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Abstract Background Next-generation sequencing has had a significant impact on genetic disease diagnosis, but the interpretation of the vast amount of genomic data it generates can be challenging. To address this, the American College of Medical Genetics and Genomics and the Association for Molecular Pathology have established guidelines for standardized variant interpretation. In this manuscript, we present the updated Hospital Israelita Albert Einstein Standards for Constitutional Sequence Variants Classification, incorporating modifications from leading genetics societies and the ClinGen initiative. Results First, we standardized the scientific publications, documents, and other reliable sources for this document to ensure an evidence-based approach. Next, we defined the databases that would provide variant information for the classification process, established the terminology for molecular findings, set standards for disease-gene associations, and determined the nomenclature for classification criteria. Subsequently, we defined the general rules for variant classification and the Bayesian statistical reasoning principles to enhance this process. We also defined bioinformatics standards for automated classification. Our workgroup adhered to gene-specific rules and workflows curated by the ClinGen Variant Curation Expert Panels whenever available. Additionally, a distinct set of specifications for criteria modulation was created for cancer genes, recognizing their unique characteristics. Conclusions The development of an internal consensus and standards for constitutional sequence variant classification, specifically adapted to the Brazilian population, further contributes to the continuous refinement of variant classification practices. The aim of these efforts from the workgroup is to enhance the reliability and uniformity of variant classification.

Hearing loss (HL) is a common sensory deficit in humans and represents an important clinical and social burden. We studied whole-genome sequencing data of a cohort of 2,097 individuals from the Brazilian Rare Genomes Project who were unaffected by hearing loss to investigate pathogenic and likely pathogenic variants associated with nonsyndromic hearing loss (NSHL). We found relevant frequencies of individuals harboring these alterations: 222 heterozygotes (10.59%) for sequence variants, 54 heterozygotes (2.58%) for copy-number variants (CNV), and four homozygotes (0.19%) for sequence variants. The top five most frequent genes and their corresponding combined allelic frequencies (AF) were GJB2 (AF = 1.57%), STRC (AF = 1%), OTOA (AF = 0.69%), TMPRSS3 (AF = 0.41%), and OTOF (AF = 0.29%). The most frequent sequence variant was GJB2:c.35del (AF = 0.72%), followed by OTOA:p. (Glu787Ter) (AF = 0.61%), while the most recurrent CNV was a microdeletion of 57.9 kb involving the STRC gene (AF = 0.91%). An important fraction of these individuals (n = 104; 4.96%) presented variants associated with autosomal dominant forms of NSHL, which may imply the development of some hearing impairment in the future. Using data from the heterozygous individuals for recessive forms and the Hardy–Weinberg equation, we estimated the population frequency of affected individuals with autosomal recessive NSHL to be 1:2,222. Considering that the overall prevalence of HL in adults ranges from 4–15% worldwide, our data indicate that an important fraction of this condition may be associated with a monogenic origin and dominant inheritance.

Abstract Since the first reported case of the new coronavirus infection in Wuhan, China, researchers and governments have witnessed an unseen rise in the number of cases. Thanks to the rapid work of Chinese scientists, the pathogen now called SARS-CoV-2 has been identified and its whole genome was deposited in public databases by early January 2020. The availability of the genome has allowed researchers to develop Reverse Transcription—Polymerase Chain Reaction (RT-PCR) assays, which are now the gold-standard for molecular diagnosis of the respiratory syndrome COVID19. Because of the rising number of cases and rapid spreading, the world has been facing a shortage of RT-PCR supplies, especially the ones involved in RNA extraction. This has been a major bottleneck to increase testing capacity in many countries that do not significantly manufacture these supplies, such as Brazil. Additionally, RT-qPCR scalability is highly dependent on equipment that usually performs testing of 96 samples at a time. In this work, we describe a cost-effective molecular NGS-based test for diagnosis of COVID19, which uses a single-step RNA extraction and presents high scalability and accuracy when compared to the gold-standard RT-qPCR. A single run of the NGS-based test using the Illumina NextSeq 550 mid-end sequencing equipment is able to multiplex 1,536 patient’s samples, providing individual semi-qualitative results (detected, not detected). Detected results are provided with fragments per million (FPM) values, which was demonstrated to correlate with RT-qPCR Cycle Threshold (CT) values. Besides, usage of the high-end Illumina Novaseq platform may yield diagnostic for up to 6144 samples in a single run. Performance results when compared with RT-qPCR show general accuracy of 96%, and 98% when only samples with CT values (gene N) lower than 30 are considered. We have also developed an online platform, termed VarsVID, to help test executors to easily scale testing numbers. Sample registering, wet-lab worksheets generation, sample sheet for sequencing and results’ display are all features provided by VarsVID. Altogether, these results will contribute to control COVID19 pandemics.

Rare diseases affect up to 13.2 million individuals in Brazil. The Brazilian Rare Genomes Project is envisioned to further the implementation of genomic medicine into the Brazilian public healthcare system. Here we report the validation results of a whole genome sequencing (WGS) procedure for implementation in clinical laboratories. In addition, we report data quality for the first 1,200 real-world patients sequenced. We sequenced a well-characterized group of 76 samples, including seven gold standard genomes, using a PCR-free WGS protocol on Illumina Novaseq 6,000 equipment. We compared the observed variant calls with their expected calls, observing good concordance for single nucleotide variants (SNVs; mean F-measure = 99.82%) and indels (mean F-measure = 99.57%). Copy number variants and structural variants events detection performances were as expected (F-measures 96.6% and 90.3%, respectively). Our WGS protocol presented excellent intra-assay reproducibility (coefficients of variation ranging between 0.03% and 0.20%) and inter-assay reproducibility (coefficients of variation ranging between 0.02% and 0.09%). Limitations of the WGS protocol include the inability to confidently detect variants such as uniparental disomy, balanced translocations, repeat expansion variants, and low-level mosaicism. In summary, the observed performance of the WGS protocol was in accordance with that seen in the best centers worldwide. The Rare Genomes Project is an important initiative to bring pivotal improvements to the quality of life of the affected individuals.

Introdução: O aumento da população idosa tem demandado o desenvolvimento de novos papéis principalmente para os idosos ativos que buscam desenvolver projetos futuros e acompanhar as mudanças tecnológicas. Objetivos: Descrever o trabalho de instrumentalização de idosos para o uso de equipamentos eletrônicos do cotidiano. Métodos: Trata-se de um relato de experiência, da intervenção desenvolvida no Projeto de Inclusão Digital do Idoso-PIDI, no período de agosto/2010 a agosto/2011. Discussão e Resultados: Quanto à caracterização do Projeto: este ocorre há 1 ano, com aulas teórico-práticas de 90 minutos 1x/semana, no período de 8 semanas no Espaço de Cultura e Extensão Universitária-ECEU da Faculdade de Medicina de Ribeirão Preto-USP. Participaram neste período cerca de 130 idosos ativos, faixa etária entre 60-85 anos de diferentes graus de escolaridade. A equipe de trabalho é formada por uma docente, alunos do curso de Terapia Ocupacional e Informática Biomédica, bolsistas do Programa Aprender com Cultura e Extensão e Ensinar com Pesquisa da Universidade de São Paulo e Apoio à Difusão do Conhecimento do CNPq. Quanto aos objetivos e à natureza das atividades desenvolvidas: O objetivo do PIDI é desenvolver ações de instrumentalização de idosos para o uso de equipamentos do cotidiano tais como o aparelho celular, controle remoto de TV/DVD, máquinas fotográficas e filmadoras, aparelhos voltados à saúde, entre outros. Caracterização das atividades: São desenvolvidas aulas teóricas utilizando multimídia e práticas utilizando aparelhos demonstrativos e do próprio idoso. São oferecidos plantões de dúvidas para atendimento individualizado e materiais de apoio como folders e apostilas. Ingresso no Projeto: Os idosos chegam por demanda espontânea, inicialmente são coletadas informações sócio-econômicas, informações sobre os aparelhos que possuem, freqüência de uso e dificuldades que apresentam para manuseio destes. Após o período de intervenção há uma avaliação do aprendizado e identificação de mudanças no cotidiano. A equipe se reúne periodicamente para discussão e avaliação dos trabalhos desenvolvidos. Conclusão: Tendo em vista as dificuldades que os idosos apresentam frente às novas tecnologias, o projeto teve como intuito instrumentalizar, melhorar a competência e as habilidades, trazer autonomia e independência. Através do contato intergeracional, os idosos puderam trocar experiências, compartilhar dificuldades e perceber que não estão sozinhos no processo de inclusão e que podem aprender e tornarem-se cada vez mais independentes quanto ao uso destas tecnologias, mudando positivamente sua vida cotidiana. Nota-se uma melhora da auto-estima por parte dos idosos e autovalorização a partir do momento que percebem sua capacidade de enfrentar novos desafios.