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Integration of next-generation sequencing in clinical diagnostic molecular pathology laboratories for analysis of solid tumours; an expert opinion on behalf of IQN Path ASBL.

ABSTRACT: The clinical demand for mutation detection within multiple genes from a single tumour sample requires molecular diagnostic laboratories to develop rapid, high-throughput, highly sensitive, accurate and parallel testing within tight budget constraints. To meet this demand, many laboratories employ next-generation sequencing (NGS) based on small amplicons. Building on existing publications and general guidance for the clinical use of NGS and learnings from germline testing, the following guidelines establish consensus standards for somatic diagnostic testing, specifically for identifying and reporting mutations in solid tumours. These guidelines cover the testing strategy, implementation of testing within clinical service, sample requirements, data analysis and reporting of results. In conjunction with appropriate staff training and international standards for laboratory testing, these consensus standards for the use of NGS in molecular pathology of solid tumours will assist laboratories in implementing NGS in clinical services.

SUBMITTER: Deans ZC

PROVIDER: S-EPMC5243883 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature

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Integration of next-generation sequencing in clinical diagnostic molecular pathology laboratories for analysis of solid tumours; an expert opinion on behalf of IQN Path ASBL.

Deans Zandra C ZC Costa Jose Luis JL Cree Ian I Dequeker Els E Edsjö Anders A Henderson Shirley S Hummel Michael M Ligtenberg Marjolijn Jl MJ Loddo Marco M Machado Jose Carlos JC Marchetti Antonio A Marquis Katherine K Mason Joanne J Normanno Nicola N Rouleau Etienne E Schuuring Ed E Snelson Keeda-Marie KM Thunnissen Erik E Tops Bastiaan B Tops Bastiaan B Williams Gareth G van Krieken Han H Hall Jacqueline A JA

Virchows Archiv : an international journal of pathology 20160927 1

The clinical demand for mutation detection within multiple genes from a single tumour sample requires molecular diagnostic laboratories to develop rapid, high-throughput, highly sensitive, accurate and parallel testing within tight budget constraints. To meet this demand, many laboratories employ next-generation sequencing (NGS) based on small amplicons. Building on existing publications and general guidance for the clinical use of NGS and learnings from germline testing, the following guideline ...[more]

PMID: 27678269

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Project description:BackgroundEarly Alzheimer's disease diagnosis is crucial for preventive therapy development. Standard neuropsychological evaluation does not identify clinically normal individuals with brain amyloidosis, the first stage of the pathology, defined as preclinical Alzheimer's disease. Spatial navigation assessment, in particular path integration, appears promising to detect preclinical symptoms, as the medial temporal lobe plays a key role in navigation and is the first cortical region affected by tau pathology.MethodsWe have conducted a cross-sectional study. We related the path integration performance of 102 individuals without dementia, aged over 50, to amyloid and tau pathologies, measured using positron emission tomography. We included 75 clinically normal individuals (19 with brain amyloidosis, 56 without) and 27 individuals with mild cognitive impairment (18 with brain amyloidosis, 9 without). We fitted linear mixed models to predict the path integration performances according to amyloid status or tau pathology in the medial temporal lobal, adjusting for age, gender, cognitive status, education, and video game experience. We decomposed the error into rotation and distance errors.ResultsWe observed that clinically normal adults with brain amyloidosis (preclinical Alzheimer's disease) had spatial navigation deficits when relying only on self-motion cues. However, they were able to use a landmark to reduce their errors. Individuals with mild cognitive impairment had deficits in path integration that did not improve when a landmark was added in the environment. The amyloid status did not influence performance among individuals with mild cognitive impairment. Among all individuals, rotation, but not distance, errors increased with the level of tau pathology in the medial temporal lobe.ConclusionOur results suggest that path integration performance in an environment without external cues allows identifying individuals with preclinical Alzheimer's disease, before overt episodic memory impairment is noticeable. Specifically, we demonstrated that poor angular estimation is an early cognitive marker of tau pathology, whereas distance estimation relates to older ages, not to Alzheimer's disease.Trial registrationEudra-CT 2018-003473-94.

Project description:BackgroundCurrently, over 300 languages are spoken in Australian homes. People without proficient English from non-English speaking countries may not receive equitable care if their health care workers do not speak their primary language. Use of professional interpreters is considered the gold standard; however, for a variety of reasons, it is often limited to key aspects of care such as diagnosis and consent. With the emergence of mobile technologies, health care workers are increasingly using digital translation tools to fill this gap. However, many of these technologies have not been developed for health care settings and their use has not been evaluated.ObjectiveThis study aimed to evaluate iPad-compatible language translation apps to determine their suitability for enabling everyday conversations in health care settings.MethodsTranslation apps were identified by searching the Apple iTunes Store and published and grey literature. Criteria for inclusion were that the apps were available at no cost, able to translate at least one of the top 10 languages spoken in Australia, and available for use on iPad. Apps that met inclusion criteria were reviewed in 2 stages. Stage 1 was the feature analysis conducted by 2 independent researchers, where apps were evaluated for offline use, input and output methods, and number of languages. Stage 2 was the analysis of suitability for everyday communication in the health care setting, conducted by 2 independent professionals with expertise in translation and cross-cultural communication. Apps that enabled key aspects of care normally within the realm of professional interpreters, such as assessment, treatment and discharge planning, and seeking consent for medical treatments, were considered unsuitable.ResultsIn total, 15 apps were evaluated. Of these, 8 apps contained voice-to-voice and voice-to-text translation options. In addition, 6 apps were restricted to using preset health phrases, whereas 1 app used a combination of free input and preset phrases. However, 5 apps were excluded before stage 2. In addition, 6 of the 10 remaining apps reviewed in stage 2 were specifically designed for health care translation purposes. Of these, 2 apps were rated as suitable for everyday communication in the health care setting-culturally and linguistically diverse Assist and Talk To Me. Both apps contained simple and appropriate preset health phrases and did not contain conversations that are normally within the realm of professional interpreters.ConclusionsAll iPad-compatible translation apps require a degree of caution and consideration when used in health care settings, and none should replace professional interpreters. However, some apps may be suitable for everyday conversations, such as those that enable preset phrases to be translated on subject matters that do not require a professional interpreter. Further research into the use of translation technology for these types of conversations is needed.

Dataset Information

Integration of next-generation sequencing in clinical diagnostic molecular pathology laboratories for analysis of solid tumours; an expert opinion on behalf of IQN Path ASBL.

Publications

Integration of next-generation sequencing in clinical diagnostic molecular pathology laboratories for analysis of solid tumours; an expert opinion on behalf of IQN Path ASBL.

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