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whole genome sequencing AND cancer

M J Alvarez-Cubero, O Santiago, C Martínez-Labarga, B Martínez-García, R Marrero-Díaz, A Rubio-Roldan, A M Pérez-Gutiérrez, P Carmona-Saez, J A Lorente, L J Martinez-Gonzalez
This study is a comparison of the efficiency of three technologies used for Y chromosome capture and the next-generation sequencing (NGS) technologies applied for determining its whole sequence. Our main findings disclose that streptavidin-biotin magnetic particle-based capture methodology offers better and a deeper sequence coverage for Y chromosome capture, compared to chromosome sorting and microdissection procedures. Moreover, this methodology is less time consuming and the most selective for capturing only Y chromosomal material, in contrast with other methodologies that result in considerable background material from other, non-targeted chromosomes...
June 21, 2018: Scientific Reports
Erjie Xia, Yinghao Wang, Adheesh Bhandari, Jizhao Niu, Fan Yang, Zhihan Yao, Ouchen Wang
Thyroid cancer is the most common malignancy of the endocrine organs. In order to further understand the tumorigenesis and progression of papillary thyroid carcinoma (PTC), the present study performed whole transcriptome sequence analysis. It was found that Cbp/p300-interacting transactivators with glutamic acid [E] and aspartic acid [D]-rich C-terminal domain 1 (CITED1) was a novel potential PTC-associated gene in thyroid cancer. The expression level and clinicopathological features of CITED1 were then assessed in The Cancer Genome Atlas (TCGA) database...
July 2018: Oncology Letters
Julie F Foley, Dhiral P Phadke, Owen Hardy, Sara Hardy, Victor Miller, Anup Madan, Kellie Howard, Kimberly Kruse, Cara Lord, Sreenivasa Ramaiahgari, Gregory G Solomon, Ruchir R Shah, Arun R Pandiri, Ronald A Herbert, Robert C Sills, B Alex Merrick
BACKGROUND: The rat genome was sequenced in 2004 with the aim to improve human health altered by disease and environmental influences through gene discovery and animal model validation. Here, we report development and testing of a probe set for whole exome sequencing (WES) to detect sequence variants in exons and UTRs of the rat genome. Using an in-silico approach, we designed probes targeting the rat exome and compared captured mutations in cancer-related genes from four chemically induced rat tumor cell lines (C6, FAT7, DSL-6A/C1, NBTII) to validated cancer genes in the human database, Catalogue of Somatic Mutations in Cancer (COSMIC) as well as normal rat DNA...
June 20, 2018: BMC Genomics
Adam G Sowalsky, Huihui Ye, Manoj Bhasin, Eliezer M Van Allen, Massimo Loda, Rosina T Lis, Laleh Montaser-Kouhsari, Carla Calagua, Fen Ma, Joshua W Russo, Rachel J Schaefer, Olga S Voznesensky, Zhenwei Zhang, Glenn J Bubley, Bruce Montgomery, Elahe A Mostaghel, Peter S Nelson, Mary-Ellen Taplin, Steven P Balk
Primary prostate cancer (PCa) can have extensive microheterogeneity, but its contribution to the later emergence of metastatic castration-resistant PCa (mCRPC) remains unclear. In this study, we microdissected residual PCa foci in radical prostatectomies from 18 men treated with neoadjuvant intensive androgen deprivation therapy (leuprolide, abiraterone acetate, and prednisone) and analyzed them for resistance mechanisms. Transcriptome profiling showed reduced but persistent androgen receptor (AR) activity in residual tumors with no increase in neuroendocrine differentiation...
June 19, 2018: Cancer Research
M Diossy, L Reiniger, Z Sztupinszki, M Krzystanek, K M Timms, C Neff, C Solimeno, D Pruss, A C Eklund, E Tóth, O Kiss, O Rusz, G Cserni, T Zombori, B Székely, J Tímár, I Csabai, Z Szallasi
Background: Based on its mechanism of action, PARP inhibitor therapy is expected to benefit mainly tumor cases with homologous recombination deficiency (HRD). Therefore, identification of tumor types with increased HRD is important for the optimal use of this class of therapeutic agents. HRD levels can be estimated using various mutational signatures from next generation sequencing data and we used this approach to determine whether breast cancer brain metastases show altered levels of HRD scores relative to their corresponding primary tumor...
June 18, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
Antti Häkkinen, Amjad Alkodsi, Chiara Facciotto, Kaiyang Zhang, Katja Kaipio, Sirpa Leppä, Olli Carpén, Seija Grénman, Johanna Hynninen, Sakari Hietanen, Rainer Lehtonen, Sampsa Hautaniemi
Motivation: DNA methylation aberrations are common in many cancer types. A major challenge hindering comparison of patient-derived samples is that they comprise of heterogeneous collection of cancer and microenvironment cells. We present a computational method that allows comparing cancer methylomes in two or more heterogeneous tumor samples featuring differing, unknown fraction of cancer cells. The method is unique in that it allows comparison also in the absence of normal cell control samples and without prior tumor purity estimates, as these are often unavailable or unreliable in clinical samples...
April 18, 2018: Bioinformatics
Srinivas R Viswanathan, Gavin Ha, Andreas M Hoff, Jeremiah A Wala, Jian Carrot-Zhang, Christopher W Whelan, Nicholas J Haradhvala, Samuel S Freeman, Sarah C Reed, Justin Rhoades, Paz Polak, Michelle Cipicchio, Stephanie A Wankowicz, Alicia Wong, Tushar Kamath, Zhenwei Zhang, Gregory J Gydush, Denisse Rotem, J Christopher Love, Gad Getz, Stacey Gabriel, Cheng-Zhong Zhang, Scott M Dehm, Peter S Nelson, Eliezer M Van Allen, Atish D Choudhury, Viktor A Adalsteinsson, Rameen Beroukhim, Mary-Ellen Taplin, Matthew Meyerson
Nearly all prostate cancer deaths are from metastatic castration-resistant prostate cancer (mCRPC), but there have been few whole-genome sequencing (WGS) studies of this disease state. We performed linked-read WGS on 23 mCRPC biopsy specimens and analyzed cell-free DNA sequencing data from 86 patients with mCRPC. In addition to frequent rearrangements affecting known prostate cancer genes, we observed complex rearrangements of the AR locus in most cases. Unexpectedly, these rearrangements include highly recurrent tandem duplications involving an upstream enhancer of AR in 70%-87% of cases compared with <2% of primary prostate cancers...
June 11, 2018: Cell
James Whitworth, Philip S Smith, Jose-Ezequiel Martin, Hannah West, Andrea Luchetti, Faye Rodger, Graeme Clark, Keren Carss, Jonathan Stephens, Kathleen Stirrups, Chris Penkett, Rutendo Mapeta, Sofie Ashford, Karyn Megy, Hassan Shakeel, Munaza Ahmed, Julian Adlard, Julian Barwell, Carole Brewer, Ruth T Casey, Ruth Armstrong, Trevor Cole, Dafydd Gareth Evans, Florentia Fostira, Lynn Greenhalgh, Helen Hanson, Alex Henderson, Jonathan Hoffman, Louise Izatt, Ajith Kumar, Ava Kwong, Fiona Lalloo, Kai Ren Ong, Joan Paterson, Soo-Mi Park, Rakefet Chen-Shtoyerman, Claire Searle, Lucy Side, Anne-Bine Skytte, Katie Snape, Emma R Woodward, Marc D Tischkowitz, Eamonn R Maher
Multiple primary tumors (MPTs) affect a substantial proportion of cancer survivors and can result from various causes, including inherited predisposition. Currently, germline genetic testing of MPT-affected individuals for variants in cancer-predisposition genes (CPGs) is mostly targeted by tumor type. We ascertained pre-assessed MPT individuals (with at least two primary tumors by age 60 years or at least three by 70 years) from genetics centers and performed whole-genome sequencing (WGS) on 460 individuals from 440 families...
June 12, 2018: American Journal of Human Genetics
Hao Liu, Wang He, Bo Wang, Kewei Xu, Jinli Han, Junjiong Zheng, Jun Ren, Lin Shao, Shiping Bo, Sijia Lu, Tianxin Lin, Jian Huang
BACKGROUND: The gold standard for bladder cancer detection is cystoscopy, which is an invasive procedure that causes discomfort in patients. The currently available non-invasive approaches either show limited sensitivity in low-grade tumours or possess unsatisfying specificity. The aim of the present study is to develop a new non-invasive strategy based on chromosomal imbalance levels to detect bladder cancer effectively. METHODS: We enrolled 74 patients diagnosed with bladder cancer (BC), 51 healthy participants and 27 patients who were diagnosed with non-malignant urinary disease (UD)...
June 15, 2018: BMC Cancer
Andrew J Aguirre, Jonathan A Nowak, Nicholas D Camarda, Richard A Moffitt, Arezou A Ghazani, Mehlika Hazar-Rethinam, Srivatsan Raghavan, Jaegil Kim, Lauren K Brais, Dorisanne Ragon, Marisa W Welch, Emma Reilly, Devin McCabe, Lori Marini, Kristin Anderka, Karla Helvie, Nelly Oliver, Ana Babic, Annacarolina Da Silva, Brandon Nadres, Emily E Van Seventer, Heather A Shahzade, Joseph P St Pierre, Kelly P Burke, Thomas E Clancy, James M Cleary, Leona A Doyle, Kunal Jajoo, Nadine J McCleary, Jeffrey A Meyerhardt, Janet E Murphy, Kimmie Ng, Anuj K Patel, Kimberly Perez, Michael H Rosenthal, Douglas A Rubinson, Marvin Ryou, Geoffrey I Shapiro, Ewa Sicinska, Stuart G Silverman, Rebecca J Nagy, Richard B Lanman, Deborah Knoerzer, Dean J Welsch, Matthew B Yurgelun, Charles S Fuchs, Levi A Garraway, Gad Getz, Jason L Hornick, Bruce E Johnson, Matthew H Kulke, Robert J Mayer, Jeffrey W Miller, Paul B Shyn, David A Tuveson, Nikhil Wagle, Jen Jen Yeh, William C Hahn, Ryan B Corcoran, Scott L Carter, Brian M Wolpin
Clinically relevant subtypes exist for pancreatic ductal adenocarcinoma (PDAC), but molecular characterization is not yet standard in clinical care. We implemented a biopsy protocol to perform time-sensitive whole exome sequencing and RNA-sequencing for patients with advanced PDAC. Therapeutically relevant genomic alterations were identified in 48% (34/71) and pathogenic/likely pathogenic germline alterations in 18% (13/71) of patients. Overall, 30% (21/71) of enrolled patients experienced a change in clinical management as a result of genomic data...
June 14, 2018: Cancer Discovery
Mingsheng Guo, Wei Yue, David C Samuels, Hui Yu, Jing He, Ying-Yong Zhao, Yan Guo
Genotyping arrays characterize genome-wide SNPs for a study cohort and were the primary technology behind genome wide association studies over the last decade. The Cancer Genome Atlas (TCGA) is one of the largest cancer consortium studies, and it collected genotyping data for all of its participants. Using TCGA SNP data genotyped using the Affymetrix 6.0 SNP array from 12,064 samples, we conducted a comprehensive comparisons across DNA sources (tumor tissue, normal tissue, and blood) and sample storage protocols (formalin-fixed paraffin-embedded (FFPE) vs...
June 11, 2018: Genomics
Hiroaki Taniguchi, Akihiro Fujimoto, Hidetoshi Kono, Mayuko Furuta, Masashi Fujita, Hidewaki Nakagawa
Hepatocyte nuclear factors (HNF) are transcription factors that crucially regulate cell-specific gene expression in many tissues, including the liver. Of these factors, HNF4A acts both as a master regulator of liver organogenesis and a tumor suppressor in the liver. In our whole genome sequencing analysis, we found seven somatic mutations (three Zn-finger mutations, three deletion mutants, and one intron mutation) of HNF4A in liver cancers. Interestingly, three out of seven mutations were clustered in its Zn-finger DNA-binding domain; G79 and F83 are positioned in the DNA recognition helix and the sidechain of M125 is sticking into the core of domain...
May 25, 2018: Oncotarget
Keiichi Hatakeyama, Takeshi Nagashima, Kenichi Urakami, Keiichi Ohshima, Masakuni Serizawa, Sumiko Ohnami, Yuji Shimoda, Shumpei Ohnami, Koji Maruyama, Akane Naruoka, Yasuto Akiyama, Masatoshi Kusuhara, Tohru Mochizuki, Ken Yamaguchi
Tumor mutational burden (TMB) is an emerging characteristic in cancer and has been associated with microsatellite instability, defective DNA replication/repair, and response to PD-1 and PD-L1 blockade immunotherapy. When estimating TMB, targeted panel sequencing is performed using a few hundred genes; however, a comparison of TMB results obtained with this platform and with whole exome sequencing (WES) has not been performed for various cancer types. In the present study, we compared TMB results using the above two platforms in 2,908 solid tumors that were obtained from Japanese patients...
2018: Biomedical Research
Veronica Ortiz, Min Yu
Whole-genome sequencing has made a significant impact on cancer research, but traditional bulk methods fail to detect information from rare cells. Recently developed single-cell sequencing methods have provided new insights and unprecedented details about cancer progression and diversity. These advancements also enable the investigation of rare cells, such as circulating tumor cells (CTCs) derived from cancer patients. In this review, we outline various single-cell sequencing techniques that can elucidate the molecular properties of CTCs...
June 8, 2018: Trends in Cell Biology
Glenn J Hanna, Eric R Kofman, Muhammad Ali Shazib, Sook-Bin Woo, Brendan Reardon, Nathaniel S Treister, Robert I Haddad, Corey S Cutler, Joseph H Antin, Eliezer M Van Allen, Ravindra Uppaluri, Robert J Soiffer
OBJECTIVES: Secondary oral squamous cell carcinoma (OSCC) is a late complication in allogeneic hematopoietic stem cell transplantation (HSCT) patients, but little is known about long-term outcomes and prognostication. Additionally, molecular alterations and immunologic insights unique to this disease remain largely unexplored. METHODS: We present a cohort of 31 patients with post-HSCT OSCC and reported on clinicopathologic predictors of survival. Whole-exome sequencing was performed on 6 (19%) matched pairs of peripheral blood (post-conditioning, pre-HSCT) and tumor samples...
June 2018: Oral Oncology
Yosr Hamdi, Maroua Boujemaa, Mariem Ben Rekaya, Cherif Ben Hamda, Najah Mighri, Houda El Benna, Nesrine Mejri, Soumaya Labidi, Nouha Daoud, Chokri Naouali, Olfa Messaoud, Mariem Chargui, Kais Ghedira, Mohamed Samir Boubaker, Ridha Mrad, Hamouda Boussen, Sonia Abdelhak
BACKGROUND: A family history of breast cancer has long been thought to indicate the presence of inherited genetic events that predispose to this disease. In North Africa, many specific epidemio-genetic characteristics have been observed in breast cancer families when compared to Western populations. Despite these specificities, the majority of breast cancer genetics studies performed in North Africa remain restricted to the investigation of the BRCA1 and BRCA2 genes. Thus, comprehensive data at a whole exome or whole genome level from local patients are lacking...
June 7, 2018: Journal of Translational Medicine
S Pamela K Shiao, Haiyan Xiao, Lixin Dong, Xiaoling Wang, Kebin Liu, Jinxiong She, Huidong Shi
Despite evidences linking methylation changes in the cancer tissues, little is known about the methylation modification in the peripheral blood. With the current study, we identified differential methylation regions (DMRs) across human genome by collecting the blood samples of colorectal cancer (CRC) patients compared to that of their blood-related family who shared genetic inheritance and environmental influences, and unrelated obese and non-obese controls by accessing publicly available Gene Expression Omnibus data...
May 22, 2018: Oncotarget
Yangrae Cho, Sunho Lee, Jong Hui Hong, Byong Joon Kim, Woon-Young Hong, Jongcheol Jung, Hyang Burm Lee, Joohon Sung, Han-Na Kim, Hyung-Lae Kim, Jongsun Jung
Calling variants from next-generation sequencing (NGS) data or discovering discordant sequences between two NGS data sets is challenging. We developed a computer algorithm, ADIScan1, to call variants by comparing the fractions of allelic reads in a tester to the universal reference genome. We then created ADIScan2 by modifying the algorithm to directly compare two sets of NGS data and predict discordant sequences between two testers. ADIScan1 detected >99.7% of variants called by GATK with an additional 724 393 SNVs...
June 5, 2018: Nucleic Acids Research
Rodolphe Marie, Marie Pødenphant, Kamila Koprowska, Loic Bærlocher, Roland C M Vulders, Jennifer Wilding, Neil Ashley, Simon J McGowan, Dianne van Strijp, Freek van Hemert, Tom Olesen, Niels Agersnap, Brian Bilenberg, Celine Sabatel, Julien Schira, Anders Kristensen, Walter Bodmer, Pieter J van der Zaag, Kalim U Mir
Sequencing the genomes of individual cells enables the direct determination of genetic heterogeneity amongst cells within a population. We have developed an injection-moulded valveless microfluidic device in which single cells from colorectal cancer derived cell lines (LS174T, LS180 and RKO) and fresh colorectal tumors have been individually trapped, their genomes extracted and prepared for sequencing using multiple displacement amplification (MDA). Ninety nine percent of the DNA sequences obtained mapped to a reference human genome, indicating that there was effectively no contamination of these samples from non-human sources...
June 6, 2018: Lab on a Chip
Sagarika Banerjee, Tian Tian, Zhi Wei, Natalie Shih, Michael D Feldman, Kristen N Peck, Angela M DeMichele, James C Alwine, Erle S Robertson
A dysbiotic microbiome can potentially contribute to the pathogenesis of many different diseases including cancer. Breast cancer is the second leading cause of cancer death in women. Thus, we investigated the diversity of the microbiome in the four major types of breast cancer: endocrine receptor (ER) positive, triple positive, Her2 positive and triple negative breast cancers. Using a whole genome and transcriptome amplification and a pan-pathogen microarray (PathoChip) strategy, we detected unique and common viral, bacterial, fungal and parasitic signatures for each of the breast cancer types...
2018: Frontiers in Microbiology
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