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Emergency Management
in Predictive Molecular Pathology Laboratories

an International Experience Discover more

About

In the time of COVID‐19, predictive molecular pathology laboratories must still timely select oncological patients for targeted treatments. However, the need to respect social distancing measures may delayresults generated by laboratory‐developed tests based on sequential steps a long hands‐on time.
Laboratory workflows should now be simplified.

 

Malapelle U, et al. J Clin Pathol 2020;0:1–5. doi:10.1136/jclinpath-2020-206957

Key Messages

  • The COVID‐19 outbreak modifies laboratory organisation to limit personnel number and working hours.
  • Despite these limitations, in our laboratory, oncological patients have timely been tested for targeted treatments.
  • This public health emergency underlines even more the concept that predictive molecular pathology should be practised in advanced laboratories by highly trained staff, even if fully automated procedures are employed.

Introduction

2020

Department of Public Health, University of Naples Federico II, Naples, Italy

Sample type

Histological: 50.0%
Cytological: 40.0%
Liquid Biopsy: 10.0%

Platform adopted

NGS: 10.0%
Idylla: 90.0%

 

Abbreviation: NGS: next generation sequencing.

Mutational rate

EGFR: 15.0%
KRAS: NR
BRAF: NR
ALK: 0.0%
ROS1: 0.0%

 

Abbreviations: ALK: Anaplastic Lymphoma Kinase; BRAF: V-Raf Murine Sarcoma Viral Oncogene Homolog B; EGFR: Epidermal Growth Factor Receptor; KRAS: Kirsten Rat Sarcoma Viral Oncogene Homolog; ROS1: ROS Proto-Oncogene 1, Receptor Tyrosine Kinase.

PD-L1 testing

≥50%: 10.0%
≥1% and <50%: 15.0%
<1%: 60.0%
Inadequate: 0.0%
NR: 15.0%

 

Abbreviations: NR: not requested; PD-L1: Programmed Death-Ligand 1.

Median TAT

5.6 days

 

Abbreviation: TAT: turnaround time.

2019

Department of Public Health, University of Naples Federico II, Naples, Italy

Sample type

Histological: 32.4%
Cytological: 26.5%
Liquid Biopsy: 41.1%

Platform adopted

NGS: 91.2%
Idylla: 8.8%

 

Abbreviation: NGS: next generation sequencing.

Mutational rate

EGFR: 17.6%
KRAS: 27.6%
BRAF: 3.8%
ALK: 0.0%
ROS1: 0.0%

 

Abbreviations: ALK: Anaplastic Lymphoma Kinase; BRAF: V-Raf Murine Sarcoma Viral Oncogene Homolog B; EGFR: Epidermal Growth Factor Receptor; KRAS: Kirsten Rat Sarcoma Viral Oncogene Homolog; ROS1: ROS Proto-Oncogene 1, Receptor Tyrosine Kinase.

PD-L1 testing

≥50%: 11.8%
≥1% and <50%: 11.8%
<1%: 26.4%
Inadequate: 0.0%
NR: 50.0%

 

Abbreviations: NR: not requested; PD-L1: Programmed Death-Ligand 1.

Median TAT

5.6 days

 

Abbreviation: TAT: turnaround time.

2020

Histopathology and Molecular Diagnostics Unit. European Institute of Oncology IRCCS, Milano, Italy

Sample type (NSCLC) for NGS (863)

Histological: 589
Cytological: 274

Platform adopted

Ion Torrent S5, Illumina NextSeq500: Idylla, EasyPGX
Ion TorrentS5

Mutational rate

EGFR: 23%
KRAS: 34%
BRAF: 7% (ex15+11); 1.5% p.V600E
ALK: 5%
ROS1: 1.8%

 

Abbreviations: ALK: Anaplastic Lymphoma Kinase; BRAF: V-Raf Murine Sarcoma Viral Oncogene Homolog B; EGFR: Epidermal Growth Factor Receptor; KRAS: Kirsten Rat Sarcoma Viral Oncogene Homolog; ROS1: ROS Proto-Oncogene 1, Receptor Tyrosine Kinase.

PD-L1 testing

≥50%: 25%
≥1% and <50%: 53%
<1%: 13%
Inadequate: 9%
NR: –

 

Abbreviations: NR: not requested; PD-L1: Programmed Death-Ligand 1.

Median TAT

8 working days for NGS; 2 working days for PD-L1

 

Abbreviation: TAT: turnaround time.

2019

Histopathology and Molecular Diagnostics Unit. European Institute of Oncology IRCCS, Milano, Italy

No data available.

2020

Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden

Sample type

Histological: 66.0%
Cytological: 34.0%

Platform adopted

NGS: 96.0%
RT-PCR: 4.0%

 

Abbreviations: NGS: next generation sequencing; RT-PCR: real time polymerase chain reaction.

Mutational rate

EGFR: 14.0%
KRAS: 31.3%
BRAF: 2.1%
ALK: 2.1%
ROS1: 2.1%

 

Abbreviations: ALK: Anaplastic Lymphoma Kinase; BRAF: V-Raf Murine Sarcoma Viral Oncogene Homolog B; EGFR: Epidermal Growth Factor Receptor; KRAS: Kirsten Rat Sarcoma Viral Oncogene Homolog; ROS1: ROS Proto-Oncogene 1, Receptor Tyrosine Kinase.

PD-L1 testing

≥50%: 40.0%
≥1% and <50%: 18.0%
<1%: 26%
Inadequate: 8.0%
NR: 8.0%

 

Abbreviations: NR: not requested; PD-L1: Programmed Death-Ligand 1.

Median TAT

11.5 days

 

Abbreviation: TAT: turnaround time.

2019

Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden

Sample type

Histological: 67.3%
Cytological: 32.7%

Platform adopted

NGS: 87.8%
RT-PCR: 12.2%

 

Abbreviations: NGS: next generation sequencing; RT-PCR: real time polymerase chain reaction.

Mutational rate

EGFR: 6.1%
KRAS: 23.3%
BRAF: 2.3%
ALK: 6.8%
ROS1: 0.0%

 

Abbreviations: ALK: Anaplastic Lymphoma Kinase; BRAF: V-Raf Murine Sarcoma Viral Oncogene Homolog B; EGFR: Epidermal Growth Factor Receptor; KRAS: Kirsten Rat Sarcoma Viral Oncogene Homolog; ROS1: ROS Proto-Oncogene 1, Receptor Tyrosine Kinase.

PD-L1 testing

≥50%: 24.5%
≥1% and <50%: 28.6%
<1%: 28.6%
Inadequate: 8.1%
NR: 10.2%

 

Abbreviations: NR: not requested; PD-L1: Programmed Death-Ligand 1.

Median TAT

11.9 days

 

Abbreviation: TAT: turnaround time.

2020

Pathology, INSERM, Nice, France

Sample type

Histological: 100.0%
Cytological: 0.0%

Platform adopted

NGS: 0.0%
Idylla: 100%

 

Abbreviation: NGS: next generation sequencing.

Mutational rate

EGFR: 12.0%
KRAS: 25.5%
BRAF: 2.0%
ALK: 3.0%
ROS1: 0.5%

 

Abbreviations: ALK: Anaplastic Lymphoma Kinase; BRAF: V-Raf Murine Sarcoma Viral Oncogene Homolog B; EGFR: Epidermal Growth Factor Receptor; KRAS: Kirsten Rat Sarcoma Viral Oncogene Homolog; ROS1: ROS Proto-Oncogene 1, Receptor Tyrosine Kinase.

Median TAT

6.3 days

 

Abbreviation: TAT: turnaround time.

2019

Pathology, INSERM, Nice, France

Sample type

Histological: 73.5%
Cytological: 26.5%

Platform adopted

NGS: 24.5%
Idylla: 75.5%

Mutational rate

EGFR: 12.0%
KRAS: 25.5%
BRAF: 2.0%
ALK: 3.0%
ROS1: 0.5%

 

Abbreviations: ALK: Anaplastic Lymphoma Kinase; BRAF: V-Raf Murine Sarcoma Viral Oncogene Homolog B; EGFR: Epidermal Growth Factor Receptor; KRAS: Kirsten Rat Sarcoma Viral Oncogene Homolog; ROS1: ROS Proto-Oncogene 1, Receptor Tyrosine Kinase.

Median TAT

6.5 days

 

Abbreviation: TAT: turnaround time.

2020

Institute of Pathology, University of Cologne, Cologne, Germany

Sample type

Histological: 84.8%
Cytological: 15.2%

Platform adopted

NGS: 90.6%
Melting Point Analysis: 9.4%

 

Abbreviations: NGS: next generation sequencing; RT-PCR: real time polymerase chain reaction.

Mutational rate

EGFR: 8.2%
KRAS: 29.0%
BRAF: 3.4%
ALK: 0.6%
ROS1: 1.0%

 

Abbreviations: ALK: Anaplastic Lymphoma Kinase; BRAF: V-Raf Murine Sarcoma Viral Oncogene Homolog B; EGFR: Epidermal Growth Factor Receptor; KRAS: Kirsten Rat Sarcoma Viral Oncogene Homolog; ROS1: ROS Proto-Oncogene 1, Receptor Tyrosine Kinase.

Median TAT

6.0 days

 

Abbreviation: TAT: turnaround time.

2019

Institute of Pathology, University of Cologne, Cologne, Germany

Sample type

Histological: 87.2%
Cytological: 12.8%

Platform adopted

NGS: 93.0%
Melting Point Analysis: 7.0%

 

Abbreviations: NGS: next generation sequencing; RT-PCR: real time polymerase chain reaction.

Mutational rate

EGFR: 7.8%
KRAS: 30.1%
BRAF: 4.9%
ALK: 2.9%
ROS1: 2.9%

 

Abbreviations: ALK: Anaplastic Lymphoma Kinase; BRAF: V-Raf Murine Sarcoma Viral Oncogene Homolog B; EGFR: Epidermal Growth Factor Receptor; KRAS: Kirsten Rat Sarcoma Viral Oncogene Homolog; ROS1: ROS Proto-Oncogene 1, Receptor Tyrosine Kinase.

Median TAT

6.0 days

 

Abbreviation: TAT: turnaround time.

2020

Surgical Pathology Unit, Department of Medicine, University of Padua, Padua, Italy

Sample type

Histological: 95.5%
Cytological: 4.5%

Platform adopted

Sequenom: 4.5%
Easy PGX: 95.5%

Mutational rate

EGFR: 13.6%
KRAS: 50.0%
BRAF: 0.0%
ALK:0.0%
ROS1:0.0%

 

Abbreviations: ALK: Anaplastic Lymphoma Kinase; BRAF: V-Raf Murine Sarcoma Viral Oncogene Homolog B; EGFR: Epidermal Growth Factor Receptor; KRAS: Kirsten Rat Sarcoma Viral Oncogene Homolog; ROS1: ROS Proto-Oncogene 1, Receptor Tyrosine Kinase.

PD-L1 testing

≥50%: 14.8%
≥1% and <50%: 7.4%
<1%: 33.4%
Inadequate: 0.0%
NR: 44.4%

 

Abbreviations: NR: not requested; PD-L1: Programmed Death-Ligand 1.

Median TAT

3.8 days

 

Abbreviation: TAT: turnaround time.

2019

Surgical Pathology Unit, Department of Medicine, University of Padua, Padua, Italy

Sample type

Histological: 96.3%
Cytological: 3.7%

Platform adopted

Sequenom: 63.0%
Easy PGX: 37.0%

Mutational rate

EGFR: 14.8%
KRAS: 50.0%
BRAF: 0.0%
ALK:0.0%
ROS1:0.0%

 

Abbreviations: ALK: Anaplastic Lymphoma Kinase; BRAF: V-Raf Murine Sarcoma Viral Oncogene Homolog B; EGFR: Epidermal Growth Factor Receptor; KRAS: Kirsten Rat Sarcoma Viral Oncogene Homolog; ROS1: ROS Proto-Oncogene 1, Receptor Tyrosine Kinase.

PD-L1 testing

≥50%: 4.5%
≥1% and <50%: 36.4%
<1%: 18.2%
Inadequate: 0.0%
NR: 40.9%

 

Abbreviations: NR: not requested; PD-L1: Programmed Death-Ligand 1.

Median TAT

3.8 days

 

Abbreviation: TAT: turnaround time.

2020

Molecular Pathology Unit, IPATIMUP, University of Porto, Porto, Portugal

Sample type

Histological: 210
Cytological: 72
Liquid Biopsy: 2

Platform adopted

NGS (Thermo-Fisher): 147 (51.7%)
Sanger sequencing: 38 (13.38%)
Idylla: 80 (28.17%)
Digital PCR: 19 (6%)

Mutational rate

EGFR: 20%
KRAS: 40%
BRAF: 3%
ALK: 5%
ROS1: 1%

 

Abbreviations: ALK: Anaplastic Lymphoma Kinase; BRAF: V-Raf Murine Sarcoma Viral Oncogene Homolog B; EGFR: Epidermal Growth Factor Receptor; KRAS: Kirsten Rat Sarcoma Viral Oncogene Homolog; ROS1: ROS Proto-Oncogene 1, Receptor Tyrosine Kinase.

PD-L1 testing

Not tested in our lab.

Median TAT

12 days

 

Abbreviation: TAT: turnaround time.

2019

Molecular Pathology Unit, IPATIMUP, University of Porto, Porto, Portugal

Sample type

Histological: 215
Cytological: 90
Liquid Biopsy: 36

Platform adopted

NGS (Thermo-Fisher):164 (48.09%)
Sanger sequencing: 29 (8.50%)
Idylla: 145 (42.52%)
Digital PCR: 3 (1%)

Mutational rate

EGFR: 20%
KRAS: 40%
BRAF: 3%
ALK: 5%
ROS1: 1%

 

Abbreviations: ALK: Anaplastic Lymphoma Kinase; BRAF: V-Raf Murine Sarcoma Viral Oncogene Homolog B; EGFR: Epidermal Growth Factor Receptor; KRAS: Kirsten Rat Sarcoma Viral Oncogene Homolog; ROS1: ROS Proto-Oncogene 1, Receptor Tyrosine Kinase.

Median TAT

12 days

 

Abbreviation: TAT: turnaround time.

Scientific Advisors

Professor Giancarlo Troncone

Department of Public Health, University of Naples Federico II, Naples, Italy

Professor Umberto Malapelle

Department of Public Health, University of Naples Federico II, Naples, Italy

Faculty

Professor Massimo Barberis

Histopathology and Molecular Diagnostics Unit. European Institute of Oncology IRCCS, Milan, Italy

Professor Matteo Fassan

Surgical Pathology Unit, Department of Medicine, University of Padua, Padua, Italy

Professor Fernando Schmitt

Molecular Pathology Unit, IPATIMUP, University of Porto, Porto, Portugal

Professor Sabine Merkelbach‐Bruse

Institute of Pathology, University of Cologne, Cologne, Germany

Professor Hans Brunnström

Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden.

Professor Paul Hofman

Department of Pathology
Nice Pasteur Hospital
University Côte d’Azur, Nice, France

Project realized with the non-conditioning contribution of

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