Legislation and Facilitation of Health Data in Denmark Short update Mads Melbye, MD, DMSc Statens Serum Institut, Copenhagen, Denmark
Legislation short facts Register research: exempted from informed consent Biobank materials: Scientific ethics aproval and exempt from informed consent >90% of applications (opt-out register) WGS and exome seq.: informed consent WGA: exempt given in most situations New model?: e-boks approach
Denmark - The Leading Country in ehealth Adoption
Research platform on 8.1 million Danes Delivery Diseases/pathology Drug use Vaccinations Childcare institutions Family, address Education, job Readmissions Hospital acquired inf. Days in hospital Health care costs Income Disability insurance CPR number Lab result* MR/CT result X-ray Blood pressure Microbiology* Haematology DNA Plasma, serum Sample tissue Spinal fluids Urine Amniotic fluids Saliva time
Basic principles of MiBa: SDN xrpt 05 xrpt xml 05 xrpt xml 05 xrpt xml 05 xml Department of clinical microbiology SDN = The National Heathcare Data Network
Nationwide sharing of patient reports on microbiological test results. National surveillance for infectious diseases and microorganisms A database for research and quality assessment projects. automatic, flexible and real time.
Access from www.sundhed.dk Patient is looking at my healthcare record
MiBAlert When a patient is hospitalized, readmitted, or transferred, important information regarding recent findings of multiresistent bacteria will be given Without sharing of this knowledge appropiate treatment may not be given and transmission to other patients may take place
patient file with MiBAlert
MiBa is called everytime a patient is put in context with EPJ
A national surveillance system combining patient administrative data microbiological test results and data on antimicrobial treatment Coorporation between : Ministry of Health The Danish Regions Statens Serum Institut Have a look: http://www.esundhed.dk/sundhedskvalitet/ha IBA
# of hospital acquired clostridium difficile infections
Consumer Data
Consumer Data and health research
PK Bi obank Dat a Sampl ei D CPR Sam pletype Sam pledat e St or agetem per at u re BiobankSour ce Pr oject Nam e PK Bi obank Dat a Sampl ei D CPR Sam pletype Sam pledat e St or agetem per at u re BiobankSour ce Pr oject Nam e PK Bi obank Dat a Sampl ei D CPR Sam pletype Sam pledat e St or agetem per at u re BiobankSour ce Pr oject Nam e PK Bi obank Dat a Sampl ei D CPR Sam pletype Sam pledat e St or agetem per at u re BiobankSour ce Pr oject Nam e PK Bi obank Dat a Sampl ei D CPR Sam pletype Sam pledat e St or agetem per at u re BiobankSour ce Pr oject Nam e Biobank Building Biobanks Register Biobanks Cancer Society: Diet, Cancer, and Health DNA biobank at Rigshospitalet (all referred patients) Patobanken (all pathological specimens) National biobank At SSI Clinical cancer biobanks Civil Registration System National registers Danish National Patient Registry Danish Family Relations Database Danish Medical Birth Registry National Pathology Registry 6 mill. specimens from 3 mill. Danes Biobank Data PK SampleID CPR SampleType SampleDate StorageTemperature BiobankSource ProjectName Biobank Registry PC Internet PC 22 mill. specimens from 5.4 mill. Danes Coordinating Centre
Access: data and biological samples Request from researcher for biological samples and register data Apply through Scientific Services at Sundhedsdatastyrelsen Applications for biological samples are evaluated by the Scientific Board at DNB Applications for register data are evaluated by Scientific Services Biological samples and register data are made available to researcher
Who can gain access? Foreign scientists Scientists in Denmark Danish companies Foreign companies
Childhood vaccination database Family doctor Bill with details National Health Insurance, National Board of Health All registrations + Information from other registries Payment to MD National Vaccination Register 1990-2016 Type, dose, date, cpr-number
Febrile seizures after MMR vaccination JAMA 2004
Discovery scans: Febrile seizues +/- MMR GWAS study I. MMR-related FS vs.controls 929/4118 II. MMR-related FS vs. MMR-unrelated FS 929/1070 III. MMR-unrelated FS vs. Controls 1070/4118 IV. FS overall vs. Controls 1999/4118 Replication genotyping 6 loci GW significant 2 loci specific for MMR-related FS 4 loci for FS in general
Variants in IFI44L and CD46 (innate immune system genes) associate with FS as an adverse event of MMR vaccinatio General FS variants point to altered ion channel function SCN1A and SCN2A: TMEM16C: 12q21.33: well-known epilepsy genes. Novel associations with FS. OR > 2, MAF~ 3%, affecting neuronal excitability. Novel target for seizure research Mg 2+ deficiency and FS susceptibility?
Mining the Phenome 31
Loss-of-function mutations Surprisingly common; we all have ~150 LoF (partial or complete) mutations across our genome Likely to have direct functional impact. But on what phenotype? Example: PCSK9 loss-of-function 40% reduction in plasma levels of LDL cholesterol Translational medicine: develop drugs that can mimic the effects of an advantageous LoF mutation by inhibiting a specific pathway
Amgen Monoclonal antibody blocking PCSK9 Regeneron and Sanofi NEJM 24 March, 2015
GENLIFE: The one million PheWAS Phenome 1,000,000 Danes: GWAS/WGS + imputation Diagnosis codes Birth characteristics Pathology Surgeries Medication Vaccinations Dental health Microbiology Haematology Blood pressure etc. PheWAS scan CTAATTGGTTTAATTATTATTTATTTGATGATACATGAAGTTGAACTCTTTACTAT AT CTAATTGGTTTAATTATTATTTATTTGATGGTACATGAAGTTGAACTCTTTACTAT AT CTAATTGGTTTAATTATTATTTATTTGATGATACATGAAGTTGAACTCTTTACTAT AT CTAATTGGTTTAATTATTATTTATTTGATGATACATGAAGTTGAACTCTTTACTAT AT CTAATTGGTTTAATTATTATTTATTTGATGATACATGAAGTTGAACTCTTTACTAT AT CTAATTGGTTTAATTATTATTTATTTGATGATACATGAAGTTGAACTCTTTACTAT AT CTAATTGGTTTAATTATTATTTATTTGATGATACATGAAGTTGAACTCTTTACTAT AT CTAATTGGTTTAATTATTATTTATTTGATGATACATGAAGTTGAACTCTTTACTAT AT CTAATTGGTTTAATTATTATTTATTTGATGGTACATGAAGTTGAACTCTTTACTAT AT CTAATTGGTTTAATTATTATTTATTTGATGATACATGAAGTTGAACTCTTTACTAT (e.g. AT CTAATTGGTTTAATTATTATTTATTTGATGATACATGAAGTTGAACTCTTTACTAT AT PheWAS target, loss-of-function mutation) Functional follow-up translational medicine
BSIG: Using million of datapoints to understand pregnancy and its complications Omics profiling of pregnancy
CELL FREE RNA AGGREGATES TRANSCRIPTS FROM DIFFERENT FETAL TISSUES DURING PREGNANCY FETAL BRAIN TRANSCRIPTS MATERNAL CIRCULATION FETAL LIVER TRANSCRIPTS PLACENTAL TRANSCRIPTS 36
Two important sources of material I. Biological Signals in Pregnancy New cohort of mothers to be (status >100 completed) Dense sampling: before pregnancy, weekly during preg., and after pregnancy II. The Danish National Birth Cohort (DNBC) 101,000 pregnant women recruited 1998-2002 Three blood samples during pregnancy Detailed history and follow-up through registry linkages
Biological Signals in Pregnancy: Sampling every week PAXgene RNA, 2½mL RNA RNA seq 2X9mL EDTA Leucosep Exome/WGS DNA WGBS Plasma PBMC Cy-TOF Metabolites Proteins Cytokines Fetal cell free RNA Proteins LC-MS HILIC+ HILIC- RP+ RP-
Global pattern of metabolite changes during pregnancy Earlier weeks Later weeks (include after-birth) Samples by gestational week 515 metabolites (p < 1e-20)