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Barreiro RAS, de Almeida TF, Gomes CDS, Monfardini F, de Farias AA, Tunes GC, de Souza GM, Duim E, de Sá Correia J, Campos Coelho AV, Caraciolo MP, Duarte YAO, Zatz M, Amaro E, Oliveira JB, Bitarello BD, Brentani H, Naslavsky MS. Assessing the risk stratification of breast cancer polygenic risk scores in a Brazilian cohort. J Mol Diagn 2024:S1525-1578(24)00150-8. [PMID: 38972593 DOI: 10.1016/j.jmoldx.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 05/10/2024] [Accepted: 06/11/2024] [Indexed: 07/09/2024] Open
Abstract
Polygenic risk scores (PRS) for breast cancer (BC) have a clear clinical utility in risk prediction. PRS transferability across populations and ancestry groups is hampered by population-specific factors, ultimately leading to differences in variant effects, such as linkage disequilibrium (LD) and differences in variant frequency (AF-diff). Thus, locally-sourced population-based phenotypic and genomic datasets are essential to assess the validity of PRS derived from signals detected across populations. Here, we assess the transferability of a BC PRS composed of 313 risk variants (313-PRS) in a Brazilian tri-hybrid admixed ancestries (European, African and Native American) whole-genome sequenced cohort, GRAR. We computed 313-PRS in GRAR (n=853) using the UK Biobank (UKBB, n=264,307) as reference. We show that although the Brazilian cohorts have a high European (EA) component, with AF-diff and to a lesser extent LD patterns similar to those found in EA populations, the 313-PRS distribution is inflated when compared to that of the UKBB, leading to potential overestimation of PRS-based risk if EA is taken as a standard. Interestingly, we find that case-controls lead to equivalent predictive power when compared to UKBB-EA samples with AUROC values of 0.66-0.62 compared to 0.63 for UKBB.
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Affiliation(s)
- Rodrigo Araujo Sequeira Barreiro
- Universidade de São Paulo, Departamento de Bioquímica, São Paulo, SP, Brazil; Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | | | - Catarina Dos Santos Gomes
- Institute of Psychiatry, University of Sao Paulo, Medical School, São Paulo, SP, Brazil; Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | | | | | | | | | - Etienne Duim
- Big Data and Analytics Department, Hospital Israelita Albert Einstein. São Paulo, SP, Brazil
| | | | | | | | - Yeda Aparecida Oliveira Duarte
- Medical-Surgical Nursing Department, School of Nursing, University of São Paulo, São Paulo, SP, Brazil; Epidemiology Department, Public Health School, University of São Paulo, São Paulo, SP, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, SP, Brazil; Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Edson Amaro
- Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | | | | | - Helena Brentani
- Institute of Psychiatry, University of Sao Paulo, Medical School, São Paulo, SP, Brazil; Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Michel Satya Naslavsky
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, SP, Brazil; Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, SP, Brazil; Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
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Segura AVC, da Silva SIO, Santiago KM, Brianese RC, Carraro DM, Torrezan GT. Misclassification of a frequent variant from PMS2CL pseudogene as a PMS2 loss of function variant in Brazilian patients. Fam Cancer 2024:10.1007/s10689-024-00411-1. [PMID: 38900223 DOI: 10.1007/s10689-024-00411-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/13/2024] [Indexed: 06/21/2024]
Abstract
PMS2, a Lynch Syndrome gene, presents challenges in genetic testing due to the existence of multiple pseudogenes. This study aims to describe a series of cases harboring a variant in the PMS2CL pseudogene that has been incorrectly assigned to PMS2 with different nomenclatures. We reviewed data from 647 Brazilian patients who underwent multigene genetic testing at a single center to identify those harboring the PMS2 V1:c.2186_2187delTC or V2:c.2182_2184delACTinsG variants, allegedly located at PMS2 exon 13. Gene-specific PCR and transcript sequencing was performed. Among the 647 individuals, 1.8% (12) carried the investigated variants, with variant allele frequencies ranging from 15 to 34%. By visually inspecting the alignments, we confirmed that both V1 and V2 represented the same variant and through gene-specific PCR and PMS2 transcript analysis, we demonstrated that V1/V2 is actually located in the PMS2CL pseudogene. Genomic databases (ExAC and gnomAD) report an incidence of 2.5 - 5.3% of this variant in the African population. Currently, V1 is classified as "uncertain significance" and V2 as "conflicting" in ClinVar, with several laboratories classifying them as "pathogenic". We identified a frequent African PMS2CL variant in the Brazilian population that is misclassified as a PMS2 variant. It is likely that V1/V2 have been erroneously assigned to PMS2 in several manuscripts and by clinical laboratories, underscoring a disparity-induced matter. Considering the limitations of short-read NGS differentiating between certain regions of PMS2 and PMS2CL, using complementary methodologies is imperative to provide an accurate diagnosis.
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Affiliation(s)
- Anthony Vladimir Campos Segura
- Clinical and Functional Genomics Group, International Research Center/CIPE, A.C.Camargo Cancer Center, 440 Taguá St, São Paulo, SP, 01508-010, Brazil
| | - Sara Iolanda Oliveira da Silva
- Clinical and Functional Genomics Group, International Research Center/CIPE, A.C.Camargo Cancer Center, 440 Taguá St, São Paulo, SP, 01508-010, Brazil
| | - Karina Miranda Santiago
- Clinical and Functional Genomics Group, International Research Center/CIPE, A.C.Camargo Cancer Center, 440 Taguá St, São Paulo, SP, 01508-010, Brazil
| | - Rafael Canfield Brianese
- Clinical and Functional Genomics Group, International Research Center/CIPE, A.C.Camargo Cancer Center, 440 Taguá St, São Paulo, SP, 01508-010, Brazil
| | - Dirce Maria Carraro
- Clinical and Functional Genomics Group, International Research Center/CIPE, A.C.Camargo Cancer Center, 440 Taguá St, São Paulo, SP, 01508-010, Brazil
- National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation, São Paulo, Brazil
| | - Giovana Tardin Torrezan
- Clinical and Functional Genomics Group, International Research Center/CIPE, A.C.Camargo Cancer Center, 440 Taguá St, São Paulo, SP, 01508-010, Brazil.
- National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation, São Paulo, Brazil.
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Buainain RP, Sodré AR, dos Santos JS, Takazaki KAG, Queiroz LDS, de Oliveira CTP, de Aguiar PHP, Marson FAL, Ortega MM. Single-Base Gene Variants in MIR-146A and SCN1A Genes Related to the Epileptogenic Process in Drug-Responsive and Drug-Resistant Temporal Lobe Epilepsy-A Preliminary Study in a Brazilian Cohort Sample. Int J Mol Sci 2024; 25:6005. [PMID: 38892194 PMCID: PMC11172889 DOI: 10.3390/ijms25116005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
The drug-resistant temporal lobe epilepsy (TLE) has recently been associated with single nucleotide variants (SNVs) in microRNA(miR)-146a (MIR-146A) (rs2910164) and Sodium Voltage-Gated Channel Alpha Subunit 1 (SCN1A) (rs2298771 and rs3812718) genes. Moreover, no studies have shown an association between these SNVs and susceptibility to drug-resistant and drug-responsive TLE in Brazil. Thus, deoxyribonucleic acid (DNA) samples from 120 patients with TLE (55 drug-responsive and 65 drug-resistant) were evaluated by real-time polymerase chain reaction (RT-PCR). A total of 1171 healthy blood donor individuals from the Online Archive of Brazilian Mutations (ABraOM, from Portuguese Arquivo Brasileiro On-line de Mutações), a repository containing genomic variants of the Brazilian population, were added as a control population for the studied SNVs. MIR-146A and SCN1A relative expression was performed by quantitative RT-PCR (qRT-PCR). The statistical analysis protocol was performed using an alpha error of 0.05. TLE patient samples and ABraOM control samples were in Hardy-Weinberg equilibrium for all studied SNVs. For rs2910164, the frequencies of the homozygous genotype (CC) (15.00% vs. 9.65%) and C allele (37.80% vs. 29.97%) were superior in patients with TLE compared to controls with a higher risk for TLE disease [odds ratio (OR) = 1.89 (95% confidence interval (95%CI) = 1.06-3.37); OR = 1.38 (95%CI = 1.04-1.82), respectively]. Drug-responsive patients also presented higher frequencies of the CC genotype [21.81% vs. 9.65%; OR = 2.58 (95%CI = 1.25-5.30)] and C allele [39.09% vs. 29.97%; OR = 1.50 (95%CI = 1.01-2.22)] compared to controls. For rs2298771, the frequency of the heterozygous genotype (AG) (51.67% vs. 40.40%) was superior in patients with TLE compared to controls with a higher risk for TLE disease [OR = 2.42 (95%CI = 1.08-5.41)]. Drug-resistant patients presented a higher AG frequency [56.92% vs. 40.40%; OR = 3.36 (95%CI = 1.04-17.30)] compared to the control group. For rs3812718, the prevalence of genotypes and alleles were similar in both studied groups. The MIR-146A relative expression level was lower in drug-resistant compared to drug-responsive patients for GC (1.6 vs. 0.1, p-value = 0.049) and CC (1.8 vs. 0.6, p-value = 0.039). Also, the SCN1A relative expression levels in samples from TLE patients were significantly higher in AG [2.09 vs. 1.10, p-value = 0.038] and GG (3.19 vs. 1.10, p-value < 0.001) compared to the AA genotype. In conclusion, the rs2910164-CC and rs2298771-AG genotypes are exerting significant risk influence, respectively, on responsive disease and resistant disease, probably due to an upregulated nuclear factor kappa B (NF-kB) and SCN1A loss of function.
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Affiliation(s)
- Renata Parissi Buainain
- Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds, São Francisco University, Bragança Paulista 12916-900, SP, Brazil or (F.A.L.M.)
- Laboratory of Molecular Biology and Genetics, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - André Rodrigues Sodré
- Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds, São Francisco University, Bragança Paulista 12916-900, SP, Brazil or (F.A.L.M.)
- Laboratory of Molecular Biology and Genetics, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Jéssica Silva dos Santos
- Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds, São Francisco University, Bragança Paulista 12916-900, SP, Brazil or (F.A.L.M.)
- Laboratory of Molecular Biology and Genetics, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Karen Antonia Girotto Takazaki
- Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds, São Francisco University, Bragança Paulista 12916-900, SP, Brazil or (F.A.L.M.)
- Laboratory of Molecular Biology and Genetics, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Luciano de Souza Queiroz
- Department of Pathology, Faculty of Medical Science, University of Campinas, Campinas 13083-970, SP, Brazil;
| | - Carlos Tadeu Parisi de Oliveira
- Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds, São Francisco University, Bragança Paulista 12916-900, SP, Brazil or (F.A.L.M.)
- Laboratory of Molecular Biology and Genetics, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
- São Francisco University Hospital, São Francisco University, Bragança Paulista 20210-030, SP, Brazil
| | - Paulo Henrique Pires de Aguiar
- Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds, São Francisco University, Bragança Paulista 12916-900, SP, Brazil or (F.A.L.M.)
- Laboratory of Molecular Biology and Genetics, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
- Department of Neurosurgery, Hospital Santa Paula, São Paulo 04556-100, SP, Brazil
| | - Fernando Augusto Lima Marson
- Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds, São Francisco University, Bragança Paulista 12916-900, SP, Brazil or (F.A.L.M.)
- Laboratory of Molecular Biology and Genetics, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Manoela Marques Ortega
- Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds, São Francisco University, Bragança Paulista 12916-900, SP, Brazil or (F.A.L.M.)
- Laboratory of Molecular Biology and Genetics, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
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Owen GI, Cordova-Delgado M, Bustos BI, Cerpa LC, Gonzalez P, Morales-Pison S, Garcia-Bloj B, Garrido M, Miquel JF, Quiñones LA. Assessing the Occurrence and Influence of Cancer Chemotherapy-Related Pharmacogenetic Alleles in the Chilean Population. Pharmaceutics 2024; 16:561. [PMID: 38675222 PMCID: PMC11054647 DOI: 10.3390/pharmaceutics16040561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/02/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Pharmacogenomic knowledge as a biomarker for cancer care has transformed clinical practice, however, as current guidelines are primarily derived from Eurocentric populations, this limits their application in Latin America, particularly among Hispanic or Latino groups. Despite advancements, systemic chemotherapy still poses challenges in drug toxicity and suboptimal response. This study explores pharmacogenetic markers related to anticancer drugs in a Chilean cohort, filling a gap in Latin American research. Notably, the influence of native South American Mapuche-Huilliche ancestry. METHODS To explore pharmacogenetic markers related to anticancer drugs, we utilized an ethnically Admixed Chilean genome-wide association studies (GWAS) dataset of 1095 unrelated individuals. Pharmacogenomic markers were selected from PharmGKB, totaling 36 level 1 and 2 evidence single nucleotide polymorphisms (SNPs) and 571 level 3 SNPs. Comparative analyses involved assessing SNP frequencies across diverse populations from the 1000 Genomes Project. Haplotypes were estimated, and linkage disequilibrium was examined. Ancestry-based association analyses explored relationships between SNPs and Mapuche-Huilliche and European ancestries. Chi-square distribution with p ≤ 0.05 and Bonferroni's multiple adjustment tests determined statistical differences between allele frequencies. RESULTS Our study reveals significant disparities in SNP frequency within the Chilean population. Notably, dihydropyrimidine dehydrogenase (DPYD) variants (rs75017182 and rs67376798), linked to an increased risk of severe fluoropyrimidine toxicity, exhibit an exceptionally low frequency (minor allele frequency (MAF) < 0.005). Nudix hydrolase 15 (NUDT15) rs116855232, associated with hematological mercaptopurine toxicity, is relatively common (MAF = 0.062), and is further linked to Mapuche-Huilliche ancestry. Thiopurine methyltransferase enzyme (TPMT), implicated in severe toxicity to mercaptopurines, SNPs rs1142345 and rs1800460 of TMPT gene demonstrate higher MAFs in Admixed Americans and the Chilean population (MAF range 0.031-0.057). Finally, the variant in the UDP-glucuronosyltransferase 1 gene (UGT1A1) rs4148323, correlated with irinotecan neutropenia, exhibits the highest MAF in East Asian (MAF = 0.136) and Chilean (MAF = 0.025) populations, distinguishing them from other investigated populations. CONCLUSIONS This study provides the first comprehensive pharmacogenetic characterization of cancer therapy-related SNPs and highlights significant disparities in SNP frequencies within the Chilean population. Our findings underscore the necessity for inclusive research and personalized therapeutic strategies to ensure the equitable and effective application of precision medicine across diverse global communities.
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Affiliation(s)
- Gareth I. Owen
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (M.C.-D.); (P.G.)
- Department of Hematology and Oncology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Santiago 8330034, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago 8331150, Chile
- Centro de Prevención y Control de Cáncer (CECAN), Santiago 8380453, Chile
| | - Miguel Cordova-Delgado
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (M.C.-D.); (P.G.)
- Department of Hematology and Oncology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Faculty of Chemical and Pharmaceutical Sciences, Universidad de Chile, Santiago 8380494, Chile
| | - Bernabé I. Bustos
- Ken and Ruth Davee Department of Neurology, Simpson Querrey Center for Neurogenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA;
| | - Leslie C. Cerpa
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8380494, Chile;
- Latin American Network for Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago 8350499, Chile
| | - Pamela Gonzalez
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (M.C.-D.); (P.G.)
| | - Sebastián Morales-Pison
- Centro de Oncología de Precisión (COP), Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago 7560908, Chile; (S.M.-P.); (B.G.-B.); (M.G.)
| | - Benjamín Garcia-Bloj
- Centro de Oncología de Precisión (COP), Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago 7560908, Chile; (S.M.-P.); (B.G.-B.); (M.G.)
| | - Marcelo Garrido
- Centro de Oncología de Precisión (COP), Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago 7560908, Chile; (S.M.-P.); (B.G.-B.); (M.G.)
- SAGA, Centro de Estudios Clínicos, Santiago 7610315, Chile
- Department of Oncología, Clínica Indisa, Santiago 7520440, Chile
| | - Juan Francisco Miquel
- Department of Gastroenterology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 8330032, Chile;
| | - Luis A. Quiñones
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8380494, Chile;
- Latin American Network for Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago 8350499, Chile
- Department of Pharmaceutical Sciences and Technology, Faculty of Chemical and Pharmaceutical Sciences, University of Chile, Santiago 8380494, Chile
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French JN, Pua VB, Laboulaye R, Leal TP, Olivas MC, Lima-Costa MF, Horta BL, Barreto ML, Tarazona-Santos E, Mata I, O’Connor TD. Comparing the effect of imputation reference panel composition in four distinct Latin American cohorts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.11.589057. [PMID: 38659746 PMCID: PMC11042191 DOI: 10.1101/2024.04.11.589057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Genome-wide association studies have been useful in identifying genetic risk factors for various phenotypes. These studies rely on imputation and many existing panels are largely composed of individuals of European ancestry, resulting in lower levels of imputation quality in underrepresented populations. We aim to analyze how the composition of imputation reference panels affects imputation quality in four target Latin American cohorts. We compared imputation quality for chromosomes 7 and X when altering the imputation reference panel by: 1) increasing the number of Latin American individuals; 2) excluding either Latin American, African, or European individuals, or 3) increasing the Indigenous American (IA) admixture proportions of included Latin Americans. We found that increasing the number of Latin Americans in the reference panel improved imputation quality in the four populations; however, there were differences between chromosomes 7 and X in some cohorts. Excluding Latin Americans from analysis resulted in worse imputation quality in every cohort, while differential effects were seen when excluding Europeans and Africans between and within cohorts and between chromosomes 7 and X. Finally, increasing IA-like admixture proportions in the reference panel increased imputation quality at different levels in different populations. The difference in results between populations and chromosomes suggests that existing and future reference panels containing Latin American individuals are likely to perform differently in different Latin American populations.
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Affiliation(s)
- Jennifer N French
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
| | - Victor Borda Pua
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
- University of Maryland Institute for Health Computing, Rockville, MD
| | - Roland Laboulaye
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
| | - Thiago Peixoto Leal
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Mario Cornejo Olivas
- Neurogenetics Working Group, Universidad Cientifica del Sur, Lima, Peru
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurologicas, Lima, Peru
| | | | - Bernardo L Horta
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas, Brazil
| | - Mauricio L Barreto
- Center for Data and Knowledge Integration for Health (CIDACS), Gonçalo Moniz Institute (IGM), Oswaldo Cruz Foundation (FIOCRUZ-BA), Salvador, Bahia, Brazil
- Collective Health Institute, Federal University of Bahia (UFBA), Salvador, Bahia, Brazil
| | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Ignacio Mata
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Timothy D. O’Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD
- Program in Health Equity and Population Health, University of Maryland School of Medicine
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Ruíz-Patiño A, Rojas L, Zuluaga J, Arrieta O, Corrales L, Martín C, Franco S, Raez L, Rolfo C, Sánchez N, Cardona AF. Genomic ancestry and cancer among Latin Americans. Clin Transl Oncol 2024:10.1007/s12094-024-03415-6. [PMID: 38581481 DOI: 10.1007/s12094-024-03415-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 02/20/2024] [Indexed: 04/08/2024]
Abstract
Latin American populations, characterized by intricate admixture patterns resulting from the intermingling of ancestries from European, Native American (NA) Asian, and African ancestries which result in a vast and complex genetic landscape, harboring unique combinations of novel variants. This genetic diversity not only poses challenges in traditional population genetics methods but also opens avenues for a deeper understanding of its implications in health. In cancer, the interplay between genetic ancestry, lifestyle factors, and healthcare disparities adds a layer of complexity to the varying incidence and mortality rates observed across different Latin American subpopulations. This complex interdependence has been unveiled through numerous studies, whether conducted on Latin American patients residing on the continent or abroad, revealing discernible differences in germline composition that influence divergent disease phenotypes such as higher incidence of Luminal B and Her2 breast tumors, EGFR and KRAS mutated lung adenocarcinomas in addition to an enrichment in BRCA1/2 pathogenic variants and a higher than expected prevalence of variants in colorectal cancer associated genes such as APC and MLH1. In prostate cancer novel risk variants have also been solely identified in Latin American populations. Due to the complexity of genetic divergence, inputs from each individual ancestry seem to carry independent contributions that interplay in the development of these complex disease phenotypes. By understanding these unique population characteristics, genomic ancestries hold a promising avenue for tailoring prognostic assessments and optimizing responses to oncological interventions.
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Affiliation(s)
- Alejandro Ruíz-Patiño
- Clinical Genetics, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia
| | - Leonardo Rojas
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia
- Thoracic Oncology Unit, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
| | - Jairo Zuluaga
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia
- Thoracic Oncology Unit, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
| | - Oscar Arrieta
- Instituto Nacional de Cancerología -INCaN, Mexico City, Mexico
| | - Luis Corrales
- Thoracic Oncology Unit, Centro de Investigación y Manejo del Cáncer (CIMCA), San José, Costa Rica
| | - Claudio Martín
- Thoracic Oncology Unit, Instituto Alexander Fleming, Buenos Aires, Argentina
| | - Sandra Franco
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia
- Breast Cancer Unit, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
| | - Luis Raez
- Oncology Department, Memorial Cancer Institute (MCI), Memorial Healthcare System, Miami, FL, USA
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Natalia Sánchez
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia
- Institute of Research, Science and Education, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
| | - Andrés Felipe Cardona
- GIGA/TERA Research Group, CTIC/Universidad El Bosque, Bogotá, Colombia.
- Thoracic Oncology Unit, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia.
- Institute of Research, Science and Education, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia.
- Direction of Research and Education, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Cra. 14 #169-49, Bogotá, Colombia.
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Dangoni GD, Teixeira ACB, da Costa SS, Scliar MO, Carvalho LML, Silva LN, Novak EM, Vince CSC, Maschietto MC, Sugayama SMM, Odone-Filho V, Krepischi ACV. Germline mutations in cancer predisposition genes among pediatric patients with cancer and congenital anomalies. Pediatr Res 2024; 95:1346-1355. [PMID: 38182823 DOI: 10.1038/s41390-023-03000-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/08/2023] [Accepted: 12/20/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND Childhood cancer has a poorly known etiology, and investigating the underlying genetic background may provide novel insights. A recognized association exists between non-chromosomal birth defects and childhood cancer susceptibility. METHODS We performed whole-exome sequencing and chromosomal microarray analysis in a cohort of childhood cancer (22 individuals, 50% with congenital anomalies) to unravel deleterious germline variants. RESULTS A diagnostic yield of 14% was found, encompassing heterozygous variants in bona fide dominant Cancer Predisposition Genes (CPGs). Considering candidate and recessive CPGs harboring monoallelic variants, which were also deemed to play a role in the phenotype, the yield escalated to 45%. Most of the deleterious variants were mapped in genes not conventionally linked to the patient's tumor type. Relevant findings were detected in 55% of the syndromic individuals, mostly variants potentially underlying both phenotypes. CONCLUSION We uncovered a remarkable prevalence of germline deleterious CPG variants, highlighting the significance of a comprehensive genetic analysis in pediatric cancer, especially when coupled with additional clinical signs. Moreover, our findings emphasized the potential for oligogenic inheritance, wherein multiple genes synergistically increase cancer risk. Lastly, our investigation unveiled potentially novel genotype-phenotype associations, such as SETD5 in neuroblastoma, KAT6A in gliomas, JAG1 in hepatoblastomas, and TNFRSF13B in Langerhans cell histiocytosis. IMPACT Novel gene-phenotype associations and candidate genes for pediatric cancer were unraveled, such as KAT6A in gliomas, SETD5 in neuroblastoma, JAG1 in hepatoblastomas, and TNFRSF13B in Langerhans cell histiocytosis. Our analysis revealed a high frequency of deleterious germline variants, particularly in cases accompanied by additional clinical signs, highlighting the importance of a comprehensive genetic evaluation in childhood cancer. Our findings also underscored the potential for oligogenic inheritance in pediatric cancer risk. Understanding the cancer etiology is crucial for genetic counseling, often influencing therapeutic decisions and offering valuable insights into molecular targets for the development of oncological therapies.
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Affiliation(s)
- Gustavo D Dangoni
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Anne Caroline B Teixeira
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Silvia S da Costa
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Marília O Scliar
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Laura M L Carvalho
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Luciana N Silva
- Department of Pediatrics, Instituto de Tratamento do Câncer Infantil (ITACI), Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Estela M Novak
- Department of Pediatrics, Instituto de Tratamento do Câncer Infantil (ITACI), Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | | | | | - Sofia M M Sugayama
- Department of Pediatrics, Instituto de Tratamento do Câncer Infantil (ITACI), Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Vicente Odone-Filho
- Department of Pediatrics, Instituto de Tratamento do Câncer Infantil (ITACI), Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Ana Cristina V Krepischi
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil.
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8
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Nunes N, Carvalho Nunes B, Zamariolli M, Cordeiro de Queiroz Soares D, Caires dos Santos L, Gollo Dantas A, Ayres Meloni V, Iole Belangero S, Gil-Da-Silva-Lopes VL, Ae Kim C, Melaragno MI. Variants in Candidate Genes for Phenotype Heterogeneity in Patients with the 22q11.2 Deletion Syndrome. Genet Res (Camb) 2024; 2024:5549592. [PMID: 38586596 PMCID: PMC10998724 DOI: 10.1155/2024/5549592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 02/29/2024] [Accepted: 03/20/2024] [Indexed: 04/09/2024] Open
Abstract
22q11.2 deletion syndrome (22q11.2DS) is a microdeletion syndrome with a broad and heterogeneous phenotype, even though most of the deletions present similar sizes, involving ∼3 Mb of DNA. In a relatively large population of a Brazilian 22q11.2DS cohort (60 patients), we investigated genetic variants that could act as genetic modifiers and contribute to the phenotypic heterogeneity, using a targeted NGS (Next Generation Sequencing) with a specific Ion AmpliSeq panel to sequence nine candidate genes (CRKL, MAPK1, HIRA, TANGO2, PI4KA, HDAC1, ZDHHC8, ZFPM2, and JAM3), mapped in and outside the 22q11.2 hemizygous deleted region. In silico prediction was performed, and the whole-genome sequencing annotation analysis package (WGSA) was used to predict the possible pathogenic effect of single nucleotide variants (SNVs). For the in silico prediction of the indels, we used the genomic variants filtered by a deep learning model in NGS (GARFIELD-NGS). We identified six variants, 4 SNVs and 2 indels, in MAPK1, JAM3, and ZFPM2 genes with possibly synergistic deleterious effects in the context of the 22q11.2 deletion. Our results provide the opportunity for the discovery of the co-occurrence of genetic variants with 22q11.2 deletions, which may influence the patients´ phenotype.
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Affiliation(s)
- Natalia Nunes
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Beatriz Carvalho Nunes
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Malú Zamariolli
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Leonardo Caires dos Santos
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Anelisa Gollo Dantas
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Vera Ayres Meloni
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Sintia Iole Belangero
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Vera Lúcia Gil-Da-Silva-Lopes
- Department of Translational Medicine, School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Chong Ae Kim
- Genetics Unit, Instituto da Criança, Universidade de São Paulo, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
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9
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Haque B, Guirguis G, Curtis M, Mohsin H, Walker S, Morrow MM, Costain G. A comparative medical genomics approach may facilitate the interpretation of rare missense variation. J Med Genet 2024:jmg-2023-109760. [PMID: 38508706 DOI: 10.1136/jmg-2023-109760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/12/2024] [Indexed: 03/22/2024]
Abstract
PURPOSE To determine the degree to which likely causal missense variants of single-locus traits in domesticated species have features suggestive of pathogenicity in a human genomic context. METHODS We extracted missense variants from the Online Mendelian Inheritance in Animals database for nine animals (cat, cattle, chicken, dog, goat, horse, pig, rabbit and sheep), mapped coordinates to the human reference genome and annotated variants using genome analysis tools. We also searched a private commercial laboratory database of genetic testing results from >400 000 individuals with suspected rare disorders. RESULTS Of 339 variants that were mappable to the same residue and gene in the human genome, 56 had been previously classified with respect to pathogenicity: 31 (55.4%) pathogenic/likely pathogenic, 1 (1.8%) benign/likely benign and 24 (42.9%) uncertain/other. The odds ratio for a pathogenic/likely pathogenic classification in ClinVar was 7.0 (95% CI 4.1 to 12.0, p<0.0001), compared with all other germline missense variants in these same 220 genes. The remaining 283 variants disproportionately had allele frequencies and REVEL scores that supported pathogenicity. CONCLUSION Cross-species comparisons could facilitate the interpretation of rare missense variation. These results provide further support for comparative medical genomics approaches that connect big data initiatives in human and veterinary genetics.
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Affiliation(s)
- Bushra Haque
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - George Guirguis
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Meredith Curtis
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hera Mohsin
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Susan Walker
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Gregory Costain
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
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10
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Duarte CAB, Dos Santos CA, de Oliveira CDD, Spautz CC, Sumita LM, Nakatani SM. Hereditary breast cancer next-generation sequencing (NGS) panel evaluation in the south region of Brazil: a novel BRCA2 candidate pathogenic variant is reported. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.08.24302195. [PMID: 38370791 PMCID: PMC10871466 DOI: 10.1101/2024.02.08.24302195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
In this article, we delineate a loosely selected cohort comprising patients with a history of early-onset breast cancer and/or a familial occurrence of cancer. The aim of this study was to gain insights into the presence of breast cancer-related gene variants in a population from a micro-region in southern Brazil, specifically the Metropolitan Region of Curitiba. This area exhibits a highly genetically mixed population, mirroring the general characteristics of the Brazilian people. Comprehensive next-generation sequencing (NGS) multigene panel testing was conducted, involving the evaluation of twelve patients. Two pathogenic variants and one candidate pathogenic variant were identified: BRCA2:c.8878C>T, p.Gln2960Ter; CHEK2:c.1100delAG>A, p.Thr367Metfs*15 and BRCA2:c.3482dupG>GA, p.Asp1161Glufs*3, a novel variant, previously unpublished, is reported.
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Affiliation(s)
- Cesar Augusto B Duarte
- Research and Development Division, Genoprimer Diagnóstico Molecular, Curitiba, Paraná, Brazil
| | | | | | | | - Laura Masami Sumita
- Clinimol Diagnóstico Molecular, Molecular Biology Clinical Laboratory, São Paulo, São Paulo, Brazil
| | - Sueli Massumi Nakatani
- Research and Development Division, Genoprimer Diagnóstico Molecular, Curitiba, Paraná, Brazil
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11
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Douillard V, Dos Santos Brito Silva N, Bourguiba-Hachemi S, Naslavsky MS, Scliar MO, Duarte YAO, Zatz M, Passos-Bueno MR, Limou S, Gourraud PA, Launay É, Castelli EC, Vince N. Optimal population-specific HLA imputation with dimension reduction. HLA 2024; 103:e15282. [PMID: 37950640 DOI: 10.1111/tan.15282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/29/2023] [Accepted: 10/14/2023] [Indexed: 11/13/2023]
Abstract
Human genomics has quickly evolved, powering genome-wide association studies (GWASs). SNP-based GWASs cannot capture the intense polymorphism of HLA genes, highly associated with disease susceptibility. There are methods to statistically impute HLA genotypes from SNP-genotypes data, but lack of diversity in reference panels hinders their performance. We evaluated the accuracy of the 1000 Genomes data as a reference panel for imputing HLA from admixed individuals of African and European ancestries, focusing on (a) the full dataset, (b) 10 replications from 6 populations, and (c) 19 conditions for the custom reference panels. The full dataset outperformed smaller models, with a good F1-score of 0.66 for HLA-B. However, custom models outperformed the multiethnic or population models of similar size (F1-scores up to 0.53, against up to 0.42). We demonstrated the importance of using genetically specific models for imputing populations, which are currently underrepresented in public datasets, opening the door to HLA imputation for every genetic population.
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Affiliation(s)
- Venceslas Douillard
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Nayane Dos Santos Brito Silva
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
- São Paulo State University, Molecular Genetics and Bioinformatics Laboratory, School of Medicine, Botucatu, Brazil
| | - Sonia Bourguiba-Hachemi
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Michel S Naslavsky
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Marilia O Scliar
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Yeda A O Duarte
- Medical-Surgical Nursing Department, School of Nursing, University of São Paulo, São Paulo, Brazil
- Epidemiology Department, Public Health School, University of São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Sophie Limou
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Pierre-Antoine Gourraud
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Élise Launay
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
- Department of Pediatrics and Pediatric Emergency, Hôpital Femme Enfant Adolescent, CHU de Nantes, Nantes, France
| | - Erick C Castelli
- São Paulo State University, Molecular Genetics and Bioinformatics Laboratory, School of Medicine, Botucatu, Brazil
| | - Nicolas Vince
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
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12
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Bravo-Garzón MA, Bornstein-Quevedo L, de Camargo VP, Sanku G, Jansen AM, de Macedo MP, Rico-Restrepo M, Chacón M. BRAF-Mutated Melanoma Journey in Latin America: Expert Recommendations From Diagnosis to Treatment. Cancer Control 2024; 31:10732748241251572. [PMID: 38751033 PMCID: PMC11100406 DOI: 10.1177/10732748241251572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 03/28/2024] [Accepted: 04/10/2024] [Indexed: 05/19/2024] Open
Abstract
OBJECTIVES • Gather a panel of Latin American experts in testing and treating BRAF-melanoma. • Describe the current landscape of BRAF-mutated melanoma in Latin America. • Outline the current gaps in testing and recommend improvements for testing and treating BRAF-mutated melanoma in the region. INTRODUCTION Melanoma prevalence in Latin America is lower than in high- and middle-income countries. However, recent data indicate that the region's incidence and mortality are rising, with more stage IV patients being diagnosed. According to international clinical practice guidelines, conducting BRAF-mutation testing in patients with stage III or stage IV melanoma and high-risk resected disease is imperative. Still, BRAF-mutation testing and targeted therapies are inconsistently available in the region. METHODS Americas Health Foundation convened a meeting of Latin American experts on BRAF-mutated melanoma to develop guidelines and recommendations for diagnosis through treatment. RESULTS AND CONCLUSIONS Some recommendations for improving diagnostics through improving access and reducing the cost of BRAF-mutation testing, enhancing efficiency in pathology laboratories, and creating country-specific local guidelines. The panel also gave treatment recommendations for neo-adjuvant therapy, adjuvant therapy, and therapy for patients with metastatic disease in Latin America.
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Affiliation(s)
- María A. Bravo-Garzón
- Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center – CTIC, Bogotá D.C., Colombia
| | | | | | | | | | | | | | - Matías Chacón
- Alexander Fleming Institute, Buenos Aires, Argentina
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13
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Ribeiro HP, Baraldi BM, Rodrigues-Soares F, Planello AC. Psychiatric Level 1A evidence pharmacogenomics in a Brazilian admixed cohort and global populations. Pharmacogenomics 2024; 25:69-78. [PMID: 38288577 DOI: 10.2217/pgs-2023-0211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
Purpose: To compare minor allele frequencies (MAFs) of psychiatric drug response variants in a Brazilian admixed cohort with global populations and other Brazilian groups. Methods: PharmGKB MAFs were gathered from publicly available genetic datasets for Brazil and worldwide. Results: Among 146 variants in CYP2D6 and CYP2C19, 41 were present in Brazil, mostly rare (MAF <1%). 11 variants showed significant MAF differences with large effect sizes compared with global populations. CYP2C19*3 (rs4986893), CYP2C19*17 (rs12248560), CYP2D6*17 (rs28371706-A) and CYP2D6*29 (rs61736512) exhibited higher frequencies in Brazil, with the latter three also differing from other Brazilian groups. Conclusion: This study highlights significant pharmacogenomic diversity in Brazil and globally, underscoring the need for more research in personalized psychiatric drug therapy.
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Affiliation(s)
- Helena Pereira Ribeiro
- Department of Morphology & Basic Pathology - Medical School, Faculdade de Medicina de Jundiaí, Jundiaí, 13202-550, Brazil
| | - Beatriz Meza Baraldi
- Department of Morphology & Basic Pathology - Medical School, Faculdade de Medicina de Jundiaí, Jundiaí, 13202-550, Brazil
| | - Fernanda Rodrigues-Soares
- Department of Pathology, Genetics, & Evolution, Institute of Biological & Natural Sciences, Universidade Federal do Triângulo Mineiro, Uberaba, 38035-180, Brazil
| | - Aline Cristiane Planello
- Department of Morphology & Basic Pathology - Medical School, Faculdade de Medicina de Jundiaí, Jundiaí, 13202-550, Brazil
- Department of Bioscience, Faculdade de Odontologia de Piracicaba/Universidade de Campinas, 13414-903, Brazil
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14
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Tallman S, Sungo MDD, Saranga S, Beleza S. Whole genomes from Angola and Mozambique inform about the origins and dispersals of major African migrations. Nat Commun 2023; 14:7967. [PMID: 38042927 PMCID: PMC10693643 DOI: 10.1038/s41467-023-43717-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
As the continent of origin for our species, Africa harbours the highest levels of diversity anywhere on Earth. However, many regions of Africa remain under-sampled genetically. Here we present 350 whole genomes from Angola and Mozambique belonging to ten Bantu ethnolinguistic groups, enabling the construction of a reference variation catalogue including 2.9 million novel SNPs. We investigate the emergence of Bantu speaker population structure, admixture involving migrations across sub-Saharan Africa and model the demographic histories of Angolan and Mozambican Bantu speakers. Our results bring together concordant views from genomics, archaeology, and linguistics to paint an updated view of the complexity of the Bantu Expansion. Moreover, we generate reference panels that better represents the diversity of African populations involved in the trans-Atlantic slave trade, improving imputation accuracy in African Americans and Brazilians. We anticipate that our collection of genomes will form the foundation for future African genomic healthcare initiatives.
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Affiliation(s)
- Sam Tallman
- University of Leicester, Department of Genetics & Genome Biology, University Road, Leicester, LE1 7RH, UK
- Genomics England, 1 Canada Square, London, E14 5AB, UK
| | | | - Sílvio Saranga
- Universidade Pedagógica, Avenida Eduardo Mondlane, CP 2107, Maputo, Mozambique
| | - Sandra Beleza
- University of Leicester, Department of Genetics & Genome Biology, University Road, Leicester, LE1 7RH, UK.
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15
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Wilson LA, Macken WL, Perry LD, Record CJ, Schon KR, Frezatti RSS, Raga S, Naidu K, Köken ÖY, Polat I, Kapapa MM, Dominik N, Efthymiou S, Morsy H, Nel M, Fassad MR, Gao F, Patel K, Schoonen M, Bisschoff M, Vorster A, Jonvik H, Human R, Lubbe E, Nonyane M, Vengalil S, Nashi S, Srivastava K, Lemmers RJLF, Reyaz A, Mishra R, Töpf A, Trainor CI, Steyn EC, Mahungu AC, van der Vliet PJ, Ceylan AC, Hiz AS, Çavdarlı B, Semerci Gündüz CN, Ceylan GG, Nagappa M, Tallapaka KB, Govindaraj P, van der Maarel SM, Narayanappa G, Nandeesh BN, Wa Somwe S, Bearden DR, Kvalsund MP, Ramdharry GM, Oktay Y, Yiş U, Topaloğlu H, Sarkozy A, Bugiardini E, Henning F, Wilmshurst JM, Heckmann JM, McFarland R, Taylor RW, Smuts I, van der Westhuizen FH, Sobreira CFDR, Tomaselli PJ, Marques W, Bhatia R, Dalal A, Srivastava MVP, Yareeda S, Nalini A, Vishnu VY, Thangaraj K, Straub V, Horvath R, Chinnery PF, Pitceathly RDS, Muntoni F, Houlden H, Vandrovcova J, Reilly MM, Hanna MG. Neuromuscular disease genetics in under-represented populations: increasing data diversity. Brain 2023; 146:5098-5109. [PMID: 37516995 PMCID: PMC10690022 DOI: 10.1093/brain/awad254] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/04/2023] [Indexed: 08/01/2023] Open
Abstract
Neuromuscular diseases (NMDs) affect ∼15 million people globally. In high income settings DNA-based diagnosis has transformed care pathways and led to gene-specific therapies. However, most affected families are in low-to-middle income countries (LMICs) with limited access to DNA-based diagnosis. Most (86%) published genetic data is derived from European ancestry. This marked genetic data inequality hampers understanding of genetic diversity and hinders accurate genetic diagnosis in all income settings. We developed a cloud-based transcontinental partnership to build diverse, deeply-phenotyped and genetically characterized cohorts to improve genetic architecture knowledge, and potentially advance diagnosis and clinical management. We connected 18 centres in Brazil, India, South Africa, Turkey, Zambia, Netherlands and the UK. We co-developed a cloud-based data solution and trained 17 international neurology fellows in clinical genomic data interpretation. Single gene and whole exome data were analysed via a bespoke bioinformatics pipeline and reviewed alongside clinical and phenotypic data in global webinars to inform genetic outcome decisions. We recruited 6001 participants in the first 43 months. Initial genetic analyses 'solved' or 'possibly solved' ∼56% probands overall. In-depth genetic data review of the four commonest clinical categories (limb girdle muscular dystrophy, inherited peripheral neuropathies, congenital myopathy/muscular dystrophies and Duchenne/Becker muscular dystrophy) delivered a ∼59% 'solved' and ∼13% 'possibly solved' outcome. Almost 29% of disease causing variants were novel, increasing diverse pathogenic variant knowledge. Unsolved participants represent a new discovery cohort. The dataset provides a large resource from under-represented populations for genetic and translational research. In conclusion, we established a remote transcontinental partnership to assess genetic architecture of NMDs across diverse populations. It supported DNA-based diagnosis, potentially enabling genetic counselling, care pathways and eligibility for gene-specific trials. Similar virtual partnerships could be adopted by other areas of global genomic neurological practice to reduce genetic data inequality and benefit patients globally.
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Affiliation(s)
- Lindsay A Wilson
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - William L Macken
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Luke D Perry
- Institute of Child Health and Centre for Neuromuscular Diseases, Neurosciences Unit, The Dubowitz Neuromuscular Centre, University College London, UCL Great Ormond Street, Great Ormond Street Hospital, London WC1N 3JH, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Christopher J Record
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Katherine R Schon
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Rodrigo S S Frezatti
- Department of Neurosciences, School of Medicine of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Sharika Raga
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Paediatric Neurology, Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Kireshnee Naidu
- Neurology Research Group, Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
- Division of Neurology, Department of Medicine, Stellenbosch University, Cape Town, South Africa
| | - Özlem Yayıcı Köken
- Faculty of Medicine, Department of Pediatric Neurology, Akdeniz University, Antalya, Turkey
| | - Ipek Polat
- Faculty of Medicine, Pediatric Neurology Department, Dokuz Eylül University, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Musambo M Kapapa
- Department of Physiotherapy, University of Zambia School of Health Sciences & University Teaching Hospital Neurology Research Office, Lusaka, Zambia
| | - Natalia Dominik
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Heba Morsy
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Melissa Nel
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Neurology Research Group, Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Mahmoud R Fassad
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Fei Gao
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Krutik Patel
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Maryke Schoonen
- Focus Area for Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Michelle Bisschoff
- Focus Area for Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Armand Vorster
- Focus Area for Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Hallgeir Jonvik
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Ronel Human
- Department of Paediatrics, Steve Biko Academic Hospital, University of Pretoria, Pretoria, South Africa
| | - Elsa Lubbe
- Department of Paediatrics, Steve Biko Academic Hospital, University of Pretoria, Pretoria, South Africa
| | - Malebo Nonyane
- Department of Paediatrics, Steve Biko Academic Hospital, University of Pretoria, Pretoria, South Africa
| | - Seena Vengalil
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Saraswati Nashi
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Kosha Srivastava
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Richard J L F Lemmers
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Alisha Reyaz
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Rinkle Mishra
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Christina I Trainor
- John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Elizabeth C Steyn
- Neurology Research Group, Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Amokelani C Mahungu
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Neurology Research Group, Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Patrick J van der Vliet
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Ahmet Cevdet Ceylan
- Department of Medical Genetics, Ankara Bilkent City Hospital, Ankara, Turkey
- Faculty of Medicine, Department of Medical Genetics, Ankara Yıldırım Beyazıt University, Ankara, Turkey
| | - A Semra Hiz
- Faculty of Medicine, Pediatric Neurology Department, Dokuz Eylül University, Izmir, Turkey
- Izmir Biomedicine and Genome Center (IBG), Izmir, Turkey
| | - Büşranur Çavdarlı
- Department of Medical Genetics, Ankara Bilkent City Hospital, Ankara, Turkey
| | - C Nur Semerci Gündüz
- Department of Medical Genetics, Ankara Bilkent City Hospital, Ankara, Turkey
- Faculty of Medicine, Department of Medical Genetics, Ankara Yıldırım Beyazıt University, Ankara, Turkey
| | - Gülay Güleç Ceylan
- Department of Medical Genetics, Ankara Bilkent City Hospital, Ankara, Turkey
- Faculty of Medicine, Department of Medical Genetics, Ankara Yıldırım Beyazıt University, Ankara, Turkey
| | - Madhu Nagappa
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Karthik B Tallapaka
- CSIR—Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Telangana, India
| | - Periyasamy Govindaraj
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | | | - Gayathri Narayanappa
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Bevinahalli N Nandeesh
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Somwe Wa Somwe
- Department of Clinical Sciences, School of Medicine and Health Sciences, University of Lusaka, Lusaka, Zambia
| | - David R Bearden
- University of Zambia Department of Educational Psychology, Lusaka, Zambia
- Department of Neurology, School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Michelle P Kvalsund
- Department of Neurology, School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Internal Medicine, University of Zambia School of Medicine, Lusaka, Zambia
| | - Gita M Ramdharry
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Yavuz Oktay
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
- Izmir Biomedicine and Genome Center (IBG), Izmir, Turkey
| | - Uluç Yiş
- Faculty of Medicine, Pediatric Neurology Department, Dokuz Eylül University, Izmir, Turkey
| | | | - Anna Sarkozy
- NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Enrico Bugiardini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Franclo Henning
- Division of Neurology, Department of Medicine, Stellenbosch University, Cape Town, South Africa
| | - Jo M Wilmshurst
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Paediatric Neurology, Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Jeannine M Heckmann
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Neurology Research Group, Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | - Izelle Smuts
- Department of Paediatrics, Steve Biko Academic Hospital, University of Pretoria, Pretoria, South Africa
| | | | | | - Pedro J Tomaselli
- Department of Neurosciences, School of Medicine of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Wilson Marques
- Department of Neurosciences, School of Medicine of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Rohit Bhatia
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - M V Padma Srivastava
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Sireesha Yareeda
- Department of Neurology, Nizam’s Institute of Medical Sciences (NIMS), Hyderabad, Telangana, India
| | - Atchayaram Nalini
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Venugopalan Y Vishnu
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Kumarasamy Thangaraj
- CSIR—Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Telangana, India
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Newcastle University Translational and Clinical Research Institute and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Francesco Muntoni
- Institute of Child Health and Centre for Neuromuscular Diseases, Neurosciences Unit, The Dubowitz Neuromuscular Centre, University College London, UCL Great Ormond Street, Great Ormond Street Hospital, London WC1N 3JH, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Jana Vandrovcova
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Mary M Reilly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
| | - Michael G Hanna
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK
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16
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Quaio CRDC, Ceroni JRM, Pereira MA, Teixeira ACB, Yamada RY, Cintra VP, Perrone E, De França M, Chen K, Minillo RM, Biondo CA, de Mello MRB, Moura LR, do Nascimento ATB, de Oliveira Pelegrino K, de Lima LB, do Amaral Virmond L, Moreno CA, Prota JRM, de Araujo Espolaor JG, Silva TYT, Moraes GHI, de Oliveira GS, Moura LMS, Caraciolo MP, Guedes RLM, Gretschischkin MC, Chazanas PLN, Nakamura CNI, de Souza Reis R, Toledo CM, Lage FSD, de Almeida GB, do Nascimento Júnior JB, Cardoso MA, de Paula Azevedo V, de Almeida TF, Cervato MC, de Oliveira Filho JB. The hospital Israelita Albert Einstein standards for constitutional sequence variants classification: version 2023. Hum Genomics 2023; 17:102. [PMID: 37968704 PMCID: PMC10652504 DOI: 10.1186/s40246-023-00549-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/02/2023] [Indexed: 11/17/2023] Open
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.
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Affiliation(s)
| | - José Ricardo Magliocco Ceroni
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Michele Araújo Pereira
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | | | - Renata Yoshiko Yamada
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Vivian Pedigone Cintra
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Eduardo Perrone
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Marina De França
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Kelin Chen
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Renata Moldenhauer Minillo
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Cheysa Arielly Biondo
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | | | - Lais Rodrigues Moura
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | | | - Karla de Oliveira Pelegrino
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Larissa Barbosa de Lima
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Luiza do Amaral Virmond
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Carolina Araujo Moreno
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Joana Rosa Marques Prota
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | | | | | - Gabriel Hideki Izuka Moraes
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Gustavo Santos de Oliveira
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Livia Maria Silva Moura
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Marcel Pinheiro Caraciolo
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Rafael Lucas Muniz Guedes
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Michel Chieregato Gretschischkin
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Pedro Lui Nigro Chazanas
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Carolina Naomi Izo Nakamura
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Rodrigo de Souza Reis
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Carmen Melo Toledo
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Fernanda Stussi Duarte Lage
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Giovanna Bloise de Almeida
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - José Bandeira do Nascimento Júnior
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Milena Andreuzo Cardoso
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Victor de Paula Azevedo
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Tatiana Ferreira de Almeida
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
| | - Murilo Castro Cervato
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil
- VarsOmics, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Joao Bosco de Oliveira Filho
- Laboratório Clínico, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, São Paulo, SP, CEP 05652-000, Brazil.
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17
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Reščenko R, Brīvība M, Atava I, Rovīte V, Pečulis R, Silamiķelis I, Ansone L, Megnis K, Birzniece L, Leja M, Xu L, Shi X, Zhou Y, Slaitas A, Hou Y, Kloviņš J. Whole-Genome Sequencing of 502 Individuals from Latvia: The First Step towards a Population-Specific Reference of Genetic Variation. Int J Mol Sci 2023; 24:15345. [PMID: 37895026 PMCID: PMC10607061 DOI: 10.3390/ijms242015345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Despite rapid improvements in the accessibility of whole-genome sequencing (WGS), understanding the extent of human genetic variation is limited by the scarce availability of genome sequences from underrepresented populations. Developing the population-scale reference database of Latvian genetic variation may fill the gap in European genomes and improve human genomics research. In this study, we analysed a high-coverage WGS dataset comprising 502 individuals selected from the Genome Database of the Latvian Population. An assessment of variant type, location in the genome, function, medical relevance, and novelty was performed, and a population-specific imputation reference panel (IRP) was developed. We identified more than 18.2 million variants in total, of which 3.3% so far are not represented in gnomAD and dbSNP databases. Moreover, we observed a notable though distinct clustering of the Latvian cohort within the European subpopulations. Finally, our findings demonstrate the improved performance of imputation of variants using the Latvian population-specific reference panel in the Latvian population compared to established IRPs. In summary, our study provides the first WGS data for a regional reference genome that will serve as a resource for the development of precision medicine and complement the global genome dataset, improving the understanding of human genetic variation.
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Affiliation(s)
- Raimonds Reščenko
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Monta Brīvība
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Ivanna Atava
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Vita Rovīte
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Raitis Pečulis
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Ivars Silamiķelis
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Laura Ansone
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Kaspars Megnis
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Līga Birzniece
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
| | - Mārcis Leja
- Faculty of Medicine, University of Latvia, LV-1004 Riga, Latvia;
- Institute of Clinical and Preventive Medicine, University of Latvia, LV-1079 Riga, Latvia
| | - Liqin Xu
- Latvia MGI Tech, LV-2167 Mārupe, Latvia; (L.X.); (X.S.); (Y.Z.); (A.S.); (Y.H.)
| | - Xulian Shi
- Latvia MGI Tech, LV-2167 Mārupe, Latvia; (L.X.); (X.S.); (Y.Z.); (A.S.); (Y.H.)
| | - Yan Zhou
- Latvia MGI Tech, LV-2167 Mārupe, Latvia; (L.X.); (X.S.); (Y.Z.); (A.S.); (Y.H.)
| | - Andis Slaitas
- Latvia MGI Tech, LV-2167 Mārupe, Latvia; (L.X.); (X.S.); (Y.Z.); (A.S.); (Y.H.)
| | - Yong Hou
- Latvia MGI Tech, LV-2167 Mārupe, Latvia; (L.X.); (X.S.); (Y.Z.); (A.S.); (Y.H.)
| | - Jānis Kloviņš
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (M.B.); (I.A.); (V.R.); (R.P.); (I.S.); (L.A.); (K.M.); (L.B.); (J.K.)
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18
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Hu JCW, Abdelhakim AH, North VS, Garcia MD, Lustig MJ, Kazim M, Odel JG. Osteopathia striata with cranial sclerosis causing a compressive optic neuropathy. Ophthalmic Genet 2023; 44:496-500. [PMID: 36446546 DOI: 10.1080/13816810.2022.2144902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 12/02/2022]
Abstract
BACKGROUND Osteopathia striata combined with cranial sclerosis (OS-CS) is an inherited skeletal dysplasia that manifests with macrocephaly, orofacial abnormalities, thickened craniofacial bones, and vertically oriented radiodensities of the long bones. CASE REPORT Here, we present a severe case of OS-CS in a 4-year-old girl causing optic neuropathy as shown by radiographic evidence, ophthalmic findings, and histopathology. Previous genetic testing in this patient revealed a de novo heterozygous mutation in AMER1 (c.1057C>T, p.Arg353Ter). Although the patient had a pre-existing, appropriately functioning, ventriculoperitoneal (VP) shunt, a subsequent MRI of the brain and orbits showed narrowing of the bilateral optic nerve canals secondary to osseous thickening causing bilateral optic nerve atrophy, worse on the left. The patient underwent staged bilateral orbital osteotomies, optic canal decompression, and bilateral frontal craniotomy, and at 11 months postoperatively, her vision remained stable. Conclusions: While up to 50% of the patients with OS-CS may experience hearing loss due to cranial nerve compression, we present a case of severe visual loss secondary to OS-CS-associated optic nerve compression.
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Affiliation(s)
- Jennifer C W Hu
- Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
| | - Aliaa H Abdelhakim
- Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
| | - Victoria S North
- Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
| | - Maria D Garcia
- Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
| | - Marc J Lustig
- Pediatric Ophthalmic Consultants of New York, New York, New York, USA
| | - Michael Kazim
- Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jeffrey G Odel
- Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
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19
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Kolb KL, Mira ALS, Auer ED, Bucco ID, de Lima e Silva CE, dos Santos PI, Hoch VBB, Oliveira LC, Hauser AB, Hundt JE, Shuldiner AR, Lopes FL, Boysen TJ, Franke A, Pinto LFR, Soares-Lima SC, Kretzschmar GC, Boldt ABW. Glucocorticoid Receptor Gene ( NR3C1) Polymorphisms and Metabolic Syndrome: Insights from the Mennonite Population. Genes (Basel) 2023; 14:1805. [PMID: 37761945 PMCID: PMC10530687 DOI: 10.3390/genes14091805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/06/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
The regulation of the hypothalamic-pituitary-adrenal (HPA) axis is associated with polymorphisms and the methylation degree of the glucocorticoid receptor gene (NR3C1) and is potentially involved in the development of metabolic syndrome (MetS). In order to evaluate the association between MetS with the polymorphisms, methylation, and gene expression of the NR3C1 in the genetically isolated Brazilian Mennonite population, we genotyped 20 NR3C1 polymorphisms in 74 affected (MetS) and 138 unaffected individuals without affected first-degree relatives (Co), using exome sequencing, as well as five variants from non-exonic regions, in 70 MetS and 166 Co, using mass spectrometry. The methylation levels of 11 1F CpG sites were quantified using pyrosequencing (66 MetS and 141 Co), and the NR3C1 expression was evaluated via RT-qPCR (14 MetS and 25 Co). Age, physical activity, and family environment during childhood were associated with MetS. Susceptibility to MetS, independent of these factors, was associated with homozygosity for rs10482605*C (OR = 4.74, pcorr = 0.024) and the haplotype containing TTCGTTGATT (rs3806855*T_ rs3806854*T_rs10482605*C_rs10482614*G_rs6188*T_rs258813*T_rs33944801*G_rs34176759*A_rs17209258*T_rs6196*T, OR = 4.74, pcorr = 0.048), as well as for the CCT haplotype (rs41423247*C_ rs6877893*C_rs258763*T), OR = 6.02, pcorr = 0.030), but not to the differences in methylation or gene expression. Thus, NR3C1 polymorphisms seem to modulate the susceptibility to MetS in Mennonites, independently of lifestyle and early childhood events, and their role seems to be unrelated to DNA methylation and gene expression.
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Affiliation(s)
- Kathleen Liedtke Kolb
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil; (K.L.K.); (A.L.S.M.); (E.D.A.); (I.D.B.); (C.E.d.L.e.S.); (P.I.d.S.); (V.B.-B.H.); (L.C.O.); (G.C.K.)
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
| | - Ana Luiza Sprotte Mira
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil; (K.L.K.); (A.L.S.M.); (E.D.A.); (I.D.B.); (C.E.d.L.e.S.); (P.I.d.S.); (V.B.-B.H.); (L.C.O.); (G.C.K.)
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
| | - Eduardo Delabio Auer
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil; (K.L.K.); (A.L.S.M.); (E.D.A.); (I.D.B.); (C.E.d.L.e.S.); (P.I.d.S.); (V.B.-B.H.); (L.C.O.); (G.C.K.)
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
| | - Isabela Dall’Oglio Bucco
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil; (K.L.K.); (A.L.S.M.); (E.D.A.); (I.D.B.); (C.E.d.L.e.S.); (P.I.d.S.); (V.B.-B.H.); (L.C.O.); (G.C.K.)
| | - Carla Eduarda de Lima e Silva
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil; (K.L.K.); (A.L.S.M.); (E.D.A.); (I.D.B.); (C.E.d.L.e.S.); (P.I.d.S.); (V.B.-B.H.); (L.C.O.); (G.C.K.)
| | - Priscila Ianzen dos Santos
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil; (K.L.K.); (A.L.S.M.); (E.D.A.); (I.D.B.); (C.E.d.L.e.S.); (P.I.d.S.); (V.B.-B.H.); (L.C.O.); (G.C.K.)
- Postgraduate Program in Internal Medicine, Medical Clinic Department, UFPR, Rua General Carneiro, 181, 11th Floor, Alto da Glória, Curitiba 80210-170, PR, Brazil
| | - Valéria Bumiller-Bini Hoch
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil; (K.L.K.); (A.L.S.M.); (E.D.A.); (I.D.B.); (C.E.d.L.e.S.); (P.I.d.S.); (V.B.-B.H.); (L.C.O.); (G.C.K.)
| | - Luana Caroline Oliveira
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil; (K.L.K.); (A.L.S.M.); (E.D.A.); (I.D.B.); (C.E.d.L.e.S.); (P.I.d.S.); (V.B.-B.H.); (L.C.O.); (G.C.K.)
| | - Aline Borsato Hauser
- Laboratory School of Clinical Analysis, Department of Pharmacy, Federal University of Paraná (UFPR), Av. Pref. Lothário Meissner, 632, Jardim Botânico, Curitiba 80210-170, PR, Brazil;
| | - Jennifer Elisabeth Hundt
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee, 160, Haus 32, 23562 Lübeck, Germany;
| | - Alan R. Shuldiner
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA;
| | - Fabiana Leão Lopes
- Human Genetics Branch, National Institute of Mental Health, 35 Convent Drive, Bethesda, MD 20892, USA;
- Institute of Psychiatry, Federal University Rio de Janeiro, Av. Venceslau Brás, 71, Rio de Janeiro 22290-140, RJ, Brazil
| | - Teide-Jens Boysen
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University of Kiel, 24105 Kiel, Germany; (T.-J.B.); (A.F.)
| | - Andre Franke
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University of Kiel, 24105 Kiel, Germany; (T.-J.B.); (A.F.)
| | - Luis Felipe Ribeiro Pinto
- Brazilian National Cancer Institute, Rua André Cavalcanti, 37, Rio de Janeiro 20231-050, RJ, Brazil; (L.F.R.P.); (S.C.S.-L.)
| | - Sheila Coelho Soares-Lima
- Brazilian National Cancer Institute, Rua André Cavalcanti, 37, Rio de Janeiro 20231-050, RJ, Brazil; (L.F.R.P.); (S.C.S.-L.)
| | - Gabriela Canalli Kretzschmar
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil; (K.L.K.); (A.L.S.M.); (E.D.A.); (I.D.B.); (C.E.d.L.e.S.); (P.I.d.S.); (V.B.-B.H.); (L.C.O.); (G.C.K.)
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
- Faculdades Pequeno Príncipe, Av. Iguaçu, 333, Curitiba 80230-020, PR, Brazil
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim, 1632, Curitiba 80250-060, PR, Brazil
| | - Angelica Beate Winter Boldt
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil; (K.L.K.); (A.L.S.M.); (E.D.A.); (I.D.B.); (C.E.d.L.e.S.); (P.I.d.S.); (V.B.-B.H.); (L.C.O.); (G.C.K.)
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
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Tinano FR, Canton APM, Montenegro LR, de Castro Leal A, Faria AG, Seraphim CE, Brauner R, Jorge AA, Mendonca BB, Argente J, Brito VN, Latronico AC. Clinical and Genetic Characterization of Familial Central Precocious Puberty. J Clin Endocrinol Metab 2023; 108:1758-1767. [PMID: 36611250 DOI: 10.1210/clinem/dgac763] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/09/2023]
Abstract
CONTEXT Central precocious puberty (CPP) can have a familial form in approximately one-quarter of the children. The recognition of this inherited condition increased after the identification of autosomal dominant CPP with paternal transmission caused by mutations in the MKRN3 and DLK1 genes. OBJECTIVE We aimed to characterize the inheritance and estimate the prevalence of familial CPP in a large multiethnic cohort; to compare clinical and hormonal features, as well as treatment response to GnRH analogs (GnRHa), in children with distinct modes of transmission; and to investigate the genetic basis of familial CPP. METHODS We retrospectively studied 586 children with a diagnosis of CPP. Patients with familial CPP (n = 276) were selected for clinical and genetic analysis. Data from previous studies were grouped, encompassing sequencing of MKRN3 and DLK1 genes in 204 patients. Large-scale parallel sequencing was performed in 48 individuals from 34 families. RESULTS The prevalence of familial CPP was estimated at 22%, with a similar frequency of maternal and paternal transmission. Pedigree analyses of families with maternal transmission suggested an autosomal dominant inheritance. Clinical and hormonal features, as well as treatment response to GnRHa, were similar among patients with different forms of transmission of familial CPP. MKRN3 loss-of-function mutations were the most prevalent cause of familial CPP, followed by DLK1 loss-of-function mutations, affecting, respectively, 22% and 4% of the studied families; both affected exclusively families with paternal transmission. Rare variants of uncertain significance were identified in CPP families with maternal transmission. CONCLUSION We demonstrated a similar prevalence of familial CPP with maternal and paternal transmission. MKRN3 and DLK1 loss-of-function mutations were the major causes of familial CPP with paternal transmission.
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Affiliation(s)
- Flávia Rezende Tinano
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 05403-900 São Paulo, Brasil
| | - Ana Pinheiro Machado Canton
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 05403-900 São Paulo, Brasil
| | - Luciana R Montenegro
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 05403-900 São Paulo, Brasil
| | - Andrea de Castro Leal
- Departamento de Saúde Integrada, Universidade do Estado do Pará (UEPA), Santarém, 68040-090 Pará, Brasil
| | - Aline G Faria
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 05403-900 São Paulo, Brasil
| | - Carlos E Seraphim
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 05403-900 São Paulo, Brasil
| | - Raja Brauner
- Pediatric Endocrinology Unit, Fondation Ophtalmologique Adolphe de Rothschild and Université Paris Descartes, 75019 Paris, France
| | - Alexander A Jorge
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 05403-900 São Paulo, Brasil
- Unidade de Endocrinologia Genética, Laboratório de Endocrinologia Celular e Molecular LIM/25, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 05403-900 São Paulo, Brasil
| | - Berenice B Mendonca
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 05403-900 São Paulo, Brasil
| | - Jesús Argente
- Department of Pediatrics, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Departments of Paediatrics and Paediatric Endocrinology, Hospital Infantil Universitario Niño Jesús, 28009 Madrid, Spain
- Instituto de Investigación La Princesa, 28009 Madrid, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029 Madrid, Spain
- IMDEA Food Institute, CEIUAM+CSIC, 28049 Madrid, Spain
| | - Vinicius N Brito
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 05403-900 São Paulo, Brasil
| | - Ana Claudia Latronico
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 05403-900 São Paulo, Brasil
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Melo A, de Carvalho LM, Ferriani VPL, Cavalcanti A, Appenzeller S, Oliveira VR, Neto HC, Rosário NA, de Oliveira Poswar F, Guimaraes MX, Kokron CM, Maia RE, Silva GD, Keller G, Ferreira MD, Vasconcelos DM, Toledo-Barros MAM, Barros SF, Neto NSR, Krieger MH, Kalil J, Mendonça LO. A brazilian nationwide multicenter study on deficiency of deaminase-2 (DADA2). Adv Rheumatol 2023; 63:23. [PMID: 37217999 DOI: 10.1186/s42358-023-00303-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/02/2023] [Indexed: 05/24/2023] Open
Abstract
INTRODUCTION The deficiency of ADA2 (DADA2) is a rare autoinflammatory disease provoked by mutations in the ADA2 gene inherited in a recessive fashion. Up to this moment there is no consensus for the treatment of DADA2 and anti-TNF is the therapy of choice for chronic management whereas bone marrow transplantation is considered for refractory or severe phenotypes. Data from Brazil is scarce and this multicentric study reports 18 patients with DADA2 from Brazil. PATIENTS AND METHODS This is a multicentric study proposed by the Center for Rare and Immunological Disorders of the Hospital 9 de Julho - DASA, São Paulo - Brazil. Patients of any age with a confirmed diagnosis of DADA2 were eligible for this project and data on clinical, laboratory, genetics and treatment were collected. RESULTS Eighteen patients from 10 different centers are reported here. All patients had disease onset at the pediatric age (median of 5 years) and most of them from the state of São Paulo. Vasculopathy with recurrent stroke was the most common phenotype but atypical phenotypes compatible with ALPS-like and Common Variable Immunodeficiency (CVID) was also found. All patients carried pathogenic mutations in the ADA2 gene. Acute management of vasculitis was not satisfactory with steroids in many patients and all those who used anti-TNF had favorable responses. CONCLUSION The low number of patients diagnosed with DADA2 in Brazil reinforces the need for disease awareness for this condition. Moreover, the absence of guidelines for diagnosis and management is also necessary (t).
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Affiliation(s)
- Adriana Melo
- Division of Clinical Immunology and Allergy, Hospital das Clínicas da Universidade de São Paulo, Universidade de São Paulo, São Paulo, Brazil
| | - Luciana Martins de Carvalho
- Division of Pediatric Rheumatology Department of Pediatrics, Clinical Hospital of Ribeirão Preto Medical School, Universidade de São Paulo, São Paulo, Brazil
| | - Virginia Paes Leme Ferriani
- Division of Pediatric Rheumatology Department of Pediatrics, Clinical Hospital of Ribeirão Preto Medical School, Universidade de São Paulo, São Paulo, Brazil
| | - André Cavalcanti
- Department of Pediatrics, Hospital das Clínicas da Universidade Federal de Pernambuco, Universidade Federal de Pernambuco, Pernambuco, Brazil
| | - Simone Appenzeller
- Department of Pediatric Rheumatology, Universidade de Campinas, São Paulo, Brazil
| | | | - Herberto Chong Neto
- Division of Allergy and Immunology, Complexo Hospital de Clínicas, Federal University of Paraná, Paraná, Brazil
| | - Nelson Augusto Rosário
- Division of Allergy and Immunology, Complexo Hospital de Clínicas, Federal University of Paraná, Paraná, Brazil
| | | | | | - Cristina Maria Kokron
- Division of Clinical Immunology and Allergy, Hospital das Clínicas da Universidade de São Paulo, Universidade de São Paulo, São Paulo, Brazil
| | - Rayana Elias Maia
- Division of Genetics, Universidade Federal de Campina Grande, Campina Grande, Paraíba, Brazil
| | - Guilherme Diogo Silva
- Department of Neurology; Hospital das Cl?nicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Gabriel Keller
- Department of Neurology; Hospital das Cl?nicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Mauricio Domingues Ferreira
- Department of Dermatology; Ambulatory for cutaneous manifestations of Primary Immunodeficiencies; Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Dewton Moraes Vasconcelos
- Department of Dermatology; Ambulatory for cutaneous manifestations of Primary Immunodeficiencies; Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Myrthes Anna Maragna Toledo-Barros
- Division of Clinical Immunology and Allergy, Hospital das Clínicas da Universidade de São Paulo, Universidade de São Paulo, São Paulo, Brazil
| | - Samar Freschi Barros
- Laboratory for Medical Investigation (LIM-19) - LIM-19; Instituto do Coração, Universidade de São Paulo, São Paulo, Brazil
| | - Nilton Salles Rosa Neto
- Department of Internal Medicine, Universidade de Santo Amaro-UNISA, São Paulo, Brazil
- Center for Rare and Immunological Disorders, Hospital 9 de Julho - Rede DASA, São Paulo, Brazil
| | - Marta Helena Krieger
- ANDAI (Associação Nacional de Doenças Autoinflamatórias - Brazilian Association for Autoinflammatory Diseases), São Paulo, Brazil
| | - Jorge Kalil
- Division of Clinical Immunology and Allergy, Hospital das Clínicas da Universidade de São Paulo, Universidade de São Paulo, São Paulo, Brazil
- Laboratory for Medical Investigation (LIM-19) - LIM-19; Instituto do Coração, Universidade de São Paulo, São Paulo, Brazil
| | - Leonardo Oliveira Mendonça
- Division of Clinical Immunology and Allergy, Hospital das Clínicas da Universidade de São Paulo, Universidade de São Paulo, São Paulo, Brazil.
- Laboratory for Medical Investigation (LIM-19) - LIM-19; Instituto do Coração, Universidade de São Paulo, São Paulo, Brazil.
- Center for Rare and Immunological Disorders, Hospital 9 de Julho - Rede DASA, São Paulo, Brazil.
- Division of Immunology and Allergy, Center for Rare and Immunological Disorders, DASA- Hospital, 9 de Julho Rua Peixoto Gomide, 285, 01409001, São Paulo, Brazil.
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Bertholim-Nasciben L, Scliar MO, Debortoli G, Thiruvahindrapuram B, Scherer SW, Duarte YAO, Zatz M, Suarez-Kurtz G, Parra EJ, Naslavsky MS. Characterization of pharmacogenomic variants in a Brazilian admixed cohort of elderly individuals based on whole-genome sequencing data. Front Pharmacol 2023; 14:1178715. [PMID: 37234706 PMCID: PMC10206227 DOI: 10.3389/fphar.2023.1178715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/10/2023] [Indexed: 05/28/2023] Open
Abstract
Introduction: Research in the field of pharmacogenomics (PGx) aims to identify genetic variants that modulate response to drugs, through alterations in their pharmacokinetics (PK) or pharmacodynamics (PD). The distribution of PGx variants differs considerably among populations, and whole-genome sequencing (WGS) plays a major role as a comprehensive approach to detect both common and rare variants. This study evaluated the frequency of PGx markers in the context of the Brazilian population, using data from a population-based admixed cohort from Sao Paulo, Brazil, which includes variants from WGS of 1,171 unrelated, elderly individuals. Methods: The Stargazer tool was used to call star alleles and structural variants (SVs) from 38 pharmacogenes. Clinically relevant variants were investigated, and the predicted drug response phenotype was analyzed in combination with the medication record to assess individuals potentially at high-risk of gene-drug interaction. Results: In total, 352 unique star alleles or haplotypes were observed, of which 255 and 199 had a frequency < 0.05 and < 0.01, respectively. For star alleles with frequency > 5% (n = 97), decreased, loss-of-function and unknown function accounted for 13.4%, 8.2% and 27.8% of alleles or haplotypes, respectively. Structural variants (SVs) were identified in 35 genes for at least one individual, and occurred with frequencies >5% for CYP2D6, CYP2A6, GSTM1, and UGT2B17. Overall 98.0% of the individuals carried at least one high risk genotype-predicted phenotype in pharmacogenes with PharmGKB level of evidence 1A for drug interaction. The Electronic Health Record (EHR) Priority Result Notation and the cohort medication registry were combined to assess high-risk gene-drug interactions. In general, 42.0% of the cohort used at least one PharmGKB evidence level 1A drug, and 18.9% of individuals who used PharmGKB evidence level 1A drugs had a genotype-predicted phenotype of high-risk gene-drug interaction. Conclusion: This study described the applicability of next-generation sequencing (NGS) techniques for translating PGx variants into clinically relevant phenotypes on a large scale in the Brazilian population and explores the feasibility of systematic adoption of PGx testing in Brazil.
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Affiliation(s)
- Luciana Bertholim-Nasciben
- School of Public Health, University of São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Marilia O. Scliar
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Guilherme Debortoli
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, ON, Canada
| | | | - Stephen W. Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Yeda A. O. Duarte
- Medical-Surgical Nursing Department, School of Nursing, University of São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Guilherme Suarez-Kurtz
- Divisão de Pesquisa Clínica e Desenvolvimento Tecnológico, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Esteban J. Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, ON, Canada
| | - Michel S. Naslavsky
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
- Hospital Israelita Albert Einstein, São Paulo, Brazil
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23
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Suarez-Kurtz G, Fernandes VC, Elias ABR. Implementation of DPYD Genotyping in Admixed American Populations: Brazil as a Model Case. Clin Pharmacol Ther 2023. [PMID: 37161547 DOI: 10.1002/cpt.2921] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/21/2023] [Indexed: 05/11/2023]
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24
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Magrino J, Munford V, Martins DJ, Homma TK, Page B, Gaubitz C, Freire BL, Lerario AM, Vilar JB, Amorin A, Leão EKE, Kok F, Menck CF, Jorge AA, Kelch BA. A thermosensitive PCNA allele underlies an ataxia-telangiectasia-like disorder. J Biol Chem 2023; 299:104656. [PMID: 36990216 PMCID: PMC10165274 DOI: 10.1016/j.jbc.2023.104656] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/25/2023] [Accepted: 03/10/2023] [Indexed: 03/29/2023] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is a sliding clamp protein that coordinates DNA replication with various DNA maintenance events that are critical for human health. Recently, a hypomorphic homozygous serine to isoleucine (S228I) substitution in PCNA was described to underlie a rare DNA repair disorder known as PCNA-associated DNA repair disorder (PARD). PARD symptoms range from UV sensitivity, neurodegeneration, telangiectasia, and premature aging. We, and others, previously showed that the S228I variant changes the protein-binding pocket of PCNA to a conformation that impairs interactions with specific partners. Here, we report a second PCNA substitution (C148S) that also causes PARD. Unlike PCNA-S228I, PCNA-C148S has WT-like structure and affinity toward partners. In contrast, both disease-associated variants possess a thermostability defect. Furthermore, patient-derived cells homozygous for the C148S allele exhibit low levels of chromatin-bound PCNA and display temperature-dependent phenotypes. The stability defect of both PARD variants indicates that PCNA levels are likely an important driver of PARD disease. These results significantly advance our understanding of PARD and will likely stimulate additional work focused on clinical, diagnostic, and therapeutic aspects of this severe disease.
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Affiliation(s)
- Joseph Magrino
- Department of Biochemistry and Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Veridiana Munford
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Davi Jardim Martins
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Thais K Homma
- Genetic Endocrinology Unit, Cellular and Molecular Endocrinology Laboratory LIM25, Endocrinology Discipline of the Faculty of Medicine of the University of São Paulo, São Paulo, Brazil; Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics LIM42, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil
| | - Brendan Page
- Department of Biochemistry and Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Christl Gaubitz
- Department of Biochemistry and Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Bruna L Freire
- Genetic Endocrinology Unit, Cellular and Molecular Endocrinology Laboratory LIM25, Endocrinology Discipline of the Faculty of Medicine of the University of São Paulo, São Paulo, Brazil; Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics LIM42, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil
| | - Antonio M Lerario
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics LIM42, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil; Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, Michigan, USA
| | - Juliana Brandstetter Vilar
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Antonio Amorin
- Neurogenetics, Neurology Department, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil
| | - Emília K E Leão
- Medical Genetics Service of the Professor Edgard Santos University Hospital - Federal University of Bahia, Salvador, Brazil
| | - Fernando Kok
- Neurogenetics, Neurology Department, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil; Mendelics Genomic Analysis, São Paulo, São Paulo, Brazil
| | - Carlos Fm Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alexander Al Jorge
- Genetic Endocrinology Unit, Cellular and Molecular Endocrinology Laboratory LIM25, Endocrinology Discipline of the Faculty of Medicine of the University of São Paulo, São Paulo, Brazil
| | - Brian A Kelch
- Department of Biochemistry and Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA.
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25
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Galvão Lopes V, Fernandes de Oliveira V, Mendonça Munhoz Dati L, Naslavsky MS, Ferreira GM, Hirata MH. Dynamics of the personalities of PCSK9 on missense variants (rs505151 and rs562556) from elderly cohort studies in Brazil. J Biomol Struct Dyn 2023; 41:15625-15633. [PMID: 37010997 DOI: 10.1080/07391102.2023.2191140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/06/2023] [Indexed: 04/04/2023]
Abstract
The Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) promotes the degradation of the low-density lipoprotein receptors (LDLR). Gain-of-function (GOF) variants of PCSK9 significantly affects lipid metabolism leading to coronary artery disease (CAD), owing to the raising the plasma low-density lipoprotein (LDL). Considering the public health matter, large-scale genomic studies have been conducted worldwide to provide the genetic architecture of populations for the implementation of precision medicine actions. Nevertheless, despite the advances in genomic studies, non-European populations are still underrepresented in public genomic data banks. Despite this, we found two high-frequency variants (rs505151 and rs562556) in the ABraOM databank (Brazilian genomic variants) from a cohort SABE study conducted in the largest city of Brazil, São Paulo. Here, we assessed the structural and dynamical features of these variants against WT through a molecular dynamics study. We sought fundamental dynamical interdomain relations through Perturb Response Scanning (PRS) and we found an interesting change of dynamical relation between prodomain and Cysteine-Histidine-Rich-Domain (CHRD) in the variants. The results highlight the pivotal role of prodomain in the PCSK9 dynamic and the implications for the development of new drugs depending on patient group genotype.
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Affiliation(s)
- Vitor Galvão Lopes
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, Brazil
| | - Victor Fernandes de Oliveira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, Brazil
| | - Livia Mendonça Munhoz Dati
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, Brazil
| | - Michel Satya Naslavsky
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, University of Sao Paulo, São Paulo, Brazil
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, Brazil
| | - Mario Hiroyuki Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, Brazil
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26
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de Castro MV, Silva MVR, Oliveira LDM, Gozzi-Silva SC, Naslavsky MS, Scliar MO, Magalhães ML, da Rocha KM, Nunes K, Castelli EC, Magawa JY, Santos KS, Cunha-Neto E, Sato MN, Zatz M. Immunological evaluation of young unvaccinated patients with Turner syndrome after COVID-19. Int J Infect Dis 2023; 129:207-215. [PMID: 36758851 PMCID: PMC9905041 DOI: 10.1016/j.ijid.2023.01.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/27/2022] [Accepted: 01/29/2023] [Indexed: 02/10/2023] Open
Abstract
OBJECTIVES The X-chromosome contains the largest number of immune-related genes, which play a major role in COVID-19 symptomatology and susceptibility. Here, we had a unique opportunity to investigate, for the first time, COVID-19 outcomes in six unvaccinated young Brazilian patients with Turner syndrome (TS; 45, X0), including one case of critical illness in a child aged 10 years, to evaluate their immune response according to their genetic profile. METHODS A serological analysis of humoral immune response against SARS-CoV-2, phenotypic characterization of antiviral responses in peripheral blood mononuclear cells after stimuli, and the production of cytotoxic cytokines of T lymphocytes and natural killer cells were performed in blood samples collected from the patients with TS during the convalescence period. Whole exome sequencing was also performed. RESULTS Our volunteers with TS showed a delayed or insufficient humoral immune response to SARS-CoV-2 (particularly immunoglobulin G) and a decrease in interferon-γ production by cluster of differentiation (CD)4+ and CD8+ T lymphocytes after stimulation with toll-like receptors 7/8 agonists. In contrast, we observed a higher cytotoxic activity in the volunteers with TS than the volunteers without TS after phorbol myristate acetate/ionomycin stimulation, particularly granzyme B and perforin by CD8+ and natural killer cells. Interestingly, two volunteers with TS carry rare genetic variants in genes that regulate type I and III interferon immunity. CONCLUSION Following previous reports in the literature for other conditions, our data showed that patients with TS may have an impaired immune response against SARS-CoV-2. Furthermore, other medical conditions associated with TS could make them more vulnerable to COVID-19.
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Affiliation(s)
- Mateus V de Castro
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil.
| | - Monize V R Silva
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Luana de M Oliveira
- Laboratório de Investigação em Dermatologia e Imunodeficiências, LIM 56, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil; Departamento de Dermatologia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Departamento de Imunologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Sarah C Gozzi-Silva
- Laboratório de Investigação em Dermatologia e Imunodeficiências, LIM 56, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil; Departamento de Imunologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Michel S Naslavsky
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil; Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Marilia O Scliar
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil; Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Monize L Magalhães
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil; Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Katia M da Rocha
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil; Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Kelly Nunes
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil; Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Erick C Castelli
- School of Medicine, Universidade Estadual Paulista, Botucatu, Brasil
| | - Jhosiene Y Magawa
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil; Instituto de Investigação em Imunologia - Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil; Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Keity S Santos
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil; Instituto de Investigação em Imunologia - Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil; Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Edecio Cunha-Neto
- Instituto de Investigação em Imunologia - Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil; Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Maria N Sato
- Laboratório de Investigação em Dermatologia e Imunodeficiências, LIM 56, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil; Departamento de Dermatologia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil; Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
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27
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Adaptive Savitzky–Golay Filters for Analysis of Copy Number Variation Peaks from Whole-Exome Sequencing Data. INFORMATION 2023. [DOI: 10.3390/info14020128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Copy number variation (CNV) is a form of structural variation in the human genome that provides medical insight into complex human diseases; while whole-genome sequencing is becoming more affordable, whole-exome sequencing (WES) remains an important tool in clinical diagnostics. Because of its discontinuous nature and unique characteristics of sparse target-enrichment-based WES data, the analysis and detection of CNV peaks remain difficult tasks. The Savitzky–Golay (SG) smoothing is well known as a fast and efficient smoothing method. However, no study has documented the use of this technique for CNV peak detection. It is well known that the effectiveness of the classical SG filter depends on the proper selection of the window length and polynomial degree, which should correspond with the scale of the peak because, in the case of peaks with a high rate of change, the effectiveness of the filter could be restricted. Based on the Savitzky–Golay algorithm, this paper introduces a novel adaptive method to smooth irregular peak distributions. The proposed method ensures high-precision noise reduction by dynamically modifying the results of the prior smoothing to automatically adjust parameters. Our method offers an additional feature extraction technique based on density and Euclidean distance. In comparison to classical Savitzky–Golay filtering and other peer filtering methods, the performance evaluation demonstrates that adaptive Savitzky–Golay filtering performs better. According to experimental results, our method effectively detects CNV peaks across all genomic segments for both short and long tags, with minimal peak height fidelity values (i.e., low estimation bias). As a result, we clearly demonstrate how well the adaptive Savitzky–Golay filtering method works and how its use in the detection of CNV peaks can complement the existing techniques used in CNV peak analysis.
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28
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Carvalho LML, Pinto CF, de Oliveira Scliar M, Otto PA, Krepischi ACV, Rosenberg C. SCAF4-related syndromic intellectual disability. Am J Med Genet A 2023; 191:570-574. [PMID: 36333968 DOI: 10.1002/ajmg.a.63032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/13/2022] [Accepted: 10/13/2022] [Indexed: 11/07/2022]
Abstract
The causal link between variants in the SCAF4 gene and a syndromic form of intellectual disability (ID) was established in 2020 by Fliedner et al. Since then, no additional cases have been reported. We performed exome sequencing in a 16-year-old Brazilian male presenting with ID, epilepsy, behavioral problems, speech impairment, facial dysmorphisms, heart malformations, and obesity. A de novo pathogenic variant [SCAF4(NM_020706.2):c.374_375dup(p.Glu126LeufsTer20)] was identified. This is the second study reporting the involvement of SCAF4 in syndromic ID, and the description of the patient's clinical features contributes to defining the phenotypic spectrum of this recently described Mendelian disorder.
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Affiliation(s)
- Laura Machado Lara Carvalho
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo (USP), Sao Paulo, Sao Paulo, Brazil
| | - Carla Franchi Pinto
- Department of Pathological Sciences, Faculty of Medical Sciences of Santa Casa de São Paulo, Sao Paulo, Sao Paulo, Brazil
| | - Marília de Oliveira Scliar
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo (USP), Sao Paulo, Sao Paulo, Brazil
| | - Paulo A Otto
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo (USP), Sao Paulo, Sao Paulo, Brazil
| | - Ana Cristina Victorino Krepischi
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo (USP), Sao Paulo, Sao Paulo, Brazil
| | - Carla Rosenberg
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo (USP), Sao Paulo, Sao Paulo, Brazil
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29
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De Oliveira TC, Secolin R, Lopes-Cendes I. A review of ancestrality and admixture in Latin America and the caribbean focusing on native American and African descendant populations. Front Genet 2023; 14:1091269. [PMID: 36741309 PMCID: PMC9893294 DOI: 10.3389/fgene.2023.1091269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/09/2023] [Indexed: 01/21/2023] Open
Abstract
Genomics can reveal essential features about the demographic evolution of a population that may not be apparent from historical elements. In recent years, there has been a significant increase in the number of studies applying genomic epidemiological approaches to understand the genetic structure and diversity of human populations in the context of demographic history and for implementing precision medicine. These efforts have traditionally been applied predominantly to populations of European origin. More recently, initiatives in the United States and Africa are including more diverse populations, establishing new horizons for research in human populations with African and/or Native ancestries. Still, even in the most recent projects, the under-representation of genomic data from Latin America and the Caribbean (LAC) is remarkable. In addition, because the region presents the most recent global miscegenation, genomics data from LAC may add relevant information to understand population admixture better. Admixture in LAC started during the colonial period, in the 15th century, with intense miscegenation between European settlers, mainly from Portugal and Spain, with local indigenous and sub-Saharan Africans brought through the slave trade. Since, there are descendants of formerly enslaved and Native American populations in the LAC territory; they are considered vulnerable populations because of their history and current living conditions. In this context, studying LAC Native American and African descendant populations is important for several reasons. First, studying human populations from different origins makes it possible to understand the diversity of the human genome better. Second, it also has an immediate application to these populations, such as empowering communities with the knowledge of their ancestral origins. Furthermore, because knowledge of the population genomic structure is an essential requirement for implementing genomic medicine and precision health practices, population genomics studies may ensure that these communities have access to genomic information for risk assessment, prevention, and the delivery of optimized treatment; thus, helping to reduce inequalities in the Western Hemisphere. Hoping to set the stage for future studies, we review different aspects related to genetic and genomic research in vulnerable populations from LAC countries.
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Affiliation(s)
- Thais C. De Oliveira
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Rodrigo Secolin
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Iscia Lopes-Cendes
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil,*Correspondence: Iscia Lopes-Cendes,
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30
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Dual Molecular Diagnoses of Recessive Disorders in a Child from Consanguineous Parents: Case Report and Literature Review. Genes (Basel) 2022; 13:genes13122377. [PMID: 36553645 PMCID: PMC9778442 DOI: 10.3390/genes13122377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
The widespread use of whole exome sequencing (WES) resulted in the discovery of multilocus pathogenic variations (MPV), defined as two or more distinct or overlapping Mendelian disorders occurring in a patient, leading to a blended phenotype. In this study, we report on a child with autosomal recessive primary microcephaly-5 (MCPH5) and nephropathic cystinosis. The proband is the first child of consanguineous parents, presenting a complex phenotype including neurodevelopmental delay, microcephaly, growth restriction, significant delay of bone maturation, lissencephaly, and abnormality of neuronal migration, photophobia, and renal tubular acidosis. WES revealed two pathogenic and homozygous variants: a c.4174C>T variant in the ASPM gene and a c.382C>T variant in the CTNS gene, explaining the complex phenotype. The literature review showed that most of the patients harboring two variants in recessive disease genes are born to consanguineous parents. To the best of our knowledge, the patient herein described is the first one harboring pathogenic variants in both the ASPM and CTNS genes. These findings highlight the importance of searching for MPV in patients with complex phenotypes investigated by genome-wide testing methods, especially for those patients born to consanguineous parents.
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31
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Challenges in selecting admixture models and marker sets to infer genetic ancestry in a Brazilian admixed population. Sci Rep 2022; 12:21240. [PMID: 36481695 PMCID: PMC9731996 DOI: 10.1038/s41598-022-25521-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
The inference of genetic ancestry plays an increasingly prominent role in clinical, population, and forensic genetics studies. Several genotyping strategies and analytical methodologies have been developed over the last few decades to assign individuals to specific biogeographic regions. However, despite these efforts, ancestry inference in populations with a recent history of admixture, such as those in Brazil, remains a challenge. In admixed populations, proportion and components of genetic ancestry vary on different levels: (i) between populations; (ii) between individuals of the same population, and (iii) throughout the individual's genome. The present study evaluated 1171 admixed Brazilian samples to compare the genetic ancestry inferred by tri-/tetra-hybrid admixture models and evaluated different marker sets from those with small numbers of ancestry informative markers panels (AIMs), to high-density SNPs (HDSNP) and whole-genome-sequence (WGS) data. Analyses revealed greater variation in the correlation coefficient of ancestry components within and between admixed populations, especially for minority ancestral components. We also observed positive correlation between the number of markers in the AIMs panel and HDSNP/WGS. Furthermore, the greater the number of markers, the more accurate the tri-/tetra-hybrid admixture models.
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32
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A Polymorphism in the TMPRSS2 Gene Increases the Risk of Death in Older Patients Hospitalized with COVID-19. Viruses 2022; 14:v14112557. [PMID: 36423166 PMCID: PMC9696669 DOI: 10.3390/v14112557] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/09/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Transmembrane serine protease type 2 (TMPRSS2) and angiotensin-converting enzyme 2 (ACE2) are the main molecules involved in the entry of SARS-CoV-2 into host cells. Changes in TMPRSS2 expression levels caused by single nucleotide polymorphisms (SNPs) may contribute to the outcome of COVID-19. The aim was to investigate the association between TMPRSS2 gene polymorphisms and the risk of death in hospitalized patients with COVID-19. METHODS We included patients with confirmed COVID-19, recruited from two hospitals in northeastern Brazil from August 2020 to July 2021. Two functional polymorphisms (rs2070788 and rs12329760) in TMPRSS2 were evaluated by real-time PCR. The Kaplan-Meier method was used to estimate death. The Cox's proportional hazards model was used to adjust for potentially confounding factors. RESULTS A total of 402 patients were followed prospectively. Survival analysis demonstrated that older patients carrying the rs2070788 GG genotype had shorter survival times when compared to those with AG or AA genotypes (p = 0.009). In multivariable analysis, the GG genotype was a factor independently associated with the risk of death in older individuals (hazard ratio = 4.03, 95% confidence interval 1.49 to 10.84). CONCLUSIONS The rs2070788 polymorphism in TMPRSS2 increases risk of death four-fold in older patients hospitalized with COVID-19.
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33
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de Castro MV, Silva MVR, Naslavsky MS, Scliar MO, Nunes K, Passos-Bueno MR, Castelli EC, Magawa JY, Adami FL, Moretti AIS, de Oliveira VL, Boscardin SB, Cunha-Neto E, Kalil J, Jouanguy E, Bastard P, Casanova JL, Quiñones-Vega M, Sosa-Acosta P, Guedes JDS, de Almeida NP, Nogueira FCS, Domont GB, Santos KS, Zatz M. The oldest unvaccinated Covid-19 survivors in South America. Immun Ageing 2022; 19:57. [PMID: 36384671 PMCID: PMC9666972 DOI: 10.1186/s12979-022-00310-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022]
Abstract
BACKGROUND Although older adults are at a high risk of severe or critical Covid-19, there are many cases of unvaccinated centenarians who had a silent infection or recovered from mild or moderate Covid-19. We studied three Brazilian supercentenarians, older than 110 years, who survived Covid-19 in 2020 before being vaccinated. RESULTS Despite their advanced age, humoral immune response analysis showed that these individuals displayed robust levels of IgG and neutralizing antibodies (NAbs) against SARS-CoV-2. Enrichment of plasma proteins and metabolites related to innate immune response and host defense was also observed. None presented autoantibodies (auto-Abs) to type I interferon (IFN). Furthermore, these supercentenarians do not carry rare variants in genes underlying the known inborn errors of immunity, including particular inborn errors of type I IFN. CONCLUSION These observations suggest that their Covid-19 resilience might be a combination of their genetic background and their innate and adaptive immunity.
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Affiliation(s)
- Mateus V de Castro
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Monize V R Silva
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Michel S Naslavsky
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Marilia O Scliar
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Kelly Nunes
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Erick C Castelli
- Department of Pathology, School of Medicine, UNESP - São Paulo State University, Botucatu, São Paulo, Brazil
| | - Jhosiene Y Magawa
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia-Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil
- Departamento de Clínica Médica, Disciplina de Imunologia Clínica e Alergia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Flávia L Adami
- Laboratory of Antigen Targeting to Dendritic Cells, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ana I S Moretti
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
| | - Vivian L de Oliveira
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
| | - Silvia B Boscardin
- Laboratory of Antigen Targeting to Dendritic Cells, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Edecio Cunha-Neto
- Instituto de Investigação em Imunologia-Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil
- Departamento de Clínica Médica, Disciplina de Imunologia Clínica e Alergia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Jorge Kalil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia-Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil
| | - Emmanuelle Jouanguy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris, Paris, France
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris, Paris, France
| | - Jean-Laurent Casanova
- Imagine Institute, University of Paris, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Mauricio Quiñones-Vega
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Proteomics (LabProt), Institute of Chemistry, LADETEC, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Patricia Sosa-Acosta
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Proteomics (LabProt), Institute of Chemistry, LADETEC, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jéssica de S Guedes
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Proteomics (LabProt), Institute of Chemistry, LADETEC, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Natália P de Almeida
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Proteomics (LabProt), Institute of Chemistry, LADETEC, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fábio C S Nogueira
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Proteomics (LabProt), Institute of Chemistry, LADETEC, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gilberto B Domont
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Keity S Santos
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia-Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil
- Departamento de Clínica Médica, Disciplina de Imunologia Clínica e Alergia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil.
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil.
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Castelli EC, de Castro MV, Naslavsky MS, Scliar MO, Silva NSB, Pereira RN, Ciriaco VAO, Castro CFB, Mendes-Junior CT, Silveira EDS, de Oliveira IM, Antonio EC, Vieira GF, Meyer D, Nunes K, Matos LRB, Silva MVR, Wang JYT, Esposito J, Cória VR, Magawa JY, Santos KS, Cunha-Neto E, Kalil J, Bortolin RH, Hirata MH, Dell’Aquila LP, Razuk-Filho A, Batista-Júnior PB, Duarte-Neto AN, Dolhnikoff M, Saldiva PHN, Passos-Bueno MR, Zatz M. MUC22, HLA-A, and HLA-DOB variants and COVID-19 in resilient super-agers from Brazil. Front Immunol 2022; 13:975918. [PMID: 36389712 PMCID: PMC9641602 DOI: 10.3389/fimmu.2022.975918] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/15/2022] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND Although aging correlates with a worse prognosis for Covid-19, super elderly still unvaccinated individuals presenting mild or no symptoms have been reported worldwide. Most of the reported genetic variants responsible for increased disease susceptibility are associated with immune response, involving type I IFN immunity and modulation; HLA cluster genes; inflammasome activation; genes of interleukins; and chemokines receptors. On the other hand, little is known about the resistance mechanisms against SARS-CoV-2 infection. Here, we addressed polymorphisms in the MHC region associated with Covid-19 outcome in super elderly resilient patients as compared to younger patients with a severe outcome. METHODS SARS-CoV-2 infection was confirmed by RT-PCR test. Aiming to identify candidate genes associated with host resistance, we investigated 87 individuals older than 90 years who recovered from Covid-19 with mild symptoms or who remained asymptomatic following positive test for SARS-CoV-2 as compared to 55 individuals younger than 60 years who had a severe disease or died due to Covid-19, as well as to the general elderly population from the same city. Whole-exome sequencing and an in-depth analysis of the MHC region was performed. All samples were collected in early 2020 and before the local vaccination programs started. RESULTS We found that the resilient super elderly group displayed a higher frequency of some missense variants in the MUC22 gene (a member of the mucins' family) as one of the strongest signals in the MHC region as compared to the severe Covid-19 group and the general elderly control population. For example, the missense variant rs62399430 at MUC22 is two times more frequent among the resilient super elderly (p = 0.00002, OR = 2.24). CONCLUSION Since the pro-inflammatory basal state in the elderly may enhance the susceptibility to severe Covid-19, we hypothesized that MUC22 might play an important protective role against severe Covid-19, by reducing overactive immune responses in the senior population.
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Affiliation(s)
- Erick C. Castelli
- Department of Pathology, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (Unipex), School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Mateus V. de Castro
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Michel S. Naslavsky
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Marilia O. Scliar
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Nayane S. B. Silva
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (Unipex), School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Raphaela N. Pereira
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (Unipex), School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Viviane A. O. Ciriaco
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (Unipex), School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Camila F. B. Castro
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (Unipex), School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
- Centro Universitário Sudoeste Paulista, Avaré, Brazil
| | - Celso T. Mendes-Junior
- Departamento de Química, Faculdade de Filosofa, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Etiele de S. Silveira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Iuri M. de Oliveira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Eduardo C. Antonio
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Gustavo F. Vieira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Laboratório de Saúde Humana In Silico, Programa de Pós-Graduação em Saúde e Desenvolvimento Humano, Universidade La Salle, Canoas, Brazil
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Kelly Nunes
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Larissa R. B. Matos
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Monize V. R. Silva
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Jaqueline Y. T. Wang
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Joyce Esposito
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Vivian R. Cória
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Jhosiene Y. Magawa
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia, Instituto Nacional de Ciências e Tecnologia-iii (INCT), São Paulo, Brazil
| | - Keity S. Santos
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia, Instituto Nacional de Ciências e Tecnologia-iii (INCT), São Paulo, Brazil
| | - Edecio Cunha-Neto
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia, Instituto Nacional de Ciências e Tecnologia-iii (INCT), São Paulo, Brazil
| | - Jorge Kalil
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia, Instituto Nacional de Ciências e Tecnologia-iii (INCT), São Paulo, Brazil
| | - Raul H. Bortolin
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Mário Hiroyuki Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | | | | | | | - Amaro N. Duarte-Neto
- Department of Pathology, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Marisa Dolhnikoff
- Department of Pathology, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Paulo H. N. Saldiva
- Department of Pathology, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
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Amaro E. Artificial intelligence and Big Data in neurology. ARQUIVOS DE NEURO-PSIQUIATRIA 2022; 80:342-347. [PMID: 35976329 PMCID: PMC9491419 DOI: 10.1590/0004-282x-anp-2022-s139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Recent advances in technology have allowed us access to a multitude of datasets pertaining to various dimensions in neurology. Together with the enormous opportunities, we also face challenges related to data quality, ethics and intrinsic difficulties related to the application of data science in healthcare. In this article we will describe the main advances in the field of artificial intelligence and Big Data applied to neurology with a focus on neurosciences based on medical images. Real-World Data (RWD) and analytics related to large volumes of information will be described as well as some of the most relevant scientific initiatives at the time of this writing.
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Affiliation(s)
- Edson Amaro
- Hospital Israelita Albert Einstein, Big Data, São Paulo SP, Brazil
- Universidade de São Paulo, Faculdade de Medicina, Instituto de Radiologia, São Paulo SP, Brazil
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