1
|
Matosinho CGR, Silva CGR, Martins ML, Silva-Malta MCF. Next Generation Sequencing of Red Blood Cell Antigens in Transfusion Medicine: Systematic Review and Meta-Analysis. Transfus Med Rev 2024; 38:150776. [PMID: 37914611 DOI: 10.1016/j.tmrv.2023.150776] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/11/2023] [Accepted: 09/01/2023] [Indexed: 11/03/2023]
Abstract
Molecular analysis of blood groups is important in transfusion medicine, allowing the prediction of red blood cell (RBC) antigens. Many blood banks use single nucleotide variant (SNV) based methods for blood group analysis. While this is a well-established approach, it is limited to the polymorphisms included in genotyping panels. Thus, variants that alter antigenic expression may be ignored, resulting in incorrect prediction of phenotypes. The popularization of next-generation sequencing (NGS) has led to its application in transfusion medicine, including for RBC antigens determination. The present review/meta-analysis aimed to evaluate the applicability of the NGS for the prediction of RBC antigens. A systematic review was conducted following a comprehensive literature search in accordance with the Preferred Reporting Items for Systematic Review and Meta-Analysis guidelines. Studies were selected based on predefined criteria and evaluated using Strengthening the Reporting of Observational studies in Epidemiology guidelines. The characteristics and results of the studies were extracted and meta-analysis was performed to verify the agreement between results from standard molecular methods and NGS. Kell (rs8176058), Duffy (rs2814778, rs12078), or Kidd (rs1085396) alleles were selected as a model for comparisons. Additionally, results are presented for other blood group systems. Of the 864 eligible studies identified, 10 met the inclusion criteria and were selected for meta-analysis. The pooled concordance proportion for NGS compared to other methods ranged from 0.982 to 0.994. The sequencing depth coverage was identified as crucial parameters for the reliability of the results. Some studies reported difficulty in analyzing more complex systems, such as Rh and MNS, requiring the adoption of specific strategies. NGS is a technology capable of predicting blood group phenotypes and has many strengths such as the possibility of simultaneously analyzing hundred individuals and gene regions, and the ability to provide comprehensive genetic analysis, which is useful in the description of new alleles and a better understanding of the genetic basis of blood groups. The implementation of NGS in the routine of blood banks depends on several factors such as cost reduction, the availability of widely validated panels, the establishment of clear quality parameters and access to bioinformatics analysis tools that are easy to access and operate.
Collapse
|
2
|
Chami A, de Souza Zózimo TR, Alves TM, Matosinho CGR, Santos C, Simões MM, Cabral WLR, de Paula Ricardo BF, da Silva Filho AL, Carvalho MRS, da Conceição Braga L. In deep bioinformatic characterization of a novel fumarate hydratase variant FH c.199T > G; (p.Tyr67Asp) in hereditary leiomyomatosis and renal cell carcinoma. Fam Cancer 2023; 22:481-486. [PMID: 37316640 DOI: 10.1007/s10689-023-00335-2] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/25/2023] [Indexed: 06/16/2023]
Abstract
Hereditary leiomyomatosis and renal cell carcinoma (HLRCC) is a rare, autosomal dominant tumor predisposition syndrome characterized by variable development of multiple skin and uterus leiomyomas and aggressive forms of renal cell carcinoma (RCC). Mutations in fumarate hydratase (FH), one of the proteins in homologous recombination repair, precede the development of HLRCC with high penetrance. Considering the risk of early metastasis of RCC, FH has been included in mutation screening panels. The identification of a pathogenic FH variant guides the screening for tumors in the carriers. However, variants of uncertain significance (VUS) are frequent findings, limiting the clinical value of the mutation screening. Here, we describe the associated phenotype and an in-depth, multi-step Bioinformatic evaluation of the germline FH c.199T > G (p.Tyr67 > Asp) variant segregated in an HLRCC family. Evidence for FH c.199T > G; (p.Tyr67Asp) pathogenicity includes the variant segregation with the disease in three affected family members, its absence in populational databases, and the deep evolutionary conservation of the Tyr67 residue. At the protein level, this residue substitution causes the loss of molecular bonds and ionic interactions, affecting molecular dynamics and protein stability. Considering ACMG/AMP criteria, we propose the reclassification of the FH c.199T > G; (p.Tyr67Asp) variant to "likely pathogenic". In addition, the in-depth, in silico approach used here allowed us to understand how and why FH c.199T > G; (p.Tyr67Asp) could cause HLRCC. This could help in clinical management decisions concerning the monitoring of unaffected family members having this variant.
Collapse
Affiliation(s)
- Anisse Chami
- Programa de Pós-Graduação em Tocoginecologia da Universidade Estadual de São Paulo - UNESP, Botucatu, SP, Brazil
- Rede Mater Dei de Saúde, Belo Horizonte, MG, Brazil
| | - Thalía Rodrigues de Souza Zózimo
- Programa de Pós-Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais - UFMG, Campus Pampulha, Belo Horizonte, MG, Brazil
| | - Thamiris Matias Alves
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas - Bloco E3 - Sala 175, Universidade Federal de Minas Gerais - UFMG, Av. Antônio Carlos, 6627 - Campus Pampulha, Belo Horizonte, 31270-901, Brazil
| | - Carolina Guimarães Ramos Matosinho
- Programa de Pós-Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais - UFMG, Campus Pampulha, Belo Horizonte, MG, Brazil
| | | | | | | | | | - Agnaldo Lopes da Silva Filho
- Programa de Pós-Graduação em Tocoginecologia da Universidade Estadual de São Paulo - UNESP, Botucatu, SP, Brazil
- Departamento de Ginecologia e Obstetrícia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Maria Raquel Santos Carvalho
- Programa de Pós-Graduação em Genética, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais - UFMG, Campus Pampulha, Belo Horizonte, MG, Brazil.
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas - Bloco E3 - Sala 175, Universidade Federal de Minas Gerais - UFMG, Av. Antônio Carlos, 6627 - Campus Pampulha, Belo Horizonte, 31270-901, Brazil.
| | - Letícia da Conceição Braga
- Núcleo de Pesquisa Básica e Translacional, Instituto Mário Penna, Belo Horizonte, MG, Brazil
- OncoTag Desenvolvimento de Produto e Serviços Para Saúde Humana, Belo Horizonte, MG, Brazil
| |
Collapse
|
3
|
Matosinho CGR, Fonseca PADS, Peixoto MGCD, Rosse IC, Lopes FCF, Zózimo T, Filho AEV, Bruneli FÂT, Carvalho MRS, Gama MAS. Phenotypic variation in milk fatty acid composition and its association with stearoyl-CoA desaturase 1 (SCD1) gene polymorphisms in Gir cows. J Anim Breed Genet 2023; 140:532-548. [PMID: 37186480 DOI: 10.1111/jbg.12777] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 03/12/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023]
Abstract
Individual variation in milk fatty acid (FA) composition has been partially attributed to stearoyl-CoA desaturase 1 (SCD1) gene polymorphisms in taurine breeds, but much less is known for Zebu breeds. This study investigated the phenotypic variation in milk FA composition, and the influence of SCD1 variants on this trait and on milk fat desaturase indices (DI) in Gir cows. The functional impact of SCD1 variants was predicted using bioinformatics tools. Milk and blood samples were collected from 312 cows distributed in 10 herds from five states of Brazil. SCD1 variants were identified through target sequencing, and milk FA composition was determined by gas chromatography. Phenotypic variation in milk FA composition fell within the range reported for taurine breeds, with SCD18 index showing the lowest variation among the DI. Fourteen SCD1 variants were identified, six of which not previously described. Regarding the A293V polymorphism, all cows were homozygous for the C allele (coding for alanine), whereas all genotypes were detected for the second SNP affecting the 293 codon (G > A), with compelling evidence for functional effects. Significant associations (based on raw p-values) were found between this SNP and C12:0, cis-9, trans-11 CLA and short-chain FA, and between another SNP (rs523411937) and C15:0 and odd-chain linear FA. A new SNP on Chr26:21277069 was associated with trans-11 C18:1, cis-9, trans-11 CLA, C18:3 n-3 and n-3 FA. These findings indicate that SCD1 polymorphisms also contributes to the phenotypic variation in milk FA composition of Gir cows, with potential use in their breeding programmes.
Collapse
Affiliation(s)
- Carolina Guimarães Ramos Matosinho
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Pablo Augusto de Souza Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
| | | | - Izinara Cruz Rosse
- Departamento de Farmácia, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | | | - Thalia Zózimo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Aníbal Eugênio Vercesi Filho
- Agência Paulista de Tecnologia dos Agronegócios e diretor do Laboratório de Biotecnologia do Instituto de Zootecnia do Governo do Estado de São Paulo, São Paulo, SP, Brazil
| | | | - Maria Raquel Santos Carvalho
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | |
Collapse
|
4
|
Perpétuo SSDA, Matosinho CGR, Chaves DG. QUALITY OF LIFE OF HEMOPHILIA A FEMALE CARRIERS OF INTRON 22 INVERSION. Hematol Transfus Cell Ther 2022. [DOI: 10.1016/j.htct.2022.09.478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
|
5
|
Matosinho CGR, Perpétuo SSDA, Chaves DG. QUALITY OF LIFE OF PATIENTS WITH VON WILLEBRAND DISEASE. Hematol Transfus Cell Ther 2022. [DOI: 10.1016/j.htct.2022.09.476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|
6
|
Matosinho CGR, Perpétuo SSDA, Chaves DG. RECLASSIFICATION OF PATIENTS WITH HEMOPHILIA A BY MOLECULAR DIAGNOSIS. Hematol Transfus Cell Ther 2022. [DOI: 10.1016/j.htct.2022.09.477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
|
7
|
Perpétuo SSDA, Matosinho CGR, Chaves DG. CLINICAL AND HEMORRHAGIC PROFILES OF PATIENTS WITH VON WILLEBRAND DISEASE. Hematol Transfus Cell Ther 2022. [DOI: 10.1016/j.htct.2022.09.480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
|
8
|
Matosinho CGR, Perpétuo SSDA, Chaves DG. CLINICAL AND HEMORRHAGIC PROFILES OF HEMOPHILIA A FEMALE CARRIERS OF INTRON 22 INVERSION. Hematol Transfus Cell Ther 2022. [DOI: 10.1016/j.htct.2022.09.475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|
9
|
Martins AAS, Paiva GM, Matosinho CGR, Coser EM, Fonseca PADS, Haase VG, Carvalho MRS. Working memory and arithmetic impairments in children with FMR1 premutation and gray zone alleles. Dement Neuropsychol 2022; 16:105-114. [PMID: 35719251 PMCID: PMC9170264 DOI: 10.1590/1980-5764-dn-2021-0035] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 10/03/2021] [Indexed: 11/22/2022] Open
Abstract
Expansive mutations in familial mental retardation 1 (FMR1) gene have been associated with different phenotypes. Full mutations are associated with intellectual disability and autism spectrum disorder; premutations are associated with math learning difficulties and working memory impairments. In gray zone, neuropsychological development has not yet been described. Objectives This study aimed to describe the frequency of FMR1 premutation and gray zone alleles in a school population sample representing a broad spectrum of variation in math achievement and detail school achievement and cognitive performance in the children identified with FMR1 premutation or gray zone alleles. Methods We described a two-phase study. In the first phase, 2,195 school-age children were screened for math achievement. In the second phase, 378 children with normal intelligence were neuropsychologically assessed and genotyped for FMR1. Of these, 121 children (61 girls) performed below percentile 25 in mathematics (MD group) and 257 children (146 girls) performed above percentile 25 (control group). Results Four pupils presented expanded alleles, one premutation and three gray zone alleles. The girl with the premutation and one boy with a gray zone allele presented impairments in working memory and arithmetic performance below percentile 6, compatible with the diagnosis of developmental dyscalculia. These children's difficulties were not associated with inaccuracy of nonsymbolic number representations or literacy impairments. Dyscalculia in these children seems to be associated mainly with working memory impairments. Conclusions FMR1 expansions in the gray zone may contribute to dyscalculia in otherwise healthy and normally intelligent children.
Collapse
Affiliation(s)
- Aline Aparecida Silva Martins
- Universidade Federal de Minas Gerais, Intituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Postgraduate Program em Genética, Belo Horizonte MG, Brazil.,Universidade Federal de Minas Gerais, Intituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Belo Horizonte MG, Brazil
| | - Giulia Moreira Paiva
- Universidade Federal de Minas Gerais, Faculdade de Filosofia e Ciências Humanas, Departamento de Psicologia, Belo Horizonte MG, Brazil.,Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Programa de Pós-Graduação em Neurociências, Belo Horizonte MG, Brazil
| | - Carolina Guimarães Ramos Matosinho
- Universidade Federal de Minas Gerais, Intituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Postgraduate Program em Genética, Belo Horizonte MG, Brazil.,Universidade Federal de Minas Gerais, Intituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Belo Horizonte MG, Brazil
| | - Elisângela Monteiro Coser
- Fundação Oswaldo Cruz, Instituto René Rachou, Departamento de Informática de Biossistemas e Genômica, Belo Horizonte MG, Brazil
| | - Pablo Augusto de Souza Fonseca
- Universidade Federal de Minas Gerais, Intituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Postgraduate Program em Genética, Belo Horizonte MG, Brazil.,Universidade Federal de Minas Gerais, Intituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Belo Horizonte MG, Brazil
| | - Vitor Geraldi Haase
- Universidade Federal de Minas Gerais, Faculdade de Filosofia e Ciências Humanas, Departamento de Psicologia, Belo Horizonte MG, Brazil.,Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Programa de Pós-Graduação em Neurociências, Belo Horizonte MG, Brazil.,Universidade Federal de Minas Gerais, Faculdade de Medicina, Postgraduate Program em Saúde da Criança e do Adolescente Belo Horizonte MG, Brazil.,Universidade Federal de Minas Gerais, Faculdade de Filosofia e Ciências Humanas, Departamento de Psicologia, Postgraduate Program em Psicologia, Belo Horizonte MG, Brazil.,Instituto Nacional de Ciência e Tecnologia em Cognição, Comportamento e Ensino, São Carlos SP, Brazil
| | - Maria Raquel Santos Carvalho
- Universidade Federal de Minas Gerais, Intituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Postgraduate Program em Genética, Belo Horizonte MG, Brazil.,Universidade Federal de Minas Gerais, Intituto de Ciências Biológicas, Departamento de Genética, Ecologia e Evolução, Belo Horizonte MG, Brazil
| |
Collapse
|
10
|
Freitas SDS, Rezende SM, de Oliveira LC, Prezotti ANL, Renni MS, Corsini CA, Amorim MVDA, Matosinho CGR, Carvalho MRS, Chaves DG. Genetic variants of VWF gene in type 2 von Willebrand disease. Haemophilia 2019; 25:e78-e85. [PMID: 30817071 DOI: 10.1111/hae.13714] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 08/01/2018] [Revised: 12/31/2018] [Accepted: 01/28/2019] [Indexed: 02/06/2023]
Abstract
INTRODUCTION von Willebrand disease (VWD) is the most common inherited bleeding disorder. Few studies have explored the molecular basis of type 2 VWD. AIM This study aimed to identify variants associated with type 2 VWD. METHODS We collected clinical and laboratory data, as well as response to desmopressin and bleeding assessment tool (BAT) score in patients diagnosed with type 2 VWD. We sequenced exons 17, 18, 20 and 28 of the VWF gene. RESULTS We identified 19 different variants in 40 unrelated patients (47.5%). Most of the variants (84.2%) were found in exon 28. A total of 10/19 variants (52.6%) were identified as "likely causative" in 17/40 patients (42.5%), according to the ISTH-SSC and EAHAD VWF gene mutations databases. Nine variants were initially identified as potentially benign. However, through analyses in silico, four of these variants were reclassified as "likely pathogenic" (Ile1380Val, Asn1435Ser, Ser1486Leu and Tyr1584Cys). Response to desmopressin was associated with three variants: Met740Ile, Arg1597Gln and Tyr1584Cys. Major bleeding was associated with variants related to VWD subtypes 2B and 2M. CONCLUSION In conclusion, we identified 19 variants, of which 14 are "likely pathogenic" and therefore associated with VWD. We suggest a possible association of pathogenic variants with major bleeding, response to desmopressin and BAT score ≥10, although this requires further confirmation.
Collapse
Affiliation(s)
- Samuel da Silva Freitas
- Fundação HEMOMINAS, Minas Gerais, Brazil.,Faculty of Medicine, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | | | - Luciana Correa de Oliveira
- Hospital das Clínicas, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | | | - Marília Sande Renni
- Instituto de Hematologia Arthur de Siqueira Cavalcanti (HEMORIO), Rio de Janeiro, Brazil
| | | | | | | | | | | |
Collapse
|