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Next generation sequencing AND cancer

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https://www.readbyqxmd.com/read/29786861/temporally-feathered-intensity-modulated-radiation-therapy-a-planning-technique-to-reduce-normal-tissue-toxicity
#1
Juan Carlos López Alfonso, Shireen Parsai, Nikhil Joshi, Andrew Godley, Chirag Shah, Shlomo A Koyfman, Jimmy J Caudell, Clifton D Fuller, Heiko Enderling, Jacob G Scott
PURPOSE: Intensity modulated radiation therapy (IMRT) has allowed optimization of three-dimensional spatial radiation dose distributions permitting target coverage while reducing normal tissue toxicity. However, radiation-induced normal tissue toxicity is a major contributor to patients' quality of life and often a dose-limiting factor in the definitive treatment of cancer with radiation therapy. We propose the next logical step in the evolution of IMRT using canonical radiobiological principles, optimizing the temporal dimension through which radiation therapy is delivered to further reduce radiation-induced toxicity by increased time for normal tissue recovery...
May 22, 2018: Medical Physics
https://www.readbyqxmd.com/read/29785153/prevalence-of-deleterious-mutations-among-patients-with-breast-cancer-referred-for-multigene-panel-testing-in-a-romanian-population
#2
Iulian Gabriel Goidescu, Gabriela Caracostea, Dan Tudor Eniu, Florin Vasile Stamatian
Aim: Multigene panel testing for Hereditary Breast and Ovarian Cancer (HBOC) using next generation sequencing is becoming more common in medical care.We report our experience regarding deleterious mutations of high and moderate-risk breast cancer genes (BRCA1/2, TP53, STK11, CDH1, PTEN, PALB2, CHEK2, ATM), as well as more recently identified cancer genes, many of which have increased risk but less well-defined penetrance. Methods: Genetic testing was performed in 130 consecutive cases with breast cancer referred to our clinic for surgical evaluation and who met the 2016 National Comprehensive Cancer Network (NCCN) criteria for genetic testing...
2018: Clujul Medical (1957)
https://www.readbyqxmd.com/read/29785135/mutation-analysis-of-brca1-2-mutations-with-special-reference-to-polymorphic-snps-in-indian-breast-cancer-patients
#3
Nidhi D Shah, Parth S Shah, Yash Y Panchal, Kalpesh H Katudia, Nikunj B Khatri, Hari Shankar P Ray, Upti R Bhatiya, Sandip C Shah, Bhavini S Shah, Mandava V Rao
Background: Germline mutations BRCA1 and BRCA2 contribute almost equally in the causation of breast cancer (BC). The type of mutations in the Indian population that cause this condition is largely unknown. Purpose: In this cohort, 79 randomized BC patients were screened for various types of BRCA1 and BRCA2 mutations including frameshift, nonsense, missense, in-frame and splice site types. Materials and methods: The purified extracted DNA of each referral patient was subjected to Sanger gene sequencing using Codon Code Analyzer and Mutation Surveyor and next-generation sequencing (NGS) methods with Ion torrent software, after appropriate care...
2018: Application of Clinical Genetics
https://www.readbyqxmd.com/read/29785006/the-era-of-immunogenomics-immunopharmacogenomics
#4
REVIEW
Makda Zewde, Kazuma Kiyotani, Jae-Hyun Park, Hua Fang, Kai Lee Yap, Poh Yin Yew, Houda Alachkar, Taigo Kato, Tu H Mai, Yuji Ikeda, Tatsuo Matsuda, Xiao Liu, Lili Ren, Boya Deng, Makiko Harada, Yusuke Nakamura
Although germline alterations and somatic mutations in disease cells have been extensively analyzed, molecular changes in immune cells associated with disease conditions have not been characterized in depth. It is clear that our immune system has a critical role in various biological and pathological conditions, such as infectious diseases, autoimmune diseases, drug-induced skin and liver toxicity, food allergy, and rejection of transplanted organs. The recent development of cancer immunotherapies, particularly drugs modulating the immune checkpoint molecules, has clearly demonstrated the importance of host immune cells in cancer treatments...
May 21, 2018: Journal of Human Genetics
https://www.readbyqxmd.com/read/29783665/identification-of-novel-somatic-tp53-mutations-in-patients-with-high-grade-serous-ovarian-cancer-hgsoc-using-next-generation-sequencing-ngs
#5
Marica Garziera, Erika Cecchin, Vincenzo Canzonieri, Roberto Sorio, Giorgio Giorda, Simona Scalone, Elena De Mattia, Rossana Roncato, Sara Gagno, Elena Poletto, Loredana Romanato, Franca Sartor, Jerry Polesel, Giuseppe Toffoli
Somatic mutations in TP53 are a hallmark of high-grade serous ovarian cancer (HGSOC), although their prognostic and predictive value as markers is not well defined. Next-generation sequencing (NGS) can identify novel mutations with high sensitivity, that may be repurposed as potential druggable anti-cancer targets and aid in therapeutic decisions. Here, a commercial NGS cancer panel comprising 26 genes, including TP53 , was used to identify new genetic markers of platinum resistance and patient prognosis in a retrospective set of patients diagnosed with epithelial ovarian cancer...
May 18, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29781987/retrospective-microrna-sequencing-complementary-dna-library-preparation-protocol-using-formalin-fixed-paraffin-embedded-rna-specimens
#6
Olivier Loudig, Christina Liu, Thomas Rohan, Iddo Z Ben-Dov
-Archived, clinically classified formalin-fixed paraffin-embedded (FFPE) tissues can provide nucleic acids for retrospective molecular studies of cancer development. By using non-invasive or pre-malignant lesions from patients who later develop invasive disease, gene expression analyses may help identify early molecular alterations that predispose to cancer risk. It has been well described that nucleic acids recovered from FFPE tissues have undergone severe physical damage and chemical modifications, which make their analysis difficult and generally requires adapted assays...
May 5, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29780747/precision-medicine-in-hormone-receptor-positive-breast-cancer
#7
REVIEW
Azadeh Nasrazadani, Roby A Thomas, Steffi Oesterreich, Adrian V Lee
In recent decades, breast cancer has become largely manageable due to successes with hormone receptor targeting. Hormone receptor-positive tumors have favorable outcomes in comparison to estrogen receptor (ESR1, ER)/progesterone receptor-negative tumors given the targetable nature of these tumors, as well as their inherently less aggressive character. Nonetheless, treatment resistance is frequently encountered due to a variety of mechanisms, including ESR1 mutations and loss of ER expression. A new era of precision medicine utilizes a range of methodologies to allow real-time analysis of individual genomic signatures in metastases and liquid biopsies with the goal of finding clinically actionable targets...
2018: Frontiers in Oncology
https://www.readbyqxmd.com/read/29780628/comprehensive-targeted-super-deep-next-generation-sequencing-enhances-differential-diagnosis-of-solitary-pulmonary-nodules
#8
Mingzhi Ye, Shiyong Li, Weizhe Huang, Chunli Wang, Liping Liu, Jun Liu, Jilong Liu, Hui Pan, Qiuhua Deng, Hailing Tang, Long Jiang, Weizhe Huang, Xi Chen, Di Shao, Zhiyu Peng, Renhua Wu, Jing Zhong, Zhe Wang, Xiaoping Zhang, Karsten Kristiansen, Jian Wang, Ye Yin, Mao Mao, Jianxing He, Wenhua Liang
Background: A non-invasive method to predict the malignancy of surgery-candidate solitary pulmonary nodules (SPN) is urgently needed. Methods: Super-depth next generation sequencing (NGS) of 35 paired tissues and plasma DNA was performed as an attempt to develop an early diagnosis approach. Results: Only ~6% of malignant nodule patients had driver mutations in the circulating tumour DNA (ctDNA) with >10,000-fold sequencing depth, and the concordance of mutation between tDNA and ctDNA was 3...
April 2018: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/29780482/an-exploration-of-nucleic-acid-liquid-biopsy-using-a-glucose-meter
#9
Yu Gu, Ting-Ting Zhang, Zhi-Feng Huang, Shan-Wen Hu, Wei Zhao, Jing-Juan Xu, Hong-Yuan Chen
The development of non-invasive techniques for the diagnosis of cancer, characterization of mutation and monitoring treatment response could greatly reduce the morbidity and mortality caused by cancer. Nevertheless, the extremely low amount of cell free nucleic acids makes liquid biopsy a very challenging task. Herein, taking advantage of the pocket size, reliable quantitative results and simple operation of the pocket-sized personal glucose meter (PGM), we report an approach of circulating microRNA-21 (miR-21) detection with high precision and low cost...
April 14, 2018: Chemical Science
https://www.readbyqxmd.com/read/29780256/the-utilization-of-next-generation-sequencing-to-detect-somatic-mutations-and-predict-clinical-prognosis-of-chinese-non-small-cell-lung-cancer-patients
#10
Liming Cao, Long Long, Min Li, Huaping Yang, Pengbo Deng, Xinru Mao, Jianxing Xiang, Bing Li, Tengfei Zhang, Chengping Hu
Purpose: The development of next-generation sequencing (NGS) has revolutionized the understanding of oncogenesis of multiple types of cancer, including non-small cell lung cancer (NSCLC). However, there has been some debate over the utility of NGS for predicting patient prognosis and determining molecular targeted therapy. Therefore, we sought to demonstrate the numerous applications of NGS in the prognostic predictions and treatment of NSCLC patients. Materials and methods: We performed NGS on either liquid or tissue tumor biopsies obtained from 53 NSCLC patients...
2018: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29778876/genome-sequence-analysis-of-a-novel-bacillus-thuringiensis-strain-blb406-active-against-aedes-aegypti-larvae-a-novel-potential-bioinsecticide
#11
Raida Zribi Zghal, Kais Ghedira, Jihen Elleuch, Marwa Kharrat, Slim Tounsi
BLB406 is a novel isolate of Bacillus thuringiensis with a larvicidal activity against Aedes aegypti larvae. It displays original plasmidic and crystal protein patterns. The present work reported molecular and bioinformatic analyses for the genome sequence of BLB406 using MiSeq Illumina next-generation sequencing technology. The reads were assembled by Velvet tool. Using RAST program and PGAAP the genome of BLB406 strain was shown to contain 6297 genes corresponding to 5924 protein coding sequences. The BLB406 genome investigation with BtToxin_scanner program shows that this strain has an original and different combination of toxins compared to the published ones: five cry genes (cry11, cry22, cry2, cry60, cry64) and two distinct vegetative insecticidal vip4 genes...
May 17, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29775621/methylation-of-nbpf1-as-a-novel-marker-for-the-detection-of-plasma-cell-free-dna-of-breast-cancer-patients
#12
REVIEW
Dandan Li, Pengchang Li, Jie Yi, Yaling Dou, Xiuzhi Guo, Yicong Yin, Danchen Wang, Chaochao Ma, Jie Wu, Ling Qiu
BACKGROUND: Recent studies revealed that tumor-specific gene methylation can be detected in the circulating cell-free DNA (cfDNA) of cancer patients; therefore, methylated cfDNA is considered a promising biomarker. Human neuroblastoma breakpoint family member 1 (NBPF1) was originally identified in a neuroblastoma (NB) patient. The present study is the first to evaluate the presence of NBPF1 gene methylation in cell-free DNA (cfDNA) in plasma of breast cancer patients. METHODS: Differentially methylated cfDNA was screened using bisulfite sequencing with a next-generation sequencer (BS-seq) among 25 breast cancer patients, 25 patients with a benign breast disease and 25 healthy female volunteers...
May 15, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29775073/diffuse-gliomas-for-nonneuropathologists-the-new-integrated-molecular-diagnostics
#13
Sunhee C Lee
Diffuse gliomas comprise the bulk of "brain cancer" in adults. The recent update to the 4th edition of the World Health Organization's classification of tumors of the central nervous system reflects an unprecedented change in the landscape of the diagnosis and management of diffuse gliomas that will affect all those involved in the management and care of patients. Of the recently discovered gene alterations, mutations in the Krebs cycle enzymes isocitrate dehydrogenases (IDHs) 1 and 2 have fundamentally changed the way the gliomas are understood and classified...
May 18, 2018: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/29774630/the-emerging-roles-of-long-non-coding-rna-in-cancer
#14
Anna Sanchez Calle, Yumi Kawamura, Yusuke Yamamoto, Fumitaka Takeshita, Takahiro Ochiya
Since comprehensive analysis of the mammalian genome has revealed that the vast majority of genomic products are transcribed in long non-coding RNAs (lncRNAs), increasing attention has been paid towards these transcripts. The applied next-generation sequencing technologies have provided accumulating evidence of dysregulated lncRNAs in cancer. The implication of this finding may be seen in many forms and at multiple levels. With impacts ranging from integrating chromatin remodeling complexes to regulating transcription and post-transcriptional processes, aberrant expression of lncRNAs may have repercussions in cell proliferation, tumor progression or metastasis...
May 17, 2018: Cancer Science
https://www.readbyqxmd.com/read/29770616/prevalence-of-germline-brca-mutations-among-women-with-carcinoma-of-the-peritoneum-or-fallopian-tube
#15
Min Chul Choi, Jin Sik Bae, Sang Geun Jung, Hyun Park, Won Duk Joo, Seung Hun Song, Chan Lee, Ji Ho Kim, Ki Chan Lee, Sunghoon Lee, Je Ho Lee
OBJECTIVE: The aim of the present study was to assess the frequency of germline mutations in patients with peritoneal carcinoma (PC) or the fallopian tube carcinoma (FTC), using a multi-gene panel. METHODS: Twenty-six patients diagnosed with either PC or FTC between January 2013 and December 2016 were recruited consecutively. Germline DNA was sequenced using a 6-gene next generation sequencing (NGS) panel following genetic counseling. Surgico-medical information was obtained from hospital records...
March 26, 2018: Journal of Gynecologic Oncology
https://www.readbyqxmd.com/read/29767721/bhd-associated-kidney-cancer-exhibits-unique-molecular-characteristics-and-a-wide-variety-of-variants-in-chromatin-remodeling-genes
#16
Hisashi Hasumi, Mitsuko Furuya, Kenji Tatsuno, Shogo Yamamoto, Masaya Baba, Yukiko Hasumi, Yasuhiro Isono, Kae Suzuki, Ryosuke Jikuya, Shinji Otake, Kentaro Muraoka, Kimito Osaka, Narihiko Hayashi, Kazuhide Makiyama, Yasuhide Miyoshi, Keiichi Kondo, Noboru Nakaigawa, Takashi Kawahara, Koji Izumi, Junichi Teranishi, Yasushi Yumura, Hiroji Uemura, Yoji Nagashima, Adam R Metwalli, Laura S Schmidt, Hiroyuki Aburatani, W Marston Linehan, Masahiro Yao
Birt-Hogg-Dubé (BHD) syndrome is a hereditary kidney cancer syndrome, which predisposes patients to develop kidney cancer, cutaneous fibrofolliculomas and pulmonary cysts. The responsible gene FLCN is a tumor suppressor for kidney cancer which plays an important role in energy homeostasis through the regulation of mitochondrial oxidative metabolism. However, the process by which FLCN-deficiency leads to renal tumorigenesis is unclear. In order to clarify molecular pathogenesis of BHD-associated kidney cancer, we conducted whole-exome sequencing analysis using next-generation sequencing technology as well as metabolite analysis using LC/MS and GC/MS...
May 14, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29765525/clinical-characteristics-of-non-small-cell-lung-cancer-harboring-mutations-in-exon-20-of-egfr-or-her2
#17
Masayuki Takeda, Kazuko Sakai, Hidetoshi Hayashi, Kaoru Tanaka, Junko Tanizaki, Takayuki Takahama, Koji Haratani, Kazuto Nishio, Kazuhiko Nakagawa
Unlike common epidermal growth factor receptor gene ( EGFR ) mutations that confer sensitivity to tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer (NSCLC), mutations in exon 20 of either EGFR or the human EGFR2 gene ( HER2 ) are associated with insensitivity to EGFR-TKIs, with treatment options for patients with such mutations being limited. Clinical characteristics, outcome of EGFR-TKI or nivolumab treatment, and the presence of coexisting mutations were reviewed for NSCLC patients with exon-20 mutations of EGFR or HER2 as detected by routine application of an amplicon-based next-generation sequencing panel...
April 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29765524/cross-platform-comparison-for-the-detection-of-ras-mutations-in-cfdna-ddpcr-biorad-detection-assay-beaming-assay-and-ngs-strategy
#18
Jessica Garcia, Julien Forestier, Eric Dusserre, Anne-Sophie Wozny, Florence Geiguer, Patrick Merle, Claire Tissot, Carole Ferraro-Peyret, Frederick S Jones, Daniel L Edelstein, Valérie Cheynet, Claire Bardel, Gaelle Vilchez, Zhenyu Xu, Pierre Paul Bringuier, Marc Barritault, Karen Brengle-Pesce, Marielle Guillet, Marion Chauvenet, Brigitte Manship, Marie Brevet, Claire Rodriguez-Lafrasse, Valérie Hervieu, Sébastien Couraud, Thomas Walter, Léa Payen
CfDNA samples from colon (mCRC) and non-small cell lung cancers (NSCLC) (CIRCAN cohort) were compared using three platforms: droplet digital PCR (ddPCR, Biorad); BEAMing/OncoBEAM™-RAS-CRC (Sysmex Inostics); next-generation sequencing (NGS, Illumina), utilizing the 56G oncology panel (Swift Biosciences). Tissue biopsy and time matched cfDNA samples were collected at diagnosis in the mCRC cohort and during 1st progression in the NSCLC cohort. Excellent matches between cfDNA/FFPE mutation profiles were observed...
April 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29765148/cancer-subtype-identification-using-somatic-mutation-data
#19
Marieke Lydia Kuijjer, Joseph Nathaniel Paulson, Peter Salzman, Wei Ding, John Quackenbush
BACKGROUND: With the onset of next-generation sequencing technologies, we have made great progress in identifying recurrent mutational drivers of cancer. As cancer tissues are now frequently screened for specific sets of mutations, a large amount of samples has become available for analysis. Classification of patients with similar mutation profiles may help identifying subgroups of patients who might benefit from specific types of treatment. However, classification based on somatic mutations is challenging due to the sparseness and heterogeneity of the data...
May 16, 2018: British Journal of Cancer
https://www.readbyqxmd.com/read/29764856/-tp53-stk11-and-egfr-mutations-predict-tumor-immune-profile-and-the-response-to-anti-pd-1-in-lung-adenocarcinoma
#20
Jerome Biton, Audrey Mansuet-Lupo, Nicolas Pécuchet, Marco Alifano, Hanane Ouakrim, Jennifer Arrondeau, Pascaline Boudou-Rouquette, Francois Goldwasser, Karen Leroy, Jeremy Goc, Marie Wislez, Claire Germain, Pierre Laurent-Puig, Marie-Caroline Dieu-Nosjean, Isabelle Cremer, Ronald Herbst, Hélène F Blons, Diane Damotte
PURPOSE: By unlocking anti-tumor immunity, antibodies targeting programmed cell death 1 (PD-1) exhibit impressive clinical results in non-small cell lung cancer, underlining the strong interactions between tumor and immune cells. However, factors that can robustly predict long-lasting responses are still needed. EXPERIMENTAL DESIGN: We performed in depth immune profiling of lung adenocarcinoma using an integrative analysis based on immunohistochemistry, flow-cytometry and transcriptomic data...
May 15, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
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