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https://www.readbyqxmd.com/read/29074871/ups-indel-a-universal-positioning-system-for-indels
#1
Mohammad Shabbir Hasan, Xiaowei Wu, Layne T Watson, Liqing Zhang
Storing biologically equivalent indels as distinct entries in databases causes data redundancy, and misleads downstream analysis. It is thus desirable to have a unified system for identifying and representing equivalent indels. Moreover, a unified system is also desirable to compare the indel calling results produced by different tools. This paper describes UPS-indel, a utility tool that creates a universal positioning system for indels so that equivalent indels can be uniquely determined by their coordinates in the new system, which also can be used to compare different indel calling results...
October 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29040455/influence-of-deep-neuromuscular-block-on-the-surgeon%C3%A5-assessment-of-surgical-conditions-during-laparotomy-a-randomized-controlled-double-blinded-trial-with-rocuronium-and-sugammadex
#2
M V Madsen, S Scheppan, E Mørk, P Kissmeyer, J Rosenberg, M R Gätke, Jonathan Thompson
No abstract text is available yet for this article.
December 1, 2017: British Journal of Anaesthesia
https://www.readbyqxmd.com/read/28993434/inherited-mutations-in-brca1-and-brca2-in-an-unselected-multiethnic-cohort-of-asian-patients-with-breast-cancer-and-healthy-controls-from-malaysia
#3
Wei Xiong Wen, Jamie Allen, Kah Nyin Lai, Shivaani Mariapun, Siti Norhidayu Hasan, Pei Sze Ng, Daphne Shin-Chi Lee, Sheau Yee Lee, Sook-Yee Yoon, Joanna Lim, Shao Yan Lau, Brennan Decker, Karen Pooley, Leila Dorling, Craig Luccarini, Caroline Baynes, Don M Conroy, Patricia Harrington, Jacques Simard, Cheng Har Yip, Nur Aishah Mohd Taib, Weang Kee Ho, Antonis C Antoniou, Alison M Dunning, Douglas F Easton, Soo Hwang Teo
BACKGROUND: Genetic testing for BRCA1 and BRCA2 is offered typically to selected women based on age of onset and family history of cancer. However, current internationally accepted genetic testing referral guidelines are built mostly on data from cancer genetics clinics in women of European descent. To evaluate the appropriateness of such guidelines in Asians, we have determined the prevalence of germ line variants in an unselected cohort of Asian patients with breast cancer and healthy controls...
October 9, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28990176/validation-of-subjective-rating-scales-for-assessment-of-surgical-workspace-during-laparoscopy
#4
G G Nervil, R Medici, J L D Thomsen, A K Staehr-Rye, S Asadzadeh, J Rosenberg, M R Gätke, M V Madsen
BACKGROUND: Recently, studies have focused on how to optimize laparoscopic surgical workspace by changes in intra-abdominal pressure, level of muscle relaxation or body position, typically evaluated by surgeons using subjective rating scales. We aimed to validate two rating scales by having surgeons assess surgical workspace in video sequences recorded during laparoscopic surgery. METHOD: Video sequences were obtained from laparoscopic procedures. Eight experienced surgeons assessed the video sequences on a categorical 5-point scale and a numerical 10-point rating scale...
November 2017: Acta Anaesthesiologica Scandinavica
https://www.readbyqxmd.com/read/28986337/improving-neuromuscular-monitoring-and-reducing-residual-neuromuscular-blockade-with-e-learning-protocol-for-the-multicenter-interrupted-time-series-invert-study
#5
Jakob Louis Demant Thomsen, Ole Mathiesen, Daniel Hägi-Pedersen, Lene Theil Skovgaard, Doris Østergaard, Jens Engbaek, Mona Ring Gätke
BACKGROUND: Muscle relaxants facilitate endotracheal intubation under general anesthesia and improve surgical conditions. Residual neuromuscular blockade occurs when the patient is still partially paralyzed when awakened after surgery. The condition is associated with subjective discomfort and an increased risk of respiratory complications. Use of an objective neuromuscular monitoring device may prevent residual block. Despite this, many anesthetists refrain from using the device. Efforts to increase the use of objective monitoring are time consuming and require the presence of expert personnel...
October 6, 2017: JMIR Research Protocols
https://www.readbyqxmd.com/read/28974067/high-intraoperative-inspiratory-oxygen-fraction-and-risk-of-major-respiratory-complications
#6
A K Staehr-Rye, C S Meyhoff, F T Scheffenbichler, M F Vidal Melo, M R Gätke, J L Walsh, K S Ladha, S D Grabitz, M I Nikolov, T Kurth, L S Rasmussen, M Eikermann
Background: High inspiratory oxygen fraction ( FIO2 ) may improve tissue oxygenation but also impair pulmonary function. We aimed to assess whether the use of high intraoperative FIO2 increases the risk of major respiratory complications. Methods: We studied patients undergoing non-cardiothoracic surgery involving mechanical ventilation in this hospital-based registry study. The cases were divided into five groups based on the median FIO2 between intubation and extubation...
July 1, 2017: British Journal of Anaesthesia
https://www.readbyqxmd.com/read/28969327/influence-of-deep-neuromuscular-block-on-the-surgeon%C3%A5-assessment-of-surgical-conditions-during-laparotomy-a-randomized-controlled-double-blinded-trial-with-rocuronium-and-sugammadex
#7
M V Madsen, S Scheppan, E Mørk, P Kissmeyer, J Rosenberg, M R Gätke
Background: During laparotomy, surgeons may experience difficult surgical conditions if the patient's abdominal wall or diaphragm is tense. Deep neuromuscular block (NMB), defined as a post-tetanic-count (PTC) between 0-1, paralyses the abdominal wall muscles and the diaphragm. We hypothesized that deep NMB (PTC 0-1) would improve subjective ratings of surgical conditions during upper laparotomy as compared with standard NMB. Methods: This was a double blinded, randomized study...
September 1, 2017: British Journal of Anaesthesia
https://www.readbyqxmd.com/read/28945494/identification-of-the-genetic-determinants-responsible-for-retinal-degeneration-in-families-of-mexican-descent
#8
Adda Villanueva, Pooja Biswas, Kameron Kishaba, John Suk, Keerti Tadimeti, Pongali B Raghavendra, Karine Nadeau, Bruno Lamontagne, Lambert Busque, Steve Geoffroy, Ian Mongrain, Géraldine Asselin, Sylvie Provost, Marie-Pierre Dubé, Eric Nudleman, Radha Ayyagari
PURPOSE: To investigate the clinical characteristics and genetic basis of inherited retinal degeneration (IRD) in six unrelated pedigrees from Mexico. METHODS: A complete ophthalmic evaluation including measurement of visual acuities, Goldman kinetic or Humphrey dynamic perimetry, Amsler test, fundus photography, and color vision testing was performed. Family history and blood samples were collected from available family members. DNA from members of two pedigrees was examined for known mutations using the APEX ARRP genotyping microarray and one pedigree using the APEX LCA genotyping microarray...
September 25, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/28933420/whole-genome-characterization-of-sequence-diversity-of-15-220-icelanders
#9
Hákon Jónsson, Patrick Sulem, Birte Kehr, Snaedis Kristmundsdottir, Florian Zink, Eirikur Hjartarson, Marteinn T Hardarson, Kristjan E Hjorleifsson, Hannes P Eggertsson, Sigurjon Axel Gudjonsson, Lucas D Ward, Gudny A Arnadottir, Einar A Helgason, Hannes Helgason, Arnaldur Gylfason, Adalbjorg Jonasdottir, Aslaug Jonasdottir, Thorunn Rafnar, Soren Besenbacher, Michael L Frigge, Simon N Stacey, Olafur Th Magnusson, Unnur Thorsteinsdottir, Gisli Masson, Augustine Kong, Bjarni V Halldorsson, Agnar Helgason, Daniel F Gudbjartsson, Kari Stefansson
Understanding of sequence diversity is the cornerstone of analysis of genetic disorders, population genetics, and evolutionary biology. Here, we present an update of our sequencing set to 15,220 Icelanders who we sequenced to an average genome-wide coverage of 34X. We identified 39,020,168 autosomal variants passing GATK filters: 31,079,378 SNPs and 7,940,790 indels. Calling de novo mutations (DNMs) is a formidable challenge given the high false positive rate in sequencing datasets relative to the mutation rate...
September 21, 2017: Scientific Data
https://www.readbyqxmd.com/read/28912480/genome-wide-rad-sequencing-data-provide-unprecedented-resolution-of-the-phylogeny-of-temperate-bamboos-poaceae-bambusoideae
#10
Xueqin Wang, Xiaying Ye, Lei Zhao, Dezhu Li, Zhenhua Guo, Huifu Zhuang
The temperate bamboos (tribe Arundinarieae, Poaceae) are strongly supported as monophyly in recent molecular studies, but taxonomic delineation and phylogenetic relationships within the tribe lack resolution. Here, we sampled 39 species (36 temperate bamboos and 3 outgroups) for restriction-site associated DNA sequencing (RAD-seq) with an emphasis on Phyllostachys clade and related clades. Using the largest data matrix for the bamboos to date, we were able to infer phylogenetic relationships with unparalleled resolution...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28872635/comprehensive-analyses-of-somatic-tp53-mutation-in-tumors-with-variable-mutant-allele-frequency
#11
Alexander J Cole, Ying Zhu, Trisha Dwight, Bing Yu, Kristie-Ann Dickson, Gregory B Gard, Jayne Maidens, Susan Valmadre, Anthony J Gill, Roderick Clifton-Bligh, Deborah J Marsh
Somatic mutation of the tumor suppressor gene TP53 is reported in at least 50% of human malignancies. Most high-grade serous ovarian cancers (HGSC) have a mutant TP53 allele. Accurate detection of these mutants in heterogeneous tumor tissue is paramount as therapies emerge to target mutant p53. We used a Fluidigm Access Array™ System with Massively Parallel Sequencing (MPS) to analyze DNA extracted from 76 serous ovarian tumors. This dataset has been made available to researchers through the European Genome-phenome Archive (EGA; EGAS00001002200)...
September 5, 2017: Scientific Data
https://www.readbyqxmd.com/read/28862766/genomic-profiles-of-lung-cancer-associated-with-idiopathic-pulmonary-fibrosis
#12
Ji An Hwang, Deokhoon Kim, Sung-Min Chun, SooHyun Bae, Joon Seon Song, Mi Young Kim, Hyun Jung Koo, Jin Woo Song, Woo Sung Kim, Jae Cheol Lee, Hyeong Ryul Kim, Chang-Min Choi, Se Jin Jang
Little is known on the pathogenesis or molecular profiles of idiopathic pulmonary fibrosis-associated lung cancer (IPF-LC). This study was performed to investigate the genomic profiles of IPF-LC and to explore the possibility of defining potential therapeutic targets in IPF-LC. We assessed genomic profiles of IPF-LC using targeted exome sequencing (OncoPanel version 2) in 35 matched tumor/normal pairs surgically resected between 2004 and 2014. Germline and somatic variant calling was performed using GATK HaplotypeCaller and MuTect with GATK SomaticIndelocator, respectively...
September 1, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28836000/antcaller-an-accurate-variant-caller-incorporating-ancient-dna-damage
#13
Boyan Zhou, Shaoqing Wen, Lingxiang Wang, Li Jin, Hui Li, Hong Zhang
Ancient DNA obtained from ancient samples, such as sediments, bones, and teeth, is an important genetic resource that can be used to reconstruct an evolutional history of humans, animals, and plants. The application of high-throughput sequencing enables the research of ancient DNA to be conducted in a whole genome scale. However, post-mortem DNA damage mainly caused by deamination of cytosine to uracil (or methylated cytosine to thymine) may confound the variant calling and downstream analysis. In this article, we develop a Python program to implement a new variant caller, "AntCaller", which extracts the information on nucleotide substitutions from sequencing data and calculates the probability of each genotype based on a Bayesian rule...
December 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28835080/-high-throughput-targeted-sequencing-panel-for-exploring-radiosensitivity-associated-genes-in-esophageal-squamous-cell-carcinoma
#14
Y Qiao, C X Hu, D A Song, S Q Li, L H Zhou, X D Jiang
Objective: To explore radiosensitivity-associated genes in esophageal squamous cell carcinoma by targeted sequencing panel. Methods: The peripheral blood from 22 esophageal squamous cell carcinoma (ESCC) patients received radiotherapy alone were collected, respectively. The genomic DNA (gDNA) of peripheral blood was extracted and used to create a library of gDNA restriction fragments. The gDNA restriction fragments were hybridized to the HaloPlex probe capture library, which comprises 356 cancer genes selected from the Catalogue of Somatic Mutations in Cancer (Cosmic) database of 2011 updated edition...
August 23, 2017: Zhonghua Zhong Liu za Zhi [Chinese Journal of Oncology]
https://www.readbyqxmd.com/read/28831090/accelerating-next-generation-sequencing-data-analysis-with-system-level-optimizations
#15
Nagarajan Kathiresan, Ramzi Temanni, Hakeem Almabrazi, Najeeb Syed, Puthen V Jithesh, Rashid Al-Ali
Next generation sequencing (NGS) data analysis is highly compute intensive. In-memory computing, vectorization, bulk data transfer, CPU frequency scaling are some of the hardware features in the modern computing architectures. To get the best execution time and utilize these hardware features, it is necessary to tune the system level parameters before running the application. We studied the GATK-HaplotypeCaller which is part of common NGS workflows, that consume more than 43% of the total execution time. Multiple GATK 3...
August 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28792971/optimized-detection-of-insertions-deletions-indels-in-whole-exome-sequencing-data
#16
COMPARATIVE STUDY
Bo-Young Kim, Jung Hoon Park, Hye-Yeong Jo, Soo Kyung Koo, Mi-Hyun Park
Insertion and deletion (INDEL) mutations, the most common type of structural variance, are associated with several human diseases. The detection of INDELs through next-generation sequencing (NGS) is becoming more common due to the decrease in costs, the increase in efficiency, and sensitivity improvements demonstrated by the various sequencing platforms and analytical tools. However, there are still many errors associated with INDEL variant calling, and distinguishing INDELs from errors in NGS remains challenging...
2017: PloS One
https://www.readbyqxmd.com/read/28637275/16gt-a-fast-and-sensitive-variant-caller-using-a-16-genotype-probabilistic-model
#17
Ruibang Luo, Michael C Schatz, Steven L Salzberg
16GT is a variant caller for Illumina whole-genome and whole-exome sequencing data. It uses a new 16-genotype probabilistic model to unify single nucleotide polymorphism and insertion and deletion calling in a single variant calling algorithm. In benchmark comparisons with 5 other widely used variant callers on a modern 36-core server, 16GT demonstrated improved sensitivity in calling single nucleotide polymorphisms, and it provided comparable sensitivity and accuracy for calling insertions and deletions as compared to the GATK HaplotypeCaller...
July 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28573656/objective-neuromuscular-monitoring-of-neuromuscular-blockade-in-denmark-an-online-based-survey-of-current-practice
#18
C M Söderström, K Z Eskildsen, M R Gätke, A K Staehr-Rye
BACKGROUND: Neuromuscular blocking agents are commonly used during general anaesthesia but can lead to postoperative residual neuromuscular blockade and associated morbidity. With appropriate objective neuromuscular monitoring (objNMM) residual blockade can be avoided. In this survey, we investigated the use of objNMM in Denmark. METHODS: We conducted an anonymous Internet-based survey distributed through e-mails to Danish public anaesthesia departments. The survey consisted of 15-17 short questions regarding the use of objNMM...
July 2017: Acta Anaesthesiologica Scandinavica
https://www.readbyqxmd.com/read/28560825/phredem-a-phred-score-informed-genotype-calling-approach-for-next-generation-sequencing-studies
#19
Peizhou Liao, Glen A Satten, Yi-Juan Hu
A fundamental challenge in analyzing next-generation sequencing (NGS) data is to determine an individual's genotype accurately, as the accuracy of the inferred genotype is essential to downstream analyses. Correctly estimating the base-calling error rate is critical to accurate genotype calls. Phred scores that accompany each call can be used to decide which calls are reliable. Some genotype callers, such as GATK and SAMtools, directly calculate the base-calling error rates from phred scores or recalibrated base quality scores...
July 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28552090/deep-neuromuscular-blockade-and-low-insufflation-pressure-during-laparoscopic-hysterectomy
#20
Matias Vested Madsen, Olav Istre, Henrik Halvor Springborg, Anne Kathrine Staehr-Rye, Jacob Rosenberg, Jørgen Lund, Mona Ring Gätke
INTRODUCTION: Establishment of sufficient muscle relaxation is essential in laparoscopic surgery. During laparoscopy, surgeons can experience abdominal contractions in their patients. Deep neuromuscular block (NMB) has the potential to prevent such episodes. In this study, we explored if deep NMB reduces the incidence of sudden abdominal contractions as compared with standard NMB. METHODS: This was a pre-planned secondary analysis of a randomized, controlled study...
May 2017: Danish Medical Journal
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