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whole genome sequencing AND cancer

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https://www.readbyqxmd.com/read/29050228/mutation-landscape-and-intra-tumor-heterogeneity-of-two-manecs-of-the-esophagus-revealed-by-multi-region-sequencing
#1
Wenqing Yuan, Zhen Liu, Wanjun Lei, Li Sun, Haijun Yang, Yu Wang, Shweta Ramdas, Xiao Dong, Ruiping Xu, Hong Cai, Jun Z Li, Yang Ke
Mixed adenoneuroendocrine carcinoma (MANEC) in the esophagus is an infrequent but highly malignant cancer with few known genomic alterations. We conducted whole-exome sequencing and whole-genome SNP genotyping for 4-6 tumor subregions and 5-6 adjacent normal tissue sites and 1-3 lymph node metastases in two esophageal MANECs to detect somatic mutations and copy number alterations, and to explore their spatial heterogeneity and underlying clonal structure. TP53 mutation, RB1 deletion or LOH, and PIK3CA, PTEN, KRAS, SOX2, DVL3, TP63 amplification appeared in all regions in both tumors...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29048467/identification-of-copy-number-variations-and-translocations-in-cancer-cells-from-hi-c-data
#2
Abhijit Chakraborty, Ferhat Ay
Motivation: Eukaryotic chromosomes adapt a complex and highly dynamic three-dimensional (3D) structure, which profoundly affects different cellular functions and outcomes including changes in epigenetic landscape and in gene expression. Making the scenario even more complex, cancer cells harbor chromosomal abnormalities (e.g., copy number variations (CNVs) and translocations) altering their genomes both at the sequence level and at the level of 3D organization. High-throughput chromosome conformation capture techniques (e...
October 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29045840/clonal-heterogeneity-influences-the-fate-of-new-adaptive-mutations
#3
Ignacio Vázquez-García, Francisco Salinas, Jing Li, Andrej Fischer, Benjamin Barré, Johan Hallin, Anders Bergström, Elisa Alonso-Perez, Jonas Warringer, Ville Mustonen, Gianni Liti
The joint contribution of pre-existing and de novo genetic variation to clonal adaptation is poorly understood but essential to designing successful antimicrobial or cancer therapies. To address this, we evolve genetically diverse populations of budding yeast, S. cerevisiae, consisting of diploid cells with unique haplotype combinations. We study the asexual evolution of these populations under selective inhibition with chemotherapeutic drugs by time-resolved whole-genome sequencing and phenotyping. All populations undergo clonal expansions driven by de novo mutations but remain genetically and phenotypically diverse...
October 17, 2017: Cell Reports
https://www.readbyqxmd.com/read/29045549/emerging-treatment-paradigms-in-brain-metastasis-in-non-small-cell-lung-cancer-an-overview-of-the-current-landscape-and-challenges-ahead
#4
D Ulahannan, J Khalifa, C Faivre-Finn, S M Lee
Advances in the last decade in genomic profiling and the identification of druggable targets amenable to biological agents, has transformed the management and survival of a subgroup of patients with brain metastasis in non-small cell lung cancer. In parallel, clinicians have re-evaluated the role of whole brain radiotherapy in selected patients with brain metastases to reduce neurocognitive toxicity. Continual progress in this understudied field is required: optimisation of the sequence of schedules for therapies in patients with brain metastases of differing genomic profiles, focusing on new strategies to overcome mechanisms of biological resistance and increasing drug penetrability into the central nervous system...
October 17, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29045504/molecular-tumor-boards-current-practice-and-future-needs
#5
D L van der Velden, C M L van Herpen, H W M van Laarhoven, E F Smit, H J M Groen, S M Willems, P M Nederlof, M H G Langenberg, E Cuppen, S Sleijfer, N Steeghs, E E Voest
Background: due to rapid technical advances, steeply declining sequencing costs, and the ever-increasing number of targeted therapies, it can be expected that extensive tumor sequencing such as Whole Exome- and -Genome Sequencing will soon be applied in standard care. Clinicians will thus be confronted with increasingly complex genetic information and multiple test-platforms to choose from. General medical training, meanwhile, can hardly keep up with the pace of innovation. Consequently, there is a rapidly growing gap between clinical knowledge and genetic potential in cancer care...
September 27, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29039585/identification-of-genome-variations-in-patients-with-lung-adenocarcinoma-using-whole-genome-re%C3%A2-sequencing
#6
Guiyuan Li, Yunqing Mei, Fan Yang, Shengming Yi, Lemin Wang
Lung adenocarcinoma is one of the types of non‑small cell lung carcinoma, which tends to be treated with surgical therapy rather than radiation therapy. It occurs in smokers and non‑smokers, and is the most common form of lung cancer among non‑smokers and women. Gene rearrangements, including ALK, ROS1 and RET, and gene mutations, including epidermal growth factor receptor (EGFR), HER2, Kristen rat sarcoma viral oncogene homolog, BRAF, phosphoinositide‑3‑kinase, catalytic, α polypeptide and MET, have been identified in lung adenocarcinoma, which enable targeted therapy in lung adenocarcinoma, for example erlotinib, gefitinib and afatinib, which are EGFR inhibitors...
October 17, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29036558/methrafo-medip-seq-methylation-estimate-using-a-random-forest-regressor
#7
Jun Ding, Ziv Bar-Joseph
Motivation: Profiling of genome wide DNA methylation is now routinely performed when studying development, cancer and several other biological processes. Although Whole genome Bisulfite Sequencing provides high-quality methylation measurements at the resolution of nucleotides, it is relatively costly and so several studies have used alternative methods for such profiling. One of the most widely used low cost alternatives is MeDIP-Seq. However, MeDIP-Seq is biased for CpG enriched regions and thus its results need to be corrected in order to determine accurate methylation levels...
July 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29032825/line-1-retrotransposon-mediated-dna-transductions-in-endometriosis-associated-ovarian-cancers
#8
Zhouchunyang Xia, Dawn R Cochrane, Michael S Anglesio, Yi Kan Wang, Tayyebeh Nazeran, Basile Tessier-Cloutier, Melissa K McConechy, Janine Senz, Amy Lum, Ali Bashashati, Sohrab P Shah, David G Huntsman
OBJECTIVE: Endometrioid (ENOC) and clear cell ovarian carcinoma (CCOC) share a common precursor lesion, endometriosis, hence the designation endometriosis associated ovarian cancers (EAOC). Long interspersed nuclear element 1 (LINE-1 or L1), is a family of mobile genetic elements activated in many cancers capable of moving neighboring DNA through 3' transductions. Here we investigated the involvement of specific L1-mediated transductions in EAOCs. METHODS: Through whole genome sequencing, we identified active L1-mediated transductions originating within the TTC28 gene in 34% (10/29) of ENOC and 31% (11/35) of CCOC cases...
October 9, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/29028887/identification-of-cancer-driver-genes-in-focal-genomic-aberrations-from-whole-exome-sequencing-data
#9
Ho Jang, Hyunju Lee
Summary: Whole-exome sequencing (WES) data have been used for identifying copy number aberrations in cancer cells. Nonetheless, the use of WES is still challenging for identification of focal aberrant regions in multiple samples that may contain cancer driver genes. In this study, we developed a wavelet-based method for identifying focal genomic aberrant regions in the WES data from cancer cells (WIFA-X). When we applied WIFA-X to glioblastoma multiforme and lung adenocarcinoma datasets, WIFA-X outperformed other approaches on identifying cancer driver genes...
September 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29027617/zebrafish-as-a-model-to-study-neuroblastoma-development
#10
REVIEW
Mattie J Casey, Rodney A Stewart
Neuroblastoma is a pediatric solid tumor arising from embryonic neural crest progenitor cells that normally generate the peripheral sympathetic nervous system. As such, the location of neuroblastoma tumors is correlated with the distribution of major post-ganglionic clusters throughout the sympathetic chain, with the highest incidence in the adrenal medulla or lumbar sympathetic ganglia (~65%). Neuroblastoma is an enigmatic tumor that can spontaneously regress with minimal treatment or become highly metastatic and develop resistance to aggressive treatments, including radiation and high-dose chemotherapy...
October 13, 2017: Cell and Tissue Research
https://www.readbyqxmd.com/read/29023722/prevalence-and-clonality-of-synchronous-primary-carcinomas-in-the-bladder-and-prostate
#11
Ying Jing, Ruiyun Zhang, Pengfei Ma, Mei-Chun Cai, Guanglei Zhuang, Haige Chen
Incidental prostate adenocarcinoma (IPCa) has been frequently discovered during postoperative histopathological evaluation of radical cystoprostatectomy specimens in patients with bladder cancer (BCa). However, there is currently no conclusive study addressing the clinical significance of IPCa and the clonal relatedness of IPCa and BCa. Here, we performed a retrospective single-center review of 919 BCa cases and an additional meta-analysis including a total of 19,868 individuals who underwent radical cystectomy for bladder cancer...
October 11, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28989557/allele-specific-copy-number-estimation-by-whole-exome-sequencing
#12
Hao Chen, Yuchao Jiang, Kara N Maxwell, Katherine L Nathanson, Nancy Zhang
Whole exome sequencing is currently a technology of choice in large-scale cancer genomics studies, where the priority is to identify cancer-associated variants in coding regions. We describe a method for estimating allele-specific copy number using whole exome sequencing data from tumor and matched normal.
June 2017: Annals of Applied Statistics
https://www.readbyqxmd.com/read/28981122/base-resolution-stratification-of-cancer-mutations-using-functional-variomics
#13
Song Yi, Ning-Ning Liu, Limei Hu, Hui Wang, Nidhi Sahni
A complete understanding of human cancer variants requires new methods to systematically and efficiently assess the functional effects of genomic mutations at a large scale. Here, we describe a set of tools to rapidly clone and stratify thousands of cancer mutations at base resolution. This protocol provides a massively parallel pipeline to achieve high stringency and throughput. The approach includes high-throughput generation of mutant clones by Gateway, confirmation of variant identity by barcoding and next-generation sequencing, and stratification of cancer variants by multiplexed interaction profiling...
November 2017: Nature Protocols
https://www.readbyqxmd.com/read/28979141/genome-scale-analysis-to-identify-prognostic-markers-in-patients-with-early-stage-pancreatic-ductal-adenocarcinoma-after-pancreaticoduodenectomy
#14
Xiwen Liao, Ketuan Huang, Rui Huang, Xiaoguang Liu, Chuangye Han, Long Yu, Tingdong Yu, Chengkun Yang, Xiangkun Wang, Tao Peng
BACKGROUND: Molecular analysis is a promising source of clinically useful prognostic biomarkers. The aim of this investigation was to identify prognostic biomarkers for patients with early-stage pancreatic ductal adenocarcinoma (PDAC) after pancreaticoduodenectomy. METHODS: An RNA sequencing dataset of PDAC was obtained from The Cancer Genome Atlas. Survival analysis and weighted gene co-expression network analysis were used to investigate the prognostic markers of early-stage PDAC after pancreaticoduodenectomy...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28978832/clinical-sequencing-in-leukemia-with-the-assistance-of-artificial-intelligence
#15
Arinobu Tojo
Next generation sequencing (NGS) of cancer genomes is now becoming a prerequisite for accurate diagnosis and proper treatment in clinical oncology. Because the genomic regions for NGS expand from a certain set of genes to the whole exome or whole genome, the resulting sequence data becomes incredibly enormous and makes it quite laborious to translate the genomic data into medicine, so-called annotation and curation. We organized a clinical sequencing team and established a bidirectional (bed-to-bench and bench-to-bed) system to integrate clinical and genomic data for hematological malignancies...
2017: [Rinshō Ketsueki] the Japanese Journal of Clinical Hematology
https://www.readbyqxmd.com/read/28978093/molecular-characterization-of-circulating-colorectal-tumor-cells-defines-genetic-signatures-for-individualized-cancer-care
#16
Say Li Kong, Xingliang Liu, Nur-Afidah Mohamed Suhaimi, Kenneth Jia Hao Koh, Min Hu, Daniel Yoke San Lee, Igor Cima, Wai Min Phyo, Esther Xing Wei Lee, Joyce A Tai, Yu Miin Foong, Jess Honganh Vo, Poh Koon Koh, Tong Zhang, Jackie Y Ying, Bing Lim, Min-Han Tan, Axel M Hillmer
Studies on circulating tumor cells (CTCs) have largely focused on platform development and CTC enumeration rather than on the genomic characterization of CTCs. To address this, we performed targeted sequencing of CTCs of colorectal cancer patients and compared the mutations with the matched primary tumors. We collected preoperative blood and matched primary tumor samples from 48 colorectal cancer patients. CTCs were isolated using a label-free microfiltration device on a silicon microsieve. Upon whole genome amplification, we performed amplicon-based targeted sequencing on a panel of 39 druggable and frequently mutated genes on both CTCs and fresh-frozen tumor samples...
September 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28977029/unforeseen-clonal-evolution-of-tumor-cell-population-in-recurrent-and-metastatic-dermatofibrosarcoma-protuberans
#17
Ensel Oh, Hae Min Jeong, Mi Jeong Kwon, Sang Yun Ha, Hyung Kyu Park, Ji-Young Song, Yu Jin Kim, Jong-Sun Choi, Eun Hee Lee, Jeeyun Lee, Yoon-La Choi, Young Kee Shin
Dermatofibrosarcoma protuberans (DFSP) is a very rare soft tissue sarcoma, generally of low-grade malignancy. DFSP is locally aggressive with a high recurrence rate, but metastasis occurs rarely. To investigate the mechanism of metastasis in DFSP, we analyzed the whole exome sequencing data of serial tumor samples obtained from a patient who had a 10-year history of recurrent and metastatic DFSP. Tracking various genomic alterations, namely somatic mutations, copy number variations, and chromosomal rearrangements, we observed a dramatic change in tumor cell population during the occurrence of metastasis in this DFSP case...
2017: PloS One
https://www.readbyqxmd.com/read/28974564/corrigendum-a-comparative-analysis-of-whole-genome-sequencing-of-esophageal-adenocarcinoma-pre-and-post-chemotherapy
#18
Ayesha Noorani, Jan Bornschein, Andy G Lynch, Maria Secrier, Achilleas Achilleos, Matthew Eldridge, Lawrence Bower, Jamie M J Weaver, Jason Crawte, Chin-Ann Ong, Nicholas Shannon, Shona MacRae, Nicola Grehan, Barbara Nutzinger, Maria O'Donovan, Richard Hardwick, Simon Tavaré, Rebecca C Fitzgerald
No abstract text is available yet for this article.
October 2017: Genome Research
https://www.readbyqxmd.com/read/28974240/association-of-a-novel-point-mutation-in-msh2-gene-with-familial-multiple-primary-cancers
#19
Hai Hu, Hong Li, Feng Jiao, Ting Han, Meng Zhuo, Jiujie Cui, Yixue Li, Liwei Wang
BACKGROUND: Multiple primary cancers (MPC) have been identified as two or more cancers without any subordinate relationship that occur either simultaneously or metachronously in the same or different organs of an individual. Lynch syndrome is an autosomal dominant genetic disorder that increases the risk of many types of cancers. Lynch syndrome patients who suffer more than two cancers can also be considered as MPC; patients of this kind provide unique resources to learn how genetic mutation causes MPC in different tissues...
October 3, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28972961/clinical-significance-of-braf-non-v600e-mutations-on-the-therapeutic-effects-of-anti-egfr-monoclonal-antibody-treatment-in-patients-with-pretreated-metastatic-colorectal-cancer-the-biomarker-research-for-anti-egfr-monoclonal-antibodies-by-comprehensive-cancer
#20
Eiji Shinozaki, Takayuki Yoshino, Kentaro Yamazaki, Kei Muro, Kensei Yamaguchi, Tomohiro Nishina, Satoshi Yuki, Kohei Shitara, Hideaki Bando, Sachiyo Mimaki, Chikako Nakai, Koutatsu Matsushima, Yutaka Suzuki, Kiwamu Akagi, Takeharu Yamanaka, Shogo Nomura, Satoshi Fujii, Hiroyasu Esumi, Masaya Sugiyama, Nao Nishida, Masashi Mizokami, Yasuhiro Koh, Yukiko Abe, Atsushi Ohtsu, Katsuya Tsuchihara
BACKGROUND: Patients with BRAF(V600E)-mutated metastatic colorectal cancer (mCRC) have a poorer prognosis as well as resistance to anti-EGFR antibodies. However, it is unclear whether BRAF mutations other than BRAF(V600E) (BRAF(non-V600E) mutations) contribute to anti-EGFR antibody resistance. METHODS: This study was composed of exploratory and inference cohorts. Candidate biomarkers identified by whole exome sequencing from super-responders and nonresponders in the exploratory cohort were validated by targeted resequencing for patients who received anti-EGFR antibody in the inference cohort...
October 3, 2017: British Journal of Cancer
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