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Novel approach to functional SNPs discovery from genome-wide data reveals promising variants for colon cancer risk. / Korbolina, Elena E.; Brusentsov, Ilja I.; Bryzgalov, Leonid O. et al.

In: Human Mutation, Vol. 39, No. 6, 01.06.2018, p. 851-859.

Research output: Contribution to journalArticlepeer-review

Harvard

Korbolina, EE, Brusentsov, II, Bryzgalov, LO, Leberfarb, EY, Degtyareva, AO & Merkulova, TI 2018, 'Novel approach to functional SNPs discovery from genome-wide data reveals promising variants for colon cancer risk', Human Mutation, vol. 39, no. 6, pp. 851-859. https://doi.org/10.1002/humu.23425

APA

Korbolina, E. E., Brusentsov, I. I., Bryzgalov, L. O., Leberfarb, E. Y., Degtyareva, A. O., & Merkulova, T. I. (2018). Novel approach to functional SNPs discovery from genome-wide data reveals promising variants for colon cancer risk. Human Mutation, 39(6), 851-859. https://doi.org/10.1002/humu.23425

Vancouver

Korbolina EE, Brusentsov II, Bryzgalov LO, Leberfarb EY, Degtyareva AO, Merkulova TI. Novel approach to functional SNPs discovery from genome-wide data reveals promising variants for colon cancer risk. Human Mutation. 2018 Jun 1;39(6):851-859. doi: 10.1002/humu.23425

Author

Korbolina, Elena E. ; Brusentsov, Ilja I. ; Bryzgalov, Leonid O. et al. / Novel approach to functional SNPs discovery from genome-wide data reveals promising variants for colon cancer risk. In: Human Mutation. 2018 ; Vol. 39, No. 6. pp. 851-859.

BibTeX

@article{f4f643b5fc644eeda3ad718111ee1104,
title = "Novel approach to functional SNPs discovery from genome-wide data reveals promising variants for colon cancer risk",
abstract = "In the majority of colorectal cancer (CRC) cases, the genetic basis of predisposition remains unexplained. The goal of the study was to assess the regulatory SNPs (rSNPs) in the human genome and to reveal SRC drivers based on the available chromatin immunoprecipitation sequencing (ChIP-Seq, ChIA-PET) and transcriptional profiling (RNA-Seq) data. We combined positional (locations within genome regulatory elements) and functional (associated with allele-specific binding and expression) criteria followed by an analysis using genome-wide association studies (GWAS) and minor allele frequency (MAF) datasets. DeSeq2 analysis through 70 CRC patients reinforced the regulatory potential. rSNPs (1,476) that were associated with significant (P < 0.01) allele-specific events resulting in thirty that exhibited a link with CRC according to the MAF and 27, with a risk of malignancy in general according to GWAS. Selected rSNPs may modify the expression of genes for tumor suppressors and the regulators of signaling pathways, including noncoding RNAs. However, the rSNPs from the most represented group affect the expression of genes related to splicing. Our findings strongly suggest that the identified variants might contribute to CRC susceptibility, which indicates that aberrant splicing is one of the key mechanisms for unraveling disease etiopathogenesis and provides useful inputs for interpreting how genotypic variation corresponds to phenotypic outcome.",
keywords = "Allele-specific events, Colorectal cancer, Functional variants, Gene regulation, SNPs, colorectal cancer, gene regulation, allele-specific events, functional variants, SUPPRESSOR, MICRORNAS, IDENTIFICATION, EPIGENETICS, SART3, TUMOR-REJECTION ANTIGEN, GENES, ASSOCIATION, EXPRESSION, RNA-SEQ DATA, Humans, Male, Polymorphism, Single Nucleotide/genetics, Genome, Human/genetics, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Colonic Neoplasms/genetics, Gene Frequency, HCT116 Cells, Risk Factors, Genotype, Alleles",
author = "Korbolina, {Elena E.} and Brusentsov, {Ilja I.} and Bryzgalov, {Leonid O.} and Leberfarb, {Elena Yu} and Degtyareva, {Arina O.} and Merkulova, {Tatyana I.}",
note = "{\textcopyright} 2018 Wiley Periodicals, Inc.",
year = "2018",
month = jun,
day = "1",
doi = "10.1002/humu.23425",
language = "English",
volume = "39",
pages = "851--859",
journal = "Human Mutation",
issn = "1059-7794",
publisher = "Wiley-Liss Inc.",
number = "6",

}

RIS

TY - JOUR

T1 - Novel approach to functional SNPs discovery from genome-wide data reveals promising variants for colon cancer risk

AU - Korbolina, Elena E.

AU - Brusentsov, Ilja I.

AU - Bryzgalov, Leonid O.

AU - Leberfarb, Elena Yu

AU - Degtyareva, Arina O.

AU - Merkulova, Tatyana I.

N1 - © 2018 Wiley Periodicals, Inc.

PY - 2018/6/1

Y1 - 2018/6/1

N2 - In the majority of colorectal cancer (CRC) cases, the genetic basis of predisposition remains unexplained. The goal of the study was to assess the regulatory SNPs (rSNPs) in the human genome and to reveal SRC drivers based on the available chromatin immunoprecipitation sequencing (ChIP-Seq, ChIA-PET) and transcriptional profiling (RNA-Seq) data. We combined positional (locations within genome regulatory elements) and functional (associated with allele-specific binding and expression) criteria followed by an analysis using genome-wide association studies (GWAS) and minor allele frequency (MAF) datasets. DeSeq2 analysis through 70 CRC patients reinforced the regulatory potential. rSNPs (1,476) that were associated with significant (P < 0.01) allele-specific events resulting in thirty that exhibited a link with CRC according to the MAF and 27, with a risk of malignancy in general according to GWAS. Selected rSNPs may modify the expression of genes for tumor suppressors and the regulators of signaling pathways, including noncoding RNAs. However, the rSNPs from the most represented group affect the expression of genes related to splicing. Our findings strongly suggest that the identified variants might contribute to CRC susceptibility, which indicates that aberrant splicing is one of the key mechanisms for unraveling disease etiopathogenesis and provides useful inputs for interpreting how genotypic variation corresponds to phenotypic outcome.

AB - In the majority of colorectal cancer (CRC) cases, the genetic basis of predisposition remains unexplained. The goal of the study was to assess the regulatory SNPs (rSNPs) in the human genome and to reveal SRC drivers based on the available chromatin immunoprecipitation sequencing (ChIP-Seq, ChIA-PET) and transcriptional profiling (RNA-Seq) data. We combined positional (locations within genome regulatory elements) and functional (associated with allele-specific binding and expression) criteria followed by an analysis using genome-wide association studies (GWAS) and minor allele frequency (MAF) datasets. DeSeq2 analysis through 70 CRC patients reinforced the regulatory potential. rSNPs (1,476) that were associated with significant (P < 0.01) allele-specific events resulting in thirty that exhibited a link with CRC according to the MAF and 27, with a risk of malignancy in general according to GWAS. Selected rSNPs may modify the expression of genes for tumor suppressors and the regulators of signaling pathways, including noncoding RNAs. However, the rSNPs from the most represented group affect the expression of genes related to splicing. Our findings strongly suggest that the identified variants might contribute to CRC susceptibility, which indicates that aberrant splicing is one of the key mechanisms for unraveling disease etiopathogenesis and provides useful inputs for interpreting how genotypic variation corresponds to phenotypic outcome.

KW - Allele-specific events

KW - Colorectal cancer

KW - Functional variants

KW - Gene regulation

KW - SNPs

KW - colorectal cancer

KW - gene regulation

KW - allele-specific events

KW - functional variants

KW - SUPPRESSOR

KW - MICRORNAS

KW - IDENTIFICATION

KW - EPIGENETICS

KW - SART3

KW - TUMOR-REJECTION ANTIGEN

KW - GENES

KW - ASSOCIATION

KW - EXPRESSION

KW - RNA-SEQ DATA

KW - Humans

KW - Male

KW - Polymorphism, Single Nucleotide/genetics

KW - Genome, Human/genetics

KW - Female

KW - Genetic Predisposition to Disease

KW - Genome-Wide Association Study

KW - Colonic Neoplasms/genetics

KW - Gene Frequency

KW - HCT116 Cells

KW - Risk Factors

KW - Genotype

KW - Alleles

UR - http://www.scopus.com/inward/record.url?scp=85044849138&partnerID=8YFLogxK

U2 - 10.1002/humu.23425

DO - 10.1002/humu.23425

M3 - Article

C2 - 29573091

AN - SCOPUS:85044849138

VL - 39

SP - 851

EP - 859

JO - Human Mutation

JF - Human Mutation

SN - 1059-7794

IS - 6

ER -

ID: 12417563