National Association of Biobanks and Biobanking Specialists: New Community for Promoting Biobanking Ideas and Projects in Russia

Genetic landscape in Russian patients with familial left ventricular noncompaction

Background

Left ventricular noncompaction (LVNC) cardiomyopathy is a disorder that can be complicated by heart failure, arrhythmias, thromboembolism, and sudden cardiac death. The aim of this study is to clarify the genetic landscape of LVNC in a large cohort of well-phenotyped Russian patients with LVNC, including 48 families (n=214).

Methods

All index patients underwent clinical examination and genetic analysis, as well as family members who agreed to participate in the clinical study and/or in the genetic testing. The genetic testing included next generation sequencing and genetic classification according to ACMG guidelines.

Results

A total of 55 alleles of 54 pathogenic and likely pathogenic variants in 24 genes were identified, with the largest number in the MYH7 and TTN genes. A significant proportion of variants -8 of 54 (14.8%) -have not been described earlier in other populations and may be specific to LVNC patients in Russia. In LVNC patients, the presence of each subsequent variant is associated with increased odds of having more severe LVNC subtypes than isolated LVNC with preserved ejection fraction. The corresponding odds ratio is 2.77 (1.37 -7.37; p <0.001) per variant after adjustment for sex, age, and family.

Conclusion

Overall, the genetic analysis of LVNC patients, accompanied by cardiomyopathy-related family history analysis, resulted in a high diagnostic yield of 89.6%. These results suggest that genetic screening should be applied to the diagnosis and prognosis of LVNC patients.

Biobanking as a Tool for Genomic Research: From Allele Frequencies to Cross-Ancestry Association Studies

In recent years, great advances have been made in the field of collection, storage, and analysis of biological samples. Large collections of samples, biobanks, have been established in many countries. Biobanks typically collect large amounts of biological samples and associated clinical information; the largest collections include over a million samples. In this review, we summarize the main directions in which biobanks aid medical genetics and genomic research, from providing reference allele frequency information to allowing large-scale cross-ancestry meta-analyses. The largest biobanks greatly vary in the size of the collection, and the amount of available phenotype and genotype data. Nevertheless, all of them are extensively used in genomics, providing a rich resource for genome-wide association analysis, genetic epidemiology, and statistical research into the structure, function, and evolution of the human genome. Recently, multiple research efforts were based on trans-biobank data integration, which increases sample size and allows for the identification of robust genetic associations. We provide prominent examples of such data integration and discuss important caveats which have to be taken into account in trans-biobank research.

The concept of the national information platform of biobanks of the Russian Federation

Aim. To create the concept of the national information platform of biobanks of the Russian Federation (NIPB RF).

Material and methods. In April 2022, an expert group consisting of 17 representatives of Russian biobanks was formed in National Association of Biobanks and Biobanking Specialists to create the concept of the NIPB RF. An analysis of international practices in this area was carried out. To assess the infrastructure of Russian biobanks in terms of information support for stored biomaterial, experts formed a questionnaire consisting of several blocks of questions. The survey was conducted from April to June 2022 among representatives of Russian biobanks. Descriptive statistics were used to analyze the results of the survey.

Results. In total, representatives of 16 biobanks took part in the survey. The storage capacity of biobanks varies from 2000 to 800000 storage units. It is shown that the majority of biobanks (81%) use information systems for entering and storing related data. Biobanks use foreign and Russian software products (53 and 47%, respectively), while a  third develop their own information systems. We formulated the NIPB RF concept as an information system designed for consolidating, processing and using data on biosamples for the development of Russian biobanking and improving the efficiency and quality of research.

Conclusion. The creation of the NIPB RF will improve the interaction between biobanks and end users and will develop biomedicine in Russia.

Influence of long-term storage of blood serum samples in a biobank for population-based seroepidemiologic studies

Aim. To assess the safety of IgG antibodies during long-term storage of blood serum samples using measles- and rubella-specific antibodies as an example.

Material and methods. The study used serum samples from the collection of the Department of Epidemiology of the Gamaleya National Research Center for Epidemiology and Microbiologya, which were tested for measles- or rubella-specific IgG antibodies immediately upon admission to the laboratory, were frozen and stored at -70оC (n=180). The samples were reexamined after 20 months (n=90) and 6 years (n=90).

Results. Reexamination after 20-month storage showed a decrease in the mean level of measles- and rubella-specific antibodies by 13,1% (from 0,36 (0,08-1,21) to 0,31 (0,02-1,2) IU/ml) and by 11,8% (from 151,4 (45-235) to 133,5 (72-198) IU/ml), respectively (p<0,05 for all). At the same time, the number of seronegative samples did not change. After a 6-year storage period, the mean level of measles-specific antibodies decreased by 33,8% (p<0,05) from 0,72 (0,4-1,79) to 0,34 (0,18-1,14) IU/ml and only two samples became seronegative. It was shown that the higher the IgG level in native samples, the more pronounced its decrease was during the second examination.

Conclusion. Storage of serum samples in a biobank for 20 months at -70оC ensures the safety of measles- and rubella-specific IgG antibodies, and is the basis for the reliability of future studies.

Development of a biobank in the structure of scientific and diagnostic and treatment institutions and prospects for interregional integration

The formation of biobanks in the structure of scientific and treatment and diagnostic institutions with prospects for interregional integration is a fundamental link in monitoring and predicting diseases of various origins, creating and testing highly effective diagnostics, and developing novel therapeutic agents.

Aim. To describe standard operating procedures and principles for the formation of bioresource collections (BRC) in medical institutions with biobanking.

Material and methods. The data of scientific and practical biomedical projects using BRC obtained from patients with genetic, multifactorial and infectious diseases in St. Petersburg and Surgut are presented. As of September 2022, the BRC collected on the basis of the Pediatric Research and Clinical Center for Infectious Diseases of the Federal Medical and Biological Agency includes biosamples from 1619 patients, and the BRC collected in the Medical Institute of Surgut State University includes biosamples from 450 patients and healthy individuals of different sex and age. The selection of biosamples from apparently healthy individuals and patients with various diseases can serve as a strategically important resource for future research in terms of etiology, epidemiology, the development of regulatory environment and scales, innovations in the development of diagnostic approaches and treatment of the Russian population.

Bioresource collection of biosamples from pregnant women at different gestational ages for the search for early biomarkers of pregnancy complications and potential for its use in research

Aim. Clinical and anamnestic characterization of the bioresource collection of biosamples from pregnant women at different gestational ages.

Material and methods. Preparation of biosamples of various biomaterial types for long-term storage; static analysis of clinical and anamnestic characteristics of women whose samples are included in the collection.

Results. As of September 1, 2022, the collection consists of 16625 biosamples of various biomaterial types from 355 pregnant women. The clinical and anamnestic characteristics of women, samples of which are presented in the collection, are presented.

Conclusion. The resulting high-quality biosamples can be used in various basic and applied research to study both the physiological and pathological course of pregnancy. Particularly promising is the possibility of searching for the earliest biomarkers of gestational complications before the onset of obstetric complications. In this regard, it is important to have complete clinical and anamnestic data on biosamples of the collection in order to expand the possibilities of its use and improve the quality of ongoing research.

Training in biobanking in the context of modern medical education

The development of biomedical research based on predictive, preventive and personalized medicine has served as a challenge to the formation and rapid development of a novel interdisciplinary scientific area  — biobanking, the main goal of which is the long-term proper storage of biological samples and related data for use in scientific and clinical research. Qualified personnel, along with the creation and development of biobank infrastructure, provide high-quality results required for biomedicine. Education and training must reflect the changing scope of knowledge and adapt to biobanking challenges. In this regard, there is an increasing need to develop and implement educational programs for staff working in and managing biobanks, as well as researchers, doctors and students who are not familiar with this area, but plan research using bioresources. The aim of this review is to present an analysis of the main biobanking directions and training programs in the world and in Russia in order to assess the existing problems and needs.

Quality management of biosampling and data collection from women at different stages of pregnancy for the search for early biomarkers of preterm birth: predicting errors and risk management

The main condition for ensuring effective sampling for creating a bioresource collection is quality management, which implies careful planning and predicting errors at all stages. Risk management of samples and data loss is ensured by correct logistics, circumspect algorithms and standardization of processes. Features of the logistic processes for creating biosample collection from the pregnant women are described in this article.

Guidelines for genetic testing of healthy adults who deposit samples and related data in bioresource collections and biobanks

Currently, a significant part of research in the fields of human and medical genetics is carried out using tissue samples, genealogical, population, medical and personal data. Their use is of particular relevance in the “genome era”, since only joint analysis of genomic data and health status of the population is crucial for understanding how genes are associated with health and disease. Genetic studies of adults without symptoms of diseases are carried out to obtain data on a possible predisposition to multifactorial diseases, to establish the carrier status of autosomal recessive mutations as part of preconception care and to assess individual sensitivity to drugs. In addition, healthy individuals can be tested to detect an inherited disease at presymptomatic stage. This situation increasingly emphasizes the importance of storing data on genome sequencing or any other patient tests for subsequent data reanalysis, as well as their safety, including biosamples from an individual and one’s family. The review article, based on international experience, summarizes guidelines for genetic testing of healthy individuals. The options for storing biological samples and related data are considered.

Management of biobanking for medical genetics research

Biobanking is one of the most important elements of the modern infrastructure for biomedical research. Organization of a biobank on the basis of the N. P. Bochkov Medical Genetics Research Center provides a centralized infrastructure for preparing biomaterial for research. Biobank has the format of a research equipment sharing center and works with two types of unique biomaterials from patients with genetic diseases: blood/blood components and vital cells of various tissue origin. The storage facility of the Biobank is equipped with low-temperature (-80° C) and cryostorage (-196° C) systems. Identification and search of samples is carried out using a bar-coding system and is implemented through the information interface of the biobank, which is integrated into the general database of patients at the Medical Genetics Research Center. Information on biomaterial samples is presented in periodically updated catalogs on the page of equipment sharing center “Biobank”. Biobank collection is available to internal and external users.

Biobank as a key component of supporting research in phthisiology and infectious diseases

Conducting fundamental and clinical research in the field of tuberculosis is an important step towards reducing related morbidity and mortality, but access to a sufficient number of high-quality samples required for research is an unsolved problem in Russia. This review is devoted to biobanking as a key component of modern research in personalized medicine, as well as to the status and prospects for developing this area in phthisiology and infectious diseases combined with tuberculosis.

Targeted Sequencing of 242 Clinically Important Genes in the Russian Population From the Ivanovo Region

We performed a targeted sequencing of 242 clinically important genes mostly associated with cardiovascular diseases in a representative population sample of 1,658 individuals from the Ivanovo region northeast of Moscow. Approximately 11% of 11,876 detected variants were not found in the Single Nucleotide Polymorphism Database (dbSNP) or reported earlier in the Russian population. Most novel variants were singletons and doubletons in our sample, and virtually no novel alleles presumably specific for the Russian population were able to reach the frequencies above 0.1-0.2%. The overwhelming majority (99.3%) of variants detected in this study in three or more copies were shared with other populations. We found two dominant and seven recessive known pathogenic variants with allele frequencies significantly increased compared to those in the gnomAD non-Finnish Europeans. Of the 242 targeted genes, 28 were in the list of 59 genes for which the American College of Medical Genetics and Genomics (ACMG) recommended the reporting of incidental findings. Based on the number of variants detected in the sequenced subset of ACMG59 genes, we approximated the prevalence of known pathogenic and novel or rare protein-truncating variants in the complete set of ACMG59 genes in the Ivanovo population at 1.4 and 2.8%, respectively. We analyzed the available clinical data and observed the incomplete penetrance of known pathogenic variants in the 28 ACMG59 genes: only 1 individual out of 12 with such variants had the phenotype most likely related to the variant. When known pathogenic and novel or rare protein-truncating variants were considered together, the overall rate of confirmed phenotypes was about 19%, with maximum in the subset of novel protein-truncating variants. We report three novel protein truncating variants in APOB and one in MYH7 observed in individuals with hypobetalipoproteinemia and hypertrophic cardiomyopathy, respectively. Our results provide a valuable reference for the clinical interpretation of gene sequencing in Russian and other populations.

Russian National Association of Biobanks and Biobanking Specialists — a tool for integrating Russian biobanks and increasing the efficiency of biomedical research Drapkina O. M

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Towards the creation of a unified glossary of Russian biobanks

To carry out research projects, clinical trials and other studies in the field of personalized medicine, it is necessary to have collections of high-quality biological samples of various types. With the development of biomedical technologies, the need for large collections of biological samples will grow every year, which necessitates the creation of various biobanks for standardized collection, storage and distribution of such samples. One of the goals of the National Association of Biobanks and Biobanking Specialists is the development of a network of Russian biobanks interacting with each other at various levels, as well as the development and implementation of organizational and legal tools for its regulation. It is required not only to standardize the access and exchange of biological samples and data, but also to create a unified terminology that will be used by biobanks throughout Russia. The main aim is to create an accurate, professional and legally correct tool containing information accessible and understandable to a wide range of researchers.

Collection and storage of DNA-containing biomaterial and isolated DNA

The advances of biomedicine include the new technologies, diagnosis and treatment techniques, as well as the practical use of new types of biological targets, in particular, nucleic acids. Genomic deoxyribonucleic acid (DNA), extracellular DNA (exDNA) and microbiome DNA obtained from different types of samples (tissues, blood and its derivatives, feces, etc.) are used as objects of genetic research. The use of new technologies for DNA analysis required the development of standardized methods for processing biological samples in order to obtain high-quality DNA samples. The research uses various methods for collecting, preparing samples and storing various DNA-containing biomaterials and isolated DNA, as well as methods for assessing the quality of samples and biobank standards. It is obvious that the use of uniform standards will allow large-scale genetic research on the basis of biobanks and research laboratories. Specialists from professional organizations such as International Society for Biological and Environmental Repositories (ISBER), Biobanking and BioMolecular Resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC), European, Middle Eastern & African Society for Biopreservationa and Biobanking (ESBB) and the Russian National Association of Biobanks and Biobanking Professionals.