keyword
MENU ▼
Read by QxMD icon Read
search

whole genome sequence cancer

keyword
https://www.readbyqxmd.com/read/29330370/a-rna-sequencing-approach-for-the-identification-of-novel-long-non-coding-rna-biomarkers-in-colorectal-cancer
#1
Atsushi Yamada, Pingjian Yu, Wei Lin, Yoshinaga Okugawa, C Richard Boland, Ajay Goel
Long non-coding RNAs (lncRNAs) have been implicated in human pathology, however, their role in colorectal carcinogenesis have not been fully elucidated. In the current study, whole-transcriptome analysis was performed in 3 pairs of colorectal cancer (CRC) and matched normal mucosa (NM) by RNA sequencing (RNA-seq). Followed by confirmation using the Cancer Genome Atlas (TCGA) dataset, we identified 27 up-regulated and 22 down-regulated lncRNAs in CRC. Up-regulation of four lncRNAs, hereby named colorectal cancer associated lncRNA (CRCAL)-1 [AC021218...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29328368/identification-of-significant-biomarkers-and-pathways-associated-with-gastric-carcinogenesis-by-whole-genome-wide-expression-profiling-analysis
#2
Hong-Jun Fei, Song-Chang Chen, Jun-Yu Zhang, Shu-Yuan Li, Lan-Lan Zhang, Yi-Yao Chen, Chun-Xin Chang, Chen-Ming Xu
The incidence of gastric cancer (GC) is extremely high in East Asia. GC is also one of the most common and lethal forms of cancer from a global perspective. However, to date, we have not been able to determine one or several genes as biomarkers in the diagnosis of GC and have also been unable to identify the genes which are important in the therapy of GC. In this study, we analyzed all genome-wide expression profiling arrays uploaded onto the Gene Expression Omnibus (GEO) database to filtrate the differentially expressed genes (DEGs) between normal stomach tissues and GC tissues...
January 11, 2018: International Journal of Oncology
https://www.readbyqxmd.com/read/29327728/diverse-modes-of-clonal-evolution-in-hbv-related-hepatocellular-carcinoma-revealed-by-single-cell-genome-sequencing
#3
Meng Duan, Junfeng Hao, Sijia Cui, Daniel L Worthley, Shu Zhang, Zhichao Wang, Jieyi Shi, Longzi Liu, Xiaoying Wang, Aiwu Ke, Ya Cao, Ruibin Xi, Xiaoming Zhang, Jian Zhou, Jia Fan, Chong Li, Qiang Gao
Hepatocellular carcinoma (HCC) is a cancer of substantial morphologic, genetic and phenotypic diversity. Yet we do not understand the relationship between intratumor heterogeneity and the associated morphologic/histological characteristics of the tumor. Using single-cell whole-genome sequencing to profile 96 tumor cells (30-36 each) and 15 normal liver cells (5 each), collected from three male patients with HBV-associated HCC, we confirmed that copy number variations occur early in hepatocarcinogenesis but thereafter remain relatively stable throughout tumor progression...
January 12, 2018: Cell Research
https://www.readbyqxmd.com/read/29325523/fanconi-anemia-with-sun-sensitivity-caused-by-a-xeroderma-pigmentosum-associated-missense-mutation-in-xpf
#4
Isabell Popp, Maqsood Punekar, Nick Telford, Stavros Stivaros, Kate Chandler, Meenakshi Minnis, Anna Castleton, Claire Higham, Louise Hopewell, D Gareth Evans, Anja Raams, Arjan F Theil, Stefan Meyer, Detlev Schindler
BACKGROUND: Fanconi anemia (FA) is an inherited genomic instability disorder with congenital and developmental abnormalities, bone marrow failure and predisposition to cancer early in life, and cellular sensitivity to DNA interstrand crosslinks. CASE PRESENTATION: A fifty-one-year old female patient, initially diagnosed with FA in childhood on the basis of classic features and increased chromosomal breakage, and remarkable sun-sensitivity is described. She only ever had mild haematological abnormalities and no history of malignancy...
January 11, 2018: BMC Medical Genetics
https://www.readbyqxmd.com/read/29325031/use-of-deep-whole-genome-sequencing-data-to-identify-structure-risk-variants-in-breast-cancer-susceptibility-genes
#5
Xingyi Guo, Jiajun Shi, Qiuyin Cai, Xiao-Ou Shu, Jing He, Wanqing Wen, Jamie Allen, Paul Pharoah, Alison Dunning, David J Hunter, Peter Kraft, Douglas F Easton, Wei Zheng, Jirong Long
Functional disruptions of susceptibility genes by large genomic structure variant (SV) deletions in germlines are known to be associated with cancer risk. However, few studies have been conducted to systematically search for SV deletions in breast cancer susceptibility genes. We analyzed deep (> 30x) whole genome sequencing (WGS) data generated in blood samples from 128 breast cancer patients of Asian and European descent with either a strong family history of breast cancer or early cancer onset disease...
January 8, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29323871/microfluidic-device-for-aptamer-based-cancer-cell-capture-and-genetic-mutation-detection
#6
Sarah Jessica Reinholt, Harold G Craighead
We present a microfluidic device for specifically capturing cancer cells and isolating their genomic DNA (gDNA) for specific amplification and sequence analysis. To capture cancer cells within the device, nucleic acid aptamers that specifically bind to cancer cells were immobilized within a channel containing micropillars designed to increase capture efficiency. The cap-tured cells were lysed in situ and their gDNA was isolated by physical entanglement within a second smaller-dimensioned micropillar array. This type of isolation allowed the gDNA to be retained and purified within the channel, and enables ampli-fication and analysis to be performed on the gDNA without the loss of the original template...
January 11, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29321190/genomic-landscape-of-pancreatic-neuroendocrine-tumours-the-international-cancer-genome-consortium
#7
Andrea Mafficini, Aldo Scarpa
Neuroendocrine tumours (NETs) may arise throughout the body and are a highly heterogeneous, relatively rare class of neoplasms difficult to study also for the lack of disease models. Despite this, knowledge on their molecular alterations has expanded in the latest years, also building from genetic syndromes causing their onset. Pancreatic NETs (PanNETs) have been among the most studied, and research so far has outlined a series of recurring features, as inactivation of MEN1, VHL, TSC1/2 genes, and hyperactivation of the PI3K/mTOR pathway...
January 10, 2018: Journal of Endocrinology
https://www.readbyqxmd.com/read/29320538/germline-and-somatic-variant-identification-using-bgiseq-500-and-hiseq-x-ten-whole-genome-sequencing
#8
Ann-Marie Patch, Katia Nones, Stephen H Kazakoff, Felicity Newell, Scott Wood, Conrad Leonard, Oliver Holmes, Qinying Xu, Venkateswar Addala, Jenette Creaney, Bruce W Robinson, Shujin Fu, Chunyu Geng, Tong Li, Wenwei Zhang, Xinming Liang, Junhua Rao, Jiahao Wang, Mingyu Tian, Yonggang Zhao, Fei Teng, Honglan Gou, Bicheng Yang, Hui Jiang, Feng Mu, John V Pearson, Nicola Waddell
Technological innovation and increased affordability have contributed to the widespread adoption of genome sequencing technologies in biomedical research. In particular large cancer research consortia have embraced next generation sequencing, and have used the technology to define the somatic mutation landscape of multiple cancer types. These studies have primarily utilised the Illumina HiSeq platforms. In this study we performed whole genome sequencing of three malignant pleural mesothelioma and matched normal samples using a new platform, the BGISEQ-500, and compared the results obtained with Illumina HiSeq X Ten...
2018: PloS One
https://www.readbyqxmd.com/read/29305224/snpitty-an-intuitive-web-application-for-interactive-b-allele-frequency-and-copy-number-visualization-of-next-generation-sequencing-data
#9
Job van Riet, Niels M G Krol, Peggy N Atmodimedjo, Erwin Brosens, Wilfred F J van IJcken, Maurice P H M Jansen, John W M Martens, Leendert H Looijenga, Guido Jenster, Hendrikus J Dubbink, Winand N M Dinjens, Harmen J G van de Werken
Exploration and visualization of next-generation sequencing data is crucial for clinical diagnostics. Software allowing simultaneous visualization of multiple regions-of-interest coupled with dynamic heuristic filtering of genetic aberrations is however lacking. Therefore, we developed the web-application SNPitty that allows interactive visualization and interrogation of variant call format (VCF) files by utilizing B-allele frequencies of single nucleotide polymorphisms and single nucleotide variants, coverage metrics and copy-numbers analysis results...
January 2, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29304755/computational-approach-to-discriminate-human-and-mouse-sequences-in-patient-derived-tumour-xenografts
#10
Maurizio Callari, Ankita Sati Batra, Rajbir Nath Batra, Stephen-John Sammut, Wendy Greenwood, Harry Clifford, Colin Hercus, Suet-Feung Chin, Alejandra Bruna, Oscar M Rueda, Carlos Caldas
BACKGROUND: Patient-Derived Tumour Xenografts (PDTXs) have emerged as the pre-clinical models that best represent clinical tumour diversity and intra-tumour heterogeneity. The molecular characterization of PDTXs using High-Throughput Sequencing (HTS) is essential; however, the presence of mouse stroma is challenging for HTS data analysis. Indeed, the high homology between the two genomes results in a proportion of mouse reads being mapped as human. RESULTS: In this study we generated Whole Exome Sequencing (WES), Reduced Representation Bisulfite Sequencing (RRBS) and RNA sequencing (RNA-seq) data from samples with known mixtures of mouse and human DNA or RNA and from a cohort of human breast cancers and their derived PDTXs...
January 5, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29301485/strategies-for-identification-of-somatic-variants-using-the-ion-torrent-deep-targeted-sequencing-platform
#11
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/29297493/the-genomics-of-prostate-cancer-emerging-understanding-with-technologic-advances
#12
Mark A Rubin, Francesca Demichelis
With the advent of next-generation sequencing technologies and large whole-exome and genome studies in prostate and other cancers, our understanding of the landscape of genomic alterations has dramatically been refined. In additional to well-known alterations in genomic regions involving 8p, 8q, 10q23, common ETS translocations and androgen receptor amplifications, newer technology have uncovered recurrent mutations in SPOP, FOXA1, MED12, IDH and complex large scale genomic alterations (eg, chromoplexy). This review surveys the enhanced landscape of genomic alterations in clinically localized and advanced prostate cancer...
January 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/29288237/genomics-driven-precision-medicine-for-advanced-pancreatic-cancer-early-results-from-the-compass-trial
#13
Kyaw Lwin Aung, Sandra E Fischer, Robert E Denroche, Gun-Ho Jang, Anna Dodd, Sean Creighton, Bernadette Southwood, Sheng-Ben Liang, Dianne Chadwick, Amy Zhang, Grainne M O'Kane, Hamzeh Adel Amin Albaba, Shari Moura, Robert C Grant, Jessica K Miller, Faridah Mbabaali, Danielle Pasternack, Ilinca M Lungu, John M S Bartlett, Sangeet Ghai, Mathieu Lemire, Spring Holter, Ashton A Connor, Richard A Moffitt, Jen Jen Yeh, Lee Timms, Paul M Krzyzanowski, Neesha C Dhani, David W Hedley, Faiyaz Notta, Julie M Wilson, Malcolm J Moore, Steven Gallinger, Jennifer J Knox
PURPOSE: To perform real time whole genome sequencing (WGS) and RNA sequencing (RNASeq) of advanced pancreatic ductal adenocarcinoma (PDAC) to identify predictive mutational and transcriptional features for better treatment selection.  Experimental Design: Patients with advanced PDAC were prospectively recruited prior to first-line combination chemotherapy. Fresh tumor tissue was acquired by image guided percutaneous core biopsy for WGS and RNASeq. Laser capture microdissection was performed for all cases...
December 29, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29286146/immune-response-associated-gene-profiling-in-japanese-melanoma-patients-using-multi-omics-analysis
#14
Yasuto Akiyama, Yoshio Kiyohara, Shusuke Yoshikawa, Masaki Otsuka, Ryota Kondou, Chizu Nonomura, Haruo Miyata, Akira Iizuka, Tadashi Ashizawa, Keiichi Ohshima, Kenichi Urakami, Takeshi Nagashima, Masatoshi Kusuhara, Takashi Sugino, Ken Yamaguchi
Project High-tech Omics-based Patient Evaluation (HOPE), including comprehensive whole-exome sequencing (WES) and gene expression profiling (GEP) using freshly resected tumor specimens, has been in progress since its implementation in 2014. Among a total of 1,685 cancer patients, 13 melanoma patients were registered in the HOPE Project and were characterized using multi-omics analyses. Among the 13 melanoma patients, 4 were deceased, and 9 were alive. The mean overall survival (OS) and relapse‑free survival (RFS) times of the melanoma patients were 16...
December 21, 2017: Oncology Reports
https://www.readbyqxmd.com/read/29282716/targeting-dna-repair-the-genome-as-a-potential-biomarker
#15
REVIEW
Ksenija Nesic, Matthew Wakefield, Olga Kondrashova, Clare L Scott, Iain A McNeish
Genomic instability and mutations are fundamental aspects of human malignancies, leading to progressive accumulation of the hallmarks of cancer. For some time, it has been clear that key mutations may be used both as prognostic and predictive biomarkers, the best-known examples being the presence of germline BRCA1 or BRCA2 mutations, which are not only associated with improved prognosis in ovarian cancer, but are also predictive of response to poly(ADP-ribose) polymerase (PARP) inhibitors. Although biomarkers as specific and powerful as these are rare in human malignancies, next generation sequencing and improved bioinformatic analyses are revealing mutational signatures, broader patterns of alterations in the cancer genome that have the power to reveal information about underlying driver mutational processes...
December 27, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/29279706/metachronous-and-synchronous-occurrence-of-5-primary-malignancies-in-a-female-patient-between-1997-and-2013-a-case-report-with-germline-and-somatic-genetic-analysis
#16
Jenny Nyqvist, Fredrik Persson, Toshima Z Parris, Khalil Helou, Elisabeth Kenne Sarenmalm, Zakaria Einbeigi, Åke Borg, Per Karlsson, Anikó Kovács
The number of patients with multiple primary malignancies has been increasing steadily in recent years. In the present study, we describe a unique case of an 81-year-old woman with 5 metachronous and synchronous primary malignant neoplasms. The patient was first diagnosed with an endometrium adenocarcinoma in 1997 and a colon adenocarcinoma in 2002. Eleven years after her colon surgery, in 2013, the patient presented with 3 other primary malignancies within a 4-month time span: an invasive malignant melanoma on the lower leg, an invasive mucinous breast carcinoma in the right breast, and a pleomorphic spindle cell sarcoma on the left upper arm...
September 2017: Case Reports in Oncology
https://www.readbyqxmd.com/read/29259192/whole-exome-sequencing-identified-sixty-five-coding-mutations-in-four-neuroblastoma-tumors
#17
Aubrey L Miller, Patrick L Garcia, Joseph G Pressey, Elizabeth A Beierle, David R Kelly, David K Crossman, Leona N Council, Richard Daniel, Raymond G Watts, Stuart L Cramer, Karina J Yoon
Neuroblastoma is a pediatric tumor characterized by histologic heterogeneity, and accounts for ~15% of childhood deaths from cancer. The five-year survival for patients with high-risk stage 4 disease has not improved in two decades. We used whole exome sequencing (WES) to identify mutations present in three independent high-risk stage 4 neuroblastoma tumors (COA/UAB-3, COA/UAB -6 and COA/UAB -8) and a stage 3 tumor (COA/UAB-14). Among the four tumors WES analysis identified forty-three mutations that had not been reported previously, one of which was present in two of the four tumors...
December 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29259186/mutational-patterns-in-chemotherapy-resistant-muscle-invasive-bladder-cancer
#18
David Liu, Philip Abbosh, Daniel Keliher, Brendan Reardon, Diana Miao, Kent Mouw, Amaro Weiner-Taylor, Stephanie Wankowicz, Garam Han, Min Yuen Teo, Catharine Cipolla, Jaegil Kim, Gopa Iyer, Hikmat Al-Ahmadie, Essel Dulaimi, David Y T Chen, R Katherine Alpaugh, Jean Hoffman-Censits, Levi A Garraway, Gad Getz, Scott L Carter, Joaquim Bellmunt, Elizabeth R Plimack, Jonathan E Rosenberg, Eliezer M Van Allen
Despite continued widespread use, the genomic effects of cisplatin-based chemotherapy and implications for subsequent treatment are incompletely characterized. Here, we analyze whole exome sequencing of matched pre- and post-neoadjuvant cisplatin-based chemotherapy primary bladder tumor samples from 30 muscle-invasive bladder cancer patients. We observe no overall increase in tumor mutational burden post-chemotherapy, though a significant proportion of subclonal mutations are unique to the matched pre- or post-treatment tumor, suggesting chemotherapy-induced and/or spatial heterogeneity...
December 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/29247978/advances-in-chromosomal-translocations-and-fusion-genes-in-sarcomas-and-potential-therapeutic-applications
#19
REVIEW
Xin Xiao, Cassandra C Garbutt, Francis Hornicek, Zheng Guo, Zhenfeng Duan
Chromosomal translocations and fusion genes are very common in human cancer especially in subtypes of sarcomas, such as rhabdomyosarcoma, Ewing's sarcoma, synovial sarcoma and liposarcoma. The discovery of novel chromosomal translocations and fusion genes in different tumors are due to the advancement of next-generation sequencing (NGS) technologies such as whole genome sequencing. Recently, many novel chromosomal translocations and gene fusions have been identified in different types of sarcoma through NGS approaches...
December 6, 2017: Cancer Treatment Reviews
https://www.readbyqxmd.com/read/29246904/homologous-recombination-deficiency-and-platinum-based-therapy-outcomes-in-advanced-breast-cancer
#20
Eric Y Zhao, Yaoqing Shen, Erin Pleasance, Katayoon Kasaian, Sreeja Leelakumari, Martin Jones, Pinaki Bose, Carolyn Ch'ng, Caralyn Reisle, Peter Eirew, Richard Corbett, Karen L Mungall, Nina Thiessen, Yussanne Ma, Jacqueline E Schein, Andrew J Mungall, Yongjun Zhao, Richard A Moore, Wendie Den Brok, Sheridan Wilson, Diego Villa, Tamara Shenkier, Caroline Lohrisch, Stephen Chia, Stephen Yip, Karen Gelmon, Howard Lim, Daniel Renouf, Sophie Sun, Kasmintan A Schrader, Sean Young, Ian Bosdet, Aly Karsan, Janessa Laskin, Marco A Marra, Steven J M Jones
Purpose: Recent studies have identified mutation signatures of homologous recombination deficiency (HRD) in over 20% of breast cancers, as well as pancreatic, ovarian, and gastric cancers. There is an urgent need to understand the clinical implications of HRD signatures. Whereas BRCA1/2 mutations confer sensitivity to platinum-based chemotherapies, it is not yet clear whether mutation signatures can independently predict platinum response.Experimental Design: In this observational study, we sequenced tumor whole genomes (100× depth) and matched normals (60×) of 93 advanced-stage breast cancers (33 platinum-treated)...
December 15, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
keyword
keyword
98001
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"