A5030760426- Genomics and Rare Diseases
- Genomics and Phylogenetic Studies
- Genomic variations and chromosomal abnormalities
- Chromosomal and Genetic Variations
- Genetic factors in colorectal cancer
- DNA Repair Mechanisms
- RNA modifications and cancer
- Genetic Associations and Epidemiology
- Cancer Genomics and Diagnostics
- Carcinogens and Genotoxicity Assessment
- Molecular Biology Techniques and Applications
- Parasites and Host Interactions
- RNA and protein synthesis mechanisms
Universidade de São Paulo
2020-2023
Hospital Sírio-Libanês
2020-2023
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 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,...
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 Xeroderma Pigmentosum variant (XP-V) is an autosomal recessive disease with increased risk to develop cutaneous neoplasms in sunlight exposed regions. These cells are deficient the translesion synthesis DNA polymerase eta. Eleven skin tumors from a genetic cluster of XP-V patients had their exome sequenced. Mutational signatures identified for most were related ultraviolet exposure, such as C>T transitions targeted pyrimidine dimers. However, four samples carry different...
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...