Method developments for the genetic analysis of complex traits (GOLD-UKBB research)

Since 2019, The National Institute of Health and Medical Research (Inserm) has set up a cross-cutting program on GenOmic variability in heaLth and Disease (GOLD) which brings together specialists in the analysis of genomic data with complementary expertise in genetic epidemiology, statistical genetics, bioinformatics and functional genomics.

The teams involved in the GOLD program want to meet the challenge of understanding the role played by genes in the development and progression of diseases. For that, they develop new statistical methods to model the role played by genes in complex phenotypes. To test these methods on real data, a project entitled “Method developments for the genetic analysis of complex traits” was submitted to UKBiobank and access to UKBiobank genetic and phenotypic data was obtained in January 2021 (application reference 59366)

Why the GOLD-UKBB research?

The development of high throughput sequencing technologies has opened-up new possibilities to sequence the human genome and identify all genetic variants in individual genomes. These variants are numerous, reaching a few millions when comparing two human genomes. Indeed, if there is only on average 0.1% sequence differences between the genomes of two individuals, at the scale of a 3 billion base pair genome, this represents ~3 million genetic variants. A majority of these variants are neutral with no impact on individual phenotype but some of them could impair individual health and lead to disease. Identifying these variants and the genes that carry them will help to understand why and how diseases occur and to better prevent and treat them. This is at the foundation of a new medicine, referred to as "genomic medicine" that takes into account patient genomes for a better diagnostic and treatment of diseases.To achieve this objective however, powerful and innovative methods are lacking to integrate longitudinal phenotype information into genetic analyses. The aim of this project is to develop such methods and train them on real datasets.

What will GOLD-UKBB research consist of?

We will develop innovative strategies and methods to analyse genetic data and link the variations observed in individual genomes to differences observed between individuals on different phenotypes that can either be binary phenotypes (affected / non affected by a given disease) or quantitative phenotypes (such as BMI or other measurable traits). The research is primary methodological and not focus on a particular disease or phenotype. The UKBioBank data would be used in different manners. First to generate some realistic synthetic data on which to train the methods and evaluate their statistical properties.  These synthetic data will mimic the patterns observed in the real data but some known genetic effects will be added in order to determine how the proposed methods recover these effects. Second, when the methods will be calibrated, they will be applied on the UKBioBank data to determine if some known or novel genetic effects could be detected through a data mining approach. Results will then need to be confirmed on other datasets and/or through experimental validation.

Regulatory information’s about GOLD-UKBB research

Who is the data controller?

Inserm

Legal base for processing?

The legal basis for processing is public interest mission

Data?

Data provided by UKBB (source) are analysed by Inserm (data recipient). Only declared investigators (see list below) will have access to this data.

Only genetic (genotyping, exome sequencing and some (50) whole genome sequencing data) and phenotypic data are requested (no biological samples or imaging data).

Research duration?

The GOLD-UKBB research duration is 36 months.

UKBB Data retention period by Inserm?

The UKBB data retention period by Inserm is 3 years.

Ethics?

The GOLD-UKBB research has been assessed by an independent ethics committee (IEC), Comité d’évaluation éthique de l’Inserm.

Who to contact?

For more information and to exercise lawful rights (to be informed, of access, of object, to request rectification and erasure), volunteers can contact UKBB, at any time, by the following means:

  • The UK Biobank free phone Participant Resource Centre is open on 0800 0 276 276 Monday – Friday 9am – 5pm. Calls from mobile phones or from overseas may be charge
  • By writing to UK Biobank at:

    1-2 Spectrum Way
    Adswood
    Stockport
    SK3 0SA

Volunteers can also contact the UK Biobank Data Protection Officer (DPO), at any time, by:

  •  Email to dpo@ukbiobank.ac.uk
  •  By post to :

    The Data Protection Officer
    UK Biobank Units
    1-2 Spectrum Way
    Adswood
    Stockport
    SK3 0SA

Volunteers have the right to contact, at any time, the UK data protection authority - Information Commissioner's Office ("ICO") - if they have any concerns about UK Biobank’s use of personal data and/or UK Biobank’s approach to data protection and the UK GDPR.

 

All of this information, and more, is available on the UKBB webpage

The DPOs of Inserm and UKBB will be able to exchange views throughout the duration of the research GOLD-UKBB to respond to requests from volunteers.

The GOLD-UKBB research is carried out in compliance with the General Data Protection Regulation (GDPR) and the regulations of French data protection authority (Cnil). 

 

Who is the GOLD-UKBB investigators?

The list of investigators (in alphabetical order) declared on GOLD-UKBB research

Nom

Prénom

Affiliation

Béroud

Christophe

UMR1251

Marseille

Cristofari

Gaël

UMR1081

Nice

Delahaye Duriez

Andrée

UMR1141

Paris

Derouin

Margot

UMR1141

Paris

Génin

Emmanuelle

UMR1078

Brest

Herzig

Anthony

UMR1078

Brest

Lanciano

Sophie

UMR1081

Nice

Leutenegger

Anne-Louise

UMR1141

Paris

Pratella

David

UMR1081

Nice

Ludwig

Thomas

UMR1078

Brest

Marenne

Gaëlle

UMR1078

Brest

Morange

Pierre-Emmanuel

UMR1263

Marseille

Perdry

Hervé

UMR1018

Paris

Saha

Saswati

UMR1090

Marseille

Salgado

David

UAR 3601 (UMS) – IFB

Marseille

Trégouet

David-Alexandre

UMR1219

Bordeaux

List updated on 02/22/2022

 

 

 

Formations EBAAI (Inserm, Aviesan et l’Institut français de bio-informatique) : initiation au traitement des données de génomique obtenues par séquençage à haut débit

11e école de bio-informatique du 13 au 18 novembre 2022 : Inscriptions closes.

Ateliers  bulk RNA-seq, ChIP-seq/ATAC-seq, variants DNA-seq et nouveau single-cell RNA-Seq) En savoir plus 

ÉcoleEBAII assemblage et annotation de génomes du 25 au 30 septembre : Inscriptions closes

Traitement de données NGS pour l'assemblage et l'annotation de novo de génomes En savoir plus

 

Voir aussi  :

Publications 

 

L’institut coordonne les réflexions et les recherches dans les domaines suivants :

  •  bioinformatique, création de plateformes intermédiaires aux centres nationaux existants adossées aux plateformes de séquençage massif,
  •  diversité génomique, maladies rares, génomique des populations, métagénomique, évolution,
  •  génétique moléculaire, régulation génétique : de la transcriptomique à l’épigénétique,
  •  dynamique du génome, éléments transposables, mutations,
  •  génétique quantitative, maladies multifactorielles, maladies rares, traits complexes.

 
L’institut Génétique, génomique, bioinformatique assure une transversalité interdisciplinaire avec tous les instituts thématiques multiorganismes.


 

 

Les orientations stratégiques :

 

 

 

Directeurs : Emmanuelle Genin (Inserm), Christian Muchardt (CNRS)

Directrice adjointe : Catherine Nguyen (Inserm)

Directrice adjointe en charge des maladies rares : Christel Thauvin (Univ. Bourgogne - CHU Dijon) pour le Suivi du PNMR3 et Interface PFMG-PNMR3

Chargées de mission : cartographie des maladies rares Pascale Cohen (université Lyon 1), génétique médicale Françoise Pulcini (Inserm), Estelle Mottez (Inserm)

Assistante administrative : Laetitia Gaillard (Inserm)

Adjointe à la direction déléguée à la coordination du programme EJP RD (programme européen conjoint sur les maladies rares) : Daria Julkowska (Inserm)

Chargés de projets (EJP RD)  : Juliane HalftermeyerYanis Mimouni 

Chargés de projets (IRDiRC)  :  Alexander Parry, Galliano Zanello

Responsable administratif et financier (EJP RD) : Blandine Castrillo

Assistante d’équipe : Aniket Sharma

Chargé de communication (EJP RD et IRDiRC) : Tanguy Onakoy 

Contact Aviesan ITMO GGB : iggb@aviesan.fr

Comité d'experts :  Laurent ABEL (Inserm, Paris), Serge AMSELEM (Inserm, Paris), Anaïs BAUDOT (Université Aix-Marseille), Jamel CHELLY (Université, Illkirch), Mark COCK (CNRS, Roscoff), Jean-François DELEUZE (CEA, Évry), Bernard DE MASSY (CNRS, Montpellier), Claude FEREC (Inserm, Brest), Philippe GLASER (Institut Pasteur, Paris), Marc HANAUER (Inserm, Paris), Cécile JULIER (Inserm, Paris), Stanislas LYONNET (Inserm, Paris), Claudine MÉDIGUE (CNRS, Évry), Hadi QUESNEVILLE (INRA, Versailles), Lluis QUINTANA-MURCI (Institut Pasteur, Paris), Ana RATH (Inserm, Paris), Hugues ROEST-CROLLIUS (CNRS, Paris), Élisabeth TOURNIER-LASSERVE (Inserm, Paris), Chantal VAURY (CNRS, Clermont-Ferrand), Jacques VAN HELDEN (Université Aix-Marseille), Jonathan WEITZMAN (Université  Paris-Diderot), Michel WERNER (CEA, Paris)

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