Utility of ultrasound‐guided liver tumor biopsy for next‐generation sequencing‐based clinical sequencing

2019 ◽  
Vol 49 (5) ◽  
pp. 579-589 ◽  
Author(s):  
Yuji Eso ◽  
Tadayuki Kou ◽  
Hiroki Nagai ◽  
Young Hak Kim ◽  
Masashi Kanai ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Liver Tumor ◽  
Next Generation ◽  
Ultrasound Guided ◽  
Tumor Biopsy ◽  
Clinical Sequencing ◽  
Generation Sequencing

scholarly journals Improved next-generation sequencing pre-capture library yields and sequencing parameters using on-bead PCR

BioTechniques ◽  
2020 ◽  
Vol 68 (1) ◽  
pp. 48-51 ◽  
Author(s):  
Christopher R McEvoy ◽  
Timothy Semple ◽  
Bhargavi Yellapu ◽  
David Y Choong ◽  
Huiling Xu ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Variant Calling ◽  
Limiting Factor ◽  
Next Generation ◽  
Tumor Biopsy ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Next Generation Sequencing Ngs ◽  
Tumor Dna ◽  
Generation Sequencing

Tumor DNA sequencing results can have important clinical implications. However, its use is often limited by low DNA input, owing to small tumor biopsy size. To help overcome this limitation we have developed a simple improvement to a commonly used next-generation sequencing (NGS) capture-based library preparation method using formalin-fixed paraffin-embedded-derived tumor DNA. By using on-bead PCR for pre-capture library generation we show that library yields are dramatically increased, resulting in decreased sample failure rates. Improved yields allowed for a reduction in PCR cycles, which translated into improved sequencing parameters without affecting variant calling. This methodology should be applicable to any NGS system in which input DNA is a limiting factor.

Utility of Endoscopic Ultrasound-Guided Biopsy for Next-Generation Sequencing of Pancreatic Exocrine Malignancies

Pancreas ◽  
2018 ◽  
Vol 47 (8) ◽  
pp. 990-995 ◽  
Author(s):  
Brent K. Larson ◽  
Richard Tuli ◽  
Laith H. Jamil ◽  
Simon K. Lo ◽  
Nan Deng ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Endoscopic Ultrasound ◽  
Next Generation ◽  
Ultrasound Guided ◽  
Guided Biopsy ◽  
Pancreatic Exocrine ◽  
Generation Sequencing ◽  
Ultrasound Guided Biopsy

scholarly journals Next-Generation Sequencing–Based Cancer Panel Data Conversion Using International Standards to Implement a Clinical Next-Generation Sequencing Research System: Single-Institution Study

10.2196/14710 ◽  
2020 ◽  
Vol 8 (4) ◽  
pp. e14710 ◽  
Author(s):  
Phillip Park ◽  
Soo-Yong Shin ◽  
Seog Yun Park ◽  
Jeonghee Yun ◽  
Chulmin Shin ◽  
...  
Keyword(s):  
Clinical Practice ◽  
Next Generation Sequencing ◽  
Clinical Data ◽  
Genomic Data ◽  
International Standards ◽  
Research System ◽  
Next Generation ◽  
Sequencing Data ◽  
Clinical Sequencing ◽  
Generation Sequencing

Background The analytical capacity and speed of next-generation sequencing (NGS) technology have been improved. Many genetic variants associated with various diseases have been discovered using NGS. Therefore, applying NGS to clinical practice results in precision or personalized medicine. However, as clinical sequencing reports in electronic health records (EHRs) are not structured according to recommended standards, clinical decision support systems have not been fully utilized. In addition, integrating genomic data with clinical data for translational research remains a great challenge. Objective To apply international standards to clinical sequencing reports and to develop a clinical research information system to integrate standardized genomic data with clinical data. Methods We applied the recently published ISO/TS 20428 standard to 367 clinical sequencing reports generated by panel (91 genes) sequencing in EHRs and implemented a clinical NGS research system by extending the clinical data warehouse to integrate the necessary clinical data for each patient. We also developed a user interface with a clinical research portal and an NGS result viewer. Results A single clinical sequencing report with 28 items was restructured into four database tables and 49 entities. As a result, 367 patients’ clinical sequencing data were connected with clinical data in EHRs, such as diagnosis, surgery, and death information. This system can support the development of cohort or case-control datasets as well. Conclusions The standardized clinical sequencing data are not only for clinical practice and could be further applied to translational research.

scholarly journals Small lung tumor biopsy samples are feasible for high quality targeted next generation sequencing

2019 ◽  
Vol 110 (8) ◽  
pp. 2652-2657 ◽  
Author(s):  
Hidenori Kage ◽  
Shinji Kohsaka ◽  
Aya Shinozaki‐Ushiku ◽  
Yoshihisa Hiraishi ◽  
Jiro Sato ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Lung Tumor ◽  
Next Generation ◽  
High Quality ◽  
Tumor Biopsy ◽  
Targeted Next Generation Sequencing ◽  
Generation Sequencing

scholarly journals New Era of Endoscopic Ultrasound-Guided Tissue Acquisition: Next-Generation Sequencing by Endoscopic Ultrasound-Guided Sampling for Pancreatic Cancer

2019 ◽  
Vol 8 (8) ◽  
pp. 1173 ◽  
Author(s):  
Imaoka ◽  
Sasaki ◽  
Hashimoto ◽  
Watanabe ◽  
Ikeda
Keyword(s):  
Pancreatic Cancer ◽  
Next Generation Sequencing ◽  
Endoscopic Ultrasound ◽  
Next Generation ◽  
Ultrasound Guided ◽  
Tissue Samples ◽  
Genomic Biomarkers ◽  
Tissue Acquisition ◽  
Chemotherapy Patients ◽  
Generation Sequencing

Pancreatic cancer is a lethal cancer with an increasing incidence. Despite improvements in chemotherapy, patients with pancreatic cancer continue to face poor prognoses. Endoscopic ultrasound-guided tissue acquisition (EUS-TA) is the primary method for obtaining tissue samples of pancreatic cancer. Due to advancements in next-generation sequencing (NGS) technologies, multiple parallel sequencing can be applied to EUS-TA samples. Genomic biomarkers for therapeutic stratification in pancreatic cancer are still lacking, however, NGS can unveil potential predictive genomic biomarkers of treatment response. Thus, the importance of NGS using EUS-TA samples is becoming recognized. In this review, we discuss the recent advances in EUS-TA application for NGS of pancreatic cancer.

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