in cancer initiation and progression. Unlike genetic alterations, epigenetic changes are potentially reversible, making them attractive and promising targets for therapeutic intervention. Studies indicated that abnormal DNA methylation is involved in dysregulation of cell cycle, apoptosis, proliferation and differentiation of osteosarcoma. However, epigenetic mechanisms of osteosarcoma metastasis remain largely unknown. MeDIP chips are performed in ZOS and ZOSM—two syngeneic primary human osteosarcoma cell lines with low and high metastatic potential which are established in our lab

2015-08-25 | E-GEOD-55961 | biostudies-arrayexpress

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