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https://www.readbyqxmd.com/read/29325452/inherited-cancer-in-the-age-of-next-generation-sequencing
#1
Kristin S Price, Ashley Svenson, Elisabeth King, Kaylene Ready, Gabriel A Lazarin
Next-generation sequencing (NGS) technology has led to the ability to test for multiple cancer susceptibility genes simultaneously without significantly increasing cost or turnaround time. With growing usage of multigene testing for inherited cancer, ongoing education for nurses and other health-care providers about hereditary cancer screening is imperative to ensure appropriate testing candidate identification, test selection, and posttest management. The purpose of this review article is to (1) provide an overview of how NGS works to detect germline mutations, (2) summarize the benefits and limitations of multigene panel testing, (3) describe risk categories of cancer susceptibility genes, and (4) highlight the counseling considerations for patients pursuing multigene testing...
January 1, 2018: Biological Research for Nursing
https://www.readbyqxmd.com/read/29325035/amplicon-based-next-generation-sequencing-of-plasma-cell-free-dna-for-detection-of-driver-and-resistance-mutations-in-advanced-non-small-cell-lung-cancer
#2
N Guibert, Y Hu, N Feeney, Y Kuang, V Plagnol, G Jones, K Howarth, J F Beeler, C P Paweletz, G R Oxnard
Background: Genomic analysis of plasma cell-free DNA is transforming lung cancer care, however available assays are limited by cost, turnaround time, and imperfect accuracy. Here we study amplicon-based plasma next-generation sequencing (NGS), rather than hybrid-capture-based plasma NGS, hypothesizing this would allow sensitive detection and monitoring of driver and resistance mutations in advanced non-small cell lung cancer (NSCLC). Methods: Plasma samples from patients with NSCLC and a known targetable genotype (EGFR, ALK/ROS1 and other rare genotypes) were collected while on therapy and analyzed, blinded to tumor genotype...
January 9, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29309945/brca1-brca2-germline-mutation-carriers-and-sporadic-pancreatic-adenocarcinoma
#3
Alex B Blair, Vincent P Groot, Georgios Gemenetzis, Jishu Wei, John L Cameron, Matthew J Weiss, Michael Goggins, Christopher L Wolfgang, Jun Yu, Jin He
BACKGROUND: The outcomes of sporadic pancreatic adenocarcinoma (PDAC) patients with germline mutations of BRCA1/BRCA2 remains unclear. The prognostic significance of BRCA1/BRCA2 mutations on survival is not well established. STUDY DESIGN: We performed targeted next-generation sequencing (NGS) to identify BRCA1/BRCA2 germline mutations in resected sporadic PDAC cases from 2000-2015. Germline BRCA mutation-carriers were matched by age and tumor location to those with BRCA1/BRCA2 wild-type genes from our institutional database...
January 5, 2018: Journal of the American College of Surgeons
https://www.readbyqxmd.com/read/29309772/gene-mutation-patterns-of-chinese-acute-myeloid-leukemia-patients-by-targeted-next-generation-sequencing-and-bioinformatic-analysis
#4
Xiaoyu Han, Wei Li, Na He, Panpan Feng, Yihua Pang, Chunyan Ji, Daoxin Ma
PURPOSES: The conventional risk stratification of acute myeloid leukemia (AML), based on cytogenetics, cannot meet the demand for accurate prognostic evaluations. In recent years, gene mutations are found to be potential markers for more accurate risk stratification, but reports on mutation screening of Chinese AML are limited. We aim to display the mutation patterns of Chinese AML patients, reveal the genotype-phenotype correlation and make a comparison with Caucasians patients. METHODS: Genome DNA from 78 patients' bone marrow were extracted for targeted gene mutation panel by next-generation sequencing (NGS) technology...
January 5, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29307989/gene-mutations-in-stool-from-gastric-and-colorectal-neoplasia-patients-by-next-generation-sequencing
#5
Omar Youssef, Virinder Sarhadi, Homa Ehsan, Tom Böhling, Monika Carpelan-Holmström, Selja Koskensalo, Pauli Puolakkainen, Arto Kokkola, Sakari Knuutila
AIM: To study cancer hotspot mutations by next-generation sequencing (NGS) in stool DNA from patients with different gastrointestinal tract (GIT) neoplasms. METHODS: Stool samples were collected from 87 Finnish patients diagnosed with various gastric and colorectal neoplasms, including benign tumors, and from 14 healthy controls. DNA was isolated from stools by using the PSP® Spin Stool DNA Plus Kit. For each sample, 20 ng of DNA was used to construct sequencing libraries using the Ion AmpliSeq Cancer Hotspot Panel v2 or Ion AmpliSeq Colon and Lung Cancer panel v2...
December 21, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/29301828/pancreatic-juice-mutation-concentrations-can-help-predict-the-grade-of-dysplasia-in-patients-undergoing-pancreatic-surveillance
#6
Masaya Suenaga, Jun Yu, Koji Shindo, Koji Tamura, Jose Alejandro N Almario, Christopher M Zaykoski, P Dane Witmer, Shah Fesharakizadeh, Michael Borges, Anne Marie Lennon, Eun J Shin, Marcia I Canto, Michael G Goggins
Purpose: The measurement of mutations in pancreatic juice samples collected from the duodenum during endoscopic ultrasound (EUS) may improve the diagnostic evaluation of patients undergoing pancreatic surveillance. Our aim was to evaluate the accuracy of using pancreatic juice mutation concentrations to predict the presence and histologic grade of neoplasia in the pancreas.Experimental Design: Digital next-generation sequencing (NGS) of pancreatic juice DNA using a targeted 12-gene panel was performed on 67 patients undergoing pancreatic evaluation during EUS including patients with pancreatic ductal adenocarcinoma, patients who subsequently underwent pancreatic resection for precursor lesions, patients undergoing surveillance for their familial/inherited susceptibility to pancreatic cancer, and normal pancreas disease controls...
January 4, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29301485/strategies-for-identification-of-somatic-variants-using-the-ion-torrent-deep-targeted-sequencing-platform
#7
Aditya Deshpande, Wenhua Lang, Tina McDowell, Smruthy Sivakumar, Jiexin Zhang, Jing Wang, F Anthony San Lucas, Jerry Fowler, Humam Kadara, Paul Scheet
BACKGROUND: 'Next-generation' (NGS) sequencing has wide application in medical genetics, including the detection of somatic variation in cancer. The Ion Torrent-based (IONT) platform is among NGS technologies employed in clinical, research and diagnostic settings. However, identifying mutations from IONT deep sequencing with high confidence has remained a challenge. We compared various computational variant-calling methods to derive a variant identification pipeline that may improve the molecular diagnostic and research utility of IONT...
January 4, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29299683/hpv-genotypes-detected-by-linear-array-and-next-generation-sequencing-in-anal-samples-from-hiv-positive-men-who-have-sex-with-men-in-mexico
#8
Luz A González-Hernández, María G Flores-Miramontes, Adriana Aguilar-Lemarroy, Krissya S Quintanilla-Peña, Fabiola L Martin-Amaya-Barajas, Moisés Ramos-Solano, Luis F Enciso Gómez, Jaime F Andrade-Villanueva, Luis F Jave-Suárez
The incidence of anal cancer has been rising, especially in HIV+ patients and has been associated with HPV infection. HIV+ patients are more at risk of HPV coinfection and are seven times more likely to have persistent HPV infection; moreover, HIV+ men have an increased risk of developing anal cancer compared to HIV+ women. The development of screening strategies for the detection of HPV in HIV+ men is of major importance; however, there is not enough information about the HPV genotypes and variants that are colonizing the anal epithelia of HIV+ men in diverse geographical regions...
January 3, 2018: Archives of Virology
https://www.readbyqxmd.com/read/29290262/gcc2-alk-as-a-targetable-fusion-in-lung-adenocarcinoma-and-its-enduring-clinical-responses-to-alk-inhibitors
#9
Junhong Jiang, Xue Wu, Xiaoling Tong, Wangzhi Wei, Anan Chen, Xiaonan Wang, Yang W Shao, Jianan Huang
OBJECTIVES: ALK, RET and ROS1 fusions have been identified as treatable targets in 5%-15% of non-small-cell lung cancers, and thanks to the advanced sequencing technologies, their new partner genes have been steadily detected. Here we identified a rare fusion of ALK (GCC2-ALK) in a patient with advanced lung adenocarcinoma and monitored the treatment efficacy of ALK inhibitors on this patient. We further performed in vitro functional studies of this fusion protein for evaluating its oncogenic potential...
January 2018: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/29285848/implementation-of-clinical-sequencing-in-cancer-genome-medicine-in-japan
#10
REVIEW
Takashi Kohno
In oncology, actionable mutations (alterations) in cancer-associated genes are critical in terms of the selection of therapeutic approaches. Next-generation sequencing (NGS) of tumor sample DNA (i.e., clinical sequencing) can guide clinical management by providing diagnostic or prognostic data, and facilitating the identification of potential treatment regimens, such as molecular-targeted and immune checkpoint blockade therapies. In the U.S., a variety of tumor-profiling multiplex gene panels have been developed and implemented for this purpose...
December 29, 2017: Cancer Science
https://www.readbyqxmd.com/read/29285234/targeted-next-generation-sequencing-in-chinese-colorectal-cancer-patients-guided-anti-egfr-treatment-and-facilitated-precision-cancer-medicine
#11
Helei Hou, Dong Liu, Chuantao Zhang, Yanxia Jiang, Guifang Lu, Na Zhou, Xiaonan Yang, Xiaoping Zhang, Zhuokun Li, Hongmei Zhu, Zhaoyang Qian, Xiaochun Zhang
Objective: Colorectal cancer (CRC) patients with both RAS and BRAF wild-type tumors determined by non-next generation sequencing (NGS) testing may still not respond due to the presence of additional mutated genes such as PIK3CA or PTEN. In this study, a broad, hybrid capture-based NGS assay was used to identify RAS, BRAF and additional targetable genetic alterations from Chinese CRC tissues. Methods: Fifty-seven cases of CRC were enrolled, and all the patients signed the informed consent...
December 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/29285217/identification-of-novel-gene-expression-signature-in-lung-adenocarcinoma-by-using-next-generation-sequencing-data-and-bioinformatics-analysis
#12
Ya-Ling Hsu, Jen-Yu Hung, Yen-Lung Lee, Feng-Wei Chen, Kuo-Feng Chang, Wei-An Chang, Ying-Ming Tsai, Inn-Wen Chong, Po-Lin Kuo
Lung adenocarcinoma is one of the leading causes of cancer-related death worldwide. We showed transcriptomic profiles in three pairs of tumors and adjacent non-tumor lung tissues using next-generation sequencing (NGS) to screen protein-coding RNAs and microRNAs. Combined with meta-analysis from the Oncomine and Gene Expression Omnibus (GEO) databases, we identified a representative genetic expression signature in lung adenocarcinoma. There were 9 upregulated genes, and 8 downregulated genes in lung adenocarcinoma...
December 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/29285045/optimization-of-rna-extraction-from-formalin-fixed-paraffin-embedded-blocks-for-targeted-next-generation-sequencing
#13
Yoojin Choi, Aeree Kim, Jinkyoung Kim, Jinhwan Lee, Soo Yeon Lee, Chungyeul Kim
Purpose: Breast cancer has a high prevalence in Korea. To achieve personalized therapy for breast cancer, long-term follow-up specimens are needed for next-generation sequencing (NGS) and multigene analysis. Formalin-fixed paraffin-embedded (FFPE) samples are easier to store than fresh frozen (FF) samples. The objective of this study was to optimize RNA extraction from FFPE blocks for NGS. Methods: RNA quality from FF and FFPE tissues (n=5), expected RNA amount per unit area, the relationship between archiving time and quantity/quality of FFPE-extracted RNA (n=14), differences in quantitative real-time polymerase chain reaction (qRT-PCR) and NGS results, and comparisons of both techniques with tissue processing at different institutions (n=96) were determined in this study...
December 2017: Journal of Breast Cancer
https://www.readbyqxmd.com/read/29281680/characteristics-of-percutaneous-core-biopsies-adequate-for-next-generation-genomic-sequencing
#14
Sharjeel H Sabir, Savitri Krishnamurthy, Sanjay Gupta, Gordon B Mills, Wei Wei, Andrea C Cortes, Kenna R Mills Shaw, Rajyalakshmi Luthra, Michael J Wallace
PURPOSE: Determine the characteristics of percutaneous core biopsies that are adequate for a next generation sequencing (NGS) genomic panel. MATERIALS AND METHODS: All patients undergoing percutaneous core biopsies in interventional radiology (IR) with samples evaluated for a 46-gene NGS panel during 1-year were included in this retrospective study. Patient and procedure variables were collected. An imaging-based likelihood of adequacy score incorporating targeting and sampling factors was assigned to each biopsied lesion...
2017: PloS One
https://www.readbyqxmd.com/read/29280996/crnet-an-efficient-sampling-approach-to-infer-functional-regulatory-networks-by-integrating-large-scale-chip-seq-and-time-course-rna-seq-data
#15
Xi Chen, Jinghua Gu, Xiao Wang, Jin-Gyoung Jung, Tian-Li Wang, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan
Motivation: NGS techniques have been widely applied in genetic and epigenetic studies. Multiple ChIP-seq and RNA-seq profiles can now be jointly used to infer functional regulatory networks (FRNs). However, existing methods suffer from either oversimplified assumption on transcription factor (TF) regulation or slow convergence of sampling for FRN inference from large-scale ChIP-seq and time-course RNA-seq data. Results: We developed an efficient Bayesian integration method (CRNET) for FRN inference using a two-stage Gibbs sampler to estimate iteratively hidden TF activities and the posterior probabilities of binding events...
December 21, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29277949/development-and-clinical-validation-of-a-circulating-tumor-dna-test-for-the-identification-of-clinically-actionable-mutations-in-non-small-cell-lung-cancer
#16
Liping Liu, Han Liu, Di Shao, Zu Liu, Jingjing Wang, Qiuhua Deng, Hailing Tang, Haihong Yang, Yalei Zhang, Yuan Qiu, Fei Cui, Meihua Tan, Pan Zhang, Zhilong Li, Jilong Liu, Wenhua Liang, Yuying Wang, Zhiyu Peng, Jian Wang, Huanming Yang, Mao Mao, Karsten Kristiansen, Mingzhi Ye, Jianxing He
Molecular analysis of potentially actionable mutations has become routine practice in oncological pathology. However, testing a wide range of oncogenes and mutations can be technically challenging because of limitations associated with tumor biopsy. Circulating tumor DNA (ctDNA) is a potential tool for the noninvasive profiling of tumors. In this study, we developed a next-generation sequencing (NGS)-based test for the detection of clinically relevant mutations in ctDNA and evaluated the feasibility of using this ctDNA NGS-based assay as an alternative to tissue genotyping...
December 26, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29277635/a-novel-and-reliable-method-to-detect-microsatellite-instability-in-colorectal-cancer-by-next-generation-sequencing
#17
Lizhen Zhu, Yanqin Huang, Xuefeng Fang, Chenglin Liu, Wanglong Deng, Chenhan Zhong, Jinghong Xu, Dong Xu, Ying Yuan
Two types of molecular tests have been established to assess the deficiency of DNA mismatch repair (MMR) system: microsatellite instability (MSI) and immunohistochemical (IHC) analysis. We have developed a reliable method to analyze the MSI status by next-generation sequencing (NGS) based on read count distribution. A total of 91 patients with primary colorectal cancer were recruited. These patients included 54 cases with the loss of expression of any MMR protein in IHC suggesting deficient MMR (dMMR), and 37 cases of colorectal cancer with staining of all four MMR proteins in IHC, suggesting proficient MMR (pMMR) in postoperative sample...
December 19, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29277564/feasibility-of-endobronchial-ultrasound-guided-transbronchial-needle-aspiration-cytology-specimens-for-next-generation-sequencing-in-non-small-cell-lung-cancer
#18
Sean P Stoy, Jeremy P Segal, Jeffrey Mueller, Larissa V Furtado, Everett E Vokes, Jyoti D Patel, Septimiu Murgu
INTRODUCTION: Next generation sequencing (NGS) testing of lung cancer is recommended by guidelines, and endobronchial ultrasound (EBUS)-guided transbronchial needle aspiration (TBNA) often provides the only material available for testing. Previous studies have demonstrated successful NGS testing on cell block samples obtained by EBUS; however, cytology smears provide a more reliable sample with better DNA quality for testing. In this study, we aimed to determine the success rate of OncoScreen (50 gene) and OncoPlus (1213 gene) panel NGS testing of cytology samples obtained by EBUS utilizing 22- and 25-gauge needles...
December 5, 2017: Clinical Lung Cancer
https://www.readbyqxmd.com/read/29275357/evaluation-of-the-relative-effectiveness-of-the-2017-updated-manchester-scoring-system-for-predicting-brca1-2-mutations-in-a-southeast-asian-country
#19
Winston Chew, Rajesh Babu Moorakonda, Eliza Courtney, Hazel Soh, Shao Tzu Li, Yanni Chen, Tarryn Shaw, John Carson Allen, Dafydd Gareth R Evans, Joanne Ngeow
BACKGROUND: Germline mutations in the BRCA1 and BRCA2 genes have significant clinical implications for both risk-reducing and early surveillance management. The third and most recent revision of the Manchester scoring system (MSS3) used to distinguish patients indicated for germline BRCA1/2 testing included further adjustments for triple negative breast cancer, high-grade serous ovarian cancer and human epidermal growth factor 2 (HER2) receptor status. This study aims to evaluate the relative effectiveness of MSS3 in a Southeast Asian population...
December 23, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29250205/next-generation-sequencing-clinical%C3%A2-applications-in-solid-tumours
#20
REVIEW
Leonhard Müllauer
Next generation sequencing (NGS) has unravelled the genetic alterations that underlie the pathogenesis of cancer. It is now becoming integrated into routine clinical diagnostics of malignant tumours. NGS supports diagnosis, identifies therapeutic targets, reveals resistance mechanisms and facilitates disease monitoring. It takes a central function in the implementation of cancer therapies adapted to the molecular alterations of tumours.
2017: Memo
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