Mutations by Next Generation Sequencing in Stool DNA from Colorectal Carcinoma Patients – A Literature Review and our Experience with this Methodology
Pages 24-32
Omar Youssef, Virinder Kaur Sarhadi, Lauri Lehtimäki, Milja Tikkanen, Arto Kokkola, Pauli Puolakkainen, Gemma Armengol and Sakari Knuutila
DOI: http://dx.doi.org/10.6000/1927-7229.2016.05.01.3
Published: 05 April 2016

Abstract: It is well-known that colorectal carcinoma is a disease involving multistep carcinogenesis (hyperplasia-adenoma-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 paraffin-embedded (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-upof 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.