GenomEUTwin

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GenomEUTwin MORGAM projects sample handling,
genotyping and analysis
Kaisa Silander National Public Health
Institute Biomedicum, Helsinki
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Sample Flow - GenomEUTwin
Genotyping Centers
Participating Centers
Biomedicum institute, Helsinki
Finnish Genome Center
Center
Biobank
Multiallelic markers
NPHI Sequenom
Biallelic markers
NPHI DNA extraction
NPHI Chip
core, Helsinki
Center
Biallelic markers
Uppsala University, Uppsala
Uppsala University
Hospital
Multiallelic markers
Uppsala University
DNA or blood
Hospital
Center
Biobank
Quality checked DNA on plate
Biallelic markers
Quality checked DNA
DNA left after genotyping
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Data provided by participating center to DNA core

• Type of sample and sample handling information
• EUid number
• Sample ID in Twin registry/Biobank
• Sex
• Family ID
• ID of father mother (if available)
• Zygosity status
• Birth date (optional)

No Material Transfer Agreement Forms are filled
when samples are sent to DNA core.
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Sample flow at NPHI DNA Core

• Sample data to db
• Link between Eutwin ID centers sample ID NPHI
  lab ID
• Concentration and volume data, gender data etc.
• Identification
• Unique labnumber for each SAMPLE
• Location stored in db
• Date when the sample was received at NPHI
• Samples are plated onto 96-well plates
• 2 x water controls
• 2 x CEPH controls
• 2 x duplicates
• Quality control and aliquotting
• Aliquots provided as dry DNA for FGC and as
  liquid for Uppsala

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DNA Aliquotting
DNA quantitation PicoGreen assay on Victor
fluorometric instrument
Dilution1 Dilution of samples using database
derived concentration
Dilution2 Dilution of samples according to
PicoGreen result.
2 µl of DNA Max. 40 ng/µl
8 µg 20 ng/µl, 400 µl
3.6 µg for FGC 4 ng/µl, 900 µl
Eutwin_P1_L1
Eutwin_P1_L2
DNA stock from center
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DNA quality control
SEX PCR (HTR2C SRY) Genotyping-ready samples
are tested for successful PCR and gender result
is compared to that reported by center
QC accepted plates are replicated into 8 ng
aliquots and dried down on 384 well PCR plates to
be genotyped at FGC
Eutwin_P1_L2
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Sample Data Flow - GenomEUTwin
Participating Centers
Genotyping Centers
Biomedicum institute, Helsinki
Uppsala University, Uppsala
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DNA samples available

• Finnish twin cohort n 1443 (with familymembers
  in subcohort NIKO)
• to be genotyped in Uppsala (n 552)

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Genomewide Linkage analysis for stature using
TwinPool

• individuals
• Australia 3110 (old genome scan data)
• Dutch 1313 (old genome scan data)
• Finns 879 (partly new Genomeutwin samples)
• Swedes 102 (new Genomeutwin samples)
• UK 2250 (old genome scan data)
• Danish 625 (new Genomeutwin samples)
• Total 3568 families, 8277 individuals

Note Analysis done by Markus Perola, using
genotype and phenotype data sent via e-mail in
excel sheets (not encrypted)!
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Stature ALL, n8277
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Stature All, chromosome 8
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Quantitative Trait Loci Mapped for Stature
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Situation after addition of 4 scans

• Chr 6 down (2.68-gt1.1 12-5)
• Chr 8 up (2.56-gt3.59 12-gt17)
• best solo lod score australia 1 1.67
• Chr 10 down (2.51-gt2.08 12-gt9)
• Australia 2 chr 15 alone the second most
  significant result!
• dissappears in the total material

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MORGAM Sample data flow
Participating Centers
Genotyping Centers
linked to phenotype
not linked to phenotype
MPC1
NPHI Helsinki
NPHI DNA Extraction Core Helsinki
MPC2
RSCI Dublin
MPC3
MORGAM Data Center Helsinki
Biobank
INSERM Paris
Blood/DNA Genotypes Phenotypes DNA sample info
MPC4
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MORGAM samples genotypes

• Study IDs in MORGAM
• Key 0 number on the blood/DNA sample tube
• Key 1 MORGAM ID number (linked to phenotype)
• Key 2 coded ID for genotyping (not linked to
  phenotype)
• Material Data Transfer Agreement signed for all
  sample transfers
• Excess DNA is returned to MPC
• MDC has collected phenotype data from all MPCs
• Sample selection done by MDC
• Sample transfers (blood DNA) monitored by MDC
• Genotyping analysis plans approved by MORGAM
  Management Group and monitored by MDC

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DNA samples available in MORGAM

• FINRISK 92 960 (ready DNA samples)
• PRIME 788 (ready DNA samples)
• ATBC 2119 (DNA in processing)
• ITALY Brianza and Pamela 817 (blood samples
  extracted)
• Northern Sweden lt300 (blood samples extracted)

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MORGAM genetic studies

• Cardiovascular disease candidate gene study
  (NPHI, Helsinki)
• Genes likely involved in cardiovascular
  pathobiology, associated with inflammation,
  thrombosis and/or lipid metabolism or associated
  with stroke
• Genotyped 105 SNPs in 32 genes on Finrisk92
• Analysis in progress
• Genes involved in pathogen response and platelet
  biology (RCSI, Dublin)
• Genotyped 12 SNPs in 10 genes on Finrisk 92
• Genes from the IL1/IL18 system and the TNF system
  (INSERM, Paris)
• Gentoyped 12 SNPs in 3 genes on Finrisk 92

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Contact information

• Finnish NPHI
• Outi Repola, DNA co-ordinator (_at_ktl.fi)
• Mervi Alanne, MORGAM DNA co-ordinator (_at_ktl.fi)
• Kaisa Silander, SNP genotyping (_at_ktl.fi)
• Markus Perola, statistical analysis (_at_ktl.fi)
• Finnish Genome Center
• Elisabeth Widen, microsatellite genotyping
  (_at_helsinki.fi)
• Uppsala University
• Ann-Christine Syvänen, SNP gentoyping
  (_at_medsci.uu.se)
• Inger Jonasson, microsatellite gentoyping
  (_at_medpat.uu.se)