ClinPrior: an algorithm for diagnosis and novel gene discovery by network-based prioritization.

BACKGROUND: Whole-exome sequencing (WES) and whole-genome sequencing (WGS) have become indispensable tools to solve rare Mendelian genetic conditions. Nevertheless, there is still an urgent need for sensitive, fast algorithms to maximise WES/WGS diagnostic yield in rare disease patients. Most tools devoted to this aim take advantage of patient phenotype information for prioritization of genomic data, although are often limited by incomplete gene-phenotype knowledge stored in biomedical databases and a lack of proper benchmarking on real-world patient cohorts. METHODS: We developed ClinPrior, a novel method for the analysis of WES/WGS data that ranks candidate causal variants based on the patient's standardized phenotypic features (in Human Phenotype Ontology (HPO) terms). The algorithm propagates the data through an interactome network-based prioritization approach. This algorithm was thoroughly benchmarked using a synthetic patient cohort and was subsequently tested on a heterogeneous prospective, real-world series of 135 families affected by hereditary spastic paraplegia (HSP) and/or cerebellar ataxia (CA). RESULTS: ClinPrior successfully identified causative variants achieving a final positive diagnostic yield of 70% in our real-world cohort. This includes 10 novel candidate genes not previously associated with disease, 7 of which were functionally validated within this project. We used the knowledge generated by ClinPrior to create a specific interactome for HSP/CA disorders thus enabling future diagnoses as well as the discovery of novel disease genes. CONCLUSIONS: ClinPrior is an algorithm that uses standardized phenotype information and interactome data to improve clinical genomic diagnosis. It helps in identifying atypical cases and efficiently predicts novel disease-causing genes. This leads to increasing diagnostic yield, shortening of the diagnostic Odysseys and advancing our understanding of human illnesses.

Prevalence of Essential Tremor on Arosa Island, Spain: a Community-based, Door-to-Door Survey.

BACKGROUND: The prevalence of essential tremor (ET) is still not well understood and the various studies performed to date have generated highly variable results. Few epidemiologic studies on the prevalence of ET have been reported from Spain. METHODS: A one-stage door-to-door survey was conducted on Arosa Island, northwestern Spain, to determine the prevalence of ET in the population aged 65 years and older. The diagnostic criteria for ET were the presence of non-dystonic head tremor or moderate- to severe-amplitude tremor on at least four tests of the revised Washington Heights-Inwood Genetic Study of Essential Tremor (WHIGET) Scale. RESULTS: A total of 65 individuals with ET (28 males, 37 females) were identified, resulting in a crude prevalence of 8.63% (adjusted rate 8.42%). Prevalence increased with advancing age. There were no significant differences in prevalence between sexes in any of the age groups. Among the prevalent cases, 12.3% (n = 8) had been previously diagnosed. Only 29.2% (n = 19) reported functional disability caused by tremor. A family history of tremor was reported in 35.4% (n = 23). DISCUSSION: The prevalence of ET was higher than that seen in similar populations in Spain and other countries. A high proportion of those with ET were previously undiagnosed. Since Arosa Island has been a relatively isolated area, these results might indicate a predominant role, at least in the elderly, for genetic factors in the development of ET.