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Biomark Res. 2018 Jun 13;6:17. doi: 10.1186/s40364-018-0133-z. eCollection 2018.

Associations of single nucleotide polymorphisms with mucinous colorectal cancer: genome-wide common variant and gene-based rare variant analyses.

Author information

1
1Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada.
2
2Discipline of Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada.
3
3Discipline of Oncology, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada.
4
4Department of Mathematics and Statistics, Faculty of Science, Memorial University of Newfoundland, St. John's, Canada.

Abstract

Background:

Colorectal cancer has significant impact on individuals and healthcare systems. Many genes have been identified to influence its pathogenesis. However, the genetic basis of mucinous tumor histology, an aggressive subtype of colorectal cancer, is currently not well-known. This study aimed to identify common and rare genetic variations that are associated with the mucinous tumor phenotype.

Methods:

Genome-wide single nucleotide polymorphism (SNP) data was investigated in a colorectal cancer patient cohort (n = 505). Association analyses were performed for 729,373 common SNPs and 275,645 rare SNPs. Common SNP association analysis was performed using univariable and multivariable logistic regression under different genetic models. Rare-variant association analysis was performed using a multi-marker test.

Results:

No associations reached the traditional genome-wide significance. However, promising genetic associations were identified. The identified common SNPs significantly improved the discriminatory accuracy of the model for mucinous tumor phenotype. Specifically, the area under the receiver operating characteristic curve increased from 0.703 (95% CI: 0.634-0.773) to 0.916 (95% CI: 0.873-0.960) when considering the most significant SNPs. Additionally, the rare variant analysis identified a number of genetic regions that potentially contain causal rare variants associated with the mucinous tumor phenotype.

Conclusions:

This is the first study applying both common and rare variant analyses to identify genetic associations with mucinous tumor phenotype using a genome-wide genotype data. Our results suggested novel associations with mucinous tumors. Once confirmed, these results will not only help us understand the biological basis of mucinous histology, but may also help develop targeted treatment options for mucinous tumors.

KEYWORDS:

Colorectal cancer; Common single nucleotide polymorphisms; Genome-wide association study; Mucinous adenocarcinoma; Rare single nucleotide polymorphisms

Conflict of interest statement

Patient consents were obtained by the Newfoundland Colorectal Cancer Registry (NFCCR) at the time of recruitment. If the patient was deceased, consent was sought from a close relative [78]. Ethics approval for this study was obtained from the Health Research Ethics Board (HREB; #15.043).The authors declare that they have no competing interests.Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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