Cancer biology and genetics laboratory

Equipe du Laboratoire de Biologie et de Génétique du Cancer
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Contact

Dr Dominique VAUR
Chef de service du Laboratoire de Biologie et de Génétique du Cancer
Dr Dominique VAUR
02 31 45 50 54
Fabrice GUICHARD
Cadre du Laboratoire de Biologie et de Génétique du Cancer
Fabrice GUICHARD
02 31 45 50 54

Secretaries

  • Opening hours: Monday to Friday, 8am to 5pm
  • Telephone: +33(0)2 31 45 50 54
  • Location: 3rd floor

Department missions

Healthcare mission

The laboratory’s activities cover the field of clinical biology, the genetics of hereditary cancers and tumour genetics.

The laboratory team realises all the main biochemical and haematological analyses that are necessary for caring for cancer patients. It provides prescribing physicians with all the necessary resources to satisfy their needs.

The department’s activity also includes constitutional genetics, for patients with hereditary predispositions to cancer, in particular breast, ovarian and digestive cancers, by testing for specific mutations in the genes involved in theses diseases. It analyses index cases via high-throughput sequencing and proposes predictive molecular diagnosis of a known mutation for family members. The department conducts complementary tests, aimed either at demonstrating the involvement of a mutation in cancers predisposition contexts (e.g. RNA study) or at conducting more in-depth molecular analysis in the absence of an identified mutation (e.g. extended genotype).

Finally, its activity in tumour genetics (tumour genotyping and cell-free circulating tumour DNA) applied essentially to colon cancer, ovarian cancer, breast cancer and prostate cancer, is essentially aimed at adapting therapeutic care for cancer patients (targeted therapies) via ‘molecular’ MDT meetings.

Research mission

The laboratory team conducts research projects in the field of cancer genetics within the INSERM U1245 unit (hereditary predisposition to cancers). Within its premises, it houses a SéSAME high-throughput sequencing platform and relies on a team of bioinformatics specialists, enabling developments specific to this field of research.

Developed projects focus essentially on research on ‘missing heritability’ within the context of cancer predisposition syndrome in breast and ovarian cancer:

  • The study of genetic heterogeneity
  • The study of the contribution of mutations that alter splicing in genes implicated in such predisposition via a high-throughput approach (RNASeq Long-Read, Midi-genes) and search for structural variants (DNASeq Long-Read).

Teaching mission

  • Lectures at the university department of Health and within the context of the Master’s Degree 2nd year ‘Omics approaches’ module
  • Hosting and supervision of Master’s Degree students (1st and 2nd year), BTS and DUT technical diploma students, medical externs and interns, and supervision of PhD scientific theses
  • FST Bioinformatics
  • FST Innovation and Research

The team

  • Head of department: Dr Dominique Vaur
  • Laboratory supervisor: Fabrice Guichard
  • Executive expert in genetics: Dr Nicolas Goardon
  • Biologists: Dr Flavie Boulouard, Dr Laurent Castera, Dr Sophie Krieger, Dr Raphaël Leman, Dr Agathe Ricou
  • Biopathology department quality manager: Florian Domin

Healthcare offer and expertise

Medical biology

In an aim to satisfy the needs of the centre’s different departments, the laboratory conducts general biology analyses for hospitalised patients and outpatient consultations (essentially blood counts, coagulation screens, ionogrammes and tumour marker tests). The department also ensures analysis of bone marrow cell counts and liquids (pleural, peritoneal, etc.). It can also be asked to receive samples from external departments for certain specific dosing techniques such as tumour markers.

Genetics

Within the framework of hereditary cancer predisposition for breast and ovarian cancer, the laboratory conducts analysis on 13 diagnostic genes (BRCA1, BRCA2, PALB2, RAD51C, RAD51D, TP53, CDH1, PTEN, MLH1, MSH2, MSH6, PMS2, EPCAM) as recommended by the Genetics and Cancer group (from a panel of 61 genes) via high-throughput sequencing (HTS) in patients (index cases) who have benefited from a prior oncogenetic consultation. The average time required to obtain results of such analysis is less than one month.

Furthermore, in an aim to adapt care for cancer patients and to allow them to benefit from certain targeted therapies, the laboratory has developed sequencing for a panel of genes of therapeutic relevance, on paraffin-embedded tumours via high-throughput sequencing (HTS), in timescales compatible with therapeutic care modalities (on average less than 3 weeks). The laboratory also conducts tests on microsatellite instabilities in tumours.

Within the context of the molecular MDT, analysis specific to patients facing therapeutic stalemate is based on the sequencing of a large panel of around 500 genes associated with fusion transcripts of around a hundred genes via simultaneous sequencing of DNA and RNA extracted from tumours.

The department’s equipment and facilities

Genetics

  • Nucleic acid extraction robot: QIAsymphony (QIAGEN)
  • Thermocyclers
  • ABI3500 capillary sequencer
  • 3 Illumina high-throughput sequencers
  • Long-read Nanopore sequencer
  • 2 distribution robots
  • Covaris E220 sonicator
  • Render farm and storage servers

General biology

  • Haematology: XN-1000 (Sysmex)
  • Haemostasis: STA Compact Max 3 (Stago)
  • Biochemistry: Cobas Pure (Roche)
  • Blood gas analyser: ABL90 Flex PLUS (Radiometer)

Results

Accreditation

The Cancer Biology and Genetics laboratory is accredited since 1 July 2014. Deployment of a quality-based approach within the anatomocytopathology laboratory led to accrediation of the Biopathology department under the reference No. 8-3264. Accreditation was then renewed for a 5-year period. The audit criteria can be consulted on the Cofrac website: https://www.cofrac.fr/

Research themes / Projects

  • COVAR: biomedical study on family segregation of genetic variants of disease (UNICANCER Genetics and Cancer group)
  • Study of splicing alterations via RNASeq (INSERM U1245)
  • Biostatistics applied to the study of rare variants (AAP emerging project CNO 2015)
  • Definition of new algorithms for splice site prediction (colloborative project LBGC-U1245 with the GGC Epissage & ENIGMA).
  • Detection of somatic CNVs
  • Constitutional mosaic, circulating tumour DNA or clonal haematopoiesis: traps and stakes involved in low allele fraction variants detected by HTS in constitutional genetics
  • Development of a national database in constitutional genetics (Genetics and Cancer group; UNICANCER consortium)
  • Exploration of the non-coding genome
  • DOMENICA study on endometrial cancer
  • HERO: HRD test evaluation in ovarian cancer

Publications

  1. Leman, R ; Muller, E ; Legros, A ; Goardon, N ; Chentli, I ; Atkinson, A & al, Validation of the Clinical Use of GIScar, an Academic-developed Genomic Instability Score Predicting Sensitivity to Maintenance Olaparib for Ovarian Cancer., Clin Cancer Res, 2023, 29, 4419-4429
  2. Leman, R ; Parfait, B ; Vidaud, D ; Girodon, E ; Pacot, L ; Le Gac, G & al, SPiP: Splicing Prediction Pipeline, a machine learning tool for massive detection of exonic and intronic variant effects on mRNA splicing., Hum Mutat, 2022, 43, 2308-2323
  3. Neviere, Z ; Coquan, E ; Brachet, PE ; Meriaux, E ; Bonnet, I ; Krieger, S & al, Outcomes of Patients with Metastatic Castration-Resistant Prostate Cancer According to Somatic Damage DNA Repair Gene Alterations., Curr Oncol, 2022, 29, 2776-2791
  4. Caputo, SM ; Golmard, L ; Léone, M ; Damiola, F ; Guillaud-Bataille, M ; Revillion, F & al, Classification of 101 BRCA1 and BRCA2 variants of uncertain significance by cosegregation study: A powerful approach., Am J Hum Genet, 2022, 108, 1907-1923
  5. Morice, PM ; Coquan, E ; Weiswald, LB ; Lambert, B ; Vaur, D ; Poulain, L, Identifying patients eligible for PARP inhibitor treatment: from NGS-based tests to 3D functional assays., Br J Cancer, 2021, 125, 7-14
  6. Boulouard, F ; Kasper, E ; Buisine, MP ; Lienard, G ; Vasseur, S ; Manase, S & al, Further delineation of the NTHL1 associated syndrome: A report from the French Oncogenetic Consortium., Clin Genet, 2021, 99, 662-672
  7. Callens, C ; Vaur, D ; Soubeyran, I ; Rouleau, E ; Just, PA ; Guillerm, E & al, Concordance Between Tumor and Germline BRCA Status in High-Grade Ovarian Carcinoma Patients in the Phase III PAOLA-1/ENGOT-ov25 Trial., J Natl Cancer Inst, 2021, 113, 917-923
  8. Bardet, S ; Goardon, N ; Lequesne, J ; Vaur, D ; Ciappuccini, R ; Leconte, A & al, Diagnostic and prognostic value of a 7-panel mutation testing in thyroid nodules with indeterminate cytology: the SWEETMAC study., Endocrine, 2021, 71, 407-417
  9. Beddok, A ; Krieger, S ; Castera, L ; Stoppa-Lyonnet, D ; Thariat, J, Management of Fanconi Anemia patients with head and neck carcinoma: Diagnosis and treatment adaptation., Oral Oncol, 108
  10. Leman, R ; Tubeuf, H ; Raad, S ; Tournier, I ; Derambure, C ; Lanos, R & al, Assessment of branch point prediction tools to predict physiological branch points and their alteration by variants., BMC Genomics, 2020, 21, 86
  11. Leman, R ; Harter, V ; Atkinson, A ; Davy, G ; Rousselin, A ; Muller, E & al , SpliceLauncher: a tool for detection, annotation and relative quantification of alternative junctions from RNAseq data., Bioinformatics, 2020, 36, 1634-1636
  12. Lopez-Perolio, I ; Leman, R ; Behar, R ; Lattimore, V ; Pearson, JF ; Castéra, L & al , Alternative splicing and ACMG-AMP-2015-based classification of PALB2 genetic variants: an ENIGMA report., J Med Genet, 2019, 56, 453-460
  13. Castéra, L ; Harter, V ; Muller, E ; Krieger, S ; Goardon, N ; Ricou, A & al , Landscape of pathogenic variations in a panel of 34 genes and cancer risk estimation from 5131 HBOC families., Genet Med, 2018, 20, 1677-1686
  14. Leman, R ; Gaildrat, P ; Le Gac, G ; Ka, C ; Fichou, Y ; Audrezet, MP & al , Novel diagnostic tool for prediction of variant spliceogenicity derived from a set of 395 combined in silico/in vitro studies: an international collaborative effort., Nucleic Acids Res, 2018, 46, 7913-7923
  15. Caputo, SM ; Léone, M ; Damiola, F ; Ehlen, A ; Carreira, A ; Gaidrat, P & al , Full in-frame exon 3 skipping of BRCA2 confers high risk of breast and/or ovarian cancer., Oncotarget, 2018, 9, 17334-17348

Partnerships

At regional level

At national level

  • INCa
    • ‘French bioinformatics networks for HTS diagnosis in oncology’
    • Participation in the project to create a national database in somatic genetics
    • Oncogenetics and PARP inhibitors
    • ITMO Cancer expert committee for precision medicine in oncology
    • Method validation in somatic genetics (HTS)
  • ANPGM
    • HTS method validation
    • HTS quality group
    • HTS report group
    • Second sample work group
    • Bioinformatics work group
  • Genetics and Cancer Group
    • Member of the Genetics and Cancer Group board
    • Practitioners group
    • Breast/ovary laboratories group
    • RNA group
    • COVAR group
    • CANSOP group
    • Tumospec project
    • French Oncogenetics Database: Project for a database of cancer predisposition genes
  • UNICANCER
    • BioPathology work group
  • Participation in the COFRAC work group – Human Health Section – HTS and Accreditation; Genetics: adaptation of accreditation to bioinformatics platforms
  • Creation, in 2018, of the BIOINFODIAG association (French network of bioinformatics for diagnosis).

At international level

  • ENIGMA: Evidence-based Network for the Interpretation of Germline Mutant Alleles
    • RNAseq method validation project
    • Tissue splicing profile project
  • GA4GH: BRCA challenge
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