المؤلفون: Jiming Chen, Guangyu Hou, Qingye Zhuang, Yuan Qiu, Tong Wang, Kaicheng Wang, Run Wu

المصدر: Virus Research

مصطلحات موضوعية: Library, 0301 basic medicine, Cancer Research, animal structures, animal diseases, viruses, AIV, avian influenza virus, IBV, infectious bronchitis virus, PBS, phosphate buffered solution, Computational biology, Biology, Article, DNA sequencing, law.invention, Duck, Feces, 03 medical and health sciences, PCR, polymerase chain reaction, law, SISPA, sequence independent single primer amplification, Next generation sequencing, Virology, Animals, RNA Viruses, Human virome, Polymerase chain reaction, DNA Primers, RT, reverse transcription, Reverse Transcriptase Polymerase Chain Reaction, Virome, virus diseases, High-Throughput Nucleotide Sequencing, RNA, PGM, Personal Genome Machine, Amplicon, Reverse transcriptase, Virus, NGS, next-generation sequencing, Detection, Ducks, 030104 developmental biology, Infectious Diseases, Mink, NDV, Newcastle disease virus, Metagenome, Metagenomics, Primer (molecular biology), Personal genomics

الوصف: Highlights • RNA-Seq libraries were constructed using three methods. • RNA virome in ducks was detected. • RNA virome in mink was detected. • Various viruses in ducks or minks were possibly first identified.
Virome (viral megagenomics) detection using next generation sequencing has been widely applied in virology, but its methods remain complicated and need optimization. In this study, we detected the viromes of RNA viruses of one mock sample, one pooled duck feces sample and one pooled mink feces sample on the Personal Genome Machine platform using the sequencing libraries prepared by three methods. The sequencing primers were added through random hybridization and ligation to fragmented viral RNA using a RNA-Seq kit in method 1, through random reverse transcription (RT) and polymerase chain reaction (PCR) in method 2 which was developed in our laboratory, and through hybridization and ligation to fragmented amplicons of random RT-PCR using a single primer in method 3. Although the results of these three samples (nine libraries) all showed that more classified viral families and genera were identified using methods 2 and 3 than using method 1, and more classified viral families and genera were identified using method 2 than using method 3, most of the differences were of no statistical significance. Moreover, 11 mammalian viral genera in minks were possibly identified for the first time through this study.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fe87a8f4c39030125577e5cac17dcac0Test
https://doi.org/10.1016/j.virusres.2017.05.003Test

المؤلفون: Hovelson, Daniel H., McDaniel, Andrew S., Cani, Andi K., Johnson, Bryan, Rhodes, Kate, Williams, Paul D., Bandla, Santhoshi, Bien, Geoffrey, Choppa, Paul, Hyland, Fiona, Gottimukkala, Rajesh, Liu, Guoying, Manivannan, Manimozhi, Schageman, Jeoffrey, Ballesteros-Villagrana, Efren, Grasso, Catherine S., Quist, Michael J., Yadati, Venkata, Amin, Anmol, Siddiqui, Javed, Betz, Bryan L., Knudsen, Karen E., Cooney, Kathleen A., Feng, Felix Y., Roh, Michael H., Nelson, Peter S., Liu, Chia-Jen, Beer, David G., Wyngaard, Peter, Chinnaiyan, Arul M., Sadis, Seth, Rhodes, Daniel R., Tomlins, Scott A.

المصدر: Neoplasia (New York, N.Y.)

مصطلحات موضوعية: Male, Proto-Oncogene Proteins B-raf, NCCN, National Comprehensive Cancer Network, CNAs, copy number alterations, DNA Mutational Analysis, PR, prostate cohort, Article, LU, lung cohort, Proto-Oncogene Proteins p21(ras), OCP, Oncomine Comprehensive Panel, indels, insertions/deletions, SCC, small cell carcinoma, Transcriptional Regulator ERG, Neoplasms, Proto-Oncogene Proteins, Humans, Anaplastic Lymphoma Kinase, QMRS, Quantitative Multiplex Reference Standard, MO, molecular cohort, beta Catenin, Aged, Retrospective Studies, MCR, minimal common region, Serine Endopeptidases, Computational Biology, High-Throughput Nucleotide Sequencing, Receptor Protein-Tyrosine Kinases, PGM, Personal Genome Machine, DNA, Neoplasm, Middle Aged, FFPE, formalin-fixed paraffin-embedded, NGS, next-generation sequencing, ErbB Receptors, GoF, gain-of-function, LoF, loss-of-function, Mutation, Trans-Activators, ras Proteins, AOHC, AcroMetrix Oncology Hotspot Control, TCGA, The Cancer Genome Atlas, Female

الوصف: Next-generation sequencing (NGS) has enabled genome-wide personalized oncology efforts at centers and companies with the specialty expertise and infrastructure required to identify and prioritize actionable variants. Such approaches are not scalable, preventing widespread adoption. Likewise, most targeted NGS approaches fail to assess key relevant genomic alteration classes. To address these challenges, we predefined the catalog of relevant solid tumor somatic genome variants (gain-of-function or loss-of-function mutations, high-level copy number alterations, and gene fusions) through comprehensive bioinformatics analysis of >700,000 samples. To detect these variants, we developed the Oncomine Comprehensive Panel (OCP), an integrative NGS-based assay [compatible with 95% accuracy for KRAS, epidermal growth factor receptor, and BRAF mutation detection as well as for ALK and TMPRSS2:ERG gene fusions. Associating positive variants with potential targeted treatments demonstrated that 6% to 42% of profiled samples (depending on cancer type) harbored alterations beyond routine molecular testing that were associated with approved or guideline-referenced therapies. As a translational research tool, OCP identified adaptive CTNNB1 amplifications/mutations in treated prostate cancers. Through predefining somatic variants in solid tumors and compiling associated potential treatment strategies, OCP represents a simplified, broadly applicable targeted NGS system with the potential to advance precision oncology efforts.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=pmid________::4d12a35876071dc9bfe5d003ea1ccf27Test
http://europepmc.org/articles/PMC4415141Test

المؤلفون: Eyal Klement, Ziv Raviv, Tzipi Braun, Avishai Lublin, Elyakum Berman, Michael Pirak, Michal Bronstein, Elinor Yechezkel, Meirav Ben Izhak, Chaim Wachtel, Adi Turjeman, Yoram Louzoun, Caroline Banet-Noach, Einav Golan, Anat Wiseman, Saar Tal, Ruth Hadas

المصدر: Gene: X, Vol 1, Iss, Pp-(2019)
Gene: X

مصطلحات موضوعية: SP, Specific primers, nt, nucleotide, 0301 basic medicine, AAvV-1, Newcastle Disease virus, lcsh:QH426-470, NCBI, National Center for Biotechnology Information, Newcastle disease virus, Computational biology, Biology, Genome, Article, DNA sequencing, 03 medical and health sciences, 0302 clinical medicine, Genetics, Sequencing, Gene, AAvV-1, Whole genome sequencing, PGM, Personal Genome Machine, General Medicine, Ion semiconductor sequencing, biology.organism_classification, WGS, Whole Genome Sequence or sequencing, lcsh:Genetics, 030104 developmental biology, NGS, 030220 oncology & carcinogenesis, Avulavirus, SISPA, Sequence Independent Single Primer Amplification, Primer (molecular biology), NGS, Next Generation Sequencing, WGS, Mutations, Personal genomics

الوصف: Background Avian avulavirus-1 (AAvV-1, previously Newcastle Disease Virus) is responsible for poultry and wild birds' disease outbreaks. Numerous whole genome sequencing methods were reported for this virus. These methods included cloning, specific primers amplification, shotgun PCR approaches, Sequence Independent Single Primer Amplification and next generation sequencing platform kits. Methods Three methods were used to sequence 173 Israeli Avian avulavirus-1 field isolates and one vaccine strain (VH). The sequencing was performed on Proton and Ion Torrent Personal Genome Machine and to a lesser extent, Illumina MiSeq and NextSeq sequencers. Target specific primers (SP) and Sequence Independent Single Primer Amplification (SISPA) products sequenced via the Ion torrent sequencer had a high error rate and truncated genomes. All the next generation sequencing platform sequencing kits generated high sequence accuracy and near-complete genomic size. Results A high level of mutations was observed in the intergenic regions between the avian avulavirus-1 genes. Within genes, multiple regions are more mutated than the Fusion region currently used for typing. Conclusions Our findings suggest that the whole genome sequencing by the Ion torrent sequencing kit is sufficient. However, when higher fidelity is desired, the Illumina NextSeq and Proton torrent sequencing kits were found to be preferable.
Highlights • PCR amplification of the viral genome, results in partial genome sequences (72% and 98% respectively). • Primer based sequencing methods have 5 to 5.6 times more N reads compared to NGS platform sequencing kits, indicating poor sequence quality. • The Ion Torrent PGM sequencing results in sequencing 99% of the viral genome. • ProtonTorrent and Illumina Nextseq sequenced 99-100% of the viral genome, leading a to full genome sequence at high coverage. • The virus is mostly mutated within a host at intergenic regions.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4be478412fb0aa5141b7a0668b9fc4a9Test
https://doi.org/10.1016/j.gene.2019.100004Test

المؤلفون: Namrata Patel, Prakash G. Koringa, Neelam M. Nathani, Tejash M. Shah, Shreya M. Patel, Chaitanya G. Joshi

المصدر: Meta Gene

مصطلحات موضوعية: SAM, Sequence Alignment Map, dbSNP, NRAMP1, Natural Resistance associated macrophage protein 1, BNBD4, Neutrophil beta-defensin 4, CHGC, Chromagranin C, NCBI, National Center for Biotechnology Information, Innate immune genes, SNP, Single Nucleotide Polymorphism, UTR, Untranslated Region, Single-nucleotide polymorphism, Biology, Genome, DNA sequencing, Article, Next generation sequencing, Indian cattle and buffalo, Genetics, Haplotype, BWA, Burrows–Wheeler Aligner, BAM, Binary Alignment Map, PCR, Polymerase Chain Reaction, TLR, Toll Like Receptor, Genetics (clinical), Tissue homeostasis, GATK, Genome Analysis Tool Kit, DEFB1, Beta defensin 1, RFLP, Restriction Fragment Length Polymorphism, Ion semiconductor sequencing, PGM, Personal Genome Machine, CHGA, Chromagranin A, SLC11, Solute Carrier Family 11, SAS, Statistical Analysis System, Single nucleotide polymorphism, SNV, Single Nucleotide Variant, CHGB, Chromagranin B, LD, Linkage Disequilibrium, NRAMP2, Natural Resistance associated macrophage protein 2, LAP, Lingual Antimicrobial Peptide, EM, Expectation Maximization, BNBD5, Neutrophil beta-defensin 5, TAP, Tracheal Antimicrobial Peptide, Reference genome

الوصف: Activation of innate immunity initiates various cascades of reactions that largely contribute to defense against physical, microbial or chemical damage, prompt for damage repair and removal of causative organisms as well as restoration of tissue homeostasis. Genetic polymorphism in innate immune genes plays prominent role in disease resistance capabilities in various breeds of cattle and buffalo. Here we studied single nucleotide variations (SNP/SNV) and haplotype structure in innate immune genes viz CHGA, CHGB, CHGC, NRAMP1, NRAMP2, DEFB1, BNBD4, BNBD5, TAP and LAP in Gir cattle and Murrah buffalo. Targeted sequencing of exonic regions of these genes was performed by Ion Torrent PGM sequencing platform. The sequence reads obtained corresponding to coding regions of these genes were mapped to reference genome of cattle BosTau7 by BWA program using genome analysis tool kit (GATK). Further variant analysis by Unified Genotyper revealed 54 and 224 SNPs in Gir and Murrah respectively and also 32 SNVs was identified. Among these SNPs 43, 36, 11,32,81,21 and 22 variations were in CHGA, CHGB, CHGC, NRAMP1, NRAMP2, DEFB1 and TAP genes respectively. Among these identified 278 SNPs, 24 were found to be reported in the dbSNP database. Variant analysis was followed by structure formation of haplotypes based on multiple SNPs using SAS software revealed a large number of haplotypes. The SNP discovery in innate immune genes in cattle and buffalo breeds of India would advance our understanding of role of these genes in determining the disease resistance/susceptibility in Indian breeds. The identified SNPs and haplotype data would also provide a wealth of sequence information for conservation studies, selective breeding and designing future strategies for identifying disease associations involving samples from distinct populations.
Highlights • Sequencing of exonic regions of 10 selected innate immune genes, 895.60 Mb data was generated. • Variant analysis using GATK pipeline revealed 278 SNPs, 32 SNVs and from these 24 were found to be reported. • 43, 36 and 11 SNPs were observed in chromagranin genes viz. CHGA, CHGB and CHGC respectively. • 32 and 81 SNPs were identified in NRAMP genes viz. NRAMP1 and NRAMP2 respectively. • 21 and 22 SNPs were observed in β-defensin genes viz. DEFB1 and TAP respectively.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::be18b3efefa25efce26b68241b11d8eeTest
https://pubmed.ncbi.nlm.nih.gov/26925373Test