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BACKGROUND: Hereditary cancer predisposition syndromes are responsible for approximately 5-10% of all diagnosed cancer cases. In order to identify individuals at risk in a cost-efficient manner, family members of individuals carrying pathogenic alterations are tested only for the specific variant that was identified in their carrier relative. The purpose of this study was to investigate the clinical use and implementation of cascade family testing (CFT) in families of breast cancer patients with pathogenic/likely pathogenic variants (PVs/LPVs) in cancer-related predisposition genes. METHODS: Germline sequencing was carried out with NGS technology using a 52-gene panel, and cascade testing was performed by Sanger sequencing or MLPA. RESULTS: In a cohort of 1785 breast cancer patients (families), 20.3% were found to have PVs/LPVs. Specifically, 52.2%, 25.1%, and 22.7% of patients had positive findings in high-, intermediate-, and low-penetrance breast cancer susceptibility genes, respectively. Although CFT was recommended to all families, only 117 families (32.3%) agreed to proceed with genetic testing. Among the first-degree relatives who underwent CFT, 70.3% were female, and 108 of 121 (89.3%) were cancer free. Additionally, 42.7%, 36.7%, and 20.6% were offspring, siblings, and parents of the subject, respectively. Our data suggest that CFT was mostly undertaken (104/117, 88.8%) in families with positive findings in high-risk genes. CONCLUSIONS: Cascade family testing can be a powerful tool for primary cancer prevention by identifying at-risk family members. It is of utmost importance to implement genetic counseling approaches leading to increased awareness and communication of genetic testing results.
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BACKGROUND/AIM: Germline copy number variation (CNV) is a type of genetic variant that predisposes significantly to inherited cancers. Today, next-generation sequencing (NGS) technologies have contributed to multi gene panel analysis in clinical practice. MATERIALS AND METHODS: A total of 2,163 patients were screened for cancer susceptibility, using a solution-based capture method. A panel of 52 genes was used for targeted NGS. The capture-based approach enables computational analysis of CNVs from NGS data. We studied the performance of the CNV module of the commercial software suite SeqPilot (JSI Medical Systems) and of the non-commercial tool panelcn.MOPS. Additionally, we tested the performance of digital multiplex ligation-dependent probe amplification (digitalMLPA). RESULTS: Pathogenic/likely pathogenic variants (P/LP) were identified in 464 samples (21.5%). CNV accounts for 10.8% (50/464) of pathogenic variants, referring to deletion/duplication of one or more exons of a gene. In patients with breast and ovarian cancer, CNVs accounted for 10.2% and 6.8% of pathogenic variants, respectively. In colorectal cancer patients, CNV accounted for 28.6% of pathogenic/likely pathogenic variants. CONCLUSION: In silico CNV detection tools provide a viable and cost-effective method to identify CNVs from NGS experiments. CNVs constitute a substantial percentage of P/LP variants, since they represent up to one of every ten P/LP findings identified by NGS multigene analysis; therefore, their evaluation is highly recommended to improve the diagnostic yield of hereditary cancer analysis.
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Variações do Número de Cópias de DNA , Neoplasias Ovarianas , Feminino , Humanos , Predisposição Genética para Doença , Neoplasias Ovarianas/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Éxons , Testes GenéticosRESUMO
Alternative splicing (AS), a crucial cellular process, is a source of transcriptomic expansion and protein variability. Its contribution to cancer development and progression among a vast repertoire of human diseases, is highlighted lately and is under extensive investigation. In this review, the relative recent aspects of AS as a hallmark of cancer are described. In parallel, the importance of the identification of splicing-related variants through next-generation sequencing technologies is discussed. Cancer therapy and the management of patients and their families can highly benefit by the classification of these variants.
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Predisposição Genética para Doença , Neoplasias , Humanos , Processamento Alternativo/genética , Neoplasias/genética , Sequenciamento de Nucleotídeos em Larga EscalaRESUMO
We present our data of a novel proposed CNA-profile risk-index, applied on a Greek ALLIC-BFM-treated cohort, aiming at further refining genomic risk-stratification. Eighty-five of 227 consecutively treated ALL patients were analyzed for the copy-number-status of eight genes (IKZF1/CDKN2A/2B/PAR1/BTG1/EBF1/PAX5/ETV6/RB1). Using the MLPA-assay, patients were stratified as: (1) Good-risk(GR)-CNA-profile (n = 51), with no deletion of IKZF1/CDKN2A/B/PAR1/BTG1/EBF1/PAX5/ETV6/RB1 or isolated deletions of ETV6/PAX5/BTG1 or ETV6 deletions with a single additional deletion of BTG1/PAX5/CDKN2A/B. (2) Poor-risk(PR)-CNA-profile (n = 34), with any deletion of ΙΚΖF1/PAR1/EBF1/RB1 or any other CΝΑ. With a median follow-up time of 49.9 months, EFS for GR-CNA-profile and PR-CNA-profile patients was 96.0% vs. 57.6% (p < 0.001). For IR-group and HR-group patients, EFS for the GR-CNA/PR-CNA subgroups was 100.0% vs. 60.0% (p < 0.001) and 88.2% vs. 55.6% (p = 0.047), respectively. Among FC-MRDd15 + patients (MRDd15 ≥ 10-4), EFS rates were 95.3% vs. 51.7% for GR-CNA/PR-CNA subjects (p < 0.001). Similarly, among FC-MRDd33 + patients (MRDd33 ≥ 10-4), EFS was 92.9% vs. 27.3% (p < 0.001) and for patients FC-MRDd33 - (MRDd33 < 10-4), EFS was 97.2% vs. 72.7% (p = 0.004), for GR-CNA/PR-CNA patients, respectively. In a multivariate analysis, the CNA-profile was the most important outcome predictor. In conclusion, the CNA-profile can establish a new genomic risk-index, identifying a distinct subgroup with increased relapse risk among the IR-group, as well as a subgroup of patients with superior prognosis among HR-patients. The CNA-profile is feasible in BFM-based protocols, further refining MRD-based risk-stratification.
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Fibroblast Growth Factor Receptor 3 (FGFR3) related skeletal dysplasias are caused by mutations in the FGFR3 gene that result in increased activation of the receptors causing alterations in the process of endochondral ossification in all long bones, and include achondroplasia, hypochondroplasia, thanatophoric dysplasia, and SADDAN. Reports of prenatal diagnosis of FGFR3 related skeletal dysplasias are not rare; however, the correlation between 2nd trimester ultrasonographic findings and underlying molecular defect in these cases is relatively poor. There is a need for specific ultrasound (U/S) predictors than can distinguish lethal from non-lethal cases and aid an earlier prenatal diagnosis. Here we present one familial and 16 sporadic cases with FGFR3 related skeletal dysplasia, and we evaluate biometric parameters and U/S findings consistent with the diagnosis of skeletal dysplasia. U/S scan performed even at the 18th week of gestation can indicate a decreased rate of development of the femora (femur length (FL) <5th centile), while the mean gestational age at diagnosis is still around the 26th week. The utility of other biometric parameters and ratios is discussed (foot length, BPD, HC, FL/foot, and FL/AC). Prenatal cytogenetic and molecular genetic analyses were performed. A final diagnosis was reached by molecular analysis. In two cases of discontinued pregnancy, fetal autopsy led to a phenotypic diagnosis and confirmed the prenatal prediction of lethality. We conclude that the combination of U/S and molecular genetic approach is helpful for establishing an accurate diagnosis of FGFR3-related skeletal dysplasias in utero and subsequently for appropriate genetic counselling and perinatal management.
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Doenças do Desenvolvimento Ósseo/diagnóstico por imagem , Doenças do Desenvolvimento Ósseo/genética , Diagnóstico Pré-Natal/métodos , Receptor Tipo 3 de Fator de Crescimento de Fibroblastos/genética , Feminino , Humanos , Mutação/genética , Gravidez , Estudos Retrospectivos , Análise de Sequência de DNA , UltrassonografiaRESUMO
BACKGROUND: Cytomegalovirus (CMV) is responsible for the most common opportunistic viral infection in patients with acquired immunodeficiency syndrome (AIDS). The colon is a common site for CMV infection in patients positive for the human immunodeficiency virus (HIV). The clinical diagnosis of CMV infection is based on the characteristic endoscopic appearance of extensive ulceration of the gastric mucosa. METHODS: A 54-year-old HIV-positive man visited our hospital because of high fever. The patient presented with diarrhea, and colonoscopy was performed. Ganciclovir was administered, with a good clinical response. However, the patient complained of the same symptoms again 6 months later. Nested polymerase chain reaction (PCR) was performed on all the patient's samples to detect CMV, followed by sequencing of the UL97 gene for CMV resistance detection. RESULTS: The PCR tests for Legionella, Chlamydia pneumoniae, Pneumocystis carinii, and Aspergillus were negative. DNA preparations from biopsy specimens of areas of colon ulceration were positive for CMV. Six months after treating the colon ulcerations, the PCR for CMV was positive, and the possible emergence of CMV mutants conferring ganciclovir resistance was examined. Direct sequencing of the PCR products revealed the known V594 mutation in the UL97 gene predisposing for ganciclovir resistance as well as the polymorphisms (579, GGC-->GGT) and (598, GGT-->GGC) in all samples tested. CONCLUSIONS: In summary, molecular biology methods can be used for early detection of CMV in characteristic colonic lesions in HIV-1-positive patients. Furthermore, detection of mutant strains resistant to antiviral drugs as well as polymorphisms elucidate the natural history of the infection.