keyword
MENU ▼
Read by QxMD icon Read
search

next generate sequencing AND cancer

keyword
https://www.readbyqxmd.com/read/28211564/the-genomics-of-inherited-bone-marrow-failure-from-mechanism-to-the-clinic
#1
REVIEW
Talia Wegman-Ostrosky, Sharon A Savage
The inherited bone marrow failure syndromes (IBMFS) typically present with significant cytopenias in at least one haematopoietic cell lineage that may progress to pancytopenia, and are associated with increased risk of cancer. Although the clinical features of the IBMFS are often diagnostic, variable disease penetrance and expressivity may result in diagnostic dilemmas. The discovery of the genetic aetiology of the IBMFS has been greatly facilitated by next-generation sequencing methods. This has advanced understanding of the underlying biology of the IBMFS and been essential in improving clinical management and genetic counselling for affected patients...
February 17, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/28211093/gsskat-rapid-gene-set-analysis-and-multiple-testing-correction-for-rare-variant-association-studies-using-weighted-linear-kernels
#2
Nicholas B Larson, Shannon McDonnell, Lisa Cannon Albright, Craig Teerlink, Janet Stanford, Elaine A Ostrander, William B Isaacs, Jianfeng Xu, Kathleen A Cooney, Ethan Lange, Johanna Schleutker, John D Carpten, Isaac Powell, Joan E Bailey-Wilson, Olivier Cussenot, Geraldine Cancel-Tassin, Graham G Giles, Robert J MacInnis, Christiane Maier, Alice S Whittemore, Chih-Lin Hsieh, Fredrik Wiklund, William J Catolona, William Foulkes, Diptasri Mandal, Rosalind Eeles, Zsofia Kote-Jarai, Michael J Ackerman, Timothy M Olson, Christopher J Klein, Stephen N Thibodeau, Daniel J Schaid
Next-generation sequencing technologies have afforded unprecedented characterization of low-frequency and rare genetic variation. Due to low power for single-variant testing, aggregative methods are commonly used to combine observed rare variation within a single gene. Causal variation may also aggregate across multiple genes within relevant biomolecular pathways. Kernel-machine regression and adaptive testing methods for aggregative rare-variant association testing have been demonstrated to be powerful approaches for pathway-level analysis, although these methods tend to be computationally intensive at high-variant dimensionality and require access to complete data...
February 16, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28208267/highly-selective-capture-surfaces-on-medical-wires-for-fishing-tumor-cells-in-whole-blood
#3
Frank D Scherag, Robert Niestroj-Pahl, Solveigh Krusekopf, Klaus Lücke, Thomas Brandstetter, Jürgen Rühe
The detection of circulating tumor cells (CTCs) in the blood of cancer patients is a challenging task. CTCs are, especially at the early stages of cancer development, extremely rare cells hidden in a vast background of regular blood cells. We describe a new strategy for the isolation of CTCs from whole blood. The key component is a medical wire coated with a multilayer assembly that allows highly specific capture of EpCAM (epithelial cell adhesion molecule) positive CTCs from blood. The assembly is generated in a layer-by-layer fashion through photochemically induced C,H insertion reactions and consists of a protective layer, which shields the contacting solution from the metal, a protein resistant layer, which prevents nonspecific interactions with proteins and a layer containing the EpCAM antibodies...
February 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28202655/constraints-in-cancer-evolution
#4
REVIEW
Subramanian Venkatesan, Nicolai J Birkbak, Charles Swanton
Next-generation deep genome sequencing has only recently allowed us to quantitatively dissect the extent of heterogeneity within a tumour, resolving patterns of cancer evolution. Intratumour heterogeneity and natural selection contribute to resistance to anticancer therapies in the advanced setting. Recent evidence has also revealed that cancer evolution might be constrained. In this review, we discuss the origins of intratumour heterogeneity and subsequently focus on constraints imposed upon cancer evolution...
February 8, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28202063/next-generation-sequencing-in-familial-breast-cancer-patients-from-lebanon
#5
Nadine Jalkh, Eliane Chouery, Zahraa Haidar, Christina Khater, David Atallah, Hamad Ali, Makia J Marafie, Mohamed R Al-Mulla, Fahd Al-Mulla, Andre Megarbane
BACKGROUND: Familial breast cancer (BC) represents 5 to 10% of all BC cases. Mutations in two high susceptibility BRCA1 and BRCA2 genes explain 16-40% of familial BC, while other high, moderate and low susceptibility genes explain up to 20% more of BC families. The Lebanese reported prevalence of BRCA1 and BRCA2 deleterious mutations (5.6% and 12.5%) were lower than those reported in the literature. METHODS: In the presented study, 45 Lebanese patients with a reported family history of BC were tested using Whole Exome Sequencing (WES) technique followed by Sanger sequencing validation...
February 15, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28199989/presence-of-cancer-associated-mutations-in-exhaled-breath-condensates-of-healthy-individuals-by-next-generation-sequencing
#6
Omar Youssef, Aija Knuuttila, Päivi Piirilä, Tom Böhling, Virinder Sarhadi, Sakari Knuutila
Exhaled breath condensate (EBC) is a non-invasive source that can be used for studying different genetic alterations occurring in lung tissue. However, the low yield of DNA available from EBC has hampered the more detailed mutation analysis by conventional methods. We applied the more sensitive amplicon-based next generation sequencing (NGS) to identify cancer related mutations in DNA isolated from EBC. In order to apply any method for the purpose of mutation screening in cancer patients, it is important to clarify the incidence of these mutations in healthy individuals...
February 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28198463/overexpression-of-fam83h-as1-indicates-poor-patient-survival-and-knockdown-impairs-cell-proliferation-and-invasion-via-met-egfr-signaling-in-lung-cancer
#7
Jie Zhang, Shumei Feng, Wenmei Su, Shengbin Bai, Lei Xiao, Lihui Wang, Dafydd G Thomas, Jules Lin, Rishindra M Reddy, Philip W Carrott, William R Lynch, Andrew C Chang, David G Beer, You-Min Guo, Guoan Chen
Whole transcriptome analyses of next generation RNA sequencing (RNA-Seq) data from human cancer samples reveled thousands of uncharacterized non-coding RNAs including long non-coding RNA (lncRNA). Recent studies indicated that lncRNAs are emerging as crucial regulators in cancer processes and potentially useful as biomarkers for cancer diagnosis and prognosis. To delineate dysregulated lncRNAs in lung cancer, we analyzed RNA-Seq data from 461 lung adenocarcinomas (LUAD) and 156 normal lung tissues. FAM83H-AS1, one of the top dysregulated lncRNAs, was found to be overexpressed in tumors relative to normal lung and significantly associated with worse patient survival in LUAD...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28196522/xpo1-in-b-cell-hematological-malignancies-from-recurrent-somatic-mutations-to-targeted-therapy
#8
REVIEW
Vincent Camus, Hadjer Miloudi, Antoine Taly, Brigitte Sola, Fabrice Jardin
Many recent publications highlight the large role of the pivotal eukaryotic nuclear export protein exportin-1 (XPO1) in the oncogenesis of several malignancies, and there is emerging evidence that XPO1 inhibition is a key target against cancer. The clinical validation of the pharmacological inhibition of XPO1 was recently achieved with the development of the selective inhibitor of nuclear export compounds, displaying an interesting anti-tumor activity in patients with massive pre-treated hematological malignancies...
February 14, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28196074/clinical-applicability-and-cost-of-a-46-gene-panel-for-genomic-analysis-of-solid-tumours-retrospective-validation-and-prospective-audit-in-the-uk-national-health-service
#9
Angela Hamblin, Sarah Wordsworth, Jilles M Fermont, Suzanne Page, Kulvinder Kaur, Carme Camps, Pamela Kaisaki, Avinash Gupta, Denis Talbot, Mark Middleton, Shirley Henderson, Anthony Cutts, Dimitrios V Vavoulis, Nick Housby, Ian Tomlinson, Jenny C Taylor, Anna Schuh
BACKGROUND: Single gene tests to predict whether cancers respond to specific targeted therapies are performed increasingly often. Advances in sequencing technology, collectively referred to as next generation sequencing (NGS), mean the entire cancer genome or parts of it can now be sequenced at speed with increased depth and sensitivity. However, translation of NGS into routine cancer care has been slow. Healthcare stakeholders are unclear about the clinical utility of NGS and are concerned it could be an expensive addition to cancer diagnostics, rather than an affordable alternative to single gene testing...
February 2017: PLoS Medicine
https://www.readbyqxmd.com/read/28194813/microrna-191-acts-as-a-tumor-promoter-by-modulating-the-tet1-p53-pathway-in-intrahepatic-cholangiocarcinoma
#10
Hao Li, Zun-Qiang Zhou, Zhang-Ru Yang, Da-Nian Tong, Jiao Guan, Bao-Jie Shi, Jia Nie, Xian-Ting Ding, Bin Li, Guang-Wen Zhou, Zheng-Yun Zhang
: Current treatment of intrahepatic cholangiocarcinoma (ICC) remains ineffective because knowledge of ICC carcinogenesis is unclear. Increasing evidence suggests that microRNAs (miRNAs), including miRNA-191, play an important role in tumorigenesis, but expression and biological functions of miRNA-191 in ICC remain to be established. This study aimed to investigate the functions and underlying mechanisms of miRNA-191 in ICC. ICC miRNA profiles were generated in 5 pairs of ICC and matched to normal bile duct tissues by next-generation sequencing technology; ICC miRNA profiles were verified in 18 pairs of ICC tissues and normal bile duct tissues by quantitative reverse transcription PCR (qRT-PCR)...
February 14, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28194276/a-case-report-of-concurrent-embryonal-rhabdomyosarcoma-and-diffuse-large-b-cell-lymphoma-in-an-adult-without-identifiable-cancer-predisposition
#11
M D Mathias, M V Ortiz, H Magnan, S R Ambati, E K Slotkin, A J Chou, M F Walsh, K Offit, C Moskowitz, A Kentsis, L H Wexler
BACKGROUND: Diffuse large B-cell lymphoma (DLBCL) is the most common form of non-Hodgkin lymphoma. Rhabdomyosarcoma, the most common soft tissue sarcoma of childhood. makes up less than 1% of solid malignancies in adults with around 400 new cases each year in the United States. They have not previously been reported concurrently. CASE PRESENTATION: A 37 year old woman presented with painful enlarging leg mass. Biopsy of the mass was consistent with embryonal rhabdomyosarcoma...
2017: Biomarker Research
https://www.readbyqxmd.com/read/28193735/comprehensive-genomic-profiling-aids-in-distinguishing-metastatic-recurrence-from-second-primary-cancers
#12
Benjamin A Weinberg, Kyle Gowen, Thomas K Lee, Sai-Hong Ignatius Ou, Robert Bristow, Lauren Krill, M Isabel Almira-Suarez, Siraj M Ali, Vincent A Miller, Stephen V Liu, Samuel J Klempner
BACKGROUND: Metastatic recurrence after treatment for locoregional cancer is a major cause of morbidity and cancer-specific mortality. Distinguishing metastatic recurrence from the development of a second primary cancer has important prognostic and therapeutic value and represents a difficult clinical scenario. Advances beyond histopathological comparison are needed. We sought to interrogate the ability of comprehensive genomic profiling (CGP) to aid in distinguishing between these clinical scenarios...
February 13, 2017: Oncologist
https://www.readbyqxmd.com/read/28193548/advances-in-understanding-tumour-evolution-through-single-cell-sequencing
#13
Jack Kuipers, Katharina Jahn, Niko Beerenwinkel
The mutational heterogeneity observed within tumours poses additional challenges to the development of effective cancer treatments. A thorough understanding of a tumour's subclonal composition and its mutational history is essential to open up the design of treatments tailored to individual patients. Comparative studies on a large number of tumours permit the identification of mutational patterns which may refine forecasts of cancer progression, response to treatment and metastatic potential. The composition of tumours is shaped by evolutionary processes...
February 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28192596/integrating-next-generation-sequencing-into-pediatric-oncology-practice-an-assessment-of-physician-confidence-and-understanding-of-clinical-genomics
#14
Liza-Marie Johnson, Jessica M Valdez, Emily A Quinn, April D Sykes, Rose B McGee, Regina Nuccio, Stacy J Hines-Dowell, Justin N Baker, Chimene Kesserwan, Kim E Nichols, Belinda N Mandrell
BACKGROUND: The incorporation of genomic testing to identify targetable somatic alterations and predisposing germline mutations into the clinical setting is becoming increasingly more common. Despite its potential usefulness, to the authors' knowledge physician confidence with regard to understanding and applying genomic testing remains unclear, particularly within the realm of pediatric oncology. METHODS: Before initiating an institutional feasibility study regarding the integration of clinical genomic testing, the authors surveyed pediatric oncologists regarding their confidence around understanding of genomic testing, perceived usefulness of test results, preferences around the disclosure of germline test results, and possible risks and benefits of testing...
February 13, 2017: Cancer
https://www.readbyqxmd.com/read/28191690/mutational-profiling-of-acral-melanomas-in-korean-populations
#15
Joon Ho Shim, Hyun-Tae Shin, Jiho Park, Ji-Hye Park, Jong-Hee Lee, Jun-Mo Yang, Duk-Hwan Kim, Kee-Taek Jang, Dong-Youn Lee
The proportion of acral melanoma (AM) is much higher in Asian populations than in Caucasians populations. Although mutational profiles associated with AM have been discovered in Caucasian populations, knowledge of its genetic alterations in the Asian populations is limited. To describe the molecular nature of AM in Korean patients, we performed mutational profilinge of AM and matched normal tissues of in patients. Fifty-one formalin-fixed paraffin-embedded AM samples and 32 matched pairs of from patients' saliva DNA were analyzed by next-generation sequencing...
February 13, 2017: Experimental Dermatology
https://www.readbyqxmd.com/read/28188963/high-risk-epithelial-ovarian-cancer-patients-for-hereditary-ovarian-cancer
#16
Seksit Chirasophon, Tarinee Manchana, Chinachote Teerapakpinyo
AIM: Risk assessment to identify patients at risk for hereditary ovarian cancer is important. The objectives of this study were to evaluate the frequency of high-risk epithelial ovarian cancer (EOC) patients and the frequency of germline mutation in these patients. METHODS: A total of 335 patients with histologically confirmed non-mucinous EOC were included. High-risk patients were defined as patients who had: (i) significant family history of breast/ovarian/colorectal/endometrial cancers; (ii) synchronous breast/endometrial/colorectal cancer; or (iii) high-grade serous carcinoma...
February 11, 2017: Journal of Obstetrics and Gynaecology Research
https://www.readbyqxmd.com/read/28188229/the-human-long-interspersed-element-1-retrotransposon-an-emerging-biomarker-of-neoplasia
#17
REVIEW
Daniel Ardeljan, Martin S Taylor, David T Ting, Kathleen H Burns
BACKGROUND: A large portion of intronic and intergenic space in our genome consists of repeated sequences. One of the most prevalent is the long interspersed element-1 (LINE-1, L1) mobile DNA. LINE-1 is rightly receiving increasing interest as a cancer biomarker. CONTENT: Intact LINE-1 elements are self-propagating. They code for RNA and proteins that function to make more copies of the genomic element. Our current understanding is that this process is repressed in most normal cells, but that LINE-1 expression is a hallmark of many types of malignancy...
February 10, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28188185/response-to-pd-1-blockade-in-microsatellite-stable-metastatic-colorectal-cancer-harboring-a-pole-mutation
#18
Jun Gong, Chongkai Wang, Peter P Lee, Peiguo Chu, Marwan Fakih
Recent clinical evidence has demonstrated that microsatellite instability (MSI) or defective mismatch repair (MMR) and high tumor mutational load can predict response to the programmed cell death 1 (PD-1) receptor inhibitor pembrolizumab in metastatic colorectal cancer (mCRC). Mutations in polymerase ε (POLE), a DNA polymerase involved in DNA replication and repair, contribute to an ultramutated but microsatellite stable (MSS) phenotype in colorectal tumors that is uniquely distinct from MSI tumors. This report presents the first case in the literature describing a clinical response to pembrolizumab in an 81-year-old man with treatment-refractory mCRC characterized by an MSS phenotype and POLE mutation identified on genomic profiling by next-generation sequencing...
February 2017: Journal of the National Comprehensive Cancer Network: JNCCN
https://www.readbyqxmd.com/read/28188106/analytical-validation-of-the-next-generation-sequencing-assay-for-a-nationwide-signal-finding-clinical-trial-molecular-analysis-for-therapy-choice-clinical-trial
#19
Chih-Jian Lih, Robin D Harrington, David J Sims, Kneshay N Harper, Courtney H Bouk, Vivekananda Datta, Jonathan Yau, Rajesh R Singh, Mark J Routbort, Rajyalakshmi Luthra, Keyur P Patel, Geeta S Mantha, Savitri Krishnamurthy, Karyn Ronski, Zenta Walther, Karin E Finberg, Sandra Canosa, Hayley Robinson, Amelia Raymond, Long P Le, Lisa M McShane, Eric C Polley, Barbara A Conley, James H Doroshow, A John Iafrate, Jeffrey L Sklar, Stanley R Hamilton, P Mickey Williams
The National Cancer Institute-Molecular Analysis for Therapy Choice (NCI-MATCH) trial is a national signal-finding precision medicine study that relies on genomic assays to screen and enroll patients with relapsed or refractory cancer after standard treatments. We report the analytical validation processes for the next-generation sequencing (NGS) assay that was tailored for regulatory compliant use in the trial. The Oncomine Cancer Panel assay and the Personal Genome Machine were used in four networked laboratories accredited for the Clinical Laboratory Improvement Amendments...
February 3, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28187453/lack-of-association-between-the-pancreatitis-risk-allele-cel-hyb-and-pancreatic-cancer
#20
Koji Shindo, Jun Yu, Masaya Suenaga, Shahriar Fesharakizadeh, Koji Tamura, Jose Alejandro Navarro Almario, Aaron Brant, Michael Borges, Abdulrehman Siddiqui, Lisa Datta, Christopher L Wolfgang, Ralph H Hruban, Alison Patricia Klein, Michael Goggins
CEL-HYB is a hybrid allele that arose from a crossover between the 3' end of the Carboxyl ester lipase (CEL) gene and the nearby CEL pseudogene (CELP) and was recently identified as a risk factor for chronic pancreatitis. Since chronic pancreatitis is a risk factor for the development of pancreatic cancer, we compared the prevalence of the CEL-HYB allele in patients with pancreatic ductal adenocarcinoma to spousal controls and disease controls. The CEL-HYB allele was detected using Sanger and next generation sequencing...
February 7, 2017: Oncotarget
keyword
keyword
67064
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"