Biology subjects

Cutting, G.

Publications and source records attributed to Cutting, G..

4 recordsLinked to original sources

bioRxiv2026

CFTR function in nasal airway cells from symptomatic and asymptomatic CF heterozygotes

Structured AbstractO_ST_ABSRationaleC_ST_ABSAn estimated 25 million people worldwide have one deleterious variant in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Chronic respiratory disease symptoms are at an increased prevalence in cystic fibrosis (CF) heterozygotes. ObjectivesDetermine the level of CFTR function in CF heterozygotes compared to individuals without CF-causing variants. Establish whether CFTR function differs between asymptomatic and symptomatic CF heterozygotes. MethodsIndividuals without respiratory symptoms or CF family history were recruited as controls. Heterozygotes were recruited from families with a CF individual harboring null alleles or c.1521_1523del (F508del) in CFTR. CFTR function was measured by short circuit current in primary human nasal epithelial cells (HNEs) from participants. Cell composition was assessed by single cell RNA sequencing. Measurements and Main ResultsCFTR function was variable in cells from control and heterozygous individuals. Mean CFTR function in asymptomatic null (8.8{+/-}0.5{micro}A/cm2 (SEM); n=30) and F508del (8.7{+/-}1.0{micro}A/cm2; n=22) heterozygotes was similar and significantly lower at 54.6% and 53.9% than controls (16.1{+/-}1.1{micro}A/cm2; n=24; p<0.0001). Mean CFTR function in symptomatic heterozygotes (8.4{+/-}1.0{micro}A/cm2; n =15) was 52.1% of controls and did not differ from asymptomatic heterozygotes (p=0.7803). Cell identities and proportions were equivalent between control and heterozygous cultures. HNEs from CF heterozygotes showed variable response to CFTR modulators. ConclusionsCFTR function in primary airway cells exhibits substantial interindividual variability and overlaps between controls and CF heterozygotes. CF heterozygotes exhibit approximately 50% of CFTR function in controls, regardless of symptom status. These findings suggest that respiratory symptoms in CF heterozygotes are influenced by factors beyond CFTR dysfunction. At a Glance CommentaryO_ST_ABSScientific Knowledge on the SubjectC_ST_ABSA growing body of evidence indicates that cystic fibrosis (CF) heterozygotes are at increased risk for a range of common and chronic respiratory diseases. Given that an estimated 10 million individuals in the United States are CF heterozygotes, this population may represent a substantial and underappreciated burden of CFTR-associated disease. However, CFTR function has not been well characterized in CF heterozygotes, and it remains uncertain whether observed clinical phenotypes reflect reduced CFTR activity. Resolving these issues will be essential for clarifying the pathobiology of common respiratory diseases and for evaluating the potential role of CFTR modulator therapy in symptomatic CF heterozygotes. What This Study Adds to the FieldAnalysis of 24 controls and 67 CF heterozygotes revealed substantial interindividual variability in CFTR function, as measured ex vivo in differentiated nasal airway epithelial cells. Mean CFTR function in CF heterozygotes was approximately 50% of that observed in controls. CFTR function did not differ significantly between symptomatic and asymptomatic heterozygotes. These findings suggest that reduced CFTR activity may contribute to symptom susceptibility in CF heterozygotes, but additional factors beyond CFTR dysfunction are likely required for the development of CF-like features. Ethical approval and participant consent statementAll participants provided written consent to the research study under IRB00116966 and/or IRB00235883 and consented to have their anonymized data published. All research was conducted in a fair and ethical manner.

genetics↗

bioRxiv2021

Leveraging TOPMed Imputation Server and Constructing a Cohort-Specific Imputation Reference Panel to Enhance Genotype Imputation among Cystic Fibrosis Patients

Cystic fibrosis (CF) is a severe genetic disorder that can cause multiple comorbidities affecting the lungs, the pancreas, the luminal digestive system and beyond. In our previous genome-wide association studies (GWAS), we genotyped [~]8,000 CF samples using a mixture of different genotyping platforms. More recently, the Cystic Fibrosis Genome Project (CFGP) performed deep ([~]30x) whole genome sequencing (WGS) of 5,095 samples to better understand the genetic mechanisms underlying clinical heterogeneity among CF patients. For mixtures of GWAS array and WGS data, genotype imputation has proven effective in increasing effective sample size. Therefore, we first performed imputation for the [~]8,000 CF samples with GWAS array genotype using the TOPMed freeze 8 reference panel. Our results demonstrate that TOPMed can provide high-quality imputation for CF patients, boosting genomic coverage from [~]0.3 - 4.2 million genotyped markers to [~]11 - 43 million well-imputed markers, and significantly improving Polygenic Risk Score (PRS) prediction accuracy. Furthermore, we built a CF-specific CFGP reference panel based on WGS data of CF patients. We demonstrate that despite having [~]3% the sample size of TOPMed, our CFGP reference panel can still outperform TOPMed when imputing some CF disease-causing variants, likely due to allele and haplotype differences between CF patients and general populations. We anticipate our imputed data for 4,656 samples without WGS data will benefit our subsequent genetic association studies, and the CFGP reference panel built from CF WGS samples will benefit other investigators studying CF.

genetics↗

bioRxiv2021

Accurate assignment of disease liability to genetic variants using only population data

PurposeThe growing size of public variant repositories prompted us to test the accuracy of predicting pathogenicity of DNA variants using population data alone. MethodsUnder the a priori assumption that the ratio of the prevalence of variants in healthy and affected populations form two distinct distributions (pathogenic and benign), we used a Bayesian method to assign probability of a variant belonging to either distribution. ResultsThe approach, termed BayPR, accurately parsed 300 of 313 expertly curated cystic fibrosis transmembrane conductance regulator (CFTR) variants: 284 of 296 pathogenic/likely pathogenic (P/LP) variants in one distribution and 16 of 17 benign/likely benign (B/LB) variants in another. BayPR produced an area under the receiver operating curve (AUC) of 0.99 for 103 functionally-confirmed missense CFTR variants, equal to or exceeding ten commonly used algorithms (AUC range: 0.54 to 0.99). Application of BayPR to expertly curated variants in eight genes associated with seven Mendelian conditions assigned [≥]80% disease-causing probability to 1,350 of 1,374 (98.3%) P/LP variants and [≤]20% to 22 of 23 (95.7%) B/LB variants. ConclusionAgnostic to variant type or functional effect, BayPR provides probabilities of pathogenicity for DNA variants responsible for Mendelian disorders using only variant counts in affected and unaffected population samples.

genetics↗

bioRxiv2019

Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework

BackgroundThe American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) clinical variant interpretation guidelines established criteria (PS3/BS3) for functional assays that specified a \"strong\" level of evidence. However, they did not provide detailed guidance on how functional evidence should be evaluated, and differences in the application of the PS3/BS3 codes is a contributor to variant interpretation discordance between laboratories. This recommendation seeks to provide a more structured approach to the assessment of functional assays for variant interpretation and guidance on the use of various levels of strength based on assay validation.\n\nMethodsThe Clinical Genome Resource (ClinGen) Sequence Variant Interpretation (SVI) Working Group used curated functional evidence from ClinGen Variant Curation Expert Panel-developed rule specifications and expert opinions to refine the PS3/BS3 criteria over multiple in-person and virtual meetings. We estimated odds of pathogenicity for assays using various numbers of variant controls to determine the minimum controls required to reach moderate level evidence. Feedback from the ClinGen Steering Committee and outside experts were incorporated into the recommendations at multiple stages of development.\n\nResultsThe SVI Working Group developed recommendations for evaluators regarding the assessment of the clinical validity of functional data and a four-step provisional framework to determine the appropriate strength of evidence that can be applied in clinical variant interpretation. These steps are: 1. Define the disease mechanism; 2. Evaluate applicability of general classes of assays used in the field; 3. Evaluate validity of specific instances of assays; 4. Apply evidence to individual variant interpretation. We found that a minimum of eleven total pathogenic and benign variant controls are required to reach moderate-level evidence in the absence of rigorous statistical analysis.\n\nConclusionsThe recommendations and approach to functional evidence evaluation described here should help clarify the clinical variant interpretation process for functional assays. Further, we hope that these recommendations will help develop productive partnerships with basic scientists who have developed functional assays that are useful for interrogating the function of a variety of genes.

genetics↗