Guidelines for implementation of cystic fibrosis newborn screening programs: Cystic Fibrosis Foundation workshop report

Newborn screening for cystic fibrosis offers the opportunity for early intervention and improved outcomes. This summary, resulting from a workshop sponsored by the Cystic Fibrosis Foundation to facilitate implementation of widespread high quality cystic fibrosis newborn screening, outlines the steps necessary for success based on the experience of existing programs. Planning should begin with a workgroup composed of those who will be responsible for the success of the local program, typically including the state newborn screening program director and cystic fibrosis care center directors. The workgroup must develop a screening algorithm based on program resources and goals including mechanisms available for sample collection, regional demographics, the spectrum of cystic fibrosis disease to be detected, and acceptable failure rates of the screen. The workgroup must also ensure that all necessary guidelines and resources for screening, diagnosis, and care be in place prior to cystic fibrosis newborn screening implementation. These include educational materials for parents and primary care providers; systems for screening and for providing diagnostic testing and counseling for screen-positive infants and their families; and protocols for care of this unique population. This summary explores the benefits and risks of various screening algorithms, including complex situations that can occur involving unclear diagnostic results, and provides guidelines and sample materials for state newborn screening programs to develop and implement high quality screening for cystic fibrosis

Next-Generation Sequencing of HIV-1 Single Genome Amplicons

The analysis of HIV-1 sequences has helped understand the viral molecular epidemiology, monitor the development of antiretroviral drug resistance, and design candidate vaccines. The introduction of single genome amplification (SGA) has been a major advancement in the field, allowing for the characterization of multiple sequences per patient while preserving linkage among polymorphisms in the same viral genome copy. Sequencing of SGA amplicons is performed by capillary Sanger sequencing, which presents low throughput, requires a high amount of template, and is highly sensitive to template/primer mismatching. In order to meet the increasing demand for HIV-1 SGA amplicon sequencing, we have developed a platform based on benchtop next-generation sequencing (NGS) (IonTorrent) accompanied by a bioinformatics pipeline capable of running on computer resources commonly available at research laboratories. During assay validation, the NGS-based sequencing of 10 HIV-1 env SGA amplicons was fully concordant with Sanger sequencing. The field test was conducted on plasma samples from 10 US Navy and Marine service members with recent HIV-1 infection (sampling interval: 2005-2010; plasma viral load: 5,884-194,984 copies/ml). The NGS analysis of 101 SGA amplicons (median: 10 amplicons/individual) showed within-individual viral sequence profiles expected in individuals at this disease stage, including individuals with highly homogeneous quasispecies, individuals with two highly homogeneous viral lineages, and individuals with heterogeneous viral populations. In a scalability assessment using the Ion Chef automated system, 41/43 tested env SGA amplicons (95%) multiplexed on a single Ion 318 chip showed consistent gene-wide coverage \u3e50×. With lower sample requirements and higher throughput, this approach is suitable to support the increasing demand for high-quality and cost-effective HIV-1 sequences in fields such as molecular epidemiology, and development of preventive and therapeutic strategies

Towards fast algorithms for the preference consistency problem based on hierarchical models

In this paper, we construct and compare algorithmic approaches to solve the Preference Consistency Problem for preference statements based on hierarchical models. Instances of this problem contain a set of preference statements that are direct comparisons (strict and non-strict) between some alternatives, and a set of evaluation functions by which all alternatives can be rated. An instance is consistent based on hierarchical preference models, if there exists an hierarchical model on the evaluation functions that induces an order relation on the alternatives by which all relations given by the preference statements are satisfied. Deciding if an instance is consistent is known to be NP-complete for hierarchical models. We develop three approaches to solve this decision problem. The first involves a Mixed Integer Linear Programming (MILP) formulation, the other two are recursive algorithms that are based on properties of the problem by which the search space can be pruned. Our experiments on synthetic data show that the recursive algorithms are faster than solving the MILP formulation and that the ratio between the running times increases extremely quickly

Computation and complexity of preference inference based on hierarchical models

Preference Inference involves inferring additional user preferences from elicited or observed preferences, based on assumptions regarding the form of the user\u27s preference relation. In this paper we consider a situation in which alternatives have an associated vector of costs, each component corresponding to a different criterion, and are compared using a kind of lexicographic order, similar to the way alternatives are compared in a Hierarchical Constraint Logic Programming model. It is assumed that the user has some (unknown) importance ordering on criteria, and that to compare two alternatives, firstly, the combined cost of each alternative with respect to the most important criteria are compared; only if these combined costs are equal, are the next most important criteria considered. The preference inference problem then consists of determining whether a preference statement can be inferred from a set of input preferences. We show that this problem is coNP-complete, even if one restricts the cardinality of the equal-importance sets to have at most two elements, and one only considers non-strict preferences. However, it is polynomial if it is assumed that the user\u27s ordering of criteria is a total ordering; it is also polynomial if the sets of equally important criteria are all equivalence classes of a given fixed equivalence relation. We give an efficient polynomial algorithm for these cases, which also throws light on the structure of the inference

Early pulmonary manifestation of cystic fibrosis in children with the DeltaF508/R117H-7T genotype

We report 3 cystic fibrosis newborn screen-positive infants with the DeltaF508/R117H-7T genotype who had Pseudomonas aeruginosa detected in oropharyngeal cultures early in life and a fourth who had pulmonary symptoms and Gram-negative growth on multiple oropharyngeal cultures. All 4 patients were followed prospectively from the time of genetic diagnosis. As many regions implement newborn screening for cystic fibrosis, there is concern regarding which mutations should be included in genetic panels used to make the cystic fibrosis diagnosis. Some have recommended that mutations not specifically associated with classic cystic fibrosis be excluded. Our cases highlight the importance of considering keeping so-called mild mutations on cystic fibrosis newborn screening panels and the need to follow children with these mutations closely

Bile acids modulate the Golgi membrane fission process via a protein kinase Ceta and protein kinase D-dependent pathway in colonic epithelial cells.

Deoxycholic acid (DCA) is a secondary bile acid that modulates signalling pathways in epithelial cells. DCA has been implicated in pathogenesis of colon carcinoma, particularly by activation of the protein kinase C (PKC) pathway. Ursodeoxycholic acid (UDCA), a tertiary bile acid, has been observed to have chemopreventive effects. The aim of this study was to investigate the effect of DCA and UDCA on the subcellular localization and activity of PKCeta and its downstream effects on Golgi structure in a colon cancer cell model. PKCeta expression was localized to the Golgi in HCT116 colon cancer cells. DCA induced fragmentation of the Golgi in these cells following activation of PKCeta and its downstream effector protein kinase D (PKD). Pretreatment of cells with UDCA or a glucocorticoid, dexamethasone, inhibited DCA-induced PKCeta/PKD activation and Golgi fragmentation. Knockdown of glucocorticoid receptor (GR) expression using small interfering RNA or inhibition using the GR antagonist mifepristone attenuated the inhibitory effect of UDCA on Golgi fragmentation. Elevated serum and faecal levels of DCA have been previously reported in patients with ulcerative colitis (UC) and colon cancer. Analysis of Golgi architecture in vivo using tissue microarrays revealed Golgi fragmentation in UC and colorectal cancer tissue. We have demonstrated that DCA can disrupt the structure of the Golgi, an organelle critical for normal cell function. Inhibition of this DCA-induced Golgi fragmentation by UDCA was mediated via the GR. This represents a potential mechanism of observed chemopreventive effects of UDCA in benign and malignant disease of the colon

Oropharyngeal flora in healthy infants: observations and implications for cystic fibrosis care

OBJECTIVE: The purpose of this preliminary study was to determine normal oropharyngeal flora in healthy, non-CF infants in order to help care givers better interpret culture results obtained from infants with CF. METHODS: Oropharyngeal cultures were obtained from 104 healthy infants \u3c12 months old. Cultures were obtained using the same methods as for CF patients and were inoculated onto routine CF culture media. Approximately 20 infants from each of 5 age groups\u3e(0-2 days, 3 days to \u3c3 \u3emonths, 3 months to \u3c6 \u3emonths, 6 months to \u3c9 months or 9 months to\u3e\u3c1 \u3eyear) were included in the well child sample. In addition, we reviewed serial results of upper airway cultures obtained during the first year of life from 20 CF-affected infants whose diagnosis was suggested by newborn screening. RESULTS: Well infants in the first 48 hr of life had very few pathogenic organisms found in their oropharyngeal cultures; 1/21 had S. aureus. Of the 83 samples from infants over 48 hr of age, we found that 27% (23/83) had S. aureus in their oropharyngeal cultures. Many infants had polymicrobial cultures. Eleven percent of culture samples had E. coli, E. cloacae, H. influenzae, or M. catarrhalis. Three of 83 cultures were positive for non-mucoid Ps. aeruginosa (3.6%), while 2 others were positive for Ps. putida. CONCLUSION: Healthy infants can have multiple gram-negative and gram-positive organisms recovered from their oropharynx. S. aureus and enteric gram-negative organisms, including non-mucoid Ps. aeruginosa, can be found in the oropharynx of well children up to 1 year of age. Care should be taken to not over interpret the presence of some of these organisms in the oropharyngeal cultures of asymptomatic CF infants

Sweat testing infants detected by cystic fibrosis newborn screening

OBJECTIVE: Describe and define limitations of early pilocarpine iontophoresis (sweat testing) for cystic fibrosis (CF) newborn screening (NBS). STUDY DESIGN: Population-based results from follow-up of CF NBS-positive newborns. RESULTS: Insufficient quantity of sweat is more likely if the sweat test is done too early, but testing is generally successful after 2 weeks of age. Sweat chloride levels drop over the first weeks of life. CF carriers have higher sweat chloride concentrations than non-carriers. CONCLUSIONS: Sweat testing can be performed effectively after 2 weeks of age for CF NBS-positive newborns. Earlier testing has a higher risk of insufficient sweat for completing testing

Information on preparing for birth & parenthood

A handbook for parents-to-be attending the Preparation for Birth and Parenthood Education programme at Cork University Maternity Hospital