ABSTRACT
Massively parallel sequencing has markedly improved mendelian diagnostic rates. This study assessed the effects of custom alterations to a diagnostic genomic bioinformatic pipeline in response to clinical need and derived practice recommendations relative to diagnostic rates and efficiency. The Genomic Annotation and Interpretation Application (GAIA) bioinformatics pipeline was designed to detect panel, exome, and genome sample integrity and prioritize gene variants in mendelian disorders. Reanalysis of selected negative cases was performed after improvements to the pipeline. GAIA improvements and their effect on sensitivity are described, including addition of a PubMed search for gene-disease associations not in the Online Mendelian Inheritance of Man database, inclusion of a process for calling low-quality variants (known as QPatch), and gene symbol nomenclature consistency checking. The new pipeline increased the diagnostic rate and reduced staff costs, resulting in a saving of US$844.34 per additional diagnosis. Recommendations for genomic analysis pipeline requirements are summarized. Clinically responsive bioinformatics pipeline improvements increase diagnostic sensitivity and increase cost-effectiveness.
Subject(s)
Exome Sequencing/methods , Genetic Diseases, Inborn/genetics , Genetic Testing/methods , Genomics/methods , Germ-Line Mutation , High-Throughput Nucleotide Sequencing/methods , Cost-Benefit Analysis , Exome , Genetic Testing/economics , Genome, Human , Genomics/economics , High-Throughput Nucleotide Sequencing/economics , Humans , INDEL Mutation , Phenotype , Polymorphism, Single Nucleotide , Sensitivity and Specificity , Exome Sequencing/economicsABSTRACT
OBJECTIVE: to establish how well postnatal ward neonatal hypoglycaemia guidelines facilitate breast feeding and adhere to UNICEF UK Baby Friendly Initiative (BFI) recommendations, and to compare compliance with different recommendations. DESIGN: an appraisal of guidelines obtained via email survey using a UNICEF UK BFI checklist tool. Information about Baby Friendly Health/Hospital Initiative (BFHI) accreditation status was obtained by email questionnaire. SETTING: tertiary neonatal centres in Australia and New Zealand. PARTICIPANTS: 22 guidelines were returned from 23 centres eligible to participate. FINDINGS: guidelines generally scored poorly. On a scale ranging from 31 to 124 of overall guideline quality, the median score was 71. On a scale of 9 to 36 for adherence to recommendations to facilitate breast feeding, the median guideline score was 20. Compliance with the recommendation to promote skin-to-skin contact and early breast feeding was poor across all centres, achieving a score of 59 out of 88. Nine of 22 guidelines mentioned skin-to-skin contact after birth and 14 advised feeding within one hour of birth. The recommendation about discussing artificial milk supplementation with parents received a score of 44 out of 88. Fourteen guidelines listed Large for Gestational Age (LGA) infants to be at risk of hypoglycaemia. Few guidelines included up-to-date references or flowcharts. KEY CONCLUSIONS: guidelines need to recommend early skin-to-skin contact and discussion with parents before artificial milk supplementation. Guidelines suggest LGA neonates are being screened unnecessarily. IMPLICATIONS FOR PRACTICE: guidelines need constant revision as evidence for best practice expands. The UNICEF UK BFI checklist provides a readily available quality improvement tool.
Subject(s)
Guideline Adherence/statistics & numerical data , Hypoglycemia , Infant Care , Infant, Newborn, Diseases , Postnatal Care , Practice Guidelines as Topic , Australia/epidemiology , Female , Health Care Surveys , Hospitals, Maternity/statistics & numerical data , Humans , Hypoglycemia/diagnosis , Hypoglycemia/epidemiology , Hypoglycemia/therapy , Infant Care/methods , Infant Care/standards , Infant, Newborn , Infant, Newborn, Diseases/diagnosis , Infant, Newborn, Diseases/therapy , New Zealand/epidemiology , Postnatal Care/methods , Postnatal Care/standards , Postnatal Care/statistics & numerical data , Pregnancy , Preventive Health Services/methods , Preventive Health Services/standardsABSTRACT
AIM: This study aims to evaluate adherence to a clinical guideline for screening and prevention of neonatal hypoglycaemia on the post-natal wards. METHODS: Retrospective chart review of 581 healthy term neonates born at a tertiary maternity hospital. Indications for hypoglycaemia screening included small for gestational age (SGA), infants of diabetic mothers (IDM; gestational, Type 1 or 2), symptomatic hypoglycaemia, macrosomia and wasted (undernourished) appearance. Outcomes were protocol entry and adherence with hypoglycaemia prevention strategies including early and frequent feeding and timely blood glucose measurement. RESULTS: Of 115 neonates screened for hypoglycaemia, 67 were IDM, 19 were SGA (including two both IDM and SGA), and two were macrosomic. One IDM and one SGA were not screened. Twenty-two neonates were screened for a reason not identifiable from the medical record, and 13 neonates were SGA by a definition different to the guideline definition, including five who were also IDM. Guideline adherence was variable. Few neonates (41 of 106, 39%) were fed in the first post-natal hour, and blood glucose measurement occurred later than recommended for 41 of 106 (39%) of neonates. CONCLUSIONS: Most IDM and SGA neonates were screened. While guideline adherence overall was comparable with other studies, neonates were fed late. We recommend staff education about benefits of early (within the first hour) frequent breastfeeding for neonates at risk.
