Biomedical subjects

Rory J Tinker

Publications and source records attributed to Rory J Tinker.

11 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

Sex-Based Disparities in Fabry Disease Cause Challenges in Newborn Screening.

INTRODUCTION: Fabry disease (FD) is a multi-systemic, X-linked lysosomal storage disorder caused by decreased α-galactosidase activity. Early diagnosis enables timely treatment, but enzyme-based newborn screening (NBS) may not detect affected females. We hypothesized that enzyme-based NBS limitations contribute to sex-based diagnostic disparities in FD and investigated these differences. METHODS: Retrospective cohort analyses used data from the Fabry Registry (FR: 2001-2023) and Tennessee NBS (2017-2024). Sex differences in diagnosis via NBS, biochemical phenotype, symptom onset, and treatment initiation were analyzed using Wilcoxon and chi-square tests. RESULTS: Among 8,657 FR individuals, 73 (67 males, 6 females) were identified via NBS. FR data show that affected females had significantly higher residual α-galactosidase activity than affected males (leukocyte median: 45.9% vs. 3.9%, plasma median: 32.5% vs. 3.9%; p < 0.0001 for both). FR females had delayed symptom onset (18.1 vs. 11.1 years), later diagnosis (35.5 vs. 30.8 years), and lower treatment rates (51.1% vs. 80.8%) compared to males (all %, p < 0.0001). Tennessee NBS detected 25 males but no females. CONCLUSION: Females with FD have delays in symptom onset, diagnosis, and treatment compared to males. Furthermore, higher residual enzyme activity causes current enzyme-based NBS to miss most females. Incorporating sex-specific cutoffs and/or molecular sequencing into NBS could improve early detection and reduce sex-based disparities.

Humans↗

PubMed2026

Coagulopathy in Neonates With Classic Galactosemia: A Life-Threatening Yet Underrecognized Complication.

INTRODUCTION: Classic galactosemia (CG) is a rare metabolic disorder caused by galactose-1-phosphate uridylyltransferase deficiency, leading to toxic metabolite accumulation and life-threatening complications such as failure to thrive, sepsis, and acute liver failure. We hypothesize that coagulopathy is an underrecognized complication of CG and that this gap is reflected by limited documentation in the medical literature. METHODS: A PubMed literature review was conducted to identify articles describing coagulopathy in CG. We filtered for guidelines, meta-analyses, reviews, and systematic reviews. Our article screening followed PRISMA guidelines. RESULTS: Of 49 identified articles, 26/49 (53%) met inclusion criteria. Only 6/49 (12%) explicitly described coagulopathy in CG, and only 1/49 (2%) discussed management. DISCUSSION: These data supports our hypothesis that coagulopathy may be an underrecognized complication of CG by clinicians and identifies a gap in current medical literature. Improved early recognition of coagulopathy in neonates with CG could prevent delays in treatment and improve outcomes.

Humans↗

PubMed2026

Sex-Specific Diagnostic Inequality in Fabry Disease: Lessons Learned from Analysis of Newborn Screening and Cascade Testing in Tennessee from 2017 to 2024.

INTRODUCTION: Fabry disease (FD) is an X-linked lysosomal storage disease caused by alpha-galactosidase A (aGAL) deficiency. Newborn screening (NBS) programs for FD have been implemented in several US states; however, its effectiveness in identifying affected females remains uncertain. We hypothesized that sex-specific inequality of NBS-based detection of FD results in different diagnostic pathways for males and females with FD. METHODS: We compared diagnostic approaches for males and females with FD using Tennessee NBS results and Vanderbilt Lysosomal Storage Disorders Database (VLSDD). Sex-specific detection differences were assessed using Fisher's exact test (α = 0.05). RESULTS: Tennessee NBS identified 25 males but no females with FD from 2017 to 2024. In VLSDD, among 81 individuals with FD, sex distribution was nearly equal (42 males, 39 females). Among males, 26/42 (62%) were diagnosed via NBS, 7/42 (17%) through known family history, and 9/42 (21%) based on clinical symptoms. All 16 males diagnosed through non-NBS were born before its implementation. In contrast, none of the 39 females were diagnosed through NBS (p value <0.05). Of these, 13/39 (33%) were diagnosed through cascade testing following their sons' detection by NBS, with a median age at diagnosis of 28 years (25th-75th percentile: 24.5-34.0). Of the remaining 26 females, 12/26 (46%) were diagnosed after a family member was diagnosed through clinical symptoms and 14/26 (54%) were diagnosed through clinical symptoms. CONCLUSIONS: NBS effectively identifies affected males but fails to detect females with FD, though it can indirectly facilitate diagnosis of older female relatives.

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

First clinical diagnosis of FAME3 via commercial Long-Read sequencing reveals mosaic repeat expansion in MARCHF6 gene.

Familial Adult Myoclonic Epilepsy type 3 (FAME3) is a rare autosomal dominant disorder characterized by cortical tremor and epilepsy, caused by a noncoding pentanucleotide repeat expansion (TTTTA/TTTCA)n in the MARCHF6 gene. Conventional genetic testing often fails to detect this expansion due to its repetitive structure and intronic location. We evaluated a 61-year-old woman with refractory myoclonic and generalized tonic-clonic seizures, whose prior genetic testing-including exome and genome sequencing-was non-diagnostic. Using PacBio HiFi long-read whole-genome sequencing and the tandem repeat genotyping tool TRGT, we identified a pathogenic MARCHF6 intronic expansion. The proband harbored one allele with 15 TTTTA repeats and a second allele with a compound expansion of 661 TTTTA and 12 TTTCA repeats. Three affected relatives shared similarly expanded alleles, but with increasing repeat size in the latter generations. Importantly, analysis using TRGT-instability revealed repeat mosaicism in all affected individuals, reflected by variability in motif counts across individual sequencing reads. This somatic heterogeneity may contribute to the phenotypic penetrance, variable expressivity and pleiotropism seen in FAME3 disease expression. To our knowledge, this is the first clinical diagnosis of FAME3 using a commercially available long-read sequencing platform, underscoring its diagnostic utility in resolving complex repeat expansion disorders and uncovering biologically relevant mosaicism.

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

RORA-neurodevelopmental disorder: A unique triad of developmental disabilities, cerebellar anomalies, and myoclonic seizures.

PURPOSE: RORA encodes the RAR-related orphan receptor-α, playing a pivotal role in cerebellar maturation and function. Here, we report the largest series of individuals with RORA-related-neurodevelopmental disorder. METHODS: Forty individuals (30 unrelated; 10 siblings from 4 families) carrying RORA pathogenic/likely pathogenic variants were collected through an international collaboration. RESULTS: The 33 variants (29 de novo, 4 inherited, and 1 shared), identified by genome/exome sequencing (n = 21), chromosomal microarray analysis (n = 7), or gene panels (n = 4), included frameshift (n = 18/33), missense (n = 9/33), and stop codon (n = 6/33). Developmental disability (n = 32/37), intellectual disability (n = 22/32), and cerebellar signs (n = 25/34) were the most striking clinical features. Cerebellar symptoms were divided into early-onset, late-onset, and progressive subgroups. Cerebellar hypoplasia, atrophy, or both (n = 16/25) were more frequent in individuals with missense variants in the DNA-binding domain. Epilepsy (n = 18/38), with prominent myoclonic seizure types (n = 11/18), was classified in (1) genetic generalized epilepsy (n = 10/18) with a syndromic diagnosis identifiable for 6: epilepsy with eyelid myoclonia (n = 5/6) and epilepsy with myoclonic absence (n = 1/6); (2) developmental and epileptic encephalopathy (n = 5/18); and (3) unclassified (n = 3/18). A participant with rapid deterioration of visual acuity and cone/rod dystrophy was reported. CONCLUSION: Missense variants in DNA-binding domain correlate to a more severe cerebellar phenotype. The RORA-related-neurodevelopmental disorder triad comprises developmental disability, cerebellar features, and a spectrum of myoclonic epilepsy.

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

Next-generation phenotyping: introducing phecodeX for enhanced discovery research in medical phenomics.

MOTIVATION: Phecodes are widely used and easily adapted phenotypes based on International Classification of Diseases codes. The current version of phecodes (v1.2) was designed primarily to study common/complex diseases diagnosed in adults; however, there are numerous limitations in the codes and their structure. RESULTS: Here, we present phecodeX, an expanded version of phecodes with a revised structure and 1,761 new codes. PhecodeX adds granularity to phenotypes in key disease domains that are under-represented in the current phecode structure-including infectious disease, pregnancy, congenital anomalies, and neonatology-and is a more robust representation of the medical phenome for global use in discovery research. AVAILABILITY AND IMPLEMENTATION: phecodeX is available at https://github.com/PheWAS/phecodeX.

Phenomics↗

PubMed2023

Phenotypic presentation of Mendelian disease across the diagnostic trajectory in electronic health records.

PURPOSE: To investigate the phenotypic presentation of Mendelian disease across the diagnostic trajectory in the electronic health record (EHR). METHODS: We applied a conceptual model to delineate the diagnostic trajectory of Mendelian disease to the EHRs of patients affected by 1 of 9 Mendelian diseases. We assessed data availability and phenotype ascertainment across the diagnostic trajectory using phenotype risk scores and validated our findings via chart review of patients with hereditary connective tissue disorders. RESULTS: We identified 896 individuals with genetically confirmed diagnoses, 216 (24%) of whom had fully ascertained diagnostic trajectories. Phenotype risk scores increased following clinical suspicion and diagnosis (P < 1 × 10-4, Wilcoxon rank sum test). We found that of all International Classification of Disease-based phenotypes in the EHR, 66% were recorded after clinical suspicion, and manual chart review yielded consistent results. CONCLUSION: Using a novel conceptual model to study the diagnostic trajectory of genetic disease in the EHR, we demonstrated that phenotype ascertainment is, in large part, driven by the clinical examinations and studies prompted by clinical suspicion of a genetic disease, a process we term diagnostic convergence. Algorithms designed to detect undiagnosed genetic disease should consider censoring EHR data at the first date of clinical suspicion to avoid data leakage.

Humans↗