keyword
MENU ▼
Read by QxMD icon Read
search

Clinical whole genome sequencing

keyword
https://www.readbyqxmd.com/read/28430103/genomic-characterization-of-recrudescent-plasmodium-malariae-after-treatment-with-artemether-lumefantrine
#1
Gavin G Rutledge, Ian Marr, G Khai Lin Huang, Sarah Auburn, Jutta Marfurt, Mandy Sanders, Nicholas J White, Matthew Berriman, Chris I Newbold, Nicholas M Anstey, Thomas D Otto, Ric N Price
Plasmodium malariae is the only human malaria parasite species with a 72-hour intraerythrocytic cycle and the ability to persist in the host for life. We present a case of a P. malariae infection with clinical recrudescence after directly observed administration of artemether/lumefantrine. By using whole-genome sequencing, we show that the initial infection was polyclonal and the recrudescent isolate was a single clone present at low density in the initial infection. Haplotypic analysis of the clones in the initial infection revealed that they were all closely related and were presumably recombinant progeny originating from the same infective mosquito bite...
August 15, 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28428978/20th-workshop-of-the-international-stroke-genetics-consortium-november-3-4-2016-milan-italy-2016-036-isgc-research-priorities
#2
Daniel Woo, Stephanie Debette, Christopher Anderson
OBJECTIVE: To develop a research priority list for the International Stroke Genetics Consortium (ISGC). BACKGROUND: Previously, stroke progress review groups and other activities provided an opportunity for members within the field to develop priorities for research. These filtered into larger categories which then published the top research priorities of their given field. However, these review groups are no longer forming and thus there has been no clear direction on what the research priorities and needs for stroke genetics research...
March 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28428775/genomics-reveals-a-unique-clone-of-burkholderia-cenocepacia-harboring-an-actively-excising-novel-genomic-island
#3
Prashant P Patil, Swapna Mali, Samriti Midha, Vikas Gautam, Lona Dash, Sunil Kumar, Jayanthi Shastri, Lipika Singhal, Prabhu B Patil
Burkholderia cenocepacia is a clinically dominant form among the other virulent species of Burkholderia cepacia complex (Bcc). In the present study, we sequenced and analyzed the genomes of seven nosocomial Bcc isolates, five of which were isolated from the bloodstream infections and two isolates were recovered from the hospital setting during the surveillance. Genome-based species identification of the Bcc isolates using a type strain explicitly identified the species as B. cenocepacia. Moreover, single nucleotide polymorphism analysis revealed that the six isolates were clonal and phylogenetically distinct from the other B...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28427202/clinical-implications-of-genomic-profiles-in-metastatic-breast-cancer-with-a-focus-on-tp53-and-pik3ca-the-most-frequently-mutated-genes
#4
Ji-Yeon Kim, Eunjin Lee, Kyunghee Park, Woong-Yang Park, Hae Hyun Jung, Jin Seok Ahn, Young-Hyuck Im, Yeon Hee Park
Breast cancer (BC) has been genetically profiled through large-scale genome analyses. However, the role and clinical implications of genetic alterations in metastatic BC (MBC) have not been evaluated. Therefore, we conducted whole-exome sequencing (WES) and RNA-Seq of 37 MBC samples and targeted deep sequencing of another 29 MBCs. We evaluated somatic mutations from WES and targeted sequencing and assessed gene expression and performed pathway analysis from RNA-Seq. In this analysis, PIK3CA was the most commonly mutated gene in estrogen receptor (ER)-positive BC, while in ER-negative BC, TP53 was the most commonly mutated gene (p = 0...
March 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28425484/mycobacterium-tuberculosis-resistance-prediction-and-lineage-classification-from-genome-sequencing-comparison-of-automated-analysis-tools
#5
Viola Schleusener, Claudio U Köser, Patrick Beckert, Stefan Niemann, Silke Feuerriegel
Whole-genome sequencing (WGS) has the potential to accelerate drug-susceptibility testing (DST) to design appropriate regimens for drug-resistant tuberculosis (TB). Several recently developed automated software tools promise to standardize the analysis and interpretation of WGS data. We assessed five tools (CASTB, KvarQ, Mykrobe Predictor TB, PhyResSE, and TBProfiler) with regards to DST and phylogenetic lineage classification, which we compared with phenotypic DST, Sanger sequencing, and traditional typing results for a collection of 91 strains...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28424332/improving-genetic-diagnosis-in-mendelian-disease-with-transcriptome-sequencing
#6
Beryl B Cummings, Jamie L Marshall, Taru Tukiainen, Monkol Lek, Sandra Donkervoort, A Reghan Foley, Veronique Bolduc, Leigh B Waddell, Sarah A Sandaradura, Gina L O'Grady, Elicia Estrella, Hemakumar M Reddy, Fengmei Zhao, Ben Weisburd, Konrad J Karczewski, Anne H O'Donnell-Luria, Daniel Birnbaum, Anna Sarkozy, Ying Hu, Hernan Gonorazky, Kristl Claeys, Himanshu Joshi, Adam Bournazos, Emily C Oates, Roula Ghaoui, Mark R Davis, Nigel G Laing, Ana Topf, Peter B Kang, Alan H Beggs, Kathryn N North, Volker Straub, James J Dowling, Francesco Muntoni, Nigel F Clarke, Sandra T Cooper, Carsten G Bönnemann, Daniel G MacArthur
Exome and whole-genome sequencing are becoming increasingly routine approaches in Mendelian disease diagnosis. Despite their success, the current diagnostic rate for genomic analyses across a variety of rare diseases is approximately 25 to 50%. We explore the utility of transcriptome sequencing [RNA sequencing (RNA-seq)] as a complementary diagnostic tool in a cohort of 50 patients with genetically undiagnosed rare muscle disorders. We describe an integrated approach to analyze patient muscle RNA-seq, leveraging an analysis framework focused on the detection of transcript-level changes that are unique to the patient compared to more than 180 control skeletal muscle samples...
April 19, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28423722/the-importance-of-the-genomic-landscape-in-waldenstr%C3%A3-m-s-macroglobulinemia-for-targeted-therapeutical-interventions
#7
REVIEW
Antonio Sacco, Adriano Fenotti, Loredana Affò, Stefano Bazzana, Domenico Russo, Marco Presta, Michele Malagola, Antonella Anastasia, Marina Motta, Christopher J Patterson, Giuseppe Rossi, Luisa Imberti, Steven P Treon, Irene M Ghobrial, Aldo M Roccaro
The Literature has recently reported on the importance of genomics in the field of hematologic malignancies, including B-cell lymphoproliferative disorders such as Waldenström's Macrolgobulinemia (WM). Particularly, whole exome sequencing has led to the identification of the MYD88L265P and CXCR4C1013G somatic variants in WM, occurring in about 90% and 30% of the patients, respectively. Subsequently, functional studies have demonstrated their functional role in supporting WM pathogenesis and disease progression, both in vitro and in vivo, thus providing the pre-clinical evidences for extremely attractive targets for novel therapeutic interventions in WM...
March 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423702/experience-with-precision-genomics-and-tumor-board-indicates-frequent-target-identification-but-barriers-to-delivery
#8
Alan H Bryce, Jan B Egan, Mitesh J Borad, A Keith Stewart, Grzegorz S Nowakowski, Asher Chanan-Khan, Mrinal M Patnaik, Stephen M Ansell, Michaela S Banck, Steven I Robinson, Aaron S Mansfield, Eric W Klee, Gavin R Oliver, Jennifer B McCormick, Norine E Huneke, Colleen M Tagtow, Robert B Jenkins, Kandelaria M Rumilla, Sarah E Kerr, Jean-Pierre A Kocher, Scott A Beck, Martin E Fernandez-Zapico, Gianrico Farrugia, Konstantinos N Lazaridis, Robert R McWilliams
BACKGROUND: The ability to analyze the genomics of malignancies has opened up new possibilities for off-label targeted therapy in cancers that are refractory to standard therapy. At Mayo Clinic these efforts are organized through the Center for Individualized Medicine (CIM). RESULTS: Prior to GTB, datasets were analyzed and integrated by a team of bioinformaticians and cancer biologists. Therapeutically actionable mutations were identified in 65% (92/141) of the patients tested with 32% (29/92) receiving genomically targeted therapy with FDA approved drugs or in an independent clinical trial with 45% (13/29) responding...
March 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423598/next-generation-mapping-reveals-novel-large-genomic-rearrangements-in-prostate-cancer
#9
Weerachai Jaratlerdsiri, Eva K F Chan, Desiree C Petersen, Claire Yang, Peter I Croucher, M S Riana Bornman, Palak Sheth, Vanessa M Hayes
Complex genomic rearrangements are common molecular events driving prostate carcinogenesis. Clinical significance, however, has yet to be fully elucidated. Detecting the full range and subtypes of large structural variants (SVs), greater than one kilobase in length, is challenging using clinically feasible next generation sequencing (NGS) technologies. Next generation mapping (NGM) is a new technology that allows for the interrogation of megabase length DNA molecules outside the detection range of single-base resolution NGS...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423517/next-generation-sequencing-of-extraskeletal-myxoid-chondrosarcoma
#10
Elizabeth J Davis, Yi-Mi Wu, Dan Robinson, Scott M Schuetze, Laurence H Baker, Jyoti Athanikar, Xuhong Cao, Lakshmi P Kunju, Arul M Chinnaiyan, Rashmi Chugh
Extraskeletal myxoid chondrosarcoma (EMC) is an indolent translocation-associated soft tissue sarcoma with a high propensity for metastases. Using a clinical sequencing approach, we genomically profiled patients with metastatic EMC to elucidate the molecular biology and identify potentially actionable mutations. We also evaluated potential predictive factors of benefit to sunitinib, a multi-targeted tyrosine kinase inhibitor with reported activity in a subset of EMC patients. Between January 31, 2012 and April 15, 2016, six patients with EMC participated in the clinical sequencing research study...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28420617/application-and-progress-of-high-throughput-sequencing-technologies-in-the-research-of-hereditary-hearing-loss
#11
Wang Cuicui, Yuan Huijun
Hearing loss (HL) is the most common birth defect. Elucidating the genetic basis of hereditary deafness can not only assist diagnosis, provide the basis for genetic counseling and the prevention of deafness, but also bring a deeper understanding of the disease pathogenesis. In the genomic era, high-throughput sequencing technologies, represented by whole genome sequencing (WGS), whole exome sequencing (WES) or target region sequencing, have been widely used in the studies of hereditary HL. Here, we summarize the application and progress of WES and target region sequencing in the research of causative genes and clinical molecular diagnosis of hereditary HL, hoping to be helpful for the development and improvement of clinical genetic diagnosis of deafness in China...
March 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28420414/integrated-genomic-analysis-of-mitochondrial-rna-processing-in-human-cancers
#12
Youssef Idaghdour, Alan Hodgkinson
BACKGROUND: The mitochondrial genome is transcribed as continuous polycistrons of RNA containing multiple genes. As a consequence, post-transcriptional events are critical for the regulation of gene expression and therefore all aspects of mitochondrial function. One particularly important process is the m(1)A/m(1)G RNA methylation of the ninth position of different mitochondrial tRNAs, which allows efficient processing of mitochondrial mRNAs and protein translation, and de-regulation of genes involved in these processes has been associated with altered mitochondrial function...
April 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28420412/intersect-then-combine-approach-improving-the-performance-of-somatic-variant-calling-in-whole-exome-sequencing-data-using-multiple-aligners-and-callers
#13
Maurizio Callari, Stephen-John Sammut, Leticia De Mattos-Arruda, Alejandra Bruna, Oscar M Rueda, Suet-Feung Chin, Carlos Caldas
Bioinformatic analysis of genomic sequencing data to identify somatic mutations in cancer samples is far from achieving the required robustness and standardisation. In this study we generated a whole exome sequencing benchmark dataset using the platinum genome sample NA12878 and developed an intersect-then-combine (ITC) approach to increase the accuracy in calling single nucleotide variants (SNVs) and indels in tumour-normal pairs. We evaluated the effect of alignment, base quality recalibration, mutation caller and filtering on sensitivity and false positive rate...
April 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28419202/genomic-characterization-of-usa300-mrsa-to-evaluate-intraclass-transmission-and-recurrence-of-ssti-among-high-risk-military-trainees
#14
Eugene V Millar, Gregory K Rice, Emad M Elassal, Carey D Schlett, Jason W Bennett, Cassie L Redden, Deepika Mor, Natasha N Law, David R Tribble, Theron Hamilton, Michael W Ellis, Kimberly A Bishop-Lilly
Background.: Military trainees are at increased risk for methicillin-resistant Staphylococcus aureus (MRSA) skin and soft tissue infection (SSTI). Whole genome sequencing (WGS) can refine our understanding of MRSA transmission and microevolution in congregate settings. Methods.: We conducted a prospective case-control study of SSTI among US Army Infantry trainees at Fort Benning, GA from July 2012-December 2014. We identified clusters of USA300 MRSA SSTI within select training classes and performed WGS on clinical isolates...
April 17, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28418892/roles-of-long-noncoding-rnas-in-colorectal-cancer-metastasis
#15
REVIEW
He Li, Si-Qing Ma, Jin Huang, Xiao-Ping Chen, Hong-Hao Zhou
Colorectal cancer (CRC) is the 3rd most common malignancies worldwide. Metastasis is responsible for more than 90% CRC patients' death. Long noncoding RNAs (lncRNAs) are an important class of transcribed RNA molecules greater than 200 nucleotides in length. With the development of whole genome sequencing technologies, they have been gained more attention. Accumulating evidences suggest that abnormal expression of lncRNAs in diverse diseases are involved in various biological functions such as proliferation, apoptosis, metastasis and differentiation by acting as epigenetic, splicing, transcriptional or post-transcriptional regulators...
March 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/28414800/semantic-prioritization-of-novel-causative-genomic-variants
#16
Imane Boudellioua, Rozaimi B Mahamad Razali, Maxat Kulmanov, Yasmeen Hashish, Vladimir B Bajic, Eva Goncalves-Serra, Nadia Schoenmakers, Georgios V Gkoutos, Paul N Schofield, Robert Hoehndorf
Discriminating the causative disease variant(s) for individuals with inherited or de novo mutations presents one of the main challenges faced by the clinical genetics community today. Computational approaches for variant prioritization include machine learning methods utilizing a large number of features, including molecular information, interaction networks, or phenotypes. Here, we demonstrate the PhenomeNET Variant Predictor (PVP) system that exploits semantic technologies and automated reasoning over genotype-phenotype relations to filter and prioritize variants in whole exome and whole genome sequencing datasets...
April 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28414188/a-case-of-splenomegaly-in-cbl-syndrome
#17
Rachel R Coe, Margaret L McKinnon, Maja Tarailo-Graovac, Colin J Ross, Wyeth W Wasserman, Jan M Friedman, Paul C Rogers, Clara D M van Karnebeek
INTRODUCTION: We present a child with unexplained splenomegaly to highlight this feature as a presenting sign of the RASopathy CBL syndrome and to draw attention to the power and utility of next generation genomic sequencing for providing rapid diagnosis and critical information to guide care in the pediatric clinical setting. CLINICAL REPORT: A 7-year-old boy presented with unexplained splenomegaly, attention deficit hyperactivity disorder, mild learning difficulties, easy bruising, mild thrombocytopenia, and subtle dysmorphic features...
April 13, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28412514/insights-from-the-genome-of-a-high-alkaline-cellulase-producing-aspergillus-fumigatus-strain-obtained-from-peruvian-amazon-rainforest
#18
Sujay Paul, Angel Zhang, Yvette Ludeña, Gretty K Villena, Fengan Yu, David H Sherman, Marcel Gutiérrez-Correa
Here, we report the complete genome sequence of a high alkaline cellulase producing Aspergillus fumigatus strain LMB-35Aa isolated from soil of Peruvian Amazon rainforest. The genome is ∼27.5mb in size, comprises of 228 scaffolds with an average GC content of 50%, and is predicted to contain a total of 8,660 protein-coding genes. Of which, 6156 are with known function; it codes for 607 putative CAZymes families potentially involved in carbohydrate metabolism. Several important cellulose degrading genes, such as endoglucanase A, endoglucanase B, endoglucanase D and beta-glucosidase, are also identified...
April 12, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28410416/correction-a-year-of-infection-in-the-intensive-care-unit-prospective-whole-genome-sequencing-of-bacterial-clinical-isolates-reveals-cryptic-transmissions-and-novel-microbiota
#19
David J Roach, Joshua N Burton, Choli Lee, Bethany Stackhouse, Susan M Butler-Wu, Brad T Cookson, Jay Shendure, Stephen J Salipante
[This corrects the article DOI: 10.1371/journal.pgen.1005413.].
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28408749/high-prevalence-of-tp53-mutations-is-associated-with-poor-survival-and-an-emt-signature-in-gliosarcoma-patients
#20
Sung-Yup Cho, Changho Park, Deukchae Na, Jee Yun Han, Jieun Lee, Ok-Kyoung Park, Chengsheng Zhang, Chang Ohk Sung, Hyo Eun Moon, Yona Kim, Jeong Hoon Kim, Jong Jae Kim, Shin Kwang Khang, Do-Hyun Nam, Jung Won Choi, Yeon-Lim Suh, Dong Gyu Kim, Sung Hye Park, Hyewon Youn, Kyuson Yun, Jong-Il Kim, Charles Lee, Sun Ha Paek, Hansoo Park
Gliosarcoma (GS) is a rare variant (2%) of glioblastoma (GBM) that poses clinical genomic challenges because of its poor prognosis and limited genomic information. To gain a comprehensive view of the genomic alterations in GS and to understand the molecular etiology of GS, we applied whole-exome sequencing analyses for 28 GS cases (6 blood-matched fresh-frozen tissues for the discovery set, 22 formalin-fixed paraffin-embedded tissues for the validation set) and copy-number variation microarrays for 5 blood-matched fresh-frozen tissues...
April 14, 2017: Experimental & Molecular Medicine
keyword
keyword
99677
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"