O-018 Clinical application of targeted next generation sequencing for colorectal cancer patients: a multicentric Belgian experience

Clinical Application of Targeted Next Generation Sequencing for Colorectal Cancers

“…Regarding the NGS platform, 10 [18,20,21,22,23,24,25,26,27,28] used the Ion Torrent Personal Genome Machine (PGM) sequencer (Life Technologies), three [29,30,31] used the MiSeq sequencer (Illumina) and one [32] used the Illumina Genome Analyser IIx. …”

“…For eight out of 10 studies using the PGM sequencer, the required quantity of DNA was 10 ng [20,21,22,23,24,25,27,28]. Two studies assessed that results were obtained using only 0.1 or 0.8 ng of DNA [18,26].…”

“…It should be noted that for studies using another platform [30,31,32], the required amount of DNA was higher (up to 3 µg of DNA) than for the PGM platform (Table 1), except for the study of Froyen et al [29], in which NGS results were obtained with <50 ng of DNA using a custom panel on the Miseq sequencer. In total, 2480 specimens were analysed across the 14 studies; more than 500 of them were biopsies (this information was reported for eight studies [18,21,22,23,24,26,27,29]).…”

“…In the analysed studies, the number of analysed genes varied from five to 183. Two studies [23,25] used more than one panel. Commercially available and homemade panels were used in 11 and four studies, respectively (Table 1) (the Ion Ampliseq cancer panel V1 was used once; the Ion Ampliseq cancer panel V2 was used twice; the Ion Ampliseq Colon and Lung panel V1 was used six times; the Ion Ampliseq Colon and Lung panel V2 was used twice; and the Truseq cancer panel was used twice).…”

“…Five out of seven studies [21,23,24,27,29] clarified their definition, TAT being “the period from sample receipt to interpretation of the result” for Malapelle et al and for Jesinghaus et al (mean TAT of 13 working days and six days, respectively), or “the time between reception of the sample in the laboratory and report release” for Fontanges et al (mean TAT of eight calendar days) or “the time from DNA isolation to results” for Tops et al and Froyen et al (TAT in between 48 and 72 h). Regardless of the definition used, five of the seven studies that reported their TAT did so within the seven recommended working days [21,23,24,25,29]. Regarding Belardinilli’s study, Froyen’s study and Tops’ study, the reported TAT are, in our understanding, more an estimation of the length of the sequencing workflow (from the start of DNA extraction to the results) but does not take into account the fact that, in clinical daily practice, samples need be pooled and are thus not immediately processed.…”