Mutations by next generation sequencing in stool DNA from colorectal carcinoma patients-a literature review and our experience with this Methodology

It is well-known that colorectal carcinoma is a disease involving multistep carcinogenesis (hyperplasiaadenoma-carcinoma-metastasizing carcinoma). It is also a disease where therapeutically important driver mutations (especially in the EGFR signaling pathway) have been identified. Since genetic muta...

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Autores: Youssef, Omar, Sarhadi, Virinder K., Lehtimäki, Lauri|||0000-0003-1586-4998, Tikkanen, Milja, Kokkola, Arto, Puolakkainen, Pauli, Armengol, Gemma|||0000-0003-2345-1106, Knuutila, Sakari
Tipo de recurso: artículo
Fecha de publicación:2016
País:España
Institución:Universitat Autònoma de Barcelona
Repositorio:Dipòsit Digital de Documents de la UAB
Idioma:inglés
OAI Identifier:oai:ddd.uab.cat:320855
Acceso en línea:https://ddd.uab.cat/record/320855
https://dx.doi.org/urn:doi:10.6000/1927-7229.2016.05.01.3
Access Level:acceso abierto
Palabra clave:Colorectal carcinoma
Dna
Mutation
Next generation sequencing
Stool specimen
SDG 3 - Good Health and Well-being
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spelling Mutations by next generation sequencing in stool DNA from colorectal carcinoma patients-a literature review and our experience with this MethodologyYoussef, OmarSarhadi, Virinder K.Lehtimäki, Lauri|||0000-0003-1586-4998Tikkanen, MiljaKokkola, ArtoPuolakkainen, PauliArmengol, Gemma|||0000-0003-2345-1106Knuutila, SakariColorectal carcinomaDnaMutationNext generation sequencingStool specimenSDG 3 - Good Health and Well-beingIt is well-known that colorectal carcinoma is a disease involving multistep carcinogenesis (hyperplasiaadenoma-carcinoma-metastasizing carcinoma). It is also a disease where therapeutically important driver mutations (especially in the EGFR signaling pathway) have been identified. Since genetic mutations can serve as good diagnostic and predictive markers, their reliable detection in the early stages of the disease and also in the follow-up of treatment efficacy is crucial. There is a fundamental problem encountered with the commonly used formalin-fixed paraffinembedded (FFPE) specimens from biopsied tumor tissue i.e. it is unlikely that the material for the mutation analysis will be available in either the early stage of the disease or during the treatment period. Therefore recently attempts have been made to identify reliable markers from plasma/serum or from stool specimens. In particular, non-invasive stool specimens have been speculated to represent the situation of ongoing tumorigenesis and thus they can be used to assess treatment efficacy in the follow-up of the patient. The key aims of this paper are firstly, to review the key methodological points when studying genomic alterations in DNA extracted from cells in stool specimens, and secondly, to review results related to biomarker screening and their therapeutic importance. A further aim is to present our new findings by focusing on the issues inherent in Next Generation Sequencing of stool specimens from patients with gastrointestinal tumors. Even though the focus of our paper is human genomic alterations in stool specimens, in our "future aspects" chapter, we also deal with the bacterial spectrum and its possible interaction with the genomic mutations. 22016-01-0120162016-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/320855https://dx.doi.org/urn:doi:10.6000/1927-7229.2016.05.01.3reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengopen accesshttp://purl.org/coar/access_right/c_abf2Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original.https://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:3208552026-06-06T12:50:31Z
dc.title.none.fl_str_mv Mutations by next generation sequencing in stool DNA from colorectal carcinoma patients-a literature review and our experience with this Methodology
title Mutations by next generation sequencing in stool DNA from colorectal carcinoma patients-a literature review and our experience with this Methodology
spellingShingle Mutations by next generation sequencing in stool DNA from colorectal carcinoma patients-a literature review and our experience with this Methodology
Youssef, Omar
Colorectal carcinoma
Dna
Mutation
Next generation sequencing
Stool specimen
SDG 3 - Good Health and Well-being
title_short Mutations by next generation sequencing in stool DNA from colorectal carcinoma patients-a literature review and our experience with this Methodology
title_full Mutations by next generation sequencing in stool DNA from colorectal carcinoma patients-a literature review and our experience with this Methodology
title_fullStr Mutations by next generation sequencing in stool DNA from colorectal carcinoma patients-a literature review and our experience with this Methodology
title_full_unstemmed Mutations by next generation sequencing in stool DNA from colorectal carcinoma patients-a literature review and our experience with this Methodology
title_sort Mutations by next generation sequencing in stool DNA from colorectal carcinoma patients-a literature review and our experience with this Methodology
dc.creator.none.fl_str_mv Youssef, Omar
Sarhadi, Virinder K.
Lehtimäki, Lauri|||0000-0003-1586-4998
Tikkanen, Milja
Kokkola, Arto
Puolakkainen, Pauli
Armengol, Gemma|||0000-0003-2345-1106
Knuutila, Sakari
author Youssef, Omar
author_facet Youssef, Omar
Sarhadi, Virinder K.
Lehtimäki, Lauri|||0000-0003-1586-4998
Tikkanen, Milja
Kokkola, Arto
Puolakkainen, Pauli
Armengol, Gemma|||0000-0003-2345-1106
Knuutila, Sakari
author_role author
author2 Sarhadi, Virinder K.
Lehtimäki, Lauri|||0000-0003-1586-4998
Tikkanen, Milja
Kokkola, Arto
Puolakkainen, Pauli
Armengol, Gemma|||0000-0003-2345-1106
Knuutila, Sakari
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Colorectal carcinoma
Dna
Mutation
Next generation sequencing
Stool specimen
SDG 3 - Good Health and Well-being
topic Colorectal carcinoma
Dna
Mutation
Next generation sequencing
Stool specimen
SDG 3 - Good Health and Well-being
description It is well-known that colorectal carcinoma is a disease involving multistep carcinogenesis (hyperplasiaadenoma-carcinoma-metastasizing carcinoma). It is also a disease where therapeutically important driver mutations (especially in the EGFR signaling pathway) have been identified. Since genetic mutations can serve as good diagnostic and predictive markers, their reliable detection in the early stages of the disease and also in the follow-up of treatment efficacy is crucial. There is a fundamental problem encountered with the commonly used formalin-fixed paraffinembedded (FFPE) specimens from biopsied tumor tissue i.e. it is unlikely that the material for the mutation analysis will be available in either the early stage of the disease or during the treatment period. Therefore recently attempts have been made to identify reliable markers from plasma/serum or from stool specimens. In particular, non-invasive stool specimens have been speculated to represent the situation of ongoing tumorigenesis and thus they can be used to assess treatment efficacy in the follow-up of the patient. The key aims of this paper are firstly, to review the key methodological points when studying genomic alterations in DNA extracted from cells in stool specimens, and secondly, to review results related to biomarker screening and their therapeutic importance. A further aim is to present our new findings by focusing on the issues inherent in Next Generation Sequencing of stool specimens from patients with gastrointestinal tumors. Even though the focus of our paper is human genomic alterations in stool specimens, in our "future aspects" chapter, we also deal with the bacterial spectrum and its possible interaction with the genomic mutations.
publishDate 2016
dc.date.none.fl_str_mv 2
2016-01-01
2016
2016-01-01
dc.type.none.fl_str_mv Article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://ddd.uab.cat/record/320855
https://dx.doi.org/urn:doi:10.6000/1927-7229.2016.05.01.3
url https://ddd.uab.cat/record/320855
https://dx.doi.org/urn:doi:10.6000/1927-7229.2016.05.01.3
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by-nc/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
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https://creativecommons.org/licenses/by-nc/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Dipòsit Digital de Documents de la UAB
instname:Universitat Autònoma de Barcelona
instname_str Universitat Autònoma de Barcelona
reponame_str Dipòsit Digital de Documents de la UAB
collection Dipòsit Digital de Documents de la UAB
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