scholarly journals Application of large-scale targeted sequencing to distinguish multiple lung primary tumors from intrapulmonary metastases

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Jiaxin Duan ◽  
Mingjian Ge ◽  
Jian Peng ◽  
Yangli Zhang ◽  
Li Yang ◽  
...  
Keyword(s):  
Somatic Mutation ◽  
Large Scale ◽  
Targeted Sequencing ◽  
Disease Stage ◽  
Primary Tumors ◽  
Lung Cancers ◽  
Appropriate Treatment ◽  
Primary Lung Tumors ◽  
Mutation Pattern ◽  
Node Metastases

Abstract The effective differentiation between multiple primary lung tumors (MPs) and intrapulmonary metastases (IMs) in patients is imperative to discover the exact disease stage and to select the most appropriate treatment. In this study, the authors was to evaluate the efficacy and validity of large-scale targeted sequencing (LSTS) as a supplement to estimate whether multifocal lung cancers (MLCs) are primary or metastatic. Targeted sequencing of 520 cancer-related oncogenes was performed on 36 distinct tumors from 16 patients with MPs. Pairing analysis was performed to evaluate the somatic mutation pattern of MLCs in each patient. A total of 25 tumor pairs from 16 patients were sequenced, 88% (n = 22) of which were classified as MPs by LSTS, consistent with clinical diagnosis. One tumor pair from a patient with lymph node metastases had highly consistent somatic mutation profiles, thus predicted as a primary-metastatic pair. In addition, some matched mutations were observed in the remaining two paired ground-glass nodules (GGNs) and classified as high-probability IMs by LSTS. Our study revealed that LSTS can potentially facilitate the distinction of MPs from IMs. In addition, our results provide new genomic evidence of the presence of cancer invasion in GGNs, even pure GGNs.

Tracking the tumor evolution of patients with recurrence of ipsilateral breast tumor.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e12582-e12582
Author(s):  
Yane Song ◽  
Li Peng ◽  
Wei Zhou ◽  
Yiru Niu ◽  
Wanning Yang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Somatic Mutation ◽  
Breast Tumor ◽  
Breast Cancer Survivors ◽  
Tumor Evolution ◽  
Recurrent Tumor ◽  
Ipsilateral Breast ◽  
Primary Tumors ◽  
Recurrent Tumors ◽  
Appropriate Treatment

e12582 Background: After primary surgical resection, quite a proportion of breast cancer survivors would experience local recurrence within 5 years. Whether local recurrent tumors arise independently or from the primary tumors, which is critical for diagnosis and appropriate treatment, remains a clinical dilemma. Phylogenetic analysis between the primary and recurrent tumor provides a new strategy helpful for determining the origin of the local recurrent tumor. Methods: DNA was extracted from FFPE samples of the primary and recurrent tumors from 12 patients with recurrence of ipsilateral breast tumor. Phylogenetic analysis between the primary and recurrent tumors in the same individual was performed based on whole exome sequencing. PyClone and SciClone were employed to detect subclones. Results: The median time to recurrence of the 12 patients was 15 months (9 to 52 months). 9 (75%) of the 12 patients recurred within 2 years. Each patient had one shared somatic mutation clone between the primary and recurrent tumor, with shared somatic mutation number ranging from 5 to 59. This observation suggests that the recurrent tumor maybe originate from the primary tumor. Conclusions: The shared somatic mutation clone indicates the primary and recurrent tumor could be of the same origin and the recurrent tumor was metastasis from primary lesion. This may provide some information to help selecting the most appropriate treatment for patients.

An Assessment of a Low-Cost Wastewater Disposal System after Twenty-Five Years of Operation

1987 ◽  
Vol 19 (5-6) ◽  
pp. 701-710 ◽  
Author(s):  
B. L. Reidy ◽  
G. W. Samson
Keyword(s):  
Large Scale ◽  
Low Cost ◽  
Wastewater Disposal ◽  
Industrial Base ◽  
Industrial Wastewaters ◽  
The Past ◽  
Gasification Process ◽  
Appropriate Treatment ◽  
Environmentally Safe ◽  
Coal Resource

A low-cost wastewater disposal system was commissioned in 1959 to treat domestic and industrial wastewaters generated in the Latrobe River valley in the province of Gippsland, within the State of Victoria, Australia (Figure 1). The Latrobe Valley is the centre for large-scale generation of electricity and for the production of pulp and paper. In addition other industries have utilized the brown coal resource of the region e.g. gasification process and char production. Consequently, industrial wastewaters have been dominant in the disposal system for the past twenty-five years. The mixed industrial-domestic wastewaters were to be transported some eighty kilometres to be treated and disposed of by irrigation to land. Several important lessons have been learnt during twenty-five years of operating this system. Firstly the composition of the mixed waste stream has varied significantly with the passage of time and the development of the industrial base in the Valley, so that what was appropriate treatment in 1959 is not necessarily acceptable in 1985. Secondly the magnitude of adverse environmental impacts engendered by this low-cost disposal procedure was not imagined when the proposal was implemented. As a consequence, clean-up procedures which could remedy the adverse effects of twenty-five years of impact are likely to be costly. The question then may be asked - when the total costs including rehabilitation are considered, is there really a low-cost solution for environmentally safe disposal of complex wastewater streams?

scholarly journals Somatic Mutation Profiling in the Liquid Biopsy and Clinical Analysis of Hereditary and Familial Pancreatic Cancer Cases Reveals KRAS Negativity and a Longer Overall Survival

Cancers ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1612
Author(s):  
Julie Earl ◽  
Emma Barreto ◽  
María E. Castillo ◽  
Raquel Fuentes ◽  
Mercedes Rodríguez-Garrote ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Overall Survival ◽  
Somatic Mutation ◽  
Disease Status ◽  
Clinical Analysis ◽  
Cytotoxic Agents ◽  
Disease Stage ◽  
Ductal Adenocarcinoma ◽  
Familial Pancreatic Cancer ◽  
Circulating Free Dna

Pancreatic ductal adenocarcinoma (PDAC) presents many challenges in the clinic and there are many areas for improvement in diagnostics and patient management. The five-year survival rate is around 7.2% as the majority of patients present with advanced disease at diagnosis that is treatment resistant. Approximately 10–15% of PDAC cases have a hereditary basis or Familial Pancreatic Cancer (FPC). Here we demonstrate the use of circulating free DNA (cfDNA) in plasma as a prognostic biomarker in PDAC. The levels of cfDNA correlated with disease status, disease stage, and overall survival. Furthermore, we show for the first time via BEAMing that the majority of hereditary or familial PDAC cases (around 84%) are negative for a KRAS somatic mutation. In addition, KRAS mutation negative cases harbor somatic mutations in potentially druggable genes such as KIT, PDGFR, MET, BRAF, and PIK3CA that could be exploited in the clinic. Finally, familial or hereditary cases have a longer overall survival compared to sporadic cases (10.2 vs. 21.7 months, respectively). Currently, all patients are treated the same in the clinic with cytotoxic agents, although here we demonstrate that there are different subtypes of tumors at the genetic level that could pave the way to personalized treatment.

scholarly journals Supraclavicular lymph node metastases from distant primary tumors: Case reports and review of the literature

2021 ◽  
Vol 81 ◽  
pp. 105720
Author(s):  
Youssef Oukessou ◽  
Yassir Hammouda ◽  
Khadija El Bouhmadi ◽  
Redallah Larbi Abada ◽  
Mohamed Roubal ◽  
...  
Keyword(s):  
Lymph Node ◽  
Lymph Node Metastases ◽  
Case Reports ◽  
Review Of The Literature ◽  
Supraclavicular Lymph Node ◽  
Primary Tumors ◽  
Node Metastases

scholarly journals Metastatic Squamous Cell Carcinoma of the Anus to the Lung Confirmed with Allelotyping

2014 ◽  
Vol 2014 ◽  
pp. 1-5 ◽  
Author(s):  
Rachel Roth ◽  
Susan Moffatt-Bruce ◽  
Marino E. Leon
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Loss Of Heterozygosity ◽  
Squamous Cell ◽  
Palliative Chemotherapy ◽  
Primary Tumors ◽  
Appropriate Treatment ◽  
Metastatic Squamous Cell Carcinoma ◽  
Hematoxylin And Eosin

Histopathologic techniques are insufficient for distinguishing primary squamous cell carcinoma (SCC) from metastatic SCC, which is clinically important. A patient with SCC of the anus was found to also have SCC of the lung, and the question of metastatic versus synchronous primary diseases was raised. Immunohistochemical and hematoxylin and eosin (H&E) staining on sections of tissue could not discriminate between the two entities. Immunostain for p16 and chromogenicin situhybridization for human papillomavirus (HPV) type 16 were positive in both tumors. Additionally, allelotyping for loss of heterozygosity displayed similar findings and confirmed the histopathological impression of anal SCC metastasis to the lung. The patient was treated with palliative chemotherapy instead of additional surgical treatment. When multiple tumors are present, determining metastatic versus synchronous primary tumors is necessary for appropriate treatment. Identification can be achieved using allelotyping for loss of heterozygosity.

scholarly journals Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Tianyun Wang ◽  
◽  
Kendra Hoekzema ◽  
Davide Vecchio ◽  
Huidan Wu ◽  
...  
Keyword(s):  
Neurodevelopmental Disorders ◽  
Large Scale ◽  
De Novo ◽  
Targeted Sequencing ◽  
Published Data ◽  
De Novo Mutations ◽  
Risk Genes ◽  
Mutation Burden ◽  
Number Of Patients ◽  
Significant Burden

Abstract Most genes associated with neurodevelopmental disorders (NDDs) were identified with an excess of de novo mutations (DNMs) but the significance in case–control mutation burden analysis is unestablished. Here, we sequence 63 genes in 16,294 NDD cases and an additional 62 genes in 6,211 NDD cases. By combining these with published data, we assess a total of 125 genes in over 16,000 NDD cases and compare the mutation burden to nonpsychiatric controls from ExAC. We identify 48 genes (25 newly reported) showing significant burden of ultra-rare (MAF < 0.01%) gene-disruptive mutations (FDR 5%), six of which reach family-wise error rate (FWER) significance (p < 1.25E−06). Among these 125 targeted genes, we also reevaluate DNM excess in 17,426 NDD trios with 6,499 new autism trios. We identify 90 genes enriched for DNMs (FDR 5%; e.g., GABRG2 and UIMC1); of which, 61 reach FWER significance (p < 3.64E−07; e.g., CASZ1). In addition to doubling the number of patients for many NDD risk genes, we present phenotype–genotype correlations for seven risk genes (CTCF, HNRNPU, KCNQ3, ZBTB18, TCF12, SPEN, and LEO1) based on this large-scale targeted sequencing effort.

Pre-surgical assessment of mediastinal lymph node metastases in Stage IA non-small-cell lung cancers

2020 ◽  
Vol 68 ◽  
pp. 61-67
Author(s):  
Yong Wang ◽  
Yeqing Zhu ◽  
Rowena Yip ◽  
Dong-Seok Lee ◽  
Raja M. Flores ◽  
...  
Keyword(s):  
Lymph Node ◽  
Lymph Node Metastases ◽  
Mediastinal Lymph Node ◽  
Small Cell ◽  
Small Cell Lung ◽  
Lung Cancers ◽  
Stage Ia ◽  
Node Metastases ◽  
Mediastinal Lymph Node Metastases
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