Overview

This section shows a general overview of information for the selected study (COSU identifier) or publication (COSP identifier). Studies may have been performed by the Sanger Institute Cancer Genome Project, or imported from the ICGC/TCGA. You can see more information on the help pages.

Reference: P53 and APC mutations are detectable in the plasma and serum of patients with colorectal cancer (CRC) or adenomas.
Paper ID: COSP46469
Authors: Gocke CD, Benko FA, Kopreski MS and McGarrity TJ
Affiliation: Department of Pathology, Penn State Geisinger-Hershey Medical Center 17033, USA. cgocke@psghs.edu
Journal: Annals of the New York Academy of Sciences, 2000;906:44-50
ISSN: 0077-8923
PMID: 10818595 (view at PubMed or Europe PMC)
Abstract: Background: A variety of tumor-related DNA has been detected in the plasma and serum of cancer patients, including RAS, the BCL2-IgH transgene, and p53. It is not known whether the APC gene, which is frequently mutated in colorectal cancer (CRC), can be identified in the plasma of CRC patients. Similarly, it is unknown whether another tumor suppressor gene altered in CRC, p53, is detectable in people with precursor lesions to CRC.The plasma of 240 colonoscopy patients was tested for mutations at two frequently altered sites (codons 175 and 248). A restriction enzyme-mediated enrichment assay was used to detect these mutants. We also tested tumor tissue from 8 patients with CRC for mutations in the mutation cluster region of the APC gene using direct DNA sequencing. Corresponding plasma from any positive patient was then similarly sequenced.Results: Three plasma p53 mutations were identified. Two of these patients had adenomas at biopsy, and 1 had a hyperplastic polyp. All were tested for the same p53 mutations, and 1 of the adenomas was positive. One of the 8 CRC patients had a 5-base-pair deletion in the cancer and the same deletion was detectable in that patient's plasma, although at an amount that we estimate at 1-5% of the total APC DNA present.Conclusions: APC mutations are detectable in the plasma of CRC patients. p53 mutants are detectable in the plasma of colorectal adenoma patients. These may have important implications for cancer screening and diagnosis in the large intestine and suggest that all malignant and premalignant DNA alterations from the colon are identifiable in the blood.
Paper Status: Curated
Genes Analysed: 21
Mutated Samples: 1
Total No. of Samples: 8

Mutation Matrix

This section shows the correlation plot between the top 20 genes and samples. There is more information in our help pages.

Genes	Mutated Samples

Non-Mutant Genes	Gene Id (COSG)

Variants

Coding Mutations
Non-Coding Mutations
CNV & Expr
Methylation
Fusions

This tab shows genes with mutations in the selected study/paper [more details]

Genes	Samples	CDS Mutation	AA Mutation

This tab shows non coding variant in the selected study/paper [more details]

Sample ID	Sample Name	ID NCV	Annotation	Zygosity	Chromosome	Genome start	Genome stop	Genome version	Strand	WT seq	Mut seq	FATHMM-MKL

This tab shows the gene expression and copy number variation data for this study [more details]

Table Information

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The table currently shows only high value (numeric) copy number data. Copy number segments are excluded if the total copy number and minor allele values are unknown.

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Sample	Gene	Expression	Expr Level (Z-Score) Over Expressed; Z-Score > 2.0 Under Expressed; Z-Score < -2.0 Normal; Z-Score within the range -2.0 to 2.0	CN Type	Minor Allele	Copy Number	CN Segment Posn.	Average Ploidy 1. N/A represents cases where the average ploidy value is not available( mostly ICGC samples). For some TCGA samples where the minor allele information is not available the average ploidy value could not be calculated. 2. For TCGA samples, the ASCAT algorithm was used to calculate the average ploidy. 3. For CGP samples, the PICNIC algorithm was used to calculate the average ploidy.	CNV

This table lists the samples in the selected study which have low/high methylation for each gene. [more details]

No data

This tab shows the fusion mutations observed in this sample [more details]

Gene	Sample Name	Id Sample(COSS)	CDS Mutation	Somatic status	Zygosity	Validated	Type

Samples

Mutant Samples
Non-Mutant Samples

This table shows mutated samples in the selected study/paper.

Sample Name	Mutation Count

This table shows samples without mutations in the selected study/paper.

Non-Mutant Samples	Sample Id (COSS)

GRCh38 · COSMIC v92