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Next gen sequencing, genomics

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https://www.readbyqxmd.com/read/29898714/calculating-the-statistical-significance-of-rare-variants-causal-for-mendelian-and-complex-disorders
#1
Aliz R Rao, Stanley F Nelson
BACKGROUND: With the expanding use of next-gen sequencing (NGS) to diagnose the thousands of rare Mendelian genetic diseases, it is critical to be able to interpret individual DNA variation. To calculate the significance of finding a rare protein-altering variant in a given gene, one must know the frequency of seeing a variant in the general population that is at least as damaging as the variant in question. METHODS: We developed a general method to better interpret the likelihood that a rare variant is disease causing if observed in a given gene or genic region mapping to a described protein domain, using genome-wide information from a large control sample...
June 13, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29690565/prostate-cancer-genomics-recent-advances-and-the-prevailing-underrepresentation-from-racial-and-ethnic-minorities
#2
REVIEW
Shyh-Han Tan, Gyorgy Petrovics, Shiv Srivastava
Prostate cancer (CaP) is the most commonly diagnosed non-cutaneous cancer and the second leading cause of male cancer deaths in the United States. Among African American (AA) men, CaP is the most prevalent malignancy, with disproportionately higher incidence and mortality rates. Even after discounting the influence of socioeconomic factors, the effect of molecular and genetic factors on racial disparity of CaP is evident. Earlier studies on the molecular basis for CaP disparity have focused on the influence of heritable mutations and single-nucleotide polymorphisms (SNPs)...
April 22, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29626926/interpreting-chromosomal-rearrangements-in-the-context-of-3-dimentional-genome-organization-a-practical-guide-for-medical-genetics
#3
REVIEW
V S Fishman, P A Salnikov, N R Battulin
In this exciting era of "next-gen cytogenetics", the use of novel molecular methods such as comparative genome hybridization and whole genome and whole exome sequencing becomes more and more common in clinics. This results in generation of large amounts of high-resolution patient-specific data and challenges the development of new approaches for interpretation of obtained information. Usually, interpretation of chromosomal rearrangements is focused on alterations of linear genome sequence, underestimating the role of spatial chromatin organization...
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29593773/sequencing-and-analysis-of-strobilanthes-cusia-nees-kuntze-chloroplast-genome-revealed-the-rare-simultaneous-contraction-and-expansion-of-the-inverted-repeat-region-in-angiosperm
#4
Haimei Chen, Junjie Shao, Hui Zhang, Mei Jiang, Linfang Huang, Zhao Zhang, Dan Yang, Molly He, Mostafa Ronaghi, Xi Luo, Botao Sun, Wuwei Wu, Chang Liu
Ban-Lan-Gen, the root tissues derived from several morphologically indistinguishable plant species, have been used widely in traditional Chinese medicines for numerous years. The identification of reliable markers to distinguish various source plant species is critical for the effective and safe use of products containing Ban-Lan-Gen. Here, we analyzed and characterized the complete chloroplast (cp) genome sequence of Strobilanthes cusia (Nees) Kuntze to identify high-resolution markers for the species determination of Southern Ban-Lan-Gen...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29385401/accurity-accurate-tumor-purity-and-ploidy-inference-from-tumor-normal-wgs-data-by-jointly-modelling-somatic-copy-number-alterations-and-heterozygous-germline-single-nucleotide-variants
#5
Zhihui Luo, Xinping Fan, Yao Su, Yu S Huang
Motivation: Tumor purity and ploidy have a substantial impact on next-gen sequence analyses of tumor samples and may alter the biological and clinical interpretation of results. Despite the existence of several computational methods that are dedicated to estimate tumor purity and/or ploidy from The Cancer Genome Atlas (TCGA) tumor-normal whole-genome-sequencing (WGS) data, an accurate, fast, and fully-automated method that works in a wide range of sequencing coverage, level of tumor purity, and level of intra-tumor heterogeneity, is still missing...
January 27, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29302837/up-regulated-pro-inflammatory-micrornas-mirnas-in-alzheimer-s-disease-ad-and-age-related-macular-degeneration-amd
#6
Aileen I Pogue, Walter J Lukiw
Alzheimer's disease (AD) of the brain neocortex and age-related macular degeneration (AMD) of the retina are two complex neurodegenerative disorders, which (i) involve the progressive dysregulation and deterioration of multiple neurobiological signaling pathways, (ii) exhibit the temporal accumulation of pro-inflammatory lesions including the amyloid beta (Aβ) peptide-containing senile plaques of AD and the drusen of AMD, and (iii) culminate in an insidious inflammatory neurodegeneration ending, respectively, in neural cell atrophy and death and progressive loss of cognition and central visual function...
January 4, 2018: Cellular and Molecular Neurobiology
https://www.readbyqxmd.com/read/29193904/somatic-mosaicism-of-an-intragenic-fancb-duplication-in-both-fibroblast-and-peripheral-blood-cells-observed-in-a-fanconi-anemia-patient-leads-to-milder-phenotype
#7
Rajalakshmi S Asur, Danielle C Kimble, Francis P Lach, Moonjung Jung, Frank X Donovan, Aparna Kamat, Raymond J Noonan, James W Thomas, Morgan Park, Peter Chines, Adrianna Vlachos, Arleen D Auerbach, Agata Smogorzewska, Settara C Chandrasekharappa
BACKGROUND: Fanconi anemia (FA) is a rare disorder characterized by congenital malformations, progressive bone marrow failure, and predisposition to cancer. Patients harboring X-linked FANCB pathogenic variants usually present with severe congenital malformations resembling VACTERL syndrome with hydrocephalus. METHODS: We employed the diepoxybutane (DEB) test for FA diagnosis, arrayCGH for detection of duplication, targeted capture and next-gen sequencing for defining the duplication breakpoint, PacBio sequencing of full-length FANCB aberrant transcript, FANCD2 ubiquitination and foci formation assays for the evaluation of FANCB protein function by viral transduction of FANCB-null cells with lentiviral FANCB WT and mutant expression constructs, and droplet digital PCR for quantitation of the duplication in the genomic DNA and cDNA...
January 2018: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/29133595/targeted-next-generation-sequencing-for-detecting-mll-gene-fusions-in-leukemia
#8
Sadia Afrin, Christine R C Zhang, Claus Meyer, Caedyn L Stinson, Thy Pham, Timothy J C Bruxner, Nicola C Venn, Toby N Trahair, Rosemary Sutton, Rolf Marschalek, J Lynn Fink, Andrew S Moore
Mixed lineage leukemia ( MLL ) gene rearrangements characterize approximately 70% of infant and 10% of adult and therapy-related leukemia. Conventional clinical diagnostics, including cytogenetics and fluorescence in situ hybridization (FISH) fail to detect MLL translocation partner genes (TPG) in many patients. Long-distance inverse (LDI)-PCR, the "gold standard" technique that is used to characterize MLL breakpoints, is laborious and requires a large input of genomic DNA (gDNA). To overcome the limitations of current techniques, a targeted next-generation sequencing (NGS) approach that requires low RNA input was tested...
February 2018: Molecular Cancer Research: MCR
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
#9
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...
July 25, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28442585/next-generation-sequencing-analysis-and-algorithms-for-pdx-and-cdx-models
#10
Garima Khandelwal, María Romina Girotti, Christopher Smowton, Sam Taylor, Christopher Wirth, Marek Dynowski, Kristopher K Frese, Ged Brady, Caroline Dive, Richard Marais, Crispin Miller
Patient-derived xenograft (PDX) and circulating tumor cell-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. As 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 to monitor the genomic, transcriptional, and epigenetic changes that accompany oncogenesis...
August 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
#11
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...
May 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/27785359/pygeno-a-python-package-for-precision-medicine-and-proteogenomics
#12
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
#13
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
#14
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/27489207/genome-wide-analysis-of-polyadenylation-events-in-schmidtea-mediterranea
#15
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
#16
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
#17
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
#18
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/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 datasets (e.g. physical, optical and 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...
October 15, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27208355/hiding-in-plain-sight-koshicola-spirodelophila-gen-et-sp-nov-chaetopeltidales-chlorophyceae-a-novel-green-alga-associated-with-the-aquatic-angiosperm-spirodela-polyrhiza
#20
Shin Watanabe, Karolina Fučíková, Louise A Lewis, Paul O Lewis
PREMISE OF THE STUDY: Discovery and morphological characterization of a novel epiphytic aquatic green alga increases our understanding of Chaetopeltidales, a poorly known order in Chlorophyceae. Chloroplast genomic data from this taxon reveals an unusual architecture previously unknown in green algae. METHODS: Using light and electron microscopy, we characterized the morphology and ultrastructure of a novel taxon of green algae. Bayesian phylogenetic analyses of nuclear and plastid genes were used to test the hypothesized membership of this taxon in order Chaetopeltidales...
May 2016: American Journal of Botany
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