The Human Phenotype Ontology in 2017.

Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.

Autism spectrum disorders in Prader-Willi and Angelman syndromes: a systematic review.

Autism spectrum disorders (ASDs) have been linked with maternally derived duplications/triplications of chromosome 15q11-13 and therefore might occur more frequently in people with Prader-Willi syndrome (PWS) when due to uniparental disomy (UPD), than in other forms of chromosomal abnormality involving this region [i.e. deletion (DEL) forms of PWS and DEL+UPD forms of Angelman's syndrome -(AS)]. Twelve studies regarding ASD in PWS and AS were reviewed. It was noteworthy that among the genetically confirmed UPD and DEL cases of PWS and AS, the rate of ASD was 25.3% (38/150; range 0-36.5%) in PWS and 1.9% in AS (2/104; range 0-100%) (Fisher's exact P<0.0001). Among the subset of cases with confirmed UPD or DEL, the rate of ASD in the UPD cases of PWS was significantly higher (20/53) than in the remaining combined samples (i.e. DEL PWS+UPD AS+DEL AS cases; 20/201) (Fisher's exact P<0.0001). ASD in UPD PWS cases (20/53) compared with DEL PWS cases (18/97) was also statistically significant (Fisher's exact P=0.0176). Thus, the limited available evidence supported the prediction that overexpression of maternally imprinted genes in 15q11-13 confers a risk for ASD. Further research will be required to confirm these findings.

A paternally inherited duplication in the Prader-Willi/Angelman syndrome critical region: a case and family study.

The Prader-Willi/Angelman Critical Region (PWACR; Chromosome 15q11-13) is of interest as a potential locus for genes conferring susceptibility to autism spectrum disorders (ASD). This report describes a female proband referred for evaluation of a possible ASD. Genetic analyses indicated that the proband, her father and one of her sisters, carried a paternally derived interstitial duplication involving 15q11-13. The proband showed evidence of ASD (PDD-NOS), borderline mental retardation, mild hypotonia and joint laxity. Her father and her sister were of normal intelligence and neither was thought to have an ASD, although speech/language difficulties and some autistic type behaviours were reported to have been present early in the development of the sister. This is one of the first reports of a child with a paternal duplication and an autism spectrum disorder. More research is required to determine whether paternally derived duplications that involve 15q11-13 are associated with developmental impairments.

Chromosome 15q11-13 abnormalities and other medical conditions in individuals with autism spectrum disorders.

OBJECTIVES: The frequency of abnormalities of 15q11-q13 and other possibly causal medical disorders including karyotypic abnormalities was investigated in an unselected series of children who were referred to one of two autism assessment centres. METHODS: Two hundred and twenty-one cases were assessed using the Autism Diagnostic Interview and Observation Schedule and, where appropriate, standardized tests of intelligence and language abilities. Medical histories and notes were reviewed, and molecular and cytogenetic investigations used to detect chromosomal abnormalities. RESULTS: One hundred and eighty-one cases were diagnosed according to International Classification of Diseases - version 10 criteria as having an autism spectrum disorder (autistic-like Pervasive Developmental Disorder) and 40 cases as having other disorders. Twenty-one (11.6%) of the children with autism spectrum disorders had a possibly causal condition compared with six (15%) of the children with other diagnoses. One child with an autism spectrum disorder had a paternally inherited familial duplication of 15q11-13. The pattern of genotype-phenotype correlation within the family indicated that this form of abnormality might carry a risk for developmental difficulties, although the risk did not appear to be specific for autism spectrum disorders. CONCLUSION: The overall rate of possibly causal medical and cytogenetic conditions in children with autism spectrum disorders was low and no different from the rate of disorder in children with other developmental/neuropsychiatric disorders that attended the same clinics. Further research is required to determine whether paternal duplication of 15q11-13 gives rise to adverse developmental outcomes.

Prader-Willi syndrome: intellectual abilities and behavioural features by genetic subtype.

BACKGROUND: Studies of chromosome 15 abnormality have implicated over-expression of paternally imprinted genes in the 15q11-13 region in the aetiology of autism. To test this hypothesis we compared individuals with Prader-Willi syndrome (PWS) due to uniparental disomy (UPD--where paternally imprinted genes are over-expressed) to individuals with the 15q11-13 deletion form of the syndrome (where paternally imprinted genes are not over-expressed). We also tested reports that PWS cases due to the larger type I (TI) form of deletion show differences to cases with the smaller type II (TII) deletion. METHOD: Ninety-six individuals with PWS were recruited from genetic centres and the PWS association. Forty-nine individuals were confirmed as having maternal UPD of chromosome 15 and were age and sex matched to 47 individuals with a deletion involving 15q11-13 (32 had the shorter (T II) deletion, and 14 had the longer (TI) deletion). Behavioural assessments were carried out blind to genetic status, using the Autism Diagnostic Observation Schedule (ADOS), the Autism Diagnostic Interview (ADI), the Autism Screening Questionnaire (ASQ), the Children's Yale-Brown Obsessive-Compulsive Scale (CY-BOCS), the Vineland Adaptive Behaviour Scales (VABS), and measurements of intellectual ability, including the Wechsler and Mullen Scales and Raven's Matrices. RESULTS: UPD cases exhibited significantly more autistic-like impairments in reciprocal social interaction on questionnaire, interview and standardised observational measures. Comparison of TI and TII deletion cases revealed few differences, but ability levels tended to be lower in the TI deletion cases. CONCLUSIONS: Findings from a large study comparing deletion and UPD forms of Prader-Willi syndrome were consistent with other evidence in indicating that paternally imprinted genes in the 15q11-13 region constitute a genetic risk factor for aspects of autistic symptomatology. These genes may therefore play a role in the aetiology of autism. By contrast with another report, there was no clear-cut relationship between the size of the deletion and the form of cognitive and behavioural phenotype.

Effect on health-related outcomes of interventions to alter the interaction between patients and practitioners: a systematic review of trials.

PURPOSE: We wanted to identify published randomized trials of interventions to alter the interaction between patients and practitioners, develop taxonomies of the interventions and outcomes, and assess the evidence that such interventions improve patients' health and well-being. METHODS: Undertaking a systematic review of randomized trials, we sought trials in primary and secondary care with health-related outcomes, which we found by searching MEDLINE, HealthSTAR, and PsycINFO bibliographic databases through 1999. We also completed one round of manual citation searching. RESULTS: Thirty-five trials were included. Most were set in primary care in North America. Trials were heterogeneous in populations, settings, interventions, and measures. Interventions frequently combined several poorly described elements. Explicit theoretical underpinning was rare, and only one study linked intervention through process to outcome measures. Health outcomes were rarely measured objectively (6 of 35), and only 4 trials with health outcomes met predefined quality criteria. Interventions frequently altered the process of interactions (significantly in 73%, 22 of 30 trials). Principal outcomes favored the intervention group in 74% of trials (26 of 35), reaching statistical significance in 14 (40%). Positive effects on health outcomes achieved statistical significance in 44% of trials (11 of 25); negative effects were uncommon (5 of 25, 20%). Simple approaches to increasing the participation of patients in the clinical encounter, such as providing practitioners with a note from patients about their concerns beforehand, showed promise, as did more complex programs providing specific information about disease and attention to emotion. Apparently similar interventions varied in effectiveness across studies. CONCLUSIONS: Successful interactions between patients and their practitioners lie at the heart of medicine, yet there are few rigorous trials of well-specified interventions to inform best practice. Trial evidence suggests that a range of approaches can achieve changes in this interaction, and some show promise in improving patients' health. To advance knowledge further, we need to replicate promising studies using rigorous methods. These should include explicit theoretical frameworks designed to link effects on key communication and interaction characteristics through to effects on health outcomes.

Prader-Willi syndrome--a study comparing deletion and uniparental disomy cases with reference to autism spectrum disorders.

Prader Willi Syndrome (PWS) is a neuro-genetic disorder. It has been reported that cases due to paternal deletion 15q11-13 (Del) behave differently to cases due to uniparental disomy (UPD). Comparison of the two forms of PWS has, to date, not included the frequency of autistic behaviours, even though there are reports of an association between maternal duplications of 15q11-13 and autism spectrum disorders (ASD). It was predicted that maternal UPD PWS cases would be more prone to ASD than Del PWS cases due to their duplicated maternally expressed genes. A preliminary test of the hypothesis was conducted using postal and telephone surveys of matched, genetically verified, UPD and Del cases using the Autism Screening Questionnaire (ASQ) and the Vineland Adaptive Behaviour Scales (VABS). As predicted, UPD cases were reported as exhibiting significantly more autistic symptomatology. They also were born to older mothers and were reported on the VABS to have more deficits in motor control problems and fewer adaptive skills in the Daily Living Skills domain. Del cases were reportedly more skilled at jigsaw puzzles. The results lend further support to the notion that abnormality in the expression of maternal imprinted 15q11-13 genes may confer a susceptibility to ASD. They also suggest that there may be cognitive differences between the groups in processing visuo-spatial information.