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Next generation sequencing AND cancer

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https://www.readbyqxmd.com/read/27935861/microrna-203-predicts-human-survival-after-resection-of-colorectal-liver-metastasis
#1
T Peter Kingham, Hoang C B Nguyen, Jian Zheng, Ioannis T Konstantinidis, Eran Sadot, Jinru Shia, Deborah Kuk, Steven Zhang, Leonard Saltz, Michael I D'Angelica, William R Jarnagin, Hani Goodarzi, Sohail F Tavazoie
BACKGROUND: Resection of colorectal liver metastasis (CRLM) can be curative. Predicting which patients may benefit from resection, however, remains challenging. Some microRNAs (miRNAs) become deregulated in cancers and contribute to cancer progression. We hypothesized that miRNA expression can serve as a prognostic marker of survival after CRLM resection. RESULTS: MiR-203 was significantly overexpressed in tumors of short-term survivors compared to long-term survivors...
December 7, 2016: Oncotarget
https://www.readbyqxmd.com/read/27933214/integrating-next-generation-sequencing-into-clinical-oncology-strategies-promises-and-pitfalls
#2
REVIEW
Peter Horak, Stefan Fröhling, Hanno Glimm
We live in an era of genomic medicine. The past five years brought about many significant achievements in the field of cancer genetics, driven by rapidly evolving technologies and plummeting costs of next-generation sequencing (NGS). The official completion of the Cancer Genome Project in 2014 led many to envision the clinical implementation of cancer genomic data as the next logical step in cancer therapy. Stemming from this vision, the term 'precision oncology' was coined to illustrate the novelty of this individualised approach...
2016: ESMO Open
https://www.readbyqxmd.com/read/27933111/aberrant-dna-hypermethylation-silenced-sox21-as1-gene-expression-and-its-clinical-importance-in-oral-cancer
#3
Cheng-Mei Yang, Tsung-Han Wang, Hung-Chih Chen, Sung-Chou Li, Ming-Chien Lee, Huei-Han Liou, Pei-Feng Liu, Yu-Kai Tseng, Yow-Ling Shiue, Luo-Ping Ger, Kuo-Wang Tsai
BACKGROUND: Long noncoding RNAs (lncRNAs) are more than 200 nucleotides in length and lack transcriptional ability. The biological function of lncRNAs in oral squamous cell carcinoma (OSCC) remains unclear. The aim of this study was to identify the dysfunction of lncRNA in OSCC. RESULTS: We analyzed the transcriptome profiles of human OSCC tissues and paired adjacent normal tissues from two patients through a next-generation sequencing approach. A total of 14 lncRNAs were upregulated (fold change ≥3) and 13 were downregulated (fold change ≤-3) in OSCC tissues compared with the adjacent normal tissues...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27932211/a-novel-class-of-somatic-mutations-in-blood-detected-preferentially-in-cd8-cells
#4
Miko Valori, Lilja Jansson, Anna Kiviharju, Pekka Ellonen, Hanna Rajala, Shady Adnan Awad, Satu Mustjoki, Pentti J Tienari
Somatic mutations have a central role in cancer but their role in other diseases such as autoimmune disorders is poorly understood. Earlier work has provided indirect evidence of rare somatic mutations in autoreactive T-lymphocytes in multiple sclerosis (MS) patients but such mutations have not been identified thus far. We analysed somatic mutations in blood in 16 patients with relapsing MS and 4 with other neurological autoimmune disease. To facilitate the detection of somatic mutations CD4+, CD8+, CD19+ and CD4-/CD8-/CD19- cell subpopulations were separated...
December 5, 2016: Clinical Immunology: the Official Journal of the Clinical Immunology Society
https://www.readbyqxmd.com/read/27931838/routine-use-of-gene-panel-testing-in-hereditary-breast-cancer-should-be-performed-with-caution
#5
REVIEW
Cedric van Marcke, Anne De Leener, Martine Berlière, Miikka Vikkula, Francois P Duhoux
Breast cancer is the most frequent cancer occurring in women. Ten percent of these cancers are considered hereditary. Among them, 30% are attributed to germline mutations in the tumor suppressor genes BRCA1 and BRCA2. Other genes of lower penetrance are also known, explaining together up to 40% of the hereditary risk of breast cancer. New techniques, such as next-generation sequencing, allow the simultaneous analysis of multiple genes in a cost-effective way. As a logical consequence, gene panel testing is entering clinical practice with the promise of personalized care...
December 2016: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/27926526/use-of-capture-based-next-generation-sequencing-to-detect-alk-fusion-in-plasma-cell-free-dna-of-patients-with-non-small-cell-lung-cancer
#6
Shaohua Cui, Wei Zhang, Liwen Xiong, Feng Pan, Yanjie Niu, Tianqing Chu, Huimin Wang, Yizhuo Zhao, Liyan Jiang
Capture-based next-generation sequencing (NGS) is a potentially useful diagnostic method to measure tumor tissue DNA in blood as it can identify concordant mutations between cell-free DNA (cfDNA) and primary tumor DNA in lung cancer patients. In this study, the sensitivity, specificity and accuracy of capture-based NGS for detecting ALK fusion in plasma cfDNA was assessed. 24 patients with tissue ALK-positivity and 15 who did not harbor ALK fusion were enrolled. 13 ALK-positive samples were identified by capture-based NGS among the 24 samples with tissue ALK-positivity...
December 1, 2016: Oncotarget
https://www.readbyqxmd.com/read/27923045/tumor-evolution-in-two-patients-with-basal-like-breast-cancer-a-retrospective-genomics-study-of-multiple-metastases
#7
Katherine A Hoadley, Marni B Siegel, Krishna L Kanchi, Christopher A Miller, Li Ding, Wei Zhao, Xiaping He, Joel S Parker, Michael C Wendl, Robert S Fulton, Ryan T Demeter, Richard K Wilson, Lisa A Carey, Charles M Perou, Elaine R Mardis
BACKGROUND: Metastasis is the main cause of cancer patient deaths and remains a poorly characterized process. It is still unclear when in tumor progression the ability to metastasize arises and whether this ability is inherent to the primary tumor or is acquired well after primary tumor formation. Next-generation sequencing and analytical methods to define clonal heterogeneity provide a means for identifying genetic events and the temporal relationships between these events in the primary and metastatic tumors within an individual...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27922044/from-tumour-heterogeneity-to-advances-in-precision-treatment-of-colorectal-cancer
#8
REVIEW
Cornelis J A Punt, Miriam Koopman, Louis Vermeulen
In recent years, the high heterogeneity of colorectal cancer (CRC) has become evident. Hence, biomarkers need to be developed that enable the stratification of patients with CRC into different prognostic subgroups and in relation to response to therapies, according to the distinctive tumour biology. Currently, only RAS-mutation status is used routinely as a negative predictive marker to avoid treatment with anti-EGFR agents in patients with metastatic CRC, and mismatch-repair status can guide the use of adjuvant chemotherapy in patients with early stage colon cancer...
December 6, 2016: Nature Reviews. Clinical Oncology
https://www.readbyqxmd.com/read/27920554/next-generation-sequence-detects-arap3-as-a-novel-oncogene-in-papillary-thyroid-carcinoma
#9
Qing-Xuan Wang, En-Dong Chen, Ye-Feng Cai, Yi-Li Zhou, Zhou-Ci Zheng, Ying-Hao Wang, Yi-Xiang Jin, Wen-Xu Jin, Xiao-Hua Zhang, Ou-Chen Wang
PURPOSE: Thyroid cancer is the most frequent malignancies of the endocrine system, and it has became the fastest growing type of cancer worldwide. Much still remains unknown about the molecular mechanisms of thyroid cancer. Studies have found that some certain relationship between ARAP3 and human cancer. However, the role of ARAP3 in thyroid cancer has not been well explained. This study aimed to investigate the role of ARAP3 gene in papillary thyroid carcinoma. METHODS: Whole exon sequence and whole genome sequence of primary papillary thyroid carcinoma (PTC) samples and matched adjacent normal thyroid tissue samples were performed and then bioinformatics analysis was carried out...
2016: OncoTargets and Therapy
https://www.readbyqxmd.com/read/27919910/ph-like-acute-lymphoblastic-leukemia-a-high-risk-subtype-in-adults
#10
Nitin Jain, Kathryn G Roberts, Elias Jabbour, Keyur Patel, Agda Karina Eterovic, Ken Chen, Patrick Zweidler-McKay, Xinyan Lu, Gloria Fawcett, Sa A Wang, Sergej Konoplev, Richard C Harvey, I-Ming Chen, Debbie Payne-Turner, Marcus Valentine, Deborah Thomas, Guillermo Garcia-Manero, Farhad Ravandi, Jorge Cortes, Steven Kornblau, Susan O'Brien, Sherry Pierce, Jeffrey Jorgensen, Kenna R Mills Shaw, Cheryl L Willman, Charles G Mullighan, Hagop Kantarjian, Marina Konopleva
Ph-like acute lymphoblastic leukemia (ALL) is a high-risk subtype of ALL in children. There are limited and conflicted data on the incidence and prognosis of Ph-like ALL in adults. Patients with newly-diagnosed B-ALL who received frontline chemotherapy at MD Anderson Cancer Center underwent gene expression profiling of leukemic cells to identify Ph-like ALL. Patients received hyper-CVAD (80%) or augmented-BFM (20%) regimen. Of 148 patients, 33.1% had Ph-like, 31.1% had Ph+, and 35.8% had other B-ALL subtypes (B-other)...
December 5, 2016: Blood
https://www.readbyqxmd.com/read/27918649/big-data-from-small-samples-informatics-of-next-generation-sequencing-in-cytopathology
#11
REVIEW
Sinchita Roy-Chowdhuri, Somak Roy, Sara E Monaco, Mark J Routbort, Liron Pantanowitz
The rapid adoption of next-generation sequencing (NGS) in clinical molecular laboratories has redefined the practice of cytopathology. Instead of simply being used as a diagnostic tool, cytopathology has evolved into a practice providing important genomic information that guides clinical management. The recent emphasis on maximizing limited-volume cytology samples for ancillary molecular studies, including NGS, requires cytopathologists not only to be more involved in specimen collection and processing techniques but also to be aware of downstream testing and informatics issues...
December 5, 2016: Cancer
https://www.readbyqxmd.com/read/27914478/germline-mutations-in-brca1-and-brca2-in-epithelial-ovarian-cancer-patients-in-brazil
#12
Simone Maistro, Natalia Teixeira, Giselly Encinas, Maria Lucia Hirata Katayama, Vivian Dionisio Tavares Niewiadonski, Larissa Garcia Cabral, Roberto Marques Ribeiro, Nelson Gaburo Junior, Ana Carolina Ribeiro Chaves de Gouvêa, Dirce Maria Carraro, Ester Cerdeira Sabino, Maria Del Pilar Estevez Diz, Roger Chammas, Geertruida Hendrika de Bock, Maria Aparecida Azevedo Koike Folgueira
BACKGROUND: Approximately 8-15% epithelial ovarian cancer patients are BRCA1 or BRCA2 germline mutation carriers. Brazilian inhabitants may have peculiar genetic characteristics associated with ethnic diversity, and studies focusing on the entire BRCA1/BRCA2 gene sequencing in Brazilian ovarian cancer patients are still lacking. The aim of this study was to evaluate BRCA1/2 mutations, through entire gene sequencing, in a Brazilian population of women with epithelial ovarian cancer. METHODS: In a cross sectional study performed in one reference centre for cancer treatment in São Paulo, Brazil, 100 patients diagnosed with epithelial ovarian cancer unselected for family history of breast and/or ovarian cancer were included...
December 3, 2016: BMC Cancer
https://www.readbyqxmd.com/read/27913932/almost-2-of-spanish-breast-cancer-families-are-associated-to-germline-pathogenic-mutations-in-the-atm-gene
#13
A Tavera-Tapia, L Pérez-Cabornero, J A Macías, M I Ceballos, G Roncador, M de la Hoya, A Barroso, V Felipe-Ponce, R Serrano-Blanch, C Hinojo, M D Miramar-Gallart, M Urioste, T Caldés, S Santillan-Garzón, J Benitez, A Osorio
PURPOSE: There is still a considerable percentage of hereditary breast and ovarian cancer (HBOC) cases not explained by BRCA1 and BRCA2 genes. In this report, next-generation sequencing (NGS) techniques were applied to identify novel variants and/or genes involved in HBOC susceptibility. METHODS: Using whole exome sequencing, we identified a novel germline mutation in the moderate-risk gene ATM (c.5441delT; p.Leu1814Trpfs*14) in a family negative for mutations in BRCA1/2 (BRCAX)...
December 2, 2016: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/27913044/clinical-validation-of-the-50-gene-ampliseq-cancer-panel-v2-for-use-on-a-next-generation-sequencing-platform-using-formalin-fixed-paraffin-embedded-and-fine-needle-aspiration-tumour-specimens
#14
Vivek Rathi, Gavin Wright, Diana Constantin, Siok Chang, Huong Pham, Kerryn Jones, Atha Palios, Sue-Anne Mclachlan, Matthew Conron, Penny McKelvie, Richard Williams
The advent of massively parallel sequencing has caused a paradigm shift in the ways cancer is treated, as personalised therapy becomes a reality. More and more laboratories are looking to introduce next generation sequencing (NGS) as a tool for mutational analysis, as this technology has many advantages compared to conventional platforms like Sanger sequencing. In Australia all massively parallel sequencing platforms are still considered in-house in vitro diagnostic tools by the National Association of Testing Authorities (NATA) and a comprehensive analytical validation of all assays, and not just mere verification, is a strict requirement before accreditation can be granted for clinical testing on these platforms...
November 29, 2016: Pathology
https://www.readbyqxmd.com/read/27912825/next-generation-sequencing-of-lung-cancers-lessons-learned-and-future-directions
#15
REVIEW
Siddhartha Devarakonda, Ashiq Masood, Ramaswamy Govindan
Targeted therapies and immune checkpoint inhibitors have significantly improved outcomes in a sizable fraction of patients with metastatic non-small cell lung cancer. Nevertheless, a majority of patients with lung cancer continue to have poor outcomes. The ability to comprehensively characterize the genomic alterations in various subtypes of lung cancer has the potential to transform cancer care by facilitating the identification of novel treatment strategies. The objective of this review is to summarize key findings from recent studies that have sequenced a large number of lung cancer samples and discuss the diagnostic, prognostic, and therapeutic relevance of these findings...
February 2017: Hematology/oncology Clinics of North America
https://www.readbyqxmd.com/read/27910944/thyroid-sclerosing-mucoepidermoid-carcinoma-with-eosinophilia-a-clinicopathologic-and-molecular-analysis-of-a-distinct-entity
#16
Akeesha A Shah, Kristin La Fortune, Caitlyn Miller, Stacey E Mills, Zubair Baloch, Virginia LiVolsi, Sanja Dacic, Alyssa L Mahaffey, Marina Nikiforova, Yuri E Nikiforov, Raja R Seethala
Sclerosing mucoepidermoid carcinoma with eosinophilia is a rare thyroid neoplasm of uncertain pathogenesis that resembles salivary gland mucoepidermoid carcinoma. This multi-institutional study characterizes the clinicopathologic and molecular features of this tumor by utilizing next-generation sequencing to assess common mutations and gene fusions involved in thyroid carcinogenesis as well as fluorescence in-situ hybridization for MAML2 translocations typical of salivary gland mucoepidermoid carcinoma. Nine cases (6 females and 3 males, mean age: 59 years, range 30-77 years) were identified...
December 2, 2016: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/27910721/care-delivery-considerations-for-widespread-and-equitable-implementation-of-inherited-cancer-predisposition-testing
#17
Deborah Cragun, Anita Y Kinney, Tuya Pal
DNA sequencing advances through next-generation sequencing (NGS) and several practice changing events, have led to shifting paradigms for inherited cancer predisposition testing. These changes necessitated a means by which to maximize health benefits without unnecessarily inflating healthcare costs and exacerbating health disparities. Areas covered: NGS-based tests encompass multi-gene panel tests, whole exome sequencing, and whole genome sequencing, all of which test for multiple genes simultaneously, compared to prior sequencing practices through which testing was performed sequentially for one or two genes...
December 2, 2016: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/27910067/next-generation-sequencing
#18
Matthieu Le Gallo, Fred Lozy, Daphne W Bell
Endometrial cancers are the most frequently diagnosed gynecological malignancy and were expected to be the seventh leading cause of cancer death among American women in 2015. The majority of endometrial cancers are of serous or endometrioid histology. Most human tumors, including endometrial tumors, are driven by the acquisition of pathogenic mutations in cancer genes. Thus, the identification of somatic mutations within tumor genomes is an entry point toward cancer gene discovery. However, efforts to pinpoint somatic mutations in human cancers have, until recently, relied on high-throughput sequencing of single genes or gene families using Sanger sequencing...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27910027/recurrent-cytogenetic-abnormalities-in-acute-myeloid-leukemia
#19
John J Yang, Tae Sung Park, Thomas S K Wan
The spectrum of chromosomal abnormality associated with leukemogenesis of acute myeloid leukemia (AML) is broad and heterogeneous when compared to chronic myeloid leukemia and other myeloid neoplasms. Recurrent chromosomal translocations such as t(8;21), t(15;17), and inv(16) are frequently detected, but hundreds of other uncommon chromosomal aberrations from AML also exist. This chapter discusses 22 chromosomal abnormalities that are common structural, numerical aberrations, and other important but infrequent (less than 1 %) translocations emphasized in the WHO classification...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27908594/rucaparib-in-relapsed-platinum-sensitive-high-grade-ovarian-carcinoma-ariel2-part-1-an-international-multicentre-open-label-phase-2-trial
#20
Elizabeth M Swisher, Kevin K Lin, Amit M Oza, Clare L Scott, Heidi Giordano, James Sun, Gottfried E Konecny, Robert L Coleman, Anna V Tinker, David M O'Malley, Rebecca S Kristeleit, Ling Ma, Katherine M Bell-McGuinn, James D Brenton, Janiel M Cragun, Ana Oaknin, Isabelle Ray-Coquard, Maria I Harrell, Elaina Mann, Scott H Kaufmann, Anne Floquet, Alexandra Leary, Thomas C Harding, Sandra Goble, Lara Maloney, Jeff Isaacson, Andrew R Allen, Lindsey Rolfe, Roman Yelensky, Mitch Raponi, Iain A McNeish
BACKGROUND: Poly(ADP-ribose) polymerase (PARP) inhibitors have activity in ovarian carcinomas with homologous recombination deficiency. Along with BRCA1 and BRCA2 (BRCA) mutations genomic loss of heterozygosity (LOH) might also represent homologous recombination deficiency. In ARIEL2, we assessed the ability of tumour genomic LOH, quantified with a next-generation sequencing assay, to predict response to rucaparib, an oral PARP inhibitor. METHODS: ARIEL2 is an international, multicentre, two-part, phase 2, open-label study done at 49 hospitals and cancer centres in Australia, Canada, France, Spain, the UK, and the USA...
November 28, 2016: Lancet Oncology
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