Biobank Samples Research Articles

Association of Angiopoetin-2 and TNF-α With Bleeding During Left Ventricular Assist Device Support: Analysis from the PREVENT Biorepository.

The purpose of this study was to describe the changes in plasma levels of angiogenic and inflammatory biomarkers, specifically Ang-2 and TNF-α, in patients receiving HeartMate II (HMII) left ventricular assist device (LVAD) and correlate them with nonsurgical bleeding. It has been shown that angiopoietin-2 (Ang-2) and tissue necrosis factor-α (TNF-α) may be linked to bleeding in LVAD patients. This study utilized biobanked samples prospectively collected from the PREVENT study, a prospective, multicenter, single-arm, nonrandomized study of patients implanted with HMII. Paired serum samples were obtained in 140 patients before implantation and at 90 days postimplantation. Baseline demographics were as follows: age 57 ± 13 years, 41% had ischemic etiology, 82% male, and 75% destination therapy indication. In the 17 patients with baseline elevation of both TNF-α and Ang-2, 10 (60%) experienced a significant bleeding event within 180 days postimplant compared with 37 of 98 (38%) patients with Ang-2 and TNF-α below the mean (p = 0.02). The hazard ratio for a bleeding event was 2.3 (95% CI: 1.2-4.6) in patients with elevated levels of both TNF-α and Ang-2. In the PREVENT multicenter study, patients with elevations in serum Angiopoietin-2 and TNF-α at baseline before LVAD implantation demonstrated increased bleeding events after LVAD implantation.

Participation bias in the UK Biobank distorts genetic associations and downstream analyses.

While volunteer-based studies such as the UK Biobank have become the cornerstone of genetic epidemiology, the participating individuals are rarely representative of their target population. To evaluate the impact of selective participation, here we derived UK Biobank participation probabilities on the basis of 14 variables harmonized across the UK Biobank and a representative sample. We then conducted weighted genome-wide association analyses on 19 traits. Comparing the output from weighted genome-wide association analyses (neffective = 94,643 to 102,215) with that from standard genome-wide association analyses (n = 263,464 to 283,749), we found that increasing representativeness led to changes in SNP effect sizes and identified novel SNP associations for 12 traits. While heritability estimates were less impacted by weighting (maximum change in h2, 5%), we found substantial discrepancies for genetic correlations (maximum change in rg, 0.31) and Mendelian randomization estimates (maximum change in βSTD, 0.15) for socio-behavioural traits. We urge the field to increase representativeness in biobank samples, especially when studying genetic correlates of behaviour, lifestyles and social outcomes.

Vitamin D status and latitude predict brain lesions in adrenoleukodystrophy.

Approximately 40% of boys with X-linked adrenoleukodystrophy (ALD) develop inflammatory demyelinating brain lesions (cerebral ALD, cALD) and are at risk for death or severe disability. Risk factors for cALD are poorly understood. Our objective was to evaluate whether vitamin D status, which influences immune function, is associated with risk for cALD. We used two independent cohorts to assess whether low vitamin D status is correlated with cALD. We used complementary proxies for vitamin D status: plasma 25-hydroxyvitamin D levels and latitude. In our first cohort, we measured 25-hydroxyvitamin D in biobanked plasma samples from ALD boys with initially normal brain MRIs followed at two expert centers. In a second cohort, we measured latitude (using home ZIP code) among ALD boys identified in a national administrative database (PHIS) covering 51 US pediatric hospitals. We used logistic regression models to estimate the odds of developing cALD in each cohort. In the first cohort, we identified 20 ALD boys with a total of 53 plasma sample timepoints who met inclusion criteria; 50% (n = 10) subsequently developed cALD. Average 25-hydroxyvitamin D levels were lower among boys who developed cALD than those who did not (median 28.9 vs 36.6 ng/ml); p = 0.019. For each 10 ng/mL decrease in 25-hydroxyvitamin D, the odds ratio for developing cALD was 6.94; p = 0.044. In the second cohort, we identified 230 ALD boys across 28 states; 57% of boys (n = 132) developed cALD. Each 2° increase in latitude conferred an odds ratio of 1.17 (95% confidence interval, 1.01, 1.35); p = 0.036 for developing cALD. Using independent cohorts, we found that ALD boys with lower pre-morbid plasma levels of 25-hydroxyvitamin D, or more northerly latitude of residence, were more likely to develop cALD. These findings offer complementary lines of evidence that vitamin D and/or ultraviolet light exposure influence cALD risk.

Abstract 3565: Establishing a multimodal data warehousing platform to accelerate discoveries in pediatric brain tumors for the Children’s Brain Tumor Network

Abstract Brain tumors are the leading cause of disease-related death in children and young adults ages 0-19 in largely populated countries such as the United States. In one year alone, 4,000 children and young adults will be diagnosed with a brain or central nervous system tumor in the United States. Brain tumors are complex and difficult to treat in growing children, with current treatments oftentimes causing significant and lifelong side effects. Furthermore, there have only been five drugs in the last 20 years approved by the FDA to treat pediatric brain tumors. Founded in 2011, the Children’s Brain Tumor Network (CBTN) is focused on accelerating the pace of translational research, the discovery of new treatments, and informing precision medicine for children diagnosed with brain tumors. CBTN comprises 32 member institutions/hospitals having over 4700 patient subjects enrolled, spanning 30+ brain tumor diagnoses, over 66,000 biobanked samples and 150 preclinical models. Longitudinal clinical data is also collected for every subject that is enrolled in the observational protocol. Through large scale data generation efforts funded by the NCI and foundational support, CBTN has whole genome, RNA-seq and other molecular characterization for over half of the enrolled patient population. Additionally, efforts have been underway to collect all pathology and radiology imaging and reporting for the subjects. With sequencing being done by multiple vendors, imaging protocols being different across multiple hospitals, and complex clinical treatment and longitudinal follow up data being translated from EHR systems, CBTN has created a rich, but complex, data landscape that is the largest of its kind in the world. In order to accelerate the process of going from data to cures, the data needs to be centralized, organized, and easily distributable. To do this, CBTN has built a first of its kind data workflow that acts as the inventory system for its various data assets. Using a modern data stack including dbt, PostgresSQL, Meltano and AWS, combined with utilization of FHIR as an interchange standard, data from multiple disparate sources such as REDcap, EHR systems, and PAC systems flow in near “real-time” to be utilized as integrated data resources The result of this modern, multimodal, and multi-institutional warehouse allows CBTN to distribute data quickly and accurately to translational researchers around the world and contribute data to key research efforts such as AACR Project Genie, Kids First Data Resource Center, NCI Childhood Cancer Data Initiative, and the NCI’s Open Targets Platform. Citation Format: Bailey K. Farrow, Nicholas Van Kuren, Nathan Young, Christopher Friedman, Meen Chul Kim, Alex Lubneuski, Jennifer Mason, Thinh (Bin) Nguyen, Zeinab Helili, Elizabeth Frenkel, Catherine Sullivan, Ariana Familiar, Yuankun Zhu, Mateusz Koptyra, Tatiana Patton, Jena Lilly, Phillip B. Storm, Adam Resnick, Allison P. Heath. Establishing a multimodal data warehousing platform to accelerate discoveries in pediatric brain tumors for the Children’s Brain Tumor Network. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3565.

Abstract 1332: Extracted mRNA from frozen buffy coat samples shows promise for use in downstream sequencing analyses

Abstract Frozen blood samples are routinely collected and stored in medical biobanks across the world, often for periods of several decades, and later used for medical research such as biomarker studies. Some common biomarker targets have included DNA alterations, protein or antibody levels or metabolomics. However, despite the potential importance of gene-expression alterations in circulating immune cells, transcriptional studies on blood samples from biobanks have been limited due to preanalytical technical difficulties of extracting high-quality RNA. In the absence of an RNA preservative, RNA degrades rapidly during the thawing process. Our aim was, therefore, to investigate the possibility of using biobanked blood samples for transcriptomics analyses. First, we used a CryoXtract CXT 350 to establish a protocol capable of isolating high-quality RNA from frozen core aliquots of buffy coat without thawing the entire sample tube. Then, we performed RNA sequencing on RNA extracted from 20 pre-diagnostic buffy coat samples from colorectal cancer patients and matched controls included in the population-based, prospective Northern Sweden Health and Disease Study (NSHDS). For all samples, two different library preparation methods were used (Illumina TruSeq Stranded mRNA poly-A selection and Illumina Stranded Total RNA with Ribo-Zero Globin). We obtained RNA yields of more than 1 µg from a majority of the NSHDS samples (mean=2.57 µg), and more than 92% of samples had RIN values of 6 or higher, indicating suitability for downstream analyses. Preliminary random forest analyses showed expected discriminatory ability between men and women based on data generated from each of the two library preparation methods. In conclusion, our newly established RNA extraction method enables extraction of RNA from frozen, biobanked buffy coat samples, collected in standard tubes, that is of sufficient quantity and quality for use in downstream whole-genome transcriptomic analyses, such as RNA sequencing. Citation Format: Erik Bovinder Ylitalo, Linda Vidman, Sophia Harlid, Bethany Van Guelpen. Extracted mRNA from frozen buffy coat samples shows promise for use in downstream sequencing analyses [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1332.

Abstract 5227: Cross-trait genome-wide association meta-analyses of clonal hematopoiesis and solid tumor risk

Abstract Clonal hematopoiesis (CH) is an age-related phenomenon where hematopoietic stem cells and their progeny acquire specific somatic mutations in a small, well-defined set of leukemogenic genes conferring them with fitness advantage leading to clonal proliferation. Mosaic chromosomal alterations (mCAs) are somatic structural variants that are manifestations of genomic instability and a sign of CH when they occur in blood. The recent availability of large-scale cohorts with blood exome sequence and genotype data has powered genome-wide association studies (GWAS) investigating the germline genetic contribution to CH and mCA risk. However, phenotypes of somatic mutation acquisition in driver genes, clonal selection and expansion, and chromosomal mosaicism are processes that are not confined to blood and contribute to neoplastic transformation across tissue types. GWAS of solid tumor susceptibility have so far identified hundreds of germline variants associated with cancer risk and it is likely that a subset of these variants contributes to solid tumor risk by affecting these somatic phenotypes in the corresponding tissues of origin and that some of the variants exert these somatic effects across tissues. We aimed to identify this subset of solid tumor risk variants by undertaking fixed effects inverse-variance weighted meta-analyses combining breast, prostate, ovarian, and endometrial cancer GWAS (total n = 237,483 cases/317,006 controls; no UK Biobank samples included) with UK Biobank-based CH (10,203 “cases”/173,918 controls) and mCA (66,011 “cases”/378,188 controls) risk GWAS in pairs where each pair involved one solid tumor type and one of either CH or mCA (for example, breast cancer and mCA constituted a pair). These analyses collectively identified 61 independent (r2<0.05) lead variants at combined cross-trait genome-wide significance (P<5 × 10−8) across 22 genomic loci where each lead variant was associated with each trait individually at P<10−3, had the same direction of allelic effect across traits, and little evidence of heterogeneity in effect (I2<40%). New loci (>1 Mb away from previously reported risk loci for a given trait) counts were: 14 new loci in the context of mCA risk, 6 new loci for CH risk, 2 for breast cancer risk, and one each for prostate, ovarian, and endometrial cancer risks. In silico functional annotation of these loci suggested lead variant-target genes that could be assigned to the discrete pathways of mitotic spindle assembly (INCENP, CENPN, ZWILCH, MAD1L1), p53 signaling (TP53, MDM4, SPI1), DNA damage repair (ATM, RAD51C, CHEK2, USP28, PARP8), and myeloid oncogenesis (WT1, HOXA9, L3MBTL3). Our novel approach combining the latest and largest blood somatic genomic trait GWAS with large-scale solid tumor risk GWAS thus yielded clear mechanistic insights into the shared inherited genetic basis of solid tumor risk and somatic genomic traits. Citation Format: Victoria Gray, George Richenberg, Pedro Quirós, Matthew Freedman, Paul Pharoah, Simon Gayther, Michelle Jones, George Vassiliou, Kate Lawrenson, Siddhartha Kar. Cross-trait genome-wide association meta-analyses of clonal hematopoiesis and solid tumor risk. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5227.

Cornus mas L. Extract Targets the Specific Molecules of the Th17/Treg Developmental Pathway in TNBS-Induced Experimental Colitis in Rats

Given that one of the crucial events in the pathogenesis of inflammatory bowel disease is the loss of homeostasis between Th17 and Treg cells, targeting the specific molecules of the Th17/Treg axis developmental pathway is a promising strategy for inflammatory bowel disease prevention and treatment. The current study aimed to assess the impact of cornelian cherry (Cornus mas L.) extract, rich in iridoids and polyphenols known for their potential anti-inflammatory activity, at two doses (20 or 100 mg/kg) on the crucial factors for Th17/Treg cell differentiation in the course of experimental colitis and compare this action with that of sulfasalazine. This study was conducted on the biobank colon tissue samples collected during the previous original experiment, in which colitis in rats was induced by trinitrobenzenesulfonic acid (TNBS). The levels of IL-6, RORγt, total STAT3, p-STAT3, and Foxp3 were determined by ELISA. The expression of PIAS3 mRNA was quantified by qPCR. Cornelian cherry extract at a dose of 100 mg/kg counteracted the TNBS-induced elevation of IL-6, RORγt, and p-STAT3 levels and a decrease in Foxp3 level and PIAS3 mRNA expression, while given concomitantly with sulfasalazine was more effective than sulfasalazine alone in reversing the TNBS-induced changes in IL-6, RORγt, total STAT3, p-STAT3, Foxp3 levels, and PIAS3 mRNA expression. The beneficial effect of cornelian cherry extract on experimental colitis may be due to its immunomodulatory activity reflected by the influence on factors regulating the Th17/Treg axis.

Clinical and genetic associations of deep learning-derived cardiac magnetic resonance-based left ventricular mass

Left ventricular mass is a risk marker for cardiovascular events, and may indicate an underlying cardiomyopathy. Cardiac magnetic resonance is the gold-standard for left ventricular mass estimation, but is challenging to obtain at scale. Here, we use deep learning to enable genome-wide association study of cardiac magnetic resonance-derived left ventricular mass indexed to body surface area within 43,230 UK Biobank participants. We identify 12 genome-wide associations (1 known at TTN and 11 novel for left ventricular mass), implicating genes previously associated with cardiac contractility and cardiomyopathy. Cardiac magnetic resonance-derived indexed left ventricular mass is associated with incident dilated and hypertrophic cardiomyopathies, and implantable cardioverter-defibrillator implant. An indexed left ventricular mass polygenic risk score ≥90th percentile is also associated with incident implantable cardioverter-defibrillator implant in separate UK Biobank (hazard ratio 1.22, 95% CI 1.05-1.44) and Mass General Brigham (hazard ratio 1.75, 95% CI 1.12-2.74) samples. Here, we perform a genome-wide association study of cardiac magnetic resonance-derived indexed left ventricular mass to identify 11 novel variants and demonstrate that cardiac magnetic resonance-derived and genetically predicted indexed left ventricular mass are associated with incident cardiomyopathy.

Rye: genetic ancestry inference at biobank scale.

Biobank projects are generating genomic data for many thousands of individuals. Computational methods are needed to handle these massive data sets, including genetic ancestry (GA) inference tools. Current methods for GA inference do not scale to biobank-size genomic datasets. We present Rye-a new algorithm for GA inference at biobank scale. We compared the accuracy and runtime performance of Rye to the widely used RFMix, ADMIXTUREand iAdmix programs and applied it to a dataset of 488221 genome-wide variant samples from the UK Biobank. Rye infers GA based on principal component analysis of genomic variant samples from ancestral reference populations and query individuals. The algorithm's accuracy is powered by Metropolis-Hastings optimization and its speed is provided by non-negative least squares regression. Rye produces highly accurate GA estimates for three-way admixed populations-African, Europeanand Native American-compared to RFMix and ADMIXTURE (${R}^2 = \ 0.998 - 1.00$), and shows 50×runtime improvement compared to ADMIXTURE on the UK Biobank dataset. Rye analysis of UK Biobank samples demonstrates how it can be used to infer GA at both continental and subcontinental levels. We discuss user consideration and options for the use of Rye; the program and its documentation are distributed on the GitHub repository: https://github.com/healthdisparities/rye.

Abstract P5-03-01: Long-term oncologic outcome of unselected triple-negative breast cancer patients according to BRCA1/2 mutations: a comprehensive single institution study

Abstract Background Triple-negative breast cancer (TNBC) is known to have a higher risk of early recurrence and relatively low risk of late recurrence compared to luminal type breast cancer. Among all subtypes of breast cancer, TNBC is more likely to have BRCA1/2 germline mutation which showed prevalence rate from about 10% to 20% in previous reports. To date, there are only few studies about the effect of BRCA1/2 mutations on the long-term oncologic prognosis in TNBC patients. We analyzed long-term oncologic outcome in unselected TNBC patients according to BRCA1/2 mutations in a comprehensive single institution. Methods Among 11,994 patients who underwent primary breast cancer surgery at Samsung Medical Center (SMC) between June 2008 and January 2016, 1,628 (13.6%) were TNBC patients. Of those, patients with inadequate and unavailable samples at SMC biobank and patients with follow-up duration less than 12 months and who had distant metastasis at presentation were excluded from the study, and 953 patients were enrolled. A retrospective study was conducted and BRCA1/2 genetic testing was done with SMC biobank samples through Next Generation Sequencing (NGS). Results Among 953 unselected TNBC patients, 122 patients (12.8%) had BRCA1/2 mutations: 91 (9.5%) were in BRCA1, and 32 (3.4%) were in BRCA2. One patient had both BRCA1/2 mutations. BRCA1/2 carriers were more likely to have personal history of ovarian cancer (9.0% vs. 0.5%, p < 0.0001), family history of breast cancer and/or ovarian cancer (40.2% vs. 9.4%, p < 0.0001), bilateral breast cancer (4.9% vs. 1.2%, p = 0.0105), and higher nuclear grade (86.0% vs. 74.0%, p = 0.0250). The median follow-up duration was 80.9 months. There were no significant differences in disease-free survival (DFS), distant metastasis-free survival (DMFS), overall survival (OS), and breast cancer-specific survival (BCSS) (p = 0.375, 0.268, 0.413, and 0.133, respectively) between BRCA1/2 carriers and non-carriers. However, BRCA1/2 carriers showed significantly worse contralateral breast cancer (CBC)-free survival than non-carriers (p < 0.0001). Sixty and 120-months cumulative recurrence rate were 18.5% and 31.2% for BRCA1/2 carriers versus 19.3% and 22.7% for non-carriers (p = 0.834 and 0.136, respectively). However, cumulative recurrence rate at 150 months showed absolute but not statistically significant difference between BRCA1/2 carriers and non-carriers (36.2% versus 23.5%, p = 0.080). Cumulative CBC recurrence rate on 60, 120- and 150-months estimates were 6.7%, 18.7% and 25.5% for BRCA1/2 carriers versus 1.1%, 2.7% and 5.2% for non-carriers which showed statistically meaningful difference (p = 0.025, 0.006 and 0.018, respectively). Sixty months, 120- and 150-months cumulative expire rate were 11.2%, 15.6% and 27.7% for BRCA1/2 carriers versus 14.3%, 20.7% and 20.7% for non-carriers (p = 0.319, 0.202 and 0.549, respectively). Discussion In this unselected cohort of patients with TNBC, we found 12.8% (122 patients among 953) prevalence of BRCA1/2 mutations. The median follow-up duration was 80.9 months. There was no significant difference in DFS, DMFS, OS and BCSS by BRCA1/2 mutation status in long-term follow up. However, BRCA1/2 carriers showed significantly worse CBC recurrence rate at 60, 120- and 150- months. And also, BRCA1/2 carriers had 12.7% higher risk of recurrence than non-carriers at 150 months, which was not statistically meaningful but showed absolute difference. Among patients with CBC recurrence, 41.3% (12 patients among 29) were BRCA1 carriers, over 85% had TNBC type of recurred CBC and approximately 80% underwent chemotherapy. In conclusion, we demonstrated that CBC recurrence risk is relatively high in TNBC patients with BRCA1 mutation and showed high chance to receive chemotherapy. Therefore, long-term follow up and appropriate genetic counseling, risk assessment should be done properly for BRCA1/2 mutation carriers in TNBC patients. Citation Format: Soo Yeon Chung, Jai Min Ryu, You Jin Jung, Yeon Jin Kim, Hye Jin Kim, Seok Jin Nam, Seok Won Kim, Jonghan Yu, Byung Joo Chae, Jeong Eon Lee, Se Kyung Lee, Sung-Won Kim, Eun Young Kim. Long-term oncologic outcome of unselected triple-negative breast cancer patients according to BRCA1/2 mutations: a comprehensive single institution study [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-03-01.

No time for complacency: The CoVaRR-Net Biobank is an essential element of laboratory preparedness for infectious disease outbreaks.

The SARS-CoV-2 pandemic highlighted the need for rapid, collaborative, and population-centric research to define health impact, develop health care policies and establish reliable diagnostic and surveillance tests. Critical for these objectives were in-depth clinical data collected in standardized fashion and large numbers of various types of human samples prior and post-viral encounter. As the pandemic evolved with the emergence of new variants of concern (VOCs), access to samples and data from infected and vaccinated individuals were needed to monitor immune durability, the possibility of increased transmissibility and virulence, and vaccine protection against new and emerging VOCs. Therefore, essential to the pandemic response is a strong laboratory and data research component, supported by effective biobanking and data sharing. Critically important to the speed of the research response is the rapid access to biobanked samples. To address critical challenges brought to light by the pandemic, the Coronavirus Variants Rapid Response Network (CoVaRR-Net), funded by the Canadian Institutes of Health Research, was established to coordinate research efforts to provide rapid evidence-based responses to emerging VOCs. The purpose of this paper is to introduce the CoVaRR-Net Biobank and define its contribution to pandemic preparedness.

Increased HIV Incidence in Wuchereria bancrofti Microfilaria Positive Individuals in Tanzania.

Infections with Wuchereria bancrofti are associated with reduced immunity against concomitant infections. Indeed, our previous study described a 2.3-fold increased HIV incidence among individuals with W. bancrofti infection, as measured by the circulating filarial antigen of the adult worm. This new study aimed to retrospectively determine microfilariae status of the participants to assess if the previously described increased HIV susceptibility was associated with the presence of MF in the same cohort. CFA positive but HIV negative biobanked human blood samples (n = 350) were analyzed for W. bancrofti MF chitinase using real time PCR. The PCR provided a positive signal in 12/350 (3.4%) samples. During four years of follow-up (1109 person years (PY)), 22 study participants acquired an HIV infection. In 39 PY of W. bancrofti MF chitinase positive individuals, three new HIV infections occurred (7.8 cases per 100 PY), in contrast to 19 seroconversions in 1070 PY of W. bancrofti MF chitinase negative individuals (1.8 cases per 100 PY, p = 0.014). In the subgroup of MF-producing Wb-infected individuals, the HIV incidence exceeded the previously described moderate increased risk for HIV seen in all Wb-infected individuals (regardless of MF status) compared with uninfected persons from the same area.

Epigenetic effects of folate and related B vitamins on brain health throughout life: Scientific substantiation and translation of the evidence for health improvement strategies.

Suboptimal status of folate and/or interrelated B vitamins (B12 , B6 and riboflavin) can perturb one-carbon metabolism and adversely affect brain development in early life and brain function in later life. Human studies show that maternal folate status during pregnancy is associated with cognitive development in the child, whilst optimal B vitamin status may help to prevent cognitive dysfunction in later life. The biological mechanisms explaining these relationships are not clear but may involve folate-related DNA methylation of epigenetically controlled genes related to brain development and function. A better understanding of the mechanisms linking these B vitamins and the epigenome with brain health at critical stages of the lifecycle is necessary to support evidence-based health improvement strategies. The EpiBrain project, a transnational collaboration involving partners in the United Kingdom, Canada and Spain, is investigating the nutrition-epigenome-brain relationship, particularly focussing on folate-related epigenetic effects in relation to brain health outcomes. We are conducting new epigenetics analysis on bio-banked samples from existing well-characterised cohorts and randomised trials conducted in pregnancy and later life. Dietary, nutrient biomarker and epigenetic data will be linked with brain outcomes in children and older adults. In addition, we will investigate the nutrition-epigenome-brain relationship in B vitamin intervention trial participants using magnetoencephalography, a state-of-the-art neuroimaging modality to assess neuronal functioning. The project outcomes will provide an improved understanding of the role of folate and related B vitamins in brain health, and the epigenetic mechanisms involved. The results are expected to provide scientific substantiation to support nutritional strategies for better brain health across the lifecycle.

Brain deficit patterns of metabolic illnesses overlap with those for major depressive disorder: A new metric of brain metabolic disease.

Metabolic illnesses (MET) are detrimental to brain integrity and are common comorbidities in patients with mental illnesses, including major depressive disorder (MDD). We quantified effects of MET on standard regional brain morphometric measures from 3D brain MRI as well as diffusion MRI in a large sample of UK BioBank participants. The pattern of regional effect sizes of MET in non-psychiatric UKBB subjects was significantly correlated with the spatial profile of regional effects reported by the largest meta-analyses in MDD but not in bipolar disorder, schizophrenia or Alzheimer's disease. We used a regional vulnerability index (RVI) for MET (RVI-MET) to measure individual's brain similarity to the expected patterns in MET in the UK Biobank sample. Subjects with MET showed a higher effect size for RVI-MET than for any of the individual brain measures. We replicated elevation of RVI-MET in a sample of MDD participants with MET versus non-MET. RVI-MET scores were significantly correlated with the volume of white matter hyperintensities, a neurological consequence of MET and age, in both groups. Higher RVI-MET in both samples was associated with obesity, tobacco smoking and frequent alcohol use but was unrelated to antidepressant use. In summary, MET effects on the brain were regionally specific and individual similarity to the pattern was more strongly associated with MET than any regional brain structural metric. Effects of MET overlapped with the reported brain differences in MDD, likely due to higher incidence of MET, smoking and alcohol use in subjects with MDD.

Increasing the security and traceability of biological samples in biobanks by blockchain technology

Background and ObjectiveOne of the main tasks in a biobank consists in storing biological samples in a high-quality condition in order to future research. At moment, there exist many applications to manage a biobank. However, in general, these are web-based applications. In these web-based applications different tasks can be done. Among them, it is possible to remark the following: informed consent, confidentiality, non-profit, respect for quality and safety standards, including traceability of samples. In this paper, we describe a blockchain smart contract to ensure the traceability of the processes done in a biobank meaning a step forward to guarantee this traceability. MethodsUse of blockchain technology to improve security, integrity and traceability of the processes carried out in a biobank. In particular IBM Hyperledger Fabric. ResultsAs a result, a set of smart contracts have been developed describing the biobank processes. ConclusionsImprovement of the security, integrity, and traceability of samples in biobanks.

Association of vitamin D status with disease severity and outcome in Indian patients with IgA nephropathy

BackgroundVitamin D deficiency has been examined as a risk factor for severity and progression of kidney disease due to its immunomodulatory effects. There is paucity of data about its impact in IgA nephropathy (IgAN).MethodsIn a retrospective cohort study, 25 (OH) vitamin D assay was performed in bio-banked baseline serum samples collected during kidney biopsy of 105 adult patients with primary IgAN diagnosed between 2015 and 2019. A level of < 10 ng/mL was defined as Vitamin D deficiency.ResultsMean age of patients was 34 ± 10.6 years, 69.5% were males. Mean baseline 25(OH) Vitamin D levels was 15.9 ± 11.9 ng/mL and 41(39%) patients had vitamin D deficiency. Serum albumin level was lower in vitamin D deficient patients compared to those who had higher vitamin D levels (3.7 ± 0.9 vs 4.1 ± 0.7 g/dl, p = 0.018)but there was no significant difference in baseline proteinuria and eGFR. Crescentic lesions were more frequent in vitamin D deficient group (19.5% vs 6.3%, p = 0.022). At median follow up of 21.5 months (6 – 56 months), there was no difference in remission (68.3% vs 65.6%, p = 0.777) and disease progression (12.5% vs 9.4%, p = 0.614) in those with and without Vitamin D deficiency respectively. On multivariate cox proportional hazard analysis, vitamin D deficiency was not a significant risk factor for renal survival (HR-1.79, 95% confidence interval:0.50–6.34, p = 0.368).ConclusionThere was no association between vitamin D deficiency and disease profile as well as renal outcome in Indian patients with IgAN.

ScONE-seq: A single-cell multi-omics method enables simultaneous dissection of phenotype and genotype heterogeneity from frozen tumors.

Single-cell multi-omics can provide a unique perspective on tumor cellular heterogeneity. Most previous single-cell whole-genome RNA sequencing (scWGS-RNA-seq) methods demonstrate utility with intact cells from fresh samples. Among them, many are not applicable to frozen samples that cannot produce intact single-cell suspensions. We have developed scONE-seq, a versatile scWGS-RNA-seq method that amplifies single-cell DNA and RNA without separating them from each other and hence is compatible with frozen biobanked samples. We benchmarked scONE-seq against existing methods using fresh and frozen samples to demonstrate its performance in various aspects. We identified a unique transcriptionally normal-like tumor clone by analyzing a 2-year frozen astrocytoma sample, demonstrating that performing single-cell multi-omics interrogation on biobanked tissue by scONE-seq could enable previously unidentified discoveries in tumor biology.

Pediatric leukemia biobank sample storage audit in a resource constraint setting: A 7-year story of 1000’s of samples

Pediatric leukemia biobank sample storage audit in a resource constraint setting: A 7-year story of 1000’s of samples

A quantified comparison of cortical atlases on the basis of trait morphometricity.

Many different brain atlases exist that subdivide the human cortex into dozens or hundreds of regions-of-interest (ROIs). Inconsistency across studies using one or another cortical atlas may contribute to the replication crisis across the neurosciences. Here, we provide a quantitative comparison between seven popular cortical atlases (Yeo, Desikan-Killiany, Destrieux, Jülich-Brain, Gordon, Glasser, Schaefer) and vertex-wise measures (thickness, surface area, and volume), to determine which parcellation retains the most information in the analysis of behavioural traits (incl. age, sex, body mass index, and cognitive ability) in the UK Biobank sample (N∼40,000). We use linear mixed models to compare whole-brain morphometricity; the proportion of trait variance accounted for when using a given atlas. Commonly-used atlases resulted in a considerable loss of information compared to vertex-wise representations of cortical structure. Morphometricity increased linearly as a function of the log-number of ROIs included in an atlas, indicating atlas-based analyses miss many true associations and yield limited prediction accuracy. Likelihood ratio tests revealed that low-dimensional atlases accounted for unique trait variance rather than variance common between atlases, suggesting that previous studies likely returned atlas-specific findings. Finally, we found that the commonly-used atlases yielded brain-behaviour associations on par with those obtained with random parcellations, where specific region boundaries were randomly generated. Our findings motivate future structural neuroimaging studies to favour vertex-wise cortical representations over coarser atlases, or to consider repeating analyses across multiple atlases, should the use of low-dimensional atlases be necessary. The insights uncovered here imply that cortical atlas choices likely contribute to the lack of reproducibility in ROI-based studies.

A genome-wide association study of tinnitus reveals shared genetic links to neuropsychiatric disorders

Tinnitus, a phantom perception of sound in the absence of any external sound source, is a prevalent health condition often accompanied by psychiatric comorbidities. Recent genome-wide association studies (GWAS) highlighted a polygenic nature of tinnitus susceptibility. A shared genetic component between tinnitus and psychiatric conditions remains elusive. Here we present a GWAS using the UK Biobank to investigate the genetic processes linked to tinnitus and tinnitus-related distress, followed by gene-set enrichment analyses. The UK Biobank sample comprised 132,438 individuals with tinnitus and genotype data. Among the study sample, 38,525 individuals reported tinnitus, and 26,889 participants mentioned they experienced tinnitus-related distress in daily living. The genome-wide association analyses were conducted on tinnitus and tinnitus-related distress. We conducted enrichment analyses using FUMA to further understand the genetic processes linked to tinnitus and tinnitus-related distress. A genome-wide significant locus (lead SNP: rs71595470) for tinnitus was obtained in the vicinity of GPM6A. Nineteen independent loci reached suggestive association with tinnitus. Fifteen independent loci reached suggestive association with tinnitus-related distress. The enrichment analysis revealed a shared genetic component between tinnitus and psychiatric traits, such as bipolar disorder, feeling worried, cognitive ability, fast beta electroencephalogram, and sensation seeking. Metabolic, cardiovascular, hematological, and pharmacological gene sets revealed a significant association with tinnitus. Anxiety and stress-related gene sets revealed a significant association with tinnitus-related distress. The GWAS signals for tinnitus were enriched in the hippocampus and cortex, and for tinnitus-related distress were enriched in the brain and spinal cord. This study provides novel insights into genetic processes associated with tinnitus and tinnitus-related distress and demonstrates a shared genetic component underlying tinnitus and psychiatric conditions. Further collaborative attempts are necessary to identify genetic components underlying the phenotypic heterogeneity in tinnitus and provide biological insight into the etiology.