Project leader: Aarno Palotie
Postdoc: Priit Palta
Exome Aggregation Consortium (ExAC) coding variant dataset has proven to be an extremely useful resource and tool to facilitate research in human medical and population genetics. We will create a similar data resource for Nordic countries, including Estonia. By providing population-specific (and through requested look-ups also individual-level) allele frequencies for human coding variants, this eScience data resource would greatly benefit the scientific community in the field of human genetics and genomics and therefore would increase the competitive advantage of genetic research towards improvement of human health in all Nordic countries. Our aim is to create the Nordic Exome Variant Catalogue by collecting available human exome variant data from all participating countries (initially data for 15 000, 5000 and 5000 whole-exome sequenced individuals from Finland, Estonia and Norway, repectively). The collected data will be aggregated by populations (countries), maintaining the cohort-specific information. This data will be stored in a secure database server at CSC (Finnish IT Center for Science).
Outcome 1: Allele frequency database publicly available to the scientific community
For this we plan to update our existing web-based user interface (SISu variant browser: http://www.sisuproject.fi/) that would allow searching and browsing the collected data as population-specific summary data – allelic distribution information for all coding variants together with corresponding functional and variant effect/consequence annotations.
Outcome 2: Access routine for individual-level WES data
We will implement an integrated inquiry system that for a small fee (to ensure sustainability) would facilitate requesting access to the cohort-specific and individual-level genotype and phenotype data directly from the population/cohort ‘owner’ and corresponding DAC.
- E-Science technologies in a workflow for personalized medicine using cancer screening as a case study.
- Whole-genome view of the consequences of a population bottleneck using 2926 genome sequences from Finland and United Kingdom.
- Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms.
- Effectiveness of cervical screening after age 60 years according to screening history: Nationwide cohort study in Sweden.
- Genome-Wide Meta-Analysis of Sciatica in Finnish Population.
- Variation at 2q35 (PNKD and TMBIM1) influences colorectal cancer risk and identifies a pleiotropic effect with inflammatory bowel disease.
- Mendelian randomisation analysis strongly implicates adiposity with risk of developing colorectal cancer.
- HEALTH BANK -A Workbench for Data Science Applications in Healthcare
- Exploration of known and unknown early symptoms of cervical cancer and development of a symptom spectrum – Outline of a data and text mining based approach.
- Finding Cervical Cancer Symptoms in Swedish Clinical Text using a Machine Learning Approach and NegEx.
- Creating a rule based system for text mining of Norwegian breast cancer pathology reports.
Project leader: Mads Melbye
Postdoc: Frederik Trier Møller
The impact of most daily products we buy on our health is currently unknown, due to a lack of access to continuously collected detailed lifestyle data. In this project we will use currently unused continuously collected electronic customer receipts, to model lifestyle determinants on disease onset and behavior and improve lifestyle advice. Initially, we aim to identify lifestyle determinants of flares in complex inflammatory diseases, such as multiple sclerosis and inflammatory bowel disease. Approximately 5% of the Danish population suffer from chronic autoimmune diseases affecting many young people, with the majority being females. Individuals affected by autoimmune diseases have an unmet need for lifestyle advice that could improve the disease course. To clarify the underlying causes of complex autoimmune disease, it is crucial to collect continuous highly-detailed lifestyle data to assess exposure to nutrients, chemicals and additives in daily life. Combined with assessment of disease activity the lifestyle determinants of disease flares could be assessed. This project leverages the existing Danish framework for conducting population-based studies of disease exposures and outcomes and a highly digitalized retail sector.
Data from costumer receipts are, with the consumers consent, already continuously collected and used in targeted marketing. Recently published research suggests that costumer receipts data reflect individual lifestyle. To date more than a 100.000 products have a digital id in Denmark that are promoting upstream traceability. Each receipt are higly individual as the consumer chooses a subset of products out of all products available, thus in effect answering a +1000 items intentional yes/no questionnaire. This multiple item answer is repeated in continous manner throughout life, underlining the potential depth of knowledge to be extracted from consumer receipts. Furthermore each product may in time be characterized in detail, including unintended contents. As such the potential public health knowledge to cost ratio seem beneficial for consumer receipts compared to traditional means to collect lifestyle information to study medium to long term outcomes. By analyzing customer receipts data information at a household level and subdivide each product into its constituents we can achieve unparalleled detail on individual exposures. In addition Denmark offers an excellent research framework to assess key health related outcomes such as death, medication, and surgery. We will monitor disease outcomes of Danish participants affected by either of the aforementioned diseases, using information from national registries, patient files and routine samples. Digital informed consent secures ethical, safe and transparent implementation of the project.
Combined, these datasources enables participating researchers to reach the initial main objective, to provide targeted prevention of disease flares in complex autoimmune disease.
Project leader: Ahti Anttila
Postdoc: Veli-Matti Partanen
NORDSCEEN (Interactive joint NORDic database on performance and outcome indicators of cervical cancer SCREENing) aims to develop a publicly available web-based interactive tool/application to access standardised, and as far as possible, evidence-based, performance and outcome indicators of cervical cancer screening, based upon up-to-date Nordic cancer screening register data. The project will develop and implement a standardised set of readily available key performance and outcome indicators, and a set of scripts for standardised retrieval of the required data items from the different collaborating screening registers. This will greatly ease the provision of relevant and tailored data to decision-makers, the press, and screening providers (as exemplified by NORDCAN and GLOBOCAN in the field of cancer burden).
Miriam Elfström (PhD, MPH) is an epidemiologist by training and divides her time between the Screening Unit at the Regional Cancer Center of Stockholm Gotland and the Department of Laboratory Medicine, Karolinska Institutet. She works closely with the regional cancer screening programs, particularly with monitoring, evaluation, and development. The focus of her research is optimizing cervical cancer prevention. Most recently, she has worked on HPV testing as a primary cervical screening tool and piloting HPV self-sampling for screening non-attenders. She is particularly interested in health systems strengthening and evaluating organization and quality assurance of cancer prevention programs. Email: firstname.lastname@example.org
I work as Project Manager at Karolinska Institutet (Medical Epidemiology and Biostatistics) and I am involved in national and EU projects related to informatics infrastructures for biomedical research and biobanking (BioMedBridges, BiobankCloud, RD-Connect, B3Africa). I have a background in computer engineering and informatics and I have experience in high-throughput data and bioinformatics, biobank data management, data harmonization and integration, project management from conception to execution and sustaining, as well as teaching at university level. I’m a fervent believer in the creed of open-source, open-access and open-science as the driving forces of contemporary science.
I have a background in computer and software engineering. I mainly work in the areas of biobanking and research management, LIMS, bio-resource cataloguing, integration of heterogeneous databases and unstructured data, experienced in designing and developing informatics systems for biomedical research/health sciences, etc. I am working as a System Developer at Karolinska Institutet.
I am a medical doctor and PhD currently specializing in public health medicine at Statens Serum Institut, Denmark. I am project managing the projects “Consumer purchase data for improvement of public health” and the eConsent app, partially funded by a NIASC seed grant, as well as Helsefonden. Historically food frequency questionnaires has been used to assess lifestyle in research but have several limitations such as (missing data, reporting bias etc.). Recently large scale sources of consumer-purchasing data has become available and could be ideal to assess lifestyle, with each supermarket visit in effect corresponding to answering a 25.000 item questionnaire. Consumer purchasing data can be unobtrusively collected continuously over the year, supporting the detection and later communication of lifestyle determinants of disease flares and onset. The seed grant from the NIASC consortium has facilitated the construction of an e-consent platform using a validated patient consent toolkit, supported by NemID/bank ID, featuring control questions to secure that the information is understood. Over the last year of the NIASC consortium grant period, pilot studies will be conducted, and the developed consumer data will be used to conduct studies within the EU project framework OH EJP