Finding Diagnostically Useful Patterns in Quantitative Phenotypic Data.

Trio-based whole-exome sequence (WES) data have established confident genetic diagnoses in ∼40% of previously undiagnosed individuals recruited to the Deciphering Developmental Disorders (DDD) study. Here we aim to use the breadth of phenotypic information recorded in DDD to augment diagnosis and disease variant discovery in probands. Median Euclidean distances (mEuD) were employed as a simple measure of similarity of quantitative phenotypic data within sets of ≥10 individuals with plausibly causative de novo mutations (DNM) in 28 different developmental disorder genes. 13/28 (46.4%) showed significant similarity for growth or developmental milestone metrics, 10/28 (35.7%) showed similarity in HPO term usage, and 12/28 (43%) showed no phenotypic similarity. Pairwise comparisons of individuals with high-impact inherited variants to the 32 individuals with causative DNM in ANKRD11 using only growth z-scores highlighted 5 likely causative inherited variants and two unrecognized DNM resulting in an 18% diagnostic uplift for this gene. Using an independent approach, naive Bayes classification of growth and developmental data produced reasonably discriminative models for the 24 DNM genes with sufficiently complete data. An unsupervised naive Bayes classification of 6,993 probands with WES data and sufficient phenotypic information defined 23 in silico syndromes (ISSs) and was used to test a "phenotype first" approach to the discovery of causative genotypes using WES variants strictly filtered on allele frequency, mutation consequence, and evidence of constraint in humans. This highlighted heterozygous de novo nonsynonymous variants in SPTBN2 as causative in three DDD probands

Prevalence, phenotype and architecture of developmental disorders caused by de novo mutation: The Deciphering Developmental Disorders Study

Individuals with severe, undiagnosed developmental disorders (DDs) are enriched for damaging de novo mutations (DNMs) in developmentally important genes. We exome sequenced 4,293 families with individuals with DDs, and meta-analysed these data with published data on 3,287 individuals with similar disorders. We show that the most significant factors influencing the diagnostic yield of de novo mutations are the sex of the affected individual, the relatedness of their parents and the age of both father and mother. We identified 94 genes enriched for damaging de novo mutation at genome-wide significance (P < 7 × 10−7), including 14 genes for which compelling data for causation was previously lacking. We have characterised the phenotypic diversity among these genetic disorders. We demonstrate that, at current cost differentials, exome sequencing has much greater power than genome sequencing for novel gene discovery in genetically heterogeneous disorders. We estimate that 42% of our cohort carry pathogenic DNMs (single nucleotide variants and indels) in coding sequences, with approximately half operating by a loss-of-function mechanism, and the remainder resulting in altered-function (e.g. activating, dominant negative). We established that most haplo insufficient developmental disorders have already been identified, but that many altered-function disorders remain to be discovered. Extrapolating from the DDD cohort to the general population, we estimate that developmental disorders caused by DNMs have an average birth prevalence of 1 in 213 to 1 in 448 (0.22-0.47% of live births), depending on parental age

Intestinal structure and function of broiler chickens on diets supplemented with a mannan oligosaccharide

A study was conducted to evaluate the response of broiler chickens to a commercial synthetic mannan oligosaccharide, Bio-MosTM (BM), included in sorghum/lupin-based diets at 0.0, 1.0, 3.0 or 5.0 g kg-1 diet. The diets were fed between 7 and 28 days of age, and both the gross response and mechanisms involved were evaluated. The highest level of BM in the diet resulted in longer (

Body and intestinal growth of broiler chicks on a commercial starter diet: 2. Development and characteristics of intestinal enzymes

1. Investigations were conducted into the development of intestinal enzyme function in broiler chickens on a commercial starter diet. The differences between intestinal regions and localisation of enzymes on the villus were assessed.2. The specific activity of maltase, sucrase, aminopeptidase N (APN) and alkaline phosphatase (AP) at all intestinal sites decreased with age. There were also variations between intestinal sites althoughthis variation depended on age. The specific activity of maltase was higher than that of the other enzymes examined, regardless of age and intestinal site. The total activities of the enzymes also increased with age at all intestinal sites.3. Results of the localisation of enzymes on the crypt : villus axis showed that activity was expressed over a large proportion of the villus. There was an increase in the total villus activity of -glucosidase (AG) , APN and AP with age. Activity per unit villus surface area was similar between ages, except for jejunal AP. At hatch enzyme activity was expressed over 44.1, 55.8 and 63.3% of villus height in the duodenum, jejunum and ileum, respectively. At 21 d of age, corresponding values were 68.7, 65.6 and 77.2%. The point of peak activity from the crypt : villus junction increased with age. In the jejunum, most enterocytes were capable of secreting active enzymes within 1 h of formation. Cells maintained their secretory capabilities until they were more than 60 h old in the case of AG.4. Although the specific activities of the enzymes were maximal at hatch, the digestive capacity of older birds may be sustained by an increase in total enzyme activity brought about by increased surfacearea. The pattern of enzyme activity along the gastrointestional tract (GIT) and crypt : villus axis is similar to that reported for some mammalian species

Body and intestinal growth of broiler chicks on a commercial starter diet: 1. Intestinal weight and mucosal development

1. A study was conducted on the pattern of development of the intestinal mucosa of the Steggles × Ross (F1) strain of broiler chickens reared on a commercial starter diet. The mechanismsunderlying the structural changes were also assessed.2. In relation to body weight, small intestinal weight peaked at 7 d of age and declined subsequently. There was also a reduction in the relative weights of the gizzard and yolk sac with age. The length ofthe small intestine and its regions increased with age.3. Crypt depth increased with age in the duodenum and jejunum while villus height increased significantly with age in all three regions of the small intestine. There were also significant changes inapparent villus surface area in the three regions, while interactions between age and intestinal region were significant in the case of crypt depth and villus height.4. There were significant differences between the age groups in the mucosal protein content of jejunal and ileal homogenates, both tending to peak at 7 d of age. The DNA content of the intestinalmucosa declined with age in the three regions of the small intestine. While there was an increase in RNA content in the duodenum and ileum, there was a reduction in the jejunum.5. Protein : DNA ratio increased between hatch and 21 d of age in all intestinal regions. Protein : RNA ratio decreased with age in the duodenum and ileum but increased in the jejunum. There were significant increases in RNA : DNA ratio in the duodenum and ileum but no changes were observed in the jejunum. The interactions between age and intestinal region were significant for all biochemicalindices assessed.6. At all ages, enterocyte proliferation at the jejunum was completed and quantifiable within 1 h of administration of 5-bromo-2´ -deoxyuridine (BrDU) . Subsequent assessment revealed an increase incrypt column count and number of BrDU-labelled cells. The rate of cell migration increased with age while there was a decline in the distance migrated in proportion to mucosal depth. The estimatedlife-span of enterocytes and time spent by enterocytes in the crypt varied with age. In d-old and 7-dold chicks, migration was complete or nearly complete within 96 h of cell birth.7. Although the intestinal mucosa of the strain was structurally developed at hatch, there was much change in structure with age, especially over the first 7 d post hatch. The rate of development wasmost rapid in the jejunum but the other regions are also important, on account of villus height or relative length of the region

Intestinal development and body growth of broiler chickens on diets supplemented with non-starch polysaccharides

The growth of broiler chicks and the mechanisms underlying responses to diets supplemented with commercial non-starch polysaccharides were evaluated. The supplements varied in viscosity and chemical structure and evaluation was conducted over two feeding periods. The viscosity of the four supplements tested ranged from 1.38 cP for alginic acid (AL) to over 2000 cP for guar gum (GG) and gum xanthan (GX). The whole diet followed a similar trend. The ileal digesta viscosity was significantly highest (

Energy landscapes shape microbial communities in hydrothermal systems on the Arctic Mid-Ocean Ridge

Methods developed in geochemical modelling combined with recent advances in molecular microbial ecology provide new opportunities to explore how microbial communities are shaped by their chemical surroundings. Here, we present a framework for analyses of how chemical energy availability shape chemotrophic microbial communities in hydrothermal systems through an investigation of two geochemically different basalt-hosted hydrothermal systems on the Arctic Mid-Ocean Ridge: the Soria Moria Vent field (SMVF) and the Loki’s Castle Vent Field (LCVF). Chemical energy landscapes were evaluated through modelling of the Gibbs energy from selected redox reactions under different mixing ratios between seawater and hydrothermal fluids. Our models indicate that the sediment-influenced LCVF has a much higher potential for both anaerobic and aerobic methane oxidation, as well as aerobic ammonium and hydrogen oxidation, than the SMVF. The modelled energy landscapes were used to develop microbial community composition models, which were compared with community compositions in environmental samples inside or on the exterior of hydrothermal chimneys, as assessed by pyrosequencing of partial 16S rRNA genes. We show that modelled microbial communities based solely on thermodynamic considerations can have a high predictive power and provide a framework for analyses of the link between energy availability and microbial community composition

Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data.

BACKGROUND: Human genome sequencing has transformed our understanding of genomic variation and its relevance to health and disease, and is now starting to enter clinical practice for the diagnosis of rare diseases. The question of whether and how some categories of genomic findings should be shared with individual research participants is currently a topic of international debate, and development of robust analytical workflows to identify and communicate clinically relevant variants is paramount. METHODS: The Deciphering Developmental Disorders (DDD) study has developed a UK-wide patient recruitment network involving over 180 clinicians across all 24 regional genetics services, and has performed genome-wide microarray and whole exome sequencing on children with undiagnosed developmental disorders and their parents. After data analysis, pertinent genomic variants were returned to individual research participants via their local clinical genetics team. FINDINGS: Around 80,000 genomic variants were identified from exome sequencing and microarray analysis in each individual, of which on average 400 were rare and predicted to be protein altering. By focusing only on de novo and segregating variants in known developmental disorder genes, we achieved a diagnostic yield of 27% among 1133 previously investigated yet undiagnosed children with developmental disorders, whilst minimising incidental findings. In families with developmentally normal parents, whole exome sequencing of the child and both parents resulted in a 10-fold reduction in the number of potential causal variants that needed clinical evaluation compared to sequencing only the child. Most diagnostic variants identified in known genes were novel and not present in current databases of known disease variation. INTERPRETATION: Implementation of a robust translational genomics workflow is achievable within a large-scale rare disease research study to allow feedback of potentially diagnostic findings to clinicians and research participants. Systematic recording of relevant clinical data, curation of a gene-phenotype knowledge base, and development of clinical decision support software are needed in addition to automated exclusion of almost all variants, which is crucial for scalable prioritisation and review of possible diagnostic variants. However, the resource requirements of development and maintenance of a clinical reporting system within a research setting are substantial. FUNDING: Health Innovation Challenge Fund, a parallel funding partnership between the Wellcome Trust and the UK Department of Health

Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data.

BACKGROUND: Human genome sequencing has transformed our understanding of genomic variation and its relevance to health and disease, and is now starting to enter clinical practice for the diagnosis of rare diseases. The question of whether and how some categories of genomic findings should be shared with individual research participants is currently a topic of international debate, and development of robust analytical workflows to identify and communicate clinically relevant variants is paramount. METHODS: The Deciphering Developmental Disorders (DDD) study has developed a UK-wide patient recruitment network involving over 180 clinicians across all 24 regional genetics services, and has performed genome-wide microarray and whole exome sequencing on children with undiagnosed developmental disorders and their parents. After data analysis, pertinent genomic variants were returned to individual research participants via their local clinical genetics team. FINDINGS: Around 80,000 genomic variants were identified from exome sequencing and microarray analysis in each individual, of which on average 400 were rare and predicted to be protein altering. By focusing only on de novo and segregating variants in known developmental disorder genes, we achieved a diagnostic yield of 27% among 1133 previously investigated yet undiagnosed children with developmental disorders, whilst minimising incidental findings. In families with developmentally normal parents, whole exome sequencing of the child and both parents resulted in a 10-fold reduction in the number of potential causal variants that needed clinical evaluation compared to sequencing only the child. Most diagnostic variants identified in known genes were novel and not present in current databases of known disease variation. INTERPRETATION: Implementation of a robust translational genomics workflow is achievable within a large-scale rare disease research study to allow feedback of potentially diagnostic findings to clinicians and research participants. Systematic recording of relevant clinical data, curation of a gene-phenotype knowledge base, and development of clinical decision support software are needed in addition to automated exclusion of almost all variants, which is crucial for scalable prioritisation and review of possible diagnostic variants. However, the resource requirements of development and maintenance of a clinical reporting system within a research setting are substantial. FUNDING: Health Innovation Challenge Fund, a parallel funding partnership between the Wellcome Trust and the UK Department of Health