title: Targeted Exome Sequencing Outcome Variations of Colorectal Tumors within and across Two Sequencing Platforms.
abstract: OBJECTIVE
  Next generation sequencing (NGS) has quickly the tool of choice for genome and exome data generation. The multitude of sequencing platforms as well as the variabilities within each platform need to be assessed. In this paper we used two platforms (ION TORRENT AND ILLUMINA) to assess single nucleotides variants in colorectal cancer (CRC) specimens.
  
  
  METHODS
  CRC specimens (n = 13) collected from 6 CRC (cancer and matched normal) patients were used to establish the mutational profile using ION TORRENT AND ILLUMINA sequencing platforms. We analyzed a set of samples from Formalin Fixed Paraffin Embedded and FF (FF) samples on both platforms to assess the effect of sample nature (FFPE vs. FF) on sequencing outcome and to evaluate the similarity/differences of SNVs across the two platforms. In addition, duplicates of FF samples were sequenced on each platform to assess variability within platform.
  
  
  RESULTS
  The comparison of FF replicates to each other gave a concordance of 77% (± 15.3%) in Ion Torrent and 70% (± 3.7%) in Illumina. FFPE vs. FF replicates gave a concordance of 40% (± 32%) in Ion Torrent and 49% (± 19%) in Illumina. For the cross platform concordance were FFPE compared to FF (Average of 75% (± 9.8%) for FFPE samples and 67% (± 32%) for FF and 70% (± 26.8%) overall average).
  
  
  CONCLUSIONS
  Our data show a significant variability within and across platforms. Also the number of detected variants depend on the nature of the specimen; FF vs. FFPE. Validation of NGS discovered mutations is a must to rule-out false positive mutants. This validation might either be performed through a second NGS platform or through Sanger sequencing.
authors.affiliation: Department of Medicine and Cancer Center, Howard University College of Medicine, Washington DC.
authors.forename: Hassan
authors.initials: H
authors.lastname: Ashktorab
authors.affiliation: Department of Medicine and Cancer Center, Howard University College of Medicine, Washington DC.
authors.forename: Hamed
authors.initials: H
authors.lastname: Azimi
authors.affiliation: Center for Cancer Research, National Cancer Institute, Frederick, USA.
authors.forename: Michael L
authors.initials: ML
authors.lastname: Nickerson
authors.affiliation: Center for Cancer Research, National Cancer Institute, Frederick, USA.
authors.forename: Sara
authors.initials: S
authors.lastname: Bass
authors.affiliation: Hithru LLC, Silver Spring, Center for Cancer Research, National Cancer Institute, Frederick, USA.
authors.forename: Sudhir
authors.initials: S
authors.lastname: Varma
authors.affiliation: Department of Pathology, Howard University College of Medicine, Washington DC.
authors.forename: Hassan
authors.initials: H
authors.lastname: Brim
keywords: Mutations; Nucleotides; Sequencing technology; Tumors