RESUMO
Chimerism monitoring following allogeneic hematopoietic cell transplantation (HCT) plays a pivotal role in evaluating engraftment status and identifying early indicators of relapse. Recent advancements in next-generation sequencing (NGS) technology have introduced AlloSeq HCT as a more sensitive alternative to short tandem repeat (STR) analysis. This study aimed to compare AlloSeq HCT with STR, focusing on the prediction of early relapse post-allogeneic HCT. Chimerism levels in 29 HCT recipients were assessed using both STR and NGS, employing a total of 125 whole blood or bone marrow aspirate samples (68 post-HCT and 57 pre-HCT samples from recipients or donors). AlloSeq HCT exhibited high concordance with STR and demonstrated the potential for early detection of chimeric changes, particularly at extremely low levels. The combined advantages of high sensitivity and automated data analysis offered by AlloSeq HCT substantiate its clinical adoption for effective chimerism monitoring.
Assuntos
Quimerismo , Transplante de Células-Tronco Hematopoéticas , Humanos , Quimeras de Transplante , Doença Crônica , Recidiva , Sequenciamento de Nucleotídeos em Larga EscalaRESUMO
Internal tandem duplication (ITD) of the FMS-like tyrosine kinase (FLT3) gene is associated with poor clinical outcomes in patients with acute myeloid leukemia. Although recent methods for detecting FLT3-ITD from next-generation sequencing (NGS) data have replaced traditional ITD detection approaches such as conventional PCR or fragment analysis, their use in the clinical field is still limited and requires further information. Here, we introduce ITDetect, an efficient FLT3-ITD detection approach that uses NGS data. Our proposed method allows for more precise detection and provides more detailed information than existing in silico methods. Further, it enables FLT3-ITD detection from exome sequencing or targeted panel sequencing data, thereby improving its clinical application. We validated the performance of ITDetect using NGS-based and experimental ITD detection methods and successfully demonstrated that ITDetect provides the highest concordance with the experimental methods. The program and data underlying this study are available in a public repository.
Assuntos
Leucemia Mieloide Aguda , Receptor 1 de Fatores de Crescimento do Endotélio Vascular , Humanos , Proteínas Tirosina Quinases/genética , Sequências de Repetição em Tandem/genética , Leucemia Mieloide Aguda/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Tirosina Quinase 3 Semelhante a fms/genética , Mutação , Duplicação GênicaRESUMO
BACKGROUND: Circulating tumor DNA (ctDNA) is a promising biomarker for early tumor detection and minimal residual disease (MRD) assessment in early-stage cancer, but quantifying minute amounts of ctDNA is challenging and well-designed studies on ctDNA in early-stage cancer are still lacking. Here, we adapted a sensitive next-generation sequencing (NGS) technology and performed parallel analysis of pre- and postoperative ctDNA and matched tumor tissues in a prospective cohort of patients with resectable pancreatic ductal adenocarcinoma (PDAC). METHODS: In total, 70 consecutive patients undergoing curative resection for resectable PDAC were enrolled. We performed integrated digital error suppression-enhanced cancer personalized profiling by deep sequencing NGS of triple-matched samples (pre/postoperative plasma cell-free DNA [cfDNA], tumor tissue, and genomic DNA) targeting 77 genes. RESULTS: Preoperative ctDNA was detected in 37.7% of the evaluable patients, with a median variant allele frequency of 0.09%. Twelve additional oncogenic mutations were detected exclusively in preoperative ctDNA but not in tissue. When quantitative concentrations of ctDNA were estimated in haploid genome equivalents per milliliter (hGE/mL), the risk of early recurrence was high in patients with postoperative ctDNA >1 hGE/mL. cfDNA variants from 24.5% of patients had features compatible with clonal hematopoiesis. CONCLUSIONS: An optimized NGS approach might add value beyond tissue analysis through the highly sensitive detection of minute amounts of ctDNA in resectable PDAC. Postoperative ctDNA concentration could be a tool for MRD assessment. Moreover, parallel analyses of matched tissues and leukocytes might be required to accurately detect clinically relevant ctDNA.
Assuntos
Adenocarcinoma , DNA Tumoral Circulante , Neoplasias Pancreáticas , Humanos , DNA Tumoral Circulante/genética , Estudos Prospectivos , Biomarcadores Tumorais , Mutação , Neoplasias Pancreáticas/genética , Neoplasias Pancreáticas/cirurgia , Neoplasias Pancreáticas/patologia , Sequenciamento de Nucleotídeos em Larga Escala , Neoplasia Residual , Neoplasias PancreáticasRESUMO
BACKGROUND/AIMS: Understanding leukemic stem cell (LSC) is important for acute myeloid leukemia (AML) treatment. However, association of LSC with patient prognosis and genetic information in AML patients is unclear. METHODS: Here we investigated the associations between genetic information and the various LSC phenotypes, namely multipotent progenitor (MPP)-like, lymphoid primed multipotent progenitor (LMPP)-like and granulocyte-macrophage progenitors (GMP)-like LSC in 52 AML patients. RESULTS: In secondary AML patients, MPP-like LSC was significantly higher than de novo AML (p = 0.0037). The proportion of MPP-like LSC was especially high in post-myeloproliferative neoplasm AML (p = 0.0485). There was no correlation between age and LSC phenotype. Mutations of KRAS and NRAS were observed in MPP-like LSC dominant patients, TP53 and ASXL1 mutations in LMPP-like LSC dominant patients, and CEBPA, DNMT3A and IDH1 mutations in GMP-like LSC dominant patients. Furthermore, KRAS mutation was significantly associated with MPP-like LSC expression (p = 0.0540), and TP53 mutation with LMPP-like LSC expression (p = 0.0276). When the patients were separated according to the combined risk including next generation sequencing data, the poorer the prognosis, the higher the LMPP-like LSC expression (p = 0.0052). This suggests that the dominant phenotype of LSC is one of the important factors in predicting the prognosis and treatment of AML. CONCLUSION: LSC phenotype in AML is closely associated with the recurrent mutations which has prognostic implication. Further research to confirm the meaning of LSC phenotype in the context of genetic aberration is warranted.
Assuntos
Leucemia Mieloide Aguda , Humanos , Leucemia Mieloide Aguda/diagnóstico , Leucemia Mieloide Aguda/genética , Mutação , Fenótipo , Prognóstico , Células-TroncoRESUMO
Despite the wide application of next-generation sequencing, Sanger sequencing still plays a necessary role in clinical laboratories. However, recent developments in the field of bioinformatics have focused mostly on next-generation sequencing, while tools for Sanger sequencing have shown little progress. In this study, SnackVar (https://github.com/Young-gonKim/SnackVar, last accessed June 22, 2020), a novel graphical user interface-based software for Sanger sequencing, was developed. All types of variants, including heterozygous insertion/deletion variants, can be identified by SnackVar with minimal user effort. The featured reference sequences of all of the genes are prestored in SnackVar, allowing for detected variants to be precisely described based on coding DNA references according to the nomenclature of the Human Genome Variation Society. Among 88 previously reported variants from four insertion/deletion-rich genes (BRCA1, APC, CALR, and CEBPA), the result of SnackVar agreed with reported results in 87 variants [98.9% (93.0%; 99.9%)]. The cause of one incorrect variant calling was proven to be erroneous base callings from poor-quality trace files. Compared with commercial software, SnackVar required less than one-half of the time taken for the analysis of a selected set of test cases. We expect SnackVar to be a cost-effective option for clinical laboratories performing Sanger sequencing.
Assuntos
Sequenciamento de Nucleotídeos em Larga Escala , Software , Sequência de Bases , Heterozigoto , Humanos , Limite de Detecção , Reprodutibilidade dos TestesRESUMO
Direct haplotyping enables noninvasive prenatal testing (NIPT) without analyzing proband, which is a promising strategy for pregnancies at risk of an inherited single-gene disorder. Here, we aimed to expand the scope of single-gene disorders that NIPT using linked-read direct haplotyping would be applicable to. Three families at risk of myotonic dystrophy type 1, lipoid congenital adrenal hyperplasia, and Fukuyama congenital muscular dystrophy were recruited. All cases exhibited distinct characteristics that are often encountered as hurdles (i.e., repeat expansion, identical variants in both parents, and novel variants with retrotransposon insertion) in the universal clinical application of NIPT. Direct haplotyping of parental genomes was performed by linked-read sequencing, combined with allele-specific PCR, if necessary. Target DMPK, STAR, and FKTN genes in the maternal plasma DNA were sequenced. Posterior risk calculations and an Anderson-Darling test were performed to deduce the maternal and paternal inheritance, respectively. In all cases, we could predict the inheritance of maternal mutant allele with > 99.9% confidence, while paternal mutant alleles were not predicted to be inherited. Our study indicates that direct haplotyping and posterior risk calculation can be applied with subtle modifications to NIPT for the detection of an expanded range of diseases.
Assuntos
Hiperplasia Suprarrenal Congênita/genética , Haplótipos , Distrofia Miotônica/genética , Teste Pré-Natal não Invasivo/métodos , Síndrome de Walker-Warburg/genética , Hiperplasia Suprarrenal Congênita/diagnóstico , Adulto , Feminino , Humanos , Masculino , Proteínas de Membrana/genética , Distrofia Miotônica/diagnóstico , Miotonina Proteína Quinase/genética , Teste Pré-Natal não Invasivo/normas , Fosfoproteínas/genética , Gravidez , Análise de Sequência de DNA/métodos , Síndrome de Walker-Warburg/diagnósticoRESUMO
BACKGROUND: Pheochromocytoma and paragangliomas (PPGL) are known as tumors with the highest level of heritability, approximately 30% of all cases. Clinical practice guidelines of PPGL recommend genetic testing for germline variants in all patients. In this study, we used whole exome sequencing to identify novel causative variants associated with PPGL to improve the detection of rare genetic variants in our cohort. METHODS: Thirty-six tested negative for pathogenic variants in previous Sanger sequencing or targeted gene panel testing for PPGL underwent whole exome sequencing. Whole exome sequencing was performed using DNA samples enriched using TruSeq Custom Enrichment Kit and sequenced with MiSeq (Illumina Inc.). Sequencing alignment and variant calling were performed using SAMtools. RESULTS: Among previously mutation undetected 36 patients, two likely pathogenic variants and 13 variants of uncertain significance (VUS) were detected in 32 pheochromocytoma-related genes. SDHA c.778G>A (p.Gly260Arg) was detected in a patient with head and neck paraganglioma, and KIF1B c.2787-2A>C in a patient with a bladder paraganglioma. Additionally, a likely pathogenic variant in BRCA2, VUS in TP53, and VUS in NFU1 were detected. CONCLUSION: Exome sequencing further identified genetic alterations by 5.6% in previously mutation undetected patients in PPGL. Implementation of targeted gene sequencing consisted of extended genes of PPGL in routine clinical screening can support the level of comprehensive patient assessment.
Assuntos
Neoplasias das Glândulas Suprarrenais/genética , Sequenciamento do Exoma/métodos , Mutação em Linhagem Germinativa/genética , Paraganglioma/genética , Feocromocitoma/genética , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Criança , Estudos de Coortes , Complexo II de Transporte de Elétrons/genética , Feminino , Predisposição Genética para Doença , Testes Genéticos/instrumentação , Neoplasias de Cabeça e Pescoço/genética , Humanos , Cinesinas/genética , Masculino , Pessoa de Meia-Idade , República da Coreia , Neoplasias da Bexiga Urinária/genética , Adulto JovemRESUMO
The accurate measurement of the Epstein-Barr virus (EBV) DNA level in the blood is required for managing EBV-associated diseases. A new commercial Abbott Real-Time EBV assay, which targets the BLLF1 gene, was evaluated on 120 clinical whole blood samples and the Qnostics EBV analytical panel. The limit of detection of the assay was 48.9â¯IU/mL (95% confidence interval, 48.1-49.8â¯IU/mL). The assay was linear from 2 to 5 log10 IU/mL (R2â¯=â¯0.997). The within-run coefficients of variation (CVs) ranged from 1.68% to 4.75% and the between-run CVs ranged from 1.73% to 12.83% for samples with high, medium, and low viral loads. EBV DNA loads measured by Abbott EBV assay strongly correlated with the results quantified by another commercial Nanogen EBV Real-Time Alert Q-PCR assay (râ¯=â¯0.879, Pâ¯<â¯0.0001). The fully automated Abbott Real-Time EBV assay targeting BLLF1 reduced both hands-on time and turnaround time and demonstrated a reliable performance for EBV DNA quantification in whole blood.
Assuntos
Automação Laboratorial/métodos , Sangue/virologia , Infecções por Vírus Epstein-Barr/virologia , Herpesvirus Humano 4/isolamento & purificação , Técnicas de Diagnóstico Molecular/métodos , Carga Viral/métodos , DNA Viral/sangue , Herpesvirus Humano 4/genética , Humanos , Reprodutibilidade dos Testes , Proteínas Virais/genéticaRESUMO
BACKGROUND: BRCA1 and BRCA2 (BRCA1/2) variants classified ambiguously as variants of uncertain significance (VUS) are a major challenge for clinical genetic testing in breast cancer; their relevance to the cancer risk is unclear and the association with the response to specific BRCA1/2-targeted agents is uncertain. To minimise the proportion of VUS in BRCA1/2, we performed the multifactorial likelihood analysis and validated this method using an independent cohort of patients with breast cancer. METHODS: We used a data set of 2115 patients with breast cancer from the nationwide multicentre prospective Korean Hereditary Breast Cancer study. In total, 83 BRCA1/2 VUSs (BRCA1, n=26; BRCA2, n=57) were analysed. The multifactorial probability was estimated by combining the prior probability with the overall likelihood ratio derived from co-occurrence of each VUS with pathogenic variants, personal and family history, and tumour characteristics. The classification was compared with the interpretation according to the American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG/AMP) guidelines. An external validation was conducted using independent data set of 810 patients. RESULTS: We were able to redefine 38 VUSs (BRCA1, n=10; BRCA2, n=28). The revised classification was highly correlated with the ACMG/AMP guideline-based interpretation (BRCA1, p for trend=0.015; BRCA2, p=0.001). Our approach reduced the proportion of VUS from 19% (154/810) to 8.9% (72/810) in the retrospective validation data set. CONCLUSION: The classification in this study would minimise the 'uncertainty' in clinical interpretation, and this validated multifactorial model can be used for the reliable annotation of BRCA1/2 VUSs.
Assuntos
Proteína BRCA1/genética , Proteína BRCA2/genética , Estudos de Associação Genética , Predisposição Genética para Doença , Variação Genética , Neoplasias da Mama/diagnóstico , Neoplasias da Mama/epidemiologia , Neoplasias da Mama/genética , Feminino , Estudos de Associação Genética/métodos , Testes Genéticos , Humanos , Análise Multivariada , Neoplasias Ovarianas/diagnóstico , Neoplasias Ovarianas/genética , Probabilidade , Prognóstico , Estudos Prospectivos , Reprodutibilidade dos Testes , República da Coreia/epidemiologiaRESUMO
BACKGROUND: Quantifying the BCR-ABL1 rearrangement is important for monitoring chronic myelogenous leukemia (CML). To standardize BCR-ABL1 quantification, the World Health Organization (WHO) established the first international genetic reference panel. Here, we compared the BCR-ABL1 levels determined using international scale (IS)-based commercially available assays. METHODS: BCR-ABL1 transcripts were quantified using two IS-based assays. 10-1, 10-2, 10-3, 10-4, 10-5 and 10-6 dilutions of the b3a2 positive RNA were used for evaluating linearity, precision, and limit of detection. Correlation of the assay was evaluated by using DNA obtained from CML patients carrying the BCR-ABL1 b3a2 and b2a2 types. RESULTS: Both Ipsogen and Asuragen assays showed fine linearity with reasonable %CV. LOD of each assay was calculated as 0.003% for Ipsogen, and 0.005% for Asuragen. By comparing the results that were lower than 10% by either one of the assay, Ipsogen and Asuragen results showed an overall good linear correlation with a tendency for the Ipsogen assay to show slightly higher levels than the Asuragen assay for b3a2 transcript. For b2a2, the tendency was opposite, with Asuragen showing higher values than the Ipsogen. CONCLUSIONS: Two commercially available IS-based BCR-ABL1 assays showed an overall good quantitative correlation. It should be taken into consideration that each assay tended to produce higher values than the other, depending on the BCR-ABL1 subtypes, suggesting that a separate conversion factor for each subtype can be more helpful when BCR-ABL1 transcript levels are converted into IS.
Assuntos
Bioensaio/normas , Proteínas de Fusão bcr-abl/genética , Testes Genéticos/métodos , Leucemia Mielogênica Crônica BCR-ABL Positiva/diagnóstico , Padrões de Referência , Bioensaio/métodos , Humanos , Leucemia Mielogênica Crônica BCR-ABL Positiva/genética , RNA Mensageiro/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Índice de Gravidade de DoençaRESUMO
Hereditary spastic paraplegia (HSP) is a genetically heterogeneous group of diseases characterized by insidiously progressive lower-extremity weakness and spasticity. Spastic paraplegia 4 (SPAST) is the most common type of uncomplicated autosomal dominant HSP (40% of such cases), and spastic paraplegia 3A (ATL1) is the second most common. Here, we conducted mutational analysis of the SPAST and/or ATL1 genes in 206 unrelated patients with HSP. DNA sequencing and multiplex ligation-dependent probe amplification was used to analyze SPAST or ATL1 pathogenic variants. To confirm splice-site pathogenic variants, mRNA transcripts were analyzed by reverse transcription-polymerase chain reactions and sequencing. Among the 52 patients with medical records and SPAST or ATL1 gene pathogenic variants or novel unclassified variants, 50 showed spasticity or weakness in their lower extremities. We identified 16 known and 18 novel SPAST pathogenic variants and 2 known and a novel splicing pathogenic variants in ATL1. We also identified 4 unclassified SPAST variants in 5 patients and an unclassified ATL1 variant in 1 patient. Further, a novel leaky-splicing variant (c.1537-11A>G) was found in SPAST, which caused skipping of exon 13 or exons 13-14. Among the 206 unrelated patients with HSP, SPAST or ATL1 pathogenic variants and potentially pathogenic variants were identified in 52 patients, a low pathogenic variant rate compared to previous results. Results from our study suggest that other genes may be involved in HSP in the Korean population.
Assuntos
Adenosina Trifosfatases/genética , Povo Asiático/genética , Proteínas de Ligação ao GTP/genética , Proteínas de Membrana/genética , Mutação/genética , Paraplegia Espástica Hereditária/diagnóstico , Paraplegia Espástica Hereditária/genética , Adolescente , Adulto , Criança , Pré-Escolar , Análise Mutacional de DNA/métodos , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , República da Coreia/epidemiologia , Paraplegia Espástica Hereditária/epidemiologia , Espastina , Adulto JovemRESUMO
Schmid-type metaphyseal chondrodysplasia (MCDS) is characterized by short stature with short legs, bowing of the long bones, coxa vara, and waddling gait. MCDS is a relatively common form of MCD. Most mutations that cause MCDS occur within the carboxyl-terminal non-collagenous domain (NC1) of the COL10A1 gene. We performed mutational analysis of the COL10A1 genes in 4 unrelated Korean patients with diagnosed MCDS. Mutational analysis of COL10A1 identified c.1904_1915delinsT (p.Gln635LeufsX10) and c.1969dupG (p.Ala657GlyfsX10), 2 novel frameshift mutations, and c.2030T>A (p.Val677Glu) and c.862G>C (p.Gly288Arg) at unusual mutational sites, which could be pathogenic. We present the first report of the molecular characteristics of MCDS in 4 Korean patients. Our findings suggest that a novel sequence variation involving an unusual mutational site of the COL10A1 gene can cause mild MCDS.
Assuntos
Colágeno Tipo XI/genética , Variação Genética , Transtornos do Crescimento/genética , Osteocondrodisplasias/diagnóstico , Osteocondrodisplasias/genética , Sequência de Aminoácidos , Povo Asiático/genética , Criança , Pré-Escolar , Análise Mutacional de DNA , Feminino , Mutação da Fase de Leitura , Humanos , Masculino , Dados de Sequência Molecular , Mutação de Sentido IncorretoRESUMO
Leber congenital amaurosis (LCA) is a genetically heterogeneous disorder and the most severe form of inherited retinal dystrophy. We report results of a diagnostic application of an extensive gene panel composed of 204 retinal dystrophy-related genes and discuss its feasibility as a diagnostic tool. Nineteen unrelated LCA patients were included in the study: two patients for validation purposes of our gene panel, 15 previously analyzed patients with no identified mutations, and two previously unanalyzed patients. Genetic diagnosis for each patient was conducted according to whether the variants were consistent with the known inheritance pattern of each gene. We identified two heterozygous or homozygous pathogenic variants in seven of 19 patients. On the basis of mutation information, clinical features were re-reviewed, and clinical diagnoses for two patients were revised from LCA to LCA-related disorders. In addition, a coverage simulation was performed to determine the optimal depth of coverage of the gene panel. Using our gene panel, we diagnosed LCA and LCA-related disorders in 36.8% of patients and one or more deleterious variants or variants of unknown significance in 89.5% of patients. Molecular diagnosis using this extensive gene panel is expected to facilitate diagnosis of retinal dystrophy and help provide proper treatment to patients, although further analyses is needed for a complete clinical validation.
Assuntos
Proteínas do Olho/genética , Heterogeneidade Genética , Amaurose Congênita de Leber/genética , Mutação , Expressão Gênica , Perfilação da Expressão Gênica , Genótipo , Heterozigoto , Homozigoto , Humanos , Amaurose Congênita de Leber/diagnóstico , Amaurose Congênita de Leber/patologia , Retina/metabolismo , Retina/patologia , Análise de Sequência de DNA/estatística & dados numéricosRESUMO
BACKGROUND: Large genomic rearrangements (LGRs) in the BRCA1/2 genes are frequently observed in breast cancer patients who are negative for BRCA1/2 small mutations. Here, we examined 221 familial breast cancer patients from 37 hospitals to estimate the contribution of LGRs, in a nationwide context, to the development of breast cancer. METHODS: Direct sequencing or mutation scanning followed by direct sequencing was performed to screen small mutations. BRCA1/2 small mutation-negative patients were screened for the presence of LGRs using a multiple ligation-dependent probe amplification (MLPA) assay. RESULTS: Using a combined strategy to detect the presence of small mutations and LGRs, we identified BRCA1/2 small mutations in 78 (35.3%) out of 221 familial breast cancer patients and BRCA1 LGRs in 3 (2.1%) out of 143 BRCA1/2 small mutation-negative patients: the deletion of exons 11-13, the deletion of exons 13-15, and whole gene deletion of exons 1-24. The novel deletion of exons 11-13 is thought to result from a non-homologous recombination event mediated by a microhomology sequence comprised of 3 or 4 base pairs: c.3416_4357 + 1863delins187 (NG_005905.2: g.33369_44944delins187). CONCLUSIONS: In this study, we showed that LGRs were found in 3.7% (3/81) of the patients who had mutations in BRCA1 or BRCA2, and 7.5% (3/40) of patients with mutations in BRCA1. This suggests that the contribution of LGRs to familial breast cancer in this population might be comparable to that in other ethnic populations. Given these findings, an MLPA to screen for mutations in the BRCA1 gene is recommended as an initial screening test in highly selective settings.
Assuntos
Proteína BRCA1/genética , Proteína BRCA2/genética , Neoplasias Ovarianas/genética , Adulto , Povo Asiático/genética , Neoplasias da Mama/sangue , Neoplasias da Mama/genética , Análise Mutacional de DNA , Éxons , Feminino , Deleção de Genes , Humanos , Mutação , Neoplasias Ovarianas/sangue , Análise de Sequência de DNARESUMO
Triple-negative breast cancer (TNBC) accounts for 12-24 % of all breast cancers. Here, we studied 221 familial breast and/or ovarian cancer patients from 37 hospitals using a comprehensive approach to identify large genomic rearrangements (LGRs) as well as sequence variants, and investigated the association between BRCA1/2 mutational status and TNBC. We performed direct sequencing or mutation scanning followed by direct sequencing. Then, 143 BRCA1/2 mutation-negative patients were screened for LGRs. In this study, the prevalence of BRCA1/2 mutations was high (36.9 %). The prevalence of BRCA1 mutations was similar to that of BRCA2 mutations: 49.4 versus 50.6 %, respectively. TNBC was diagnosed in 35.2 % of BRCA1/2 mutation carriers and 57.1 % of BRCA1 mutation carriers. Conversely, two-thirds of TNBC patients carried BRCA1/2 mutation(s), and about half were BRCA1 mutation carriers. When stratified by the mutated gene, TNBC prevalence in BRCA1 mutation carriers was significantly lower when there was a family history of ovarian cancer. Our multinomial logistic regression model demonstrated that no single factor was sufficient, and at least two factors, such as a patient with family history of both breast cancer and ovarian cancer or a patient diagnosed at a relatively young age (<40 years) with a TNBC phenotype, are necessary to indicate BRCA1/2 genetic testing in this population. Our results suggest that TNBC is a strong predictor for the presence of a BRCA1 mutation in this population, but additional risk factors should also be evaluated to ascertain a 10 % or higher prior probability of BRCA1/2 mutation testing.
Assuntos
Genes BRCA1 , Genes BRCA2 , Mutação , Neoplasias de Mama Triplo Negativas/genética , Adulto , Idade de Início , Neoplasias da Mama/epidemiologia , Neoplasias da Mama/genética , Neoplasias da Mama/patologia , Feminino , Humanos , Pessoa de Meia-Idade , Estadiamento de Neoplasias , Neoplasias Ovarianas/genética , Prevalência , Prognóstico , República da Coreia/epidemiologia , Fatores de Risco , Neoplasias de Mama Triplo Negativas/epidemiologia , Neoplasias de Mama Triplo Negativas/patologia , Adulto JovemRESUMO
Hypochondroplasia (HCH) is an autosomal dominant inherited skeletal dysplasia, usually caused by a heterozygous mutation in the fibroblast growth factor receptor 3 gene (FGFR3). A 27-year-old HCH woman with a history of two consecutive abortions of HCH-affected fetuses visited our clinic for preimplantation genetic diagnosis (PGD). We confirmed the mutation in the proband (FGFR3:c.1620C>A, p.N540K), and established a nested allele-specific PCR and sequence analysis for PGD using single lymphocyte cells. We performed this molecular genetic analysis to detect the presence of mutation among 20 blastomeres from 18 different embryos, and selected 9 embryos with the wild-type sequence (FGFR3:c.1620C). A successful pregnancy was achieved through a frozen-thawed cycle and resulted in the full-term birth of a normal neonate. To the best of our knowledge, this is the first report of a successful pregnancy and birth using single-cell allele-specific PCR and sequencing for PGD in an HCH patient.
RESUMO
Multiple epiphyseal dysplasia (MED) is a genetically heterogeneous group of diseases characterized by variable degrees of epiphyseal abnormality primarily involving the hip and knee joints. The purpose of this study was to investigate the frequency of mutations in individuals with a clinical and radiographic diagnosis of MED and to test the hypothesis that characteristic radiological findings may be helpful in predicting the gene responsible. The radiographs of 74 Korean patients were evaluated by a panel of skeletal dysplasia experts. Six genes known to be associated with MED (COMP, MATN3, COL9A1, COL9A2, COL9A3, and DTDST) were screened by sequencing. Mutations were found in 55 of the 63 patients (87%). MATN3 mutations were found in 30 patients (55%), followed by COMP mutations in 23 (41%), and COL9A2 and DTDST mutations in one patient (2%) each. Comparisons of radiographic findings in patients with COMP and MATN3 mutations showed that albeit marked abnormalities in hip and knee joints were observed in both groups, the degree of involvement and the morphology of dysplastic epiphyses differed markedly. The contour of the pelvic acetabulum, the presence of metaphyseal vertical striations, and/or the brachydactyly of the hand were also found to be highly correlated with the genotypes. The study confirms that MATN3 and COMP are the genes most frequently responsible for MED and that subtle radiographic signs may give precious indications on which gene(s) should be prioritized for mutational screening in a given individual.
Assuntos
Proteínas da Matriz Extracelular/genética , Glicoproteínas/genética , Osteocondrodisplasias/genética , Adolescente , Adulto , Proteínas de Transporte de Ânions/genética , Povo Asiático/etnologia , Povo Asiático/genética , Proteína de Matriz Oligomérica de Cartilagem , Criança , Pré-Escolar , Estudos de Coortes , Colágeno Tipo IX/genética , Feminino , Estudos de Associação Genética , Heterogeneidade Genética , Testes Genéticos , Genoma Humano , Humanos , Deformidades Congênitas dos Membros/diagnóstico por imagem , Deformidades Congênitas dos Membros/genética , Deformidades Congênitas dos Membros/patologia , Masculino , Proteínas Matrilinas , Mutação de Sentido Incorreto , Osteocondrodisplasias/diagnóstico por imagem , Osteocondrodisplasias/etnologia , Osteocondrodisplasias/patologia , Radiografia , Deleção de Sequência , Índice de Gravidade de Doença , Transportadores de Sulfato , Adulto JovemRESUMO
Multiple epiphyseal dysplasia is caused by heterogeneous genotypes involving more than six genes. Recessive mutations in the DTDST gene cause a phenotype of recessive multiple epiphyseal dysplasia (rMED). The authors report a 9-yr old Korean girl with the rMED phenotype having novel compound heterozygous mutations in the DTDST gene, which were inherited from both parents. This is the first Korean rMED case attributed to DTDST mutations, and expands the spectrum of diseases caused by DTDST mutations.
Assuntos
Proteínas de Transporte de Ânions/genética , Genes Recessivos , Heterozigoto , Mutação , Osteocondrodisplasias/genética , Animais , Povo Asiático/genética , Criança , Análise Mutacional de DNA , Feminino , Genótipo , Humanos , Coreia (Geográfico) , Fenótipo , Transportadores de SulfatoRESUMO
BACKGROUND: Neurofibromatosis type 2 (NF2) is an autosomal dominant syndrome caused by the NF2 tumor suppressor gene. However, the NF2 mutation characteristics in Korean patients are not sufficiently understood. In this study, we conducted a comprehensive mutational analysis in 7 Korean NF2 patients by performing direct sequencing and gene-dosage assessment. METHODS: We analyzed all exons and flanking regions of NF2 by direct sequencing and screened the deletions or duplications involving NF2 by multiplex ligation-dependent probe amplification. RESULTS: Four novel NF2 mutations, including 2 splice-site mutations (c.364-1G>A and c.886-3C>G), 1 frameshift mutation (c.524delA), and 1 missense mutation (c.397T>C; p.Cys133Arg), were identified in our patients. No large deletion or duplication was identified in our series. Subsequently, we identified an abnormal splicing product by using reverse transcription-PCR and direct sequencing in 2 patients with a novel splice-site mutation. The missense mutation c.397T>C was predicted to have harmful effects on protein function. CONCLUSIONS: The detection rate of NF2 mutations in Korean patients (57%) is similar to those in other populations. Our results provided a greater insight into the mutational spectrum of the NF2 gene in Korean subjects.