ArticleGenes, chromosomes & cancer2012
A new whole genome amplification method for studying clonal evolution patterns in malignant colorectal polyps.
Article in Genes, chromosomes & cancer, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 27 citations in OpenAlex.
- Discovery of Long Non-Coding RNA MALAT1 Amplification in Precancerous Colorectal Lesions.International journal of molecular sciences · 2022Article
- Molecular characterization of ulcerative colitis-associated colorectal carcinomas.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2021Article
- Clinical responses to PD-1 inhibition and their molecular characterization in six patients with mismatch repair-deficient metastatic cancer of the digestive system.Journal of cancer research and clinical oncology · 2021Article
- Newly established gastrointestinal cancer cell lines retain the genomic and immunophenotypic landscape of their parental cancers.Scientific reports · 2020Article
- Molecular characterization of colorectal adenomas reveals POFUT1 as a candidate driver of tumor progression.International journal of cancer · 2020Article
- Variations in the Mitochondrial Genome of a Goldfish-Like Hybrid [Koi Carp (♀) × Blunt Snout Bream (♂)] Indicate Paternal Leakage.Frontiers in genetics · 2020Article
- Single-cell genetic analysis of clonal dynamics in colorectal adenomas indicates CDX2 gain as a predictor of recurrence.International journal of cancer · 2019Article
- [Crohn's disease-associated colorectal carcinogenesis : TP53 mutations and copy number gains of chromosome arm 5p as (early) markers of tumor progression].Der Pathologe · 2018Review
- Consensus molecular subtype classification of colorectal adenomas.The Journal of pathology · 2018Article
- Dynamics of Genome Alterations in Crohn's Disease-Associated Colorectal Carcinogenesis.Clinical cancer research : an official journal of the American Association for Cancer Research · 2018Article
- Endothelial protein C receptor is overexpressed in colorectal cancer as a result of amplification and hypomethylation of chromosome 20q.The journal of pathology. Clinical research · 2017Article
- Evolutionary dynamics in pre-invasive neoplasia.Current opinion in systems biology · 2017Article
- Methods and novel technology for microRNA quantification in colorectal cancer screening.Clinical epigenetics · 2017Review
- Genomic Landscape of Colorectal Mucosa and Adenomas.Cancer prevention research (Philadelphia, Pa.) · 2016Article
- Patterns of Chromosomal Aberrations in Solid Tumors.Recent results in cancer research. Fortschritte der Krebsforschung. Progres dans les recherches sur le cancer · 2015Review
- Article
- Mechanisms of topoisomerase I (TOP1) gene copy number increase in a stage III colorectal cancer patient cohort.PloS one · 2013Article
- The consequences of chromosomal aneuploidy on the transcriptome of cancer cells.Biochimica et biophysica acta · 2012Review
- Article
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Authors and funding
7 authors at 3 institutions in 3 countries.
Funding
Abstract
To identify the genetic drivers of colorectal tumorigenesis, we applied array comparative genomic hybridization (aCGH) to 13 formalin-fixed paraffin-embedded (FFPE) samples of early, localized human colon adenocarcinomas arising in high-grade adenomas (so-called "malignant polyps"). These lesions are small and hence the amount of DNA is limited. Additionally, the quality of DNA is compromised due to the fragmentation as a consequence of formalin fixation. To overcome these problems, we optimized a newly developed isothermal whole genome amplification system (NuGEN Ovation® WGA FFPE System). Starting with 100 ng of FFPE DNA, the amplification system produced 4.01 ± 0.29 μg (mean ± standard deviation) of DNA. The excellent quality of amplified DNA was further indicated by a high signal-to-noise ratio and a low derivative log(2) ratio spread. Both, the amount of amplified DNA and aCGH performance were independent of the age of the FFPE blocks and the associated degradation of the extracted DNA. We observed losses of chromosome arms 5q and 18q in the adenoma components of the malignant polyp samples, while the embedded early carcinomas revealed losses of 8p, 17p, and 18, and gains of 7, 13, and 20. Aberrations detected in the adenoma components were invariably maintained in the embedded carcinomas. This approach demonstrates that using isothermally whole genome amplified FFPE DNA is technically suitable for aCGH. In addition to demonstrating the clonal origin of the adenoma and carcinoma part within a malignant polyp, the gain of chromosome arm 20q was an indicator for progression from adenoma to carcinoma.
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