Elsevier

Meta Gene

Volume 7, February 2016, Pages 95-104
Meta Gene

Copy number variants associated with 18p11.32, DCC and the promoter 1B region of APC in colorectal polyposis patients

https://doi.org/10.1016/j.mgene.2015.12.005Get rights and content
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Highlights

  • Catalogue of 139 CNVs unique to the polyposis patients which represent candidates for involvement in their disease

  • Identification of CNVs in four unrelated polyposis patients in APC, DCC, MLH1 and CTNNB1 which are likely to be associated with disease in affected individuals

  • A recurrent deletion at 18p11.32 was identified that affected 9% of the polyposis patients which harbours a lncRNA

Abstract

Familial Adenomatous Polyposis (FAP) is the second most common inherited predisposition to colorectal cancer (CRC) associated with the development of hundreds to thousands of adenomas in the colon and rectum. Mutations in APC are found in ~ 80% polyposis patients with FAP. In the remaining 20% no genetic diagnosis can be provided suggesting other genes or mechanisms that render APC inactive may be responsible. Copy number variants (CNVs) remain to be investigated in FAP and may account for disease in a proportion of polyposis patients. A cohort of 56 polyposis patients and 40 controls were screened for CNVs using the 2.7M microarray (Affymetrix) with data analysed using ChAS (Affymetrix). A total of 142 CNVs were identified unique to the polyposis cohort suggesting their involvement in CRC risk. We specifically identified CNVs in four unrelated polyposis patients among CRC susceptibility genes APC, DCC, MLH1 and CTNNB1 which are likely to have contributed to disease development in these patients. A recurrent deletion was observed at position 18p11.32 in 9% of the patients screened that was of particular interest. Further investigation is necessary to fully understand the role of these variants in CRC risk given the high prevalence among the patients screened.

Abbreviations

ALL
acute lymphoblastic leukaemia
BH
Bengamini and Hochberg
CHAS
Chromosome Analysis Suite
CN
copy number
CNV
copy number variation
COSMIC
Catalogue of Somatic Mutations in Cancer
CRC
colorectal cancer
DGV
Database of genomic variants
DNA
deoxyribose nucleic acid
FAP
familial adenomatous polyposis
HMDD
human microRNA disease database
Kb
kilobase
KEGG
Kyoto Encyclopaedia of Genes and Genomes
lncRNA
link RNA
LOH
loss of heterozygosity
mapd
median absolute pairwise difference
miR
microRNA
MLPA
multiplex ligation-dependant probe amplification
MMR
mismatch repair
ng
nanogram
NTC
no template control
QC
quality control
RNA
ribose nucleic acid
SNP
single nucleotide polymorphism
TAM
Tool for the annotation of microRNAs
TCGA
The Cancer Genome Atlas
UCSC
University of California, Santa Cruz

Keywords

Cancer
polyposis
CNV
long non-coding RNAs
diagnostic testing

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