Investigation of the needs for national and local biobank services and improvement of biobank awareness

Background and aims: Biobank is a repository where human-derived samples and associated data are collected and stored for future research purposes. Biobanks have an essential role in the development of medicine from the symptom- and diagnose-based cure to proactive, preventive and personalized medicine. In Finland, Biobank Law came into effect in 2013, after which ten biobanks have been registered. Finnish Clinical Biobank Tampere received its operating license in 2015. The Finnish biobank operations are still relatively new and require development to meet the biobank users’ needs. This study aimed to increase the visibility of Finnish Clinical Biobank Tampere among the local academic researchers and to improve their biobank awareness by the means of marketing. Another aim of this study was to investigate the needs for biobank services among academic researchers and pharmaceutical companies. Methods: This study composed of two parts: a local part for academic researchers and a national part for pharmaceutical companies. Online questionnaires were used to explore the needs for biobank services and to find out the level of academic researchers’ level of biobank awareness. Two rounds of questionnaires were used in the local part to investigate the possible changes in biobank awareness. To increase the academic researchers’ biobank awareness, different marketing methods were planned and implemented between the questionnaires: a presentation, an email, and a leaflet. The researchers on the first round were divided into three reference groups to test the effect of each marketing method. After the second questionnaire, the effect of each method was analyzed with statistical analyses to find out the most effective method(s) for further use. Results: Presentation given face-to-face appeared to be the most effective marketing method in raising both biobank visibility and the sense of having received enough information about the biobank operations. Email and leaflet were not as effective methods. The number of study participants was too small for email marketing to succeed. Leaflet alone was not an efficient method, but together with presentation, led to best results in increasing biobank awareness. Although increased during this study, the biobank awareness among academic researchers in Tampere is still low. Academic researchers’ interests towards different biobank sample and data types are widely distributed, whereas pharmaceutical companies are primarily interested in data and nationally unified biobank services. Conclusion: Local marketing, preferably personal meetings, and local service development should be prioritized to increase collaboration between the biobank and academic researchers. Enhanced collaboration would probably lead to researchers’ further interest towards biobanks in a national level as well. National coordination is needed to unify the Finnish biobank services. Presumably, that would increase the interest of pharmaceutical companies towards utilization of biobanks in their research

Annotation and curation of human genomic variations: an ELIXIR Implementation Study

Background: ELIXIR is an intergovernmental organization, primarily based around European countries, established to host life science resources, including databases, software tools, training material and cloud storage for the scientific community under a single infrastructure. Methods: In 2018, ELIXIR commissioned an international survey on the usage of databases and tools for annotating and curating human genomic variants with the aim of improving ELIXIR resources. The 27-question survey was made available on-line between September and December 2018 to rank the importance and explore the usage and limitations of a wide range of databases and tools for annotating and curating human genomic variants, including resources specific for next generation sequencing, research into mitochondria and protein structure. Results: Eighteen countries participated in the survey and a total of 92 questionnaires were collected and analysed. Most respondents (89%, n=82) were from academia or a research environment. 51% (n=47) of respondents gave answers on behalf of a small research group (10 people). The survey showed that the scientific community considers several resources supported by ELIXIR crucial or very important. Moreover, it showed that the work done by ELIXIR is greatly valued. In particular, most respondents acknowledged the importance of key features and benefits promoted by ELIXIR, such as the verified scientific quality and maintenance of ELIXIR-approved resources. Conclusions ELIXIR is a "one-stop-shop" that helps researchers identify the most suitable, robust and well-maintained bioinformatics resources for delivering their research tasks

An assessment of prevalence of Type 1 CFI rare variants in European AMD, and why lack of broader genetic data hinders development of new treatments and healthcare access

PurposeAdvanced age-related macular degeneration (AAMD) risk is associated with rare complement Factor I (FI) genetic variants associated with low FI protein levels (termed 'Type 1'), but it is unclear how variant prevalences differ between AMD patients from different ethnicities.MethodsCollective prevalence of Type 1 CFI rare variant genotypes were examined in four European AAMD datasets. Collective minor allele frequencies (MAFs) were sourced from the natural history study SCOPE, the UK Biobank, the International AMD Genomics Consortium (IAMDGC), and the Finnish Biobank Cooperative (FINBB), and compared to paired control MAFs or background population prevalence rates from the Genome Aggregation Database (gnomAD). Due to a lack of available genetic data in non-European AAMD, power calculations were undertaken to estimate the AAMD population sizes required to identify statistically significant association between Type 1 CFI rare variants and disease risk in different ethnicities, using gnomAD populations as controls.ResultsType 1 CFI rare variants were enriched in all European AAMD cohorts, with odds ratios (ORs) ranging between 3.1 and 7.8, and a greater enrichment was observed in dry AMD from FINBB (OR 8.9, 95% CI 1.49-53.31). The lack of available non-European AAMD datasets prevented us exploring this relationship more globally, however a statistical association may be detectable by future sequencing studies that sample approximately 2,000 AAMD individuals from Ashkenazi Jewish and Latino/Admixed American ethnicities.ConclusionsThe relationship between Type 1 CFI rare variants increasing odds of AAMD are well established in Europeans, however the lack of broader genetic data in AAMD has adverse implications for clinical development and future commercialisation strategies of targeted FI therapies in AAMD. These findings emphasise the importance of generating more diverse genetic data in AAMD to improve equity of access to new treatments and address the bias in health care.Peer reviewe

Recontacting biobank participants to collect lifestyle, behavioural and cognitive information via online questionnaires : lessons from a pilot study within FinnGen

OBJECTIVES: To recontact biobank participants and collect cognitive, behavioural and lifestyle information via a secure online platform. DESIGN: Biobank-based recontacting pilot study. SETTING: Three Finnish biobanks (Helsinki, Auria, Tampere) recruiting participants from February 2021 to July 2021. PARTICIPANTS: All eligible invitees were enrolled in FinnGen by their biobanks (Helsinki, Auria, Tampere), had available genetic data and were >18 years old. Individuals with severe neuropsychiatric disease or cognitive or physical disabilities were excluded. Lastly, 5995 participants were selected based on their polygenic score for cognitive abilities and invited to the study. Among invitees, 1115 had successfully participated and completed the study questionnaire(s). OUTCOME MEASURES: The primary outcome was the participation rate among study invitees. Secondary outcomes included questionnaire completion rate, quality of data collected and comparison of participation rate boosting strategies. RESULTS: The overall participation rate was 18.6% among all invitees and 23.1% among individuals aged 18-69. A second reminder letter yielded an additional 9.7% participation rate in those who did not respond to the first invitation. Recontacting participants via an online healthcare portal yielded lower participation than recontacting via physical letter. The completion rate of the questionnaire and cognitive tests was high (92% and 85%, respectively), and measurements were overall reliable among participants. For example, the correlation (r) between self-reported body mass index and that collected by the biobanks was 0.92. CONCLUSION: In summary, this pilot suggests that recontacting FinnGen participants with the goal to collect a wide range of cognitive, behavioural and lifestyle information without additional engagement results in a low participation rate, but with reliable data. We suggest that such information be collected at enrolment, if possible, rather than via post hoc recontacting.publishedVersionPeer reviewe

An assessment of prevalence of Type 1 CFI rare variants in European AMD, and why lack of broader genetic data hinders development of new treatments and healthcare access

PurposeAdvanced age-related macular degeneration (AAMD) risk is associated with rare complement Factor I (FI) genetic variants associated with low FI protein levels (termed ‘Type 1’), but it is unclear how variant prevalences differ between AMD patients from different ethnicities.MethodsCollective prevalence of Type 1 CFI rare variant genotypes were examined in four European AAMD datasets. Collective minor allele frequencies (MAFs) were sourced from the natural history study SCOPE, the UK Biobank, the International AMD Genomics Consortium (IAMDGC), and the Finnish Biobank Cooperative (FINBB), and compared to paired control MAFs or background population prevalence rates from the Genome Aggregation Database (gnomAD). Due to a lack of available genetic data in non-European AAMD, power calculations were undertaken to estimate the AAMD population sizes required to identify statistically significant association between Type 1 CFI rare variants and disease risk in different ethnicities, using gnomAD populations as controls.ResultsType 1 CFI rare variants were enriched in all European AAMD cohorts, with odds ratios (ORs) ranging between 3.1 and 7.8, and a greater enrichment was observed in dry AMD from FINBB (OR 8.9, 95% CI 1.49–53.31). The lack of available non-European AAMD datasets prevented us exploring this relationship more globally, however a statistical association may be detectable by future sequencing studies that sample approximately 2,000 AAMD individuals from Ashkenazi Jewish and Latino/Admixed American ethnicities.ConclusionsThe relationship between Type 1 CFI rare variants increasing odds of AAMD are well established in Europeans, however the lack of broader genetic data in AAMD has adverse implications for clinical development and future commercialisation strategies of targeted FI therapies in AAMD. These findings emphasise the importance of generating more diverse genetic data in AAMD to improve equity of access to new treatments and address the bias in health care.</p

Tajuttoman autettavan kylkiasentoon kääntäminen selältään ja mahaltaan sekä traumapotilaan blokkikääntö: opetusvideot ensiapukoulutukseen

Tajuttomuudella tarkoitetaan tilaa, jossa tajunnantaso on heikentynyt. Kun henkilö on tajuton, hän ei ole heräteltävissä, eli ei reagoi puhutteluun ja ravisteluun. Tajuton autettava on aina käännettävä kylkiasentoon avointen hengitysteiden turvaamiseksi. Selkävammaa epäiltäessä selkäydinvamma on mahdollinen. Siirroissa on käytettävä blokkikääntötekniikkaa, jonka avulla vältetään vamman pahentumista. Tämän toiminnallisen opinnäytetyön tuotoksena teimme kolme opetusvideota Kareliaammattikorkeakoululla järjestettävään ensiapukoulutukseen. Opetusvideoiden tavoitteena oli tuoda tietoa Karelia-ammattikorkeakoulussa ensiapukurssia suorittaville tajuttoman kylkiasentoon kääntämisestä selältään ja mahaltaan sekä traumapotilaan blokkikäännöstä. Opetusvideoilla on kerrottu myös teoriatietoa tajuttomuudesta ja rankavammasta. Opetusvideoista saimme palautetta ohjaajiltamme, toimeksiantajaltamme sekä yhdeltä ensiapukurssia suorittavalta opiskelijaryhmältä. Palautteen mukaan opetusvideoiden sisältö oli selkeää, helposti ymmärrettävää sekä visuaalinen ilme oli hyvä. Opetusvideot myös tukivat oppimista. Saadun palautteen perusteella voidaan todeta, että opetusvideot onnistuivat hyvin. Jatkokehitysideana opinnäytetyön tuotoksille on, että opetusvideoita voisi hyödyntää myös hoitoalan ulkopuolisilla työpaikoilla ensiapukoulutuksessa