Implementation Insights Vancouver General Hospital, BC. Challenges we faced. Work-flow integration 11/14/2016
|
|
- Roger Parks
- 6 years ago
- Views:
Transcription
1 Implementation Insights Vancouver General Hospital, BC Challenges we faced Will vary depending on what your starting point is (SBT vs Serology) Space Training - Bench and analysis Computerization Integration into LIMS Work-flow integration How much change do you need to take the lab from molecular to NGS? still need pre- and post-pcr areas, so not much change from current set up tissue or sample collection will probably stay the same as current methods (ACD blood, BMT with multiple transfusions?) DNA extractions will also probably stay the same (note the use of EDTA in elution buffer) computerization might be an issue 1
2 Challenges with space Currently we are still running SSO/SSP, our sequencing core has moved into the old serology lab Bench height and width is different Benches dimension need to be able to take equipment (size and weight a MiSeq weighs more than Terasaki typing plates)! Freezer/fridge space Do you keep individual loci amplicon? Or only pooled samples? How long are libraries good for? Challenges with Training Staff training involves; bench/hands on training analysis resulting training Also, disseminating information to clinics and physicians. Challenges with training Bench work; Remarkably similar to current molecular techniques. Micro-volumes require additional experience to achieve consistency Multiplex of high number of samples can be confusing and will require more care awareness during processing Many more steps involved in library preparation (compared to SSO/SSP), time-management is more relevant 2
3 Bench Training Walk through protocol and technology 3 test runs (non-valuable samples; with smaller batch sizes initially), 3 real runs (with standard batch size, concordance with SSO/SSP) All QC tests passed for all 6 runs Training schedule ~5 months Actions to overcome bench challenges Practice good micro-pipetting technique on nonvaluable samples Develop monitoring procedures, and good practice, to ensure no sample mix up when handling many samples Protocols and workflows which are more flexible will permit technicians to develop a time management plan that works for them Challenges with training Analysis; Previous experience with SBT data and the associated software makes the learning curve less steep level of competence comes with analysis of a POOR run not a good run! Simplified workflow of analysis is essential to maintain consistency across calls 3
4 Actions to overcome challenges with analysis training Familiarization with software Lab meetings to show how the software looks, how to navigate through analysis pipeline, examples of results, examples of reports, integration into current reporting procedure Clear SOP (even better, cheat sheets!) Practise datasets (good and bad data). Compare analysis with trainee and trainer, work through challenging calls together Challenges with equipment Due to the significantly higher throughput capabilities of the technology, even simple things will need to be re-assessed; ordering reagents and supplies will be more frequent. Plan accordingly Multichannel pipettes will have to be maintained regularly and calibrated (which is an ASHI standard) CONNECTIVITY Computer specification for software will vary depending on software used; Most can be run on a stand alone desktop, either as individual licenses or as client servers Some will require a dedicated server to run software 4
5 Challenges with connectivity Standard hospital computers are not 64-bit. Data storage requirements for an Immunology lab for the last 40 years ~ 500mb/month, current data storage requirements for an Immunology lab ~100gb/month Data storage security concerns Optimal multiplexing strategy Optimal multiplexing strategy; expected sample throughput, frequency of testing, the assay TAT, the degree of batching (for regions of high genomic complexity, higher read depth can be used to compensate to improve accuracy) for batching samples, there must exist guidelines for standard multiplexing and read depth to ensure equivalence of test results. Validation of barcodes DATA REPORTING Clinical interpretation: Seamless, unambiguous, clinically relevant interpretation for end user Clinical report generation; What to include and what not to include intronic differences, variants of unknown significance 5
6 Integration with LIMS Automatic transfer of fastq files to data analysis software Direct import from analysis software to Histotrac (or equivalent) Update of Tie- breakers All methods tested were excellent and easily implementable in the lab Customer support is critical Although cost is of course important, should not be the deciding factor Tech feedback Top 5 reasons to go NGS The learning curve might be steep, depending on where you start from (serology, SBT), but easily streamlined for a medium-large throughput lab One pass testing; no need to go back and order additional tests (careful with those class 2 s!) Maintain autonomy from other sequencing labs, business model Creating a pre-to-post transplant continuum Cos all your friends are doing it! 6
7 THANK YOU Introduction For clinical purposes, NGS has all but replaced it s methodological predecessor, Sanger sequencing. It s faster, cheaper but ALONE, is it sensitive and specific enough to catch every variant while avoiding false-positives? Is cost a barrier to introduction of NGS in HLA labs? Pro s Pushing Transplant diagnostics into the 21st century Con s High set up costs Comparable to current molecular testing costs Fewer supplementary assays More complex training than current molecular testing techniques Minor pipetting error could result in loss of amplicon and consequently no data Limits repeated testing (especially hi-res repeats when Ab detected) Steep learning curve for data analysis 7
8 Interesting article The Scientist Q&A: Confirming NGS results with Sanger (Ambry Genetics CEO, Aaron Elliot) e/q-a--confirming-next-gen-sequencing- Results-with-Sanger/ Is cost a barrier to introduction of NGS in HLA labs? multi-plexing is a double edged sword; if it works, drastically lowers cost, but if theres an error, lose a lot in terms of reagent and time higher start-up costs cost of positive/negative controls (for each library preparation as well as for each sequencing instrument run) 8
9 Costs Evaluation costs Validation/accreditation costs Capital equipment costs Tech costs training costs Capital Equipment Instrument Cost* Investment Illumina MiSeq $100,000 Illumina MiSeq Support (Years 2 & 3) $34,000 Size selection equipment (Optional) $10,000 Plate fluorometer (Optional) $20,000 qpcr machine (Optional) $30,000 5x PCR machine $35, bit computer with 16+ GB RAM $3, x Liquid handler (Optional, pre & post PCR) $50,000+ (each) m four US Labs, rounded to $1,000 workflow integration Upstream integration Sample collection and DNA extractions Library preparation workflows Sample batching Liquid handling automation Data processing and analysis workflows Data transfer automation Analysis automation Long term data storage Approval workflow and tracking LIMS integration Export to NMDP standard Import directly into LIMS 9
10 Work-flow integration multiple QC steps; initially time-consuming but in the long run, will save bench time. Eventually QC steps can be pared down to minimum. to confirm or not to confirm with different assay typing takes longer than antibodies consequence on activation of patient labs not previously engaged in HLA typing could become involved in testing, as the workflow is fairly simple and indeed not drastically different for a wide range of diagnostic tests (cancer panel vs hla panel) however interpretation is KEY Automation 10
11 Work-flow integration WHAT IS OUR CURRENT TAT FOR NGS? Currently not suitable for deceased donor typing Challenges in data interpretation Can be summarised in 3 words; TIME, WORKLOAD, AMBIGUITIES Average time spent analysing and interpreting NGS data time allotment data analysis is still a bottle-neck partly because batches can be so large very few ambiguities gone are the days of chains Challenges in data interpretation determining QC characteristics associations 11
12 Challenges in data interpretation loss of 2nd allele in homozygous! determining true homozygousity drop outs amplicon coverage- accurate pooling required Challenges in data interpretation Submission of new alleles to CTR dictionary getting used to no chains! G group problem is now the reverse of the problem before (cant match too specific vs cant match not specific enough) NGS Data Analysis Approaches Reference- bases alignment, followed by HLA call based on the variants detected during alignment call is only as good at the alignment, coverage often insufficient Database based approach against known alleles novel allele detection and homozygous alleles are difficult to detect 12
13 Complex genetics Duplications High level of segmental duplications Lots of similar genes and lots of similar pseudogenes Duplicated segments can be more similar within an individual than they are to the corresponding segments of a reference genome Complex genetics Particularly DRB Tandem repeats can still be problematic (however no other technique has overcome this issue fully) However Many alleles are already known (even partially), both in terms of sequence and frequencies within a population HLA regions is relatively small, with a high degree of linkage disequilibrim, therefore many haplotypes have been described 13
14 Validation requirements 50 samples (plus 20 blind), over 3 runs Set up as you would routine testing (run size, sample type) Evaluation of; Run to run variability Tech to tech variability Quality Testing Must evaluate potential allele dropouts Documentation for; Sample preparation Monitor fidelity of barcoding methods rotate control samples with different barcode sequences Instrument performance measures internal control sample for instrument run performance Quality Testing Analytic performance criteria Incorporating vendor specifications Base quality, read length, average coverage, uniformity of coverage Independently validate software program Ensure genotyping algorithms are appropriate for sequencing strategy and sequencing error modalities 14
15 KNOW YOUR ASSAY S LIMITATIONS! Issues to consider inclusion of positive control sample, library QC use of phix for cross lot QC, run QC Top 5 reasons to go NGS The learning curve might be steep, depending on where you start from (serology, SBT), but easily streamlined for a medium-large throughput lab one pass testing; no need to go back and order additional tests (careful with those class 2 s!), auto-antibody issue Cos all your friends are doing it potential for epitope etc, rejection assay that detects donor-derived cellfree DNA in recipient plasma (Journal of Molecular Diagnostics) Circulating cell-free DNA enables noninvasive diagnosis of heart transplant rejection. De Vlaminck et al. Sci Transl Med Jun 18;6(241)?maintain autonomy from (cancer) other sequencing labs, business model Creating a pre-to-post transplant continuum? 15
16 11/14/2016 Single Molecule, Real-Time (SMRT ) Sequencing Unique capability to reveal the unknown Very Long 1 Read lengths Single Molecule Real Time Sequencing is capable of generating long reads to enable resolution of variation 2 High Accuracy Achieves >99.999% consensus accuracy Lack of systematic sequencing errors Coverage 4 3 High Uniformity Lack of GC content or sequence complexity bias Sequence native DNA No DNA amplification Epigenome characterization Roche s Single Molecule Real-Time Sequencer Accessible Benefits of Single Molecule Real-Time Sequencing Long read lengths High accuracy Sensitivity to detect minor variants at low frequencies Designed To Deliver: Simultaneous base-modification detection High coverage uniformity Short run times (minutes to few hours) Analytically validated workflows and analysis algorithms An optional, simplified supplied and supported compute pipeline Products in development and not available for global distribution. For Research Use Only. Not for use in diagnostic procedures. SMRT is a trademark of Pacific Biosciences 16
17 LOCATION SPACE ASHI Standards require (wipe tests for both); Pre-PCR and Thermocyclers, vortexer, centrifuge (no change from current molecular requirements) Post-PCR areas DNA quantitation equipment, thermocyclers, vortexer, centrifuge, library preparation auxiliary equipment, sequencer DNA extraction area EQUIPMENT (specific) Auxiliary equipment (not just the sequencer) is required for any HLA kit on the market DNA quantitation (and qualitation) equipment (fluorometers, spectrophotometers, gel equipment, RT-PCR etc) Library preparation equipment (magnetic stands for beads (remarkably expensive!), Pippin prep), thermocyclers) 17
18 Challenges with space Currently we are still running SSO/SSP, our sequencing core has moved into the old serology lab Bench height is different Benches dimension need to be able to take equipment (size and weight a MiSeq weighs more than Terisaki plates)! Freezer/fridge space Do you keep individual loci amplicon? Or only pooled samples? How long are libraries good for? DNA quantitation equipment Equipment (standard) Vortexers (plate and tube) Centrifuges (plate and tube) Amplification thermocyclers Multichannel pipette 18
19 Other equipment Challenges with equipment Due to the significantly higher throughput capabilities of the technology, even simple things will need to be re-assessed; ordering reagents and supplies will be more frequent. Plan accordingly Multichannel pipettes will have to be maintained regularly and calibrated (which is an ASHI standard), but when pipetting for heavy loads and with microvolumes, any tiny variability will cause samples to fail Equipment (general) Liquid handlers are highly recommended for both Pre- and Post-PCR steps Budget allowing (otherwise, get the 1 for Pre- PCR) Are programmable for other uses within the laboratory 19
20 Challenges with equipment Sequencers and liquid handlers have relatively large footprints, and can be very heavy and sensitive Must be on weight bearing bench No located on the same bench as a centrifuge or hightraffic area as vibrations can affect both the sequencer and the liquid handler Highly recommended NOT to move sequencers (alignment of internal optics) or liquid handlers (alignment and very heavy) unless absolute need..pick a permanent place Equipment (specific) Staff training involves; TRAINING bench/hands on training analysis resulting training Also, disseminating information to clinics and physician. Whilst the reported typings (if remaining at 4 digits) will look the same, the loss of chains and the ambiguities (no more XX) will need to be clarified with the programs 20
21 Challenges with training Bench work; Remarkably similar to current molecular techniques. Micro-volumes require additional experience to achieve consistency Multiplex of high number of samples can be confusing and will require more care awareness during processing Many more steps involved in library preparation (compared to SSO/SSP), time-management is more relevant Actions to overcome bench challenges Practice good micro-pipetting technique on nonvaluable samples Develop monitoring procedures, and good practice, to ensure no sample mix up when handling many samples (do not overwhelm the tech identify a suitable number of multiplex-able sample and use that as a standard) Protocols and workflows which are more flexible will permit technicians to develop a time management plan that works for them Challenges with training Analysis; Previous experience with SBT data and the associated software makes the learning curve less steep level of competence comes with analysis of a POOR run not a good run! Simplified workflow of analysis is essential to maintain consistency across calls 21
22 Actions to overcome challenges with analysis training Familiarization with software Lab meetings to show how the software looks, how to navigate through analysis pipeline, examples of results, examples of reports, integration into current reporting procedure Clear SOP (even better, cheat sheets!) Practise datasets (good and bad data). Compare analysis with trainee and trainer, work through challenging calls together ADDITIONAL During the validation phase of assay development, it is important to test assay performance using reference material Positive control material Must establish what constitutes a fail or a pass positive control Requirement to include a Negative control 22
23 Bench Training Walk through protocol and technology 3 test runs (non-valuable samples; with smaller batch sizes initially), 3 real runs (with standard batch size, concordance with SSO/SSP) All QC tests passed for all 6 runs Equipment Training Monitoring sequencing runs SOP will outline run metrics, positive control for sequencing portion of protocol (cross run variability) Maintenance of sequencers (do not knock bench while machine is running etc, wash maintenance schedule) CONNECTIVITY Computer specification for software will vary depending on software used; Most can be run on a stand alone desktop, either as individual licenses or as client servers Some will require a dedicated server to run software 23
24 Challenges with connectivity Standard hospital computers are not 64-bit. Data storage requirements for an Immunology lab for the last 40 years ~ 500mb/month, current data storage requirements for an Immunology lab ~350gb/month Data storage security concerns (there is a paper published that individuals could be identified from anonymous NGS data; Science : Identifying personal genomes by surname inference) BIOINFORMATICS essential to have a strategy to detect and investigate false Challenges of Bioinformatics 24
25 COST COMPARISON Demonstrating cost effectiveness of clinical NGS is key to payor reimbursement, hospital uptake OTHER CHALLENGES The question is not technological can it be done but rather practical how can NGS technology be developed into a mainstream clinical typing tool? Quality control standardisation lack thereof current NGS technologies have higher error rates and novel error modes compared to traditional sequencing what is an appropriate orthogonal technology? i mean, we assume SSO/SSP is right. What is the true measure of truth 25
26 BMT samples; the way we request samples may need to change what if the patient has had multiple transfusions and we are not detecting patient cells but donor DNA DNA often low, cell count low in certain types malignancies How we overcame challenges FLOW DIAGRAMS OF VENDORS 26
27 Illumina TruSight Life Technologies (Thermo Fisher) NXType 27
28 FLOW DIAGRAMS IN PRACTICE CAP NGS checklist recommends orthogonal analytical confirmation of all encountered mutations from an assay before the mutation is reported as clinically actionable (is this relevant for HLA possibly not) FDA-Cleared instrumentation Optimal multiplexing strategy; includes taking into account the following expected sample throughput, frequency of testing, the assay TAT, the degree of batching (for regions of high genomic complexity, higher read depth can be used to compensate to improve accuracy) for batching samples, there must exist guidelines for standard multiplexing and read depth to ensure equivalence of test results. 28
29 DATA REPORTING Clinical interpretation: Seamless, unabiguous, clinically relevant interpretation for end user Clinical report generation; What to include and what not to include intronic differences, variants of unknown significance Parallel analysis of control samples Raw reads (DAT files, BCL files) Demultiplexing Deconvoluted reads (FASTQ files) Alignment to reference genome Aligned reads (BAM files) Coverage calculations, local alignment On target alignment Variation analysis QC raw and QC passed run yield, read quality, run parameters QC barcoding deconvolution, sample read distribution QC alignment (mapping quality), library complexity QC coverage depth, coverage uniformity, allellelic frequency, strand bias, GC content Filtration Clinical report Truth QC controls 29
Next Generation Sequencing of HLA: Challenges and Opportunities in the era of Precision Medicine. Dr. Paul Keown, 2016
Next Generation Sequencing of HLA: Challenges and Opportunities in the era of Precision Medicine Dr. Paul Keown, 2016 Statement of Conflict & Collaboration Therapeutics collaborations Novartis, Roche,
More informationIntroducing NGS and Holotype HLA EAP User Experiences
Agenda Introducing NGS and Holotype HLA EAP User Experiences David Lowe University of Liverpool Julio Delgado ARUP and University of Utah Alex Sheh Red Cross, Dedham Dimitri Monos CHOP Tim Hague CEO @
More informationVALIDATION OF HLA TYPING BY NGS
VALIDATION OF HLA TYPING BY NGS Eric T. Weimer, Ph.D., D(ABMLI) Assistant Professor, Pathology and Laboratory Medicine Associate Director, Clinical Flow Cytometry, HLA, and Immunology Laboratories CONFLICT
More informationMarcelo Fernández-Viña
Marcelo Fernández-Viña Histocompatibility, Immunogenetics and Disease Profiling Laboratory Stanford Blood Center HLA: Quo Vadis (Where are going to)? Development and Implementation of Next Generation Sequencing
More informationHLA-Typing Strategies
HLA-Typing Strategies Cologne, 13.5.2017 Joannis Mytilineos MD, PhD Department of Transplantation Immunology Institute for Clinical Transfusion Medicine and Immunogenetics German Red Cross Blood Transfusion
More informationEFI 2016 DEBATE: WHOLE GENE VERSUS EXONIC SEQUENCING. Dr Katy Latham Stance: Whole gene sequencing should be the norm for HLA typing
EFI 2016 DEBATE: WHOLE GENE VERSUS EXONIC SEQUENCING Dr Katy Latham Stance: Whole gene sequencing should be the norm for HLA typing Why we should be utilising whole gene sequencing Ambiguity generated
More informationIs NGS for everyone? Is NGS for everyone? Factors to consider in selecting a platform and approach. Costs as incentive and barrier
NEX-GENERAION SEQUENCING (NGS) WORKSHOP November 10-11, 2016 Embassy Suites by Hilton Dallas - DFW Airport South Is NGS for everyone? Lee Ann Baxter-Lowe University of Southern California Children s Hospital
More informationFunctional DNA Quality Analysis Improves the Accuracy of Next Generation Sequencing from Clinical Specimens
Functional DNA Quality Analysis Improves the Accuracy of Next Generation Sequencing from Clinical Specimens Overview We have developed a novel QC, the SuraSeq DNA Quantitative Functional Index (QFI ).
More informationHigh Cross-Platform Genotyping Concordance of Axiom High-Density Microarrays and Eureka Low-Density Targeted NGS Assays
High Cross-Platform Genotyping Concordance of Axiom High-Density Microarrays and Eureka Low-Density Targeted NGS Assays Ali Pirani and Mohini A Patil ISAG July 2017 The world leader in serving science
More informationRIPTIDE HIGH THROUGHPUT RAPID LIBRARY PREP (HT-RLP)
Application Note: RIPTIDE HIGH THROUGHPUT RAPID LIBRARY PREP (HT-RLP) Introduction: Innovations in DNA sequencing during the 21st century have revolutionized our ability to obtain nucleotide information
More informationLiquidBiopsy LIQUIDBIOPSY. Automated Rare Template Isolation Platform
LiquidBiopsy LIQUIDBIOPSY Automated Rare Template Isolation Platform Enabling cancer research with highly multiplexed molecular analysis of serially collected blood samples The LiquidBiopsy Platform simplifies
More informationAmplicon Library Preparation Method Manual. GS FLX Titanium Series October 2009
GS FLX Titanium Series 1. Workflow 3. Procedure The procedure to prepare Amplicon libraries is shown in Figure 1. It consists of a PCR amplification, performed using special Fusion Primers for the Genome
More informationOutline General NGS background and terms 11/14/2016 CONFLICT OF INTEREST. HLA region targeted enrichment. NGS library preparation methodologies
Eric T. Weimer, PhD, D(ABMLI) Assistant Professor, Pathology & Laboratory Medicine, UNC School of Medicine Director, Molecular Immunology Associate Director, Clinical Flow Cytometry, HLA, and Immunology
More informationGet to Know Your DNA. Every Single Fragment.
HaloPlex HS NGS Target Enrichment System Get to Know Your DNA. Every Single Fragment. High sensitivity detection of rare variants using molecular barcodes How Does Molecular Barcoding Work? HaloPlex HS
More informationSummary of Proposed Revisions to the 2013 Standards November 2014
Summary of Proposed Revisions to the 2013 Standards November 2014 The following revisions are proposed to the 2013 ASHI Standards. These revisions went through multiple reviews by the ASHI Board of Directors
More informationSMRT Analysis Barcoding Overview (v6.0.0)
SMRT Analysis Barcoding Overview (v6.0.0) Introduction This document applies to PacBio RS II and Sequel Systems using SMRT Link v6.0.0. Note: For information on earlier versions of SMRT Link, see the document
More informationAssay Validation Services
Overview PierianDx s assay validation services bring clinical genomic tests to market more rapidly through experimental design, sample requirements, analytical pipeline optimization, and criteria tuning.
More informationTargeted Sequencing in the NBS Laboratory
Targeted Sequencing in the NBS Laboratory Christopher Greene, PhD Newborn Screening and Molecular Biology Branch Division of Laboratory Sciences Gene Sequencing in Public Health Newborn Screening February
More informationQuality Control of Next Generation Sequence Data
Quality Control of Next Generation Sequence Data January 17, 2018 Kane Tse, Assistant Bioinformatics Coordinator Canada s Michael Smith Genome Sciences Centre BC Cancer Agency Canada s Michael Smith Genome
More informationGENOMICS WORKFLOW SOLUTIONS THAT GO WHERE THE SCIENCE LEADS. Genomics Solutions Portfolio
GENOMICS WORKFLOW SOLUTIONS THAT GO WHERE THE SCIENCE LEADS Genomics Solutions Portfolio WORKFLOW SOLUTIONS FROM EXTRACTION TO ANALYSIS Application-based answers for every step of your workflow Scientists
More informationFully Automated Library Quantification for Illumina Sequencing on the NGS STAR
Fully Automated Library Quantification for Illumina Sequencing on the NGS STAR Introduction Hamilton Robotics, an industry leader in liquid handling and laboratory automation equipment, has partnered with
More informationHyperCap, an automatable workflow on the Agilent Bravo B
Automation Note February 2018 HyperCap, an automatable workflow on the Agilent Bravo B 1. OVERVIEW As the demand for next-generation sequencing (NGS) grows, laboratories must adapt to manage increased
More informationWELCOME. Norma J. Nowak, PhD Executive Director, NY State Center of Excellence in Bioinformatics and Life Sciences (CBLS)
WELCOME Norma J. Nowak, PhD Executive Director, NY State Center of Excellence in Bioinformatics and Life Sciences (CBLS) Director, UB Genomics and Bioinformatics Core (GBC) o o o o o o o o o o o o Grow
More informationQuality assurance in NGS (diagnostics)
Quality assurance in NGS (diagnostics) Chris Mattocks National Genetics Reference Laboratory (Wessex) Research Diagnostics Quality assurance Any systematic process of checking to see whether a product
More informationNGS Sample QC with the Agilent 2200 TapeStation. Rainer Nitsche Application Engineer Agilent Technologies, Inc.
NGS Sample QC with the Agilent 2200 TapeStation Rainer Nitsche Application Engineer Agilent Technologies, Inc. The Agilent 2100 Bioanalyzer First commercially available Lab-on-a-Chip product Introduced
More informationSequencing and PCR. Training: Ion S5 and S5 XL Systems workflow training
Training: Ion S5 and S5 XL Systems workflow training This interactive course focuses on the Ion S5 and Ion S5 XL Systems operation and the Ion AmpliSeq workflow on the Ion Chef System for sequencing. The
More informationMicroSEQ TM ID Rapid Microbial Identification System:
MicroSEQ TM ID Rapid Microbial Identification System: the complete solution for reliable genotypic microbial identification 1 The world leader in serving science Rapid molecular methods for pharmaceutical
More informationLab methods: Exome / Genome. Ewart de Bruijn
Lab methods: Exome / Genome 27 06 2013 Ewart de Bruijn Library prep is only a small part of the complete DNA analysis workflow DNA isolation library prep enrichment flowchip prep sequencing bioinformatics
More informationDNA concentration and purity were initially measured by NanoDrop 2000 and verified on Qubit 2.0 Fluorometer.
DNA Preparation and QC Extraction DNA was extracted from whole blood or flash frozen post-mortem tissue using a DNA mini kit (QIAmp #51104 and QIAmp#51404, respectively) following the manufacturer s recommendations.
More informationSureSelect XT HS. Target Enrichment
SureSelect XT HS Target Enrichment What Is It? SureSelect XT HS joins the SureSelect library preparation reagent family as Agilent s highest sensitivity hybrid capture-based library prep and target enrichment
More informationGENOMICS WORKFLOW SOLUTIONS THAT GO WHERE THE SCIENCE LEADS. Genomics Solutions Portfolio
GENOMICS WORKFLOW SOLUTIONS THAT GO WHERE THE SCIENCE LEADS Genomics Solutions Portfolio WORKFLOW SOLUTIONS FROM EXTRACTION TO ANALYSIS Application-based answers for every step of your workflow Scientists
More informationAKESOgen, Inc, 3155 Northwoods Place, NW, Norcross, GA 30071, USA Tel: +1 (770) Page 1
Page 1 HLA Sequencing Based Typing Workflow: A- Sample Collection: iswab-discovery (Mawi DNA Technologies) - Sample was transported by standard US postal services mail, no cold chain of any sort was involved
More informationsolid S Y S T E M s e q u e n c i n g See the Difference Discover the Quality Genome
solid S Y S T E M s e q u e n c i n g See the Difference Discover the Quality Genome See the Difference With a commitment to your peace of mind, Life Technologies provides a portfolio of robust and scalable
More informationWelcome to the NGS webinar series
Welcome to the NGS webinar series Webinar 1 NGS: Introduction to technology, and applications NGS Technology Webinar 2 Targeted NGS for Cancer Research NGS in cancer Webinar 3 NGS: Data analysis for genetic
More informationIncrease Sequencing Efficiency with the SeqCap EZ Prime Exome
Sequencing Solutions Technical Note June 2018 How To Increase Sequencing Efficiency with the SeqCap EZ Prime Exome Applications Whole Exome Sequencing Products SeqCap EZ Prime Exome SeqCap EZ HyperCap
More informationIntroducing QIAseq. Accelerate your NGS performance through Sample to Insight solutions. Sample to Insight
Introducing QIAseq Accelerate your NGS performance through Sample to Insight solutions Sample to Insight From Sample to Insight let QIAGEN enhance your NGS-based research High-throughput next-generation
More informationIllumina s Suite of Targeted Resequencing Solutions
Illumina s Suite of Targeted Resequencing Solutions Colin Baron Sr. Product Manager Sequencing Applications 2011 Illumina, Inc. All rights reserved. Illumina, illuminadx, Solexa, Making Sense Out of Life,
More informationMHC Region. MHC expression: Class I: All nucleated cells and platelets Class II: Antigen presenting cells
DNA based HLA typing methods By: Yadollah Shakiba, MD, PhD MHC Region MHC expression: Class I: All nucleated cells and platelets Class II: Antigen presenting cells Nomenclature of HLA Alleles Assigned
More informationHID Real-Time PCR Analysis Software v1.3
PRODUCT BULLETIN Human identification HID Real-Time PCR Analysis Software v1.3 Enhanced data analysis for QuantStudio 5 and 7500 Real-Time PCR Systems with Quantifiler kit Applied Biosystems Quantifiler
More informationab High Sensitivity DNA Library Preparation Kit (For Illumina )
ab185905 High Sensitivity DNA Library Preparation Kit (For Illumina ) Instructions for Use For the preparation of a DNA library using sub-nanogram amounts of DNA input for next generation sequencing applications
More informationab High Sensitivity DNA Library Preparation Kit (For Illumina )
ab185905 High Sensitivity DNA Library Preparation Kit (For Illumina ) Instructions for Use For the preparation of a DNA library using sub-nanogram amounts of DNA input for next generation sequencing applications
More informationBR-9516B. SNP genotyping analysis for medium to ultra-high throughput. GENOMELAB TM SNPSTREAM GENOTYPING SERIES
BR-9516B SNP genotyping analysis for medium to ultra-high throughput. GENOMELAB TM SNPSTREAM GENOTYPING SERIES Where power meets flexibility. The GenomeLab SNPstream Genotyping System provides an automated,
More informationNEXTflex Cystic Fibrosis Amplicon Panel. (For Illumina Platforms) Catalog # (Kit contains 8 reactions) Bioo Scientific Corp V17.
NEXTflex Cystic Fibrosis Amplicon Panel (For Illumina Platforms) Catalog #4231-01 (Kit contains 8 reactions) Bioo Scientific Corp. 2017 V17.02 This product is for research use only. Not for use in diagnostic
More informationA*01:02, 68:02 B*15:10, 58:02 DRB1*03:01, 12:01
lifetechnologies.com For In Vitro Diagnostic Use. The 3500 Dx and 3500xL Dx Genetic Analyzers CS2 and system accessories meet the requirements for IVD instrumentation in the United States. 2013 Life Technologies
More informationHaloPlex HS. Get to Know Your DNA. Every Single Fragment. Kevin Poon, Ph.D.
HaloPlex HS Get to Know Your DNA. Every Single Fragment. Kevin Poon, Ph.D. Sr. Global Product Manager Diagnostics & Genomics Group Agilent Technologies For Research Use Only. Not for Use in Diagnostic
More informationSchedule of Accreditation issued by United Kingdom Accreditation Service 2 Pine Trees, Chertsey Lane, Staines-upon-Thames, TW18 3HR, UK
2 Pine Trees, Chertsey Lane, Staines-upon-Thames, TW18 3HR, UK Royal Liverpool and Broadgreen University Hospitals NHS Trust Liverpool Clinical Laboratories (LCL) Department of Histocompatibility and Immunogenetics
More informationDeep Sequencing technologies
Deep Sequencing technologies Gabriela Salinas 30 October 2017 Transcriptome and Genome Analysis Laboratory http://www.uni-bc.gwdg.de/index.php?id=709 Microarray and Deep-Sequencing Core Facility University
More informationAnalytical verification methods for the Oncomine Lung cfdna Assay using the Ion S5 XL System
WHITE PAPER Oncomine Lung cfdna Assay and Ion S5 XL System Analytical verification methods for the Oncomine Lung cfdna Assay using the Ion S5 XL System Key highlights Investigate tumor heterogeneity and
More informationEmbrace the Future of Electrophoresis
Embrace the Future of Electrophoresis Analysis of 12 samples in as little as 3 minutes Unattended analysis of up to 96 samples Resolution down to 3 5 bp for fragments
More informationAlmac Diagnostics. NGS Panels: From Patient Selection to CDx. Dr Katarina Wikstrom Head of US Operations Almac Diagnostics
Almac Diagnostics NGS Panels: From Patient Selection to CDx Dr Katarina Wikstrom Head of US Operations Almac Diagnostics Overview Almac Diagnostics Overview Benefits and Challenges of NGS Panels for Subject
More informationFrom Liquid Biopsy and FFPE Samples to Results
From Liquid Biopsy and FFPE Samples to Results Fully automated purification, reliable quantification and bisulfite conversion of cell-free circulating DNA and DNA from FFPE samples Fully automated purification,
More informationDNBseq TM SERVICE OVERVIEW Plant and Animal Whole Genome Re-Sequencing
TM SERVICE OVERVIEW Plant and Animal Whole Genome Re-Sequencing Plant and animal whole genome re-sequencing (WGRS) involves sequencing the entire genome of a plant or animal and comparing the sequence
More informationFrom Liquid Biopsy and FFPE Samples to Results
www.autogen.com 774-233-3000 From Liquid Biopsy and FFPE Samples to Results Fully automated purification, reliable quantification and bisulfite conversion of cell-free circulating DNA and DNA from FFPE
More informationIn The Name of GOD. HLA Typing. By: M. Farzanehkhah NoAvaran MAYA Teb Co.
In The Name of GOD HLA Typing 21.04.2016 By: M. Farzanehkhah NoAvaran MAYA Teb Co. Haplotypes: An HLA haplotype is a series of HLA genes (loci alleles) by chromosome, one passed from mother and one from
More informationTHE WHOLE GENE: APPLICATION AND IMPLEMENTATION OF WHOLE GENE SEQUENCING IN THE CLINICAL LABORATORY.
THE WHOLE GENE: APPLICATION AND IMPLEMENTATION OF WHOLE GENE SEQUENCING IN THE CLINICAL LABORATORY. Dr. Katy Latham Anthony Nolan Research Institute, London, UK EFI 2018: NGS teaching session OBJECTIVES
More informationPerformance Characteristics drmid Dx for Illumina NGS systems
Performance Characteristics drmid Dx for Illumina NGS systems MANUFACTURER Multiplicom N.V. Galileïlaan 18 2845 Niel BELGIUM Revision date: August, 2017 Page 1 of 7 TABLE OF CONTENTS 1. TEST PRINCIPLE...
More informationAgilent NGS Solutions : Addressing Today s Challenges
Agilent NGS Solutions : Addressing Today s Challenges Charmian Cher, Ph.D Director, Global Marketing Programs 1 10 years of Next-Gen Sequencing 2003 Completion of the Human Genome Project 2004 Pyrosequencing
More informationProtein and transcriptome quantitation using BD AbSeq Antibody-Oligonucleotide
Protein and transcriptome quantitation using BD AbSeq Antibody-Oligonucleotide technology and the 10X Genomics Chromium Single Cell Gene Expression Solution Jocelyn G. Olvera, Brigid S. Boland, John T.
More informationNEXT GENERATION SEQUENCING Whole Gene Sequencing
NEXT GENERATION SEQUENCING Whole Gene Sequencing Ingrid Faé Educational Session 3: Next generation sequencing Stockholm, Friday, June 27 th 2014 Department for Blood Group Serology and Transfusion Medicine
More informationSURESELECTXT LOW INPUT TARGET ENRICHMENT
SURESELECTXT LOW INPUT TARGET ENRICHMENT Low Input FFPE Optimized Streamlined Workflow SureSelect XT Low Input What is it? SureSelect XT Low Input is a low-input, FFPE-optimized library preparation kit.
More informationFrom Bands to Base Pairs: Implementation of WGS in a PulseNet Laboratory
From Bands to Base Pairs: Implementation of WGS in a PulseNet Laboratory Sara Wagner Microbiologist WI State Lab of Hygiene InFORM Meeting Nov 19, 2015 Objectives Describe WGS implementation at WSLH What
More informationAutomated target enrichment using SeqCapEZ DNA kits on ACSIA NGS Capture Edition
Application Note Automated target enrichment using SeqCapEZ DNA kits on ACSIA NGS Capture Edition Anh Thu VU, PrimaDiag Parc Biocitech, 102 Avenue Gaston Roussel, 93230 Romainville, France E-mail: anhthu.vu@primadiag.com
More informationSEQUENCING FROM SAMPLE TO SEQUENCE READY
SEQUENCING FROM SAMPLE TO SEQUENCE READY ACCESS ARRAY SYSTEM HIGH-QUALITY LIBRARIES NOT ONCE, BUT EVERY TIME n The highest quality amplicons more sensitive, accurate, and specific n Full support for all
More information454 Sample Prep / Workflow at the BioMedical Genomics Center (BMGC) University of Minnesota. Sushmita Singh
454 Sample Prep / Workflow at the BioMedical Genomics Center (BMGC) University of Minnesota Sushmita Singh 1 Consultation 2 Sample Prep (client) 3 Sample Prep (Core) Sequencing 4 Data QC 1 Consultation
More informationNext Generation Sequencing. Target Enrichment
Next Generation Sequencing Target Enrichment Next Generation Sequencing Your Partner in Every Step from Sample to Data NGS: Revolutionizing Genetic Analysis with Single-Molecule Resolution Next generation
More informationPurpose: To sequence 16S microbial DNA isolated from animal fecal matter and perform compositional analysis of bacterial communities.
Purpose: To sequence 16S microbial DNA isolated from animal fecal matter and perform compositional analysis of bacterial communities. Reference: This protocol was adapted from: A custom and streamlined
More information2017 HTS-CSRS COMMUNITY PUBLIC WORKSHOP
2017 HTS-CSRS COMMUNITY PUBLIC WORKSHOP GenomeNext Overview Olympus Platform The Olympus Platform provides a continuous workflow and data management solution from the sequencing instrument through analysis,
More informationRedefine what s possible with the Axiom Genotyping Solution
Redefine what s possible with the Axiom Genotyping Solution From discovery to translation on a single platform The Axiom Genotyping Solution enables enhanced genotyping studies to accelerate your research
More informationSNP GENOTYPING WITH iplex REAGENTS AND THE MASSARRAY SYSTEM
SNP GENOTYPING Accurate, sensitive, flexible MassARRAY System SNP GENOTYPING WITH iplex REAGENTS AND THE MASSARRAY SYSTEM Biomarker validation Routine genetic testing Somatic mutation profiling Up to 400
More informationEPIGENTEK. EpiNext DNA Library Preparation Kit (Illumina) Base Catalog # P-1051 PLEASE READ THIS ENTIRE USER GUIDE BEFORE USE
EpiNext DNA Library Preparation Kit (Illumina) Base Catalog # PLEASE READ THIS ENTIRE USER GUIDE BEFORE USE Uses: The EpiNext DNA Library Preparation Kit (Illumina) is suitable for preparing a DNA library
More informationSNP GENOTYPING WITH iplex REAGENTS AND THE MASSARRAY SYSTEM
SNP GENOTYPING Accurate, sensitive, flexible MassARRAY System SNP GENOTYPING WITH iplex REAGENTS AND THE MASSARRAY SYSTEM Biomarker validation Routine genetic testing Somatic mutation profiling Up to 400
More informationLaktaseCheck real time PCR Kit
Instruction for Use Dr. Schröders LaktaseCheck real time PCR Kit Test for the analysis of the C/T polymorphism at position -13910 within the regulatory region of the lactase gen in man. G01010-96 96 gerbion
More informationDNA METHYLATION RESEARCH TOOLS
SeqCap Epi Enrichment System Revolutionize your epigenomic research DNA METHYLATION RESEARCH TOOLS Methylated DNA The SeqCap Epi System is a set of target enrichment tools for DNA methylation assessment
More informationABA iplex Pro Chimeric ID Panel Protocol
ABA iplex Pro Chimeric ID Panel Protocol This document gives the assay protocol for the Assays by Agena (ABA) iplex Pro Chimeric ID Panel (Chimeric ID). The Chimeric ID Panel accurately determines the
More informationBIOO LIFE SCIENCE PRODUCTS. NEXTflex TM 16S V4 Amplicon-Seq Kit 4 (Illumina Compatible) BIOO Scientific Corp V13.01
BIOO LIFE SCIENCE PRODUCTS NEXTflex TM 16S V4 Amplicon-Seq Kit 4 (Illumina Compatible) Catalog #: 4201-01 (16 reactions) BIOO Scientific Corp. 2013 V13.01 TABLE OF CONTENTS GENERAL INFORMATION... 1 Product
More informationComplete Success Begins with Sample Quality Control. Agilent 4150 and 4200 TapeStation Systems
Complete Success Begins with Sample Quality Control Agilent 4150 and 4200 TapeStation Systems Complete Success Begins with Sample Quality Control Agilent TapeStation systems are automated electrophoresis
More informationPCR SYSTEMS. a new era in high-productivity qpcr. Applied Biosystems ViiA 7 Real-Time PCR System
PCR SYSTEMS a new era in high-productivity qpcr Applied Biosystems ViiA 7 Real-Time PCR System a new era in high-productivity qpcr The ViiA 7 Real-Time PCR System delivers the proven reliability, sensitivity,
More informationIsoFluxTM. System. The next generation of CTC Analysis is here
IsoFluxTM System The next generation of CTC Analysis is here Product Overview IsoFlux System The next generation of circulating tumor cell analysis is here The IsoFlux System enriches intact rare cells
More informationSummary of key processes for tumor BRCA testing. Q&A Session Hadassah Medical Center, Jerusalem Sabine Merkelbach-Bruse
Summary of key processes for tumor BRCA testing Q&A Session 29.01.2018 Hadassah Medical Center, Jerusalem Sabine Merkelbach-Bruse Review of key processes Overview Summary of key processes Quality assurance
More informationNext Generation Oncology Sequencing in your Laboratory. Built by pioneers in cancer genomics and liquid biopsy approaches PROGENEUS
PROGENEUS Next Generation Oncology Sequencing in your Laboratory Built by pioneers in cancer genomics and liquid biopsy approaches For Research Use Only. Not for iagnostic Purposes. personalgenome.com/progeneus
More informationEvaluation of the Autogen FlexSTAR automated DNA extractor, for suitability in routine diagnostic use
Evaluation of the Autogen FlexSTAR automated DNA extractor, for suitability in routine diagnostic use Performed by Dr H Martin, E Gee, G Flavell and S Marshall 2015 Initial machine evaluation Aim: To extract
More informationLiquidator 96. CCDB Simplifies Genomic Workflow Liquidator 96 Used in DNA Barcoding
CCDB Simplifies Genomic Workflow Liquidator 96 Used in DNA Barcoding The Canadian Centre for DNA Barcoding (CCDB) uses the throughout its barcoding workflow. The CCDB is developing a barcode reference
More informationOvercome limitations with RNA-Seq
Buyer s Guide Simple, customized RNA-Seq workflows Evaluating options for next-generation RNA sequencing Overcome limitations with RNA-Seq Next-generation sequencing (NGS) has revolutionized the study
More informationImplementation of Automated Sample Quality Control in Whole Exome Sequencing
Journal of Life Sciences 11 (2017) 261-268 doi: 10.17265/1934-7391/2017.06.001 D DAVID PUBLISHING Implementation of Automated Sample Quality Control in Whole Exome Sequencing Elisa Viering 1, Jana Molitor
More informationSupplemental File 1: Modified Nextera XT DNA Sample Preparation Guide (Illumina, USA, Part # rev. C, October 2012).
Supplemental File 1: Modified Nextera XT DNA Sample Preparation Guide (Illumina, USA, Part # 15031942 rev. C, October 2012). Required Kit content: Box1 ATM Amplicon Tagment Mix TD Tagment DNA Buffer NPM
More informationFFPE in your NGS Study
FFPE in your NGS Study Richard Corbett Canada s Michael Smith Genome Sciences Centre Vancouver, British Columbia Dec 6, 2017 Our mandate is to advance knowledge about cancer and other diseases and to use
More informationCAPTURE-BASED APPROACH FOR COMPREHENSIVE DETECTION OF IMPORTANT ALTERATIONS
CAPTURE-BASE APPROACH FOR COMPREHENSIVE ETECTION OF IMPORTANT ALTERATIONS SEQUENCE MUTATIONS MICROSATELLITE INSTABILITY AMPLIFICATIONS GENOMIC REARRANGEMENTS For Research Use Only. Not for iagnostic Purposes.
More informationIllumina TruSeq RNA Access Library Prep Kit Automated on the Biomek FX P Dual-Hybrid Liquid Handler
Illumina TruSeq RNA Access Library Prep Kit Automated on the Biomek FX P Dual-Hybrid Liquid Handler Introduction David Horvath, M.S., Senior Applications Scientist, Beckman Coulter, Inc.; Tim Hill, Scientist,
More informationPerformance of the Newly Developed Non-Invasive Prenatal Multi- Gene Sequencing Screen
1 // Performance of the Newly Developed Non-Invasive Prenatal Multi- Gene Sequencing Screen ABSTRACT Here we describe the analytical performance of the newly developed non-invasive prenatal multi-gene
More informationCertificate of Analysis of the Holotype HLA 24/7 Configuration A1 & CE
Certificate of Analysis of the Holotype HLA 24/7 Configuration A1 & CE Product name Holotype HLA 24/7 Configuration A1 & CE Reference number H52 LOT number 00027 (N4/002-P5/006-E1/004-R2/006) Expiration
More informationAgilent 2200 TapeStation System ACCELERATE YOUR SAMPLE QC WITH CONFIDENCE
Agilent 2200 TapeStation System ACCELERATE YOUR SAMPLE QC WITH CONFIDENCE Agilent 2200 TapeStation SYSTEM Accelerate your sample QC Confidence means a QC workflow that delivers reproducible, user-independent
More informationNext Generation Sequencing
Educational Session 28th EFI Conference, Stockholm Kaimo Hirv ZENTRUM FÜR HUMANGENETIK UND LABORATORIUMSDIAGNOSTIK (MVZ) Dr. Klein, Dr. Rost und Kollegen Lochhamer Str. 29 82152 Martinsried Tel: 0800-GENETIK
More informationsparq HiFi PCR Master Mix
sparq HiFi PCR Master Mix Cat. No. 95192-050 Size: 50 reactions Store at -25 C to -15 C 95192-250 250 reactions Description The sparq HiFi PCR Master Mix is a high efficiency, high-fidelity, and low bias
More informationILLUMINA SEQUENCING SYSTEMS
ILLUMINA SEQUENCING SYSTEMS PROVEN QUALITY. TRUSTED SOLUTIONS. Every day, researchers are using Illumina next-generation sequencing (NGS) systems to better understand human health and disease, as well
More informationSurely Better Target Enrichment from Sample to Sequencer
sureselect TARGET ENRICHMENT solutions Surely Better Target Enrichment from Sample to Sequencer Agilent s market leading SureSelect platform provides a complete portfolio of catalog to custom products,
More informationProcedure & Checklist - Preparing SMRTbell Libraries using PacBio Barcoded Universal Primers for Multiplex SMRT Sequencing
Procedure & Checklist - Preparing SMRTbell Libraries using PacBio Barcoded Universal Primers for Multiplex SMRT Sequencing Before You Begin This document describes methods for generating barcoded PCR products
More informationDevelopment of quantitative targeted RNA-seq methodology for use in differential gene expression
Development of quantitative targeted RNA-seq methodology for use in differential gene expression Dr. Jens Winter, Market Development Group Biological Biological Research Content EMEA QIAGEN Universal Workflows
More informationThe MiniSeq System. Explore the possibilities. Discover demonstrated NGS workflows for molecular biology applications.
The MiniSeq System. Explore the possibilities. Discover demonstrated NGS workflows for molecular biology applications. Let your work flow with Illumina NGS. The MiniSeq System delivers powerful and cost-effective
More informationAxygen AxyPrep Magnetic Bead Purification Kits. A Corning Brand
Axygen AxyPrep Magnetic Bead Purification Kits A Corning Brand D Sample Prep Solutions for Genomics Obtaining Pure Nucleic Acids from Your Sample is Precious The purification of high quality DNA is the
More information