News Article | May 4, 2017
Crohn's disease (CD) results from a complex interplay between host genetic factors and endogenous microbial communities. In the current study, the Ghannoum lab used Ion Torrent sequencing to characterize the gut bacterial microbiota (bacteriome) and fungal community (mycobiome) in patients with CD and their non-diseased first degree relatives (NCDR) in 9 familial clusters living in Northern France/Belgium, and in healthy individuals from 4 families living in the same area (non-CD unrelated, NCDU). Significant microbial interactions were identified and validated using single- and mixed-species biofilms. CD and non-diseased first degree relatives groups clustered together in the mycobiome, but not in bacteriome. Recent research is showing that this fungal-bacterial interaction is detrimental to the host, novel prevention and treatment approaches are needed to interfere with this cooperation and restore the microbiome balance. In this webinar, attendees will learn about the mycobiome contribute to digestive tract health and Crohn’s disease. They will also learn how individual steps in their microbiomics workflow can be standardized to greatly improve the quality and reproducibility of the data generated. Dr. Mahmoud Ghannoum, professor and director at the Center for Medical Mycology, Case Western Reserve University and University Hospitals Case Medical Center, will be a speaker for this event along with Dr. Shuiquan Tang, scientist at Zymo Research Corp. Ghannoum received a Master of Science in medicinal chemistry and doctorate in microbial physiology from University of Technology in England, and an MBA from the Weatherhead School of Management at Case. Presently he is a tenured Professor and Director of the Center for Medical Mycology, Case Western Reserve University and University Hospitals Case Medical Center (UH). He is also a fellow of the Infectious Disease Society of America and past President of the Medical Mycological Society of the Americas (MMSA). Tang received a doctorate of chemical engineering and applied chemistry from the University of Toronto. He joined Zymo Research in 2014, and has since been instrumental in the research and development of Zymo's microbiomics and metagenomics programs. His past experiences include work in the fields of environmental microbiology and biological process engineering, with an emphasis on bioinformatics, metagenomics and anaerobic cultivation. LabRoots will host the webinar May 22, 2017, beginning at 8:00 a.m. PDT, 11:00 a.m. ET. To read more about this event, discover the continuing education credits offered, or to register for free, click here. About Zymo Research Corp. Zymo Research Corp. is a privately held nucleic acid purification company based in Irvine, California, USA. Since its inception in 1994 it has been serving the academic and biopharmaceutical scientific communities by providing DNA and RNA purification products. In early 2016 Zymo Research developed ZymoBIOMICS®, a comprehensive line of microbiomics related products including two microbial standards, to assist researchers in accurate microbial profiling. In addition its microbiomic, epigenetic, and nucleic acid purification products, Zymo Research also provides genetic, epigenetic and transcriptome analysis services. Follow Zymo Research Corporation on Facebook, LinkedIn, Twitter, and Instagram. About LabRoots LabRoots is the leading scientific social networking website and producer of educational virtual events and webinars. Contributing to the advancement of science through content sharing capabilities, LabRoots is a powerful advocate in amplifying global networks and communities. Founded in 2008, LabRoots emphasizes digital innovation in scientific collaboration and learning, and is a primary source for current scientific news, webinars, virtual conferences, and more. LabRoots has grown into the world’s largest series of virtual events within the Life Sciences and Clinical Diagnostics community.
News Article | May 22, 2017
(PRLEAP.COM) Family ReEntry, a nonprofit leader that assists families affected by the criminal justice system, today announced the appointment of three key new board members, who will help guide the organization on its program expansion and advocacy efforts.Carlah Esdaile Bragg, David Light and Christian Morris have accepted nomination to serve on the Family ReEntry board of directors. The commitment enlists the skills, knowledge and advisory of all activities for the organization to increase its services that restore dignity and renew families that have been impacted by incarceration and the justice system.Jeff Grant, Executive Director of Family ReEntry, said, "Carlah, David and Christian bring exceptional experience, expertise and relationships to our board. They each have a special, different perspective that is ideal for guiding the future of Family ReEntry."Bragg is a lifelong resident of New Haven, CT with an understanding of local and statewide conditions, community needs and strategies. She is currently the Director of Marketing and Community Relations for Cornell Scott - Hill Health Center, Connecticut's oldest and one of the largest community health centers in the state, providing medical, behavioral health and dental services to more than 30,000 residents. She is an advocate, holding various positions with the NAACP. Bragg served on the City of New Haven Fresh Start planning team and serves on the City of New Haven Reentry Advisory Committee, and the Reentry Roundtable Faith Based Committee.Light is a biotech scientist and entrepreneur from Branford, CT. A graduate of Yale University, David studied molecular, cellular and developmental biology. At Ion Torrent, David invented a particle that enabled the commercial viability of DNA semiconductor sequencing and helped lead to the acquisition of Ion Torrent by Life Technologies. At Life Technologies, David was Head of Chemistry R&D, and when Life Tech was acquired by Thermo Fisher Scientific, Light transitioned to Director of Product Management in order to directly handle the commercialization of the technologies that he helped develop. For the past six years, David has guest lectured at Yale where he teaches undergraduates about DNA sequencing. Light is also a founding board member of the ShuLounge of New Haven. a novel congregation catering to a vibrant and diverse community."I'm honored to be a member of the board of directors at Family ReEntry and support its vital and impactful work, which has special meaning to me and my family, who have directly felt the effects and difficulties resulting from incarceration," Light explained.Morris, who first consulted with Family ReEntry on strategic business planning, now brings added value to the organization with his background in technology and software business application solutions. Morris is co-founder of SmartPath Labs, a technology and business advisory firm focused on new market adoption and strategic partnerships for emerging technology companies. As the former Executive Vice President of CometaWorks, Morris delivered technology solutions across financial services, healthcare, educational institutions, and entertainment sectors. Previously, Morris served on the board of Sound Affects, a nonprofit organization dedicated to changing how the war on cancer is fought and financed with a mission to increase the implementation of promising new treatments by empowering individuals to directly support bio-entrepreneur's research. Morris lives in Westport, CT.With the assistance of the three newest members, the board of Family ReEntry seeks to advise the organization in supporting, not just the individuals who are reentering society after incarceration, but the families and friends of those individuals as they transition. Family ReEntry provides vital services to help individuals and families in the areas of prevention, intervention, diversion, in-prison and reentry.Currently, there are over 2.3 million people incarcerated in the United States and over 70 million with criminal records. "It is vital that we reach these individuals at critical junctures in their lives and provide them with enough support so that they can have every opportunity to achieve, learn and grow as citizens who are not forced to return to the kind of activity that caused them to be incarcerated in the first place," said Grant, a man who knows very well of the difficulties that formerly incarcerated individuals can face. He served almost 14 months in Federal prison for a white-collar crime he committed in 2001 when he was a lawyer. Grant said. "As the first person in the country formerly incarcerated for a white-collar crime to be appointed as Executive Director of a major criminal justice nonprofit, I try to be a role model that there is hope after prison.""The situation can seem overwhelming to those most affected, but there is help," Grant explained. "Men and woman and their families who come through Family ReEntry are succeeding in making positive contributions and improving their lives. While national averages show a large percentage of this population returning to prison, we are seeing that Family ReEntry's work is significantly lowering that percentage."Family ReEntry is a 501c3 nonprofit, which was founded in 1984 as a reentry support group for men at the Isaiah House in Bridgeport. It has since grown to include policy advocacy, and intervention, prevention, in-prison, reentry, fatherhood and youth & family programs. Over the past 33 years, effective advocacy efforts and community-based programs developed by Family ReEntry have significantly reduced the likelihood that clients will re-offend, be re-arrested, or be re-incarcerated. Its programs provide a spectrum of services designed to disrupt the intergenerational cycle of incarceration. Family ReEntry addresses the specific needs of each client and their families through individualized case management and support services. It works to create a positive social network for each client, helping make their transition from prison back into the community a successful, self-sufficient one, while strengthening their families and the community. Family ReEntry operates its programs in strategic locations that encompass eight municipal regions and judicial geographic areas, two parole districts and five prisons. Approximately, sixty-percent of those served by Family ReEntry are from greater Bridgeport Connecticut's largest city. The organization has offices in Bridgeport, Norwalk and New Haven, CT. Programs are also held in Stamford, Waterbury, Derby, New London and Norwich, CT. More information is available at www.familyreentry.org and on its social media including, Facebook Instagram and YouTube
News Article | May 24, 2017
"Cost was a limiting factor for panels with a large number of amplicons. For researchers that need to change their gene content frequently, the lower price for oligos is really great," said Pan Zhang, Ph.D., M.D., director, Sequencing and Microarray Center at Coriell Institute for Medical Research. Adam Ameur, Ph.D., Bioinformatics Scientist, National Genomics Infrastructure, SciLifeLab at Uppsala University, added: "The majority of the projects we provide service for have only a few samples, so it is good to have a small pack size. Previously, we have been limited because of the cost, so this may open up other studies in which we look at larger genes with fewer samples." Ion AmpliSeq On-Demand Panels are custom designed by customers on the Ion AmpliSeq Designer tool (www.ampliseq.com) by selecting from a growing repository of highly optimized gene targets that are relevant in germline disorder research. The tool's disease-gene database, which allows gene selection based on disease research area, has been informed by public repositories, such as the Medical Subject Headings (MeSH) database, and includes primer sets based on 1,000's of proven designs that are also wet lab verified to guarantee performance. Panels are then ordered instantaneously in practical pack sizes that fit experiment needs and lower upfront costs. "Targeted sequencing using customer-designed custom panels has proven to be a popular method for driving translational research, but for uncommon, complex diseases such as germline disorders, most labs do not have the number of samples to justify the significant investment of time and money," said Joydeep Goswami, president of Clinical Next-Generation Sequencing and Oncology at Thermo Fisher Scientific. "By simplifying the way users can customize their content and pack delivery size, clinical researchers can focus on targets of interest that will drive greater discovery without the high upfront cost and risk of waste." Thermo Fisher will provide demonstrations of the new Ion AmpliSeq Designer Software for delegates who request them at ESHG 2017. The company is also hosting a workshop featuring talks from early access users of Ion AmpliSeq On-Demand Panels and other new technology from Thermo Fisher. The complementary workshop, titled New Products to Enable Discovery of De Novo and Germline Mutations, will take place Sunday, May 28 at 11:15 am CET in the Ballerup Room at the Bella Center Copenhagen (BCC). Workshop presenters include: Additional Ion Torrent NGS products to be highlighted at ESHG 2017 include: For more information on the Ion AmpliSeq On-Demand Panels, stop by Thermo Fisher's booth (#438) or visit www.thermofisher.com/ampliseqondemand.html. For more information on the workshop at ESHG, visit www.thermofisher.com/eshg17. Ion AmpliSeq On-Demand Panels, Ion ReproSeq PGS Kits and Ion 510 Chip are For Research Use Only; not for use in diagnostic procedures. About Thermo Fisher Scientific Thermo Fisher Scientific Inc. is the world leader in serving science, with revenues of $18 billion and more than 55,000 employees globally. Our mission is to enable our customers to make the world healthier, cleaner and safer. We help our customers accelerate life sciences research, solve complex analytical challenges, improve patient diagnostics and increase laboratory productivity. Through our premier brands – Thermo Scientific, Applied Biosystems, Invitrogen, Fisher Scientific and Unity Lab Services – we offer an unmatched combination of innovative technologies, purchasing convenience and comprehensive support. For more information, please visit www.thermofisher.com. To view the original version on PR Newswire, visit:http://www.prnewswire.com/news-releases/new-on-demand-targeted-next-generation-sequencing-panels-for-inherited-disease-research-deliver-user-customization-without-high-upfront-cost-300461447.html
News Article | May 24, 2017
A targeted NGS approach is the preferred method for researchers who study germline disorders in an effort to understand complex diseases that require analysis of multiple genes. Compared to the time-consuming and costly whole exome or whole genome sequencing, targeted NGS has become an especially beneficial approach in clinical research settings where a more practical, efficient and economical way to resequence tens-to-hundreds of specific gene targets is often required. "Cost was a limiting factor for panels with a large number of amplicons. For researchers that need to change their gene content frequently, the lower price for oligos is really great," said Pan Zhang, Ph.D., M.D., director, Sequencing and Microarray Center at Coriell Institute for Medical Research. Adam Ameur, Ph.D., Bioinformatics Scientist, National Genomics Infrastructure, SciLifeLab at Uppsala University, added: "The majority of the projects we provide service for have only a few samples, so it is good to have a small pack size. Previously, we have been limited because of the cost, so this may open up other studies in which we look at larger genes with fewer samples." Ion AmpliSeq On-Demand Panels are custom designed by customers on the Ion AmpliSeq Designer tool (www.ampliseq.com) by selecting from a growing repository of highly optimized gene targets that are relevant in germline disorder research. The tool's disease-gene database, which allows gene selection based on disease research area, has been informed by public repositories, such as the Medical Subject Headings (MeSH) database, and includes primer sets based on 1,000's of proven designs that are also wet lab verified to guarantee performance. Panels are then ordered instantaneously in practical pack sizes that fit experiment needs and lower upfront costs. "Targeted sequencing using customer-designed custom panels has proven to be a popular method for driving translational research, but for uncommon, complex diseases such as germline disorders, most labs do not have the number of samples to justify the significant investment of time and money," said Joydeep Goswami, president of Clinical Next-Generation Sequencing and Oncology at Thermo Fisher Scientific. "By simplifying the way users can customize their content and pack delivery size, clinical researchers can focus on targets of interest that will drive greater discovery without the high upfront cost and risk of waste." Thermo Fisher will provide demonstrations of the new Ion AmpliSeq Designer Software for delegates who request them at ESHG 2017. The company is also hosting a workshop featuring talks from early access users of Ion AmpliSeq On-Demand Panels and other new technology from Thermo Fisher. The complementary workshop, titled New Products to Enable Discovery of De Novo and Germline Mutations, will take place Sunday, May 28 at 11:15 am CET in the Ballerup Room at the Bella Center Copenhagen (BCC). Workshop presenters include: Additional Ion Torrent NGS products to be highlighted at ESHG 2017 include: For more information on the Ion AmpliSeq On-Demand Panels, stop by Thermo Fisher's booth (#438) or visit www.thermofisher.com/ampliseqondemand.html. For more information on the workshop at ESHG, visit www.thermofisher.com/eshg17. Ion AmpliSeq On-Demand Panels, Ion ReproSeq PGS Kits and Ion 510 Chip are For Research Use Only; not for use in diagnostic procedures. About Thermo Fisher Scientific Thermo Fisher Scientific Inc. is the world leader in serving science, with revenues of $18 billion and more than 55,000 employees globally. Our mission is to enable our customers to make the world healthier, cleaner and safer. We help our customers accelerate life sciences research, solve complex analytical challenges, improve patient diagnostics and increase laboratory productivity. Through our premier brands – Thermo Scientific, Applied Biosystems, Invitrogen, Fisher Scientific and Unity Lab Services – we offer an unmatched combination of innovative technologies, purchasing convenience and comprehensive support. For more information, please visit www.thermofisher.com.
News Article | February 15, 2017
Les résultats de Mount Sinaï, de l'Université de Washington, et des laboratoires de Cold Spring Harbor seront présentés à AGBT ANN ARBOR, Michigan, 15 février 2017 /PRNewswire/ -- Swift Biosciences a annoncé aujourd'hui la mise sur le marché de son kit de préparation de bibliothèque Accel-NGS® XL, la solution de séquençage la plus rapide pour le séquençage du génome entier sur les plateformes Pacific Biosciences® (PacBio®). Ce kit de préparation de bibliothèque, spécialement optimisé pour la technologie de séquençage d'une simple molécule en temps réel (SMRT®) de PacBio, fournit des lectures de séquençage significativement plus longues avec un simple workflow à tube unique utilisant des introductions d'échantillons réduites. Swift Biosciences accepte dès maintenant des commandes pour le kit Accel-NGS XL —vendu exclusivement par Swift. « Grâce à son workflow convivial de quatre heures et ses plus longues lectures, le kit Accel-NGS XL améliore considérablement les applications de séquençage de génome entier, telles que le séquençage d'haplotypes et d'assemblages de novo, sur n'importe quel génome y compris le génome microbien, végétal, animal, et humain », a déclaré Haley Fiske, directrice commerciale de Swift Biosciences. « Ces améliorations de la qualité et du workflow aident les utilisateurs de PacBio à obtenir des résultats plus significatifs dans chaque passage tout en doublant leur productivité. » Dans le cadre de l'assemblée générale AGBT 2017, Swift Biosciences et plusieurs collaborateurs scientifiques ont présenté deux affiches dévoilant les données de séquençage générées grâce à cette nouvelle chimie. La première affiche, intitulée « Une méthode améliorant la longueur de lecture du séquençage SMRT », a affiché les résultats, générés en collaboration avec Mount Sinaï et les laboratoires de Cold Spring Harbor, à partir de divers génomes y compris les génomes végétaux, bactériens et l'ADN de référence humain. Les données à l'appui ont produit des lectures moyennes allant jusqu'à 20Kb, avec une introduction d'échantillon réduite de 50% et sans artefact de dimère adaptateur. Sur la deuxième affiche, intitulée « Méthodes de construction de bibliothèque améliorées pour la plateforme de séquençage Pacific Biosciences utilisant le kit de préparation de bibliothèque Accel-NGS XL pour PacBio appliqué à des clones BAC problématiques pour l'amélioration de la référence du génome humain », Robert Fulton, directeur du développement et de gestion de projet au McDonnell Genome Institute de l'Université de Washington, a présenté les résultats de séquençage de clones BAC humains qui démontrent des rendements de bibliothèque accrus avec de plus longues lectures de séquençage. « Swift Biosciences est la première société à offrir des solutions de préparation de bibliothèque sur les trois principales plateformes de séquençage, Pacific Biosystems, Illumina® et Ion Torrent™ », a ajouté Timothy Harkins, Ph.D., président-directeur général de Swift Biosciences. « Nous sommes stratégiquement axés sur l'expansion du marché NGS en simplifiant les workflows complexes avec nos technologies de bibliothèque innovantes et en apportant de nouvelles applications à chacune des plateformes de séquençage de prochaine génération (next generation sequencing, NGS). Nos bibliothèques fournissent les données de la plus haute qualité dans les applications les plus problématiques. Swift est la 'The NGS library company'. »
News Article | February 15, 2017
- Swift Biosciences lanza su nuevo kit de biblioteca de larga inserción para mejorar la calidad de los datos en las plataformas de secuenciación PacBio Los resultados de Mount Sinai, Washington University y de Cold Spring Harbor Laboratories se presentarán en AGBT ANN ARBOR, Michigan, 15 de febrero de 2017 /PRNewswire/ -- Swift Biosciences anunció hoy el lanzamiento comercial de su kit de preparación de biblioteca Accel-NGS® XL, la solución de secuenciación más rápida para toda la secuenciación del genoma en las plataformas Pacific Biosciences® (PacBio®). Este kit de preparación de biblioteca, optimizado especialmente para la tecnología de secuenciación Single Molecule, Real-Time (SMRT®) de PacBio, proporciona lecturas de secuenciación mucho más largas con un solo flujo de trabajo de un solo tubo utilizando menos entradas de muestras. Swift Biosciences ya acepta pedidos para el kit Accel-NGS XL— vendido de forma exclusiva por medio de Swift. "Con su flujo de trabajo sencillo de cuatro horas y longitudes de lectura mayores, el kit Accel-NGS XL mejora de forma sustancial todas las aplicaciones de secuenciación del genoma, como el montaje de novo y la secuenciación de haplotipo, en cualquier genoma que incluyen microbiales, planta, animales y humanos", afirmó Haley Fiske, responsable comercial de Swift Biosciences. "Estas mejoras de calidad y flujo de trabajo ayuda a los usuarios de PacBio para generar resultados más destacados desde cada puesta en marcha con una productividad que es del doble". Swift Biosciences y diversos colaboradores científicos presentaron dos posters en la reunión general de la AGBT 2017 mostrando los datos de secuenciación generados con esta nueva química. El primer poster, titulado "A Method to Improve Read Length of SMRT Sequencing", mostró los resultados, generados en colaboración con Mount Sinai y Cold Spring Harbor Laboratories, desde diversos genomas, incluyendo el ADN de referencia de plantas, bacterias y humanos. Los datos de apoyo produjeron unas lecturas medias de hasta 20Kb, con un 50% menos de entrada de muestra y sin dispositivos de adaptador de dímero. En el segundo poster, titulado "Improved Library Construction Methods for the Pacific Biosciences Sequencing Platform Using Swift Accel-NGS XL Library Prep Kit for PacBio Applied to Challenging BAC Clones for Human Genome Reference Improvement", Robert Fulton, director de desarrollo de proyectos y gestión del McDonnell Genome Institute of Washington University, presentó los resultados de la secuenciación de clones humanos BAC, demostrando unos rendimientos de biblioteca superiores con lecturas de secuenciación más largas. "Swift Biosciences es la primera compañía que ofrece soluciones de preparación de biblioteca en las tres principales plataformas de secuenciación, incluyendo Pacific Biosystems, Illumina®, e Ion Torrent™", destacó Timothy Harkins, Ph.D., director general y consejero delegado de Swift Biosciences. "Estamos centrados de forma estratégica en la ampliación del mercado NGS por medio de la simplificación de los flujos de trabajo complejos por medio de las tecnologías de biblioteca innovadoras y por el suministro de aplicaciones nuevas para cada una de las plataformas NGS. Nuestras bibliotecas proporcionan los datos de la mayor calidad en las aplicaciones más complejas. Swift es por ello la 'The NGS library company'".
News Article | March 1, 2017
The experiments were not randomized and the investigators were not blinded to allocation during experiments and outcome assessment. ARC-Net, University of Verona: approval number 1885 from the Integrated University Hospital Trust (AOUI) Ethics Committee (Comitato Etico Azienda Ospedaliera Universitaria Integrata) approved in their meeting of 17 November 2010, documented by the ethics committee 52070/CE on 22 November 2010 and formalized by the Health Director of the AOUI on the order of the General Manager with protocol 52438 on 23 November 2010. APGI: Sydney South West Area Health Service Human Research Ethics Committee, western zone (protocol number 2006/54); Sydney Local Health District Human Research Ethics Committee (X11-0220); Northern Sydney Central Coast Health Harbour Human Research Ethics Committee (0612-251M); Royal Adelaide Hospital Human Research Ethics Committee (091107a); Metro South Human Research Ethics Committee (09/QPAH/220); South Metropolitan Area Health Service Human Research Ethics Committee (09/324); Southern Adelaide Health Service/Flinders University Human Research Ethics Committee (167/10); Sydney West Area Health Service Human Research Ethics Committee (Westmead campus) (HREC2002/3/4.19); The University of Queensland Medical Research Ethics Committee (2009000745); Greenslopes Private Hospital Ethics Committee (09/34); North Shore Private Hospital Ethics Committee. Baylor College of Medicine: Institutional Review Board protocol numbers H-29198 (Baylor College of Medicine tissue resource), H-21332 (Genomes and Genetics at the BCM-HGSC), and H-32711(Cancer Specimen Biobanking and Genomics). Patients were recruited and consent obtained for genomic sequencing through the ARC-Net Research Centre at Verona University, Australian Pancreatic Cancer Genome Initiative (APGI), and Baylor College of Medicine as part of the ICGC (www.icgc.org). A patient criterion for admission to the study was that they were clinically sporadic. This information was acquired through direct interviews with participants and a questionnaire regarding their personal history and that of relatives with regard to pancreas cancers and any other cancers during anamnesis. Clinical records were also used to clarify familial history based on patient indications. Samples were prospectively and consecutively acquired through institutions affiliated with the Australian Pancreatic Cancer Genome Initiative. Samples from the ARC-Net biobank are the result of consecutive collections from a single centre. All tissue samples were processed as previously described5151. Representative sections were reviewed independently by at least one additional pathologist with specific expertise in pancreatic diseases. Samples either had full face frozen sectioning performed in optimal cutting temperature (OCT) medium, or the ends excised and processed in formalin to verify the presence of tumour in the sample to be sequenced and to estimate the percentage of neoplastic cells in the sample relative to stromal cells. Macrodissection was performed if required to excise areas that did not contain neoplastic epithelium. Tumour cellularity was determined using SNP arrays (Illumina) and the qpure tool9. PanNET is a rare tumour type and the samples were collected via an international network. We estimate that with 98 unique patients in the discovery cohort, we will achieve 90% power for 90% of genes to detect mutations that occur at a frequency of ~10% above the background rate for PanNET (assuming a somatic mutation frequency of more than 2 per Mb)52. Cancer and matched normal colonic mucosa were collected at the time of surgical resection from the Royal Brisbane and Women’s Hospital and snap frozen in liquid nitrogen. A biallelic germline mutation in the MUTYH gene was detected by restriction fragment length polymorphism analysis and confirmed by automated sequencing to be the G382D mutation (or ENST00000450313.5 G396D, ClinVar#5294) in both alleles53. The primary antibodies used for immunohistochemical staining were: cytokeratin 8/18 (5D3, Novocastra), chromogranin A (DAK-A3, Dako), and CD99 (O13, Biolegend). Antibodies and staining conditions have been described elsewhere39. Whole-genome sequencing with 100-bp paired reads was performed with a HiSEQ2000 (Illumina). Sequence data were mapped to a GRCh37 using BWA and BAM files are available in the EGA (accession number: EGAS00001001732). Somatic mutations and germline variants were detected using a previously described consensus mutation calling strategy11. Mutations were annotated with gene consequence using SNPeff. The pathogenicity of germline variants was predicted using cancer-specific and locus-specific genetic databases, medical literature, computational predictions with ENSEMBL Variant Effect Predictor (VEP) annotation, and second hits identified in the tumour genome. Intogen27 was used to find somatic genes that were significantly mutated. Somatic structural variants were identified using the qSV tool as previously described10, 11, 17. Coding mutations are included in supplementary tables and all mutations have been uploaded to the International Cancer Genome Consortium Data Coordination Center. Mutational signatures were predicted using a published framework14. Essentially, the 96-substitution classification was determined for each sample. The signatures were compared to other validated signatures and the prevalence of each signature per megabase was determined. Somatic copy number was estimated using high density SNP arrays and the GAP tool12. Arm level copy number data were clustered using Ward’s method, Euclidian distance. GISTIC13 was used to identify recurrent regions of copy number change. The whole genome sequence data was used to determine the length of the telomeres in each sample using the qMotif tool. Essentially, qMotif determines telomeric DNA content by calculating the number of reads that harbour the telomere motif (TTAGG), and then estimates the relative length of telomeres in the tumour compared to the normal. qMotif is available online (http://sourceforge.net/projects/adamajava). Telomere length was validated by qPCR as previously described54. RNASeq library preparation and sequencing were performed as previously described55. Essentially, sequencing reads were mapped to transcripts corresponding to ensemble 70 annotations using RSEM. RSEM data were normalized using TMM (weighted trimmed mean of M-values) as implemented in the R package ‘edgeR’. For downstream analyses, normalized RSEM data were converted to counts per million (c.p.m.) and log transformed. Genes without at least 1 c.p.m. in 20% of the sample were excluded from further analysis55. Unsupervised class discovery was performed using consensus clustering as implemented in the ConsensusClusterPlus R package56. The top 2,000 most variable genes were used as input. Differential gene expression analysis between representative samples was performed using the R package ‘edgeR’57. Ontology and pathway enrichment analysis was performed using the R package ‘dnet’58. PanNET class enrichment using published gene signatures44 was performed using Gene Set Variation Analysis (GSVA) as described previously55. Two strategies were used to verify fusion transcripts. For verification of EWSR1–BEND2 fusions, cDNAs were synthesized using the SuperScript VILO cDNA synthesis kit (Thermofisher) with 1 μg purified total RNA. For each fusion sequence, three samples were used: the PanNET sample containing the fusion, the PanNET sample without that fusion, and a non-neoplastic pancreatic sample. The RT–PCR product were evaluated on the Agilent 2100 Bioanalyzer (Agilent Technologies) and verified by sequencing using the 3130XL Genetic Analyzer (Life Technologies). Primers specific for EWSR1–BEND2 fusion genes are available upon request. To identify the EWSR1 fusion partner in the case ITNET_2045, a real-time RT–PCR translocation panel for detecting specific Ewing sarcoma fusion transcripts was applied as described59. Following identification of the fusion partner, PCR amplicons were subjected to sequencing using the 3130XL Genetic Analyzer. EWSR1 rearrangements were assayed on paraffin-embedded tissue sections using a commercial split-signal probe (Vysis LSI EWSR1 (22q12) Dual Colour, Break Apart Rearrangement FISH Probe Kit) that consists of a mixture of two FISH DNA probes. One probe (~500 kb) is labelled in SpectrumOrange and flanks the 5′ side of the EWSR1 gene, extending through intron 4, and the second probe (~1,100 kb) is labelled in SpectrumGreen and flanks the 3′ side of the EWSR1 gene, with a 7-kb gap between the two probes. With this setting, the assay enables the detection of rearrangements with breakpoints spanning introns 7–10 of the EWSR1 gene. Hybridization was performed according to the manufacturer’s instructions and scoring of tissue sections was assessed as described elsewhere60, counting at least 100 nuclei per slide. Recurrently mutated genes identified by whole-genome sequencing were independently evaluated in a series of 62 PaNETs from the ARC-Net Research Centre, University of Verona. Four Ion Ampliseq Custom panels (Thermofisher) were designed to target the entire coding regions and flanking intron–exon junctions of the following genes: MEN1, DAXX, ATRX, PTEN and TSC2 (panel 1); DEPDC5, TSC1 and SETD2 (panel 2); ARID1A and MTOR (panel 3); CHEK2 and MUTYH (panel 4). Twenty nanograms of DNA were used per multiplex PCR amplification. The quality of the obtained libraries was evaluated by the Agilent 2100 Bioanalyzer on chip electrophoresis. Emulsion PCR was performed with the OneTouch system (Thermofisher). Sequencing was run on the Ion Torrent Personal Genome Machine (PGM, Thermofisher) loaded with 316 or 318 chips. Data analysis, including alignment to the hg19 human reference genome and variant calling, was done using Torrent Suite Software v4.0 (Thermofisher). Filtered variants were annotated using a custom pipeline based on the Variant Effector Predictor (VEP) software. Alignments were visually verified with the Integrative Genomics Viewer: IGV v2.3 (Broad Institute). There is no contiguous structure available for CHEK2, so we produced a model of isoform C using PDBid 3i6w61 as a template for predicting the structure of sequence O96017. Modelling was carried out within the YASARA suite of programs62 and consisted of an initial BLAST search for suitable templates followed by alignment, building of loops not present in selected template structure and energy minimization in explicit solvent. Modelling was carried out in the absence of a phosphopeptide ligand, which was added on completion by aligning the model with structure 1GXC and merging the ligand contained therein with the model structure. Similarly, MUTYH is represented by discontinuous structures and so this too was modelled using PDBids 3N5N and 4YPR as templates together with sequence NP_036354.1. Having constructed both models, amino acid substitutions were carried out to make the wild-type sequences conform to the variants described above. Each substitution was carried out independently and the resulting variant structures were subject to simulated annealing energy minimization using the AMBER force field. The resulting energy-minimized structures formed the basis of the predictions. CHEK2 site mutants were generated by site-directed mutagenesis of wild-type pCMV–FLAG CHEK2 (primer sequences in Supplementary Table 16). Proteins were expressed in HEK293T, a highly transfectable derivative of HEK293 cells that were retrieved from the cell culture bank at the QIMR Berghofer medical research institute. Cells were authenticated by STR profiling and were negative for mycoplasma. Transfected cells were lysed in NP-40 modified RIPA with protease and phosphatase inhibitors. Protein expression levels were analysed by western blotting with anti-FLAG antibodies and imaging HRP luminescent signal on a CCD camera (Fuji) and quantifying in MultiGauge software (Fuji). Kinase assays were performed using recombinant GST–CDC25C (amino acids 200–256) as substrate, essentially as described63. Kinase assay quantification was performed by scintillation counting of excised gel bands in OptiPhase scintillant (Perkin Elmer) using a Tri-Carb 2100TR beta counter (Packard). Counts for each reaction set were expressed as a fraction of the wild type. All experiments were performed at least three times. The date of diagnosis and the date and cause of death for each patient were obtained from the Central Cancer Registry and treating clinicians. Median survival was estimated using the Kaplan–Meier method and the difference was tested using the log-rank test. P values of less than 0.05 were considered statistically significant. The hazard ratio and its 95% confidence interval were estimated using Cox proportional hazard regression modelling. The correlation between DAXX or ATRX mutational status and other clinico-pathological variables was calculated using the χ2 test. Statistical analysis was performed using StatView 5.0 Software (Abacus Systems). Disease-specific survival was used as the primary endpoint. Genome sequencing data presented in this study have been submitted to the European Genome-Phenome Archive under accession number EGAS00001001732 (https://www.ebi.ac.uk/ega/search/site/EGAS00001001732).
News Article | February 15, 2017
ANN ARBOR, Mich., Feb. 15, 2017 /PRNewswire/ -- Swift Biosciences today announced the commercial release of its Accel-NGS® XL Library Prep Kit, the fastest sequencing solution for whole genome sequencing on Pacific Biosciences® (PacBio®) platforms. This library preparation kit, specially optimized for PacBio's Single Molecule, Real-Time (SMRT®) sequencing technology, provides significantly longer sequencing reads with a simple, single-tube workflow utilizing lower sample inputs. Swift Biosciences is now accepting orders for the Accel-NGS XL kit -- sold exclusively by Swift. "With its easy four-hour workflow and longer read lengths, the Accel-NGS XL kit substantially improves whole genome sequencing applications, such as de novo assembly and haplotype sequencing, on any genome including microbial, plant, animal, and human," said Haley Fiske, Chief Commercial Officer of Swift Biosciences. "These quality and workflow improvements help PacBio users generate more meaningful results from every run with twice the productivity." Swift Biosciences and several scientific collaborators presented two posters at the AGBT 2017 General Meeting showcasing sequencing data generated with this new chemistry. The first poster, entitled "A Method to Improve Read Length of SMRT Sequencing," displayed results, generated in collaboration with Mount Sinai and Cold Spring Harbor Laboratories, from diverse genomes including plant, bacterial and human reference DNA. The supporting data produced average reads up to 20Kb, with 50% less sample input and no adapter dimer artifacts. In the second poster, entitled "Improved Library Construction Methods for the Pacific Biosciences Sequencing Platform Using Swift Accel-NGS XL Library Prep Kit for PacBio Applied to Challenging BAC Clones for Human Genome Reference Improvement," Robert Fulton, Director of Project Development and Management at McDonnell Genome Institute of Washington University, presented results from human BAC clone sequencing, demonstrating higher library yields with longer sequencing reads. "Swift Biosciences is the first company to offer library preparation solutions on all three major sequencing platforms, including Pacific Biosystems, Illumina®, and Ion Torrent™," stated Timothy Harkins, Ph.D., President and CEO of Swift Biosciences. "We are strategically focused on expanding the NGS market by simplifying complex workflows through our innovative library technologies and bringing new applications to each of the NGS platforms. Our libraries provide the highest quality data in the most challenging of applications. Swift is 'The NGS library company.'"
News Article | November 23, 2016
This report studies Genome Sequencing Equipment in Global market, especially in North America, Europe, China, Japan, Southeast Asia and India, focuses on top manufacturers in global market, with production, price, revenue and market share for each manufacturer, covering Illumina Thermo Fisher Scientific BGI Roche Qiagen Pacific Biosciences Sequenom DAAN Gene Agilent Technologies Berry Genomics Hunan China Sun Pharmaceutical Machinery Jilin Zixin Pharmaceutical Industrial View Full Report With Complete TOC, List Of Figure and Table: http://globalqyresearch.com/global-genome-sequencing-equipment-market-research-report-2016 Market Segment by Regions, this report splits Global into several key Regions, with production, consumption, revenue, market share and growth rate of Genome Sequencing Equipment in these regions, from 2011 to 2021 (forecast), like North America Europe China Japan Southeast Asia India Split by product type, with production, revenue, price, market share and growth rate of each type, can be divided into Pacific Bio Ion Torrent sequencing Illumina SOLiD sequencing Split by application, this report focuses on consumption, market share and growth rate of Genome Sequencing Equipment in each application, can be divided into Medicine Biology Geology Agriculture Others Global Genome Sequencing Equipment Market Research Report 2016 1 Genome Sequencing Equipment Market Overview 1.1 Product Overview and Scope of Genome Sequencing Equipment 1.2 Genome Sequencing Equipment Segment by Type 1.2.1 Global Production Market Share of Genome Sequencing Equipment by Type in 2015 1.2.2 Pacific Bio 1.2.3 Ion Torrent sequencing 1.2.4 Illumina 1.2.5 SOLiD sequencing 1.3 Genome Sequencing Equipment Segment by Application 1.3.1 Genome Sequencing Equipment Consumption Market Share by Application in 2015 1.3.2 Medicine 1.3.3 Biology 1.3.4 Geology 1.3.5 Agriculture 1.3.6 Others 1.4 Genome Sequencing Equipment Market by Region 1.4.1 North America Status and Prospect (2011-2021) 1.4.2 Europe Status and Prospect (2011-2021) 1.4.3 China Status and Prospect (2011-2021) 1.4.4 Japan Status and Prospect (2011-2021) 1.4.5 Southeast Asia Status and Prospect (2011-2021) 1.4.6 India Status and Prospect (2011-2021) 1.5 Global Market Size (Value) of Genome Sequencing Equipment (2011-2021) 7 Global Genome Sequencing Equipment Manufacturers Profiles/Analysis 7.1 Illumina 7.1.1 Company Basic Information, Manufacturing Base and Its Competitors 7.1.2 Genome Sequencing Equipment Product Type, Application and Specification 22.214.171.124 Type I 126.96.36.199 Type II 7.1.3 Illumina Genome Sequencing Equipment Production, Revenue, Price and Gross Margin (2015 and 2016) 7.1.4 Main Business/Business Overview 7.2 Thermo Fisher Scientific 7.2.1 Company Basic Information, Manufacturing Base and Its Competitors 7.2.2 Genome Sequencing Equipment Product Type, Application and Specification 188.8.131.52 Type I 184.108.40.206 Type II 7.2.3 Thermo Fisher Scientific Genome Sequencing Equipment Production, Revenue, Price and Gross Margin (2015 and 2016) 7.2.4 Main Business/Business Overview 7.3 BGI 7.3.1 Company Basic Information, Manufacturing Base and Its Competitors 7.3.2 Genome Sequencing Equipment Product Type, Application and Specification 220.127.116.11 Type I 18.104.22.168 Type II 7.3.3 BGI Genome Sequencing Equipment Production, Revenue, Price and Gross Margin (2015 and 2016) 7.3.4 Main Business/Business Overview 7.4 Roche 7.4.1 Company Basic Information, Manufacturing Base and Its Competitors 7.4.2 Genome Sequencing Equipment Product Type, Application and Specification 22.214.171.124 Type I 126.96.36.199 Type II 7.4.3 Roche Genome Sequencing Equipment Production, Revenue, Price and Gross Margin (2015 and 2016) 7.4.4 Main Business/Business Overview 7.5 Qiagen 7.5.1 Company Basic Information, Manufacturing Base and Its Competitors 7.5.2 Genome Sequencing Equipment Product Type, Application and Specification 188.8.131.52 Type I 184.108.40.206 Type II 7.5.3 Qiagen Genome Sequencing Equipment Production, Revenue, Price and Gross Margin (2015 and 2016) 7.5.4 Main Business/Business Overview 7.6 Pacific Biosciences 7.6.1 Company Basic Information, Manufacturing Base and Its Competitors 7.6.2 Genome Sequencing Equipment Product Type, Application and Specification 220.127.116.11 Type I 18.104.22.168 Type II 7.6.3 Pacific Biosciences Genome Sequencing Equipment Production, Revenue, Price and Gross Margin (2015 and 2016) 7.6.4 Main Business/Business Overview 7.7 Sequenom 7.7.1 Company Basic Information, Manufacturing Base and Its Competitors 7.7.2 Genome Sequencing Equipment Product Type, Application and Specification 22.214.171.124 Type I 126.96.36.199 Type II 7.7.3 Sequenom Genome Sequencing Equipment Production, Revenue, Price and Gross Margin (2015 and 2016) 7.7.4 Main Business/Business Overview 7.8 DAAN Gene 7.8.1 Company Basic Information, Manufacturing Base and Its Competitors 7.8.2 Genome Sequencing Equipment Product Type, Application and Specification 188.8.131.52 Type I 184.108.40.206 Type II 7.8.3 DAAN Gene Genome Sequencing Equipment Production, Revenue, Price and Gross Margin (2015 and 2016) 7.8.4 Main Business/Business Overview 7.9 Agilent Technologies 7.9.1 Company Basic Information, Manufacturing Base and Its Competitors 7.9.2 Genome Sequencing Equipment Product Type, Application and Specification 220.127.116.11 Type I 18.104.22.168 Type II 7.9.3 Agilent Technologies Genome Sequencing Equipment Production, Revenue, Price and Gross Margin (2015 and 2016) 7.9.4 Main Business/Business Overview 7.10 Berry Genomics 7.10.1 Company Basic Information, Manufacturing Base and Its Competitors 7.10.2 Genome Sequencing Equipment Product Type, Application and Specification 22.214.171.124 Type I 126.96.36.199 Type II 7.10.3 Berry Genomics Genome Sequencing Equipment Production, Revenue, Price and Gross Margin (2015 and 2016) 7.10.4 Main Business/Business Overview 7.11 Hunan China Sun Pharmaceutical Machinery 7.12 Jilin Zixin 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News Article | February 22, 2017
DNA is the hereditary material in our cells and contains the instructions for them to live, behave, grow, and develop. These instructions are based on the order of the DNA bases, called nucleotides. To unlock the instructions, carried by a DNA molecule, we need to read these nucleotide sequences (by performing DNA sequencing). There are various methods for sequencing DNA, including Sanger sequencing, Illumina, 454, Ion Torrent sequencing, SMRT sequencing (Pacific Biosciences), and Nanopore sequencing. Nanopore sequencing is a modern and promising technique, in which many researchers are interested. This method benefits from the potential advantages of label-free sequencing as well as the long reads, both of which help in easing the sequencing requirements. In this method, the DNA zips through a tiny pore (nanopore) in a membrane. Each nucleotide which passes through the nanopore results in a unique characteristic change, uncovering the sequence of the biomolecule. Analyzing the DNA, directly taken from the cell, as opposed to synthesized molecules, is another advantage of this method, enhancing the sequencing accuracy. Nanopore sequencing methods are based on two types of nanopores: (1) solid-state nanopores, and (2) protein-based nanopores. In a review published in the journal, Recent Patents on Nanotechnology, by Roozbeh Abedini-Nassab, recent advances presented in various articles and patents in the field of solid state nanopore sequencing, including sequencing methods, membrane materials and their fabrication techniques, drilling methods, and biomolecule translocation speed control ideas are investigated. This review shows how nanotechnology is helping in revealing crucial biological information, which can be used later in solving problems in biological research. For more information about the article, please visit http://www.