Cold Spring Harbor, NY, United States
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Russnes H.G.,University of Oslo | Russnes H.G.,Dana-Farber Cancer Institute | Navin N.,University of Texas M. D. Anderson Cancer Center | Hicks J.,Cold Spring Harbor Laboratories | Borresen-Dale A.-L.,University of Oslo
Journal of Clinical Investigation | Year: 2011

Rapid and sophisticated improvements in molecular analysis have allowed us to sequence whole human genomes as well as cancer genomes, and the findings suggest that we may be approaching the ability to individualize the diagnosis and treatment of cancer. This paradigmatic shift in approach will require clinicians and researchers to overcome several challenges including the huge spectrum of tumor types within a given cancer, as well as the cell-to-cell variations observed within tumors. This review discusses how next-generation sequencing of breast cancer genomes already reveals insight into tumor heterogeneity and how it can contribute to future breast cancer classification and management.


- 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'".


- 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,...


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.'"


Ergebnisse von Mount Sinai, Washington University und Cold Spring Harbor Laboratories werden auf AGBT vorgestellt ANN ARBOR, Michigan, 15. Februar 2017 /PRNewswire/ -- Swift Biosciences gab heute die kommerzielle Veröffentlichung seines Accel-NGS® XL Library Prep Kit bekannt, der...


Plummer P.N.,Griffith University | Freeman R.,Griffith University | Taft R.J.,University of Queensland | Vider J.,Griffith University | And 12 more authors.
Cancer Research | Year: 2013

Bone marrow-derived endothelial progenitor cells (EPC) contribute to the angiogenesis-dependent growth of tumors in mice and humans. EPCs regulate the angiogenic switch via paracrine secretion of proangiogenic growth factors and by direct luminal incorporation into sprouting nascent vessels. miRNAs have emerged as key regulators of several cellular processes including angiogenesis; however, whether miRNAs contribute to bone marrow-mediated angiogenesis has remained unknown. Here, we show that genetic ablation of miRNA-processing enzyme Dicer, specifically in the bone marrow, decreased the number of circulating EPCs, resulting in angiogenesis suppression and impaired tumor growth. Furthermore, genome-wide deep sequencing of small RNAs revealed tumor EPC-intrinsic miRNAs including miR-10b and miR-196b, which have been previously identified as key regulators of HOX signaling and adult stem cell differentiation. Notably, we found that both miR-10b and miR-196b are responsive to vascular endothelial growth factor stimulation and show elevated expression in human high-grade breast tumor vasculature. Strikingly, targeting miR-10b and miR-196b led to significant defects in angiogenesis-mediated tumor growth in mice. Targeting these miRNAs may constitute a novel strategy for inhibiting tumor angiogenesis. ©2012 AACR.


Mager E.M.,University of Miami | Brix K.V.,University of Miami | Gerdes R.M.,Cold Spring Harbor Laboratories | Ryan A.C.,Hydroqual Inc | Grosell M.,University of Miami
Ecotoxicology and Environmental Safety | Year: 2011

As the first step toward parameterization of a chronic lead (Pb) biotic ligand model (BLM) for Ceriodaphnia dubia, 7-d toxicity tests were performed in waters modified to evaluate the influences of hardness, DOM (as Suwannee River NOM and Aldrich humic acid (HA)), pH (buffered with 4mM MOPS) and alkalinity on the chronic toxicity of Pb. Calculated EC20s for the control base water test and each of the most extreme modified test waters were as follows in γgL-1 Pb (95% confidence interval): base water control=45 (14-53), 5mM CaSO4=22 (12-30), 32mgL-1 DOM=523 (388-573), 2.5mM NaHCO3=73 (21-120) and pH 6.4 buffered with MOPS=3.9γgL-1 Pb (1-5). Results indicate that hardness does not protect against chronic toxicity of Pb to C. dubia, whereas HA does protect at the highest concentration tested (597γM). Additionally, our findings suggest that low pH increases the chronic toxicity of Pb whereas increased alkalinity is protective. The findings reported herein support the need for a chronic Pb BLM as an alternative approach to hardness-based regulations. © 2010 Elsevier Inc.


Karni-Schmidt O.,Columbia University | Castillo-Martin M.,Columbia University | HuaiShen T.,Columbia University | Gladoun N.,Columbia University | And 6 more authors.
American Journal of Pathology | Year: 2011

The TP63 gene, a member of the TP53 tumor suppressor gene family, can be expressed as at least six isoforms due to alternative promoter use and alternative splicing. The lack of p63 isoform-specific antibodies has limited the analysis of the biological significance of p63. We report a novel set of well-defined antibodies to examine p63 isoforms in mouse and human urothelium during embryogenesis and tumor progression, respectively. We provide evidence that basal and intermediate urothelial cells express p63 isoforms, with the TAp63 variant the first to be detected during development, whereas umbrella cells are characterized by a p63-negative phenotype. Notably, we report that p63-null mice develop a bladder with an abnormal urothelium, constituted by a single layer of cells that express uroplakin II and low molecular weight cytokeratins, consistent with an umbrella cell phenotype. Finally, analysis of 202 human bladder carcinomas revealed a new categorization of invasive tumors into basal-like (positive for ΔNp63 and high molecular weight cytokeratins and negative for low molecular weight cytokeratins) versus luminal-like (negative for ΔNp63 and high molecular weight cytokeratins and positive for low molecular weight cytokeratins) phenotypes, with ΔNp63 expression associated with an aggressive clinical course and poor prognosis. This study highlights the relevance of p63 isoforms in both urothelial development and bladder carcinoma progression, with ΔNp63 acting as an oncogene in certain invasive bladder tumors. Copyright © 2011 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.


Patent
Cold Spring Harbor Laboratories and Philips | Date: 2010-09-15

The present invention relates to a method for assisting in diagnosing breast cancer and/or monitoring breast cancer progression in a given sample based on the analysis of differential DNA methylation patterns. More particularly, the method is directed to the identification of one or more epigenetic markers that derive from the application of a variety of statistical methods in order to point out the prognostic significance of the difference in methylation states at one or more genomic loci and predict whether the sample analyzed has a good or bad prognosis following treatment.


Patent
Cold Spring Harbor Laboratories and Philips | Date: 2010-01-25

Provided is a method for the analysis of breast cancer disorders, comprising determining the genomic methylation status of one or more CpG dinucleotides. Furthermore, a computer program product stored on a computer-readable medium comprising software code adapted to perform the steps of the method when executed on a data-processing apparatus is provided. A device comprising means for supporting a clinician is also provided.

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