Genomic, transcriptomic, and protein landscape profile of CFTR and cystic fibrosis.

Cystic Fibrosis (CF) is caused most often by removal of amino acid 508 (Phe508del, deltaF508) within CFTR, yet dozens of additional CFTR variants are known to give rise to CF and many variants in the genome are known to contribute to CF pathology. To address CFTR coding variants, we developed a sequence-to-structure-to-dynamic matrix for all amino acids of CFTR using 233 vertebrate species, CFTR structure within a lipid membrane, and 20 ns of molecular dynamic simulation to assess known variants from the CFTR1, CFTR2, ClinVar, TOPmed, gnomAD, and COSMIC databases. Surprisingly, we identify 18 variants of uncertain significance within CFTR from diverse populations that are heritable and a likely cause of CF that have been understudied due to nonexistence in Caucasian populations. In addition, 15 sites within the genome are known to modulate CF pathology, where we have identified one genome region (chr11:34754985-34836401) that contributes to CF through modulation of expression of a noncoding RNA in epithelial cells. These 15 sites are just the beginning of understanding comodifiers of CF, where utilization of eQTLs suggests many additional genomics of CFTR expressing cells that can be influenced by genomic background of CFTR variants. This work highlights that many additional insights of CF genetics are needed, particularly as pharmaceutical interventions increase in the coming years.

Nocturnal Oximetry-based Evaluation of Habitually Snoring Children.

RATIONALE: The vast majority of children around the world undergoing adenotonsillectomy for obstructive sleep apnea-hypopnea syndrome (OSA) are not objectively diagnosed by nocturnal polysomnography because of access availability and cost issues. Automated analysis of nocturnal oximetry (nSpO2), which is readily and globally available, could potentially provide a reliable and convenient diagnostic approach for pediatric OSA. METHODS: Deidentified nSpO2 recordings from a total of 4,191 children originating from 13 pediatric sleep laboratories around the world were prospectively evaluated after developing and validating an automated neural network algorithm using an initial set of single-channel nSpO2 recordings from 589 patients referred for suspected OSA. MEASUREMENTS AND MAIN RESULTS: The automatically estimated apnea-hypopnea index (AHI) showed high agreement with AHI from conventional polysomnography (intraclass correlation coefficient, 0.785) when tested in 3,602 additional subjects. Further assessment on the widely used AHI cutoff points of 1, 5, and 10 events/h revealed an incremental diagnostic ability (75.2, 81.7, and 90.2% accuracy; 0.788, 0.854, and 0.913 area under the receiver operating characteristic curve, respectively). CONCLUSIONS: Neural network-based automated analyses of nSpO2 recordings provide accurate identification of OSA severity among habitually snoring children with a high pretest probability of OSA. Thus, nocturnal oximetry may enable a simple and effective diagnostic alternative to nocturnal polysomnography, leading to more timely interventions and potentially improved outcomes.

Five cases of missed cystic fibrosis heterozygous mutations identified after a positive newborn screen on a sibling.

In Michigan (MI), NBS for CF was started in October 2007 using the IRT/DNA protocol. In 2016, a component of the Hologic molecular test kit used by the MI NBS lab was recalled (40 CF mutation 2nd tier test). This recall had a major impact on states using the Hologic test kits in their NBS programs. Michigan specimens were sent to another state's NBS Lab for 2nd tier testing using the Luminex 60 mutation test kit until the Luminex kit could be procured and validated in MI. In this report, we present five cases born during this time period. These cases were initially reported out as having normal NBS results for CF but had heterozygous F508 del (c.1521_1523delCTT) mutations later identified. Of the five cases, one was diagnosed with CF (Case1), one with CF related metabolic syndrome (CRMS), and the other three were carriers.

Improving the Rate of Sufficient Sweat Collected in Infants Referred for Sweat Testing in Michigan.

Objective. Sweat collected for testing should have quantity not sufficient (QNS) rate of ≤10% in babies ≤3 months of age. Michigan (MI) cystic fibrosis (CF) centers' QNS rates were 12% to 25% in 2009. This project was initiated to reduce sweat QNS rates in MI. Methods/Steps. (a) Each center's sweat testing procedures were reviewed by a consultant. (b) Each center received a report with recommendations to improve QNS rates. (c) Technicians visited other participating centers to observe their procedures. Results. A total of 778 infants were identified as positive via CF newborn screening over a 2-year period. The mean age at time of sweat test was 23.2 days (SD ± 13.0 days). The overall QNS percent decreased from 14.4% to 9.5% (P = .04) during the study. Conclusion. This project and teamwork approach led to a decrease of sweat test QNS rates, opportunities to solve a common problem, and improved quality of care.

Evaluation of genetic counseling among cystic fibrosis carriers, Michigan Newborn Screening.

OBJECTIVE: A quality improvement (QI) strategy to improve the rate of genetic counseling (GC) services was initiated in cystic fibrosis (CF) care Center E in 2010. This statewide study was conducted to determine: (1) GC rates before and after implementation of the QI strategy at Center E; (2) characteristics associated with not receiving GC; and (3) topic areas addressed during GC. METHODS: The retrospective study included 1,097 CF carriers born from 2008 to 2011 identified through Michigan's Newborn Screening Program. Rate of GC services was determined for Center E and the other four CF centers before and after the QI change. Bivariate and multivariable logistic regression was used to determine associations between select characteristics and not receiving GC. Topic areas discussed during GC sessions were assessed using frequency tables. RESULTS: Rate of GC services in Center E increased from 23% in 2008-2010 to 91% in 2011, while at the other centers approximately 92% received GC services across those years. In 2008-2010, being seen at Center E and black race were significantly associated with increased likelihood of not receiving GC services in adjusted analyses. In 2011, neither characteristic was associated with receipt of GC. Of 16 target topic areas, all were discussed in 85% of GC sessions. CONCLUSIONS: Implementing a QI strategy of providing sweat test results at the GC appointment within Center E resulted in more CF carriers receiving comprehensive GC services. Center-specific procedure differences should be assessed to increase rate of GC services following a positive CF newborn screen.

Predictors of insufficient sweat production during confirmatory testing for cystic fibrosis.

Michigan's Newborn Screening (NBS) Program began statewide screening for cystic fibrosis (CF) in October 2007. Confirmatory sweat testing is performed in infants having initial immunoreactive trypsinogen concentrations ≥ 99.8th percentile or ≥ 96 th percentile and at least one CF mutation identified by DNA analysis. Some infants fail to produce a sufficient quantity of sweat (QNS-quantity not sufficient) to test for CF, meaning disease confirmation is delayed and sweat testing is later repeated. In this study, we evaluate predictors of QNS results. Information from the linked birth certificates and NBS diagnostic confirmation data were used. The study population was resident infants born in Michigan in 2008 who underwent a sweat test. Bivariate analyses revealed that preterm birth, low birth weight, CF care center, and race were significantly associated with QNS sweat testing results. Adjusted analyses indicated that preterm infants were 2.4 times more likely to have QNS results (95% CI 0.9, 6.4). When age at time of test, accounting for gestational age (gestational age at delivery plus postdelivery age of life=corrected age), was used in the multivariable model, infants <39 weeks were 7.4 times more likely to have QNS results (95% CI 2.5, 21.8). Waiting to sweat test until an infant is aged 39 weeks or more (corrected age) would likely reduce the rate of QNS results, thereby reducing the burden of repeat sweat testing on families and healthcare providers. Further research is necessary to understand the impact of potential delays in diagnosis/treatment relative to postponing sweat testing.