Novel genes associated with colorectal cancer are revealed by high resolution cytogenetic analysis in a patient specific manner.

Genomic abnormalities leading to colorectal cancer (CRC) include somatic events causing copy number aberrations (CNAs) as well as copy neutral manifestations such as loss of heterozygosity (LOH) and uniparental disomy (UPD). We studied the causal effect of these events by analyzing high resolution c...

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Autores principales:	Hisham Eldai, Sathish Periyasamy, Saeed Al Qarni, Maha Al Rodayyan, Sabeena Muhammed Mustafa, Ahmad Deeb, Ebthehal Al Sheikh, Mohammed Afzal, Mishal Johani, Zeyad Yousef, Mohammad Azhar Aziz
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/44bd526d8f984689bb57070726ffe059
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spelling	oai:doaj.org-article:44bd526d8f984689bb57070726ffe0592021-11-18T08:49:04ZNovel genes associated with colorectal cancer are revealed by high resolution cytogenetic analysis in a patient specific manner.1932-620310.1371/journal.pone.0076251https://doaj.org/article/44bd526d8f984689bb57070726ffe0592013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24204606/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Genomic abnormalities leading to colorectal cancer (CRC) include somatic events causing copy number aberrations (CNAs) as well as copy neutral manifestations such as loss of heterozygosity (LOH) and uniparental disomy (UPD). We studied the causal effect of these events by analyzing high resolution cytogenetic microarray data of 15 tumor-normal paired samples. We detected 144 genes affected by CNAs. A subset of 91 genes are known to be CRC related yet high GISTIC scores indicate 24 genes on chromosomes 7, 8, 18 and 20 to be strongly relevant. Combining GISTIC ranking with functional analyses and degree of loss/gain we identify three genes in regions of significant loss (ATP8B1, NARS, and ATP5A1) and eight in regions of gain (CTCFL, SPO11, ZNF217, PLEKHA8, HOXA3, GPNMB, IGF2BP3 and PCAT1) as novel in their association with CRC. Pathway and target prediction analysis of CNA affected genes and microRNAs, respectively indicates TGF-β signaling pathway to be involved in causing CRC. Finally, LOH and UPD collectively affected nine cancer related genes. Transcription factor binding sites on regions of >35% copy number loss/gain influenced 16 CRC genes. Our analysis shows patient specific CRC manifestations at the genomic level and that these different events affect individual CRC patients differently.Hisham EldaiSathish PeriyasamySaeed Al QarniMaha Al RodayyanSabeena Muhammed MustafaAhmad DeebEbthehal Al SheikhMohammed AfzalMishal JohaniZeyad YousefMohammad Azhar AzizPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 10, p e76251 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Hisham Eldai Sathish Periyasamy Saeed Al Qarni Maha Al Rodayyan Sabeena Muhammed Mustafa Ahmad Deeb Ebthehal Al Sheikh Mohammed Afzal Mishal Johani Zeyad Yousef Mohammad Azhar Aziz Novel genes associated with colorectal cancer are revealed by high resolution cytogenetic analysis in a patient specific manner.
description	Genomic abnormalities leading to colorectal cancer (CRC) include somatic events causing copy number aberrations (CNAs) as well as copy neutral manifestations such as loss of heterozygosity (LOH) and uniparental disomy (UPD). We studied the causal effect of these events by analyzing high resolution cytogenetic microarray data of 15 tumor-normal paired samples. We detected 144 genes affected by CNAs. A subset of 91 genes are known to be CRC related yet high GISTIC scores indicate 24 genes on chromosomes 7, 8, 18 and 20 to be strongly relevant. Combining GISTIC ranking with functional analyses and degree of loss/gain we identify three genes in regions of significant loss (ATP8B1, NARS, and ATP5A1) and eight in regions of gain (CTCFL, SPO11, ZNF217, PLEKHA8, HOXA3, GPNMB, IGF2BP3 and PCAT1) as novel in their association with CRC. Pathway and target prediction analysis of CNA affected genes and microRNAs, respectively indicates TGF-β signaling pathway to be involved in causing CRC. Finally, LOH and UPD collectively affected nine cancer related genes. Transcription factor binding sites on regions of >35% copy number loss/gain influenced 16 CRC genes. Our analysis shows patient specific CRC manifestations at the genomic level and that these different events affect individual CRC patients differently.
format	article
author	Hisham Eldai Sathish Periyasamy Saeed Al Qarni Maha Al Rodayyan Sabeena Muhammed Mustafa Ahmad Deeb Ebthehal Al Sheikh Mohammed Afzal Mishal Johani Zeyad Yousef Mohammad Azhar Aziz
author_facet	Hisham Eldai Sathish Periyasamy Saeed Al Qarni Maha Al Rodayyan Sabeena Muhammed Mustafa Ahmad Deeb Ebthehal Al Sheikh Mohammed Afzal Mishal Johani Zeyad Yousef Mohammad Azhar Aziz
author_sort	Hisham Eldai
title	Novel genes associated with colorectal cancer are revealed by high resolution cytogenetic analysis in a patient specific manner.
title_short	Novel genes associated with colorectal cancer are revealed by high resolution cytogenetic analysis in a patient specific manner.
title_full	Novel genes associated with colorectal cancer are revealed by high resolution cytogenetic analysis in a patient specific manner.
title_fullStr	Novel genes associated with colorectal cancer are revealed by high resolution cytogenetic analysis in a patient specific manner.
title_full_unstemmed	Novel genes associated with colorectal cancer are revealed by high resolution cytogenetic analysis in a patient specific manner.
title_sort	novel genes associated with colorectal cancer are revealed by high resolution cytogenetic analysis in a patient specific manner.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/44bd526d8f984689bb57070726ffe059
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_version_	1718421256748924928

Novel genes associated with colorectal cancer are revealed by high resolution cytogenetic analysis in a patient specific manner.

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