Submit Search
Upload
Aug2014 abrf interlaboratory study plans
•
Download as PPTX, PDF
•
1 like
•
1,660 views
GenomeInABottle
Follow
ABRF update
Read less
Read more
Health & Medicine
Report
Share
Report
Share
1 of 19
Download now
Recommended
140127 abrf interlaboratory study proposal
140127 abrf interlaboratory study proposal
GenomeInABottle
Bioinformatica e genomica comparata: nuove strategie sperimentali e computazionali per la produzione e analisi di dati NGS finalizzati a sviluppare processi e prodotti innovativi per la salute dell’uomo, l’ambiente e l’agroalimentare.
Ernesto Picardi – Bioinformatica e genomica comparata: nuove strategie sperim...
Ernesto Picardi – Bioinformatica e genomica comparata: nuove strategie sperim...
eventi-ITBbari
What is the impact of assay failure in your laboratory and how do you monitor for it? The most heavily degraded samples are not suitable for standard exome coverage: sometimes it’s not even a matter of getting bad sequencing, you might get nothing at all! FFPE artifacts increase with storage time Artifacts go against the statistical power of your variant calling analysis Molecular reference standards help filter out bad mappings and spurious variants Bioinformatics pipelines allow adding Molecular Reference Standards in your joint variant calling pipeline Genome In A Bottle Reference Standards are invaluable for validating variant calling analysis NIST and its collaborators shared datasets created with most NGS technologies Horizon Diagnostics shared annotated, merged variant calls from NIST for the Ashkenazim Trio ~35K variants are predicted having high or moderate impact within the Trio GM24385 (Ashkenazim Son) includes 352 small variants with high/moderate impact which are absent in Father and Mother Routinely monitor the performance of your workflows and assays with independent external controls
Molecular QC: Interpreting your Bioinformatics Pipeline
Molecular QC: Interpreting your Bioinformatics Pipeline
Candy Smellie
With technological breakthroughs in single cell isolation, whole genome amplification (WGA) and NGS library preparation, experiments using single cells are now possible. However, challenges still exist. In particular, methods for the unbiased and complete amplification of a single genome and for the efficient conversion of that amplified DNA into a sequencer-compatible library face several technical limitations including incomplete amplification, the introduction of PCR errors, GC-bias and locus or allelic drop-out. The presentation covers the impact of these factors and how one can mitigate it.
DNA Sequencing from Single Cell
DNA Sequencing from Single Cell
QIAGEN
Introduction to RNASeq Data Generation and Quality Control
Rnaseq basics ngs_application1
Rnaseq basics ngs_application1
Yaoyu Wang
Introducing Biochain Next Generation Sequencing Products
BioChain Next Generation Sequencing Products
BioChain Next Generation Sequencing Products
biochain
NGS DNA TECHS
2011 jeroen vanhoudt_ngs
2011 jeroen vanhoudt_ngs
Din Apellidos
Course: Bioinformatics for Biomedical Research (2014). Session: 2.1.2- Next Generation Sequencing. Technologies and Applications. Part II: NGS Applications I. Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
NGS Applications I (UEB-UAT Bioinformatics Course - Session 2.1.2 - VHIR, Bar...
NGS Applications I (UEB-UAT Bioinformatics Course - Session 2.1.2 - VHIR, Bar...
VHIR Vall d’Hebron Institut de Recerca
Recommended
140127 abrf interlaboratory study proposal
140127 abrf interlaboratory study proposal
GenomeInABottle
Bioinformatica e genomica comparata: nuove strategie sperimentali e computazionali per la produzione e analisi di dati NGS finalizzati a sviluppare processi e prodotti innovativi per la salute dell’uomo, l’ambiente e l’agroalimentare.
Ernesto Picardi – Bioinformatica e genomica comparata: nuove strategie sperim...
Ernesto Picardi – Bioinformatica e genomica comparata: nuove strategie sperim...
eventi-ITBbari
What is the impact of assay failure in your laboratory and how do you monitor for it? The most heavily degraded samples are not suitable for standard exome coverage: sometimes it’s not even a matter of getting bad sequencing, you might get nothing at all! FFPE artifacts increase with storage time Artifacts go against the statistical power of your variant calling analysis Molecular reference standards help filter out bad mappings and spurious variants Bioinformatics pipelines allow adding Molecular Reference Standards in your joint variant calling pipeline Genome In A Bottle Reference Standards are invaluable for validating variant calling analysis NIST and its collaborators shared datasets created with most NGS technologies Horizon Diagnostics shared annotated, merged variant calls from NIST for the Ashkenazim Trio ~35K variants are predicted having high or moderate impact within the Trio GM24385 (Ashkenazim Son) includes 352 small variants with high/moderate impact which are absent in Father and Mother Routinely monitor the performance of your workflows and assays with independent external controls
Molecular QC: Interpreting your Bioinformatics Pipeline
Molecular QC: Interpreting your Bioinformatics Pipeline
Candy Smellie
With technological breakthroughs in single cell isolation, whole genome amplification (WGA) and NGS library preparation, experiments using single cells are now possible. However, challenges still exist. In particular, methods for the unbiased and complete amplification of a single genome and for the efficient conversion of that amplified DNA into a sequencer-compatible library face several technical limitations including incomplete amplification, the introduction of PCR errors, GC-bias and locus or allelic drop-out. The presentation covers the impact of these factors and how one can mitigate it.
DNA Sequencing from Single Cell
DNA Sequencing from Single Cell
QIAGEN
Introduction to RNASeq Data Generation and Quality Control
Rnaseq basics ngs_application1
Rnaseq basics ngs_application1
Yaoyu Wang
Introducing Biochain Next Generation Sequencing Products
BioChain Next Generation Sequencing Products
BioChain Next Generation Sequencing Products
biochain
NGS DNA TECHS
2011 jeroen vanhoudt_ngs
2011 jeroen vanhoudt_ngs
Din Apellidos
Course: Bioinformatics for Biomedical Research (2014). Session: 2.1.2- Next Generation Sequencing. Technologies and Applications. Part II: NGS Applications I. Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
NGS Applications I (UEB-UAT Bioinformatics Course - Session 2.1.2 - VHIR, Bar...
NGS Applications I (UEB-UAT Bioinformatics Course - Session 2.1.2 - VHIR, Bar...
VHIR Vall d’Hebron Institut de Recerca
DNA sequence analysis and genotyping of biological samples using innovative instrumentation, such as next-generation sequencing (NGS) platforms, is often limited by the small amount of sample available. The REPLI-g Single Cell Kit is specially designed to uniformly amplify genomic DNA from single cells (1 to <1000 bacterial or tumor cells) or purified genomic DNA with complete genome coverage. Additional protocols are also available for use with fresh or dried blood or fresh or frozen tissue. Dedicated buffers and reagents undergo a unique, controlled decontamination procedure to avoid amplification of contaminating DNA, ensuring highly reliable results every time. Accurate amplification of genomes with negligible sequence bias and no genomic drop-outs is achieved with innovative Multiple Displacement Amplification (MDA) technology. In contrast to PCR-based WGA technologies, high fidelity rates are increased up to 1000-fold, avoiding costly false positive or negative results.
Whole Genome Amplification from Single Cell
Whole Genome Amplification from Single Cell
QIAGEN
Tumor heterogeneity has been known for a while but quantifying heterogeneity is still a challenge. NGS is the method of choice in the analysis of tumor heterogeneity, however, there are some inherent challenges associated with it. These include false positives, gaps in the gene due to overrepresentation and incomplete representation of low-frequency transcripts – all contributing to an inaccurate picture. Conventional library prep strategies for NGS are based on PCR, which introduces sequence-based bias and amplification noise, leading to these inaccuracies. In this webinar, we will cover 1. Principles of UMI and the new QIAseq product porfolio 2. How UMI along with SPE (single primer extension) allows for increased uniformity across difficult-to-sequence regions, removal of library construction bias, improved data analysis and sequencing optimization 3. How data generated from using UMI and SPE is directly comparable to analysis derived from whole transcriptome and exome sequencing 4. Application of UMI and SPE in the discovery of novel gene fusions and in the analysis of gene expression and genetic variation
QIAseq Targeted DNA, RNA and Fusion Gene Panels
QIAseq Targeted DNA, RNA and Fusion Gene Panels
QIAGEN
Alignment algorithms are not just about placing reads in best-matching locations to a reference genome. They are now being expected to handle small insertions, deletions, gapped alignment of reads across intron boundaries and even span breakpoints of structural variations, fusions and copy number changes. At the same time, variant-calling algorithms can only reach their full potential by being intimately matched to the aligner's output or by doing local assemblies themselves. Knowing when these tools can be expected to perform well and when they will produce technical artifacts or be incapable of detecting features is critical when interpreting any analysis based on their output. This presentation will compare the performance of the alignment and variant calling tools used by sequencing service providers including Illumina Genome Network, Complete Genomics and The Broad Institute. Using public samples analyzed by each pipeline, we will look at the level of concordance and dive into investigating problematic variants and regions of the genome.
Knowing Your NGS Upstream: Alignment and Variants
Knowing Your NGS Upstream: Alignment and Variants
Golden Helix Inc
Course: Bioinformatics for Biomedical Research (2014). Session: 2.3- Introduction to NGS Variant Calling Analysis. Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Introduction to NGS Variant Calling Analysis (UEB-UAT Bioinformatics Course -...
Introduction to NGS Variant Calling Analysis (UEB-UAT Bioinformatics Course -...
VHIR Vall d’Hebron Institut de Recerca
SANGER SEQUENCING - 1st generation sequencing Sanger Sequencing Workflow: PCR amplification (target enrichment) PCR purification (primer, dNTPs) Sequencing reaction (bi-directional) Sequencing purification (primer, dNTPs, ddNTPs) Electrophoretic run on sequencer Sequencing lecture Alignment to reference SANGER SEQUENCING: LIMITATIONS Analytical sensitivity*: 99% PCR-Based no detection deletion/duplication rearrangements del/dup BRCA = 4-28% of all BRCA mutations in most population** Level of mosaicism > 20% Low throughput (82496 capillary tubes) Labor intensive Time consuming High cost (large size gene or more genes)
20160219 - S. De Toffol - Dal Sanger al NGS nello studio delle mutazioni BRCA