BRCA1 / 2 testing by massive sequencing highlights, shadows or pitfalls?
|
|
- Clinton Ellis
- 8 years ago
- Views:
Transcription
1 BRCA1 / 2 testing by massive sequencing highlights, shadows or pitfalls? Giovanni Luca Scaglione, PhD Laboratory of Clinical Molecular Diagnostics and Personalized Medicine, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Rome, Italy
2 Twenty years since the discovery of BRCA BRCA1 gene positionally cloned and sequenced 1, BRCA2 gene identified and sequenced 3, BRCA mutation life time cancer risks: breast (60 85%), ovarian (15 40%) Synthetic lethality of PARP inhibition in BRCA-deficient cell lines 8, Clinical antitumour activity of PARP inhibitor shown in BRCA-mutation associated cancer 10 Initiation of Phase III trials of PARP inhibitors in BRCA-mutant ovarian and breast cancers 2014: BRCA as PGx gene? 1. Friedman et al. Nat Genet 1994;8: ; 2. Miki et al. Science 1994;266:66 71; 3. Wooster et al. Nature 1995;378: ; 4. Tavtigian et al. Nat Genet 1996;12: ; 5. Brose et al. J Natl Cancer Inst 2002;94: ; 6. Thompson et al. J Natl Cancer Inst 2002;94: ; 7. Wooster, Weber. N Engl J Med 2003;348: ; 8. Farmer et al. Nature 2005;434: ; 9. Brody. N Engl J Med 2005;353: ; 10. Fong et al. N Engl J Med 2009;361:
3 Highlights Summary Working on 454 GS junior (Roche Diagnostics) 1. Up to 12 patients & multigenic profile within a run 2. Complete BRCA1/2 screening (100% coding regions) 3. Fast variant call report by means of bioinformatics tool: Amplicon Suite Shadows 1. Pre-NGS Quality Control >>> Fragment Analysis 2. NGS data robustness: Inter-run & Intra-run >>> Read coverage profile 3. Post-NGS Validation Experiments >>> Sanger Chemistry Pitfalls 1. PCR Bias (Primer Binding Energies, GC-content) 2. empcr errors 3. CNV Copy Number Variations
4 Summary Patients Sample 1. w/ breast cancer 2. and/or ovarian cancer 3. w/ a positive family history Collection whole blood sample (K 3 EDTA) 8-12 patients per run (3/4 day) DNA extraction
5 Complete BRCA1/2 screening (100% coding regions) Genomic DNA Fragment Library Barcoded Library Multiplex PCR, Amplification of Specific Targets 5 PCR multiplex 93 Amplicons Universal PCR, Addition of MIDs and 454 adaptor sequences
6 Complete BRCA1/2 screening (100% coding regions) Plex A B C D E empcr water-in-oil emulsion
7 Summary Gene Scan Profile Pre-emulsion QC step check-point Sanger Pre-NGS Quality Control (Fragment Analysis) Mut + or Re-Extraction Mut - NGS
8 Complete BRCA1/2 screening (100% coding regions) Pyrosequencing GS 454 Junior 454 GS Junior Clinical Lab Report Data Analysis
9 Summary Quantitative Analysis: Read Coverage > 38x NGS data robustness: Inter-run & Intra-run read cover profile
10 Case Report Read Coverage Warning!
11 Summary Fast variant call report by means of bioinformatics tool: Amplicon Suite
12 Summary QC Mut - NGS Mut + Sanger Post-NGS Validation Experiments (Sanger Chemistry)
13 Summary >Library Preparation< 1. Contamination (not completely excluded) 2. PCR Bias (Primer Binding Energies, GC-content) 3. Chimeras (up to 45%, high sequence similarity) 4. PCR errors (454 protocol TAQ error rate 1:9000 bases) >empcr< 1. empcr errors 2. Artificial Duplicates >Sequencing< Pitfalls Known Error Patterns 1. Well Cross-Talk Type I ( Ghost well ) 2. Well Cross-Talk Type II ( Optical Bleeding ) 3. Homopolymer Errors
14 Pitfalls Known Error Patterns >Library Preparation< 1. Contamination (not completely excluded) 2. PCR Bias (Primer Binding Energies, GC-content) Plex 3. Chimeras A B (up C D to 45%, E high sequence similarity) 4. PCR errors (454 protocol TAQ error rate 1:9000 bases) n=117 >empcr< 1. empcr errors 2. Artificial Duplicates >Sequencing< n of reads per plex 1. Well Cross-Talk Type [95% Conf. I ( Ghost Interval] well ) Variabl e (Mean ± SE) 2. Plex A Well Cross-Talk 120 ± 4 Type 107 II - ( Optical 124 Bleeding ) Plex B 180 ± Homopolymer Errors Plex C 130 ± Plex D 110 ± Plex E 150 ±
15 Case Report Read Coverage Warning! BRCA1 exon x MLPA Negative
16 Case Report Read Coverage Warning!
17 >Library Preparation< Pitfalls Known Error Patterns 1. Contamination (not completely excluded) 2. PCR Bias (Primer Binding Energies, GC-content) 3. Chimeras (up to 45%, high sequence similarity) 4. PCR errors (454 protocol TAQ error rate 1:9000 bases) >empcr< 1. empcr errors 2. Artificial Duplicates >Sequencing< 1. Well Cross-Talk Type I ( Ghost well ) 2. Well Cross-Talk Type II ( Optical Bleeding ) 3. Homopolymer Errors
18 Plex B - Amplicon Read Coverage PLEX B Variable n of reads per plex (Mean ± SE) [95% Conf. Interval ] Plex A 120 ± Plex B 180 ± Plex C 130 ± Plex D 110 ± Plex E 150 ±
19 Conclusions Amplicon Suite tool could be tuned for the Copy Number Variation (CNV) analysis in BRCA1/2 testing due to his highly flexible and fast capability of finding out data from GS Junior 454 runs The analysis performed not only in the inter-run series but also in intra-run series is the driving force in the setup of CNV analysis NGS data analysis could not be separated from amplicon library data analysis
20 Thank You
Data Analysis for Ion Torrent Sequencing
IFU022 v140202 Research Use Only Instructions For Use Part III Data Analysis for Ion Torrent Sequencing MANUFACTURER: Multiplicom N.V. Galileilaan 18 2845 Niel Belgium Revision date: August 21, 2014 Page
More informationSEQUENCING. From Sample to Sequence-Ready
SEQUENCING From Sample to Sequence-Ready ACCESS ARRAY SYSTEM HIGH-QUALITY LIBRARIES, NOT ONCE, BUT EVERY TIME The highest-quality amplicons more sensitive, accurate, and specific Full support for all major
More informationThe Power of Next-Generation Sequencing in Your Hands On the Path towards Diagnostics
The Power of Next-Generation Sequencing in Your Hands On the Path towards Diagnostics The GS Junior System The Power of Next-Generation Sequencing on Your Benchtop Proven technology: Uses the same long
More information14/12/2012. HLA typing - problem #1. Applications for NGS. HLA typing - problem #1 HLA typing - problem #2
www.medical-genetics.de Routine HLA typing by Next Generation Sequencing Kaimo Hirv Center for Human Genetics and Laboratory Medicine Dr. Klein & Dr. Rost Lochhamer Str. 9 D-8 Martinsried Tel: 0800-GENETIK
More informationGenetic Analysis. Phenotype analysis: biological-biochemical analysis. Genotype analysis: molecular and physical analysis
Genetic Analysis Phenotype analysis: biological-biochemical analysis Behaviour under specific environmental conditions Behaviour of specific genetic configurations Behaviour of progeny in crosses - Genotype
More informationIntroduction to next-generation sequencing data
Introduction to next-generation sequencing data David Simpson Centre for Experimental Medicine Queens University Belfast http://www.qub.ac.uk/research-centres/cem/ Outline History of DNA sequencing NGS
More informationAutomated DNA sequencing 20/12/2009. Next Generation Sequencing
DNA sequencing the beginnings Ghent University (Fiers et al) pioneers sequencing first complete gene (1972) first complete genome (1976) Next Generation Sequencing Fred Sanger develops dideoxy sequencing
More informationNazneen Aziz, PhD. Director, Molecular Medicine Transformation Program Office
2013 Laboratory Accreditation Program Audioconferences and Webinars Implementing Next Generation Sequencing (NGS) as a Clinical Tool in the Laboratory Nazneen Aziz, PhD Director, Molecular Medicine Transformation
More informationJuly 7th 2009 DNA sequencing
July 7th 2009 DNA sequencing Overview Sequencing technologies Sequencing strategies Sample preparation Sequencing instruments at MPI EVA 2 x 5 x ABI 3730/3730xl 454 FLX Titanium Illumina Genome Analyzer
More informationNext generation DNA sequencing technologies. theory & prac-ce
Next generation DNA sequencing technologies theory & prac-ce Outline Next- Genera-on sequencing (NGS) technologies overview NGS applica-ons NGS workflow: data collec-on and processing the exome sequencing
More informationHistory of DNA Sequencing & Current Applications
History of DNA Sequencing & Current Applications Christopher McLeod President & CEO, 454 Life Sciences, A Roche Company IMPORTANT NOTICE Intended Use Unless explicitly stated otherwise, all Roche Applied
More informationNext Generation Sequencing
Next Generation Sequencing Technology and applications 10/1/2015 Jeroen Van Houdt - Genomics Core - KU Leuven - UZ Leuven 1 Landmarks in DNA sequencing 1953 Discovery of DNA double helix structure 1977
More informationOverview of Next Generation Sequencing platform technologies
Overview of Next Generation Sequencing platform technologies Dr. Bernd Timmermann Next Generation Sequencing Core Facility Max Planck Institute for Molecular Genetics Berlin, Germany Outline 1. Technologies
More informationTCRG TCRA/D IGH IGK/L
Assays immunoseq Assay The inquiry to insight solution for profiling T- and B-cell s Immunosequencing solutions for multiple species and loci Illuminate the adaptive immune system with bias-controlled
More informationUsefulness of polymorphic markers in exclusion of BRCA1/BRCA2 mutations in families with aggregation of breast/ovarian cancers
J. Appl. Genet. 44(3), 2003, pp. 419-423 Short communication Usefulness of polymorphic markers in exclusion of BRCA1/BRCA2 mutations in families with aggregation of breast/ovarian cancers Bohdan GÓRSKI,
More informationGenome Sequencer System. Amplicon Sequencing. Application Note No. 5 / February 2007. www.roche-applied-science.com
Genome Sequencer System Application Note No. 5 / February 2007 Amplicon Sequencing www.roche-applied-science.com 1 Amplicon Sequencing Corresponding author: Tom Jarvie, 454 Life Sciences Corporation, Branford,
More informationNext Generation Sequencing: Technology, Mapping, and Analysis
Next Generation Sequencing: Technology, Mapping, and Analysis Gary Benson Computer Science, Biology, Bioinformatics Boston University gbenson@bu.edu http://tandem.bu.edu/ The Human Genome Project took
More informationDNA Sequence Analysis
DNA Sequence Analysis Two general kinds of analysis Screen for one of a set of known sequences Determine the sequence even if it is novel Screening for a known sequence usually involves an oligonucleotide
More informationValidation parameters: An introduction to measures of
Validation parameters: An introduction to measures of test accuracy Types of tests All tests are fundamentally quantitative Sometimes we use the quantitative result directly However, it is often necessary
More informationCore Facility Genomics
Core Facility Genomics versatile genome or transcriptome analyses based on quantifiable highthroughput data ascertainment 1 Topics Collaboration with Harald Binder and Clemens Kreutz Project: Microarray
More informationBacReady TM Multiplex PCR System
BacReady TM Multiplex PCR System Technical Manual No. 0191 Version 10112010 I Description.. 1 II Applications 2 III Key Features.. 2 IV Shipping and Storage. 2 V Simplified Procedures. 2 VI Detailed Experimental
More informationGenScript BloodReady TM Multiplex PCR System
GenScript BloodReady TM Multiplex PCR System Technical Manual No. 0174 Version 20040915 I Description.. 1 II Applications 2 III Key Features.. 2 IV Shipping and Storage. 2 V Simplified Procedures. 2 VI
More informationDevelopment of a Workflow to Detect Sequence Variants in the BRCA1 and BRCA2 Genes
Your Innovative Research BRCA1 and BRCA2 Variant Detection Development of a Workflow to Detect Sequence Variants in the BRCA1 and BRCA2 Genes The oncogenetics group in the DNA Diagnostics division of the
More informationHereditary Ovarian cancer: BRCA1 and BRCA2. Karen H. Lu MD September 22, 2013
Hereditary Ovarian cancer: BRCA1 and BRCA2 Karen H. Lu MD September 22, 2013 Outline Hereditary Breast and Ovarian Cancer (HBOC) BRCA1/2 genes How to identify What it means to you What it means to your
More informationAppendix 2 Molecular Biology Core Curriculum. Websites and Other Resources
Appendix 2 Molecular Biology Core Curriculum Websites and Other Resources Chapter 1 - The Molecular Basis of Cancer 1. Inside Cancer http://www.insidecancer.org/ From the Dolan DNA Learning Center Cold
More informationGene Expression Assays
APPLICATION NOTE TaqMan Gene Expression Assays A mpl i fic ationef ficienc yof TaqMan Gene Expression Assays Assays tested extensively for qpcr efficiency Key factors that affect efficiency Efficiency
More informationOncology Insights Enabled by Knowledge Base-Guided Panel Design and the Seamless Workflow of the GeneReader NGS System
White Paper Oncology Insights Enabled by Knowledge Base-Guided Panel Design and the Seamless Workflow of the GeneReader NGS System Abstract: This paper describes QIAGEN s philosophy and process for developing
More informationEvaluation of a Microfluidic System for Performance of Fully Automated Companion Diagnostics for Personalized Medicine
Evaluation of a Microfluidic System for Performance of Fully Automated Companion Diagnostics for Personalized Medicine Gwendolyn Spizz, I. Cristina McGuire, Rubina Yasmin, Whitney Honey, Zongyuan Chen,
More information360 Master Mix. , and a supplementary 360 GC Enhancer.
Product Bulletin AmpliTaq Gold 360 Master Mix and 360 DNA Polymerase AmpliTaq Gold 360 Master Mix AmpliTaq Gold 360 DNA Polymerase 360 Coverage for a Full Range of Targets AmpliTaq Gold 360 Master Mix
More informationGenetic Testing for Hereditary Breast and Ovarian Cancer - BRCA1/2 ANALYSIS -
Genetic Testing for Hereditary Breast and Ovarian Cancer - BRCA1/2 ANALYSIS - January 2005 SCIENTIFIC BACKGROUND Breast cancer is considered to be one of the most prevalent cancer in women. The overall
More informationAnalysis of the DNA Methylation Patterns at the BRCA1 CpG Island
Analysis of the DNA Methylation Patterns at the BRCA1 CpG Island Frédérique Magdinier 1 and Robert Dante 2 1 Laboratory of Molecular Biology of the Cell, Ecole Normale Superieure, Lyon, France 2 Laboratory
More informationBioruptor NGS: Unbiased DNA shearing for Next-Generation Sequencing
STGAAC STGAACT GTGCACT GTGAACT STGAAC STGAACT GTGCACT GTGAACT STGAAC STGAAC GTGCAC GTGAAC Wouter Coppieters Head of the genomics core facility GIGA center, University of Liège Bioruptor NGS: Unbiased DNA
More informationSingle-Cell DNA Sequencing with the C 1. Single-Cell Auto Prep System. Reveal hidden populations and genetic diversity within complex samples
DATA Sheet Single-Cell DNA Sequencing with the C 1 Single-Cell Auto Prep System Reveal hidden populations and genetic diversity within complex samples Single-cell sensitivity Discover and detect SNPs,
More information6/10/2015. Hereditary Predisposition for Breast Cancer: Looking at BRCA1/BRCA2 Testing & Beyond. Hereditary Cancers. BRCA1 and BRCA2 Review
Hereditary Predisposition for Breast Cancer: Looking at BRCA1/BRCA2 Testing & Beyond Arturo Anguiano MD, FACMG International Medical Director, Medical Affairs Vice Chairman, Genetics; Medical Director,
More informationbitter is de pil Linos Vandekerckhove, MD, PhD
4//24 Current HIV care HIV copies/ ml plasma Viral load Welcome to the Digital droplet PCR age! bitter is de pil Linos Vandekerckhove, MD, PhD Latent HIV reservoir Time at Ghent University Hospital 2 HIV
More informationNuevas tecnologías basadas en biomarcadores para oncología
Nuevas tecnologías basadas en biomarcadores para oncología Simposio ASEBIO 14 de marzo 2013, PCB Jose Jimeno, MD, PhD Co-Founder / Vice Chairman Pangaea Biotech SL Barcelona, Spain PANGAEA BIOTECH BUSINESS
More informationDefinition of Minimum Performance Requirements for Analytical Methods of GMO Testing European Network of GMO Laboratories (ENGL)
Definition of Minimum Performance Requirements for Analytical Methods of GMO Testing European Network of GMO Laboratories (ENGL) 13 October 2008 Date of application: 13 April 2009 INTRODUCTION The scope
More informationThe author(s) shown below used Federal funds provided by the U.S. Department of Justice and prepared the following final report:
The author(s) shown below used Federal funds provided by the U.S. Department of Justice and prepared the following final report: Document Title: Author(s): Resolution of DNA Mixtures and Analysis of Degraded
More informationNon-invasive prenatal detection of chromosome aneuploidies using next generation sequencing: First steps towards clinical application
Non-invasive prenatal detection of chromosome aneuploidies using next generation sequencing: First steps towards clinical application PD Dr. rer. nat. Markus Stumm Zentrum für Pränataldiagnostik Kudamm-199
More informationPreciseTM Whitepaper
Precise TM Whitepaper Introduction LIMITATIONS OF EXISTING RNA-SEQ METHODS Correctly designed gene expression studies require large numbers of samples, accurate results and low analysis costs. Analysis
More informationSanger Sequencing. Troubleshooting Guide. Failed sequence
Sanger Sequencing Troubleshooting Guide Below are examples of the main problems experienced in ABI Sanger sequencing. Possible causes for failure and their solutions are listed below each example. The
More informationTargeted. sequencing solutions. Accurate, scalable, fast TARGETED
Targeted TARGETED Sequencing sequencing solutions Accurate, scalable, fast Sequencing for every lab, every budget, every application Ion Torrent semiconductor sequencing Ion Torrent technology has pioneered
More informationDescription: Molecular Biology Services and DNA Sequencing
Description: Molecular Biology s and DNA Sequencing DNA Sequencing s Single Pass Sequencing Sequence data only, for plasmids or PCR products Plasmid DNA or PCR products Plasmid DNA: 20 100 ng/μl PCR Product:
More informationHow is genome sequencing done?
How is genome sequencing done? Using 454 Sequencing on the Genome Sequencer FLX System, DNA from a genome is converted into sequence data through four primary steps: Step One DNA sample preparation; Step
More informationBest Practices for Maintaining Quality in Molecular Diagnostics Gyorgy Abel, MD, PhD
Best Practices for Maintaining Quality in Molecular Diagnostics Gyorgy Abel, MD, PhD Director, Clinical Chemistry Molecular Diagnostics / Immunology Department of Laboratory Medicine Lahey Clinic Medical
More informationBreast cancer and the role of low penetrance alleles: a focus on ATM gene
Modena 18-19 novembre 2010 Breast cancer and the role of low penetrance alleles: a focus on ATM gene Dr. Laura La Paglia Breast Cancer genetic Other BC susceptibility genes TP53 PTEN STK11 CHEK2 BRCA1
More informationNGS data analysis. Bernardo J. Clavijo
NGS data analysis Bernardo J. Clavijo 1 A brief history of DNA sequencing 1953 double helix structure, Watson & Crick! 1977 rapid DNA sequencing, Sanger! 1977 first full (5k) genome bacteriophage Phi X!
More informationGenomics Services @ GENterprise
Genomics Services @ GENterprise since 1998 Mainz University spin-off privately financed 6-10 employees since 2006 Genomics Services @ GENterprise Sequencing Service (Sanger/3730, 454) Genome Projects (Bacteria,
More informationMolecular and Cell Biology Laboratory (BIOL-UA 223) Instructor: Ignatius Tan Phone: 212-998-8295 Office: 764 Brown Email: ignatius.tan@nyu.
Molecular and Cell Biology Laboratory (BIOL-UA 223) Instructor: Ignatius Tan Phone: 212-998-8295 Office: 764 Brown Email: ignatius.tan@nyu.edu Course Hours: Section 1: Mon: 12:30-3:15 Section 2: Wed: 12:30-3:15
More informationHow many of you have checked out the web site on protein-dna interactions?
How many of you have checked out the web site on protein-dna interactions? Example of an approximately 40,000 probe spotted oligo microarray with enlarged inset to show detail. Find and be ready to discuss
More informationPARP inhibition basic science and clinical challenge. Thomas Helleday, PhD
PARP inhibition basic science and clinical challenge Thomas Helleday, PhD Poly (ADP-ribose) Polymerase 1 (PARP1) Reprinted by permission from Macmillan Publishers Ltd: Rouleau M et al. Nat Rev Cancer 2010;10:293-301
More informationIntroduction to transcriptome analysis using High Throughput Sequencing technologies (HTS)
Introduction to transcriptome analysis using High Throughput Sequencing technologies (HTS) A typical RNA Seq experiment Library construction Protocol variations Fragmentation methods RNA: nebulization,
More informationGenomic Medicine The Future of Cancer Care. Shayma Master Kazmi, M.D. Medical Oncology/Hematology Cancer Treatment Centers of America
Genomic Medicine The Future of Cancer Care Shayma Master Kazmi, M.D. Medical Oncology/Hematology Cancer Treatment Centers of America Personalized Medicine Personalized health care is a broad term for interventions
More informationHow Can Institutions Foster OMICS Research While Protecting Patients?
IOM Workshop on the Review of Omics-Based Tests for Predicting Patient Outcomes in Clinical Trials How Can Institutions Foster OMICS Research While Protecting Patients? E. Albert Reece, MD, PhD, MBA Vice
More informationFULLY AUTOMATED AND VALIDATED HIGH VOLUME DNA EXTRACTION USING CHEMAGEN MAGNETIC BEADS BASED KITS
FULLY AUTOMATED AND VALIDATED HIGH VOLUME DNA EXTRACTION USING CHEMAGEN MAGNETIC BEADS BASED KITS Tom Janssens & Ivo Salden UZ Gasthuisberg, Center for Human Genetics, Leuven Perkin Elmer Webinar 27th
More informationTranslating DNA repair pathways into therapeutic targets: beyond the BRCA1/2 and PARP inhibitor saga. Jorge S Reis-Filho, MD PhD FRCPath
Translating DNA repair pathways into therapeutic targets: beyond the BRCA1/2 and PARP inhibitor saga Jorge S Reis-Filho, MD PhD FRCPath Summary How do PARP inhibitors work? Synthetic lethality Potential
More informationLa capture de la fonction par des approches haut débit
Colloque Génomique Environnementale LYON 2011 La capture de la fonction par des approches haut débit Pierre PEYRET J. Denonfoux, N. Parisot, E. Dugat-Bony, C. Biderre-Petit, D. Boucher, G. Fonty, E. Peyretaillade
More informationRecombinant DNA and Biotechnology
Recombinant DNA and Biotechnology Chapter 18 Lecture Objectives What Is Recombinant DNA? How Are New Genes Inserted into Cells? What Sources of DNA Are Used in Cloning? What Other Tools Are Used to Study
More informationAdvances in RainDance Sequence Enrichment Technology and Applications in Cancer Research. March 17, 2011 Rendez-Vous Séquençage
Advances in RainDance Sequence Enrichment Technology and Applications in Cancer Research March 17, 2011 Rendez-Vous Séquençage Presentation Overview Core Technology Review Sequence Enrichment Application
More informationThe Need for a PARP in vivo Pharmacodynamic Assay
The Need for a PARP in vivo Pharmacodynamic Assay Jay George, Ph.D., Chief Scientific Officer, Trevigen, Inc., Gaithersburg, MD For further infomation, please contact: William Booth, Ph.D. Tel: +44 (0)1235
More informationTargeted Variant Test Requisition Form (3/4/2015)
Targeted Variant Test Requisition Form (3/4/2015) Instructions: Please provide clinical features of family members. All testing must be ordered by a qualified healthcare provider. See Test Selection Box
More informationAssuring the Quality of Next-Generation Sequencing in Clinical Laboratory Practice. Supplementary Guidelines
Assuring the Quality of Next-Generation Sequencing in Clinical Laboratory Practice Next-generation Sequencing: Standardization of Clinical Testing (Nex-StoCT) Workgroup Principles and Guidelines Supplementary
More informationNEIGE. diagnosis In oncogenetics. Nicolas Sévenet 02 juillet 2012. n.sevenet@bordeaux.unicancer.fr
NEIGE g for molecular NExt g generation sequencing diagnosis In oncogenetics Nicolas Sévenet 02 juillet 2012 n.sevenet@bordeaux.unicancer.fr t@b d i f Reports 15 years Next generation sequencing 06/2011
More informationQuantifiler Human DNA Quantification Kit Quantifiler Y Human Male DNA Quantification Kit
Product Bulletin Human Identification Quantifiler Human DNA Quantification Kit Quantifiler Y Human Male DNA Quantification Kit The Quantifiler kits produce reliable and reproducible results, helping to
More informationAnnex to the Accreditation Certificate D-PL-13372-01-00 according to DIN EN ISO/IEC 17025:2005
Deutsche Akkreditierungsstelle GmbH German Accreditation Body Annex to the Accreditation Certificate D-PL-13372-01-00 according to DIN EN ISO/IEC 17025:2005 Period of validity: 26.03.2012 to 25.03.2017
More informationNext Generation Sequencing
Next Generation Sequencing DNA sequence represents a single format onto which a broad range of biological phenomena can be projected for high-throughput data collection Over the past three years, massively
More informationNew Directions in Treatment of Ovarian Cancer. Amit M. Oza Princess Margaret Hospital University of Toronto
New Directions in Treatment of Ovarian Cancer Amit M. Oza Princess Margaret Hospital University of Toronto Newly diagnosed: scenario Ist line Surgery chemotherapy Cure If can t cure can we turn into chronic
More informationReal-time quantitative RT -PCR (Taqman)
Real-time quantitative RT -PCR (Taqman) Author: SC, Patti Lab, 3/03 This is performed as a 2-step reaction: 1. cdna synthesis from DNase 1-treated total RNA 2. PCR 1. cdna synthesis (Advantage RT-for-PCR
More informationMultiplex your most important
Multiplex your most important genetic assays on one platform GenomeLab GeXP Genetic Analysis System Blood Banking Capillary Electrophoresis Centrifugation Flow Cytometry Genomics Lab Automation Lab Tools
More informationPROVIDER POLICIES & PROCEDURES
PROVIDER POLICIES & PROCEDURES BRCA GENETIC TESTING The purpose of this document is to provide guidance to providers enrolled in the Connecticut Medical Assistance Program (CMAP) on the requirements for
More informationTECHNOLOGIES, PRODUCTS & SERVICES for MOLECULAR DIAGNOSTICS, MDx ABA 298
DIAGNOSTICS BUSINESS ANALYSIS SERIES: TECHNOLOGIES, PRODUCTS & SERVICES for MOLECULAR DIAGNOSTICS, MDx ABA 298 By ADAMS BUSINESS ASSOCIATES MAY 2014. May 2014 ABA 298 1 Technologies, Products & Services
More informationIMMEDIATE HOT LINE: Effective March 2, 2015
MEDICARE COVERAGE OF LABORATORY TESTING Please remember when ordering laboratory tests that are billed to Medicare/Medicaid or other federally funded programs, the following requirements apply: 1. Only
More informationReal-Time PCR Vs. Traditional PCR
Real-Time PCR Vs. Traditional PCR Description This tutorial will discuss the evolution of traditional PCR methods towards the use of Real-Time chemistry and instrumentation for accurate quantitation. Objectives
More informationInstitutional Partnership Program
GENEWIZ Outsourcing Services Institutional Partnership Program Solid Science. Superior Service. DNA Sequencing Partners to Fuel Your Success Institutions whose success depends on significant life science
More informationEnhancing PCR & STR Experiments. Sharron Ohgi Senior Research Associate sohgi@biomatrica.com
Enhancing PCR & STR Experiments Sharron Ohgi Senior Research Associate sohgi@biomatrica.com Outline PCR experiments Sample challenges Introducing Biomatrica s PCRboost o Performance examples o Summary
More informationHow Sequencing Experiments Fail
How Sequencing Experiments Fail v1.0 Simon Andrews simon.andrews@babraham.ac.uk Classes of Failure Technical Tracking Library Contamination Biological Interpretation Something went wrong with a machine
More informationThe Ethics of Research with Stored Samples and Data
The Ethics of Research with Stored Samples and Data Sara Chandros Hull, Ph.D. Office of the Clinical Director, NHGRI and Department of Bioethics National Institutes of Health Disclaimers/Disclosures No
More informationGenetic diagnostics the gateway to personalized medicine
Micronova 20.11.2012 Genetic diagnostics the gateway to personalized medicine Kristiina Assoc. professor, Director of Genetic Department HUSLAB, Helsinki University Central Hospital The Human Genome Packed
More informationIntroduction To Epigenetic Regulation: How Can The Epigenomics Core Services Help Your Research? Maria (Ken) Figueroa, M.D. Core Scientific Director
Introduction To Epigenetic Regulation: How Can The Epigenomics Core Services Help Your Research? Maria (Ken) Figueroa, M.D. Core Scientific Director Gene expression depends upon multiple factors Gene Transcription
More informationACMG clinical laboratory standards for next-generation sequencing
American College of Medical Genetics and Genomics ACMG Practice Guidelines ACMG clinical laboratory standards for next-generation sequencing Heidi L. Rehm, PhD 1,2, Sherri J. Bale, PhD 3, Pinar Bayrak-Toydemir,
More informationReliable PCR Components for Molecular Diagnostic Assays
Reliable PCR Components for Molecular Diagnostic Assays Terri McDonnell, MBA, PMP Senior Program Manager, Molecular Diagnostics March 2014 In this webinar we will: Discuss requirements for amplification
More informationBRCA and Breast/Ovarian Cancer -- Analytic Validity Version 2003-6 2-1
ANALYTIC VALIDITY Question 8: Is the test qualitative or quantitative? Question 9: How often is a test positive when a mutation is present (analytic sensitivity)? Question 10: How often is the test negative
More informationComplete Genomics Sequencing
TECHNOLOGY OVERVIEW Complete Genomics Sequencing Introduction With advances in nanotechnology, high-throughput instruments, and large-scale computing, it has become possible to sequence a complete human
More informationAn Overview of DNA Sequencing
An Overview of DNA Sequencing Prokaryotic DNA Plasmid http://en.wikipedia.org/wiki/image:prokaryote_cell_diagram.svg Eukaryotic DNA http://en.wikipedia.org/wiki/image:plant_cell_structure_svg.svg DNA Structure
More informationempcr Amplification Method Manual - Lib-A
GS Junior Titanium Series May 2010 (Rev. April 2011) For life science research only. Not for use in diagnostic procedures. 1. WORKFLOW The emulsion-based clonal amplification (empcr amplification) of a
More informationProtocol. Introduction to TaqMan and SYBR Green Chemistries for Real-Time PCR
Protocol Introduction to TaqMan and SYBR Green Chemistries for Real-Time PCR Copyright 2008, 2010 Applied Biosystems. All rights reserved. Ambion and Applied Biosystems products are for Research Use Only.
More informationPh.D. in Bioinformatics and Computational Biology Degree Requirements
Ph.D. in Bioinformatics and Computational Biology Degree Requirements Credits Students pursuing the doctoral degree in BCB must complete a minimum of 90 credits of relevant work beyond the bachelor s degree;
More informationExploiting science for engineering: BRCA2 targeted therapies
20.109 MOD1 DNA ENGINEERING Fall 2010 Exploiting science for engineering: BRCA2 targeted therapies Orsi Kiraly Engelward lab Homologous recombination is important No HR chromosomal aberrations cell death
More informationThe 100,000 genomes project
The 100,000 genomes project Tim Hubbard @timjph Genomics England King s College London, King s Health Partners Wellcome Trust Sanger Institute ClinGen / Decipher Washington DC, 26 th May 2015 The 100,000
More informationVLLM0421c Medical Microbiology I, practical sessions. Protocol to topic J10
Topic J10+11: Molecular-biological methods + Clinical virology I (hepatitis A, B & C, HIV) To study: PCR, ELISA, your own notes from serology reactions Task J10/1: DNA isolation of the etiological agent
More informationNew generation sequencing: current limits and future perspectives. Giorgio Valle CRIBI - Università di Padova
New generation sequencing: current limits and future perspectives Giorgio Valle CRIBI Università di Padova Around 2004 the Race for the 1000$ Genome started A few questions... When? How? Why? Standard
More informationab185916 Hi-Fi cdna Synthesis Kit
ab185916 Hi-Fi cdna Synthesis Kit Instructions for Use For cdna synthesis from various RNA samples This product is for research use only and is not intended for diagnostic use. Version 1 Last Updated 1
More informationMoBEDAC -- Integrated data and analysis for the indoor and built environment. Folker Meyer Argonne National Laboratory GSC 13 Shenzhen, China
MoBEDAC -- Integrated data and analysis for the indoor and built environment Folker Meyer Argonne National Laboratory GSC 13 Shenzhen, China NGS is causing paradigm shift Environmental clone libraries
More informationNext Generation Sequencing. mapping mutations in congenital heart disease
Next Generation Sequencing mapping mutations in congenital heart disease AV Postma PhD Academic Medical Center Amsterdam, the Netherlands Overview talk Congenital heart disease and genetics Next generation
More informationSanger Sequencing and Quality Assurance. Zbigniew Rudzki Department of Pathology University of Melbourne
Sanger Sequencing and Quality Assurance Zbigniew Rudzki Department of Pathology University of Melbourne Sanger DNA sequencing The era of DNA sequencing essentially started with the publication of the enzymatic
More information14.3 Studying the Human Genome
14.3 Studying the Human Genome Lesson Objectives Summarize the methods of DNA analysis. State the goals of the Human Genome Project and explain what we have learned so far. Lesson Summary Manipulating
More informationCurrent Motif Discovery Tools and their Limitations
Current Motif Discovery Tools and their Limitations Philipp Bucher SIB / CIG Workshop 3 October 2006 Trendy Concepts and Hypotheses Transcription regulatory elements act in a context-dependent manner.
More informationG E N OM I C S S E RV I C ES
GENOMICS SERVICES THE NEW YORK GENOME CENTER NYGC is an independent non-profit implementing advanced genomic research to improve diagnosis and treatment of serious diseases. capabilities. N E X T- G E
More informationOverview sequence projects
Overview sequence projects Bioassist NGS meeting 15-01-2010 Barbera van Schaik KEBB - Bioinformatics Laboratory b.d.vanschaik@amc.uva.nl NGS at the Academic Medical Center Sequence facility Laboratory
More information