Future of biobanks - bigger, longer, and more dimensional

Genome-Wide Meta-Analysis Identifies Multiple Novel Rare Variants to Predict Common Human Infectious Diseases Risk

Infectious diseases still threaten global human health, and host genetic factors have been indicated as determining risk factors for observed variations in disease susceptibility, severity, and outcome. We performed a genome-wide meta-analysis on 4624 subjects from the 10,001 Dalmatians cohort, with 14 infection-related traits. Despite a rather small number of cases in some instances, we detected 29 infection-related genetic associations, mostly belonging to rare variants. Notably, the list included the genes CD28, INPP5D, ITPKB, MACROD2, and RSF1, all of which have known roles in the immune response. Expanding our knowledge on rare variants could contribute to the development of genetic panels that could assist in predicting an individual's life-long susceptibility to major infectious diseases. In addition, longitudinal biobanks are an interesting source of information for identifying the host genetic variants involved in infectious disease susceptibility and severity. Since infectious diseases continue to act as a selective pressure on our genomes, there is a constant need for a large consortium of biobanks with access to genetic and environmental data to further elucidate the complex mechanisms behind host-pathogen interactions and infectious disease susceptibility.

Landscape of Pediatric Biobanking: Challenges and Current Efforts

Diseases that manifest themselves in the pediatric age group frequently have a more diverse spectrum of abnormalities and a greater rarity than diseases that are primarily seen in adults. The complexity and the relatively small populations with specific diseases are factors that have hindered progress in the treatment of pediatric disorders. Personalized medical therapies that are specifically tailored for individuals with unusual or unique problems have great potential to assist in overcoming these factors that have been a bottleneck to pediatric medical success. Personalization of therapies will necessarily be data driven and will require delineation of the proteomic, genomic, epigenomic, and immune characteristics of patients in comparison to the general population. It follows that there is a need to provide researchers with accessible high-quality pediatric tissue collections to facilitate the acquisition of the molecular information needed to support personalized medicine. Because of the unusual nature of many pediatric diseases, sample pools from individual institutions are often too small to adequately power definitive studies. Thus, etiological and translational research in this area are increasingly relying on biobanking networks to provide investigators with adequate numbers of tissue samples. Several pediatric biobanking networks have been formed, which are aimed at increasing the power of research studies and desired pools of high-quality samples. However, despite the concerted efforts, these multicenter networks and collaborations have met with mixed outcomes owing to increasing complexities and heterogeneity in the biobanking arena. While there have been challenges and roadblocks, there also have been some positive outcomes that have had paradigm impacts on diagnosis, study, and treatment of specific diseases. This article highlights the need for establishing pediatric biobanks, how current efforts in pediatric biobanking are influencing the pediatric research landscape, and attempts to identify practical impediments that continue to hamper advancements for the future.

Biobanking for Translational Diabetes Research in India

India is declared as the diabetic capital of the world. Clinically well-annotated blood samples will advance diabetes research for better diagnostic and treatment methods. Building a disease-specific biobank with high-quality peripheral blood mononuclear cells (PBMCs) and clinical follow-up data system will serve as a good platform for clinical research in diabetes. Processing and storage of high-quality biospecimen for translational research in diabetes demand the implementation of good clinical laboratory practices. “Certification or accreditation programs” that improve biorepository processes and frameworks are lacking in Indian context. To sustain and translate the research into clinical practice, good governance of the biobank and financial resources is required. For ethical issues related to health needs of the people and participants in the research, issues related to research process, translational research, and commercialization, data sharing should be addressed. For India to be an innovation and sustainable country Indian government is supporting translational research facilities, including biobanks. India has developed biobanks for various diseases; however, diabetes-specific research biorepository is lacking. Given the dangers of diabetic burden, India should set up a diabetes disease-specific repository learning from the global organizations and customize to the needs of Indian context. It is important to have private agencies get involved to develop biobanks and future research as there are commercial goals to translate research into practice. New technologies of specimen storing and preservation, data management, and data sharing should be adopted for developing cost-effective long-standing disease-specific population biobank in India.

Mortality patterns in Southern Adriatic islands of Croatia: a registry-based study

Aim

To investigate the mortality patterns on the Southern Adriatic islands of Croatia and compare them with those in two, mainly coastal, mainland counties.

Methods

In this registry-based study we used the official mortality register data to analyze the mortality patterns on seven Croatian islands (Brač, Hvar, Korčula, Lastovo, Mljet, Šolta, and Vis) and Pelješac peninsula in the 1998-2013 period and calculated the average lifespan, life expectancy, and standardized mortality ratios (SMR). We compared the leading causes of death with those in the mainland population of two southernmost Croatian counties.

Results

The average lifespan of the island population was 3-10 years longer for men and 2-7 years longer for women than that on the mainland. All-cause SMRs were significantly lower for both men and women on Korčula, Brač, Mljet, and Pelješac but significantly higher for women on Šolta (1.22; 95% confidence intervals 1.07-1.38). The leading causes of death on the islands were cardiovascular diseases, with higher percentages in men and lower in women in comparison with those on the mainland. There were no substantial differences in the life expectancy at birth.

Conclusions

Despite longer lifespan, lack of differences in life expectancy at birth suggests that the recent generations of islanders no longer show beneficial mortality patterns, possibly due to diminishing adherence to the Mediterranean diet and lifestyle. Restoring the traditional lifestyles is a public health priority, with the ultimate aim of reducing inequalities and improving the health of island inhabitants.

Dietary Factors Associated with Plasma Thyroid Peroxidase and Thyroglobulin Antibodies

The knowledge about dietary habits and their influence in the development of autoimmune thyroid disease is insufficient. The aim of this study was to analyse the association of dietary factors and plasma thyroid peroxidase antibodies (TPO-Ab) and/or thyroglobulin antibodies (Tg-Ab). The study enrolled 1887 participants originating from the South Croatia. Participants with elevated plasma TPO-Ab and/or Tg-Ab were defined as cases (n = 462) and those with TPO-Ab and/or Tg-Ab within referent values were defined as controls (n = 1425). Dietary intake was evaluated according to a food frequency questionnaire containing 58 food items. Principal component analysis was used to group food items into dietary groups. We used logistic regression analysis to examine dietary groups associated with positive plasma TPO-Ab and/or Tg-Ab. The results indicate that the dietary group with frequent consumption of animal fats and butter is associated with positive plasma TPO-Ab and/or Tg-Ab (p = 0.01). The dietary group with frequent consumption of vegetables as well as the dietary group with high consumption of dried fruit, nuts, and muesli are associated with negative findings of TPO-Ab and/or Tg-Ab (p = 0.048 and p = 0.02, respectively). We showed that the anti-inflammatory dietary groups are associated with the negative findings of plasma TPO-Ab and/or Tg-Ab.

Market-driven production of biospecimens and the role of NHS hospital-led biobanks

Biobanks are vital for biospecimen production in research, despite the regulatory, recruitment and commercial difficulties they face. We conducted interviews with clinicians, researchers, volunteers who recruit biobank participants, regulators and NHS managers about the integration of a biobank into an NHS hospital. We show that medical waste collected for biomedical research acquires its socio-ethical and economic value from the level of integration (both technologically and organisationally) of the biobank into the NHS hospital. There is extensive investment in a range of intellectual and commercial relationships and labour among stakeholders involved in the production of biospecimens. It is not only the boundaries of research, clinical care and commercialisation of biospecimens that blur but also those of volunteerism and citizenship. Hospital-led biobanks provide an opportunity to study the intertwining of biomedical innovation and healthcare.

Host genetics and susceptibility to congenital and childhood cytomegalovirus infection: a systematic review

Aim

To summarize available evidence on the role of host genetics in the susceptibility to congenital and childhood cytomegalovirus (CMV) infections by conducting a systematic review of published studies.

Methods

We searched online databases (PubMed, Web of Science, Scopus and HuGe Navigator) for relevant studies with well-defined inclusion and exclusion criteria and assessed the risk of bias using novel Confounding-Selection-Information bias score (CSI).

Results

5105 studies were initially identified, but only 5 met all the inclusion criteria and were analyzed in detail. Polymorphisms of the toll-like receptors (TLRs) and mannose-binding lectin (MBL) genes were shown to have an impact on the CMV infection in infants. Polymorphisms of the TLR2 (rs3804100, rs1898830), TLR4 (rs4986791), and TLR9 (rs352140) were shown to have a role in congenital CMV infection. Low MBL levels were associated with CMV infection in Chinese individuals, a finding that was not replicated in Caucasians. The overall credibility of evidence was weak.

Conclusions

Based on currently available very limited amount of evidence, it is uncertain whether congenital and childhood CMV infections are under host genetic control. Additional primary studies are needed with more specific research hypotheses that will enable gradual understanding of specific mechanisms of the CMV pathogenesis. More genetic studies in the future will facilitate better understanding of host susceptibility and likely enable novel preventative and curative measures.

Mediterranean diet in the southern Croatia - does it still exist?

AIM

To assess the adherence to the Mediterranean diet in the population of Dalmatia in southern Croatia.

METHODS

A cross-sectional study was performed within the 10001 Dalmatians cohort, encompassing 2768 participants from Korčula and Vis islands and the City of Split, who were recruited during 2011-2014. Using the data obtained from food frequency questionnaire we calculated the Mediterranean Diet Serving Score (MDSS). Multivariate logistic regression was used to identify the characteristics associated with the adherence to the Mediterranean diet, with age, sex, place of residence, education attainment, smoking, and physical activity as covariates.

RESULTS

The median MDSS score was 11 out of maximum 24 points (interquartile range 8-13), with the highest score recorded on the island of Vis. Participants reported a dietary pattern that had high compliance with the Mediterranean diet guidelines for consumption of cereals (87% met the criteria), potatoes (73%), olive oil (69%), and fish (61%), moderate for consumption of fruit (54%) and vegetables (31%), and low for consumption of nuts (6%). Overall, only 23% of the participants were classified as being adherent to the Mediterranean diet, with a particularly low percentage among younger participants (12%) compared to the older ones (34%). Men were less likely to show good adherence (odds ratio 0.52, 95% confidence interval 0.42-0.65).

CONCLUSION

This study revealed rather poor compliance with the current recommendations on the Mediterranean diet composition in the population of Dalmatia. Public health intervention is especially needed in younger age groups and in men, who show the greatest departure from traditional Mediterranean diet and lifestyle.

The impact of IL-6 and IL-28B gene polymorphisms on treatment outcome of chronic hepatitis C infection among intravenous drug users in Croatia

Background

Several genes and their single nucleotide polymorphisms (SNPs) are associated with either spontaneous resolution of hepatitis C infection or better treatment-induced viral clearance. We tested a cohort of intravenous drug users (IVDU) diagnosed with chronic hepatitis C virus (HCV) for treatment response and its association with the SNPs in the interleukin-6 (rs1800795-IL6) and the interleukin-28B (rs12979860-IL28B) genes.

Methods

The study included 110 Croatian IVDU positive for anti-HCV antibody. Genotyping was performed by polymerase chain reaction (PCR) based approach. Patients were treated by standard pegylated-interferon/ribavirin and followed throughout a period of four years, during which sustained virological response (SVR) was determined. All data were analysed with statistical package SPSS 19.0 (IBM Corp, Armonk, NY, USA) and PLINK v1.07 software.

Results

Patients showed a significantly better response to treatment according to the number of copies of the C allele carried at rs1800795-IL6 (P = 0.034). All but one of the patients with CC genotype achieved SVR (93%), whereas the response rate of patients with GG genotype was 64%. The association of rs1800795-IL6 with SVR status remained significant after further adjustment for patients’ age, fibrosis staging, and viral genotype (OR 2.15, 95% CI 1.16–4.68, P = 0.019). Distributions of allele frequencies at the locus rs12979860-IL28B among the study cohort and the underlying general population were suggestive of a protective effect of CC genotype in acquiring chronic hepatitis C in the Croatian IVDU population.

Discussion

The rs1800795-IL6 polymorphism is associated with positive response to treatment in IVDU patients positive for HCV infection. A protective role of rs12979860-IL28B CC genotype in acquiring chronic hepatitis C is suggested for Croatian IVDU population.

Soluble transferrin receptor levels are positively associated with insulin resistance but not with the metabolic syndrome or its individual components

The metabolic syndrome (MetS) is known to be associated with elevated serum ferritin levels. The possible association with other Fe markers has been less well studied. We aimed to investigate the cross-sectional association of soluble transferrin receptor (sTfR) and ferritin levels with the MetS components, insulin resistance and glycosylated Hb (HbA1C). The sample consisted of 725 adults, aged 19-93 years (284 men, 151 premenopausal and 290 postmenopausal women), from the Croatian island of Vis. Serum sTfR and ferritin levels were measured by immunoturbidimetry and electrochemiluminescence assays, respectively. The MetS was defined using modified international consensus criteria. Logistic and linear regression analyses were conducted to investigate the associations adjusting for age, fibrinogen, smoking status, alcohol consumption and BMI. Prevalence of the MetS was 48·7 %. Standardised values of ferritin were positively associated with all of the MetS components (except high blood pressure and waist circumference) in men (P0·05). sTfR levels could be spuriously elevated in subjects with insulin resistance and without association with the MetS or its components. We conclude that different markers of Fe metabolism are not consistently associated with cardiometabolic risk.

Whole-exome sequencing in an isolated population from the Dalmatian island of Vis

We have whole-exome sequenced 176 individuals from the isolated population of the island of Vis in Croatia in order to describe exonic variation architecture. We found 290 577 single nucleotide variants (SNVs), 65% of which are singletons, low frequency or rare variants. A total of 25 430 (9%) SNVs are novel, previously not catalogued in NHLBI GO Exome Sequencing Project, UK10K-Generation Scotland, 1000Genomes Project, ExAC or NCBI Reference Assembly dbSNP. The majority of these variants (76%) are singletons. Comparable to data obtained from UK10K-Generation Scotland that were sequenced and analysed using the same protocols, we detected an enrichment of potentially damaging variants (non-synonymous and loss-of-function) in the low frequency and common variant categories. On average 115 (range 93–140) genotypes with loss-of-function variants, 23 (15–34) of which were homozygous, were identified per person. The landscape of loss-of-function variants across an exome revealed that variants mainly accumulated in genes on the xenobiotic-related pathways, of which majority coded for enzymes. The frequency of loss-of-function variants was additionally increased in Vis runs of homozygosity regions where variants mainly affected signalling pathways. This work confirms the isolate status of Vis population by means of whole-exome sequence and reveals the pattern of loss-of-function mutations, which resembles the trails of adaptive evolution that were found in other species. By cataloguing the exomic variants and describing the allelic structure of the Vis population, this study will serve as a valuable resource for future genetic studies of human diseases, population genetics and evolution in this population.

The role of host genetic factors in respiratory tract infectious diseases: systematic review, meta-analyses and field synopsis

Host genetic factors have frequently been implicated in respiratory infectious diseases, often with inconsistent results in replication studies. We identified 386 studies from the total of 24,823 studies identified in a systematic search of four bibliographic databases. We performed meta-analyses of studies on tuberculosis, influenza, respiratory syncytial virus, SARS-Coronavirus and pneumonia. One single-nucleotide polymorphism from IL4 gene was significant for pooled respiratory infections (rs2070874; 1.66 [1.29–2.14]). We also detected an association of TLR2 gene with tuberculosis (rs5743708; 3.19 [2.03–5.02]). Subset analyses identified CCL2 as an additional risk factor for tuberculosis (rs1024611; OR = 0.79 [0.72–0.88]). The IL4-TLR2-CCL2 axis could be a highly interesting target for translation towards clinical use. However, this conclusion is based on low credibility of evidence - almost 95% of all identified studies had strong risk of bias or confounding. Future studies must build upon larger-scale collaborations, but also strictly adhere to the highest evidence-based principles in study design, in order to reduce research waste and provide clinically translatable evidence.

The Future of Biobanking: A Conceptual Look at How Biobanks Can Respond to the Growing Human Biospecimen Needs of Researchers

Biobanking of human biological specimens has evolved from the simple private collection of often poorly annotated residual clinical specimens, to well annotated and organized collections setup by commercial and not-for-profit organizations. The activities of biobanks is now the focus of international and government agencies in recognition of the need to adopt best practices and provide scientific, ethical and legal guidelines for the industry. The demand for more, high quality and clinically annotated biospecimens will increase, primarily due to the unprecedented level of genomic, post genomic and personalized medicine research activities going on. Demand for more biospecimens provides new challenges and opportunities for developing strategies to build biobanking into a business that is better able to supply the biospecimen needs of the future. A paradigm shift is required particularly in organization and funding, as well as in how and where biospecimens are collected, stored and distributed. New collection sites, organized as Research Ready Hospitals (RRHs) and new public-private partnership models are needed for sustainability and increased biospecimen availability. Biobanks will need to adopt industry-wide standard operating procedures, better and "non-destructive" methods for quality assessment, less expensive methods for sample storage/distribution, and objective methods to manage scarce biospecimens. Ultimately, the success of future biobanks will rely greatly on the success of public-private partnerships, number and diversity of available biospecimens, cost management and the realization that an effective biobank is one that provides high quality and affordable biospecimens to drive research that leads to better health and quality of life for all.

Is experimentally induced pain associated with socioeconomic status? Do poor people hurt more?

Background

The association of pain and socioeconomic status is widely reported, yet much less clearly understood. The aim of this study was to investigate the association of experimentally induced pain threshold and tolerance with socioeconomic status.

Material/Methods

The study sample consisted of 319 adult subjects from the population of the island of Vis, Croatia, which was previously shown to have a high level of social homogeneity. A manual dolorimeter was used to measure mechanical pressure pain threshold (least stimulus intensity) and pain tolerance (maximum tolerance stimulus intensity) on both hands. Pain tolerance interval was defined as the difference between pain tolerance and threshold. Years of schooling and material status were used as socioeconomic estimates.

Results

Both of the socioeconomic estimates were significantly correlated with pain threshold, tolerance, and tolerance interval (P<0.001). The mixed modeling analysis, controlled for the effects of age, gender, and 4 psychological variables, indicated that education was not a significant predictor in any of the 3 models. However, lower material status was significantly associated with lower pain tolerance (P=0.038) and narrower pain tolerance interval (P=0.032), but not with pain threshold (P=0.506). The overall percentages of explained variance were lower in the tolerance interval model (20.2%) than in pain tolerance (23.1%) and threshold (33.1%), suggesting the increasing share of other confounding variables in pain tolerance and even more so in tolerance interval model.

Conclusions

These results suggest a significant association between experimentally induced pain tolerance and tolerance interval with material status, suggesting that poor people indeed do hurt more.