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Clinical "MUTATOME" Of Myelodysplastic Syndrome;Comparison To Primary Acute Myelogenous Leukemia

BLOOD 2013年第21期122卷 518-518页

作者： Makishima, Hideki LaFramboise, Thomas Przychodzen, Bartlomiej P. Yoshida, Kenichi Ruffalo, Matthew Gomez-Segui, Ines Husseinzadeh, Holleh D. Shiraishi, Yuichi Sanada, Masashi Nagata, Yasunobu Sato, Yusuke Sato-Otsubo, Aiko Chiba, Kenichi Tanaka, Hiroko Nakamaki, Tsuyoshi Hofmann, Wolf-Karsten Miyawaki, Shuichi Shih, Lee-Yung Chiba, Shigeru Miyano, Satoru Hosono, Naoko Polprasert, Chantana Thota, Swapna Dienes, Brittney Guinta, Kathryn M. Sauntharatajah, Yogen Sekeres, Mikkael A. Ogawa, Seishi Maciejewski, Jaroslaw P. Translational Hematology and Oncology Research Cleveland Clinic Taussig Cancer Institute Cleveland OH USA Department of Electrical Engineering and Computer Science Case Western Reserve University Cleveland OH USA Department of Pathology and Tumor biology Kyoto University Kyoto Japan Electrical Engineering and Computer Science Case Western Reserve University Cleveland OH USA Hematology Department University Hospital La Fe Valencia Spain Laboratory of DNA Information Analysis Human Genome Center Institute of Medical Science The University of Tokyo Tokyo Japan Department of Pathology and Tumor Biology Graduate School of Medicine Kyoto University Kyoto Japan Cancer Genomics Project Graduate School of Medicine The University of Tokyo Tokyo Japan Laboratory of Sequence Data Analysis Human Genome Center Institute of Medical Science The University of Tokyo Tokyo Japan Division of Hematology Department of Medicine Showa University School of Medicine Tokyo Japan Department of Hematology and Oncology University Hospital Mannheim Mannheim Germany Division of Hematology Department of Internal Medicine Tokyo Metropolitan Ohtsuka Hospital Tokyo Japan Chang Gung Memorial Hospital Taoyuan Taiwan Department of Hematology Faculty of Medicine University of Tsukuba Tsukuba Japan Translational Hematology Oncology Research Cleveland Clinic Taussig Cancer Institute Cleveland OH USA Department of Translational Hematology and Oncology Research Taussig Cancer Institute Cleveland Clinic Cleveland OH USA Translational Hematology and Oncology Research Taussig Cancer Institute Cleveland Clinic Cleveland OH USA Leukemia Program Department of Hematologic Oncology and Blood Disorders Taussig Cancer Institute Cleveland Clinic Cleveland OH USA

Chromosomal aberrations and somatic mutations constitute key elements of the pathogenesis of myelodysplastic syndromes (MDS), a clonal hematologic malignancy characterized by cytopenias, a dysplastic bone marrow and propensity to clonal evolution. Next generation sequencing (NGS) enables definition of somatic mutational patterns and clonal architecture as a discovery platform, and for clinical *** systematically applied NGS to 707 cases of MDS and MDS-related disorders. 205 cases (low-risk MDS: N=78, high-risk MDS: N=42, MDS/MPN: N=48 and sAML: N=37) were tested by whole exome sequencing (WES). For validation in an additional 502 patients (low-risk MDS: N=192, high-risk MDS: N=104, MDS/MPN: N=111 and sAML: N=95), targeted deep NGS was applied for 60 index genes which were most commonly affected in the cohort analyzed by WES. For NGS data analysis a statistical pipeline was developed to focus on: i) identification of the most relevant somatic mutations, and ii) minimization of false positive results. We studied serial samples from 21 exemplary informative patients. We also compared somatic mutational patterns to those seen in primary AML TCGA cohort (N=201). Given the size of the cohort, there was, for example, a 87% chance of seeing mutations at a frequency of 1% and a 98% of seeing those with a frequency of 2%. While focusing on the most common events, we observed 1117 somatic mutations in 199 genes. The 88 genes mutated mutated in >1% of cases with MDS carried 388 mutations in MDS+sAML (2.5/case), 128 in MDS/MPN (2.7/case) and 398 in pAML (2.0/case). The average number of mutations per case increased during progression (2.2 in lower-risk, 2.8 in higher-risk MDS, 3.4 in sAML). In MDS, the 30 most frequently affected genes were present at least once in 70% of patients. The 30 most frequently mutated genes in MDS/MPN were mutated in 82% of patients. Individual mutations were also sub-grouped according to their function. When we compared three MDS subcateg

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Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

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Human genomics 2016年第1期10 Suppl 1卷 12页

作者： A. K. Srivastava Y. Wang R. Huang C. Skinner T. Thompson L. Pollard T. Wood F. Luo R. Stevenson R. Polimanti J. Gelernter X. Lin I. Y. Lim Y. Wu A. L. Teh L. Chen I. M. Aris S. E. Soh M. T. Tint J. L. MacIsaac F. Yap K. Kwek S. M. Saw M. S. Kobor M. J. Meaney K. M. Godfrey Y. S. Chong J. D. Holbrook Y. S. Lee P. D. Gluckman N. Karnani A. Kapoor D. Lee A. Chakravarti C. Maercker F. Graf M. Boutros G. Stamoulis F. Santoni P. Makrythanasis A. Letourneau M. Guipponi N. Panousis M. Garieri P. Ribaux E. Falconnet C. Borel S. E. Antonarakis S. Kumar J. Curran J. Blangero S. Chatterjee J. Akiyama D. Auer C. Berrios L. Pennacchio T. R. Donti G. Cappuccio M. Miller P. Atwal A. Kennedy A. Cardon C. Bacino L. Emrick J. Hertecant F. Baumer B. Porter M. Bainbridge P. Bonnen B. Graham R. Sutton Q. Sun S. Elsea Z. Hu P. Wang Y. Zhu J. Zhao M. Xiong David A. Bennett A. Hidalgo-Miranda S. Romero-Cordoba S. Rodriguez-Cuevas R. Rebollar-Vega E. Tagliabue M. Iorio E. D’Ippolito S. Baroni B. Kaczkowski Y. Tanaka H. Kawaji A. Sandelin R. Andersson M. Itoh T. Lassmann Y. Hayashizaki P. Carninci A. R. R. Forrest C. A. Semple E. A. Rosenthal B. Shirts L. Amendola C. Gallego M. Horike-Pyne A. Burt P. Robertson P. Beyers C. Nefcy D. Veenstra F. Hisama R. Bennett M. Dorschner D. Nickerson J. Smith K. Patterson D. Crosslin R. Nassir N. Zubair T. Harrison U. Peters G. Jarvik F. Menghi K. Inaki X. Woo P. Kumar K. Grzeda A. Malhotra H. Kim D. Ucar P. Shreckengast K. Karuturi J. Keck J. Chuang E. T. Liu B. Ji A. Tyler G. Ananda G. Carter H. Nikbakht M. Montagne M. Zeinieh A. Harutyunyan M. Mcconechy N. Jabado P. Lavigne J. Majewski J. B. Goldstein M. Overman G. Varadhachary R. Shroff R. Wolff M. Javle A. Futreal D. Fogelman L. Bravo W. Fajardo H. Gomez C. Castaneda C. Rolfo J. A. Pinto K. C. Akdemir L. Chin S. Patterson C. Statz S. Mockus S. N. Nikolaev X. I. Bonilla L. Parmentier B. King F. Bezrukov G. Kaya V. Zoete V. Seplyarskiy H. Sharpe T. McKee K. Popadin N. Basset-Seguin R. Ben Chaabene M. Andrianova C. Verdan K. Grosdemange O. Sumara M. E JCSRI Greenwood Genetic Center Greenwood USA School of Computing Clemson University Clemson USA Biochemical Genetics Laboratory Greenwood Genetic Center Greenwood USA Department Psychiatry Yale Sch Med and VA CT Healthcare Center West Haven USA Department Genetics Yale Sch Med and VA CT Healthcare Center West Haven USA Department Neurobiology Yale Sch Med and VA CT Healthcare Center West Haven USA Singapore Institute for Clinical Sciences Singapore Singapore National University of Singapore Singapore Singapore University of British Columbia Vancouver Canada KK Women’s and Children’s Hospital Singapore Singapore University of Southampton and University Hospital Southampton NHS Foundation Trust Southampton UK University of Auckland Auckland New Zealand McKusick-Nathans Institute of Genetic Medicine Johns Hopkins University School of Medicine Baltimore USA Esslingen University of Applied Sciences Esslingen Germany German Cancer Research Center Heidelberg Germany Department of Genetic Medicine and Development University of Geneva Medical School Geneva Switzerland Geneva University Hospitals-HUG Service of Genetic Medicine Geneva Switzerland GE3 Institute of Genetics and Genomics of Geneva University of Geneva Medical School Geneva Switzerland South Texas Diabetes and Obesity Institute School of Medicine University of Texas Rio-Grande Valley Edinburg USA South Texas Diabetes and Obesity Institute School of Medicine University of Texas Rio-Grande Valley Brownsville USA Institute of Genetic Medicine Johns Hopkins University Baltimore USA Genomics Division Lawrence Berkeley National Laboratory Berkeley USA Molecular and Human Genetics Baylor College of Medicine Houston USA Department of Translational Medical Sciences Federico II University Naples Italy Metabolon Inc Durham USA Section of Pediatric Neurology and Neuroscience Baylor College of Medicine Houston USA Tawam Hospital Abu Dhabi United Arab Emirates Stanford Medical School Stanford USA Sch

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s

关键词： Pulmonary Arterial Hypertension Oral Squamous Cell Carcinoma Deep Neural Network Autosomal Recessive Polycystic Kidney Disease Whole Genome Bisulfite Sequencing

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Hybrid clutter canceler with feedback guided predicative filtering on a heterogeneous parallel processing system

Hybrid clutter canceler with feedback guided predicative fil...

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International Waveform Diversity and Design Conference, WDD 2012

作者： Brinkhus, Jeffrey M. Jezak, Joseph A. Berdanier, Charles Levitan, Steven P. Chiarulli, Donald M. Electical and Computer Engineering University of Pittsburgh United States Computer Engineering Graduate Program University of Pittsburgh United States Electrical Engineering Wright State University United States Computer Science Department University of Pittsburgh United States

ISBN: (纸本)9781509005987

In this paper we describe a novel clutter cancellation platform based on a two stage approach that combines a feedback guided predictive front-end hybrid clutter canceller with high performance back-end filtering and target detection. The front-end architecture is based on an FPGA implementation of a Kalman filter that predicts target locations in real time and removes the target signals from the incoming data prior to hybrid cancellation. The back-end is user configurable and exploits high performance GPU and multi-core parallel hardware to simultaneously compute multiple clutter suppression and target detection algorithms coupled to an intelligent selection strategy for selecting the most accurate result. These target locations are fed back to the FPGA Kalman filter periodically to update the target predictions. © 2012 IEEE.

关键词： Kalman filters

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Verification of open platform board and bluetooth dongle for wireless controlling binaural hearing aids

Verification of open platform board and bluetooth dongle for...

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IEEE-EMBS International Conference on biomedical and Health Informatics, BHI 2012. In Conj. with the 8th Int. Symp.on Medical Devices and Biosensors and the 7th Int. Symp. on biomedical and Health engineering

作者： Kim, Dong-Wook Lim, Hyung Gyu Seong, Ki-Woong Lee, Jyung-Hyun Park, Hee-Joon Song, Byung-Seop Kim, Myoung-Nam Cho, Jin-Ho Department of Electrical Engineering and Computer Science Graduate School Kyungpook National University Daegu Korea Republic of Graduate School of Electrical Engineering and Computer Science Kyungpook National University Daegu 702-701 Korea Republic of Institute of Biomedical Engineering Research Kyungpook National University Daegu Korea Republic of Department of Biomedical Engineering Kyungpook National University Hospital Daegu Korea Republic of Department Biomedical Engineering Keimyoung University Daegu Korea Republic of Department of Rehabilitation Engineering Daegu University Daegu Korea Republic of Department of Biomedical Engineering School of Medicine Kyungpook National University Daegu Korea Republic of

ISBN: (纸本)9781457721779

Recently, the development of binaural hearing aids are rapidly developing with the improvement of wireless communication technology and integrated circuit design. The binaural hearing aids manufacturers are developing control technology using the multimedia equipment and smart-phone for its hearing aids control. In this paper, we designed and implemented the hearing aids system that is combined open platform board and bluetooth dongle for development of binaural hearing aids. And also, we implemented android based control GUI (graphical user interface) for hearing aids volume and fitting parameters control. From the experiment results, we verified open platform board and bluetooth dongle that was successfully controlled the hearing aids system volume using smart-phone GUI. © 2012 IEEE.

关键词： Bluetooth

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Chromosome Classification for Metaphase Selection

Chromosome Classification for Metaphase Selection

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International Symposium on Communications and Information Technologies

作者： Ravi Uttamatanin Peerapol Yuvapoositanon Apichart Intarapanich Saowaluck Kaewkamnerd Sissades Tongsima The Electrical Engineering Graduate Program Faculty of Engineering Mahanakorn University of Technology Bangkok Thailand Electronic Engineering Department Mahanakorn University of Technology Bangkok Thailand National Electronics and Computer Technology Center Pathumtani Thailand National Center for Genetic Engineering and Biotechnology Pathumtani Thailand

ISBN: (纸本)9781467355797

Identification of good metaphase spread is an important step in chromosome analysis for genetic disorder detection. In this paper, we propose a rule for chromosome classification to identify good metaphase spreads. The chromosome shapes were classified into four main classes. The first and the second classes refer to individual chromosomes with straight and bended shapes, respectively. The third class is characterized as those chromosomes with overlapping bodies and the forth class is for the non-chromosomal artifacts. Good metaphase spreads should largely contain the first and the second classes while the number of the third class should be kept minimal. Several image parameters were examined and used for creating rule-based classification. The threshold value for each parameter is determined using statistical model. We observed that the empirical probability density function of the parameters can be represented by Gaussian model and, hence, the threshold value can be easily determined. The proposed rules can efficiently and accurately classify the individual chromosome with > 90% accuracy.

关键词： Chromosome Metaphase selection Metaphase spread Rule base classification Gaussian model

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Forces of Orthodontic Closed Coil Springs Measured using Fiber Bragg Gratings

Forces of Orthodontic Closed Coil Springs Measured using Fib...

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Latin America Optics and Photonics Conference, LAOP 2012

作者： Milczewski, Maura Scandelari Dinisio, Felipe Gonçalves Martelli, Cicero Borges, Paulo César Kalinowski, Hypolito José da Cunha, José Carlos Munhoz Federal University of Technology - Paraná Curitiba80230-901 Brazil Graduate Program on Electrical Engineering and Applied Computer Science Canada Department of Mechanical Engineering Brazilian Dentistry Association Paraná Brazil

The aim of this study is to compare forces generated by three different orthodontic closed coil springs supplied by three companies, optical fiber Bragg gratins are used to evaluate the force of closing of springs. &#... 详细信息

ISBN: (纸本)9781557529589

关键词： Fiber Bragg gratings

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Accelerated DSP functions on the CBE for the X-Midas Toolkit

Accelerated DSP functions on the CBE for the X-Midas Toolkit

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International Waveform Diversity and Design Conference, WDD 2012

作者： Jezak, Joseph A. Berdanier, Charles Levitan, Steven P. Chiarulli, Donald M. Computer Engineering Graduate Program University of Pittsburgh United States USAF AFRL/RYMDA Wright Patterson Air Force Base United States Department of Electrical and Computer Engineering University of Pittsburgh United States Department of Computer Science University of Pittsburgh United States

ISBN: (纸本)9781509005987

We characterize the impact of the Cell Broadband Engine architecture, on commonly used radar DSP algorithms. We use the capabilities of the CBE to accelerate several key computational kernels including Matrix Multiplication, Matrix Inversion, and the Finite Impulse Response (FIR) filter. These algorithms are implemented and benchmarked as library routines within the X-Midas Toolkit. We observe speedups as large as 1200x for complex matrix multiplication, but speedups of 40x to 60x are more typical. We find that system I/O overhead within the X-Midas toolkit severely limited the performance of the applications. © 2012 IEEE.

关键词： FIR filters

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Smart environmental architecture for node localization in a wireless sensor network

Smart environmental architecture for node localization in a ...

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8th International Conference on Intelligent Environments, IE 2012

作者： Jauregui-Ortiz, Salvador Siller, Mario Ramos, Felix Scalabrin, Edson Electrical Engineering and Computer Science Department Center of Research and Advanced Studies Guadalajara Jalisco Mexico Graduate Program in Computer Science Pontifical Catholic University Parana Brazil Curitiba Parana Brazil

ISBN: (纸本)9780769547411

As far as we know, there is not a Node Localization Algorithm (NLA) that presents the same accuracy for all possible scenarios. We believe that a NLA should be able to interpret the dynamic information of the environment. In this sense, simple NLAs are rather focused and might perform well for specific scenarios and applications. Therefore, information fusion and context awareness seems to be an appropriate approach to address this issue. We propose the Smart Environmental Architecture for Node Localization (SEA-NL), which is composed by two main elements: (i) the Smart Beacon Nodes (SBNs) and (ii) the Logical Position of Nodes (LPN). In (i) the obstruction level indicator is estimated and can improve the estimation of distances among nodes. In (ii) environment information and a one to one relation between a node and an object are used and can also improve location estimation. Via simulation, our architecture was tested indoors and outdoors considering three localization algorithms: the Weighed Centroid Localization (WCL), the Centroid Localization, and the Triangular Centroid Localization. Finally, we present an accuracy comparison among NLAs used in isolated way, and by using the SBNs, the LPN, and the SEA-NL, where our architecture improves WCL up to ~30.88%. © 2012 IEEE.

关键词： Information fusion

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Smart antenna using a combination of D3LS and NCLS algorithms

Smart antenna using a combination of D3LS and NCLS algorithm...

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2012 9th International Conference on electrical engineering/Electronics, computer, Telecommunications and Information Technology, ECTI-CON 2012

作者： Nilsuwan, Phichet Boonpoonga, Akkarat Tagapanij, Jukkrit Sirisuk, Phaophak Electrical Engineering Graduate Program Faculty of Engineering Mahanakorn University of Technology Bangkok Thailand Department of Electrical and Computer Engineering Faculty of Engineering King Mongkut's University of Technology North Bangkok Bangkok Thailand Department of Telecommunication Engineering Mahanakorn University of Technology Bangkok Thailand International College King Mongkut's Institute of Technology Ladkrabang Bangkok Thailand

ISBN: (纸本)9781467320245

This paper presents a smart antenna system using a combination of nonconventional least square (NCLS) optimization and direct data domain least square (D3LS) for direction-of-arrival (DOA) estimation and beamforming, respectively. In the proposed system, NCLS optimization is utilized to estimate DOA of incoming signal first. The estimated DOA is then assisted for initial processing of D3LS in beamforming. The performance in term of estimated signal amplitude and estimated DOA of the proposed system is evaluated via simulations. © 2012 IEEE.

关键词： Direction of arrival

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Performance evaluation of D3LS and NCLS smart antenna in mobile communications

Performance evaluation of D3LS and NCLS smart antenna in mob...

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2012 17th International Symposium on Antennas and Propagation, ISAP 2012

作者： Boonpoonga, Akkarat Nilsuwan, Phichet Tagapanij, Jukkrit Sirisuk, Phaophak Department of Electrical and Computer Engineering Faculty of Engineering King Mongkut's University of Technology North Bangkok Bangkok Thailand Electrical Engineering Graduate Program Faculty of Engineering Mahanakorn University of Technology Bangkok Thailand Department of Telecommunication Engineering Mahanakorn University of Technology Bangkok Thailand International College King Mongkut's Institute of Technology Ladkrabang Bangkok Thailand

ISBN: (纸本)9784885522703

A smart antenna was proposed to improve wireless communication systems. The smart antenna may comprises direction-of-arrival (DOA) estimation and/or adaptive antenna. The DOA estimation technique is used to estimate direction of transmitted signals. An adaptive antenna has ability of suppressing undesired signals namely interference or jammers in specific directions while receive only the desired one. There are a number of methods proposed to conduct in such way, including multiple signal classification (MUSIC), least mean squares (LMS), sample matrix inversion (SMI), recursive least squares (RLS), and their derivative forms as seen in the literatures in [1]. These methods require a training sequence or known information for adaptation and/or DOA estimation. Although a constant modulus algorithm (CMA) was proposed without the need of training sequence, it has a slow convergence. © 2012 IEICE.

关键词： Multiple signal classification

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