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Targeted Exon Sequencing Successfully Discovers Rare Causative Genes and Clarifies the Molecular Epidemiology of Japanese Deafness Patients

Maiko Miyagawa, Takehiko Naito, Shin-ya Nishio, Naoyuki Kamatani, Shin-ichi Usami, Andreas R. Janecke
2013 PLoS ONE  
Target exon resequencing using Massively Parallel DNA Sequencing (MPS) is a new powerful strategy to discover causative genes in rare Mendelian disorders such as deafness.  ...  In addition, using a large number of patients, the present study clarified the molecular epidemiology of deafness in Japanese.  ...  Comparison with Another Algorithm for Pooled DNA Samples We also analyzed all the data with VIPR, a program established and validated for use with pooled samples [24] .  ... 
doi:10.1371/journal.pone.0071381 pmid:23967202 pmcid:PMC3742761 fatcat:3ycqekeunre5vks47e52l3h4m4

Polymorphisms of Vasoactive Intestinal Peptide Receptor-1 Gene and Their Genetic Effects on Broodiness in Chickens

M. Zhou, M. Lei, Y. Rao, Q. Nie, H. Zeng, M. Xia, F. Liang, D. Zhang, X. Zhang
2008 Poultry Science  
One hundred twenty-eight variation sites were identified in the 11,136bp region of the chicken VIPR-1 gene.  ...  The partial cloning and sequencing of the VIPR-1 gene showed that the average nucleotide diversity was 0.00669 ± 0.00093 in Red Jungle Fowls (RJF), and 0.00582 ± 0.00026 in domestic chickens.  ...  In each population, 2 loci were considered in LD (r 2 ≥ 0.33), in strongly LD (r 2 ≥ 0.6), in complete disequilibrium (r 2 = 1).  ... 
doi:10.3382/ps.2007-00495 pmid:18420979 fatcat:76mhgptarjf3ln6bxtjw6fw66q

Viral interference with antigen presentation

Jonathan W. Yewdell, Ann B. Hill
2002 Nature Immunology  
viral transmission) of viral gene products that interfere with antigen presentation in vitro.  ...  REVIEW www.nature.com/natureimmunology • november 2002 • volume 3 no 11 • nature immunology 1019 CD8 + T cells play an important role in immunity to viruses.  ...  VIPRs may yet teach us something about antigen presentation.  ... 
doi:10.1038/ni1102-1019 pmid:12407410 fatcat:2vb5d4m3dbbnvbniij2rlyrhly

Microarrays for Pathogen Detection and Analysis

K. S. McLoughlin
2011 Briefings in Functional Genomics  
DNA microarrays have emerged as a viable platform for detection of pathogenic organisms in clinical and environmental samples.  ...  While pathogen detection arrays have been used primarily in a research context, several groups are aggressively working to develop arrays for clinical diagnostics, food safety testing, environmental monitoring  ...  VIPR VIPR (Viral Identification using a PRobabilistic algorithm) [34] is a technique developed for analysis of viral diagnostic microarrays.  ... 
doi:10.1093/bfgp/elr027 pmid:21930658 pmcid:PMC3245552 fatcat:um7x35qvjvandhmbu5ohfsvwci

Functional Coding Variants in SLC6A15, a Possible Risk Gene for Major Depression

Carina Quast, Serena Cuboni, Daniel Bader, André Altmann, Peter Weber, Janine Arloth, Simone Röh, Tanja Brückl, Marcus Ising, Anna Kopczak, Angelika Erhardt, Felix Hausch (+3 others)
2013 PLoS ONE  
DNA from 400 depressed patients and 400 controls was screened for genetic variants using a pooled targeted re-sequencing approach.  ...  In total, we identified 405 genetic variants, including twelve non-synonymous variants.  ...  Results Variant Identification Using NGS In total, 405 genetic variants were detected in the sequencing runs.  ... 
doi:10.1371/journal.pone.0068645 pmid:23874702 pmcid:PMC3712998 fatcat:hl7ofnirsvfp3gdw433uxze5jm

Multiplex Reverse Transcription-PCR for Simultaneous Surveillance of Influenza A and B Viruses

Bin Zhou, Yi-Mo Deng, John R. Barnes, October M. Sessions, Tsui-Wen Chou, Malania Wilson, Thomas J. Stark, Michelle Volk, Natalie Spirason, Rebecca A. Halpin, Uma Sangumathi Kamaraj, Tao Ding (+6 others)
2017 Journal of Clinical Microbiology  
Sequence information from influenza virus genomes is instrumental in determining mechanisms underpinning antigenic evolution and antiviral resistance.  ...  The strategy was validated on thousands of seasonal influenza A and B virus-positive specimens using multiple next-generation sequencing platforms.  ...  With the closest viral genome as a guide, the consensus genome of the sample was generated by using the 'bam2cons_iter.sh' script from the ViPR pipeline (https://github.com/CSB5/vipr).  ... 
doi:10.1128/jcm.00957-17 pmid:28978683 pmcid:PMC5703814 fatcat:v3efz3uxcfcgreh57lz5mcn5oq

A comprehensive collection of systems biology data characterizing the host response to viral infection

Brian D. Aevermann, Brett E. Pickett, Sanjeev Kumar, Edward B. Klem, Sudhakar Agnihothram, Peter S. Askovich, Armand Bankhead, Meagen Bolles, Victoria Carter, Jean Chang, Therese R.W. Clauss, Pradyot Dash (+56 others)
2014 Scientific Data  
This program generated 47 transcriptomic and proteomic datasets from 30 studies that investigate in vivo and in vitro host responses to viral infections.  ...  By comparing data from mutant versus wild-type virus and host strains, RNA versus protein differential expression, and infection with genetically similar strains, these data can be used to further investigate  ...  Acknowledgements Data described here was funded in whole or in part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health  ... 
doi:10.1038/sdata.2014.33 pmid:25977790 pmcid:PMC4410982 fatcat:7n47nith2ndg7njw2o5iks3rtq

Software Dedicated to Virus Sequence Analysis "Bioinformatics Goes Viral" [chapter]

Martin Hölzer, Manja Marz
2017 Advances in Virus Research  
Above all, there is an urgent need for dedicated software tools to tackle various challenges in virology.  ...  The attention of bioinformaticians to this challenging field is currently unsatisfying in respect to its medical and biological importance.  ...  R.  ... 
doi:10.1016/bs.aivir.2017.08.004 pmid:29029728 pmcid:PMC7172532 fatcat:e7fyqwbkcze3xhvzywnyapn7z4

Advanced Molecular and Immunological Diagnostic Methods to Detect SARS-CoV-2 Infection

John Charles Rotondo, Fernanda Martini, Martina Maritati, Elisabetta Caselli, Carla Enrica Gallenga, Matteo Guarino, Roberto De Giorgio, Chiara Mazziotta, Maria Letizia Tramarin, Giada Badiale, Mauro Tognon, Carlo Contini
2022 Microorganisms  
Real Time-PCR-based assays for the detection of viral RNA are currently considered the gold-standard method for SARS-CoV-2 diagnosis and can be used efficiently on pooled nasopharyngeal, or oropharyngeal  ...  First of all, the preventive vaccine, which has been implemented in record time, is effective in more than 95% of cases.  ...  Second, continued viral variants generated by people from continents where vaccination programs are limited, can often lead to difficulties in identification and negatively affect the current vaccination  ... 
doi:10.3390/microorganisms10061193 pmid:35744711 pmcid:PMC9231257 fatcat:stpv5btcizfk7dbqqwoslcvl4a

Multifunctional CRISPR-Cas9 with engineered immunosilenced human T cell epitopes

Shayesteh R. Ferdosi, Radwa Ewaisha, Farzaneh Moghadam, Sri Krishna, Jin G. Park, Mo R. Ebrahimkhani, Samira Kiani, Karen S. Anderson
2019 Nature Communications  
them by T cell assays using healthy donor PBMCs.  ...  We also report pre-existing human CD8+T cell immunity in the majority of healthy individuals screened.  ...  We thank the Center for Computational and Integrative Biology (CCIB) DNA core facility at Massachusetts General Hospital and Genomics and Bioinformatics (TCGB) core at UCLA for the DNA and RNA sequencing  ... 
doi:10.1038/s41467-019-09693-x pmid:31015529 pmcid:PMC6478683 fatcat:mtesk6r265c4bmwlhqb4xuipme

Single molecule, near full-length genome sequencing of dengue virus

Thiruni N. Adikari, Nasir Riaz, Chathurani Sigera, Preston Leung, Braulio M. Valencia, Kirston Barton, Martin A. Smith, Rowena A. Bull, Hui Li, Fabio Luciani, Praveen Weeratunga, Tun-Linn Thein (+7 others)
2020 Scientific Reports  
Pairwise genetic distances of within host variants identified from the Nano-Q tool were less than that of between host variants, thus enabling the phylogenetic segregation of variants from the same host  ...  We introduce an assay to amplify near full-length dengue virus genomes as intact molecules, sequence these amplicons with third generation "nanopore" technology without fragmenting and use the sequence  ...  Within-host variant identification.  ... 
doi:10.1038/s41598-020-75374-1 pmid:33097792 fatcat:pgfpi5ov6zdcfcscdn6yoc4e3i

Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples using nanopore sequencing

Alexander G. Shaw, Manasi Majumdar, Catherine Troman, Áine O'Toole, Blossom Benny, Dilip Abraham, Ira Praharaj, Gagandeep Kang, Salmaan Sharif, Muhammad Masroor Alam, Shahzad Shaukat, Mehar Angez (+14 others)
2020 Journal of Clinical Microbiology  
Variant analysis of sequencing reads also allowed identification of polioviruses and enteroviruses in artificial mixtures and was able to distinguish complex mixtures of polioviruses in environmental samples  ...  Direct detection of viral RNA using PCR allows faster detection but has traditionally faced challenges related to poor sensitivity and difficulties in sequencing common samples containing poliovirus and  ...  ACKNOWLEDGMENTS We thank the members of the ARTIC network for helpful discussions in the development of this work. We thank James Hadfield for support and development of the RAMPART software package.  ... 
doi:10.1128/jcm.00920-20 pmid:32611795 pmcid:PMC7448630 fatcat:tix3iff7vbfqzgzvcmmm72puaq

Multifunctional CRISPR/Cas9 with engineered immunosilenced human T cell epitopes [article]

Shayesteh R. Ferdosi, Radwa Ewaisha, Farzaneh Moghadam, Sri Krishna, Jin G. Park, Mo R. Ebrahimkhani, Samira Kiani, Karen S. Anderson
2018 bioRxiv   pre-print
The application of Cas9 for genetic and epigenetic therapies in humans raises concerns over immunogenicity of this foreign protein.  ...  We report pre-existing human CD8+ T cell immunity to Streptococcus pyogenes Cas9 in the majority of healthy individuals screened.  ...  The use of CRISPR/Cas9 in humans may eventually necessitate creating HLA type-specific Cas9 variants, particularly for applications that require long-term Cas9 expression.  ... 
doi:10.1101/360198 fatcat:4keh6cmd2vhzfk7oft4gearhha

A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection

Tran Thi Ngoc Dung, Pham Thanh Duy, October M. Sessions, Uma K. Sangumathi, Voong Vinh Phat, Pham Thi Thanh Tam, Nguyen Thi Nguyen To, Tran My Phuc, Tran Thi Hong Chau, Nguyen Ngoc Minh Chau, Ngoc Nguyen Minh, Guy E. Thwaites (+2 others)
2017 BMC Genomics  
Acknowledgements We thank the children and parents enrolled in this trial and the staff of Children's Hospital 2 in HCMC, Vietnam.  ...  Assembled sequences are deposited in GenBank under accession numbers KY634534-KY634860. Authors' contributions  ...  LoFreq2 was then used to detect the single nucleotide variants present in the sample [35] .  ... 
doi:10.1186/s12864-017-3714-6 pmid:28438140 pmcid:PMC5404283 fatcat:w4y5htipsjeedfyu4sjbtl5ldy

Hacking the diversity of SARS-CoV-2 and SARS-like coronaviruses in human, bat and pangolin populations [article]

Nicholas John Dimonaco, Mazdak Salavati, Barbara Shih
2020 bioRxiv   pre-print
Lastly, we have characterised several high impact variants (inframe insertion/deletion or stop gain) in bat-CoV and pangolin-CoV populations, some of which are found in the same amino acid position and  ...  Following de novo gene annotation prediction, analysis on gene-gene similarity network, codon usage bias and variant discovery were carried out.  ...  Using taxonomic data made available by the Virus Pathogen Database and Analysis Resource (ViPR) [66] 429 Host-Source No.  ... 
doi:10.1101/2020.11.24.391763 fatcat:dthnhvi6wzdjtdfrplasiyhnei
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