Identification of different mutational profiles in cancers arising in specific colon segments by next generation sequencing

Oncotarget
Duarte Mendes OliveiraAntonia Rizzuto

Abstract

The objective of this study was to investigate the mutational profiles of cancers arising in different colon segments. To this aim, we have analyzed 37 colon cancer samples by use of the Ion AmpliSeq™ Comprehensive Cancer Panel. Overall, we have found 307 mutated genes, most of which already implicated in the development of colon cancer. Among these, 15 genes were mutated in tumors originating in all six colon segments and were defined "common genes" (i.e. APC, PIK3CA, TP53) whereas 13 genes were preferentially mutated in tumors originating only in specific colon segments and were defined "site-associated genes" (i.e. BLNK, PTPRD). In addition, the presence of mutations in 10 of the 307 identified mutated genes (NBN, SMUG1, ERBB2, PTPRT, EPHB1, ALK, PTPRD, AURKB, KDR and GPR124) were found to be of clinical relevance. Among clinically relevant genes, NBN and SMUG1 were identified as independent prognostic factors that predicted poor survival in colon cancer patients. In conclusion, the findings reported here indicate that tumors arising in different colon segments present differences in the type and/or frequency of genetic variants, with two of them being independent prognostic factors that predict poor survival in colon cancer...Continue Reading

References

Jun 1, 1990·Cell·E R Fearon, B Vogelstein
Nov 19, 2002·Nature Immunology·Alexandra FlemmingHassan Jumaa
Mar 7, 2003·The New England Journal of Medicine·Henry T Lynch, Albert de la Chapelle
Oct 7, 2004·Cell Cycle·Yardena Samuels, Victor E Velculescu
Jan 8, 2005·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Ernest T Hawk, Bernard Levin
Aug 23, 2005·Genes, Chromosomes & Cancer·Masamitsu SatoTakashi Kohno
Sep 9, 2006·Science·Tobias SjöblomVictor E Velculescu
Dec 21, 2006·Molecular and Cellular Biology·Irina IssaevaEli Canaani
Oct 13, 2007·Science·Laura D WoodBert Vogelstein
Oct 17, 2007·Genes & Development·Anil K Rustgi
Oct 15, 2008·Proceedings of the National Academy of Sciences of the United States of America·Rebecca J LearyVictor E Velculescu
Dec 17, 2008·Cancer Research·David A SolomonTodd Waldman
May 29, 2009·CA: a Cancer Journal for Clinicians·Ahmedin JemalMichael J Thun
Nov 26, 2009·Gastroenterology·David P TaylorLisa A Cannon-Albright
Feb 19, 2010·Nature·Graham R BignellMichael R Stratton
Apr 1, 2010·Nature Methods·Ivan A AdzhubeiShamil R Sunyaev
Nov 26, 2010·Annual Review of Pathology·Eric R Fearon
Sep 13, 2011·Genome Research·Giovanni CirielloNikolaus Schultz
Jan 13, 2012·CA: a Cancer Journal for Clinicians·Rebecca SiegelAhmedin Jemal
Feb 14, 2012·Nature Medicine·Doron LipsonPhilip J Stephens
Jun 23, 2012·Nature·Catherine S GrassoScott A Tomlins
Jul 20, 2012·Nature·UNKNOWN Cancer Genome Atlas Network
Aug 17, 2012·Nature·Somasekar SeshagiriFrederic J de Sauvage
Sep 11, 2012·Nature·UNKNOWN Cancer Genome Atlas Research Network
May 1, 2011·Experimental and Therapeutic Medicine·Kosuke FunatoTetsu Akiyama
Dec 5, 2012·Cancer Discovery·Jennifer N Wu, Charles W M Roberts
Nov 5, 2013·World Journal of Gastroenterology : WJG·Tae-Min KimYeun-Jun Chung
Jan 8, 2014·Current Genomics·Francesco BerardinelliAntonio Antoccia
Mar 14, 2014·Frontiers in Oncology·Gieri Cathomas
Oct 28, 2014·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Dae-Hwan KimSeunghee Lee
Apr 17, 2015·Science Translational Medicine·Siân JonesVictor E Velculescu
Sep 5, 2015·Gastroenterology Report·Jonathan M KocarnikAmanda I Phipps

❮ Previous
Next ❯

Citations

Mar 7, 2021·International Journal of Molecular Sciences·Sripriya Raja, Bennett Van Houten

❮ Previous
Next ❯

Methods Mentioned

BETA
exome sequencing
surgical resection
PCR
Chip

Software Mentioned

R
Thermofisher
Torrent Suite
Polyphen2
Variant Caller
Torrent Variant Caller
SIFT
Mutation Mapper

Related Concepts

Related Feeds

Cancer Sequencing

Several sequencing approaches are employed to understand and examine tumor development and progression. These include whole genome as well as RNA sequencing. Here is the latest research on cancer sequencing.

Adenomatous Polyposis Coli

Adenomatous polyposis coli is a protein encoded by the APC gene and acts as a tumor suppressor. Discover the latest research on adenomatous polyposis coli here.

Related Papers

Lung Cancer : Journal of the International Association for the Study of Lung Cancer
Laura BonannoStefano Indraccolo
The Breast : Official Journal of the European Society of Mastology
Laura-Ancuta PopIoana Berindan-Neagoe
Lung Cancer : Journal of the International Association for the Study of Lung Cancer
Satu Mäki-NevalaSakari Knuutila
Cancer Control : Journal of the Moffitt Cancer Center
Timothy N HembreeAlberto A Chiappori
© 2022 Meta ULC. All rights reserved