Characteristics and utilisation of the Mayo Clinic Biobank, a clinic-based prospective collection in the USA: cohort profile

Prevalence and associations of multiple hypnotic prescriptions in a clinical sample

STUDY OBJECTIVES

We examined the prevalence of multiple hypnotic prescriptions and its association with clinical and demographic characteristics from the electronic health record (EHR) in the Mayo Clinic Biobank.

METHODS

Adult participants enrolled in the Mayo Clinic Biobank with an EHR number of ≥ 1 year were included (n = 52,940). Clinical and demographic characteristics were compared between participants who were and were not prescribed any hypnotic approved for insomnia by the US Food and Drug Administration and/or trazodone and in those prescribed a single vs multiple (≥ 2) hypnotics. A phenotype-based, phenome-wide association study (PheWAS) examining associations between hypnotic prescriptions and diagnoses across the EHR was performed adjusting for demographic and other confounders.

RESULTS

A total of 17,662 (33%) participants were prescribed at least 1 hypnotic and 5,331 (10%) received ≥ 2 hypnotics. Participants who were prescribed a hypnotic were more likely to be older, female, White, with a longer EHR, and a greater number of diagnostic codes (all P < .001). Those with multiple hypnotic prescriptions were more likely to be younger, female, with a longer EHR, and a greater number of diagnostic codes (all P < .001) compared with those prescribed a single hypnotic. The PheWAS revealed that participants with multiple hypnotic prescriptions had higher rates of mood disorders, anxiety disorders, suicidal ideation, restless legs syndrome, and chronic pain (all P < 1 e-10).

CONCLUSIONS

Receiving multiple hypnotic prescriptions is common and associated with a greater prevalence of psychiatric, chronic pain, and sleep-related movement disorders. Future studies should examine potential genetic associations with multiple hypnotic prescriptions to personalize treatments for chronic insomnia.

CITATION

Kolla BP, Mansukhani MP, Chakravorty S, Frank JA, Coombes BJ. Prevalence and associations of multiple hypnotic prescriptions in a clinical sample. J Clin Sleep Med. 2024;20(5):793-800.

Community Outreach and Engagement in Cancer Research Through a Biobank Clinic at Shaukat Khanum Memorial Cancer Hospital and Research Centre, Pakistan

INTRODUCTION

Cancer's increasing prevalence across the globe emphasizes the urgency for continued research, prevention, and accessible healthcare to mitigate its impact on individuals and communities. While there have been significant advances made towards controlling cancer morbidity and mortality in recent decades, Pakistan continues to experience a markedly elevated burden of the disease. With this study, we aim to raise awareness about biobank research within the cancer patient community, fostering participation and collaboration to advance the fight against cancer through vital research contributions.

METHODS

In October 2022, we initiated the biobank clinic at Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC). Here, patients underwent screening and received invitations to voluntarily participate in biobank research. During these interactions, we engaged patients in discussions about the significance of biobank research, addressed their concerns, and encouraged their participation in advancing our research endeavors. Two-sample independent t-tests were performed to compare the mean number of participants in pre-clinic and post-clinic cohorts.

RESULTS

This research involved a total of 958 participants, with 312 participants enrolled before the clinic and 646 participants enrolled after the clinic. We have observed a noticeable increase in the participation of cancer patients in our research endeavors since the inception of the biobank clinic (p-value<0.001). Over an 11-month time frame, we scheduled appointments for 759 patients, and out of those, 656 patients availed themselves to visit the clinic. Impressively, we achieved the enrollment of 646 patients into the clinic, reflecting an exceptional consent rate of 98.47% for their active involvement in our research initiatives. This underscores our commitment to conducting comprehensive discussions and providing thorough explanations regarding the ethical and procedural aspects of our research.

CONCLUSION

Biobank clinic plays a pivotal role in raising cancer awareness and fostering research participation, especially in regions with limited healthcare infrastructure and lower literacy rates. It emerges as a community-engagement model that aligns research with local needs, ensuring its relevance and benefit to the population.

High-Dimensional Clustering of 4000 Irritable Bowel Syndrome Patients Reveals Seven Distinct Disease Subsets

BACKGROUND AND AIMS

Irritable bowel syndrome (IBS) is a pain disorder classified by bowel habits, disregarding other factors that may influence the clinical course. The aim of this study was to determine if IBS patients can be clustered based on clinical, dietary, lifestyle, and psychosocial factors.

METHODS

Between 2013 and 2020, the Mayo Clinic Biobank surveyed and received 40,291 responses to a questionnaire incorporating Rome III criteria. Factors associated with IBS were determined and latent class analysis, a model-based clustering, was performed on IBS cases.

RESULTS

We identified 4021 IBS patients (mean 64 years; 75% women) and 12,063 controls. Using 26 variables separating cases from controls, the optimal clustering revealed 7 latent clusters. These were characterized by perceived health impairment (moderate or severe), psychoneurological factors, and bowel dysfunction (diarrhea or constipation predominance). Health impairment clusters demonstrated more pain, with the severe cluster also having more psychiatric comorbidities. The next 3 clusters had unique enrichment of psychiatric, neurological, or both comorbidities. The bowel dysfunction clusters demonstrated less abdominal pain, with diarrhea cluster most likely to report pain improvement with defecation. The constipation cluster had the highest exercise score and consumption of fruits, vegetables, and alcohol. The distribution of clusters remained similar when Rome IV criteria were applied. Physiologic tests were available on a limited subset (6%), and there were no significant differences between clusters.

CONCLUSIONS

In this cohort of older IBS patients, 7 distinct clusters were identified demonstrating varying degrees of gastrointestinal symptoms, comorbidities, dietary, and lifestyle factors. Further research is required to assess whether these unique clusters could be used to direct clinical trials and individualize patient management.

Phenotypic distinctions in depression and anxiety: a comparative analysis of comorbid and isolated cases

BACKGROUND

Anxiety and depression are frequently comorbid yet phenotypically distinct. This study identifies differences in the clinically observable phenome across a wide variety of physical and mental disorders comparing patients with diagnoses of depression without anxiety, anxiety without depression, or both depression and anxiety.

METHODS

Using electronic health records for 14 994 participants with depression and/or anxiety in the Mayo Clinic Biobank, a phenotype-based phenome-wide association study (Phe2WAS) was performed to test for differences between these groups across a broad range of clinical diagnoses observed in the electronic health record. Additional analyses were performed to determine the temporal sequencing of diagnoses.

RESULTS

Compared to patients diagnosed only with anxiety, those diagnosed only with depression were more likely to have diagnoses of obesity (OR 1.75; p = 1 × 10-27), sleep apnea (OR 1.71; p = 1 × 10-22), and type II diabetes (OR 1.74; p = 9 × 10-18). Compared to those diagnosed only with depression, those diagnosed only with anxiety were more likely to have diagnoses of palpitations (OR 1.91; p = 2 × 10-25), benign skin neoplasms (OR 1.61; p = 2 × 10-17), and cardiac dysrhythmias (OR 1.45; p = 2 × 10-12). Patients with comorbid depression and anxiety were more likely to have diagnoses of other mental health disorders, substance use disorders, sleep problems, and gastroesophageal reflux relative to isolated depression.

CONCLUSIONS

While depression and anxiety are closely related, this study suggests that phenotypic distinctions exist between depression and anxiety. Improving phenotypic characterization within the broad categories of depression and anxiety could improve the clinical assessment of depression and anxiety.

A large meta-analysis identifies genes associated with anterior uveitis

Anterior Uveitis (AU) is the inflammation of the anterior part of the eye, the iris and ciliary body and is strongly associated with HLA-B*27. We report AU exome sequencing results from eight independent cohorts consisting of 3,850 cases and 916,549 controls. We identify common genome-wide significant loci in HLA-B (OR = 3.37, p = 1.03e-196) and ERAP1 (OR = 0.86, p = 1.1e-08), and find IPMK (OR = 9.4, p = 4.42e-09) and IDO2 (OR = 3.61, p = 6.16e-08) as genome-wide significant genes based on the burden of rare coding variants. Dividing the cohort into HLA-B*27 positive and negative individuals, we find ERAP1 haplotype is strongly protective only for B*27-positive AU (OR = 0.73, p = 5.2e-10). Investigation of B*27-negative AU identifies a common signal near HLA-DPB1 (rs3117230, OR = 1.26, p = 2.7e-08), risk genes IPMK and IDO2, and several additional candidate risk genes, including ADGFR5, STXBP2, and ACHE. Taken together, we decipher the genetics underlying B*27-positive and -negative AU and identify rare and common genetic signals for both subtypes of disease.

Age-Dependent Sex Differences in the Prevalence of Selective Serotonin Reuptake Inhibitor Treatment: A Retrospective Cohort Analysis

Background: Antidepressants are among the most prescribed medications in the United States. The aim of this study was to explore the prevalence of antidepressant prescriptions and investigate sex differences and age-sex interactions in adults enrolled in the Right Drug, Right Dose, Right Time: Using Genomic Data to Individualize Treatment (RIGHT) study. Materials and Methods: We conducted a retrospective analysis of the RIGHT study. Using electronic prescriptions, we assessed 12-month prevalence of antidepressant treatment. Sex differences and age-sex interactions were evaluated using multivariable logistic regression and flexible recursive smoothing splines. Results: The sample consisted of 11,087 participants (60% women). Antidepressant prescription prevalence was 22.24% (27.96% women, 13.58% men). After adjusting for age and enrollment year, women had significantly greater odds of antidepressant prescription (odds ratio = 2.29; 95% confidence interval = 2.07, 2.54). Furthermore, selective serotonin reuptake inhibitors (SSRIs) had a significant age-sex interaction. While SSRI prescriptions in men showed a sustained decrease with age, there was no such decline for women until after reaching ∼50 years of age. There are important limitations to consider in this study. Electronic prescription data were cross-sectional; information on treatment duration or adherence was not collected; this cohort is not nationally representative; and enrollment occurred over a broad period, introducing confounding by changes in temporal prescribing practices. Conclusions: Underscored by the significant interaction between age and sex on odds of SSRI prescription, our results warrant age to be incorporated as a mediator when investigating sex differences in mental illness, especially mood disorders and their treatment.

CWH43 Variants Are Associated With Disease Risk and Clinical Phenotypic Measures in Patients With Normal Pressure Hydrocephalus

Background and Objectives

Variants in the CWH43 gene have been associated with normal pressure hydrocephalus (NPH). We aimed to replicate these findings, identify additional CWH43 variants, and further define the clinical phenotype associated with CWH43 variants.

Methods

We determined the prevalence of CWH43 variants by whole-genome sequencing (WGS) in 94 patients with NPH. The odds of having CWH43 variant carriers develop NPH were determined through comparison with 532 Mayo Clinic Biobank volunteers without a history of NPH. For patients with NPH, we documented the head circumference, prevalence of disproportionate enlargement of subarachnoid hydrocephalus (DESH), microvascular changes on MRI quantified by the Fazekas scale, and ambulatory response to ventriculoperitoneal shunting.

Results

We identified rare (MAF <0.05) coding CWH43 variants in 15 patients with NPH. Ten patients (Leu533Terfs, n = 8; Lys696Asnfs, n = 2) harbored previously reported predicted loss-of-function variants, and combined burden analysis confirmed risk association with NPH (OR 2.60, 95% CI 1.12-6.03, p = 0.027). Additional missense variations observed included Ile292Thr (n = 2), Ala469Ser (n = 2), and Ala626Val (n = 1). Though not quite statistically significant, in single variable analysis, the odds of having a head circumference above the 75th percentile of normal controls was more than 5 times higher for CWH43 variant carriers compared with that for noncarriers (unadjusted OR 5.67, 95% CI 0.96-108.55, p = 0.057), and this was consistent after adjusting for sex and height (OR 5.42, 95% CI 0.87-106.37, p = 0.073). DESH was present in 56.7% of noncarriers and only 21.4% of carriers (p = 0.016), while sulcal trapping was also more prevalent among noncarriers (67.2% vs 35.7%, p = 0.030). All 8 of the 15 variant carriers who underwent ventriculoperitoneal shunting at our institution experienced ambulatory improvements.

Discussion

CWH43 variants are frequent in patients with NPH. Predicted loss-of-function mutations were the most common; we identified missense mutations that require further study. Our findings suggest that congenital factors, rather than malabsorption or vascular dysfunction, are primary contributors to the CWH43-related NPH clinical syndrome.

A Rapid Review on the Value of Biobanks Containing Genetic Information

OBJECTIVES

Increasing access to health data through biobanks containing genetic information has the potential to expand the knowledge base and thereby improve screening, diagnosis, and treatment options for many diseases. Nevertheless, although privacy concerns and risks surrounding genetic data sharing are well documented, direct evidence in favor of the hypothesized benefits of data integration is scarce, which complicates decision making in this area. Therefore, the objective of this study is to summarize the available evidence on the research and clinical impacts of biobanks containing genetic information, so as to better understand how to quantify the value of expanding genomic data access.

METHODS

Using a rapid review methodology, we performed a search of MEDLINE/PubMed and Embase databases; and websites of biobanks and genomic initiatives published from 2010 to 2022. We classified findings into 11 indicators including outputs (a direct product of the biobank activities) and outcomes (changes in scientific and clinical capacity).

RESULTS

Of 8479 abstracts and 101 gray literature sources were reviewed, 96 records were included. Although most records did not report key indicators systematically, the available evidence concentrated on research indicators such as publications and gene-disorder association discoveries (63% of studies), followed by research infrastructure (26%), and clinical indicators (11%) such as supporting the diagnosis of individual patients.

CONCLUSIONS

Existing evidence on the benefits of biobanks is skewed toward easily quantifiable research outputs. Measuring a comprehensive set of outputs and outcomes inspired by value frameworks is necessary to generate better evidence on the benefits of genomic data sharing.

Batch-effect correction with sample remeasurement in highly confounded case-control studies

Batch effects are pervasive in biomedical studies. One approach to address the batch effects is repeatedly measuring a subset of samples in each batch. These remeasured samples are used to estimate and correct the batch effects. However, rigorous statistical methods for batch-effect correction with remeasured samples are severely underdeveloped. Here we developed a framework for batch-effect correction using remeasured samples in highly confounded case-control studies. We provided theoretical analyses of the proposed procedure, evaluated its power characteristics and provided a power calculation tool to aid in the study design. We found that the number of samples that need to be remeasured depends strongly on the between-batch correlation. When the correlation is high, remeasuring a small subset of samples is possible to rescue most of the power.

Multitarget Stool DNA Testing Has High Positive Predictive Value for Colorectal Neoplasia on the Second Round of Testing

BACKGROUND & AIMS

Multitarget stool DNA (mt-sDNA) testing is a stool-based screening test for colorectal cancer (CRC). In a single instance of testing, the pivotal Food and Drug Administration-approval study (NCT01397747) found that 16% of mt-sDNA tests were positive, and the positive predictive value (PPV) for CRC or advanced precursor lesions (APL) was 27.3%. We aimed to examine real-world longitudinal performance by determining the test-positive rate and PPV of mt-sDNA on the second round of testing.

METHODS

Colonoscopy and pathology reports were reviewed retrospectively for patients with a negative mt-sDNA on the first round of screening and a positive mt-sDNA on the second round. The test-positivity rate and PPV for CRC, APL, and any colorectal neoplasia were calculated for the second mt-sDNA and compared with baseline PPVs from a previously published cohort of patients from our institution who tested positive on the first round of screening.

RESULTS

A total of 2758 patients completed a second test at a median of 3.2 years after the first test. Of these, 422 (15%) had a positive second mt-sDNA. The PPV was 0.25% for CRC, 24% for APL, and 67% for any colorectal neoplasia. There was no significant difference in PPV on the second mt-sDNA test compared with the first round (24% vs 28% for APL; P = .12).

CONCLUSIONS

mt-sDNA test positive rate and PPV were similar between the first and second rounds of screening. These observations confirm the utility of a second round of mt-sDNA screening and may inform estimates of mt-sDNA effectiveness for CRC screening.

Cohort study examining associations between ceramide levels and risk of multimorbidity among persons participating in the Mayo Clinic Biobank

OBJECTIVE

Ceramides have been associated with several ageing-related conditions but have not been studied as a general biomarker of multimorbidity (MM). Therefore, we determined whether ceramide levels are associated with the rapid development of MM.

DESIGN

Retrospective cohort study.

SETTING

Mayo Clinic Biobank.

PARTICIPANTS

1809 persons in the Mayo Clinic Biobank ≥65 years without MM at the time of enrolment, and with ceramide levels assayed from stored plasma.

PRIMARY OUTCOME MEASURE

Persons were followed for a median of 5.7 years through their medical records to identify new diagnoses of 20 chronic conditions. The number of new conditions was divided by the person-years of follow-up to calculate the rate of accumulation of new chronic conditions.

RESULTS

Higher levels of C18:0 and C20:0 were associated with a more rapid rate of accumulation of chronic conditions (C18:0 z score RR: 1.30, 95% CI: 1.10 to 1.53; C20:0 z score RR: 1.26, 95% CI: 1.07 to 1.49). Higher C18:0 and C20:0 levels were also associated with an increased risk of hypertension and coronary artery disease.

CONCLUSIONS

C18:0 and C20:0 were associated with an increased risk of cardiometabolic conditions. When combined with biomarkers specific to other diseases of ageing, these ceramides may be a useful component of a biomarker panel for predicting accelerated ageing.

Cardiovascular Risk and Diseases in Patients With and Without Leptin-Melanocortin Pathway Variants

OBJECTIVE

To study differences in cardiovascular risk factors and diseases between patients with and without genetic variants in the leptin-melanocortin pathway.

METHODS

A cross-sectional study of patients with a history of severe obesity genotyped in June 2019 as participants of the Mayo Clinic Biobank was conducted in March 2022 to assess differences in cardiovascular risk and diseases between carriers of a heterozygous variant in the leptin-melanocortin pathway and noncarriers. Cardiovascular risk factors included hypertension, diabetes, dyslipidemia, and smoking. Cardiovascular disease includes coronary artery disease, peripheral artery disease, and cerebrovascular accidents. Patients with a history of bariatric surgery were excluded. We used logistic regression models to estimate the odds ratio and 95% CI, adjusting for age, body mass index (BMI), and sex.

RESULTS

Among a total of 168 carriers (8%; 121 [72%] female; mean [SD] age, 65.1 [14.9] years; BMI, 44.0 [7.4] kg/m2) and 2039 noncarriers (92%; 1446 [71%] female; mean [SD] age, 64.9 [14.4] years; BMI, 42.9 [6.6] kg/m2), carriers had higher prevalence odds of hypertension (odds ratio, 3.26; 95% CI, 2.31 to 4.61; P<.001) and reported higher number of cardiovascular risk factors compared with noncarriers (2.4 [1.1] vs 2.0 [1.1]; P<.001). There were no significant differences in the adjusted odds associated with diabetes, dyslipidemia, smoking, or cardiovascular disease.

CONCLUSION

Despite having similar body weight and BMI, carriers of heterozygous variants in the leptin-melanocortin pathway had higher rates of hypertension than noncarriers. These findings point to an association between hypertension and leptin-melanocortin pathway variants.

The importance of social activity to risk of major depression in older adults

BACKGROUND

Several social determinants of health (SDoH) have been associated with the onset of major depressive disorder (MDD). However, prior studies largely focused on individual SDoH and thus less is known about the relative importance (RI) of SDoH variables, especially in older adults. Given that risk factors for MDD may differ across the lifespan, we aimed to identify the SDoH that was most strongly related to newly diagnosed MDD in a cohort of older adults.

METHODS

We used self-reported health-related survey data from 41 174 older adults (50-89 years, median age = 67 years) who participated in the Mayo Clinic Biobank, and linked ICD codes for MDD in the participants' electronic health records. Participants with a history of clinically documented or self-reported MDD prior to survey completion were excluded from analysis (N = 10 938, 27%). We used Cox proportional hazards models with a gradient boosting machine approach to quantify the RI of 30 pre-selected SDoH variables on the risk of future MDD diagnosis.

RESULTS

Following biobank enrollment, 2073 older participants were diagnosed with MDD during the follow-up period (median duration = 6.7 years). The most influential SDoH was perceived level of social activity (RI = 0.17). Lower level of social activity was associated with a higher risk of MDD [hazard ratio = 2.27 (95% CI 2.00-2.50) for highest v. lowest level].

CONCLUSION

Across a range of SDoH variables, perceived level of social activity is most strongly related to MDD in older adults. Monitoring changes in the level of social activity may help identify older adults at an increased risk of MDD.

Positive association between research competitiveness of Chinese academic hospitals and the scale of their biobanks: A national survey

Biobanks are important research infrastructure developed rapidly by Chinese hospitals. The objective of this study is to investigate the association between the comprehensive research competitiveness of hospitals and the development of hospital biobanks. In 2018, we conducted a national survey among Chinese biobank managers and directors. An online questionnaire was used to collect data of biobank characteristics. Of the 70 academic hospital biobanks responded to our survey, 49 of their hospitals were listed in the Science and Technology Evaluation Metrics (STEM) and 46 of their hospitals were listed in the Fudan Hospital Rankings, respectively, in 2018. Hospital scores from the STEM and Fudan Hospital Rankings were identified from their official websites. Multivariate linear regression analyses were used to assess the associations of STEM scores and Fudan Hospital Rankings with the scale of biobanks. The overall STEM score, Scientific and Technological Output, and Academic Impact in hospitals with large-scale biobanks were 48.35%, 55.16%, and 58.65% higher than those with small-scale biobanks, respectively. The scale of biobanks was positively associated with STEM score (β = 0.367, p = 0.009), Scientific and Technological Output (β = 0.441, p = 0.001), and Academic Impact (β = 0.304, p = 0.044) after adjustment for potential confounders. For Fudan Hospital Rankings, the comprehensive score and sustainable development ability score were higher in hospitals with large-scale biobanks. Further analyses showed that the scale of the biobanks was positively associated with a higher comprehensive score (β = 0.313, p = 0.037) and a sustainable development ability score (β = 0.463, p < 0.001). The scale of hospital biobanks was positively associated with the research competitiveness of Chinese hospitals.

Employment Characteristics and Risk of Hospitalization Among Older Adults Participating in the Mayo Clinic Biobank

Objective

To determine the relationship between characteristics of employment and future hospitalization in older adults.

Patients and Methods

We conducted a survey of adults aged 65 years or older participating in the Mayo Clinic Biobank. Using a frequency-matched, case-control design, we compared patients who were hospitalized within 5 years of biobank enrollment (cases) with those who were not hospitalized (controls). We assessed the duration of work, age at first job, number of jobs, disability, retirement, and reasons for leaving work. We performed logistic regression analysis to assess the association of these factors with hospitalization, accounting for age, sex, comorbid conditions, and education level.

Results

Among 3536 participants (1600 cases and 1936 controls; median age, 68.5 years; interquartile range, 63.4-73.9 years), cases were older, more likely to be male, and had lower education levels. Comorbid illnesses had the largest association with hospitalization (odds ratio [OR], 4.09; 95% CI, 3.37-4.97 [highest vs lowest quartile]). On adjusted analyses, odds of hospitalization increased with the presence of disability (OR, 1.31; 95% CI, 1.01-1.69) and decreased with having 1 or 2 lifetime jobs vs no employment (OR, 0.77; 95% CI, 0.60-1.00). The length of work, furlough, age of retirement, childcare issues, and reasons for leaving a job were not associated with hospitalization.

Conclusion

This study reports an association between disability during work and hospitalization. On the basis of our findings, it may be important to obtain a more detailed work history from patients because it may provide further insight into their future health.

Progression and survival of MBL: a screening study of 10 139 individuals

Monoclonal B-cell lymphocytosis (MBL) is a common hematological premalignant condition that is understudied in screening cohorts. MBL can be classified into low-count (LC) and high-count (HC) types based on the size of the B-cell clone. Using the Mayo Clinic Biobank, we screened for MBL and evaluated its association with future hematologic malignancy and overall survival (OS). We had a two-stage study design including discovery and validation cohorts. We screened for MBL using an eight-color flow-cytometry assay. Medical records were abstracted for hematological cancers and death. We used Cox regression to evaluate associations and estimate hazard ratios and 95% confidence intervals (CIs), adjusting for age and sex. We identified 1712 (17%) individuals with MBL (95% LC-MBL), and the median follow-up time for OS was 34.4 months with 621 individuals who died. We did not observe an association with OS among individuals with LC-MBL (P = .78) but did among HC-MBL (hazard ratio, 1.8; 95% CI, 1.1-3.1; P = .03). Among the discovery cohort with a median of 10.0 years follow-up, 31 individuals developed hematological cancers with two-thirds being lymphoid malignancies. MBL was associated with 3.6-fold risk of hematological cancer compared to controls (95% CI, 1.7-7.7; P < .001) and 7.7-fold increased risk for lymphoid malignancies (95% CI:3.1-19.2; P < .001). LC-MBL was associated with 4.3-fold risk of lymphoid malignancies (95% CI, 1.4-12.7; P = .009); HC-MBL had a 74-fold increased risk (95% CI, 22-246; P < .001). In this large screening cohort, we observed similar survival among individuals with and without LC-MBL, yet individuals with LC-MBL have a fourfold increased risk of lymphoid malignancies. Accumulating evidence indicates that there are clinical consequences to LC-MBL, a condition that affects 8 to 10 million adults in the United States.

Biobanking potential for biomedical research in endocrinology

Biobanking is an actively developing scientific area that provides tools for conducting biomedical research, increasing the reliability and reproducibility of their results. In endocrinology, more and more attention is paid to the study of molecular and genetic markers of diseases for the selection of new points of influence in treatment, the development of targeted therapy and a strategy for personalized prevention. This approach is designed to solve the problems of endocrine disorders, their complications, causing significant damage to the individual and he population health, and reduce the financial burden of chronic endocrine disorders. To increase the reliability and reproducibility of research results, requirements for working with biological material should be strictly complied. The use of biobanking will increase the validity of data obtained in clinical trials in endocrinology. There are successful examples of Russian and foreign studies using the capabilities of biobanks aimed at studying diabetes, polycystic ovary syndrome, adenomas and other endocrine disorders. The article discusses the prospects for partnership with biobanks in the framework of endocrinology research. The purpose of this review is to analyze the literature to systematize knowledge for application of biobanking in biomedical research in the field of endocrinology.

Development of a multiomics model for identification of predictive biomarkers for COVID-19 severity: a retrospective cohort study

BACKGROUND

COVID-19 is a multi-system disorder with high variability in clinical outcomes among patients who are admitted to hospital. Although some cytokines such as interleukin (IL)-6 are believed to be associated with severity, there are no early biomarkers that can reliably predict patients who are more likely to have adverse outcomes. Thus, it is crucial to discover predictive markers of serious complications.

METHODS

In this retrospective cohort study, we analysed samples from 455 participants with COVID-19 who had had a positive SARS-CoV-2 RT-PCR result between April 14, 2020, and Dec 1, 2020 and who had visited one of three Mayo Clinic sites in the USA (Minnesota, Arizona, or Florida) in the same period. These participants were assigned to three subgroups depending on disease severity as defined by the WHO ordinal scale of clinical improvement (outpatient, severe, or critical). Our control cohort comprised of 182 anonymised age-matched and sex-matched plasma samples that were available from the Mayo Clinic Biorepository and banked before the COVID-19 pandemic. We did a deep profiling of circulatory cytokines and other proteins, lipids, and metabolites from both cohorts. Most patient samples were collected before, or around the time of, hospital admission, representing ideal samples for predictive biomarker discovery. We used proximity extension assays to quantify cytokines and circulatory proteins and tandem mass spectrometry to measure lipids and metabolites. Biomarker discovery was done by applying an AutoGluon-tabular classifier to a multiomics dataset, producing a stacked ensemble of cutting-edge machine learning algorithms. Global proteomics and glycoproteomics on a subset of patient samples with matched pre-COVID-19 plasma samples was also done.

FINDINGS

We quantified 1463 cytokines and circulatory proteins, along with 902 lipids and 1018 metabolites. By developing a machine-learning-based prediction model, a set of 102 biomarkers, which predicted severe and clinical COVID-19 outcomes better than the traditional set of cytokines, were discovered. These predictive biomarkers included several novel cytokines and other proteins, lipids, and metabolites. For example, altered amounts of C-type lectin domain family 6 member A (CLEC6A), ether phosphatidylethanolamine (P-18:1/18:1), and 2-hydroxydecanoate, as reported here, have not previously been associated with severity in COVID-19. Patient samples with matched pre-COVID-19 plasma samples showed similar trends in muti-omics signatures along with differences in glycoproteomics profile.

INTERPRETATION

A multiomic molecular signature in the plasma of patients with COVID-19 before being admitted to hospital can be exploited to predict a more severe course of disease. Machine learning approaches can be applied to highly complex and multidimensional profiling data to reveal novel signatures of clinical use. The absence of validation in an independent cohort remains a major limitation of the study.

FUNDING

Eric and Wendy Schmidt.

The Implication of Latent Information Quality to the Reproducibility of Secondary Use of Electronic Health Records

Reproducibility is an important quality criterion for the secondary use of electronic health records (EHRs). However, multiple barriers to reproducibility are embedded in the heterogeneous EHR environment. These barriers include complex processes for collecting and organizing EHR data and dynamic multi-level interactions occurring during information use (e.g., inter-personal, inter-system, and cross-institutional). To ensure reproducible use of EHRs, we investigated four information quality dimensions and examine the implications for reproducibility based on a real-world EHR study. Four types of IQ measurements suggested that barriers to reproducibility occurred for all stages of secondary use of EHR data. We discussed our recommendations and emphasized the importance of promoting transparent, high-throughput, and accessible data infrastructures and implementation best practices (e.g., data quality assessment, reporting standard).

Prevalence of Heavy Chain MGUS by Race and Family History Risk Groups Using a High Sensitivity Screening Method

The mass spectrometry assay found over threefold numbers of individuals with MGUS than gel-based assays across 3 risk groups.

Relative differences in MGUS using the sensitive mass spectrometry assay were similar by race, family history, and age as prior MGUS studies.

Mass-spectrometry (MS) assays detect lower levels of monoclonal proteins and result in earlier detection of monoclonal gammopathy of undetermined significance (MGUS). We examined heavy chain MGUS prevalence using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS among 3 risk groups, ages 50 or older: 327 African Americans (AA) and 1223 European Americans (EA) from a clinical biobank and 1093 unaffected first-degree relatives (FDR) of patients with hematologic disorders. Age- and sex-adjusted prevalence rates were directly standardized to 2010 United States population. Prevalence ratios were estimated for comparisons of AA and FDR to the EA group using the Poisson distribution. Results were also compared with population-based prevalence using conventional gel-based methods. Risk groups had similar sex and age distributions. MALDI-TOF MGUS prevalence was higher in the AA (16.5% [95% confidence interval (CI), 12.2%, 20.8%]) and FDR (18.3% [95% CI, 16.6%, 21.6%]) than in EA (10.8% [95% CI, 8.8%, 12.7%]), translating to prevalence ratios of 1.73 (95% CI, 1.31, 2.29) and 1.90 (95% CI, 1.55, 2.34), respectively. MALDI-TOF EA prevalence was over threefold higher than conventional estimates but showed similar age trends. Thus, the MALDI-TOF assay found greater numbers with MGUS but similar relative differences by race, family history, and age as prior studies.

A hybrid model to identify fall occurrence from electronic health records

INTRODUCTION

Falls are a leading cause of unintentional injury in the elderly. Electronic health records (EHRs) offer the unique opportunity to develop models that can identify fall events. However, identifying fall events in clinical notes requires advanced natural language processing (NLP) to simultaneously address multiple issues because the word "fall" is a typical homonym.

METHODS

We implemented a context-aware language model, Bidirectional Encoder Representations from Transformers (BERT) to identify falls from the EHR text and further fused the BERT model into a hybrid architecture coupled with post-hoc heuristic rules to enhance the performance. The models were evaluated on real world EHR data and were compared to conventional rule-based and deep learning models (CNN and Bi-LSTM). To better understand the ability of each approach to identify falls, we further categorize fall-related concepts (i.e., risk of fall, prevention of fall, homonym) and performed a detailed error analysis.

RESULTS

The hybrid model achieved the highest f1-score on sentence (0.971), document (0.985), and patient (0.954) level. At the sentence level (basic data unit in the model), the hybrid model had 0.954, 1.000, 0.988, and 0.999 in sensitivity, specificity, positive predictive value, and negative predictive value, respectively. The error analysis showed that that machine learning-based approaches demonstrated higher performance than a rule-based approach in challenging cases that required contextual understanding. The context-aware language model (BERT) slightly outperformed the word embedding approach trained on Bi-LSTM. No single model yielded the best performance for all fall-related semantic categories.

CONCLUSION

A context-aware language model (BERT) was able to identify challenging fall events that requires context understanding in EHR free text. The hybrid model combined with post-hoc rules allowed a custom fix on the BERT outcomes and further improved the performance of fall detection.

Lay understandings of drug-gene interactions: The right medication, the right dose, at the right time, but what are the right words?

As pharmacogenomic (PGx) testing increases in popularity, lay concepts of drug‐gene interactions set the stage for shared decision making in precision medicine. Few studies explore what recipients of PGx results think is happening in their bodies when a drug‐gene interaction is discovered. To characterize biobank participants’ understanding of PGx research results, we conducted a focus group study, which took place after PGx variants conferring increased risk of dihydropyrimidine dehydrogenase (DPD) deficiency were disclosed to biobank contributors. DPD deficiency confers an increased risk of adverse reaction to commonly used cancer chemotherapeutics. Ten focus groups were conducted, ranging from two to eight participants. Fifty‐four individuals participated in focus groups. A framework approach was used for descriptive and explanatory analysis. Descriptive themes included participants’ efforts to make sense of PGx findings as they related to: (1) health implications, (2) drugs, and (3) genetics. Explanatory analysis supplied a functional framework of how participant word choices can perform different purposes in PGx communication. Results bear three main implications for PGx research‐related disclosure. First, participants’ use of various terms suggest participants generally understanding their PGx results, including how positive PGx results differ from positive disease susceptibility genetic results. Second, PGx disclosure in biobanking can involve participant conflation of drug‐gene interactions with allergies or other types of medical reactions. Third, the functional framework suggests a need to move beyond a deficit model of genetic literacy in PGx communication. Together, findings provide an initial evidence base for supporting bidirectional expert‐recipient PGx results communication.

Investigating ELOVL7 coding variants in multiple system atrophy

Multiple system atrophy (MSA) is a rare sporadic, progressive parkinsonism characterised by autonomic dysfunction. A recent genome-wide association study reported an association at the Elongation of Very Long Fatty Acids Protein 7 (ELOVL7) locus with MSA risk. In the current study four independent and unrelated cohorts were assessed, consisting of pathologically confirmed MSA cases, Parkinson's disease (PD) cases, and two unrelated, healthy control groups. All exons of ELOVL7 were sequenced in pathologically confirmed MSA cases; data for PPMI samples and Biobank controls was extracted from whole genome sequence. Coding variants in ELOVL7 were extremely rare, and we observed no significant association of ELOVL7 coding variants with risk of MSA.

No Association Between Pharmacogenomics Variants and Hospital and Emergency Department Utilization: A Mayo Clinic Biobank Retrospective Study

Background

The use of pharmacogenomics data is increasing in clinical practice. However, it is unknown if pharmacogenomics data can be used more broadly to predict outcomes like hospitalization or emergency department (ED) visit. We aim to determine the association between selected pharmacogenomics phenotypes and hospital utilization outcomes (hospitalization and ED visits).

Methods

This cohort study utilized 10,078 patients from the Mayo Clinic Biobank in the RIGHT protocol with sequence and interpreted phenotypes for 10 selected pharmacogenes including CYP2D6, CYP2C9, CYP2C19, CYP3A5, HLA B 5701, HLA B 5702, HLA B 5801, TPMT, SLCO1B1, and DPYD. The primary outcome was hospitalization with ED visits as a secondary outcome. We used Cox proportional hazards model to test the association between each pharmacogenomics phenotype and the risk of the outcomes.

Results

During the follow-up period (median [in years] = 7.3), 13% (n=1354) and 8% (n=813) of the subjects experienced hospitalization and ED visits, respectively. Compared to subjects who did not experience hospitalization, hospitalized patients were older (median age [in years]: 67 vs 65), poorer self-rated health (15% vs 4.7% for fair/poor), and higher disease burden (median number of chronic conditions: 7 vs 4) at baseline. There was no association of hospitalization with any of the pharmacogenomics phenotypes. The pharmacogenomics phenotypes were not associated with disease burden, a well-established risk factor for hospital utilization outcomes. Similar findings were observed for patients with ED visits during the follow-up period.

Conclusion

We found no association of 10 well-established pharmacogenomics phenotypes with either hospitalization or ED visits in this relatively large biobank population and outside the context of specific drug use related to these genes. Traditional risk factors for hospitalization like age and self-rated health were much more likely to predict hospitalization and/or ED visits than this pharmacogenomics information.

Communicating unexpected pharmacogenomic results to biobank contributors: A focus group study

OBJECTIVES

The goals of this study were to explore 1) the impact of returning unexpected pharmacogenomic (PGx) results to biobank contributors, and 2) participant views about improving communication.

METHODS

We conducted a qualitative focus group study with biobank participants (N = 54) who were notified by mail of an individual research result indicating increased risk for adverse events associated with the common cancer drug 5-fluorouracil (5-FU). We employed a framework approach for analysis.

RESULTS

Our results revealed three themes illustrating participants' questions and uncertainty, especially regarding how to share results with health providers and family members, and remember them over time. Participants valued results for themselves and others, and for the future of medicine. Risk perception was framed by health identity. "Toxicity narratives," or familiarity with another's adverse reaction to chemotherapy, increased the sense of importance participants reported.

CONCLUSION

These focus group results highlight research participant remaining questions and high valuation of PGx results, even when unexpected.

PRACTICE IMPLICATIONS

We identify PGx research participants' needs for clear clinical translation messaging that attends to health identity, pragmatics of sharing information with family members, and patient perceptions of barriers to transferring research results to a clinical context.

Genome-wide detection of tandem DNA repeats that are expanded in autism

Tandem DNA repeats vary in the size and sequence of each unit (motif). When expanded, these tandem DNA repeats have been associated with more than 40 monogenic disorders1. Their involvement in disorders with complex genetics is largely unknown, as is the extent of their heterogeneity. Here we investigated the genome-wide characteristics of tandem repeats that had motifs with a length of 2-20 base pairs in 17,231 genomes of families containing individuals with autism spectrum disorder (ASD)2,3 and population control individuals4. We found extensive polymorphism in the size and sequence of motifs. Many of the tandem repeat loci that we detected correlated with cytogenetic fragile sites. At 2,588 loci, gene-associated expansions of tandem repeats that were rare among population control individuals were significantly more prevalent among individuals with ASD than their siblings without ASD, particularly in exons and near splice junctions, and in genes related to the development of the nervous system and cardiovascular system or muscle. Rare tandem repeat expansions had a prevalence of 23.3% in children with ASD compared with 20.7% in children without ASD, which suggests that tandem repeat expansions make a collective contribution to the risk of ASD of 2.6%. These rare tandem repeat expansions included previously undescribed ASD-linked expansions in DMPK and FXN, which are associated with neuromuscular conditions, and in previously unknown loci such as FGF14 and CACNB1. Rare tandem repeat expansions were associated with lower IQ and adaptive ability. Our results show that tandem DNA repeat expansions contribute strongly to the genetic aetiology and phenotypic complexity of ASD.

Characteristics Associated With Recruitment and Re-contact in Mayo Clinic Biobank

Objective: To better understand the characteristics associated with a participant's willingness to consent to the Mayo Clinic Biobank (MCB) and examine factors associated with willingness to participate in follow-up studies embedded within MCB that require re-contact and participant approval. Participants and Methods: Consent rates were compared across patient demographics to the MCB. Rates of participation to follow-up studies were also compared across demographics and request types. Results: Among 272,102 Mayo Clinic patients invited to the MCB, 48,314 (19%) consented across the three recruitment sites within 90 days of initial invitation. A significant age by gender interaction was identified, showing young males consent at a lower rate than young females and older males consent at a higher rate than older females. Over the recruitment time frame of 2009-2015, there was a significant decrease in consent rates (decline of 2.5%/year). Of the 57,041 consented MCB participants, 33,487 participants (59%) have been invited to participate in follow-up studies via re-contact. Follow-up studies of the MCB may require participants to provide additional samples, complete questionnaires, and/or release their identity to a research team. MCB participants have been invited to enroll in a median of two studies (IQR: 1-3). Seventy-one percent of participants consented to at least one follow-up study, with individual follow-up study consent rates ranging from 14 to 87% depending on study type, with a median consent rate of 61% (IQR: 47-70%). Studies requesting return of a questionnaire had the highest participation rates. White participants, older participants, and participants with some college or a degree were significantly more likely to participate to follow-up studies, while there was no association with gender. Conclusion: Consent rates among younger and non-white patients were lower than in older, white patients. However, we also found that participation rates among those already enrolled in the biobank were much higher than those seen in new recruitment efforts, external to an existing biobank. We thus demonstrate an important way that biobanks can advance precision medicine goals: through provision of populations from which studies can draw participants for future studies.