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Fussiger H, Pereira BLDS, Padilha JPD, Donis KC, Siebert M, Brusius-Facchin AC, Baldo G, Saute JAM, Chen K, Virmond LA, Silva MFB, Minillo RM, Almeida TF, Pelegrino KO, Ferreira AFM, Colichio GBC, Oliveira APA, Teixeira ACB, Carlos CD, da Matta MC, Lima MM, Yamada RY, Cintra VP, Campilongo GP, Camargo SK, Oliveira TFG, Coelho AVC, de Albuquerque RS, de Souza EA, Júnior MAP, Caraciolo MP, Cervato MC, Gomes CS, Moura LMS, Guedes RLM, Barreiro RAS, Reis RS, Val FC, Oliveira JB, Siebert M, Brusius‐Facchin AC, Baldo G, Saute JAM. Copy number variations in SPAST and ATL1 are rare among Brazilians. Clin Genet 2022; 103:580-584. [PMID: 36537231 DOI: 10.1111/cge.14280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
Copy number variations (CNV) may represent a significant proportion of SPG4 and SPG3A diagnosis, the most frequent autosomal dominant subtypes of hereditary spastic paraplegias (HSP). We aimed to assess the frequency of CNVs in SPAST and ATL1 and to update the molecular epidemiology of HSP families in southern Brazil. A cohort study that included 95 Brazilian index cases with clinical suspicion of HSP was conducted between April 2011 and September 2022. Multiplex Ligation Dependent Probe Amplification (MLPA) was performed in 41 cases without defined diagnosis by different massive parallel sequencing techniques (MPS). Diagnosis was obtained in 57/95 (60%) index cases, 15/57 (26.3%) being SPG4. Most frequent autosomal recessive HSP subtypes were SPG7 followed by SPG11, SPG76 and cerebrotendinous xanthomatosis. No CNVs in SPAST and ATL1 were found. Copy number variations are rare among SPG4 and SPG3A families in Brazil. Considering the possibility of CNVs detection by specific algorithms with MPS data, we consider that this is likely the most cost-effective approach to investigate CNVs in these genes in low-risk populations, with MLPA being reserved as an orthogonal confirmatory test.
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Affiliation(s)
- Helena Fussiger
- Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Janice Pacheco Dias Padilha
- Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Karina Carvalho Donis
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
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- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Marina Siebert
- Laboratory Research Unit, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | | | - Guilherme Baldo
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Jonas Alex Morales Saute
- Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,Department of Internal Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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- Laboratory Research Unit, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre Brazil
| | | | - Guilherme Baldo
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
| | - Jonas Alex Morales Saute
- Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre Brazil
- Department of Internal Medicine Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
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Chagas BS, Gurgel APAD, Paiva Júnior SSL, Lima RCP, Cordeiro MN, Moura RR, Coelho AVC, Nascimento KCG, Silva Neto JC, Crovella S, Freitas AC. Synergic effect of oral contraceptives, GSTP1 polymorphisms, and high-risk HPV infection in development of cervical lesions. Genet Mol Res 2017; 16:gmr-16-03-gmr.16039742. [PMID: 28829907 DOI: 10.4238/gmr16039742] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Human papillomavirus (HPV) infection is considered a risk factor for cervical cancer. Even if the high-risk HPV (HR-HPV) infection is necessary, environmental co-factors and genetic susceptibility also play an important role in cervical cancer development. In this study, a possible association of rs1695 GSTP1 polymorphisms, HR-HPV infection, and oral contraceptive use with cancer lesion development in women was investigated. The study population comprised 441 Brazilian women from the Northeast region including 98 HPV-infected women with high-grade squamous intraepithelial lesions, 77 HPV-infected women with low-grade squamous intraepithelial lesions, and 266 HPV-negative women with no lesion, used as a control. Our data did not show a significant association between the GSTP1 polymorphism A/G (rs1695) and any HPV-related cervical abnormalities. However, considering the use of oral contraceptives, the GSTP1 rs1695 polymorphism was associated with higher susceptibility to the development of cervical lesions in HR-HPV-infected women. Our study suggests a synergic effect of oral contraceptive use, GSTP1 polymorphisms, and HR-HPV infection in the development of cervical lesions. Together, these risk factors may induce neoplastic transformation of the cervical squamous epithelium, setting conditions for secondary genetic events leading to cervical cancer.
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Affiliation(s)
- B S Chagas
- Laboratório de Estudos Moleculares e Terapia Experimental, Departamento de Genética, , , Brasil
| | - A P A D Gurgel
- Departamento de Engenharia e Meio Ambiente, Universidade Federal da Paraíba, Rio Tinto, PB, Brasil
| | - S S L Paiva Júnior
- Unidade Acadêmica de Serra Talhada, Universidade Federal Rural de Pernambuco, Serra Talhada, PE, Brasil
| | - R C P Lima
- Laboratório de Estudos Moleculares e Terapia Experimental, Departamento de Genética, , , Brasil
| | - M N Cordeiro
- Laboratório de Estudos Moleculares e Terapia Experimental, Departamento de Genética, , , Brasil
| | - R R Moura
- Laboratório de Variabilidade e Genética Humana, Departamento de Genética, , , Brasil.,Instituto de Saúde Materno-Infantil, IRCCS Burlo Garofolo, , Itália
| | - A V C Coelho
- Laboratório de Variabilidade e Genética Humana, Departamento de Genética, , , Brasil
| | - K C G Nascimento
- Laboratório de Estudos Moleculares e Terapia Experimental, Departamento de Genética, , , Brasil
| | - J C Silva Neto
- Laboratório de Pesquisa Molecular e Citológica, Departamento de Histologia, , , Brasil
| | - S Crovella
- Laboratório de Variabilidade e Genética Humana, Departamento de Genética, , , Brasil.,Instituto de Saúde Materno-Infantil, IRCCS Burlo Garofolo, , Itália.,, , Itália
| | - A C Freitas
- Laboratório de Estudos Moleculares e Terapia Experimental, Departamento de Genética, , , Brasil
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Coelho AVC, Silva SPS, Zandonà L, Stocco G, Decorti G, Crovella S. Role of inosine triphosphate pyrophosphatase gene variant on fever incidence during zidovudine antiretroviral therapy. Genet Mol Res 2017; 16:gmr-16-01-gmr.16019373. [PMID: 28128422 DOI: 10.4238/gmr16019373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Zidovudine, the antiretroviral drug used to treat HIV infection, commonly causes adverse effects, such as systemic fever and gastrointestinal alterations. In the present study, the potential role of inosine triphosphate pyrophosphatase (ITPA) gene variant on the incidence of adverse events during antiretroviral therapy (ART) of HIV with zidovudine was discussed. Individuals from Northeastern Brazil (N = 204) receiving treatment for HIV-1 infection were recruited. Zidovudine-related adverse effects developed during the treatment were registered. The rs1127354 polymorphism in the ITPA gene was genotyped using real-time PCR to assess whether this single nucleotide polymorphism was associated with the occurrence of zidovudine-related adverse effects. We observed a significant association between the ITPA variant genotype and the reported systemic fever (odds ratio = 7.17, 95% confidence interval = 1.19-43.15; P = 0.032). Zidovudine use could indirectly lead to an increase in the levels of inosine monophosphate in an antimetabolite-like manner, which is converted to inosine triphosphate (ITP). The rs1127354 variant caused a decrease in ITPA activity, thereby leading to ITP accumulation. This in turn resulted in cytotoxicity, which was manifested by neutropenia and fever. Therefore, we hypothesized a pharmacogenetic model involving the ITPA variant genotype in multifactorial components that act together to determine the onset of zidovudine-related adverse effects.
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Affiliation(s)
- A V C Coelho
- Departamento de Genética, Universidade Federal de Pernambuco Federal de Pernambuco, Recife, PE, Brasil
| | - S P S Silva
- Programa de Pós-Graduação em Inovação Terapêutica, Universidade Federal de Pernambuco Federal de Pernambuco, Recife, PE, Brasil
| | - L Zandonà
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - G Stocco
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - G Decorti
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - S Crovella
- Departamento de Genética, Universidade Federal de Pernambuco Federal de Pernambuco, Recife, PE, Brasil.,Institute for Maternal and Child Health, Scientific Institute for Research, Hospitalization and Care Burlo Garofolo, Trieste, Italy
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Costa MOLP, Heráclio SA, Coelho AVC, Acioly VL, Souza PRE, Correia MTS. Comparison of conventional Papanicolaou cytology samples with liquid-based cervical cytology samples from women in Pernambuco, Brazil. ACTA ACUST UNITED AC 2015; 48:831-8. [PMID: 26247400 PMCID: PMC4568811 DOI: 10.1590/1414-431x20154252] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 03/09/2015] [Indexed: 11/22/2022]
Abstract
In the present study, we compared the performance of a ThinPrep cytological method
with the conventional Papanicolaou test for diagnosis of cytopathological changes,
with regard to unsatisfactory results achieved at the Central Public Health
Laboratory of the State of Pernambuco. A population-based, cross-sectional study was
performed with women aged 18 to 65 years, who spontaneously sought gynecological
services in Public Health Units in the State of Pernambuco, Northeast Brazil, between
April and November 2011. All patients in the study were given a standardized
questionnaire on sociodemographics, sexual characteristics, reproductive practices,
and habits. A total of 525 patients were assessed by the two methods (11.05% were
under the age of 25 years, 30.86% were single, 4.4% had had more than 5 sexual
partners, 44% were not using contraception, 38.85% were users of alcohol, 24.38% were
smokers, 3.24% had consumed drugs previously, 42.01% had gynecological complaints,
and 12.19% had an early history of sexually transmitted diseases). The two methods
showed poor correlation (k=0.19; 95%CI=0.11–0.26; P<0.001). The
ThinPrep method reduced the rate of unsatisfactory results from 4.38% to 1.71%
(χ2=5.28; P=0.02), and the number of cytopathological changes diagnosed
increased from 2.47% to 3.04%. This study confirmed that adopting the ThinPrep method
for diagnosis of cervical cytological samples was an improvement over the
conventional method. Furthermore, this method may reduce possible losses from
cytological resampling and reduce obstacles to patient follow-up, improving the
quality of the public health system in the State of Pernambuco, Northeast Brazil.
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Affiliation(s)
- M O L P Costa
- Laboratório Central de Saúde Pública do Estado de Pernambuco, Recife, PE, BR
| | - S A Heráclio
- Laboratório Central de Saúde Pública do Estado de Pernambuco, Recife, PE, BR
| | - A V C Coelho
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, BR
| | - V L Acioly
- Laboratório Central de Saúde Pública do Estado de Pernambuco, Recife, PE, BR
| | - P R E Souza
- Departamento de Biologia, Universidade Federal Rural de Pernambuco, Recife, PE, BR
| | - M T S Correia
- Departamento de Bioquímica, Universidade Federal de Pernambuco, Recife, PE, BR
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5
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Coelho AVC, Moura RR, Cavalcanti CAJ, Guimarães RL, Sandrin-Garcia P, Crovella S, Brandão LAC. A rapid screening of ancestry for genetic association studies in an admixed population from Pernambuco, Brazil. Genet Mol Res 2015; 14:2876-84. [PMID: 25867437 DOI: 10.4238/2015.march.31.18] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Genetic association studies determine how genes influence traits. However, non-detected population substructure may bias the analysis, resulting in spurious results. One method to detect substructure is to genotype ancestry informative markers (AIMs) besides the candidate variants, quantifying how much ancestral populations contribute to the samples' genetic background. The present study aimed to use a minimum quantity of markers, while retaining full potential to estimate ancestries. We tested the feasibility of a subset of the 12 most informative markers from a previously established study to estimate influence from three ancestral populations: European, African and Amerindian. The results showed that in a sample with a diverse ethnicity (N = 822) derived from 1000 Genomes database, the 12 AIMs had the same capacity to estimate ancestries when compared to the original set of 128 AIMs, since estimates from the two panels were closely correlated. Thus, these 12 SNPs were used to estimate ancestry in a new sample (N = 192) from an admixed population in Recife, Northeast Brazil. The ancestry estimates from Recife subjects were in accordance with previous studies, showing that Northeastern Brazilian populations show great influence from European ancestry (59.7%), followed by African (23.0%) and Amerindian (17.3%) ancestries. Ethnicity self-classification according to skin-color was confirmed to be a poor indicator of population substructure in Brazilians, since ancestry estimates overlapped between classifications. Thus, our streamlined panel of 12 markers may substitute panels with more markers, while retaining the capacity to control for population substructure and admixture, thereby reducing sample processing time.
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Affiliation(s)
- A V C Coelho
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brasil
| | - R R Moura
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brasil
| | - C A J Cavalcanti
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brasil
| | - R L Guimarães
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brasil
| | - P Sandrin-Garcia
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brasil
| | | | - L A C Brandão
- Laboratório de Imunopatologia Keizo Asami, Universidade Federal de Pernambuco, Recife, PE, Brasil
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Catamo E, Addobbati C, Segat L, Sotero Fragoso T, Tavares Dantas A, de Ataide Mariz H, Ferreira da Rocha Junior L, Branco PintoDuarte AL, Coelho AVC, de Moura RR, Polesello V, Crovella S, Sandrin Garcia P. Comprehensive analysis of polymorphisms in the HLA-G 5' upstream regulatory and 3' untranslated regions in Brazilian patients with systemic lupus erythematosus. ACTA ACUST UNITED AC 2015; 85:458-65. [PMID: 25762019 DOI: 10.1111/tan.12545] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 01/28/2015] [Accepted: 02/12/2015] [Indexed: 01/02/2023]
Abstract
This study aims to comprehensively analyze human leucocyte antigen (HLA)-G polymorphisms association with susceptibility to systemic lupus erythematosus (SLE) development and clinical manifestations. The HLA-G 5' upstream regulatory region (URR), 3' untranslated region (UTR) and a cytosine deletion at exon 3 (ΔC, HLA-G*0105N allele) were analyzed in 114 SLE patients and 128 healthy controls from North East Brazil. The +3003T>C (rs1707) C allele and the HG010101c extended HLA-G allele were significantly more frequent in SLE patients than healthy controls (+3003C allele frequency: 12% in SLE patients vs 6% in controls; odds ratio (OR), 2.10, 95% confidence interval (CI), 1.06-4.28, P = 0.026; HG010101c frequency: 11.8% in SLE patients and 6.3% in controls; OR, 2.14, 95% CI, 1.01-4.51, P = 0.046) and were associated with susceptibility for disease development. Other polymorphisms were associated with different clinical manifestations. Although HLA-G role in SLE disease is far from being elucidated yet, our association study results along with a systematic review and meta-analysis suggest that HLA-G might be able to slightly modulate the complex SLE phenotype (pooled OR, 1.14, 95% CI, 1.02-1.27, P = 0.021).
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Affiliation(s)
- E Catamo
- University of Trieste, Trieste, Italy
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