Detection of new regulatory SNPs associated with colorectal cancer predisposition
A new approach to the search for regulatory SNPs (rSNPs) based on the use of ENCODE project data on ChIP-seq and RNA-seq experiments was developed. The approach was successfully used for the detection of rSNPs associated with colorectal cancer susceptibility. To start out with, we used raw sequence...
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| Format: | Article |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2017-02-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/853 |
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| author | E. Yu. Leberfarb L. O. Bryzgalov I. I. Brusentsov T. I. Merkulova |
| author_facet | E. Yu. Leberfarb L. O. Bryzgalov I. I. Brusentsov T. I. Merkulova |
| author_sort | E. Yu. Leberfarb |
| collection | DOAJ |
| description | A new approach to the search for regulatory SNPs (rSNPs) based on the use of ENCODE project data on ChIP-seq and RNA-seq experiments was developed. The approach was successfully used for the detection of rSNPs associated with colorectal cancer susceptibility. To start out with, we used raw sequence data of 15 independent ChIP-seq experiments run on colorectal cancer cell line HCT-116, which allowed us to generate the initial pool of 7985 SNPs located in regulatory regions. For further selection of functional SNPs, we used the ChIP-seq binding bias analysis and revealed 775 SNPs that are more likely to influence transcription regulation in HCT-116 cells. Then the RNA-seq bias analysis in HCT-116 cells was performed. As a result, we confirmed the functionality of 231 SNPs, which were classified as rSNPs. In order to select rSNPs potentially associated with colorectal cancer we chose those in strong linkage disequilibrium with SNPs asso-ciated with this pathology according to GWAS and ClinVar data. Functional annotation analysis of genes containing the rSNPs selected confirmed the involvement of BAIAP2L1 and BUB3 genes in colorectal cancer predisposition. We also found two genes (RRAGD and FZD6) playing a role in the RAS/MAРK and WNT signaling pathways. Although the involvement of the RAS/MAРK and WNT pathways in colon cancer is a well-known fact, these two genes are still unknown candidates. Moreover, we found 14 new candidate genes with promise for further study of colorectal cancer predisposition. |
| format | Article |
| id | doaj-art-0d048e3a7df045598b9284d548352625 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2017-02-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-0d048e3a7df045598b9284d5483526252025-02-01T09:58:03ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592017-02-0120679780310.18699/VJ16.197543Detection of new regulatory SNPs associated with colorectal cancer predispositionE. Yu. Leberfarb0L. O. Bryzgalov1I. I. Brusentsov2T. I. Merkulova3Institute of Cytology and Genetics SB RASInstitute of Cytology and Genetics SB RASInstitute of Cytology and Genetics SB RASInstitute of Cytology and Genetics SB RASA new approach to the search for regulatory SNPs (rSNPs) based on the use of ENCODE project data on ChIP-seq and RNA-seq experiments was developed. The approach was successfully used for the detection of rSNPs associated with colorectal cancer susceptibility. To start out with, we used raw sequence data of 15 independent ChIP-seq experiments run on colorectal cancer cell line HCT-116, which allowed us to generate the initial pool of 7985 SNPs located in regulatory regions. For further selection of functional SNPs, we used the ChIP-seq binding bias analysis and revealed 775 SNPs that are more likely to influence transcription regulation in HCT-116 cells. Then the RNA-seq bias analysis in HCT-116 cells was performed. As a result, we confirmed the functionality of 231 SNPs, which were classified as rSNPs. In order to select rSNPs potentially associated with colorectal cancer we chose those in strong linkage disequilibrium with SNPs asso-ciated with this pathology according to GWAS and ClinVar data. Functional annotation analysis of genes containing the rSNPs selected confirmed the involvement of BAIAP2L1 and BUB3 genes in colorectal cancer predisposition. We also found two genes (RRAGD and FZD6) playing a role in the RAS/MAРK and WNT signaling pathways. Although the involvement of the RAS/MAРK and WNT pathways in colon cancer is a well-known fact, these two genes are still unknown candidates. Moreover, we found 14 new candidate genes with promise for further study of colorectal cancer predisposition.https://vavilov.elpub.ru/jour/article/view/853regulatory snps (rsnp)colorectal cancernext generation sequencingencode project |
| spellingShingle | E. Yu. Leberfarb L. O. Bryzgalov I. I. Brusentsov T. I. Merkulova Detection of new regulatory SNPs associated with colorectal cancer predisposition Вавиловский журнал генетики и селекции regulatory snps (rsnp) colorectal cancer next generation sequencing encode project |
| title | Detection of new regulatory SNPs associated with colorectal cancer predisposition |
| title_full | Detection of new regulatory SNPs associated with colorectal cancer predisposition |
| title_fullStr | Detection of new regulatory SNPs associated with colorectal cancer predisposition |
| title_full_unstemmed | Detection of new regulatory SNPs associated with colorectal cancer predisposition |
| title_short | Detection of new regulatory SNPs associated with colorectal cancer predisposition |
| title_sort | detection of new regulatory snps associated with colorectal cancer predisposition |
| topic | regulatory snps (rsnp) colorectal cancer next generation sequencing encode project |
| url | https://vavilov.elpub.ru/jour/article/view/853 |
| work_keys_str_mv | AT eyuleberfarb detectionofnewregulatorysnpsassociatedwithcolorectalcancerpredisposition AT lobryzgalov detectionofnewregulatorysnpsassociatedwithcolorectalcancerpredisposition AT iibrusentsov detectionofnewregulatorysnpsassociatedwithcolorectalcancerpredisposition AT timerkulova detectionofnewregulatorysnpsassociatedwithcolorectalcancerpredisposition |