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International Biobank and Cohort Studies: Developing a Harmonious Approach February 7-8, 2005, Atlanta; GA PowerPoint Presentation
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International Biobank and Cohort Studies: Developing a Harmonious Approach February 7-8, 2005, Atlanta; GA. Jan-Eric Litton Karolinska Institutet, Stockholm Sweden. Karolinska Institutet GenomEUtwin Karolinska Institutet Biobank LifeGene. Karolinska Institutet Stockholm, Sweden.

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slide1
International Biobank and Cohort Studies: Developing a Harmonious ApproachFebruary 7-8, 2005, Atlanta; GA

Jan-Eric Litton

Karolinska Institutet, Stockholm

Sweden

  • Karolinska Institutet
  • GenomEUtwin
  • Karolinska Institutet Biobank
  • LifeGene
slide2

Karolinska Institutet

Stockholm, Sweden

slide3

Stockholm

… an archipelago with 30.000 ilands

slide4

War and cholera

led to the royal decree ...

A letter from

King Karl XIII to

the Collegium Medicum in 1810 authorized the

immediate establishment of a ”college for the corps

of field surgeons”.

slide5

From a school for army surgeons to a

medical university

1810 The Royal Carolinska Medico-Surgical

Institute was founded ”forthe creation of

skilled Army Surgeons”.

1811 Jöns Jacob Berzelius became one of KI’s

first professors and laid the foundation

for the Institute’s natural-scientific orientation.

1895 Alfred Nobel appointed Karolinska Institutet

to decide who should be awarded the

Nobel Prize in Physiology or Medicine.

1993 A comprehensive reorganization of

KI began: 150 departments became 27.

slide6

GenomEUtwin

  • The European Consortium of Twin Registries for Analyses of Complex Traits; www.genomeutwin.org
  • Aims to capitalize special advantages of Europe in population genetics
  • The goal is to identify critical genetic and life-style risk factors for common diseases using European strengths in genetics, epidemiology and biocomputing
slide7

GenomEUtwin

  • Funded by EU as one of three Centers of Excellence in Genomics in 2002, PI: Leena Peltonen
  • Twin cohort from Denmark, Finland, Italy Netherlands, Norway and Sweden (England and Australia) over 600 000 twin pairs total, 65% dizygotic
  • MORGAM cohort from 9 European countries, total of > 144 000 participants
slide8

GenomEUtwin

  • Twin Cohorts have been used for decades to estimate to role of genetics in the background of common diseases
  • Gathering phenotype info for decades
  • In Sweden
    • Civic # 1947
    • Swedish Cancer Registry 1958
    • The Cause of Dead Registry, started 1756, modern classification 1961
slide9

TwinNET

  • Ten first months
  • a database structure established
  • Database completion
    • A common, secure database established in Europe for all relevant scientific information in GenomEUtwin
slide10

TwinNET

  • EUid number (EUIDNUM) 752000021210
    • The EUidnumber consists of four parts:
      •  Country code 3 digits – ISO 3166
      •  Randomized number 7 digits
      •  Identification number 1 digit

Check sum 1 digit

slide14

ODBC – JDBC and more

Federated data approch

  • Data stay untouched
    • Integrates
    • heterogeneous local or
    • remote data sources
    • through wrappers
  • Just need to know what
  • data should be available
  • to whom and how to access them
  • It makes all data look
  • like it is one virtual database
  • hiding the data layer complexity
slide15

TwinNET

  • Relational wrappers list
    • DB2 family
    • Informix (Informix Client SDK)
    • Oracle (SQLNet or Net8 client)
    • MSQL Server (ODBC driver version 3.0 or later)
    • Sybase (Sybase open client)
    • Teradata (Teradata CLI)
    • ODBC (ODBC driver version 3.x)
  • Non-relational wrappers list
    • Lotus Extended search
    • Excel
    • Flatfile (CSV format)
    • XML (1.0 specifications)
    • OLE DB
    • BLAST
    • Documentum (Documentum client API)
    • Entrez (version 1.0)
slide16

FinnishTwin Registry

Genotypes

SwedishTwin Registry

TwinNET

GenomEUtwin centres databases

GenomEUtwin user

Federated database HUB

FinnishTwin Registry

Genotypes

SwedishTwin Registry

slide17

TwinNET December 2004

SQL

SMdb

Genotype

submission database

Helsinki

IBM xSeries 325

2xOpteron, 4GB, SAN

WEB

Database federation – Information Integrator

Genotypes

Phenotypes

SSH

Excel sheet

SSH

SSH

Stockholm

GT

GT

GT

DK

FGCHelsinki

Mol Med Rudbeck lab

Uppsala

NO

FI

SE

slide18

Karolinska Institutet Biobank

  • Karolinska Institute Biobank constitutes a national, non-commercial resource for collection, handling and storage of human biological material aiming at promoting scientific excellence within molecular and
  • genetic research.
  • Biobank Informatic is a central part of the Karolinska Institutets Biobank
slide19

Biobank Information

Management System - vision

A system that will enable a researcher to search and navigate the enormous amounts of information available for samples and their donors in various data sources.

slide20

Biobank Information

Management System

slide21

Biobank Information

Management System

slide22

Biobank Information

Management System

  • DDQB- Absract Data Model

Data Abstraction Model (DAM)

C

Database

C

User View

C

Access Methods

F

F

F

F

F

F

F

Abstract Query

slide23

Biobank Information

Management System

slide24

LifeGene

A Swedish Population-based Project

on

Lifestyle, Genomics and Health

slide25

LifeGene

  • Study of aetiology of diseases with high health care and economic impact
  • Prospective highly motivated and well characterized cohort with 5-800,000
  • Ascertainment of nuclear families
  • Ages 0-39: infections, asthma and allergy, obesity and diabetes, mental disorders and cognitive dysfunction
  • Ages 40-64: CVD, diabetes, neurodegenerative disorders, cancer