Articles

The Belgian next generation sequencing guidelines for haematological and solid tumours

BJMO - volume 11, issue 2, march 2017

Ir A. Hébrant PhD, G. Froyen PhD, B. Maes MD, PhD, R. Salgado MD, PhD, M. Le Mercier PhD, N. D’Haene MD, PhD, S. De Keersmaecker PhD, K. Claes PhD, J. Van der Meulen MD, P. Aftimos MD, J. Van Houdt PhD, K. Cuppens MD, K. Vanneste PhD, E. Dequeker PhD, S. Van Dooren PhD, J. Van Huysse MD, F. Nollet PhD, S. Van Laere PhD, B. Denys MD, V. Ghislain , C. Van Campenhout PhD, M. Van den Bulcke PhD

SUMMARY

Targeted next generation sequencing is a complex procedure including the ‘wet bench’ and ‘dry bench’ parts. Both parts are composed of many steps for which optimal assay conditions and settings must be determined.

The aim of these guidelines is to provide generic, platform independent, recommendations for targeted next generation sequencing tests to detect acquired somatic mutations in DNA, in (haemato)-oncology that are complementary to the ISO 15189 norm (medical laboratories) in order to:

  1. facilitate the implementation of the required quality metrics for the detection of somatic variants by next generation sequencing in oncology and haemato-oncology in the Belgian laboratories,
  2. harmonise test validation and verification,
  3. harmonise clinical interpretation and reporting of variants and,
  4. assure and maintain optimal test performance by establishing procedures and modalities for internal quality control and external quality assessments.

(BELG J MED ONCOL 2017;11(2):56–67)

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Clinical application of targeted next generation sequencing for lung cancer patients

BJMO - volume 9, issue 7, december 2015

M. Le Mercier PhD, N. De Nève MSc, O. Blanchard MSc, M. Remmelink MD, PhD, B. Weynand MD, PhD, I. Salmon MD, PhD, N. D’Haene MD, PhD

Summary

The successes of targeted agents in patients with molecularly defined tumours and improvements in genomic technology have generated enthusiasm for incorporating genomic profiling into clinical cancer practice and molecular testing has now become a standard of care for lung cancer. International guidelines recommend testing for EGFR mutations and ALK gene rearrangement to guide patient selection for therapy. However, different potentially targetable oncogenes, such as KRAS, PIK3CA, BRAF, ERBB2 or MET, for which agents are being evaluated, have been proposed as valuable for managing patients with lung cancer. Recently, the development of next generation sequencing has enabled simultaneous detection of many clinically relevant mutations in different genes in a single test. In this study, we have evaluated the clinical utility of targeted next generation sequencing, using a 22 genes panel, for patients with lung cancer on 234 samples, including cytology, biopsies and surgical resections, from two different institutions tested in routine daily practice since validation and accreditation of the method (BELAC ISO15189). On the 234 samples tested, only one case could not be sequenced due to an insufficient quantity of available tissue. Among the 233 cases tested, 223 (95.7%) samples were sequenced successfully. The median turnaround time between reception of the sample in the laboratory and report release was one week. The most frequent mutations were found in TP53 (42.1%) and KRAS (35.9%). Of successfully sequenced cases, 137 potentially actionable mutations were identified in 130 patients (58.3%), including 80 KRAS mutations, 26 EGFR mutations, fourteen BRAF mutations, eight PIK3CA mutations, three PTEN mutations, two ERBB2 insertions, two NRAS mutations and two MAP2K1 mutations. Overall, next generation sequencing can be applied in daily practice even for small samples, such as lung biopsies or cell blocks. Moreover, it provides clinically relevant information for lung cancer patients.

(BELG J MED ONCOL 2015;9(7):272–78)

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