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https://www.readbyqxmd.com/read/28706301/a-haystack-heuristic-for-autoimmune-disease-biomarker-discovery-using-next-gen-immune-repertoire-sequencing-data
#1
Leonard Apeltsin, Shengzhi Wang, H-Christian von Büdingen, Marina Sirota
Large-scale DNA sequencing of immunological repertoires offers an opportunity for the discovery of novel biomarkers for autoimmune disease. Available bioinformatics techniques however, are not adequately suited for elucidating possible biomarker candidates from within large immunosequencing datasets due to unsatisfactory scalability and sensitivity. Here, we present the Haystack Heuristic, an algorithm customized to computationally extract disease-associated motifs from next-generation-sequenced repertoires by contrasting disease and healthy subjects...
July 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28688118/a-pair-of-dicer1-positive-monozygotic-twins-one-with-pleuropulmonary-blastoma-another-with-acute-transient-hepatitis
#2
Sihui Li, Siyu Cai, Xisi Wang, Dawei Zhang, Libing Fu, Qi Zeng, Xiaoxia Peng, Xiaoli Ma
Pleuropulmonary blastoma (PPB) is the most common primary malignant neoplasm of the lung in children that is associated with a germline mutation in DICER1. In this report, we share an interesting case of a pair of monozygotic twins: one of them developed PPB when she was 4-year old, while the other developed acute transient hepatitis when she was 5-year old. Next-Gen sequencing for DICER1 mutations of their family revealed that both twins and their mother had c.C3675A mutation. The mother also had a history of multinodular goiter...
July 8, 2017: Pediatric Blood & Cancer
https://www.readbyqxmd.com/read/28660979/gel-seq-whole-genome-and-transcriptome-sequencing-by-simultaneous-low-input-dna-and-rna-library-preparation-using-semi-permeable-hydrogel-barriers
#3
Gordon D Hoople, Andrew Richards, Yan Wu, Kota Kaneko, Xiaolin Luo, Gen-Sheng Feng, Kun Zhang, Albert P Pisano
The advent of next generation sequencing has fundamentally changed genomics research. Unfortunately, standard protocols for sequencing the genome and the transcriptome are incompatible. This forces researchers to choose between examining either the DNA or the RNA for a particular sample. Here we describe a new device and method, collectively dubbed Gel-seq, that enables researchers to simultaneously sequence both DNA and RNA from the same sample. This technology makes it possible to directly examine the ways that changes in the genome impact the transcriptome in as few as 100 cells...
June 29, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28442585/next-gen-sequencing-analysis-and-algorithms-for-pdx-and-cdx-models
#4
Garima Khandelwal, Maria Romina Girotti, Christopher Smowton, Sam Taylor, Chris Wirth, Marek Dynowski, Kristopher K Frese, Ged Brady, Caroline Dive, Richard Marais, Crispin Miller
Patient-derived xenograft (PDX) and CTC-derived explant (CDX) models are powerful methods for the study of human disease. In cancer research, these methods have been applied to multiple questions including the study of metastatic progression, genetic evolution and therapeutic drug responses. Since PDX and CDX models can recapitulate the highly heterogeneous characteristics of a patient tumor, as well as their response to chemotherapy, there is considerable interest in combining them with next-generation sequencing (NGS) in order to monitor the genomic, transcriptional, and epigenetic changes that accompany oncogenesis...
April 25, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28289279/next-gen-sequencing-identifies-non-coding-variation-disrupting-mirna-binding-sites-in-neurological-disorders
#5
P Devanna, X S Chen, J Ho, D Gajewski, S D Smith, A Gialluisi, C Francks, S E Fisher, D F Newbury, S C Vernes
Understanding the genetic factors underlying neurodevelopmental and neuropsychiatric disorders is a major challenge given their prevalence and potential severity for quality of life. While large-scale genomic screens have made major advances in this area, for many disorders the genetic underpinnings are complex and poorly understood. To date the field has focused predominantly on protein coding variation, but given the importance of tightly controlled gene expression for normal brain development and disorder, variation that affects non-coding regulatory regions of the genome is likely to play an important role in these phenotypes...
March 14, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28224057/identification-and-characterization-of-microsatellite-markers-in-pinus-kesiya-var-langbianensis-pinaceae
#6
Nian-Hui Cai, Yu-Lan Xu, Da-Wei Wang, Shi Chen, Gen-Qian Li
PREMISE OF THE STUDY: Microsatellite primers were developed in Pinus kesiya var. langbianensis (Pinaceae), a species native to southwestern China, to investigate its genetic diversity and population structure in order to provide information for the conservation and management of this species. METHODS AND RESULTS: Using next-generation sequencing, a total of 2349 putative simple sequence repeat primer pairs were designed. Eighteen polymorphic markers in 60 individuals belonging to four populations of P...
February 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/27901429/no-panacea-next-gen-sequencing-will-not-mitigate-adoptees-lack-of-genetic-family-health-history
#7
Stephanie M Fullerton
No abstract text is available yet for this article.
December 2016: American Journal of Bioethics: AJOB
https://www.readbyqxmd.com/read/27785359/pygeno-a-python-package-for-precision-medicine-and-proteogenomics
#8
Tariq Daouda, Claude Perreault, Sébastien Lemieux
pyGeno is a Python package mainly intended for precision medicine applications that revolve around genomics and proteomics. It integrates reference sequences and annotations from Ensembl, genomic polymorphisms from the dbSNP database and data from next-gen sequencing into an easy to use, memory-efficient and fast framework, therefore allowing the user to easily explore subject-specific genomes and proteomes. Compared to a standalone program, pyGeno gives the user access to the complete expressivity of Python, a general programming language...
2016: F1000Research
https://www.readbyqxmd.com/read/27745839/structural-chromosomal-rearrangements-require-nucleotide-level-resolution-lessons-from-next-generation-sequencing-in-prenatal-diagnosis
#9
Zehra Ordulu, Tammy Kammin, Harrison Brand, Vamsee Pillalamarri, Claire E Redin, Ryan L Collins, Ian Blumenthal, Carrie Hanscom, Shahrin Pereira, India Bradley, Barbara F Crandall, Pamela Gerrol, Mark A Hayden, Naveed Hussain, Bibi Kanengisser-Pines, Sibel Kantarci, Brynn Levy, Michael J Macera, Fabiola Quintero-Rivera, Erica Spiegel, Blair Stevens, Janet E Ulm, Dorothy Warburton, Louise E Wilkins-Haug, Naomi Yachelevich, James F Gusella, Michael E Talkowski, Cynthia C Morton
In this exciting era of "next-gen cytogenetics," integrating genomic sequencing into the prenatal diagnostic setting is possible within an actionable time frame and can provide precise delineation of balanced chromosomal rearrangements at the nucleotide level. Given the increased risk of congenital abnormalities in newborns with de novo balanced chromosomal rearrangements, comprehensive interpretation of breakpoints could substantially improve prediction of phenotypic outcomes and support perinatal medical care...
November 3, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/27706155/alignerboost-a-generalized-software-toolkit-for-boosting-next-gen-sequencing-mapping-accuracy-using-a-bayesian-based-mapping-quality-framework
#10
Qi Zheng, Elizabeth A Grice
Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present...
October 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27624755/coetzeea-brasiliensis-gen-nov-sp-nov-isolated-from-larvae-of-anopheles-darlingi
#11
Peter Kämpfer, Stefanie P Glaeser, Osvaldo Marinotti, Lionel Guy, Sebastian Håkansson, Wanderli P Tadei, Hans-Jürgen Busse, Olle Terenius
A Gram-stain-negative, rod-shaped strain, Braz8T, isolated from larvae of Anopheles darlingi was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Braz8T was related most closely to species of the genus Thorsellia, with 95.6, 96.5 and 96.6 % similarity to the type strains of Thorsellia anophelis, Thorsellia kandunguensis and Thorsellia kenyensis, respectively, and formed a separate branch in the phylogenetic tree next to the monophyletic cluster of the genus Thorsellia...
December 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27489207/genome-wide-analysis-of-polyadenylation-events-in-schmidtea-mediterranea
#12
Vairavan Lakshmanan, Dhiru Bansal, Jahnavi Kulkarni, Deepak Poduval, Srikar Krishna, Vidyanand Sasidharan, Praveen Anand, Aswin Seshasayee, Dasaradhi Palakodeti
In eukaryotes, 3' untranslated regions (UTRs) play important roles in regulating posttranscriptional gene expression. The 3'UTR is defined by regulated cleavage/polyadenylation of the pre-mRNA. The advent of next-generation sequencing technology has now enabled us to identify these events on a genome-wide scale. In this study, we used poly(A)-position profiling by sequencing (3P-Seq) to capture all poly(A) sites across the genome of the freshwater planarian, Schmidtea mediterranea, an ideal model system for exploring the process of regeneration and stem cell function...
October 13, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27488298/clinical-decision-making-integrating-advances-in-the-molecular-understanding-of-spine-tumors
#13
REVIEW
C Rory Goodwin, Nancy Abu-Bonsrah, Mark H Bilsky, Jeremy J Reynolds, Laurence D Rhines, Ilya Laufer, Alexander C Disch, Arpad Bozsodi, Shreyaskumar R Patel, Ziya L Gokaslan, Daniel M Sciubba, Chetan Bettegowda
STUDY DESIGN: Literature review. OBJECTIVE: To describe advancements in molecular techniques, biomarkers, technology, and targeted therapeutics and the potential these modalities hold to predict treatment paradigms, clinical outcomes, and/or survival in patients diagnosed with primary spinal column tumors. SUMMARY OF BACKGROUND DATA: Advances in molecular technologies and techniques have influenced the prevention, diagnosis, and overall management of patients diagnosed with cancer...
October 15, 2016: Spine
https://www.readbyqxmd.com/read/27470940/herbihabitans-rhizosphaerae-gen-nov-sp-nov-a-member-of-the-family-pseudonocardiaceae-isolated-from-rhizosphere-soil-of-the-herb-limonium-sinense-girard
#14
Chang-Feng Zhang, Meng-Jie Ai, Ju-Xian Wang, Shao-Wei Liu, Li-Li Zhao, Jing Su, Cheng-Hang Sun, Li-Yan Yu, Yu-Qin Zhang
The taxonomic position of an actinobacterium, designated CPCC 204279T, which was isolated from a rhizosphere soil sample of the herb Limonium sinense collected from Xinjiang Province, China, was established using a polyphasic approach. Whole-cell hydrolysates of strain CPCC 204279T contained galactose and arabinose as diagnostic sugars and meso-diaminopimelic acid as the diamino acid. The muramic acid residues in the peptidoglycan were N-acetylated. The predominant menaquinone was MK-9(H4). The phospholipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides...
October 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27446181/-omics-tools-for-better-understanding-the-plant-endophyte-interactions
#15
REVIEW
Sanjana Kaul, Tanwi Sharma, Manoj K Dhar
Endophytes, which mostly include bacteria, fungi and actinomycetes, are the endosymbionts that reside asymptomatically in plants for at least a part of their life cycle. They have emerged as a valuable source of novel metabolites, industrially important enzymes and as stress relievers of host plant, but still many aspects of endophytic biology are unknown. Functions of individual endophytes are the result of their continuous and complex interactions with the host plant as well as other members of the host microbiome...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27390188/tartrate-resistant-acid-phosphatase-deficiency-in-the-predisposition-to-systemic-lupus-erythematosus
#16
Jie An, Tracy A Briggs, Audrey Dumax-Vorzet, Marta E Alarcón-Riquelme, Alexandre Belot, Michael Beresford, Ian N Bruce, Claudia Carvalho, Laurence Chaperot, Johan Frostegård, Joel Plumas, Gillian I Rice, Timothy J Vyse, Alice Wiedeman, Yanick J Crow, Keith B Elkon
OBJECTIVE: Mutations in the ACP5 gene, which encodes tartrate-resistant acid phosphatase (TRAP), cause the immuno-osseous disorder spondyloenchondrodysplasia, which includes as disease features systemic lupus erythematosus (SLE) and a type I interferon (IFN) signature. Our aims were to identify TRAP substrates, determine the consequences of TRAP deficiency in immune cells, and assess whether ACP5 mutations are enriched in sporadic cases of SLE. METHODS: Interaction between TRAP and its binding partners was tested by a yeast 2-hybrid screening, confocal microscopy, and immunoprecipitation/Western blotting...
January 2017: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/27388436/next-generation-sequencing-of-an-88-year-old-specimen-of-the-poorly-known-species-liagora-japonica-nemaliales-rhodophyta-supports-the-recognition-of-otohimella-gen-nov
#17
Masahiro Suzuki, Takahiro Segawa, Hiroshi Mori, Ayumi Akiyoshi, Ryo Ootsuki, Akira Kurihara, Hidetoshi Sakayama, Taiju Kitayama, Tsuyoshi Abe, Kazuhiro Kogame, Hiroshi Kawai, Hisayoshi Nozaki
Liagora japonica is a red algal species distributed in temperate regions of Japan. This species has not been collected from its type locality on the Pacific coast of Japan since 1927 and seems to have become extinct in this area. For molecular characterization of L. japonica, we extracted DNA from the topotype material of L. japonica collected in 1927, analyzed seven genes using Illumina next-generation sequencing, and compared these data with sequences from modern samples of similar red algae collected from the Japan Sea coast of Japan...
2016: PloS One
https://www.readbyqxmd.com/read/27376026/editorial-hereditary-cancer-risk-assessment-new-perspectives-and-challenges-for-the-next-gen-sequencing-era
#18
Israel Gomy
No abstract text is available yet for this article.
2016: Frontiers in Oncology
https://www.readbyqxmd.com/read/27318200/genome-puzzle-master-gpm-an-integrated-pipeline-for-building-and-editing-pseudomolecules-from-fragmented-sequences
#19
Jianwei Zhang, Dave Kudrna, Ting Mu, Weiming Li, Dario Copetti, Yeisoo Yu, Jose Luis Goicoechea, Yang Lei, Rod A Wing
MOTIVATION: Next generation sequencing technologies have revolutionized our ability to rapidly and affordably generate vast quantities of sequence data. Once generated, raw sequences are assembled into contigs or scaffolds. However, these assemblies are mostly fragmented and inaccurate at the whole genome scale, largely due to the inability to integrate additional informative data sets (e.g. physical, optical & genetic maps). To address this problem, we developed a semi-automated software tool - Genome Puzzle Master (GPM) - that enables the integration of additional genomic signposts to edit and build "new-gen-assemblies" that result in high-quality "annotation-ready" pseudomolecules...
June 17, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27225403/rapid-drug-susceptibility-testing-of-drug-resistant-mycobacterium-tuberculosis-isolates-directly-from-clinical-samples-by-use-of-amplicon-sequencing-a-proof-of-concept-study
#20
Rebecca E Colman, Julia Anderson, Darrin Lemmer, Erik Lehmkuhl, Sophia B Georghiou, Hannah Heaton, Kristin Wiggins, John D Gillece, James M Schupp, Donald G Catanzaro, Valeriu Crudu, Ted Cohen, Timothy C Rodwell, David M Engelthaler
Increasingly complex drug-resistant tuberculosis (DR-TB) is a major global health concern and one of the primary reasons why TB is now the leading infectious cause of death worldwide. Rapid characterization of a DR-TB patient's complete drug resistance profile would facilitate individualized treatment in place of empirical treatment, improve treatment outcomes, prevent amplification of resistance, and reduce the transmission of DR-TB. The use of targeted next-generation sequencing (NGS) to obtain drug resistance profiles directly from patient sputum samples has the potential to enable comprehensive evidence-based treatment plans to be implemented quickly, rather than in weeks to months, which is currently needed for phenotypic drug susceptibility testing (DST) results...
August 2016: Journal of Clinical Microbiology
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