Development of the Precision Link Biobank at Boston Children's Hospital: Challenges and Opportunities

Age-Dependent Differences in Blood Levels of Glial Fibrillary Acidic Protein but Not Ubiquitin Carboxy-Terminal Hydrolase L1 in Children

OBJECTIVES

Despite the growing evidence of the clinical utility of blood-brain biomarkers in adults with traumatic brain injury (TBI), less is known about the performance of these biomarkers in children. We characterize age-dependent differences in levels of ubiquitin carboxy-terminal hydrolase L1 (UCH-L1) and glial fibrillary acidic protein (GFAP) in children without TBI.

METHODS

Plasma biobank specimens from children and adolescents aged 0-<19 years without TBI were obtained, and UCH-L1 and GFAP levels were quantified. The relationship between age and biomarker expression was determined using previously defined aged epochs (<3.5 years, 3.5 years to <11 years, 11 years and older), then biomarker levels were compared with established thresholds for ruling out the need for a head CT in adults with a mild TBI (mTBI) (UCH-L1 400 pg/mL, GFAP 35 pg/mL).

RESULTS

The age range of the 366 control patients was 3 months-18 years. There was a significant negative association between age and GFAP but not UCH-L1. Only 1.4% of samples exceeded the UCH-L1 cutoff; however, 20% of samples exceeded the GFAP cutoff and 100% children younger than 3.5 years had values that exceeded the cutoff.

DISCUSSION

Age seems to modify physiologic plasma GFAP levels. Diagnostic cutoffs for TBI based on GFAP but not UCH-L1 and may need to be adjusted in children younger than 11 years.

GSDMB/ORMDL3 Rare/Common Variants Are Associated with Inhaled Corticosteroid Response among Children with Asthma

Inhaled corticosteroids (ICS) are efficacious in the treatment of asthma, which affects more than 300 million people in the world. While genome-wide association studies have identified genes involved in differential treatment responses to ICS in asthma, few studies have evaluated the effects of combined rare and common variants on ICS response among children with asthma. Among children with asthma treated with ICS with whole exome sequencing (WES) data in the PrecisionLink Biobank (91 White and 20 Black children), we examined the effect and contribution of rare and common variants with hospitalizations or emergency department visits. For 12 regions previously associated with asthma and ICS response (DPP10, FBXL7, NDFIP1, TBXT, GLCCI1, HDAC9, TBXAS1, STAT6, GSDMB/ORMDL3, CRHR1, GNGT2, FCER2), we used the combined sum test for the sequence kernel association test (SKAT) adjusting for age, sex, and BMI and stratified by race. Validation was conducted in the Biorepository and Integrative Genomics (BIG) Initiative (83 White and 134 Black children). Using a Bonferroni threshold for the 12 regions tested (i.e., 0.05/12 = 0.004), GSDMB/ORMDL3 was significantly associated with ICS response for the combined effect of rare and common variants (p-value = 0.003) among White children in the PrecisionLink Biobank and replicated in the BIG Initiative (p-value = 0.02). Using WES data, the combined effect of rare and common variants for GSDMB/ORMDL3 was associated with ICS response among asthmatic children in the PrecisionLink Biobank and replicated in the BIG Initiative. This proof-of-concept study demonstrates the power of biobanks of pediatric real-life populations in asthma genomic investigations.

Effectiveness of multimodal participant recruitment in SPARK, a large, online longitudinal research study of autism

Background

SPARK launched in 2016 to build a US cohort of autistic individuals and their family members. Enrollment includes online consent to share data and optional consent to provide saliva for genomic analysis. SPARK's recruitment strategies include social media and support of a nation-wide network of clinical sites. This study evaluates SPARK's recruitment strategies to enroll a core study population.

Methods

Individuals who joined between January 31, 2018, and May 29, 2019 were included in the analysis. Data include sociodemographic characteristics, clinical site referral, the website URL used to join, how the participant heard about SPARK, enrollment completion (online registration, study consents, and returning saliva sample), and completion of the baseline questionnaire. Logistic regressions were performed to evaluate the odds of core participant status (completing enrollment and baseline questionnaire) by recruitment strategy.

Results

In total, 31,715 individuals joined during the study period, including 40% through a clinical site. Overall, 88% completed online registration, 46% returned saliva, and 38% were core participants. Those referred by a clinical site were almost twice as likely to be core participants. Those who directly visited the SPARK website or performed a Google search were more likely to be core participants than those who joined through social media.

Discussion

Being a core participant may be associated with the "personal" connection and support provided by a clinical site and/or site staff, as well as greater motivation to seek research opportunities. Findings from this study underscore the value of adopting a multimodal recruitment approach that combines social media and a physical presence.

Plasma Neurofilament Light Chain Is Elevated in Adaptor Protein Complex 4-Related Hereditary Spastic Paraplegia

BACKGROUND

Adaptor protein complex 4-associated hereditary spastic paraplegia (AP-4-HSP) is caused by pathogenic biallelic variants in AP4B1, AP4M1, AP4E1, and AP4S1.

OBJECTIVE

The aim was to explore blood markers of neuroaxonal damage in AP-4-HSP.

METHODS

Plasma neurofilament light chain (pNfL) and glial fibrillary acidic protein (GFAP) levels were measured in samples from patients and age- and sex-matched controls (NfL: n = 46 vs. n = 46; GFAP: n = 14 vs. n = 21) using single-molecule array assays. Patients' phenotypes were systematically assessed using the AP-4-HSP natural history study questionnaires, the Spastic Paraplegia Rating Scale, and the SPATAX disability score.

RESULTS

pNfL levels increased in AP-4-HSP patients, allowing differentiation from controls (Mann-Whitney U test: P = 3.0e-10; area under the curve = 0.87 with a 95% confidence interval of 0.80-0.94). Phenotypic cluster analyses revealed a subgroup of individuals with severe generalized-onset seizures and developmental stagnation, who showed differentially higher pNfL levels (Mann-Whitney U test between two identified clusters: P = 2.5e-6). Plasma GFAP levels were unchanged in patients with AP-4-HSP.

CONCLUSIONS

pNfL is a potential disease marker in AP-4-HSP and can help differentiate between phenotypic subgroups. © 2023 International Parkinson and Movement Disorder Society.

Translating Precision Health for Pediatrics: A Scoping Review

Precision health aims to personalize treatment and prevention strategies based on individual genetic differences. While it has significantly improved healthcare for specific patient groups, broader translation faces challenges with evidence development, evidence appraisal, and implementation. These challenges are compounded in child health as existing methods fail to incorporate the physiology and socio-biology unique to childhood. This scoping review synthesizes the existing literature on evidence development, appraisal, prioritization, and implementation of precision child health. PubMed, Scopus, Web of Science, and Embase were searched. The included articles were related to pediatrics, precision health, and the translational pathway. Articles were excluded if they were too narrow in scope. In total, 74 articles identified challenges and solutions for putting pediatric precision health interventions into practice. The literature reinforced the unique attributes of children and their implications for study design and identified major themes for the value assessment of precision health interventions for children, including clinical benefit, cost-effectiveness, stakeholder values and preferences, and ethics and equity. Tackling these identified challenges will require developing international data networks and guidelines, re-thinking methods for value assessment, and broadening stakeholder support for the effective implementation of precision health within healthcare organizations. This research was funded by the SickKids Precision Child Health Catalyst Grant.

A cervical cancer biorepository for pharmacogenomics research in Zimbabwe

BACKGROUND

Research infrastructures such as biorepositories are essential to facilitate genomics and its growing applications in health research and translational medicine in Africa. Using a cervical cancer cohort, this study describes the establishment of a biorepository consisting of biospecimens and matched phenotype data for use in genomic association analysis and pharmacogenomics research.

METHOD

Women aged > 18 years with a recent histologically confirmed cervical cancer diagnosis were recruited. A workflow pipeline was developed to collect, store, and analyse biospecimens comprising donor recruitment and informed consent, followed by data and biospecimen collection, nucleic acid extraction, storage of genomic DNA, genetic characterization, data integration, data analysis and data interpretation. The biospecimen and data storage infrastructure included shared -20 °C to -80 °C freezers, lockable cupboards, secured access-controlled laptop, password protected online data storage on OneDrive software. The biospecimen or data storage, transfer and sharing were compliant with the local and international biospecimen and data protection laws and policies, to ensure donor privacy, trust, and benefits for the wider community.

RESULTS

This initial establishment of the biorepository recruited 410 women with cervical cancer. The mean (± SD) age of the donors was 52 (± 12) years, comprising stage I (15%), stage II (44%), stage III (47%) and stage IV (6%) disease. The biorepository includes whole blood and corresponding genomic DNA from 311 (75.9%) donors, and tumour biospecimens and corresponding tumour DNA from 258 (62.9%) donors. Datasets included information on sociodemographic characteristics, lifestyle, family history, clinical information, and HPV genotype. Treatment response was followed up for 12 months, namely, treatment-induced toxicities, survival vs. mortality, and disease status, that is disease-free survival, progression or relapse, 12 months after therapy commencement.

CONCLUSION

The current work highlights a framework for developing a cancer genomics cohort-based biorepository on a limited budget. Such a resource plays a central role in advancing genomics research towards the implementation of personalised management of cancer.

Comprehensive characterization of putative genetic influences on plasma metabolome in a pediatric cohort

BACKGROUND

The human exposome is composed of diverse metabolites and small chemical compounds originated from endogenous and exogenous sources, respectively. Genetic and environmental factors influence metabolite levels, while the extent of genetic contributions across metabolic pathways is not yet known. Untargeted profiling of human metabolome using high-resolution mass spectrometry (HRMS) combined with genome-wide genotyping allows comprehensive identification of genetically influenced metabolites. As such previous studies of adults discovered and replicated genotype-metabotype associations. However, these associations have not been characterized in children.

RESULTS

We conducted the largest genome by metabolome-wide association study to date of children (N = 441) using 619,688 common genetic variants and 14,342 features measured by HRMS. Narrow-sense heritability (h²) estimates of plasma metabolite concentrations using genomic relatedness matrix restricted maximum likelihood (GREML) method showed a bimodal distribution with high h² (> 0.8) for 15.9% of features and low h² (< 0.2) for most of features (62.0%). The features with high h² were enriched for amino acid and nucleic acid metabolism, while carbohydrate and lipid concentrations showed low h². For each feature, a metabolite quantitative trait loci (mQTL) analysis was performed to identify genetic variants that were potentially associated with plasma levels. Fifty-four associations among 29 features and 43 genetic variants were identified at a genome-wide significance threshold p < 3.5 × 10^-12 (= 5 × 10^-8/14,342 features). Previously reported associations such as UGT1A1 and bilirubin; PYROXD2 and methyl lysine; and ACADS and butyrylcarnitine were successfully replicated in our pediatric cohort. We found potential candidates for novel associations including CSMD1 and a monostearyl alcohol triglyceride (m/z 781.7483, retention time (RT) 89.3 s); CALN1 and Tridecanol (m/z 283.2741, RT 27.6). A gene-level enrichment analysis using MAGMA revealed highly interconnected modules for dADP biosynthesis, sterol synthesis, and long-chain fatty acid transport in the gene-feature network.

CONCLUSION

Comprehensive profiling of plasma metabolome across age groups combined with genome-wide genotyping revealed a wide range of genetic influence on diverse chemical species and metabolic pathways. The developmental trajectory of a biological system is shaped by gene-environment interaction especially in early life. Therefore, continuous efforts on generating metabolomics data in diverse human tissue types across age groups are required to understand gene-environment interaction toward healthy aging trajectories.

Collecting Biospecimens and Obtaining Biobank Consent From Patients in an Academic Health Care Setting: Practical and Ethical Considerations

Academic health centers and health systems increasingly ask patients to enroll in research biobanks as part of standard care, raising important practical and ethical questions for integrating biobank consent processes into health care settings. This article aims to assist academic health centers and health systems considering implementing these integrated consent processes by outlining the 5 main issues-and the key practical and ethical considerations for each issue-that Indiana University Health and the Indiana Biobank faced when integrating biobank consent into their health system, as well as the key obstacles encountered. The 5 main issues to consider include the specimen to collect (leftover, new collection, or add-ons to clinical tests), whether to use opt-in or opt-out consent, where to approach patients, how to effectively use digital tools for consent, and how to appropriately simplify consent information.

Using a 3 stage process to create a consumer research contact list in a paediatric health setting: the PARTICIPATE project

The impact of child health research can be far reaching; affecting children's immediate health, their adult health, the health of future generations and the economic wellbeing of countries. Consumer and community involvement is increasingly recognised as key to successful research recruitment. Systematic approaches to research recruitment include research registries or research contact lists.

OBJECTIVE

Develop a process of creating a consumer research contact list for participating in future research opportunities at a children's health service.

METHODS

A healthcare improvement approach using a 3 stage framework; 1) evidence review and consultation 2) co-production of a research communications plan with stakeholders (including consumers), including a draft research information brochure 3) prototyping involved iteratively testing the brochure, surveying parents or carers who attended outpatient clinics or the hospital Emergency Department, and conducting follow up telephone calls.

RESULTS

There was overall support for the creation of a research contact list, but some unknowns remain. 367 parents or carers completed the survey and 36 participated in a follow up telephone call. Over half would be willing to join a research contact list and more than 90% of the children of parents or carers surveyed were not currently participating in research. Several potential barriers identified by health service staff were dispelled. Research communications and a future contact list should be available in electronic form.

CONCLUSIONS

There was strong support for creating a research contact list. The approach will inform our future directions including creation of an electronic research contact list easily accessible by consumers of the children's health service. Recruiting enough children to participate in research studies can be challenging. Establishing a registry or list of young people willing to be contacted to participate in research is one way of addressing this problem. At our children's health service, we wanted to explore the idea of developing a research contact list and we were particularly keen to involve consumers and community members in this process, which involved: 1.Reviewing other examples of research contact lists and consulting with a range of people, including consumers and community members, 2. Co-producing a research communications plan with parents, young people, health service staff and research staff, including a draft research information brochure for families, and 3. Testing the acceptability of the brochure by surveying parents or carers who attended outpatient clinics or the hospital Emergency Department, and conducting follow up telephone calls with them. 367 parents or carers completed a survey and 36 participated in a follow up telephone call. Over half were willing to join a research contact list and more than 90% of the children of parents or carers surveyed were not currently participating in research. Several potential barriers raised by consumers and health professionals in the first stage of the project were not found to be a concern for the parents or carers surveyed. Responses showed research communications and a future contact list should be available in electronic form. These findings will inform the future creation of an electronic research contact list, easily accessible by consumers of the children's health service.

Adolescent Assent and Reconsent for Biobanking: Recent Developments and Emerging Ethical Issues

Research biobanks that enroll minors face important practical, ethical, and regulatory challenges in reconsenting participants when they reach the age of 18. Federal regulations governing research in the United States provide minimal guidance and allow for a range of practices, including waiving the requirement to obtain reconsent. Some commentators have argued that institutional review boards should indeed grant such waivers, given the low risks of biobank-based research and the impracticality of contacting all participants when they turn 18. There is also significant ethical debate about the age at which adolescents can make authentic, autonomous decisions regarding their research participation. This paper reviews these issues in detail, describes the current state of the ethical discussion, and outlines evidence-based policies for enrolling minors into research biobanks.

Methods and implementation of a pediatric asthma pharmacogenomic study in the emergency department setting

OBJECTIVES

The emergency department (ED) is a challenging setting to conduct pharmacogenomic studies and integrate that data into fast-paced and potentially life-saving treatment decisions. Therefore, our objective is to present the methods and feasibility of a pilot pharmacogenomic study set in the ED that measured pediatric bronchodilator response (BDR) during acute asthma exacerbations.

METHODS

This is an exploratory pilot study that collected buccal swabs for DNA and measured BDR during ED encounters for pediatric asthma exacerbations. We evaluated the study's feasibility with a qualitative analysis of ED provider surveys and quantitatively by the proportion of eligible patients enrolled.

RESULTS

We enrolled 59 out of 90 patients (65%) that were identified and considered eligible during a 5-month period (target enrollment 60 patients over 12 months). The median patient age was 7 years (interquartile range 4-9 years), 61% (N = 36) were male, and 92% (N = 54) were African American. Quality DNA collection was successful for all 59 patients. The ED provider survey response rate was 100%. Most ED providers reported that the study did not impact their workflow (98% of physicians, 88% of nurses, and 90% of respiratory therapists). ED providers did report difficulties with spirometry in the younger age group.

CONCLUSIONS

Pharmacogenomic studies can be conducted in the ED setting, and enroll a younger patient population with a high proportion of minority participants. By disseminating this study's methods and feasibility analysis, we aim to increase interest in pharmacogenomic studies set in the ED and aimed toward future ED-based pharmacogenomic decision-making.

Incorporating Biobank Consent into a Healthcare Setting: Challenges for Patient Understanding

Biobank participants often do not understand much of the information they are provided as part of the informed consent process, despite numerous attempts at simplifying consent forms and improving their readability. We report the first assessment of biobank enrollees' comprehension under an "integrated consent" process, where patients were asked to enroll in a research biobank as part of their normal healthcare experience. A number of healthcare systems have implemented similar integrated consent processes for biobanking, but it is unknown how much patients understand after enrolling under these conditions. Methods: We recruited patients who enrolled in a biobank while in a healthcare setting when receiving ordinary care. We assessed knowledge of consent materials using 11 true/false questions drawn from a well-known biobank knowledge test. After reviewing the results from 114 participants, we revised the consent form and repeated the knowledge assessment with 144 different participants. Results: Participants scored poorly on the knowledge test in both rounds, with no significant differences in overall scores or individual items between the rounds. In Phase 1, participants answered 53% of the questions correctly, 25% incorrectly, and 22% "I don't know." In Phase 2, participants answered 53% of questions correctly, 24% incorrectly, and 23% "I don't know." Participants scored particularly poorly on questions about data sharing and accessing medical records. Conclusions: Enrollees under an integrated consent model had significant misunderstandings that persisted despite an attempt to improve information specifically about those topics in a consent form. These results raise challenges for current approaches that attribute misunderstanding to overly complex consent forms. They also suggest that the pressures of the clinic may compound other problems with patient understanding of biobank consent. As health systems increasingly blend research and care, they may need to rethink their approach to educating patients about participation in a biobank.

A high-throughput phenotyping algorithm is portable from adult to pediatric populations

OBJECTIVE

Multimodal automated phenotyping (MAP) is a scalable, high-throughput phenotyping method, developed using electronic health record (EHR) data from an adult population. We tested transportability of MAP to a pediatric population.

MATERIALS AND METHODS

Without additional feature engineering or supervised training, we applied MAP to a pediatric population enrolled in a biobank and evaluated performance against physician-reviewed medical records. We also compared performance of MAP at the pediatric institution and the original adult institution where MAP was developed, including for 6 phenotypes validated at both institutions against physician-reviewed medical records.

RESULTS

MAP performed equally well in the pediatric setting (average AUC 0.98) as it did at the general adult hospital system (average AUC 0.96). MAP's performance in the pediatric sample was similar across the 6 specific phenotypes also validated against gold-standard labels in the adult biobank.

CONCLUSIONS

MAP is highly transportable across diverse populations and has potential for wide-scale use.

GenoPheno: cataloging large-scale phenotypic and next-generation sequencing data within human datasets

Precision medicine promises to revolutionize treatment, shifting therapeutic approaches from the classical one-size-fits-all to those more tailored to the patient's individual genomic profile, lifestyle and environmental exposures. Yet, to advance precision medicine's main objective-ensuring the optimum diagnosis, treatment and prognosis for each individual-investigators need access to large-scale clinical and genomic data repositories. Despite the vast proliferation of these datasets, locating and obtaining access to many remains a challenge. We sought to provide an overview of available patient-level datasets that contain both genotypic data, obtained by next-generation sequencing, and phenotypic data-and to create a dynamic, online catalog for consultation, contribution and revision by the research community. Datasets included in this review conform to six specific inclusion parameters that are: (i) contain data from more than 500 human subjects; (ii) contain both genotypic and phenotypic data from the same subjects; (iii) include whole genome sequencing or whole exome sequencing data; (iv) include at least 100 recorded phenotypic variables per subject; (v) accessible through a website or collaboration with investigators and (vi) make access information available in English. Using these criteria, we identified 30 datasets, reviewed them and provided results in the release version of a catalog, which is publicly available through a dynamic Web application and on GitHub. Users can review as well as contribute new datasets for inclusion (Web: https://avillachlab.shinyapps.io/genophenocatalog/; GitHub: https://github.com/hms-dbmi/GenoPheno-CatalogShiny).

Children's rare disease cohorts: an integrative research and clinical genomics initiative

While genomic data is frequently collected under distinct research protocols and disparate clinical and research regimes, there is a benefit in streamlining sequencing strategies to create harmonized databases, particularly in the area of pediatric rare disease. Research hospitals seeking to implement unified genomics workflows for research and clinical practice face numerous challenges, as they need to address the unique requirements and goals of the distinct environments and many stakeholders, including clinicians, researchers and sequencing providers. Here, we present outcomes of the first phase of the Children’s Rare Disease Cohorts initiative (CRDC) that was completed at Boston Children’s Hospital (BCH). We have developed a broadly sharable database of 2441 exomes from 15 pediatric rare disease cohorts, with major contributions from early onset epilepsy and early onset inflammatory bowel disease. All sequencing data is integrated and combined with phenotypic and research data in a genomics learning system (GLS). Phenotypes were both manually annotated and pulled automatically from patient medical records. Deployment of a genomically-ordered relational database allowed us to provide a modular and robust platform for centralized storage and analysis of research and clinical data, currently totaling 8516 exomes and 112 genomes. The GLS integrates analytical systems, including machine learning algorithms for automated variant classification and prioritization, as well as phenotype extraction via natural language processing (NLP) of clinical notes. This GLS is extensible to additional analytic systems and growing research and clinical collections of genomic and other types of data.

Experiences implementing scalable, containerized, cloud-based NLP for extracting biobank participant phenotypes at scale

OBJECTIVE

To develop scalable natural language processing (NLP) infrastructure for processing the free text in electronic health records (EHRs).

MATERIALS AND METHODS

We extend the open-source Apache cTAKES NLP software with several standard technologies for scalability. We remove processing bottlenecks by monitoring component queue size. We process EHR free text for patients in the PrecisionLink Biobank at Boston Children's Hospital. The extracted concepts are made searchable via a web-based portal.

RESULTS

We processed over 1.2 million notes for over 8000 patients, extracting 154 million concepts. Our largest tested configuration processes over 1 million notes per day.

DISCUSSION

The unique information represented by extracted NLP concepts has great potential to provide a more complete picture of patient status.

CONCLUSION

NLP large EHR document collections can be done efficiently, in service of high throughput phenotyping.

The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system

PURPOSE

Clinicians and researchers must contextualize a patient's genetic variants against population-based references with detailed phenotyping. We sought to establish globally scalable technology, policy, and procedures for sharing biosamples and associated genomic and phenotypic data on broadly consented cohorts, across sites of care.

METHODS

Three of the nation's leading children's hospitals launched the Genomic Research and Innovation Network (GRIN), with federated information technology infrastructure, harmonized biobanking protocols, and material transfer agreements. Pilot studies in epilepsy and short stature were completed to design and test the collaboration model.

RESULTS

Harmonized, broadly consented institutional review board (IRB) protocols were approved and used for biobank enrollment, creating ever-expanding, compatible biobanks. An open source federated query infrastructure was established over genotype-phenotype databases at the three hospitals. Investigators securely access the GRIN platform for prep to research queries, receiving aggregate counts of patients with particular phenotypes or genotypes in each biobank. With proper approvals, de-identified data is exported to a shared analytic workspace. Investigators at all sites enthusiastically collaborated on the pilot studies, resulting in multiple publications. Investigators have also begun to successfully utilize the infrastructure for grant applications.

CONCLUSIONS

The GRIN collaboration establishes the technology, policy, and procedures for a scalable genomic research network.

Assessment of coverage for endogenous metabolites and exogenous chemical compounds using an untargeted metabolomics platform

Physiological status and pathological changes in an individual can be captured by metabolic state that reflects the influence of both genetic variants and environmental factors such as diet, lifestyle and gut microbiome. The totality of environmental exposure throughout lifetime - i.e., exposome - is difficult to measure with current technologies. However, targeted measurement of exogenous chemicals and untargeted profiling of endogenous metabolites have been widely used to discover biomarkers of pathophysiologic changes and to understand functional impacts of genetic variants. To investigate the coverage of chemical space and interindividual variation related to demographic and pathological conditions, we profiled 169 plasma samples using an untargeted metabolomics platform. On average, 1,009 metabolites were quantified in each individual (range 906 - 1,038) out of 1,244 total chemical compounds detected in our cohort. Of note, age was positively correlated with the total number of detected metabolites in both males and females. Using the robust Qn estimator, we found metabolite outliers in each sample (mean 22, range from 7 to 86). A total of 50 metabolites were outliers in a patient with phenylketonuria including the ones known for phenylalanine pathway suggesting multiple metabolic pathways perturbed in this patient. The largest number of outliers (N=86) was found in a 5-year-old boy with alpha-1-antitrypsin deficiency who were waiting for liver transplantation due to cirrhosis. Xenobiotics including drugs, diets and environmental chemicals were significantly correlated with diverse endogenous metabolites and the use of antibiotics significantly changed gut microbial products detected in host circulation. Several challenges such as annotation of features, reference range and variance for each feature per age group and gender, and population scale reference datasets need to be addressed; however, untargeted metabolomics could be immediately deployed as a biomarker discovery platform and to evaluate the impact of genomic variants and exposures on metabolic pathways for some diseases.

Optimizing Retrieval of Biospecimens Using the Curated Cancer Clinical Outcomes Database (C3OD)

To fully support their role in translational and personalized medicine, biorepositories and biobanks must continue to advance the annotation of their biospecimens with robust clinical and laboratory data. Translational research and personalized medicine require well-documented and up-to-date information, but the infrastructure used to support biorepositories and biobanks can easily be out of sync with the host institution. To assist researchers and provide them with accurate pathological, epidemiological, and bio-molecular data, the Biospecimen Repository Core Facility (BRCF) at the University of Kansas Medical Center (KUMC) merges data from medical records, the tumor registry, and pathology reports using the Curated Cancer Clinical Outcomes Database (C3OD). In this report, we describe the utilization of C3OD to optimally retrieve and dispense biospecimen samples using these 3 data sources and demonstrate how C3OD greatly increases the efficiency of obtaining biospecimen samples for the researchers.