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NGS gene panels in onco-haematology

Pictogramme horloge Benoit QUILICHINI Pictogramme horloge April 2019

Technological progress is the main driver behind medical advances. Recent years have seen the growth of molecular techniques, in particular the advent of NGS high-throughput sequencing (next generation sequencing). From now on, this new technology allows the analysis of gene panels, which have key applications in onco-haematology.

The diagnosis, determination of prognosis and monitoring of malign haemopathies is based on comparing cellular haematology, histological, cytogenetic and molecular biology data. Eurofins Biomnis has a global platform, on which anatomopathologists and medical biologists work closely together. The list of molecular biomarkers increases every year and is expected to continue to grow as a result of the many studies carried out in the field of targeted therapies and the ongoing identification of new markers for diagnostic and prognostic purposes.

The increasing complexity of the molecular tests to be performed for each patient naturally leads to the adoption of gene analysis using panels, which can now be performed by NGS. These combined analyses reduce the time needed in the diagnostic process and patient care pathway.

The concept of personalised medicine:
The right diagnosis and treatment for the right patient, at the right time and the right price

The management of myeloproliferative neoplasms (MPN), as defined by the WHO 2017 classification, requires molecular analyses to confirm the diagnosis. This molecular approach also allows a prognosis to be established and in certain cases, can help shape the treatment regimen for patients.

It is with this in mind that our laboratory offers a new range of molecular tests and gene panels that use NGS, in addition to conventional (hematological karyotype) and molecular (FISH) cytology and cytogenetics.

For a suspected case of myeloproliferative neoplasms (outside of CMML the search for the JAK2 V617F mutation by PCR is proposed as a first line of action. If this test is negative, combined testing for the JAK2 (all exons), CALR, MPL mutations (‘MPN-Diagnosis 1’ panel) or JAK2 (all exons), CALR, MPL, CSF3R, SETBP1 and SRSF2 mutations (‘MPN-Diagnosis 2’ panel) is indicated according to the clinical context. In addition, for establishing a prognosis and to assist in therapeutic decision-making, the ‘MPN-Prognosis’ panel may be considered.

For the same purpose,, NGS panels are available for chronic myelomonocytic leukaemia (CMML), myelodysplastic syndromes (MDS) and acute myeloid leukaemia (AML). The purpose of these panels is diagnosis (CMML and AML), prognosis (CMML, MDS and AML) or providing guidance for deciding on treatment (CMML, MDS and AML) In addition, we also offer analyses of individual genes: TP53 for chronic lymphocytic leukaemia and MDS (5q- syndrome), BRAF for hairy cell leukaemia and cKIT for mastocytosis.

All of our new panels and tests are listed in the table below.

New NGS panels and individual gene analyses for specific pathologies

Indication(s)Genes listRead on
NGS Panel
“NMP-Diagnostic 1”
Polycythemia Vera (PV)
Primary Myelofibrosis (PMF)
Essential Thrombocythemia (ET)
JAK2 / CALR / MPLPanel sheet
NGS Panel
“NMP-Diagnostic 2”
Polycythemia Vera (PV)
Primary Myelofibrosis (PMF)
Essential Thrombocythemia (ET)
Chronic Neutrophilia Leukemia (CNL)
Atypical CML – BCR-ABL negative
JAK2/CALR/MPL/
CSF3R/SETBP1/SRSF2
Panel sheet
NGS Panel
“NMP-Pronostic”
Myeloproliferative neoplasmsASXL1/CALR/CBL/CSF3R/
DNMT3A/EZH2/FLT3/IDH1/
IDH2/JAK2/KIT/KRAS/MPL/
NPM1/NRAS/RUNX1/SETBP1/
SF3B1/SRSF2/TET2/TP53/
U2AF1/ZRSR2
Panel sheet
NGS Panel “CMML”Chronic Myelomonocytic LeukemiaASXL1/CBL/DNMT3A/
EZH2/FLT3/IDH1/IDH2/
JAK2/KRAS/NPM1/NRAS/
RUNX1/SETBP1/SF3B1/
SRSF2/TET2/TP53/
U2AF1/ZRSR2
Panel sheet
NGS Panel “MDS “Myelodysplastic syndromesASXL1/BRAF/CALR/CBL/
CEBPA/CSF3R/DNMT3A/
ETV6/EZH2/FLT3/HRAS/
IDH1/IDH2/JAK2/KIT/
KRAS/MPL/NPM1/NRAS/
PTPN11/RUNX1/SETBP1/
SF3B1/SRSF2/TET2/
TP53/U2AF1/WT1/ZRSR2
Panel sheet
NGS Panel “AML”Acute myeloid leukaemiaASXL1/BRAF/CALR/CBL/
CEBPA/CSF3R/DNMT3A/
ETV6/EZH2/FLT3/HRAS/
IDH1/IDH2/JAK2/KIT/
KRAS/MPL/NPM1/NRAS/
PTPN11/RUNX1/SETBP1/
SF3B1/SRSF2/TET2/
TP53/U2AF1/WT1/ZRSR2
Panel sheet
TP53
Isolated test
Chronic lymphocytic leukemia – MDSTP53
BRAF
Isolated test
Hairy cell leukemiaBRAF
CKIT
Isolated test
MastocytosiscKIT

For more information

 

References

  1. Swerdlow SH, Campo E, Harris NL., Jaffe ES, Pileri SA, Stein H, Thiele J (Eds): WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues (Revised 4th edition). lARC: Lyon 2017.
  • Itzykson R, Fenaux P, Bowen D, et al. Diagnosis and Treatment of Chronic Myelomonocytic Leukemias in Adults, Recommendations From the European Hematology Association and the European LeukemiaNet, Hemasphere 2018;2 (6):pe150.
  • Döhner H, Este E, Grimwade D, et al. Diagnosis and management of AML in adults: 2017 ELN recommendations from an international expert panel. Blood. 2017;129(4):424-47.

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