Biomedical subjects

Josh F Peterson

Publications and source records attributed to Josh F Peterson.

8 recordsLinked to original sources

PubMed2026

An EHR-based framework for modeling growth curves and constructing growth centile charts for genetic disorders.

Growth modeling is central to human genetics, as deviations from typical growth can signal an underlying disorder. In this cohort study, we developed a generalizable framework for generating growth charts across genetic conditions using electronic health records (EHR). Leveraging 22 years of longitudinal EHR data from 452,470 patients across 15 genetic conditions and unaffected individuals, we generated sex- and condition-specific growth charts using Generalized Additive Models for Location, Scale, and Shape, and quantified differences in size, timing, and intensity using SuperImposition by Translation and Rotation (SITAR). SITAR-derived growth parameters showed strong concordance with established annotations in OMIM and Orphanet, and identified previously unreported growth patterns. We stratified cystic fibrosis by CFTR functional class and observed greater growth impairment in individuals with homozygous minimal-function variants compared to those with residual function. This framework provides a generalizable approach for leveraging EHR data to refine genotype-phenotype relationships and enable continuous updating of growth charts across genetic conditions.

Journal Article↗

PubMed2026

Genotype-Guided Antidepressant Prescribing for Patients With Depression: A Randomized Clinical Trial.

IMPORTANCE: The effectiveness of pharmacogenetics to guide prescribing of selective serotonin reuptake inhibitors (SSRIs) for depression remains unclear, despite the well-established association between SSRI pharmacokinetics and genetic variation. OBJECTIVE: To determine whether pharmacogenetic-guided prescribing of SSRIs improves treatment response in patients with depression. DESIGN, SETTING, AND PARTICIPANTS: The ADOPT PGx (A Depression and Opioid Pragmatic Trial in Pharmacogenetics) Depression pragmatic randomized clinical trial was conducted from August 10, 2021, through April 27, 2024, at primary care, psychiatry, or family medicine clinics at enrolling sites throughout the US. Patients were aged 8 years or older and had experienced depression for 3 months or longer. INTERVENTION: Patients were randomized to genotype-guided SSRI prescribing (intervention group) or usual care (control group). Actionable drug metabolism phenotypes were defined as those for which pharmacogenetic clinical guidelines recommend alternative medication selection or dose adjustment. MAIN OUTCOMES AND MEASURES: The primary outcome was change in Patient-Reported Outcomes Measurement Information System (PROMIS) depression T scores at 3 months among patients with the actionable phenotype. Secondary end points included adverse effect severity of SSRIs at 3 months and depression remission (measured with PROMIS depression scores and Patient Health Questionnaire-8 [PHQ-8] scores) at 6 months. RESULTS: This study of 1460 patients included 1239 adults (84.9%) (mean [SD] age, 40.6 [16.7] years) and 221 children (15.1%) (mean [SD] age, 14.6 [1.8] years). Most patients were female (1096 [75.1%]). A total of 692 patients (47.4%) had an actionable phenotype; 351 (50.7%) were assigned to the intervention, and 341 (49.3%) were assigned to usual care. At baseline, 463 of the 692 patients (66.9%) reported having depressive symptoms for more than 2 years, 603 (87.1%) were receiving pharmacologic treatment, and 354 (51.2%) were receiving nonpharmacologic treatment. At 3 months, no significant differences were observed between the intervention and usual care groups in change in PROMIS depression T scores (mean [SD] change, -4.3 [8.4] vs -4.0 [8.1]; P = .68), medication adverse effect burden (mean [SD] change, 8.2 [4.3] vs 7.8 [4.5]; P = .37), or Patient Health Questionnaire-8 score change (mean [SD] change, -3.3 [5.2] vs -2.7 [4.8]; P  = .13). However, at 6 months, the PROMIS depression T-score remission rate (score ≤16) was higher in the intervention group compared with the usual care group (153 of 317 patients [48.3%] vs 122 of 310 patients [39.4%]; P = .02). CONCLUSIONS AND RELEVANCE: In this randomized clinical trial, genotype-guided prescribing of SSRIs did not improve control of depression symptoms at 3 months compared with usual care but was associated with higher depression remission rates at 6 months. These findings suggest a possible longer-term clinical benefit and indicate that future studies should focus on the durability and long-term impact of genotype-guided prescribing in the management of depressive symptoms. TRIAL REGISTRATION: ClinicalTrials.gov Identifiers: NCT04445792 (Master Protocol Research Program platform trial) and NCT05966155 (ADOPT PGx Depression trial).

Humans↗

PubMed2026

Evaluating pregnancy and neonatal outcomes in mothers with genetic disease using electronic health care records.

PURPOSE: The effect of Mendelian disorders on pregnancy and neonatal outcomes is poorly understood because of their rarity and the challenge of compiling complete prenatal and postnatal records. METHODS: Using electronic health records from a single academic center, we developed a retrospective cohort of maternal-infant dyads. Cases were mothers with molecularly confirmed Mendelian disorders paired with live-born infants; controls had no documented genetic disease. Outcomes were evaluated overall, by organ system, and by individual disorder. RESULTS: The cohort included 58,912 dyads, 241 with genetic diagnoses and 58,671 controls. Although overall outcomes were generally favorable, mothers with genetic disorders had higher rates of cesarean delivery and neonatal intensive care unit admission, earlier gestational age, and lower Apgar scores. Neonatal risks were greatest among neurological and cardiovascular disorders. Known associations were replicated, including increased neonatal intensive care unit admission in 22q11.2 deletion syndrome, cesarean delivery in Turner syndrome, and gestational diabetes in cystic fibrosis. We also provided descriptive electronic-health-record-based case reports and case series for 35 disorders previously lacking published pregnancy outcome data. CONCLUSION: This study identifies elevated perinatal risks in specific Mendelian disease groups and demonstrates how electronic-health-record-linked data can support prenatal counseling, risk stratification, and individualized care for individuals with genetic disorders.

Humans↗

PubMed2025

Covering medical care costs for participants in the eMERGE Network: Challenges for equity and implementation.

PURPOSE: To investigate the complexities of covering study-recommended medical care costs for individuals (in order to prevent lack of adherence due to financial reasons), which have received little attention. METHODS: We explored the deliberations, decisions, and challenges faced by the Electronic Medical Records and Genomics (eMERGE) Network during the implementation of a genomic research project recommending clinical care based on high-risk results defined largely by polygenic risk scores. Two surveys were disseminated to eMERGE sites: to identify preferences about payment for specific care recommendations (survey 1) and to understand the operational processes of covering medical care costs (survey 2). RESULTS: Paying for a subset of care recommendations for the funded study duration was identified as the most feasible approach for covering medical care costs for participants who received high-risk genomic results. Each eMERGE site, by necessity, used diverse approaches to pay for medical care costs. CONCLUSION: eMERGE researchers balanced competing concerns about bias, equity, study design, regulatory compliance, and cost in designing a unified approach to cover some of the recommended medical care costs in the study. Many implementation challenges were encountered. Findings can inform researchers and regulatory bodies about the implications and complications of covering medical care costs in translational research studies focused on prevention.

Humans↗

PubMed2025

Characterizing trends in clinical genetic testing: A single-center analysis of EHR data from 1.8 million patients over two decades.

A lack of structural data in electronic health records (EHRs) makes assessing the impact of genetic testing on clinical practice challenging. We extracted clinical genetic tests from the EHRs of more than 1.8 million patients seen at Vanderbilt University Medical Center from 2002 to 2022. With these data, we quantified the use of clinical genetic testing in healthcare and described how testing patterns and results changed over time. We assessed trends in types of genetic tests, tracked usage across medical specialties, and introduced a new measure, the genetically attributable fraction (GAF), to quantify the proportion of observed phenotypes attributable to a genetic diagnosis over time. We identified 104,392 tests and 19,032 molecularly confirmed diagnoses. The proportion of patients with genetic testing in their EHRs increased from 1.0% in 2002 to 6.1% in 2022, and testing became more comprehensive with the growing use of multi-gene panels. The number of unique diseases diagnosed with genetic testing increased from 51 in 2002 to 509 in 2022, and there was a rise in the number of variants of uncertain significance. The phenome-wide GAF for 6,505,620 diagnoses made in 2022 was 0.46%, and the GAF was greater than 5% for 74 phenotypes, including pancreatic insufficiency (67%), chorea (64%), atrial septal defect (24%), microcephaly (17%), paraganglioma (17%), and ovarian cancer (6.8%). Our study provides a comprehensive quantification of the increasing role of genetic testing at a major academic medical institution and demonstrates its growing utility in explaining the observed medical phenome.

Humans↗

PubMed2024

Cost-effectiveness of population-wide genomic screening for Lynch Syndrome and polygenic risk scores to inform colorectal cancer screening.

PURPOSE: Genomic screening to identify individuals with Lynch Syndrome (LS) and those with a high polygenic risk score (PRS) promises to personalize colorectal cancer (CRC) screening. Understanding its clinical and economic impact is needed to inform screening guidelines and reimbursement policies. METHODS: We developed a Markov model to simulate individuals over a lifetime. We compared LS+PRS genomic screening with standard of care (SOC) for a cohort of US adults at age 30. The Markov model included health states of no CRC, CRC stages (A-D), and death. We estimated incidence, mortality, and discounted economic outcomes of the population under different interventions. RESULTS: Screening 1000 individuals for LS+PRS resulted in 1.36 fewer CRC cases and 0.65 fewer deaths compared with SOC. The incremental cost-effectiveness ratio was $124,415 per quality-adjusted life year; screening had a 69% probability of being cost-effective using a willingness-to-pay threshold of $150,000/quality-adjusted life year . Setting the PRS threshold at the 90th percentile of the LS+PRS screening program to define individuals at high risk was most likely to be cost-effective compared with 95th, 85th, and 80th percentiles. CONCLUSION: Population-level LS+PRS screening is marginally cost-effective, and a threshold of 90th percentile is more likely to be cost-effective than other thresholds.

Humans↗

PubMed2024

Diagnostic delay in monogenic disease: A scoping review.

PURPOSE: Diagnostic delay in monogenic disease is reportedly common. We conducted a scoping review investigating variability in study design, results, and conclusions. METHODS: We searched the academic literature on January 17, 2023, for original peer reviewed journals and conference articles that quantified diagnostic delay in monogenic disease. We abstracted the reported diagnostic delay, relevant study design features, and definitions. RESULTS: Our search identified 259 articles quantifying diagnostic delay in 111 distinct monogenetic diseases. Median reported diagnostic delay for all studies collectively in monogenetic diseases was 5.0 years (IQR 2-10). There was major variation in the reported delay within individual monogenetic diseases. Shorter delay was associated with disorders of childhood metabolism, immunity, and development. The majority (67.6%) of articles that studied delay reported an improvement with calendar time. Study design and definitions of delay were highly heterogenous. Three gaps were identified: (1) no studies were conducted in the least developed countries, (2) delay has not been studied for the majority of known, or (3) most prevalent genetic diseases. CONCLUSION: Heterogenous study design and definitions of diagnostic delay inhibit comparison across studies. Future efforts should focus on standardizing delay measurements, while expanding the research to low-income countries.

Humans↗

PubMed2023

The phenotype-genotype reference map: Improving biobank data science through replication.

Population-scale biobanks linked to electronic health record data provide vast opportunities to extend our knowledge of human genetics and discover new phenotype-genotype associations. Given their dense phenotype data, biobanks can also facilitate replication studies on a phenome-wide scale. Here, we introduce the phenotype-genotype reference map (PGRM), a set of 5,879 genetic associations from 523 GWAS publications that can be used for high-throughput replication experiments. PGRM phenotypes are standardized as phecodes, ensuring interoperability between biobanks. We applied the PGRM to five ancestry-specific cohorts from four independent biobanks and found evidence of robust replications across a wide array of phenotypes. We show how the PGRM can be used to detect data corruption and to empirically assess parameters for phenome-wide studies. Finally, we use the PGRM to explore factors associated with replicability of GWAS results.

Humans↗