RESUMO
EGFR mutations are a major prognostic factor in lung adenocarcinoma. However, current detection methods require sufficient samples and are costly. Deep learning is promising for mutation prediction in histopathological image analysis but has limitations in that it does not sufficiently reflect tumor heterogeneity and lacks interpretability. In this study, we developed a deep learning model to predict the presence of EGFR mutations by analyzing histopathological patterns in whole slide images (WSIs). We also introduced the EGFR mutation prevalence (EMP) score, which quantifies EGFR prevalence in WSIs based on patch-level predictions, and evaluated its interpretability and utility. Our model estimates the probability of EGFR prevalence in each patch by partitioning the WSI based on multiple-instance learning and predicts the presence of EGFR mutations at the slide level. We utilized a patch-masking scheduler training strategy to enable the model to learn various histopathological patterns of EGFR. This study included 868 WSI samples from lung adenocarcinoma patients collected from three medical institutions: Hallym University Medical Center, Inha University Hospital, and Chungnam National University Hospital. For the test dataset, 197 WSIs were collected from Ajou University Medical Center to evaluate the presence of EGFR mutations. Our model demonstrated prediction performance with an area under the receiver operating characteristic curve of 0.7680 (0.7607-0.7720) and an area under the precision-recall curve of 0.8391 (0.8326-0.8430). The EMP score showed Spearman correlation coefficients of 0.4705 (p = 0.0087) for p.L858R and 0.5918 (p = 0.0037) for exon 19 deletions in 64 samples subjected to next-generation sequencing analysis. Additionally, high EMP scores were associated with papillary and acinar patterns (p = 0.0038 and p = 0.0255, respectively), whereas low EMP scores were associated with solid patterns (p = 0.0001). These results validate the reliability of our model and suggest that it can provide crucial information for rapid screening and treatment plans.
Assuntos
Adenocarcinoma de Pulmão , Aprendizado Profundo , Receptores ErbB , Neoplasias Pulmonares , Mutação , Humanos , Receptores ErbB/genética , Adenocarcinoma de Pulmão/genética , Adenocarcinoma de Pulmão/patologia , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/patologia , Análise Mutacional de DNA , Feminino , Interpretação de Imagem Assistida por ComputadorRESUMO
BACKGROUND: Primary electrical disorders (PEDs) are a group of cardiac rhythm abnormalities that occur in the absence of detectable structural heart disease and are a significant cause of sudden cardiac death (SCD). The initiation of cardiac muscle contraction and relaxation is orchestrated by the action potential (AP), generated through ionic changes across the membrane. Mutations in the AP-related gene CACNA2D1 have been identified as a causative factor for PED. METHODS: We recruited a Chinese family with a history of arrhythmia. The proband has experienced palpitations and chest tightness for over 40 years, with symptoms worsening over the past year. Whole exome sequencing (WES) was used to determine the genetic etiologies in this family. RESULTS: A novel heterozygous missense mutation (NM_000722.3: c.1685G > C;p.G562A) of CACNA2D1 gene was detected. Genotyping of the proband's parents indicated that the arrhythmia phenotype in the proband was caused by a de novo mutation. CONCLUSIONS: WES was utilized to explore the genetic etiology in a family with arrhythmia, leading to the identification of a novel mutation in the CACNA2D1 gene. This study not only expands the mutation spectrum of the CACNA2D1 gene but also contributes to genetic counseling and clinical diagnosis for this family.
Assuntos
Arritmias Cardíacas , Sequenciamento do Exoma , Predisposição Genética para Doença , Heterozigoto , Mutação de Sentido Incorreto , Linhagem , Fenótipo , Humanos , Masculino , Arritmias Cardíacas/genética , Arritmias Cardíacas/diagnóstico , Arritmias Cardíacas/fisiopatologia , Feminino , China , Análise Mutacional de DNA , Adulto , Povo Asiático/genética , Canais de Cálcio/genética , Pessoa de Meia-Idade , Hereditariedade , Frequência Cardíaca/genética , Potenciais de Ação , População do Leste AsiáticoRESUMO
Microsatellite instability (MSI) occurs across a number of cancers and is associated with different clinical characteristics when compared to microsatellite stable (MSS) cancers. As MSI cancers have different characteristics, routine MSI testing is now recommended for a number of cancer types including colorectal cancer (CRC). Using gene panels for sequencing of known cancer mutations is routinely performed to guide treatment decisions. By adding a number of MSI regions to a small gene panel, the efficacy of simultaneous MSI detection in a series of CRCs was tested. Tumour DNA from formalin-fixed, paraffin-embedded (FFPE) tumours was sequenced using a 23-gene panel kit (ATOM-Seq) provided by GeneFirst. The mismatch repair (MMR) status was obtained for each patient from their routine pathology reports, and compared to MSI predictions from the sequencing data. By testing 29 microsatellite regions in 335 samples the MSI status was correctly classified in 314/319 samples (98.4% concordance), with sixteen failures. By reducing the number of regions in silico, comparable performance could be reached with as few as eight MSI marker positions. This test represents a quick, and accurate means of determining MSI status in FFPE CRC samples, as part of a routine gene mutation assay, and can easily be incorporated into a research or diagnostic setting. This could replace separate mutation and MSI tests with no loss of accuracy, thus improving testing efficiency.
Assuntos
Neoplasias Colorretais , Formaldeído , Instabilidade de Microssatélites , Mutação , Fixação de Tecidos , Humanos , Neoplasias Colorretais/genética , Neoplasias Colorretais/diagnóstico , Formaldeído/química , Inclusão em Parafina , Feminino , Masculino , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Reparo de Erro de Pareamento de DNA/genética , Análise Mutacional de DNA/métodos , Idoso , Pessoa de Meia-IdadeRESUMO
BACKGROUND: Gastric cancer (GC), a molecularly heterogeneous disease, is the third leading cause of cancer death worldwide. The majority of GC cases worldwide occur in East Asia, predominantly China. Mutational Signature Framework offers an elegant approach to identify mutational processes present in tumors. METHODS: To identify mutational signature patterns, we conducted whole exome sequencing (WES) analysis in Chinese patients with GC. Mutect2 and MutsigCV were used to identify significantly mutated genes in 175 Chinese GC cases using paired tumor-normal tissues. We investigated mutational signatures using Catalogue of Somatic Mutations in Cancer (COSMIC) Version 2 (V2) and Version 3 (V3). RESULTS: We identified 104 mutated genes with P < 0.01. Seven genes (OR6B1, B2M, ELF3, RHOA, RPL22, TP53, ARIDIA) had q < 0.0001, including six previously associated with GC. Mutational signatures (COSMIC-V3) observed include 14 single base substitutions (SBS), one doublet base substitution (DBS) Signature A, and one InDel (ID2). The most frequent SBS signatures (SBS05, SBS01, SBS15, SBS20, SBS40) were also observed in 254 White GC cases from The Cancer Genome Atlas (TCGA) Project. However, SBS01 and SBS20 showed significant differences between Whites vs. All Asians (19.3% vs. 11.3% for SBS 1 (P = 0.012) and 11.4% vs. 5.9% for SBS20 (P = 0.025), respectively). Using COSMIC V2, signatures 6, 15, and 1 were the most frequent in Chinese GC cases. Further, most Chinese GC cases carried multiple signatures. CONCLUSIONS: This effort represents the most detailed mutational signatures analysis of GC cases from China to date. Results hold promise for new insights in understanding risk and prognosis factors in GC.
Assuntos
Povo Asiático , Sequenciamento do Exoma , Mutação , Neoplasias Gástricas , Humanos , Neoplasias Gástricas/genética , Masculino , Feminino , Pessoa de Meia-Idade , Idoso , Povo Asiático/genética , China/epidemiologia , Adulto , Biomarcadores Tumorais/genética , Idoso de 80 Anos ou mais , Análise Mutacional de DNA , População do Leste AsiáticoRESUMO
MET is a receptor tyrosine kinase (RTK) responsible for initiating signaling pathways involved in development and wound repair. MET activation relies on ligand binding to the extracellular receptor, which prompts dimerization, intracellular phosphorylation, and recruitment of associated signaling proteins. Mutations, which are predominantly observed clinically in the intracellular juxtamembrane and kinase domains, can disrupt typical MET regulatory mechanisms. Understanding how juxtamembrane variants, such as exon 14 skipping (METΔEx14), and rare kinase domain mutations can increase signaling, often leading to cancer, remains a challenge. Here, we perform a parallel deep mutational scan (DMS) of the MET intracellular kinase domain in two fusion protein backgrounds: wild-type and METΔEx14. Our comparative approach has revealed a critical hydrophobic interaction between a juxtamembrane segment and the kinase âºC-helix, pointing to potential differences in regulatory mechanisms between MET and other RTKs. Additionally, we have uncovered a ß5 motif that acts as a structural pivot for the kinase domain in MET and other TAM family of kinases. We also describe a number of previously unknown activating mutations, aiding the effort to annotate driver, passenger, and drug resistance mutations in the MET kinase domain.
Assuntos
Proteínas Proto-Oncogênicas c-met , Proteínas Proto-Oncogênicas c-met/genética , Proteínas Proto-Oncogênicas c-met/metabolismo , Humanos , Domínios Proteicos/genética , Mutação , Motivos de Aminoácidos , Análise Mutacional de DNARESUMO
Background: Early and minimally invasive detection of epidermal growth factor receptor (EGFR) mutations in non-small cell lung cancer (NSCLC) patients is a promising tool to select patients for targeted therapy in order to improve their prognosis. This study aimed to identify a sensitive, cost-effective, and easily accessible noninvasive method for detecting the EGFR-targetable mutations in the plasma exosomal DNA (exoDNA)+ of patients with NSCLC. Methods: This retrospective observational study was conducted over 10 months, from December 2022 to October 2023, at Masih Daneshvari Hospital in Tehran, Iran. A total of 30 patients with stage II-IV NSCLC and targetable mutation in the EGFR gene were included in the study. Nested PCR and Sanger sequencing were used to evaluate EGFR mutations in the DNA extracted from circulating exosomes. Results: The study found a sensitivity of 76.6% for EGFR mutation detection on exoDNA compared to tissue results. No significant impact was observed based on tumor staging, histology, mutation type, smoking status, gender, or age. Conclusion: Therapeutically targetable driver mutations in the EGFR gene can be accurately detected using nested PCR followed by direct sequencing of plasma exoDNA from patients with NSCLC. This approach facilitates timely and more personalized treatment for NSCLC patients, ultimately improving patient prognosis. Additionally, this method reduces the reliance on invasive tissue biopsies and their associated complications.
Assuntos
Carcinoma Pulmonar de Células não Pequenas , Receptores ErbB , Exossomos , Neoplasias Pulmonares , Mutação , Reação em Cadeia da Polimerase , Humanos , Receptores ErbB/genética , Feminino , Masculino , Exossomos/genética , Reação em Cadeia da Polimerase/métodos , Pessoa de Meia-Idade , Mutação/genética , Carcinoma Pulmonar de Células não Pequenas/genética , Carcinoma Pulmonar de Células não Pequenas/sangue , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/sangue , Neoplasias Pulmonares/patologia , Neoplasias Pulmonares/diagnóstico , Idoso , Estudos Retrospectivos , Adulto , Análise Mutacional de DNA/métodos , Sensibilidade e EspecificidadeRESUMO
In today's globalized society, ophthalmologists can examine people of different ethnicities regardless of where they live. The frequency of disease-causing genes varies according to a patient's ethnic background. We explain genetic findings for Japanese patients with inherited eye diseases. Ocular genetics has made great advances over the past 30 years. For example, detecting mutations at nucleotide position 11778 in mitochondrial DNA was useful in the genetic diagnosis of Leber's hereditary optic neuropathy (LHON). I evaluated the genotype-phenotype relationship in cases of corneal dystrophy and inherited retinal dystrophy (IRD). I identified the entire exon sequence of the eyes shut homolog (EYS) gene in patients with autosomal recessive retinitis pigmentosa (RP). EYS gene mutations are the most frequent cause of autosomal recessive RP. RPGRIP1 may be a common causative gene with early-onset severe retinal dystrophy, including Leber congenital amaurosis. However, some genes have complex structures that are difficult to analyze, including the OPN1LW/OPN1MW gene cluster in blue cone monochromacy and the IKBKG/NEMO genes in incontinentia pigmenti. This review will also present two cases with uniparental disomy, a case of IRD with double mutations, and a case with RP complicated with LHON-like neuropathy. Precise understanding of the effects of genetic variants may reveal differences in the clinical characteristics of patients with the same variant. When starting genome medicine, accurately diagnosing the patient, making accurate prediction, determining the genetic pattern, and providing genetic counseling are important. Above all, that both the doctors and patients understand genetic diseases correctly is important.
Assuntos
Proteínas do Olho , Mutação , Humanos , Análise Mutacional de DNA , DNA Mitocondrial/genética , População do Leste Asiático , Proteínas do Olho/genética , Japão/epidemiologiaRESUMO
BACKGROUND: Congenital heart disease (CHD) is a lifelong abnormality present from birth. Multiple studies have shown that mutations in genes involved in heart development could cause congenital heart disease. The CITED2 gene works as a transcription factor in the hypoxic pathway for the development of the heart. Therefore, five CHD types, ventricular septal defect, atrial septal defect, atrioventricular septal defect, tetralogy of fallot, and patent ductus arteriosus, were evaluated by conducting a targeted single nucleotide polymorphism (SNP) analysis of the CITED2 gene variant rs375393125 (T > C). This study aimed to identify the association of CITED2 gene mutations in CHD patients. METHODS: Three hundred fifty samples, 250 from patients and 100 from controls, were collected for this genetic analysis. Allele-specific PCR and gel electrophoresis were used to identify the target missense mutations. The genotypic results of the CHDs were further validated through Sanger sequencing. RESULTS: The frequency of the homozygous mutant (CC) in CHD patients was 48.4%, and of the heterozygous mutant (TC) genotype was 11.4%; these percentages are higher than controls (1%). The control samples had only one heterozygous TC and no homozygous CC genotype. The chi-square value was obtained at 103.9 with a probability of 0.05, more significant than the significance value of 21.03. The odds ratio was 43.7, which is > 1. The calculated value of ANOVA was 11.6, which was more significant than the F critical value of 3.7. As a result of sequencing, the mutant sample of each selected CHD type was found heterozygous or homozygous, and the results were like those obtained through conventional PCR. CONCLUSION: The samples of CHD patients showed mutations. Therefore, the CITED2 gene SNP might be associated with CHD.
Assuntos
Predisposição Genética para Doença , Cardiopatias Congênitas , Mutação de Sentido Incorreto , Fenótipo , Polimorfismo de Nucleotídeo Único , Proteínas Repressoras , Transativadores , Humanos , Cardiopatias Congênitas/genética , Cardiopatias Congênitas/diagnóstico , Feminino , Estudos de Casos e Controles , Proteínas Repressoras/genética , Masculino , Transativadores/genética , Frequência do Gene , Homozigoto , Lactente , Heterozigoto , Análise Mutacional de DNA , Pré-Escolar , Fatores de Risco , Estudos de Associação Genética , Criança , China/epidemiologia , AdolescenteAssuntos
Ectodisplasinas , Humanos , Ectodisplasinas/genética , Masculino , Mutação , Displasia Ectodérmica Anidrótica Tipo 1/genética , Displasia Ectodérmica Anidrótica Tipo 1/diagnóstico , Pré-Escolar , Lactente , Criança , Displasia Ectodérmica/genética , Displasia Ectodérmica/diagnóstico , Hemizigoto , Análise Mutacional de DNA , Testes Genéticos/métodosRESUMO
PURPOSE: To ascertain the characteristics of achromatopsia (ACHM) in Japan by analyzing the genetic and phenotypic features of patients with ACHM. METHODS: The medical records of 52 patients from 47 Japanese families who were clinically diagnosed with ACHM were reviewed in this retrospective observational study. RESULTS: Thirty-six causative variants of ACHM were identified in 26 families via whole-exome sequencing: PDE6C (12 families), CNGA3 (10 families), CNGB3 (two families), and GNAT2 (two families). However, none of the 6 causative variants that are known to cause ACHM, or the 275 other genes listed in RetNet, were observed in 19 families. A significant trend toward older age and worsening of ellipsoid zone disruption on optical coherence tomography images was observed (P < 0.01). Progressive ellipsoid zone disruptions were observed in 13 eyes of seven patients during the follow-up visits. These patients harbored one or more variants in PDE6C. CONCLUSION: The ACHM phenotype observed in this study was similar to those observed in previous reports; however, the causative gene variants differed from those in Europe. The low identification ratio of causative genes in whole-exome sequencing suggests the presence of unique hotspots in Japanese patients with ACHM that were not detectable via ordinal whole-exome sequencing.
Assuntos
Defeitos da Visão Cromática , Sequenciamento do Exoma , Tomografia de Coerência Óptica , Humanos , Defeitos da Visão Cromática/genética , Defeitos da Visão Cromática/diagnóstico , Masculino , Feminino , Estudos Retrospectivos , Japão/epidemiologia , Adulto , Pessoa de Meia-Idade , Criança , Adolescente , Adulto Jovem , Mutação , Linhagem , Acuidade Visual , Nucleotídeo Cíclico Fosfodiesterase do Tipo 6/genética , Fenótipo , Pré-Escolar , Proteínas do Olho/genética , Idoso , Eletrorretinografia , Canais de Cátion Regulados por Nucleotídeos Cíclicos/genética , Análise Mutacional de DNARESUMO
When monitoring minimal residual disease (MRD) after tumor treatment, there are higher requirements of the lower limit of detection than when detecting for drug resistance mutations and circulating tumor cell mutations during therapy. Traditional Sanger sequencing has 5%-20% wild-type mutation detection, so its limit of detection cannot meet the corresponding requirements. The wild-type blocking technologies that have been reported to overcome this include blocker displacement amplification (BDA), non-extendable locked nucleic acid (LNA), hot-spot-specific probes (HSSP), etc. These technologies use specific oligonucleotide sequences to block wild-type or recognize wild-type and then combine this with other methods to prevent wild-type amplification and amplify mutant amplification, leading to characteristics like high sensitivity, flexibility, and convenience. This protocol uses BDA, a wild-type blocking PCR combined with Sanger sequencing, to optimize the detection of RHOA G17V low-frequency somatic mutations, and the detection sensitivity can reach 0.5%, which can provide a basis for MRD monitoring of angioimmunoblastic T-cell lymphoma.
Assuntos
Mutação , Reação em Cadeia da Polimerase , Humanos , Reação em Cadeia da Polimerase/métodos , Neoplasia Residual/genética , Análise de Sequência de DNA/métodos , Análise Mutacional de DNA/métodosRESUMO
PURPOSE: The management of indeterminate thyroid nodules remains a topic of ongoing debate, particularly regarding the differentiation of malignancy. Somatic mutation analysis offers crucial insights into tumor characteristics. This study aimed to assist the clinical management of indeterminate nodules with somatic mutation analysis. METHODS: Aspiration samples from 20 indeterminate thyroid nodules were included in the study. A next-generation sequencing panel containing 67 genes was used for molecular profiling. The results were compared with pathology data from surgical material, which is considered the gold standard. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated. RESULTS: Variants in six genes (NRAS, BRAF, TP53, TERT, PTEN, PIK3CA) were detected in 10 out of 20 samples. We identified nine Tier 1 or 2 variants in 10 (67â¯%) out of 15 malignant nodules (NRAS, BRAF, TP53, TERT, PTEN, PIK3CA) and one Tier 2 (PIK3CA) variant in one out of five benign nodules. The study demonstrated an NPV of 40â¯%, a PPV of 90â¯%, a specificity of 80â¯%, and a sensitivity of 60â¯%. CONCLUSION: Based on the detected molecular markers, at least nine patients (45â¯%) could be managed correctly without needing a repeat FNAB attempt. This study underscores the clinical practicality of molecular tests in managing nodules with indeterminate cytology. Additionally, this study emphasizes the importance of considering the patient's age when determining the DNA- or RNA-based genetic testing method. Finally, we discussed the significance of the somatic mutation profile and its impact on the current pathological classification.
Assuntos
Sequenciamento de Nucleotídeos em Larga Escala , Mutação , Nódulo da Glândula Tireoide , Humanos , Nódulo da Glândula Tireoide/genética , Nódulo da Glândula Tireoide/patologia , Nódulo da Glândula Tireoide/diagnóstico , Feminino , Pessoa de Meia-Idade , Masculino , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Adulto , Análise Mutacional de DNA/métodos , Idoso , Neoplasias da Glândula Tireoide/genética , Neoplasias da Glândula Tireoide/patologia , Neoplasias da Glândula Tireoide/diagnóstico , Biomarcadores Tumorais/genética , Sensibilidade e Especificidade , Biópsia por Agulha Fina , CitologiaRESUMO
Cobas EGFR mutation Test v2 was FDA-approved as qualitative liquid biopsy for actionable EGFR variants in non-small cell lung cancer (NSCLC). It generates semiquantitative index (SQI) values that correlate with mutant allele levels, but decision thresholds for clinical use in NSCLC surveillance are lacking. We conducted long-term ctDNA monitoring in 20 subjects with EGFR-mutated NSCLC; resulting in a 155 on-treatment samples. We defined optimal SQI intervals to predict/rule-out progression within 12 weeks from sampling and performed orthogonal calibration versus deep-sequencing and digital PCR. SQI showed significant diagnostic power (AUC 0.848, 95% CI 0.782-0.901). SQI below 5 (63% of samples) had 93% (95% CI 87-96%) NPV, while SQI above 10 (25% of samples) had 69% (95% CI 56-80%) PPV. Cobas EGFR showed perfect agreement with sequencing (Kappa 0.860; 95% CI 0.674-1.00) and digital PCR. SQI values strongly (r: 0.910, 95% 0.821-0.956) correlated to mutant allele concentrations with SQI of 5 and 10 corresponding to 6-9 (0.2-0.3%) and 64-105 (1.1-1.6%) mutant allele copies/mL (VAF) respectively. Our dual-threshold classifier of SQI 0/5/10 yielded informative results in 88% of blood draws with high NPV and good overall clinical utility for patient-centric surveillance of metastatic NSCLC.
Assuntos
Carcinoma Pulmonar de Células não Pequenas , Receptores ErbB , Neoplasias Pulmonares , Mutação , Humanos , Carcinoma Pulmonar de Células não Pequenas/genética , Carcinoma Pulmonar de Células não Pequenas/patologia , Receptores ErbB/genética , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/patologia , Masculino , Feminino , Pessoa de Meia-Idade , Idoso , Biópsia Líquida/métodos , DNA Tumoral Circulante/genética , DNA Tumoral Circulante/sangue , Análise Mutacional de DNA/métodos , Metástase NeoplásicaRESUMO
BACKGROUND: Retinitis pigmentosa (RP) is a heterogeneous group of inherited retinal diseases. However, it is still not well understand about the relationship between PCDH15 variants and RP. METHODS: In this study, we enrolled a Chinese autosomal recessive retinitis pigmentosa (arRP) pedigree and identified the causative gene in the proband by targeted whole exome sequencing (WES). The variants were validated in the family members by Sanger sequencing and co-segregation analysis. RESULTS: Novel compound heterozygous, Frame shift variants of the PCDH15 gene, NM_001384140.1:c.4368 - 2147_4368-2131del and NM_001384140.1:c exon19:c.2505del: p. T836Lfs*6 were identified in the arRP pedigree, which co-segregated with the clinical RP phenotypes. The PCDH15 protein is highly conserved among species. CONCLUSION: This is the first study to identify novel compound heterozygous variants c.4368 - 2147_4368-2131del and c.2505del(p.T836Lfs*6) in the PCDH15 gene which might be disease-causing variants, and extending the variant spectra. All above findings may be contribute to genetic counseling, molecular diagnosis and clinical management of arRP disease.
Assuntos
Proteínas Relacionadas a Caderinas , Retinose Pigmentar , Adulto , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Proteínas Relacionadas a Caderinas/genética , China/epidemiologia , Análise Mutacional de DNA , População do Leste Asiático/genética , Sequenciamento do Exoma , Heterozigoto , Linhagem , Fenótipo , Retinose Pigmentar/genéticaRESUMO
Usher syndrome (USH) is a recessive genetic disorder manifested by congenital sensorineural hearing loss and progressive retinitis pigmentosa, which leads to audiovisual impairment. We report a patient with Usher syndrome type 1 with new compound heterozygous MYO7A variants. A total of four members from the USH family were included. Medical history and retinal examinations were taken and genomic DNA from peripheral blood was extracted in the proband and other members. 381 retinal disease-associated genes were screened using targeted sequence capture array technology and Sanger sequencing was used to confirm the screening results. Scanning laser ophthalmoscope showed bone spicule pigmentary deposits in the mid-peripheral retina and whitish and thin retinal blood vessels especially in the arterioles. Optical coherence tomography showed that the centrality of the macular ellipsoid band disappeared in both eyes, and only remained near the fovea. Visual field examination showed a progressive loss of the visual field in a concentric pattern in both eyes. The electroretinography showed a significant decrease in the amplitudes of a- and b-waves in the scotopic and photopic condition. DNA sequencing identified the compound heterozygous variants including c.1003+1G > A: p. (?) and c.5957_5958del: p.G1987Lfs*50 of MYO7A, with the latter being novel. In this study, we found a novel compound heterozygous variant in MYO7A, which enriched the mutation spectrum and expanded our understanding of the heterogeneity of phenotype and genotype of Usher syndrome type 1.
Assuntos
Eletrorretinografia , Miosina VIIa , Síndromes de Usher , Adulto , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Análise Mutacional de DNA , Heterozigoto , Mutação , Miosina VIIa/genética , Linhagem , Tomografia de Coerência Óptica , Síndromes de Usher/genética , Campos Visuais/fisiologiaRESUMO
PURPOSE: To study the clinical and genetic features of a cohort of RP children. METHODS: We identified 46 RP patients with pathogenic or likely pathogenic mutations among 96 patients with a clinical diagnosis of retinitis pigmentosa. All of the patients underwent comprehensive clinical examinations and genetic testing. A retrospective study was conducted on 46 children with retinitis pigmentosa. The genetic and clinical characteristics of children with different genotypes were analyzed. RESULTS: Among the 46 children, 13 inherited X-linked gene mutations, including 9 RPGR and 4 RP2 mutations. There were 10 cases of autosomal dominant genes and 23 cases of autosomal recessive genes. XLRP accounted for a larger proportion of children, as observed in previous studies on RP. We found that RPGR genes were the most commonly mutated genes in RP children. The most frequently mutated gene was RPGR (9.3%), followed by RP2 (4.2%) and RPE65 (4.2%). Forty-six patients had mutations in 21 different genes, 19 of which were novel mutations.Most children with XLRP have a high degree of myopia, poor vision, and severe clinical symptoms. Frameshift mutations were more common in XLRP, followed by nonsense mutations. The onset of XLRP is relatively serious since childhood. Most children with ADRP have relatively good visual acuity and mild clinical symptoms, and missense mutations are common. The clinical manifestations of ARRP in children are more severe than those of ADRP in children but milder than those of XLRP in children, and missense mutations are common. The manifestations of RPE65 mutations are also severe and appear early. CONCLUSIONS: Our results revealed that XLRP gene mutations were more common in children than in adults, as observed in previous studies on RP. The proportion of RP children with ADRP is relatively small. The new findings in our study polished the spectrum of novel mutations and the proportions of different genotypes in pediatric patients. The onset of XLRP occurred earlier. The genes with a high incidence in children were all relatively severe gene types of RP. This comprehensive database may provide essential information regarding the initial stage of RP.
Assuntos
Proteínas do Olho , Mutação , Retinose Pigmentar , Humanos , Retinose Pigmentar/genética , Retinose Pigmentar/diagnóstico , Masculino , Criança , Feminino , Estudos Retrospectivos , Pré-Escolar , Proteínas do Olho/genética , Adolescente , Acuidade Visual/fisiologia , Eletrorretinografia , Análise Mutacional de DNA , Lactente , Genes Ligados ao Cromossomo X/genética , Genótipo , Proteínas de Membrana , Proteínas de Ligação ao GTPRESUMO
Breast cancer (BC) has emerged as the most common malignancy among females. The genomic profile of BC is diverse in nature and complex due to heterogeneity among various geographically different ethnic groups. The primary objective of this study was to carry out a comprehensive mutational analysis of Indian BC cases by performing whole exome sequencing. The cohort included patients with a median age of 48 years. TTN, TP53, MUC16, SYNE1, and OBSCN were the frequently altered genes found in our cohort. The PIK3CA and KLC3 genes are driver genes implicated in various cellular functions and cargo transportation through microtubules, respectively. Except for CCDC168 and PIK3CA, several gene pairings were found to be significantly linked with co-occurrence. Irrespective of their hormonal receptor status, RTK/RAS was observed with frequently altered signaling pathways. Further analysis of the mutational signature revealed that SBS13, SBS6, and SBS29 were mainly observed in our cohort. This study supplements the discovery of diagnostic biomarkers and provides new therapeutic options for the improved management of BC.
Assuntos
Neoplasias da Mama , Sequenciamento do Exoma , Mutação , Humanos , Feminino , Neoplasias da Mama/genética , Pessoa de Meia-Idade , Adulto , Índia/epidemiologia , Biomarcadores Tumorais/genética , Idoso , Análise Mutacional de DNARESUMO
We proposed a single-color fluorogenic DNA decoding sequencing method designed to improve sequencing accuracy, increase read length and throughput, as well as decrease scanning time. This method involves the incorporation of a mixture of four types of 3'-O-modified nucleotide reversible terminators into each reaction. Among them, two nucleotides are labeled with the same fluorophore, while the remaining two are unlabeled. Only one nucleotide can be extended in each reaction, and an encoding that partially defines base composition can be obtained. Through cyclic interrogation of a template twice with different nucleotide combinations, two sets of encodings are sequentially obtained, enabling the determination of the sequence. We demonstrate the feasibility of this method using established sequencing chemistry, achieving a cycle efficiency of approximately 99.5â¯%. Notably, this strategy exhibits remarkable efficacy in the detection and correction of sequencing errors, achieving a theoretical error rate of 0.00016â¯% at a sequencing depth of ×2, which is lower than Sanger sequencing. This method is theoretically compatible with the existing sequencing-by-synthesis (SBS) platforms, and the instrument is simpler, which may facilitate further reductions in sequencing costs, thereby broadening its applications in biology and medicine. Moreover, we demonstrate the capability to detect known mutation sites using information from only a single sequencing run. We validate this approach by accurately identifying a mutation site in the human mitochondrial DNA.
Assuntos
Corantes Fluorescentes , Mutação , Corantes Fluorescentes/química , Humanos , Análise de Sequência de DNA/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , DNA/genética , Genótipo , Técnicas de Genotipagem/métodos , Análise Mutacional de DNA/métodos , DNA Mitocondrial/genéticaRESUMO
Telomerase reverse transcriptase promoter (TERTp) mutations are frequently targeted tumor markers, however, they reside in regions with high GC content, which poses challenges when examined with simple molecular techniques or even with next-generation sequencing (NGS). In bladder cancer (BC), TERTp mutations are particularly frequent, however, none of the available tools have demonstrated efficacy in detecting TERTp mutations via a simple noninvasive technique. Therefore, we developed a novel PCR-based method for the detection of the two most common TERTp mutations and demonstrated its use for the analysis of BC samples. The developed SHARD-PCR TERTp mutation detection technique requires PCR and restriction digestion steps that are easily implementable even in less well-equipped laboratories. Cell lines with known mutational status were utilized for method development. Matching urine and tumor tissue samples from BC patients were analyzed, and the results were validated by next-generation sequencing. Analysis of eighteen urine and corresponding tumor tissue samples by SHARD-PCR revealed perfect matches in sample pairs, which paralleled the corresponding NGS results: fourteen samples exhibited mutations at the -124 position, two samples showed mutations at the -146 position, and no mutations were detected in two samples. Our study serves as a proof-of-concept and is limited by its small sample size, nonetheless, it demonstrates that SHARD-PCR is a simple, economic and highly reliable method for detecting TERTp mutations, which are common in different cancer types. For bladder cancer, SHARD-PCR can be performed with the use of noninvasive samples and could replace or complement currently used techniques.
Assuntos
Mutação , Reação em Cadeia da Polimerase , Regiões Promotoras Genéticas , Telomerase , Neoplasias da Bexiga Urinária , Humanos , Neoplasias da Bexiga Urinária/genética , Neoplasias da Bexiga Urinária/diagnóstico , Telomerase/genética , Reação em Cadeia da Polimerase/métodos , Masculino , Feminino , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Idoso , Pessoa de Meia-Idade , Análise Mutacional de DNA/métodos , Biomarcadores Tumorais/genética , Linhagem Celular TumoralRESUMO
BACKGROUND: Oculocutaneous albinism (OCA) is a genetically heterogeneous condition that is associated with reduced or absent melanin pigment in the skin, hair, and eyes, resulting in reduced vision, high sensitivity to light, and rapid and uncontrolled eye movements. To date, seventeen genes have been associated with OCA including syndromic and non-syndromic forms of the condition. METHODS: Whole exome sequencing (WES) was performed to identify pathogenic variants in nine Pakistani families with OCA, with validation and segregation of candidate variants performed using Sanger sequencing. Furthermore, the pathogenicity of the identified variants was assessed using various in-silico tools and 3D protein structural analysis software. RESULTS: WES identified biallelic variants in three genes explaining the OCA in these families, including four variants in TYR, three in OCA2, and two in HPS1, including two novel variants c.667C > T: p.(Gln223*) in TYR, and c.2009 T > C: p.(Leu670Pro) in HPS1. CONCLUSIONS: Overall, this study adds further knowledge of the genetic basis of OCA in Pakistani communities and facilitates improved management and counselling services for families suffering from severe genetic diseases in Pakistan.