keyword
MENU ▼
Read by QxMD icon Read
search

next generation sequence

keyword
https://www.readbyqxmd.com/read/28821183/improvement-of-the-threespine-stickleback-genome-using-a-hi-c-based-proximity-guided-assembly
#1
Catherine L Peichel, Shawn T Sullivan, Ivan Liachko, Michael A White
Scaffolding genomes into complete chromosome assemblies remains challenging even with the rapidly increasing sequence coverage generated by current next-generation sequence technologies. Even with scaffolding information, many genome assemblies remain incomplete. The genome of the threespine stickleback (Gasterosteus aculeatus), a fish model system in evolutionary genetics and genomics, is not completely assembled despite scaffolding with high-density linkage maps. Here, we first test the ability of a Hi-C based proximity-guided assembly (PGA) to perform a de novo genome assembly from relatively short contigs...
September 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28820494/immune-response-patterns-and-next-generation-sequencing-diagnostics-for-the-detection-of-mycoses-in-patients-with-septic-shock-results-of-a-combined-clinical-and-experimental-investigation
#2
Sebastian O Decker, Annette Sigl, Christian Grumaz, Philip Stevens, Yevhen Vainshtein, Stefan Zimmermann, Markus A Weigand, Stefan Hofer, Kai Sohn, Thorsten Brenner
Fungi are of increasing importance in sepsis. However, culture-based diagnostic procedures are associated with relevant weaknesses. Therefore, culture- and next-generation sequencing (NGS)-based fungal findings as well as corresponding plasma levels of β-d-glucan, interferon gamma (INF-γ), tumor necrosis factor alpha (TNF-α), interleukin (IL)-2, -4, -6, -10, -17A, and mid-regional proadrenomedullin (MR-proADM) were evaluated in 50 septic patients at six consecutive time points within 28 days after sepsis onset...
August 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28819852/enumeration-dielectrophoretic-capture-and-molecular-analysis-of-circulating-tumor-cells
#3
Stephanie S Yee, Erica L Carpenter
The identification of therapeutically targetable mutations in circulating tumor cells (CTCs) from cancer patient blood is increasingly used to personalize patient care. Here, we describe a novel approach for the enumeration, capture, and molecular analysis of CTCs from blood using an FDA-approved CTC enrichment and enumeration platform followed by dielectrophoretic capture and next-generation sequencing.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28819851/rarecyte-%C3%A2-ctc-analysis-step-3-using-the-cytepicker-%C3%A2-module-for-individual-cell-retrieval-and-subsequent-whole-genome-amplification-of-circulating-tumor-cells-for-genomic-analysis
#4
Jackie L Stilwell, Paulina Varshavskaya, Jeffrey L Werbin, Joshua J Nordberg, Arturo B Ramirez, Steve Quarre, Jay Tzucker, Jennifer Chow, Brennan Enright, Eric P Kaldjian
The CytePicker module built into the RareCyte CyteFinder instrument allows researchers to easily retrieve individual cells from microscope slides for genomic analyses, including array CGH, targeted sequencing, and next-generation sequencing. Here, we describe the semiautomated retrieval of CTCs from the blood processed by AccuCyte (see Chapter 13) and amplification of genomic DNA so that molecular analysis can be performed.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28819720/immunohistochemical-null-phenotype-for-mismatch-repair-proteins-in-colonic-carcinoma-associated-with-concurrent-mlh1-hypermethylation-and-msh2-somatic-mutations
#5
Tao Wang, Zsofia K Stadler, Liying Zhang, Martin R Weiser, Olca Basturk, Jaclyn F Hechtman, Efsevia Vakiani, Lenard B Saltz, David S Klimstra, Jinru Shia
Microsatellite instability, a well-established driver pathway in colorectal carcinogenesis, can develop in both sporadic and hereditary conditions via different molecular alterations in the DNA mismatch repair (MMR) genes. MMR protein immunohistochemistry (IHC) is currently widely used for the detection of MMR deficiency in solid tumors. The IHC test, however, can show varied staining patterns, posing challenges in the interpretation of the staining results in some cases. Here we report a case of an 80-year-old female with a colonic adenocarcinoma that exhibited an unusual "null" IHC staining pattern with complete loss of all four MMR proteins (MLH1, MSH2, MSH6, and PMS2)...
August 17, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28819548/a-random-forest-classifier-for-detecting-rare-variants-in-ngs-data-from-viral-populations
#6
Raunaq Malhotra, Manjari Jha, Mary Poss, Raj Acharya
We propose a random forest classifier for detecting rare variants from sequencing errors in Next Generation Sequencing (NGS) data from viral populations. The method utilizes counts of varying length of k-mers from the reads of a viral population to train a Random forest classifier, called MultiRes, that classifies k-mers as erroneous or rare variants. Our algorithm is rooted in concepts from signal processing and uses a frame-based representation of k-mers. Frames are sets of non-orthogonal basis functions that were traditionally used in signal processing for noise removal...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28819152/dissecting-the-genomic-activity-of-a-transcriptional-regulator-by-the-integrative-analysis-of-omics-data
#7
Giulio Ferrero, Valentina Miano, Marco Beccuti, Gianfranco Balbo, Michele De Bortoli, Francesca Cordero
In the study of genomic regulation, strategies to integrate the data produced by Next Generation Sequencing (NGS)-based technologies in a meaningful ensemble are eagerly awaited and must continuously evolve. Here, we describe an integrative strategy for the analysis of data generated by chromatin immunoprecipitation followed by NGS which combines algorithms for data overlap, normalization and epigenetic state analysis. The performance of our strategy is illustrated by presenting the analysis of data relative to the transcriptional regulator Estrogen Receptor alpha (ERα) in MCF-7 breast cancer cells and of Glucocorticoid Receptor (GR) in A549 lung cancer cells...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819017/adrenocortical-carcinoma-and-succinate-dehydrogenase-gene-mutations
#8
Tobias Else, Antonio Marcondes Lerario, Jessica Everett, Lori Haymon, Deborah Wham, Michael Mullane, Tremika LeShan Wilson, Irene Rainville, Huma Rana, Andrew J Worth, Nathaniel W Snyder, Ian A Blair, Rana McKay, Kerry Kilbridge, Gary D Hammer, Justine Barletta, Anand Vaiyda
OBJECTIVE: Germline loss-of-function mutations in succinate dehydrogenase (SDHx) genes results in rare tumor syndromes that include pheochromocytoma, paraganglioma, and others. Here we report a case series of patients with adrenocortical carcinoma (ACC) that harbor SDHx germline mutations. PATIENTS AND RESULTS: We report four unrelated patients with ACC and SDHx mutations. All cases presented with Cushing syndrome and large adrenal masses that were confirmed to be ACC on pathology...
August 17, 2017: European Journal of Endocrinology
https://www.readbyqxmd.com/read/28818953/new-horizons-for-precision-medicine-in-biliary-tract-cancers
#9
REVIEW
Juan W Valle, Angela Lamarca, Lipika Goyal, Jorge Barriuso, Andrew X Zhu
Biliary tract cancers (BTC), including cholangiocarcinoma and gallbladder cancer, are poor-prognosis and low-incidence cancers, although the incidence of intrahepatic cholangiocarcinoma is rising. A minority of patients present with resectable disease but relapse rates are high; benefit from adjuvant capecitabine chemotherapy has been demonstrated. Cisplatin/gemcitabine combination chemotherapy has emerged as the reference first-line treatment regimen; there is no standard second-line therapy. Selected patients may be suitable for liver-directed therapy (e...
August 17, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28818896/genome-sequences-of-three-novel-isolates-of-human-parainfluenza-virus-2-associated-with-acute-respiratory-infection
#10
J L Kennedy, J C Kincaid, K C Schwalm, A N Stoner, T J Abramo, T M Thompson, O Hardin, C Putt, D L Dinwiddie
Using target capture of viral nucleic acid and next-generation sequencing, we generated the genome sequences of three novel human parainfluenza virus 2 isolates. Isolates ACRI_0185 (GenBank accession number MF077311), ACRI_0230 (MF077312), and ACRI_0248 (MF077313) were collected in October 2016, February 2017, and March 2017, respectively, from pediatric patients with acute respiratory infection in Arkansas.
August 17, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28818736/co-option-of-endogenous-viral-sequences-for-host-cell-function
#11
REVIEW
John A Frank, Cédric Feschotte
Eukaryotic genomes are littered with sequences of diverse viral origins, termed endogenous viral elements (EVEs). Here we used examples primarily drawn from mammalian endogenous retroviruses to document how the influx of EVEs has provided a source of prefabricated coding and regulatory sequences that were formerly utilized for viral infection and replication, but have been occasionally repurposed for cellular function. While EVE co-option has benefited a variety of host biological functions, there appears to be a disproportionate contribution to immunity and antiviral defense...
August 14, 2017: Current Opinion in Virology
https://www.readbyqxmd.com/read/28818680/clinical-validation-of-copy-number-variant-detection-from-targeted-next-generation-sequencing-panels
#12
Jennifer Kerkhof, Laila C Schenkel, Jack Reilly, Sheri McRobbie, Erfan Aref-Eshghi, Alan Stuart, C Anthony Rupar, Paul Adams, Robert A Hegele, Hanxin Lin, David Rodenhiser, Joan Knoll, Peter J Ainsworth, Bekim Sadikovic
Next-generation sequencing (NGS) technology has rapidly replaced Sanger sequencing in the assessment of sequence variations in clinical genetics laboratories. One major limitation of current NGS approaches is the ability to detect copy number variations (CNVs) greater than approximately 50bp. Since these represent a major mutational burden in many genetic disorders, parallel CNV assessment using alternate supplemental methods, along with the NGS analysis, is normally required resulting in increased labor, costs, and turnaround times...
August 14, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28818651/genomic-characterization-of-a-paediatric-mrsa-outbreak-by-next-generation-sequencing
#13
Elisabetta Ugolotti, Eddi Di Marco, Roberto Bandettini, Roberto Biassoni
INTRODUCTION: Twelve strains of meticillin-resistant Staphylococcus aureus (MRSA) isolated during a suspected outbreak in a Paediatric Intensive Care Unit were analyzed by Whole Genome Sequence (WGS). AIM: To define the clonality of MRSA strains to a high discriminative power and to evaluate the presence of genetic determinants responsible for antibiotic resistance and for virulence. RESULTS: Ten out of 12 strains belonged to the MLST ST2625, while the other two were ST8...
August 14, 2017: Journal of Hospital Infection
https://www.readbyqxmd.com/read/28818634/mining-na%C3%A3-ve-rabbit-antibody-repertoires-by-phage-display-for-monoclonal-antibodies-of-therapeutic-utility
#14
Haiyong Peng, Thomas Nerreter, Jing Chang, Junpeng Qi, Xiuling Li, Pabalu Karunadharma, Gustavo Martinez, Mohammad Fallahi, Jo Soden, Jim Freeth, Roger R Beerli, Ulf Grawunder, Michael Hudecek, Christoph Rader
Owing to their high affinities and specificities, rabbit monoclonal antibodies (mAbs) have demonstrated value and potential primarily as basic research and diagnostic reagents, but in some cases also as therapeutics. To accelerate access to rabbit mAbs bypassing immunization, we generated a large naïve rabbit antibody repertoire represented by a phage display library encompassing >10 billion independent antibodies in chimeric rabbit/human Fab format and validated it by next-generation sequencing. Panels of rabbit mAbs selected from this library against two emerging cancer targets, ROR1 and ROR2, revealed high diversity, affinity, and specificity...
August 14, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28818608/potential-resistance-mechanisms-revealed-by-targeted-sequencing-from-lung-adenocarcinoma-patients-with-primary-resistance-to-epidermal-growth-factor-receptor-egfr-tyrosine-kinase-inhibitors-tkis
#15
Jia Zhong, Lei Li, Zhijie Wang, Hua Bai, Gai Fei, Jian Chunduan, Jun Zhao, Minglei Zhuo, Yuyang Wang, Shuhang Wang, Wanchun Zang, Meina Wu, Tongtong An, Guanhua Rao, Jie Wang
BACKGROUND: EGFR-TKIs have greatly improved the prognosis of lung adenocarcinoma. However, approximately 5%-10% lung adenocarcinoma patients with EGFR sensitive mutations have primary resistance to EGFR-TKIs treatment. The underlying mechanism is unknown. METHODS: This study used next-generation sequencing (NGS) to explore the mechanisms of primary resistance by analyzing 11 patients with primary resistance and 11 patients sensitive to EGFR-TKIs. NGS targeted sequencing was performed on the Illumina X platform for 483 cancer-related genes...
August 14, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28818390/three-novel-recessive-mutations-in-lama2-syne1-and-ttn-are-identified-in-a-single-case-with-congenital-muscular-dystrophy
#16
Liang Wu, Bingwu Xiang, Huan Zhang, Xiaoxiao He, Celina Shih, Xiang Chen, Tao Cai
Congenital muscular dystrophies (CMD) are a group of heterogeneous disorders. Here, targeted next generation sequencing of 168 CMD-associated genes was performed on collected clinic samples to identify potential mutations. A loss-of-function mutation (c.4676-4682delGCTGCAA; p.Cys1560Thrfs*33) of the LAMA2 gene in a consanguineous family was identified and confirmed by Sanger sequencing. The second recessive mutation in SYNE1 (c.2881C>T; p.Arg961Trp) was found in the SAP motif, which was predicted to be involved in chromosomal organization...
July 6, 2017: Neuromuscular Disorders: NMD
https://www.readbyqxmd.com/read/28818389/common-and-variable-clinical-histological-and-imaging-findings-of-recessive-ryr1-related-centronuclear-myopathy-patients
#17
Osorio Abath Neto, Cristiane de Araújo Martins Moreno, Edoardo Malfatti, Sandra Donkervoort, Johann Böhm, Júlio Brandão Guimarães, A Reghan Foley, Payam Mohassel, Jahannaz Dastgir, Diana Xerxes Bharucha-Goebel, Soledad Monges, Fabiana Lubieniecki, James Collins, Līvija Medne, Mariarita Santi, Sabrina Yum, Brenda Banwell, Emmanuelle Salort-Campana, John Rendu, Julien Fauré, Uluc Yis, Bruno Eymard, Chrystel Cheraud, Raphaël Schneider, Julie Thompson, Xaviere Lornage, Lilia Mesrob, Doris Lechner, Anne Boland, Jean-François Deleuze, Umbertina Conti Reed, Acary Souza Bulle Oliveira, Valérie Biancalana, Norma B Romero, Carsten G Bönnemann, Jocelyn Laporte, Edmar Zanoteli
Mutations in RYR1 give rise to diverse skeletal muscle phenotypes, ranging from classical central core disease to susceptibility to malignant hyperthermia. Next-generation sequencing has recently shown that RYR1 is implicated in a wide variety of additional myopathies, including centronuclear myopathy. In this work, we established an international cohort of 21 patients from 18 families with autosomal recessive RYR1-related centronuclear myopathy, to better define the clinical, imaging, and histological spectrum of this disorder...
May 30, 2017: Neuromuscular Disorders: NMD
https://www.readbyqxmd.com/read/28818315/screening-for-familial-cancer-risk-focus-on-breast-cancer
#18
REVIEW
Christine Rousset-Jablonski, Anne Gompel
A breast or an ovarian cancer occurring at a young age and/or in a family where other cases preexist suggests that those patients should be candidates for screening for mutations. Despite decades of medical research, less than 30% of cases with a suggestive personal and/or family history of hereditary breast cancer have an identified causative gene mutation. The vast majority of these cases are due to a mutation in one of the highly penetrant breast cancer genes (BRCA1, BRCA2, PTEN, TP53, CDH1, and STK11) and various guidelines direct the management of these patients...
August 7, 2017: Maturitas
https://www.readbyqxmd.com/read/28818101/a-new-method-for-sequencing-the-hypervariable-plasmodium-falciparum-gene-var2csa-from-clinical-samples
#19
Antoine Dara, Mark A Travassos, Matthew Adams, Sarah Schaffer DeRoo, Elliott F Drábek, Sonia Agrawal, Miriam K Laufer, Christopher V Plowe, Joana C Silva
BACKGROUND: VAR2CSA, a member of the Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) family, mediates the binding of P. falciparum-infected erythrocytes to chondroitin sulfate A, a surface-associated molecule expressed in placental cells, and plays a central role in the pathogenesis of placental malaria. VAR2CSA is a target of naturally acquired immunity and, as such, is a leading vaccine candidate against placental malaria. This protein is very polymorphic and technically challenging to sequence...
August 17, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28818065/case-reports-of-two-pedigrees-with-recessive-arrhythmogenic-right-ventricular-cardiomyopathy-associated-with-homozygous-thr335ala-variant-in-dsg2
#20
Sami Qadri, Olli Anttonen, Juho Viikilä, Eija H Seppälä, Samuel Myllykangas, Tero-Pekka Alastalo, Miia Holmström, Tiina Heliö, Juha W Koskenvuo
BACKGROUND: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited cardiac disease, involving changes in ventricular myocardial tissue and leading to fatal arrhythmias. Mutations in desmosomal genes are thought to be the main cause of ARVC. However, the exact molecular genetic etiology of the disease still remains largely inconclusive, and this along with large variabilities in clinical manifestations complicate clinical diagnostics. CASE PRESENTATION: We report two families (n = 20) in which a desmoglein-2 (DSG2) missense variant c...
August 17, 2017: BMC Medical Genetics
keyword
keyword
83023
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"