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Daniel Valenzuela, Tuukka Norri, Niko Välimäki, Esa Pitkänen, Veli Mäkinen
BACKGROUND: Typical human genome differs from the reference genome at 4-5 million sites. This diversity is increasingly catalogued in repositories such as ExAC/gnomAD, consisting of >15,000 whole-genomes and >126,000 exome sequences from different individuals. Despite this enormous diversity, resequencing data workflows are still based on a single human reference genome. Identification and genotyping of genetic variants is typically carried out on short-read data aligned to a single reference, disregarding the underlying variation...
May 9, 2018: BMC Genomics
Zhentang Li, Yi Wang, Fei Wang
BACKGROUND: The rapid development of next-generation sequencing (NGS) technology has continuously been refreshing the throughput of sequencing data. However, due to the lack of a smart tool that is both fast and accurate, the analysis task for NGS data, especially those with low-coverage, remains challenging. RESULTS: We proposed a decision-tree based variant calling algorithm. Experiments on a set of real data indicate that our algorithm achieves high accuracy and sensitivity for SNVs and indels and shows good adaptability on low-coverage data...
April 19, 2018: BMC Bioinformatics
Darrell O Ricke, Anna Shcherbina, Adam Michaleas, Philip Fremont-Smith
High-throughput sequencing (HTS) of single nucleotide polymorphisms (SNPs) enables additional DNA forensic capabilities not attainable using traditional STR panels. However, the inclusion of sets of loci selected for mixture analysis, extended kinship, phenotype, biogeographic ancestry prediction, etc., can result in large panel sizes that are difficult to analyze in a rapid fashion. GrigoraSNP was developed to address the allele-calling bottleneck that was encountered when analyzing SNP panels with more than 5000 loci using HTS...
April 16, 2018: Journal of Forensic Sciences
Daichi Shigemizu, Fuyuki Miya, Shintaro Akiyama, Shujiro Okuda, Keith A Boroevich, Akihiro Fujimoto, Hidewaki Nakagawa, Kouichi Ozaki, Shumpei Niida, Yonehiro Kanemura, Nobuhiko Okamoto, Shinji Saitoh, Mitsuhiro Kato, Mami Yamasaki, Tatsuo Matsunaga, Hideki Mutai, Kenjiro Kosaki, Tatsuhiko Tsunoda
Insertions and deletions (indels) have been implicated in dozens of human diseases through the radical alteration of gene function by short frameshift indels as well as long indels. However, the accurate detection of these indels from next-generation sequencing data is still challenging. This is particularly true for intermediate-size indels (≥50 bp), due to the short DNA sequencing reads. Here, we developed a new method that predicts intermediate-size indels using BWA soft-clipped fragments (unmatched fragments in partially mapped reads) and unmapped reads...
April 4, 2018: Scientific Reports
Samira Asgharzade, Mohammad Amin Tabatabaiefar, Javad Mohammadi-Asl, Morteza Hashemzadeh Chaleshtori
BACKGROUND: Recent studies have confirmed the utility of targeted next-generation sequencing (NGS), providing a remarkable opportunity to find variants in known disease genes, especially in genetically heterogeneous disorders such as hearing loss (HL). METHODS: After excluding mutations in the most common autosomal recessive non-syndromic HL (ARNSHL) genes via Sanger sequencing and genetic linkage analysis, we performed NGS in the proband an Iranian family with ARNSHL...
May 2018: International Journal of Pediatric Otorhinolaryngology
Nam S Vo, Vinhthuy Phan
Motivation: The detection of genomic variants has great significance in genomics, bioinformatics and biomedical research and applications. However, despite a lot of effort, Indels and structural variants are still under-characterized compared to SNPs. Current approaches based on next-generation sequencing data usually require large numbers of reads (high coverage) to be able to detect such types of variants accurately. However Indels, especially those close to each other, are still hard to detect accurately...
March 24, 2018: Bioinformatics
Nasrollah Saleh-Gohari, Kolsoum Saeidi, Roya Zeighaminejad
AIMS: Fucosidosis is a rare autosomal recessive lysosomal storage disorder caused by α-L-fucosidase deficiency as a result of FUCA1 gene mutations. Here, we studied clinical features and the molecular basis of fucosidosis in a family from Iran, including two probands and nine family members. METHODS: DNA sample of two probands were screened for gene defects using a next generation sequencing technique. The sequencing processes were performed on an Illumina Hiseq 4000 platform...
March 27, 2018: Journal of Clinical Pathology
Shanshan Ren, Koen Bertels, Zaid Al-Ars
GATK HaplotypeCaller (HC) is a popular variant caller, which is widely used to identify variants in complex genomes. However, due to its high variants detection accuracy, it suffers from long execution time. In GATK HC, the pair-HMMs forward algorithm accounts for a large percentage of the total execution time. This article proposes to accelerate the pair-HMMs forward algorithm on graphics processing units (GPUs) to improve the performance of GATK HC. This article presents several GPU-based implementations of the pair-HMMs forward algorithm...
2018: Evolutionary Bioinformatics Online
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...
April 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
Katarzyna Piórkowska, Kacper Żukowski, Katarzyna Ropka-Molik, Mirosław 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...
March 20, 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...
February 2018: 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
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