Представлена вторая версия руководства по интерпретации данных последовательности ДНК человека, полученных методами массового параллельного секвенирования. Первая версия руководства была опубликована в журнале «Медицинская генетика» в 2017 г. Она основана на рекомендациях и руководяcтвах по интерпретации результатов массового параллельного секвенирования (MPS), разработанных в Европе и США ACMG, CAP, ESHG и FDA. Обсуждение документа было проведено на профильных научных мероприятиях в течение 2017-2018 гг. Поступившие замечания и поправки к документу отражены в его текущей версии.
This is a second version of guidelines for the interpretation of massive parallel sequencing (MPS) variants. First version was published in Medical Genetics journal in 2017. They were based on ACMG, CAP, ESHG and FDA guidelines and recommendations. Leading authorities on medical genetics and bioinformatics updated and finalized them. First version of guidelines was presented and discussed on all Russian conference «NGS in medical genetics» and all Russian conference «New technologies for diagnosing hereditary diseases». All members of these conferences and members of Russian Society of Medical Genetics could introduce amendments and give comments. Current version include reviewed notes and comments.
Наследственные болезни обмена веществ представляют собой обширный класс генетических заболеваний и вносят значительный вклад в детскую заболеваемость, при этом их диагностика с использованием биохимических методов зачастую вызывает затруднения. В СПбГКУЗ МГЦ были разработаны и внедрены три панели для секвенирования 88 генов, ответственных за развитие трех групп наследственных болезней обмена (НБО), и протестировано 84 ребенка, у которых данные заболевания были заподозрены по данным тандемной масс-спектрометрии (ТМС), либо по наличию клинических симптомов. У 6 детей методом NGS полностью установлена генетическая причина заболевания. Патогенные мутации выявлялись значительно чаще при повышении биохимических маркеров, демонстрируя ведущую роль предварительного биохимического скрининга в проведении NGS анализа. NGS значительно повышает результативность клинической диагностики НБО. Биохимическое тестирование и NGS играют взаимодополняющие роли, и их комплексное использование в алгоритме селективного скрининга позволяет повысить точность диагностики НБО.
Inborn errors of metabolism are an extensive class of genetic diseases and contribute significantly to childhood morbidity, and their diagnosis using biochemical methods is often difficult. Three panels for sequencing of 88 genes responsible for the development of three groups of inborn errors of metabolism (IEM) were developed and introduced in St.Petersburg Medical and Genetic Center and 84 children were tested for which these diseases were suspected by tandem mass-spectrometry or by the presence of clinical symptoms. In 6 children, the NGS method fully established the genetic cause of the disease. Pathogenic mutations were detected significantly more frequently with increased biochemical markers, demonstrating the leading role of pre-biochemical screening in performing NGS analysis. NGS significantly improves the clinical diagnostic effectiveness of IEM. Biochemical testing and NGS play complementary roles and their complex use in selective screening algorithm allows to increase accuracy of IEM diagnostics.
NGS is a powerful tool for the diagnostics of inherited diseases. A number of studies devoted to the development and validation of targeted NGS panels are published. Here we present not only development and validation of an assay, but report our experience on introduction of a new approach into the real clinical practice. The assay is intended for the diagnostics of frequent newborn inherited diseases: cystic fibrosis, phenylketonuria and galactosemia. The analysis is performed on the Ion PGM™ sequencing platform and allows the detection of single-nucleotide variations as well as copy number variants. We developed the software performing data quality control, providing decision-support variant annotation and generating the medical report that enables clinical application of the assay. Analytical validation of the assay was performed by bi-directional Sanger sequencing of the most part of the targeted region. Clinical validation was performed by multicenter blind testing of clinical and control samples. Sensitivity and specificity of the assay are above 99%. We have developed statements for test ordering, test acquisition form and practical recommendations for the results interpretation. The test has been successfully applied for the confirmatory diagnostics in a clinical laboratory during a year. Thus, the developed assay is a comprehensive ready-to-use CE-IVD solution for clinical diagnostics.
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