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Mykyta Artomov, Alexander J Stratigos, Ivana Kim, Raj Kumar, Martin Lauss, Bobby Y Reddy, Benchun Miao, Carla Daniela Robles-Espinoza, Aravind Sankar, Ching-Ni Njauw, Kristen Shannon, Evangelos S Gragoudas, Anne Marie Lane, Vivek Iyer, Julia A Newton-Bishop, D Timothy Bishop, Elizabeth A Holland, Graham J Mann, Tarjinder Singh, Mark J Daly, Hensin Tsao
Background: Extraordinary progress has been made in our understanding of common variants in many diseases, including melanoma. Because the contribution of rare coding variants is not as well characterized, we performed an exome-wide, gene-based association study of familial cutaneous melanoma (CM) and ocular melanoma (OM). Methods: Using 11 990 jointly processed individual DNA samples, whole-exome sequencing was performed, followed by large-scale joint variant calling using GATK (Genome Analysis ToolKit)...
December 1, 2017: Journal of the National Cancer Institute
Jayesh J Sheth, Riddhi Bhavsar, Dhairya Patel, Aishwarya Joshi, Frenny J Sheth
BACKGROUND: Harlequin ichthyosis (HI) is a severe genetic disorder caused by the mutation in the ABCA12 gene. Infants born with this condition have markedly thickened, hard stratum corneum skin all over the body. METHODS: A female child born with a thick white plate of skin with deep cracks all over the body was investigated for genes associated with congenital Ichthyosis by Next Generation sequencing. The variant relevant to the clinical indications was identified using Picard and GATK version 3...
January 29, 2018: International Journal of Dermatology
Yu Zheng, Hai-Lin Wang, Jian-Kang Li, Li Xu, Laurent Tellier, Xiao-Lin Li, Xiao-Yan Huang, Wei Li, Tong-Tong Niu, Huan-Ming Yang, Jian-Guo Zhang, Dong-Ning Liu
AIM: To study the genes responsible for retinitis pigmentosa. METHODS: A total of 15 Chinese families with retinitis pigmentosa, containing 94 sporadically afflicted cases, were recruited. The targeted sequences were captured using the Target_Eye_365_V3 chip and sequenced using the BGISEQ-500 sequencer, according to the manufacturer's instructions. Data were aligned to UCSC Genome Browser build hg19, using the Burroughs Wheeler Aligner MEM algorithm. Local realignment was performed with the Genome Analysis Toolkit (GATK v...
2018: International Journal of Ophthalmology
Yiqi Wang, Gen Li, Mark Ma, Fazhong He, Zhuo Song, Wei Zhang, Chengkun Wu
BACKGROUND: Whole-genome sequencing (WGS) plays an increasingly important role in clinical practice and public health. Due to the big data size, WGS data analysis is usually compute-intensive and IO-intensive. Currently it usually takes 30 to 40 h to finish a 50× WGS analysis task, which is far from the ideal speed required by the industry. Furthermore, the high-end infrastructure required by WGS computing is costly in terms of time and money. In this paper, we aim to improve the time efficiency of WGS analysis and minimize the cost by elastic cloud computing...
January 19, 2018: BMC Genomics
K Piórkowska, K Żukowski, K Ropka-Molik, M Tyra
The present study shows the characterization of the chromosome 15 (SSC15) region that is highly rich in quantitative traits loci (QTLs) associated with pork quality, growth performance, fat and meat carcass contents. The analytic method that was utilized included targeted enrichment DNA sequencing and RNA hybridisation probes. The research included two pig breeds (Puławska and Polish Landrace) that are significantly different in terms of carcass and meat quality features. Filtered sequences were aligned to the Sscrofa10...
January 12, 2018: Gene
Yu-Chin Hsu, Yu-Ting Hsiao, Tzu-Yuan Kao, Jan-Gowth Chang, Grace S Shieh
Due to lack of normal samples in clinical diagnosis and to reduce costs, detection of small-scale mutations from tumor-only samples is required but remains relatively unexplored. We developed an algorithm (GATKcan) augmenting GATK with two statistics and machine learning to detect mutations in cancer. The averaged performance of GATKcan in ten experiments outperformed GATK in detecting mutations of randomly sampled 231 from 241 TCGA endometrial tumors (EC). In external validations, GATKcan outperformed GATK in TCGA breast cancer (BC), ovarian cancer (OC) and melanoma tumors, in terms of Matthews correlation coefficient (MCC) and precision, where MCC takes both sensitivity and specificity into account...
November 21, 2017: Scientific Reports
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
M V Madsen, S Scheppan, E Mørk, P Kissmeyer, J Rosenberg, M R Gätke
No abstract text is available yet for this article.
December 1, 2017: British Journal of Anaesthesia
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
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
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
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
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
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
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
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
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
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
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
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]
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