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NCAD v1.0: a database for non-coding variant annotation and interpretation

Journal of Genetics and Genomics 2024年第2期51卷 230-242页

作者： Xiaoshu Feng Sihan Liu Ke Li Fengxiao Bu Huijun Yuan Institute of Rare Diseases West China HospitalSichuan UniversityChengduSichuan 610044China

The application of whole genome sequencing is expanding in clinical diagnostics across various genetic disorders, and the significance of non-coding variants in penetrant diseases is increasingly being demonstrated. Therefore, it is urgent to improve the diagnostic yield by exploring the pathogenic mechanisms of variants in non-coding regions. However, the interpretation of non-coding variants remains a significant challenge, due to the complex functional regulatory mechanisms of non-coding regions and the current limitations of available databases and tools. Hence, we develop the non-coding variant annotation database (NCAD, http://***/), encompassing comprehensive insights into 665,679,194 variants, regulatory elements, and element interaction details. Integrating data from 96 sources, spanning both GRCh37 and GRCh38 versions, NCAD v1.0 provides vital information to support the genetic diagnosis of non-coding variants, including allele frequencies of 12 diverse populations, with a particular focus on the population frequency information for 230,235,698 variants in 20,964 Chinese individuals. Moreover, it offers prediction scores for variant functionality, five categories of regulatory elements, and four types of non-coding RNAs. With its rich data and comprehensive coverage, NCAD serves as a valuable platform, empowering researchers and clinicians with profound insights into non-coding regulatory mechanisms while facilitating the interpretation of non-coding variants.

关键词： Non-coding variants Annotation variant interpretation Database

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Current scenario of the genetic testing for rare neurological disorders exploiting next generation sequencing

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Neural Regeneration Research 2021年第3期16卷 475-481页

作者： Chiara Di Resta Giovanni Battista Pipitone Paola Carrera Maurizio Ferrari Vita-Salute San Raffaele University MilanItaly Unit of Genomics for Human Disease Diagnosis Division of Genetics and Cell BiologyIRCCS San Raffaele Scientific InstituteMilanItaly Clinical Molecular Biology Laboratory IRCCS San Raffaele HospitalMilanItaly

Next generation sequencing is currently a cornerstone of genetic testing in routine diagnostics,allowing for the detection of sequence variants with so far unprecedented large scale,mainly in genetically heterogenous diseases,such as neurological disorders.It is a fast-moving field,where new wet enrichment protocols and bioinformatics tools are constantly being developed to overcome initial limitations.Despite the as yet undiscussed advantages,however,there are still some challenges in data analysis and the interpretation of variants.In this review,we address the current state of next generation sequencing diagnostic testing for inherited human disorders,particularly giving an overview of the available high-throughput sequencing approaches;including targeted,whole-exome and whole-genome sequencing;and discussing the main critical aspects of the bioinformatic process,from raw data analysis to molecular diagnosis.

关键词： clinical practice genetic testing neurogenesis next generation sequencing sequencing approaches variant interpretation

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