A5081522671- Chromosomal and Genetic Variations
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- T-cell and Retrovirus Studies
- RNA modifications and cancer
- Genomic variations and chromosomal abnormalities
- Genomics and Rare Diseases
- Genetic Associations and Epidemiology
- CRISPR and Genetic Engineering
- Cancer-related molecular mechanisms research
- MicroRNA in disease regulation
- Circular RNAs in diseases
- Parasites and Host Interactions
- Carcinogens and Genotoxicity Assessment
- DNA Repair Mechanisms
- Molecular Biology Techniques and Applications
- Genetic factors in colorectal cancer
- Cancer Genomics and Diagnostics
Hospital Sírio-Libanês
2017-2025
Universidade de São Paulo
2017-2023
Abstract As whole-genome sequencing (WGS) becomes the gold standard tool for studying population genomics and medical applications, data on diverse non-European admixed individuals are still scarce. Here, we present a high-coverage WGS dataset of 1,171 highly elderly Brazilians from census-based cohort, providing over 76 million variants, which ~2 absent large public databases. enables identification ~2,000 previously undescribed mobile element insertions without previous description, nearly...
Abstract Background: Retrocopies, also known as processed pseudogenes, are structural variations resulting from the duplication of protein-coding genes via reverse transcription their mature messenger RNA by LINE-1 enzymatic machinery. These retrocopies can be fixed, present in all genomes a given species, or unfixed—classified here retroCNVs—when they polymorphic, either germline somatic. While fixed have been extensively studied, understanding retroCNVs remains limited due to lack...
Abstract Background: Glioblastoma (GBM) is the most aggressive type of primary brain tumor in adults, with a median survival approximately 15 months. Unfortunately, prognosis for GBM has remained unfavorable decades. The genetic and transcriptomic heterogeneity complicates treatment, underscoring need more comprehensive understanding its molecular basis. Recently, retrotransposons have been shown to influence gene expression formation chimeric transcripts. Although they are associated...
Transposable elements make up a significant portion of the human genome. Accurately locating these mobile DNAs is vital to understand their role as source structural variation and somatic mutation. To this end, laboratories have developed strategies selectively amplify or otherwise enrich transposable element insertion sites in genomic DNA. Here we describe technique, Transposon Insertion Profiling by sequencing (TIPseq), map Long INterspersed Element 1 (LINE-1, L1) retrotransposon...
Abstract As whole-genome sequencing (WGS) becomes the gold standard tool for studying population genomics and medical applications, data on diverse non-European admixed individuals are still scarce. Here, we present a high-coverage WGS dataset of 1,171 highly elderly Brazilians from census-based cohort, providing over 76 million variants, which ~2 absent large public databases. enabled identifying ~2,000 novel mobile element insertions, nearly 5Mb genomic segments human genome reference, 140...
Xeroderma pigmentosum variant (XP-V) is an autosomal recessive disease with increased risk of developing cutaneous neoplasms in sunlight-exposed regions. These cells are deficient the translesion synthesis (TLS) DNA polymerase eta, responsible for bypassing different types lesions. From exome sequencing 11 skin tumors a genetic XP-V patients' cluster, classical mutational signatures related to sunlight exposure, such as C>T transitions targeted pyrimidine dimers, were identified. However,...
Abstract As whole-genome sequencing (WGS) becomes the gold standard tool for studying population genomics and medical applications, data on diverse non-European admixed individuals are still scarce. Here, we present a high-coverage WGS dataset of 1,171 highly elderly Brazilians from census-based cohort, providing over 76 million variants, which ~ 2 absent large public databases. enabled identifying 2,000 novel mobile element insertions, nearly 5 Mb genomic segments human genome reference,...
Background Transposable elements (TEs) constitute a significant portion of mammalian genomes, accounting for about 50% the total DNA. Intragenic TEs are particular interest as they co-transcribed with their host genes in pre-mRNA, potentially leading to formation novel chimeric transcripts and exonization TEs. The abundance RNA sequencing data currently available offers unique opportunity explore transcriptomic variations. However, limitation is capability existing computational tools. Here,...
A BI-RADS category of 4 from a mammogram indicates suspicious breast lesions, which require core biopsies for diagnosis and have an approximately one third chance being malignant. Human plasma contains many circulating microRNAs, variations in their levels been associated with pathologies, including cancer. Here, we present novel methodology to identify malignant lesions women mammography. First, used the miRNome array qRT-PCR define microRNAs that were differentially represented blood...
Abstract Motivation Retrocopies or processed pseudogenes are gene copies resulting from mRNA retrotransposition. These duplicates can be fixed, somatically inserted polymorphic in the genome. However, knowledge regarding unfixed retrocopies (retroCNVs) is still limited, and development of computational tools for effectively identifying genotyping them an urgent need. Results Here, we present sideRETRO, a pipeline dedicated not only to detecting retroCNVs whole-genome whole-exome sequencing...
ABSTRACT Retrocopies or processed pseudogenes are gene copies resulting from mRNA retrotransposition. These duplicates can be fixed, somatically inserted dimorphic in the genome. However, knowledge regarding unfixed retrocopies (retroCNVs) is still limited, and development of computational tools for effectively identifying genotyping them an urgent need. Here, we present sideRETRO, a pipeline dedicated not only to detecting retroCNVs whole-genome whole-exome sequencing data but also...
ABSTRACT Next-generation sequencing (NGS) is currently the gold standard technique for large-scale genome and transcriptome studies. However, downstream processing of NGS data a critical bottleneck that requires difficult decisions regarding analysis methods parameters. Simulated or synthetic datasets are practical cost-effective alternatives overcoming these difficulties. have known true values provide standardized scenario driving development methodologies tuning cut-off values. Although...
Abstract BI-RADS 4 category reports suspicious breast lesions in mammograms, which have 23-34% chance of malignancy and require core biopsies for diagnosis confirmation. New biomarkers are needed been sought to improve diagnose those patients. Once the human plasma contains a large number circulating microRNAs (miRNAs), variations their levels associated with pathologic conditions, including cancer. We hypothesized that miRNA level can be used separate malignant from benign In this context,...