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At least 19 recordsLinked to original sources

Family genetic risk communication and reverse cascade testing in the BabySeq project.

PURPOSE: Genomic sequencing of newborns can initiate disease surveillance and therapy for children and may identify at-risk relatives through reverse cascade testing. We explored genetic risk communication and reverse cascade testing among families of newborns who underwent exome sequencing and were identified as having a risk for an autosomal dominant disease. METHODS: We conducted semistructured interviews with parents of newborns enrolled in the BabySeq Project who had a pathogenic or likely pathogenic variant associated with an autosomal dominant childhood- and/or adult-onset disease returned. We used directed content analysis to derive themes. RESULTS: From 11 families, all first-degree relatives (n = 32, 100%), 29 second-degree relatives (76%), and 26 third-degree relatives (43%) were informed of their risk. All parents (n = 22, 69% of first-degree relatives), 4 (11%) second-degree relatives, and 1 (2%) third-degree relatives underwent cascade testing. Most parents preferred to handle risk communication themselves. Parents with positive cascade testing but no associated symptoms were less inclined to share findings with relatives but highly motivated to share results if the variant's associated disease severity was high, as perceived with adult-onset conditions. One new subtheme, family member traits, was identified and defined as a relative's propensity to anxiety/concern after risk communications but did not diminish risk communication. CONCLUSION: Findings can inform more effective notification and testing practices for families of newborns at risk for hereditary genetic conditions.

Humans

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 (&#x3b1; = 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

Incidental MSH6 Germline Pathogenic Variant Identified through Tumor-only Comprehensive Genomic Profiling in a Patient with Small Cell Lung Cancer.

A 55-year-old woman was diagnosed with limited-disease small cell lung cancer (LD-SCLC) after incidental detection of a lung nodule. First-line chemotherapy achieved partial response, but recurrence occurred after one year. During second-line therapy, comprehensive genomic profiling (CGP) revealed a germline MSH6 frameshift mutation. Although lung tumor immunohistochemistry showed the retained expression of mismatch repair (MMR) protein, a prior colon cancer specimen showed the loss of MSH6 expression and deficient MMR expression. Germline genetic testing confirmed Lynch syndrome. Cascade testing identified the same mutation in her daughter. This case outlines a tumor-to-germline workflow with testing of at-risk relatives and highlights the importance of prudent interpretation of presumed germline variants.

Humans

Utility of High-Throughput Genomic Analysis for Genetic Counseling in Large Family with Wilson Disease Carrying a Novel 28-bp ATP7B Splice-Junction Deletion.

Background/Objectives: Wilson disease (WD) is an autosomal recessive disorder of copper metabolism caused by pathogenic variants in the ATP7B gene. Early diagnosis and appropriate treatment are essential for preventing irreversible complications. This study demonstrated the clinical utility of integrated high-throughput genomic analysis for molecular diagnosis and genetic counseling in a large Thai family affected by WD. Methods: A 32-year-old woman with clinical features suggestive of WD underwent clinical, biochemical, and molecular genetic evaluations, including sequencing of the entire ATP7B gene and SNP microarray. Fluorescent PCR followed by capillary electrophoresis was used for segregation analysis in available family members. SNP microarray analysis and whole-exome sequencing were performed on the proband's husband to identify pathogenic variants in the ATP7B gene and other disease-associated genes for reproductive risk assessment. Results: The proband presented with hepatic dysfunction, Kayser-Fleischer rings, low serum ceruloplasmin, and a family history of fatal liver disease. She also developed progressive weakness, with nerve conduction findings consistent with axonal sensorimotor polyneuropathy predominantly affecting the lower limbs. Sequencing identified a novel homozygous 28-bp splice-junction deletion, c.4022-24_4025del, which disrupted the canonical splice acceptor site at the intron 19/exon 20 boundary and was classified as pathogenic variant. Segregation analysis confirmed carrier status in the proband's father and identified heterozygous carrier or homozygous wild-type status among her living siblings. SNP microarray analysis revealed a 46.7 Mb copy-neutral long contiguous stretch of homozygosity (CN-LCSH) encompassing ATP7B, with CN-LCSH regions accounting for 2.046% of the total autosomal genome. These findings potentially reflected segmental uniparental isodisomy or identity by descent, while the overall homozygosity pattern did not support recent consanguinity. Combined genomic analyses of the proband's husband revealed no pathogenic or likely pathogenic ATP7B variants. Based on the available testing, all offspring are expected to be heterozygous carriers, and the risk of an affected child is considered very low. Conclusions: This study highlights the value of integrated genomic analysis for molecular diagnosis, cascade testing, and reproductive risk counseling. Further functional studies should be conducted to validate their pathogenicity.

ATP7B

Guidelines for Genetic Testing of Peripheral Nerve Disorders.

Inherited peripheral neuropathies (IPNs) comprise a clinically and genetically heterogeneous group of disorders affecting approximately 1 in 2500 individuals and represent one of the most common inherited neurologic diseases. The rapidly expanding identification of disease-causing genes and the widespread implementation of next-generation sequencing (NGS) have fundamentally transformed the diagnostic evaluation of these disorders. Contemporary molecular testing has substantially increased diagnostic yield, shortened the diagnostic delay, refined disease classification, and strengthened genotype-phenotype correlations. In the United States, NGS-based multigene panels have become the most cost-effective first-line molecular diagnostic approach for most patients with suspected inherited neuropathies, whereas phenotype-directed single-gene testing remains appropriate in selected clinical circumstances and in healthcare systems in which access to comprehensive sequencing is limited. Despite these advances, challenges continue to affect diagnostic accuracy, including interpretation of variants of uncertain significance, detection of copy number variants and repeat expansions, technical limitations associated with highly homologous genomic regions such as SORD, and variability in gene content and analytic performance among commercially available testing platforms. Accurate diagnosis therefore requires integration of clinical phenotype, electrodiagnostic findings, family history, and molecular data. Establishing a precise genetic diagnosis has become increasingly important because it improves prognostic accuracy, guides genetic counseling and cascade testing, identifies patients with treatable hereditary neuropathies such as transthyretin amyloidosis, and facilitates enrollment in gene-specific clinical trials and emerging precision therapies. An evidence-based, phenotype-driven approach that incorporates contemporary molecular technologies is essential to maximize diagnostic efficiency while recognizing the strengths and limitations of currently available genetic testing strategies.

Charcot&#x2013;Marie&#x2013;tooth disease

Challenges of genomic testing for patients and clinicians in Latin America: Foundations of a qualitative multi-country study.

Genomic medicine is expanding across Latin America (LATAM), yet access to essential ancillary services such as genetic counselling remains limited. 'Latin-SEQ' is a study that provides whole exome sequencing (WES) for neuromuscular diseases across 18 countries, aiming to improve diagnostic rates and generate region-specific genetic insights. However, funding constraints exclude genetic counselling and cascade testing, raising concerns about equitable and harm-free care. This paper reports early findings from 'Latin-SEQ Plus,' a mixed-methods study exploring patient and healthcare practitioner (HCP) perspectives on WES and genetic counselling. Data were generated via surveys with patients and HCPs, and participatory workshops with HCPs across six countries. We found that patients strongly valued genetic testing for diagnostic clarity, improved care, and family planning. HCPs acknowledged the diagnostic benefits of WES but highlighted absence of local genetic counselling services, inconsistent pre and post-test practices, and uncertainty in managing incidental findings and variants of uncertain significance (VUS). Psychological impacts related to WES results are not always addressed, underscoring risks of psychological and emotional harm for patients. Access to WES and genetic counselling is limited in LATAM due to financial hardship and the absence of a clear genetic counselling infrastructure. Our findings also reveal a mismatch between patient expectations and HCPs' capacity to deliver comprehensive genomic care. We argue for urgent investment in genetic counselling infrastructure, HCP training, culturally tailored resources, and policy frameworks to support equitable implementation of genomic medicine in LATAM.

Humans

Genomics-informed neuropsychiatric care for neurodevelopmental disorders: Results from a multidisciplinary clinic.

PURPOSE: Patients with neurodevelopmental disorders (NDDs) have high rates of neuropsychiatric comorbidities. Genomic medicine may help guide care because pathogenic variants are identified in up to 50% of patients with NDDs. We evaluate the impact of a genomics-informed, multidisciplinary, neuropsychiatric specialty clinic on the diagnosis and management of patients with NDDs. METHODS: We performed a retrospective study of 316 patients from the University of California, Los Angeles Care and Research in Neurogenetics Clinic, a genomics-informed multidisciplinary clinic. RESULTS: Among the 246 patients who underwent genetic testing, 41.8% had a pathogenic or likely pathogenic variant. Patients had 62 different genetic diagnoses, with 12 diagnoses shared by 2 or more patients, whereas 50 diagnoses were found in only single patients. Genetic diagnosis resulted in direct changes to clinical management in all patients with a pathogenic or likely pathogenic variant, including cascade testing (30.6%), family counseling (22.2%), medication changes (13.9%), clinical trial referral (2.8%), medical surveillance (30.6%), and specialty referrals (69.4%). CONCLUSIONS: A genomics-informed model can provide significant clinical benefits to patients with NDDs, directly affecting management across multiple domains for most diagnosed patients. As precision treatments advance, establishing a genetic diagnosis will be critical for proper management. With the growing number of rare neurogenetic disorders, clinician training should emphasize core principles of genomic medicine over individual syndromes.

Humans

CanVar-UK: A collaborative platform for germline interpretation in cancer susceptibility genes.

Germline variants in cancer susceptibility genes (CSGs) are typically inherited rather than arising de novo. Hence, wide cascade testing of families across geographies is common, meaning consistency in variant classification is particularly critical. Variant interpretation requires collation of variant-level data from diverse sources, as well as assembly of comprehensive clinical data, often necessitating sharing of information between genomic testing centers. Here, we describe CanVar-UK, a freely accessible web platform bespoke designed to support interpretation of germline CSG variants. CanVar-UK contains variant-level data for over 1.1 million single-nucleotide variants (SNVs), comprising all possible coding SNVs in 116 established CSGs. The data sources with which variants are annotated include in silico scores from 11 clinically relevant tools, population allele frequencies from gnomAD v4.1, case counts from multiple cohorts, including National Health Service (NHS) clinical laboratory testing, variant-level readouts from 47 selected functional and splicing datasets across 19 CSGs, genetic epidemiology studies, and live linkage to existing consensus classifications in the ClinVar database. The diagnostic discussion forum is only available to registered diagnostic scientist users. Through this, a variant-tagged email message can be dispatched in real time across the diagnostic forum community of >1,500 users, with all exchanges and classifications captured and stored in the platform. Already widely used by NHS diagnostic clinical scientists in the UK, CanVar-UK has a rapidly growing international diagnostic user base (>800 UK and >600 non-UK registered users). Survey of the NHS diagnostic user community illustrates the wide-ranging utility of CanVar-UK within their clinical workflows for interpretation of germline CSG variants.

Journal Article

Financing and health system capacity for precision medicine in Asia: a six country landscape analysis.

BACKGROUND: Precision medicine (PM) adoption is accelerating across Asia, but implementation remains uneven due to differences in financing, infrastructure, governance, and health-system readiness. OBJECTIVES: To examine how six Asian countries (Singapore, South Korea, China, Malaysia, Thailand, and Indonesia) adopt, finance, and integrate PM technologies, and identify common implementation patterns and challenges. METHODS: A landscape review of peer-reviewed literature, government publications, and HTA reports (2010-2026) was conducted, supplemented by stakeholder consultations. PM applications were grouped into public health screening (hereditary breast and ovarian cancer [HBOC] and familial hypercholesterolemia [FH] cascade testing), next-generation sequencing (NGS) applications (rare diseases, oncology, pharmacogenomics), and AI-enabled PM. Evidence was synthesized across access, awareness, reimbursement, and implementation. RESULTS: Public health genomic screening demonstrated the highest implementation readiness, followed by precision oncology, while rare disease diagnostics remained infrastructure-dependent and pharmacogenomics and AI-enabled PM platforms were at earlier stages. Four readiness profiles emerged: highly aligned systems; reimbursement-constrained systems with strong governance and infrastructure; systems strengthening governance, public financing and infrastructure; and strategy-led systems expanding implementation through pilot programs and referral centers. CONCLUSIONS: PM implementation across Asia remains heterogeneous. The identified readiness profiles highlight governance, financing, and infrastructure priorities for sustainable and equitable PM diffusion.

Asia

LDLR Variant Classification Through Activity-Normalized Prime Editing Screening.

BACKGROUND: Inherited variants in the LDL (low-density lipoprotein) receptor (LDLR) gene are the most common cause of familial hypercholesterolemia, significantly increasing coronary artery disease risk. Early identification of pathogenic LDLR variants enables prompt lipid-lowering therapy and cascade testing of at-risk relatives; however, most LDLR variants observed in the population have uncertain or absent clinical classifications, leaving many patients without actionable information. METHODS: We developed the first activity-normalized prime editing screening pipeline to measure the impact of 5184 LDLR coding variants on LDL-cholesterol (LDL-C) uptake. Each prime editing guide RNA is paired with a genotypic outcome reporter to correct for variable editing efficiency, overcoming a key limitation of previous pooled genome editing screens. A statistical framework further improves variant effect estimates by jointly analyzing all missense variants at each amino acid position. RESULTS: We show that prime editing of the reporter construct correlates with endogenous variant installation frequency, validating the activity normalization approach. The resulting scores capture a continuous spectrum of functional effects, robustly separate pathogenic versus benign ClinVar variants, and show concordance with LDL-C levels in UK Biobank participants. We calibrate functional evidence strengths to the ACMG/AMP variant interpretation framework, enabling integration into a clinical variant classification workflow. By combining functional, computational, population, and contextual evidence, 322 of 434 LDLR variants currently classified as variants of uncertain significance, conflicting, or absent from ClinVar appear to meet evidence thresholds for reclassification and can be prioritized for expert review, substantially expanding the pool of actionable variant classifications. The screen also reveals a cluster of gain-of-function variants in LDLR class A repeat 5, at least some of which enhance LDL-C uptake through increased apolipoprotein B interaction, with implications for therapeutic genome editing. Last, prime editing uniquely detects splice-altering coding variants missed by cDNA-based screens and pathogenicity predictors, revealing an advantage of endogenous variant installation. CONCLUSIONS: Altogether, activity-normalized prime editing provides a scalable framework for LDLR variant classification that substantially expands the proportion of variants with evidence for genetic diagnosis and reveals novel biology with therapeutic relevance.

CRISPR screening

A Novel SLC25A4 Variant Causing Mitochondrial Dysfunction, Myopathy and Cardiomyopathy: A Functional and Molecular Characterization.

SLC25A4, solute carrier family 25 member 4, gene is a member of the mitochondrial carrier subfamily within the solute carrier protein family. Pathogenic variants in SLC25A4 are associated with a spectrum of mitochondrial disorders that exhibit variable inheritance patterns and clinical manifestations. Specifically, dominantly inherited variants are typically associated with progressive external ophthalmoplegia with mitochondrial DNA deletions, recessively inherited variants are linked to myopathy and cardiomyopathy, and de novo variants can result in early-onset fatal disease presentations. In this study, we aimed to identify and characterize the disease-causing mutation(s) in a nine-year-old female patient from a consanguineous Saudi family. The patient was asymptomatic until the age of 3 years, when she presented with cardiomyopathy and myopathy. Comprehensive genetic analysis inclusive of whole exome sequencing and segregation analysis using Sanger sequencing identified an SLC25A4 variant (NM_001151.4: exon 2: c.112-1G>C) as the most likely cause of the disease. To assess transcript-level effects, we performed RT-PCR on RNA extracted from the patient's cultured lymphoblast cell lines (LCLs) and fibroblast cell lines (FCLs). RT-PCR analysis demonstrated that the variant causes aberrant splicing, resulting in a 6 bp in-frame deletion (p.Gln37_Val38del) in the ANT1 protein. Quantitative RT-PCR demonstrated reduced SLC25A4 transcript levels in both FCLs and LCLs. Quantitative PCR analysis of mitochondrial DNA demonstrated a trend toward increased mtDNA copy number in patient-derived FCLs compared with controls, suggesting a possible compensatory response to mitochondrial dysfunction. Furthermore, Seahorse assays revealed marked reductions in both oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) in patient-derived FCLs compared with controls. These findings expand the molecular and functional spectrum of SLC25A4-associated disease and may inform clinical practice, including genetic interventions such as preimplantation genetic diagnosis, premarital genetic screening, targeted genetic counseling, and cascade testing of at-risk family members.

Humans

[Evaluation of cascade filtration on a test sample].

Double filtration or filtration in series can be consider as an effective means of removing proteins such as IgG, IgM, immune complexes, lipoproteins from plasma. In this study, we evaluated, using a biological and technical protocol: Kuraray (2A and 4A) and Dideco (Albusave) filters. Results were good by analysis of the sieving coefficient, but the method had 2 inconveniences: problem of slogging of the columns after filtering 2 liters and too high a reject coefficient of albumin. No effective solutions exist to avoid these two problems. Nevertheless, the filtration in series technic seems to be a good method for removing cholesterol and we have undertaken new studies to improve this system.

Blood Component Removal

Gentamicin inhibits agonist stimulation of the phosphatidylinositol cascade in primary cultures of rabbit proximal tubular cells and in rat renal cortex.

A growing body of evidence indicates that aminoglycoside antibiotics interact with phosphoinositides and this has led to the hypothesis that these drugs perturb the phosphatidylinositol (PI) cascade. To test this hypothesis we examined the effect of gentamicin on agonist stimulation of the PI cascade in primary culture of rabbit proximal tubular cells (RPTC) and in rat renal cortex. Parathyroid (PTH) (10(-6) M) stimulated a significant increase in total inositol phosphates, inositol monophosphate and inositol trisphosphate, but not inositol bisphosphate in RPTC with the peak effect at 2 min. This effect was completely inhibited in RPTC exposed to 10(-3) M gentamicin for 48 and 24 hr. In other experiments we demonstrated that angiotensin II, phenylephrine, bradykinin and arginine vasopressin (all at 10(-6) M) stimulated inositol trisphosphate generation in control RPTC but not in cells exposed to 10(-3) M gentamicin for 24 h. In contrast gentamicin did not block PTH-stimulation of cyclic AMP generation, which indicates that gentamicin did not prevent PTH from interacting with its plasma membrane receptor. PTH also stimulated redistribution of protein kinase C from the cytosolic to the membrane fraction of RPTC. This effect was completely abolished in RPTC exposed to 10(-3) M gentamicin for 2 days. PTH given i.p. to rats stimulated the redistribution of protein kinase C from the cytosolic to the membrane fraction of renal cortex. This effect was completely inhibited in rats injected with gentamicin, 100 mg/kg per day for 2 days. The

Animals

Beneficial effect of cyclooxygenase inhibition on adverse hemodynamic responses after protamine.

The hypothesis that adverse effects observed when heparin is antagonized by protamine are mediated by metabolites of the arachidonic acid cascade was tested during general anesthesia (enflurane, fentanyl) in 16 pigs classified into two groups. In the first group (n = 9), effects of intravenously administered protamine on systemic hemodynamics, blood/gas tensions, and arterial and mixed-venous prostanoid levels were studied. The second group (n = 7) was pretreated with indomethacin 10 mg/kg, and the same measurements were made. All pigs received heparin 150 units/kg. When protamine 1.1 +/- 0.1 mg/kg was administered over 3 minutes, marked hemodynamic alterations were observed in group 1: pulmonary artery pressure and pulmonary vascular resistance increased, and left ventricular end-diastolic and systemic arterial pressures decreased. Arterial and mixed-venous PO2 values deteriorated in all pigs in group 1 at the end of protamine infusion. These alterations were accompanied by significantly elevated prostanoid levels in arterial and mixed-venous plasma samples: Thromboxane A2, prostaglandin F2 alpha, KH2-PGF2 alpha (a metabolite of prostaglandin F2 alpha), and prostacyclin were maximally elevated at completion of protamine and remained significantly above control values at 5 minutes but were not significantly different from control after 10 minutes. Blocking the cyclooxygenase cascade by pretreatment of the pigs with indomethacin (group 2) prevented hemodynamic and blood gas alterations. It is concluded that in pigs the detrimental side effects associated with the use of protamine to reverse heparin are mediated by metabolites of the cyclooxygenase cascade.(ABSTRACT TRUNCATED AT 250 WORDS)

Anesthesia, General

The tap test: confirmation of a simple, rapid, inexpensive, and reliable indicator of fetal pulmonary maturity.

The tap test was previously described, and preliminary experience suggested it might be a rapid, inexpensive, and reliable indicator of fetal lung maturity. In this expanded series of 332 patients delivered of infants within 72 hours of amniotic fluid analysis, the predictive values for mature test results at 2, 5, and 10 minutes were 98.9% (182 of 184), 97.4% (221 of 227), and 97.1% (233 of 240), respectively. Predictive values for immature test results were 41.2% (61 of 148), 54.3% (57 of 105), and 60.9% (56 of 92). For the phospholipid profile the predictive value was 96.9% (186 of 192) for a mature test result and 40.7% (57 of 140) for an immature result. These observations, coupled with its methodologic simplicity, make the tap test a good first step in a cascade scheme of tests for fetal lung maturity and a valuable test in a facility where the phospholipid profile is not available 24 hours a day.

Amniotic Fluid

Cholesterol palmitate in amniotic fluid: confirmation of a simple, rapid, inexpensive, and reliable indicator of fetal pulmonary maturity.

The cholesterol test was previously described and preliminary experience suggested it might be a rapid, inexpensive, and reliable indicator of fetal lung maturity. In this expanded series of 1342 patients delivered of infants within 72 hours of amniotic fluid analysis, the predictive value for mature test was 98.6%. Predictive value for immature test was 55.4%. For the phospholipid profile the predictive value was 97.0% for a mature test result, 31.2% for an immature result. These observations, coupled with its methodologic simplicity, make the cholesterol palmitate test a good first step in a cascade scheme of tests for fetal lung maturity and a valuable test in a facility where the phospholipid profile is not available 24 hours a day.

Amniocentesis