New germline GATA1 variant in females with anemia and thrombocytopenia.

Familial forms of bone marrow defects are rare disorders and description of new cases are valuable opportunities to clarify the molecular machinery that triggers hematopoiesis and blood formation, as well as risk to malignant transformation. We investigated the genetic scenario and possible patterns of transmission in a rare case of familial myeloid disorder with a history of exposure to pesticides. Blood counts of two proband sisters, age 41 and 42, revealed mild anemia, neutrophilia and thrombocytopenia with bone marrow finding mimicking primary myelofibrosis in the cellular phase. We analyzed the coding regions of 78 myeloid neoplasms-related genes and 16 encoding xenobiotic metabolizing genes using Next-Generation Sequencing. The GATA1 variant c.788C > T, p.T263M, located in the C-terminal zinc finger domain of GATA1, was detected in the DNA of the two sisters. The screening of the other kindreds also revealed the p.T263M variant in the mother and two daughters with the same bone marrow disorder. This is the first report of an alteration in the GATA1 CF domain causing anemia, thrombocytopenia and megakaryocyte proliferation with mild myelofibrosis, correlating a new GATA1 germline variant with myeloid disorder.

Novel mutations associated with pyruvate kinase deficiency in Brazil.

BACKGROUND: Pyruvate kinase deficiency is a hereditary disease that affects the glycolytic pathway of the red blood cell, causing nonspherocytic hemolytic anemia. The disease is transmitted as an autosomal recessive trait and shows a marked variability in clinical expression. This study reports on the molecular characterization of ten Brazilian pyruvate kinase-deficient patients and the genotype-phenotype correlations. METHOD: Sanger sequencing and in silico analysis were carried out to identify and characterize the genetic mutations. A non-affected group of Brazilian individuals were also screened for the most commonly reported variants (c.1456C>T and c.1529G>A). RESULTS: Ten different variants were identified in the PKLR gene, of which three are reported here for the first time: p.Leu61Gln, p.Ala137Val and p.Ala428Thr. All the three missense variants involve conserved amino acids, providing a rationale for the observed enzyme deficiency. The allelic frequency of c.1456C>T was 0.1% and the 1529G>A variant was not found. CONCLUSION: This is the first comprehensive report on molecular characterization of pyruvate kinase deficiency from South America. The results allowed us to correlate the severity of the clinical phenotype with the identified variants.

Novel mutations associated with pyruvate kinase deficiency in Brazil

Abstract Background: Pyruvate kinase deficiency is a hereditary disease that affects the glycolytic pathway of the red blood cell, causing nonspherocytic hemolytic anemia. The disease is transmitted as an autosomal recessive trait and shows a marked variability in clinical expression. This study reports on the molecular characterization of ten Brazilian pyruvate kinase-deficient patients and the genotype-phenotype correlations. Method: Sanger sequencing and in silico analysis were carried out to identify and characterize the genetic mutations. A non-affected group of Brazilian individuals were also screened for the most commonly reported variants (c.1456C>T and c.1529G>A). Results: Ten different variants were identified in the PKLR gene, of which three are reported here for the first time: p.Leu61Gln, p.Ala137Val and p.Ala428Thr. All the three missense variants involve conserved amino acids, providing a rationale for the observed enzyme deficiency. The allelic frequency of c.1456C>T was 0.1% and the 1529G>A variant was not found. Conclusion: This is the first comprehensive report on molecular characterization of pyruvate kinase deficiency from South America. The results allowed us to correlate the severity of the clinical phenotype with the identified variants.

Screening of genetic alterations related to non-syndromic hearing loss using MassARRAY iPLEX® technology.

BACKGROUND: Recent advances in molecular genetics have enabled to determine the genetic causes of non-syndromic hearing loss, and more than 100 genes have been related to the phenotype. Due to this extraordinary genetic heterogeneity, a large percentage of patients remain without any molecular diagnosis. This condition imply the need for new methodological strategies in order to detect a greater number of mutations in multiple genes. In this work, we optimized and tested a panel of 86 mutations in 17 different genes screened using a high-throughput genotyping technology to determine the molecular etiology of hearing loss. METHODS: The technology used in this work was the MassARRAY iPLEX® platform. This technology uses silicon chips and DNA amplification products for accurate genotyping by mass spectrometry of previous reported mutations. The generated results were validated using conventional techniques, as direct sequencing, multiplex PCR and RFLP-PCR. RESULTS: An initial genotyping of control subjects, showed failures in 20 % of the selected alterations. To optimize these results, the failed tests were re-designed and new primers were synthesized. Then, the specificity and sensitivity of the panel demonstrated values above 97 %. Additionally, a group of 180 individuals with NSHL without a molecular diagnosis was screened to test the diagnostic value of our panel, and mutations were identified in 30 % of the cases. In 20 % of the individuals, it was possible to explain the etiology of the HL. Mutations in GJB2 gene were the most prevalent, followed by other mutations in in SLC26A4, CDH23, MT-RNR1, MYO15A, and OTOF genes. CONCLUSIONS: The MassARRAY technology has the potential for high-throughput identification of genetic variations. However, we demonstrated that optimization is required to increase the genotyping success and accuracy. The developed panel proved to be efficient and cost-effective, being suitable for applications involving the molecular diagnosis of hearing loss.

Optimization of simultaneous screening of the main mutations involved in non-syndromic deafness using the TaqMan® OpenArray™ Genotyping platform.

BACKGROUND: Hearing loss is the most common sensory deficit in humans, affecting approximately 10% of the global population. In developed countries, one in every 500 individuals suffers from severe to profound bilateral sensorineural hearing loss. For those up to 5 years old, the proportion is higher, at 2.7 in 1000 individuals, and for adolescents the average is 3.5 in 1000. Among the causes of hearing loss, more than 50% are related to genetic factors. To date, nearly 150 loci and 64 genes have been associated with hearing loss. Mutations in the GJB2 gene, which encodes connexin 26, constitute the main genetic cause. So far, more than 300 variations have been described in this gene.As a response to the clinical and genetic heterogeneity of hearing loss and the importance of correct molecular diagnosis of individuals with hereditary hearing loss, this study worked in the optimization for a diagnostic protocol employing a high-throughput genotyping technology. METHODS: For this work, was used the TaqMan® OpenArray™ Genotyping platform. This is a high performance, high-throughput technology based on real-time PCR, which enables the evaluation of up to 3072 SNPs (Single Nucleotide Polymorphisms), point mutations, small deletions, and insertions, using a single genotyping plate. For the study, were selected the layout allowing to analyze 32 alterations in 96 individuals simultaneously. In the end, the generated results were validated by conventional techniques, as direct sequencing, Multiplex PCR and RFLP-PCR. RESULTS: A total of 376 individuals were analyzed, of which 94 were healthy controls, totaling 4 plates in duplicate. All 31 of the changes analyzed were present in the nuclear genes GJB2, GJB6, CRYL1, TMC1, SLC26A4, miR-96, and OTOF, and in the mitochondrial genes MT-RNR1 and MT-TS1. The reactions were subsequently validated by established techniques (direct sequencing, multiplex PCR, and RFLP-PCR) that had previously been used to perform molecular screening of hearing loss at the Human Genetics Laboratory of the Center for Molecular Biology and Genetic Engineering (CBMEG), at the State University of Campinas (UNICAMP). In total, 11,656 genotyping reactions were performed. Of these, only 351 reactions failed, representing approximately 3.01% of the total. The average accuracy of genotyping using the OpenArray™ plates was 96.99%. CONCLUSIONS: The results demonstrated the accuracy, low cost, and good reproducibility of the technique, indicating that the TaqMan® OpenArray™ Genotyping Platform is a useful and reliable tool for application in molecular diagnostic testing of hearing loss.

Etiologic and diagnostic evaluation: algorithm for severe to profound sensorineural hearing loss in Brazil.

OBJECTIVE: Evaluation of the effectiveness of imaging and genetic testing, and establishment of a cost-effective diagnostic protocol for the etiologic diagnosis of sensorineural hearing loss (SNHL) in Brazil. DESIGN: Prospective cohort study. STUDY SAMPLE: Analysis of 100 unrelated Brazilian patients with severe to profound bilateral SNHL submitted to cochlear implant (CI) between 2002 and 2010 at the University of Campinas hospital. The study was based upon three groups: individuals with congenital, progressive, and sudden SNHL. RESULTS: After the diagnostic investigation, the number of cases with unknown etiology was reduced from 72 to 42 (a 42% reduction); 25% of cases were due to environmental factors, 19% to genetic causes, and 14% to inner-ear abnormalities or other clinical features. The genetic and imaging findings contributed to the diagnosis of SNHL in 19% and 20% of the cases analysed, respectively. Molecular testing mainly contributed to the diagnosis of patients with congenital SNHL, while the contribution of radiologic examination was higher for individuals with progressive or sudden SNHL. A sequential diagnostic protocol was proposed based on these data. CONCLUSIONS: The proposed diagnostic workup algorithm could provide better optimization of etiologic diagnosis, as well as reduced costs, compared to a simultaneous testing approach.

Molecular analysis of SLC26A4 gene in patients with nonsyndromic hearing loss and EVA: identification of two novel mutations in Brazilian patients.

UNLABELLED: The SLC26A4 gene has been described as the second gene involved in most cases of sensorineural non-syndromic hearing loss, since the first is the GJB2 gene. Recessive mutations in the SLC26A4 gene encoding pendrin, an anion transporter, are responsible for non-syndromic hearing loss associated with an enlarged vestibular aqueduct (EVA) and Pendred syndrome, which causes early hearing loss and affects the thyroid gland. Typically, the hearing loss is profound and prelingual. However, in some individuals, hearing impairment may develop later in childhood and then progress. Over 200 different SLC26A4 mutations have been reported, with each ethnic population having its own distinctive mutant allele series including a few prevalent founder mutations. OBJECTIVE: Perform the screening of the 20 coding exons of SLC26A4 gene in Brazilian deaf individuals with EVA. PATIENTS AND METHODS: Among the 23 unrelated non-syndromic hearing loss Brazilian patients with EVA, in whom no deafness-causing mutations of the GJB2 gene, the direct sequencing was performed to screen the 20 exons and their flanking regions of the SLC26A4 gene. RESULTS: The sequencing results revealed 9 cases (39%) carrying 13 different SLC26A4 mutations, including 11 known mutations (279delT, V138F, T193I, IVS8+1G>A, T410M, Q413R, R409H, L445W, IVS15+5G>A, V609G, and R776C) and 2 novel mutation (G149R and P142L). CONCLUSION: The SLC26A4 mutations have a high carrying rate in non-syndromic hearing loss Brazilian patients. The identification of a disease-causing mutation can be used to establish a genotypic diagnosis and provide important information to the patients and their families.

Association between phenotype, performance with hearing aids, and genotype of childhood hearing loss in children with and without genetic alteration.

PURPOSE: To establish the frequency of genetic mutations related to sensorineural hearing loss (SNHL); to verify if there is association between the degree of SNHL and the presence of genetic alteration; and to verify if the Minimal Response Levels (MRL) with hearing aids vary according to the genetic alteration. METHODS: Thirty hearing aids users with ages between 8 and 111 months were evaluated. The evaluation procedures used were: pure-tone audiometry; the auditory steady state response (ASSR) on sound field, with and without hearing aids; and genetic study of the hearing loss. RESULTS: Three genetic mutations were diagnosed: 35delG, A1555G and A827G, and the children with these mutations showed higher degree of SNHL. There was no difference between the genetic patterns regarding the degree of SNHL, except for patients with A827G mitochondrial mutation, because all subjects with this mutation had profound SNHL. The difference between the MRL obtained with and without amplification, considering the presence of mutation and the degree of SNHL, was higher in children with moderate SNHL without genetic alterations, both in behavioral and electrophysiological evaluations. CONCLUSION: Genetic mutations were found in 36.7% of the sample, justifying the importance of genetic tracking in the hearing habilitation process. Children with genetic mutations showed higher degrees of hearing loss. The different mutation patterns do not directly determine the degree of hearing loss. The best thresholds with amplification were found in children with moderate hearing loss without genetic alterations.

Associação entre fenótipo, desempenho com próteses auditivas e genótipo da deficiência auditiva infantil em crianças com e sem alteração genética / Association between phenotype, performance with hearing aids, and genotype of childhood hearing loss in children with and without genetic alteration

OBJETIVO: Estabelecer a frequência de mutações genéticas relacionadas à deficiência auditiva neurossensorial (DANS); verificar se há associação entre grau da DANS e presença de alteração genética e verificar se os Níveis Mínimos de Resposta (NMR) com próteses auditivas variam em função da alteração genética. MÉTODOS: Foram avaliadas 30 crianças, com idades entre 8 e 111 meses, usuárias de próteses auditivas. Os procedimentos de avaliação utilizados foram: audiometria tonal e resposta auditiva de estado estável (RAEE) em campo livre, com e sem as próteses auditivas e estudo genético da DANS. RESULTADOS: Foram diagnosticadas três mutações genéticas: 35delG, A1555G e A827G, sendo que as crianças com tais mutações apresentaram maior grau de DANS. Não houve diferença entre os padrões genéticos em relação ao grau de DANS, com exceção dos pacientes com mutação mitocondrial A827G, pois todos com essa mutação eram portadores de DANS de grau profundo. A diferença entre os NMR obtidos sem e com o uso da amplificação, considerando a presença de mutação e grau de DANS, foi maior nas crianças portadoras de DANS de grau moderado sem alteração genética, tanto na avaliação comportamental quanto na eletrofisiológica. CONCLUSÃO: As mutações genéticas foram encontradas em 36,7% da amostra, o que justifica a importância do rastreamento genético no processo de habilitação auditiva. Crianças com mutações genéticas apresentam o maior grau de DANS. Os diferentes padrões de mutações não determinam diretamente o grau da DANS. Os melhores limiares com o uso da amplificação foram encontrados nas crianças com DANS moderada, sem alteração genética.

PURPOSE: To establish the frequency of genetic mutations related to sensorineural hearing loss (SNHL); to verify if there is association between the degree of SNHL and the presence of genetic alteration; and to verify if the Minimal Response Levels (MRL) with hearing aids vary according to the genetic alteration. METHODS: Thirty hearing aids users with ages between 8 and 111 months were evaluated. The evaluation procedures used were: pure-tone audiometry; the auditory steady state response (ASSR) on sound field, with and without hearing aids; and genetic study of the hearing loss. RESULTS: Three genetic mutations were diagnosed: 35delG, A1555G and A827G, and the children with these mutations showed higher degree of SNHL. There was no difference between the genetic patterns regarding the degree of SNHL, except for patients with A827G mitochondrial mutation, because all subjects with this mutation had profound SNHL. The difference between the MRL obtained with and without amplification, considering the presence of mutation and the degree of SNHL, was higher in children with moderate SNHL without genetic alterations, both in behavioral and electrophysiological evaluations. CONCLUSION: Genetic mutations were found in 36.7% of the sample, justifying the importance of genetic tracking in the hearing habilitation process. Children with genetic mutations showed higher degrees of hearing loss. The different mutation patterns do not directly determine the degree of hearing loss. The best thresholds with amplification were found in children with moderate hearing loss without genetic alterations.