Cancer biology and genetics laboratory

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Dr Dominique VAUR
Chef de service du Laboratoire de Biologie et de Génétique du Cancer
Dr Dominique VAUR
02 31 45 50 64
Fabrice GUICHARD
Cadre du Laboratoire de Biologie et de Génétique du Cancer
Fabrice GUICHARD
02 31 45 50 64

Secretaries

  • Opening hours: from 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, within the context of patients with hereditary predispositions to cancer, in particular breast and ovarian cancers, by testing for specific predisposing genes for breast and/or ovarian cancer. 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 cancer 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 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 (oncogenetics). 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)

Teaching mission

  • Lectures at the university department of pharmaceutical science 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

The team

  • Head of department: Dr Dominique Vaur
  • Laboratory executive: 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: Hafsa Chevaucher

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. Modalities for conducting samples are described in the following document:

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 benefit from a prior oncogenetic consultation. The average time required to obtain results of such analysis is less than one month. The prescription form, together with modalities for conducting samples can be consulted here:

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. The prescription form for somatic genetic analyses can be consulted here:

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 list of available analyses can be consulted in the Biology and cancer genetics laboratory analysis catalogue (EN-0452.24/ May 2021).

The department’s equipment and facilities

Genetics

  • Nucleic acid extraction robot: QIAsymphony (QIAGEN)
  • Thermocyclers
  • ABI3500 capillary sequencer
  • 2 Illumina high-throughput sequencers
  • 2 distribution robots
  • Render farm and storage servers

General biology

  • Haematology: XN-1000 (Sysmex)
  • Haemostasis: STA Compact Max 3 (Stago)
  • Biochemistry: Cobas 6000 (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. In March 2018, an accreditation renewal audit was conducted in the Biopathology department as per the NF EN ISO 15189 standard. Accreditation was then renewed for a 5-year period. The audit criteria can be consulted on the Cofrac website: https://www.cofrac.fr/

2019 activity data

In 2019, for hereditary predispositions to breast and ovarian cancer, the laboratory sequenced 3,345 index cases over a panel of 34 genes using high-throughput sequencing (HTS), in an average timescale of 24 days, and conducted 1,183 presymptomatic tests in family members. This activity has earned the laboratory a position as France’s leading oncogenetics laboratory, offering the shortest test result timescales. The laboratory also conducted 1,330 somatic genetic analyses on tumours.

Research themes / Projects

  • COVAR: biomedical study on family segregation of genetic variants of disease (UNICANCER Genetics and Cancer group)
  • Genetic determinism of early phenotype cancers (INSERM U1245)
  • 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).
  • Identification and implication of major gene regulatory sequences in predisposition to breast and ovarian cancer (AAP emerging projects CNO 2016)
  • Detection of somatic CNVs
  • Study of bioinformatic tools for the detection of CNVs via HTS (Cancéropôle Nord-Ouest project)
  • Detection of microsatellite instabilities in tumours via HTS
  • Development of a local database system aimed at exploiting and validating genetic tumour data
  • UTOLA: Phase II study evaluating Olaparib as maintenance treatment in endometrial cancer
  • PROCARBO project: Research in variants leading to sensitivity to PARP inhibitors on circulating tumour DNA, in metastatic prostate cancer
  • 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)

Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. Davy, G ; Rousselin, A ; Goardon, N ; Castéra, L ; Harter, V ; Legros, A & al , Detecting splicing patterns in genes involved in hereditary breast and ovarian cancer., Eur J Hum Genet, 2017, 25, 1147-1154
  7. Muller, E ; Goardon, N ; Brault, B ; Rousselin, A ; Paimparay, G ; Legros, A & al , OutLyzer: software for extracting low-allele-frequency tumor mutations from sequencing background noise in clinical practice., Oncotarget, 2016, 7, 79485-79493
  8. Castéra, L ; Krieger, S ; Rousselin, A ; Legros, A ; Baumann, JJ ; Bruet, O & al , Next-generation sequencing for the diagnosis of hereditary breast and ovarian cancer using genomic capture targeting multiple candidate genes., Eur J Hum Genet, 2014, 22, 1305-13
  9. Houdayer, C ; Caux-Moncoutier, V ; Krieger, S ; Barrois, M ; Bonnet, F ; Bourdon, V & al , Guidelines for splicing analysis in molecular diagnosis derived from a set of 327 combined in silico/in vitro studies on BRCA1 and BRCA2 variants., Hum Mutat, 2012, 33, 1228-38
  10. Théry, JC ; Krieger, S ; Gaildrat, P ; Révillion, F ; Buisine, MP ; Killian, A & al , Contribution of bioinformatics predictions and functional splicing assays to the interpretation of unclassified variants of the BRCA genes., Eur J Hum Genet, 2011, 19, 1052-8

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

Useful documents for healthcare professionals

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