Illumina's technology has potential clinical applications in molecular diagnostics. Their sequencing platforms like MiSeq and analysis software like KaryoStudioDx can enable molecular cytogenetic testing and targeted gene panels. MiSeq allows scalable amplicon sequencing from hundreds to thousands of targets in 1-2 days at lower costs than Sanger sequencing. Illumina aims to submit their iScan platform and arrays for FDA approval for post-natal cytogenetic testing. Their SNP microarrays can detect more types of chromosomal abnormalities than microarrays and help characterize regions associated with disease.
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.
Massively Parallel Sequencing - integrating the Ion PGM™ sequencer into your ...Thermo Fisher Scientific
This document summarizes the integration of massively parallel sequencing (MPS) using the Ion PGMTM sequencer into a forensic laboratory. The project aims to begin transforming STR profiling to genomic technologies, add additional SNP markers in a single workflow, and enable non-human DNA testing. Initial results show sequencing of amplified STR products is possible but alignment is challenging. A custom panel of 280 targets including STRs, SNPs, and amelogenin was also tested with most targets detected across samples. Ongoing work focuses on improving sensitivity, reproducibility, and analyzing mixed samples. Implementation of MPS as a routine forensic service is estimated within 3-5 years.
Utilization of NGS to Identify Clinically-Relevant Mutations in cfDNA: Meet t...QIAGEN
Pancreatic cancer is a uniquely lethal malignancy characterized by frequent mutations in KRAS, CDKN2A, SMAD4, TP53 and many others. We have shown that KRAS mutation can be detected in cell-free, circulating tumor DNA (ctDNA) isolated from the plasma in a subset of patients and is associated with poor prognosis. The ability to simultaneously detect multiple pancreatic cancer-specific mutations in ctDNA would open a new avenue for detection of clinically-relevant mutations. In this study, we performed ultra-deep sequencing of ctDNA from advanced pancreatic cancer patients prior to treatment with Gemcitabine and Erlotinib following target enrichment. Somatic, non-synonymous variants were identified in 29 different genes at allele frequencies typically less than 0.5%. Updated results of ultra-deep NGS analysis will be presented.
"Massively parallel sequencing in forensic genetics
Dr. Walther Parson
assoc. Prof. Institute of Legal Medicine, Innsbruck, Austria
adj. Prof. Penn State University, PA, USA"
The document describes Phase II of the ABRF Next Generation Sequencing Study which aims to establish reference data sets for evaluating DNA sequencing performance across multiple platforms and laboratories. Phase II will sequence various human and bacterial genomic samples to assess accuracy, coverage, and limits of detection using different platforms and library preparation methods. A collaboration with NIST Genome in a Bottle will provide standardized samples to the participating laboratories. The study aims to provide a resource for ongoing method development and evaluation of sequencing performance.
Next generation sequencing (NGS) of circulating tumor DNA (ctDNA) from patient plasma is becoming more widespread in oncology clinical trials. The noninvasive nature of acquiring these samples is particularly important when resection of representative tumor samples is not advised or not possible. However, profiling of ctDNA has challenges to overcome, such as low concentration of ctDNA shed from the tumor and a low signal:noise ratio caused by somatic alterations with less than 1% variant allele fraction. Improving the sensitivity of these assays to detect low allele frequency events with high confidence requires robust sequencing of low input libraries while employing error correction to reduce background noise. To overcome these challenges, we have incorporated unique molecular identifiers (UMIs) into our NGS workflow. Using these novel adapters paired with our proprietary bioinformatics pipeline (AstraZeneca), the number of false positive variants reported for allele fractions less than 0.5% was reduced tenfold. We also refined our curation based on the mapping quality and strand bias in the vicinity of each variant to further reduce the background noise. The use of xGen® Dual Index UMI Adapters—Tech Access (Integrated DNA Technologies) has enabled us to sequence thousands of plasma samples from diverse tumor indications and at differing time points during our trials. The generated data are highly informative with the potential to answer critical questions relating to individual response or resistance to experimental therapies. During this webinar, we discuss our current NGS ctDNA workflow and our future plans to increase our sequencing sensitivity with these novel UMI adapters.
NGS for Infectious Disease Diagnostics: An Opportunity for Growth Alira Health
Infectious diseases are a major public health concern causing over 3.5 million deaths worldwide. Diagnosing patients as quickly and effectively as possible is crucial for managing disease outbreaks. Next-generation sequencing (NGS) provides unique capabilities to understand the genetic profile of infectious disease patients that no other technology can match.
Whole-genome metagenomics allows clinicians to take a deeper dive into pathogens by generating big-data about their characteristics. This data can be rapidly analyzed using complex bioinformatics software algorithms to achieve clinical-grade diagnostic accuracy. In a healthcare system shifting towards personalized medicine, NGS can provide clinicians the tools that they need to prescribe individualized treatments to save patients who were previously untreatable. The result is improved quality of care, better treatment regimes, and cost-saving healthcare.
Alzheimer’s disease (AD) is a devastating neurodegenerative disease that is genetically complex. Although great progress has been made in identifying fully penetrant mutations in genes that cause early-onset AD, these still represent a very small percentage of AD cases. Large-scale, genome-wide association studies (GWAS) have identified at least 20 additional genetic risk loci for the more common form: late-onset AD. However, the identified SNPs are typically not the actual risk variants, but are in linkage disequilibrium with the presumed causative variants [1].
To help identify causative genetic variants, we have combined highly accurate, long-read sequencing with hybrid-capture technology. In this collaborative webinar*, we present this method and show how combining IDT xGen® Lockdown® Probes with PacBio SMRT® Sequencing allows targeting and sequencing of candidate genes from genomic DNA and corresponding transcripts from cDNA. Using a panel of target capture probes for 35 AD candidate genes, we demonstrate the power of this approach by looking at data for two individuals with AD. Some additional benefits of this method include the ability to leverage long reads, phase heterozygous variants, and link corresponding transcript isoforms to their respective alleles.
Reference: 1. Van Cauwenberghe C, Van Broeckhoven C, Sleegers K. (2016) The genetic landscape of Alzheimer disease: clinical implications and perspectives. Genet Med, 18(5):421–430.
* This presentation represents a collaboration between Pacific Biosciences and Integrated DNA Technologies. The individual opinions expressed may not reflect shared opinions of Pacific Biosciences and Integrated DNA Technologies.
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.
Massively Parallel Sequencing - integrating the Ion PGM™ sequencer into your ...Thermo Fisher Scientific
This document summarizes the integration of massively parallel sequencing (MPS) using the Ion PGMTM sequencer into a forensic laboratory. The project aims to begin transforming STR profiling to genomic technologies, add additional SNP markers in a single workflow, and enable non-human DNA testing. Initial results show sequencing of amplified STR products is possible but alignment is challenging. A custom panel of 280 targets including STRs, SNPs, and amelogenin was also tested with most targets detected across samples. Ongoing work focuses on improving sensitivity, reproducibility, and analyzing mixed samples. Implementation of MPS as a routine forensic service is estimated within 3-5 years.
Utilization of NGS to Identify Clinically-Relevant Mutations in cfDNA: Meet t...QIAGEN
Pancreatic cancer is a uniquely lethal malignancy characterized by frequent mutations in KRAS, CDKN2A, SMAD4, TP53 and many others. We have shown that KRAS mutation can be detected in cell-free, circulating tumor DNA (ctDNA) isolated from the plasma in a subset of patients and is associated with poor prognosis. The ability to simultaneously detect multiple pancreatic cancer-specific mutations in ctDNA would open a new avenue for detection of clinically-relevant mutations. In this study, we performed ultra-deep sequencing of ctDNA from advanced pancreatic cancer patients prior to treatment with Gemcitabine and Erlotinib following target enrichment. Somatic, non-synonymous variants were identified in 29 different genes at allele frequencies typically less than 0.5%. Updated results of ultra-deep NGS analysis will be presented.
"Massively parallel sequencing in forensic genetics
Dr. Walther Parson
assoc. Prof. Institute of Legal Medicine, Innsbruck, Austria
adj. Prof. Penn State University, PA, USA"
The document describes Phase II of the ABRF Next Generation Sequencing Study which aims to establish reference data sets for evaluating DNA sequencing performance across multiple platforms and laboratories. Phase II will sequence various human and bacterial genomic samples to assess accuracy, coverage, and limits of detection using different platforms and library preparation methods. A collaboration with NIST Genome in a Bottle will provide standardized samples to the participating laboratories. The study aims to provide a resource for ongoing method development and evaluation of sequencing performance.
Next generation sequencing (NGS) of circulating tumor DNA (ctDNA) from patient plasma is becoming more widespread in oncology clinical trials. The noninvasive nature of acquiring these samples is particularly important when resection of representative tumor samples is not advised or not possible. However, profiling of ctDNA has challenges to overcome, such as low concentration of ctDNA shed from the tumor and a low signal:noise ratio caused by somatic alterations with less than 1% variant allele fraction. Improving the sensitivity of these assays to detect low allele frequency events with high confidence requires robust sequencing of low input libraries while employing error correction to reduce background noise. To overcome these challenges, we have incorporated unique molecular identifiers (UMIs) into our NGS workflow. Using these novel adapters paired with our proprietary bioinformatics pipeline (AstraZeneca), the number of false positive variants reported for allele fractions less than 0.5% was reduced tenfold. We also refined our curation based on the mapping quality and strand bias in the vicinity of each variant to further reduce the background noise. The use of xGen® Dual Index UMI Adapters—Tech Access (Integrated DNA Technologies) has enabled us to sequence thousands of plasma samples from diverse tumor indications and at differing time points during our trials. The generated data are highly informative with the potential to answer critical questions relating to individual response or resistance to experimental therapies. During this webinar, we discuss our current NGS ctDNA workflow and our future plans to increase our sequencing sensitivity with these novel UMI adapters.
NGS for Infectious Disease Diagnostics: An Opportunity for Growth Alira Health
Infectious diseases are a major public health concern causing over 3.5 million deaths worldwide. Diagnosing patients as quickly and effectively as possible is crucial for managing disease outbreaks. Next-generation sequencing (NGS) provides unique capabilities to understand the genetic profile of infectious disease patients that no other technology can match.
Whole-genome metagenomics allows clinicians to take a deeper dive into pathogens by generating big-data about their characteristics. This data can be rapidly analyzed using complex bioinformatics software algorithms to achieve clinical-grade diagnostic accuracy. In a healthcare system shifting towards personalized medicine, NGS can provide clinicians the tools that they need to prescribe individualized treatments to save patients who were previously untreatable. The result is improved quality of care, better treatment regimes, and cost-saving healthcare.
Alzheimer’s disease (AD) is a devastating neurodegenerative disease that is genetically complex. Although great progress has been made in identifying fully penetrant mutations in genes that cause early-onset AD, these still represent a very small percentage of AD cases. Large-scale, genome-wide association studies (GWAS) have identified at least 20 additional genetic risk loci for the more common form: late-onset AD. However, the identified SNPs are typically not the actual risk variants, but are in linkage disequilibrium with the presumed causative variants [1].
To help identify causative genetic variants, we have combined highly accurate, long-read sequencing with hybrid-capture technology. In this collaborative webinar*, we present this method and show how combining IDT xGen® Lockdown® Probes with PacBio SMRT® Sequencing allows targeting and sequencing of candidate genes from genomic DNA and corresponding transcripts from cDNA. Using a panel of target capture probes for 35 AD candidate genes, we demonstrate the power of this approach by looking at data for two individuals with AD. Some additional benefits of this method include the ability to leverage long reads, phase heterozygous variants, and link corresponding transcript isoforms to their respective alleles.
Reference: 1. Van Cauwenberghe C, Van Broeckhoven C, Sleegers K. (2016) The genetic landscape of Alzheimer disease: clinical implications and perspectives. Genet Med, 18(5):421–430.
* This presentation represents a collaboration between Pacific Biosciences and Integrated DNA Technologies. The individual opinions expressed may not reflect shared opinions of Pacific Biosciences and Integrated DNA Technologies.
Illumina is a global leader in genomic technologies that provides sequencing and microarray solutions. Their portfolio includes the MiSeq, NextSeq 500, HiSeq 2500, and HiSeq X Ten sequencing platforms. Illumina serves customers in human health, research, reproductive health, forensics, cancer, agriculture and more. Their reproductive and genetic health portfolio addresses the continuum from preconception to pregnancy to genetic conditions. Products highlighted include VeriSeq PGS for embryo screening, Karyomapping for inherited disorder screening, and their non-invasive prenatal testing solution in development. The NextSeq 550 was also introduced as a platform that enables both sequencing and array scanning applications on a single system.
IDT provides a range of solutions for targeted next generation sequencing. Labs processing hundreds to thousands of samples can create highly uniform, custom panels using xGen® Lockdown Probes. The new xGen Acute Myeloid Leukemia (AML) panel is a predesigned set of Lockdown Probes that captures 260 genes identified by whole genome and exome sequencing of 200 patient samples. The AML panel can be used as stand-alone or customized with additional probes to detect other targets of interest.
The document discusses various topics related to molecular profiling and personalized medicine. It describes first generation molecular profiling techniques like gene sequencing, microarrays, and PCR. It then covers next generation sequencing technologies like Roche 454, Illumina, and ABI SOLID. It also discusses second generation techniques for DNA and RNA profiling including exome sequencing, ChIP-seq, and RNA-seq. Finally, it briefly mentions third generation sequencing and epigenetic profiling.
Dr. Ben Hause - Next Generation Sequencing to Identify Viruses Associated wit...John Blue
Next Generation Sequencing to Identify Viruses Associated with Bovine Respiratory Disease - Dr. Ben Hause, Clinical Assistant Professor, Kansas State University, from the 2016 NIAA Annual Conference: From Farm to Table - Food System Biosecurity for Animal Agriculture, April 4-7, 2016, Kansas City, MO, USA.
More presentations at http://www.trufflemedia.com/agmedia/conference/2016_niaa_farm_table_food_system_biosecurity
Digital RNAseq Technology Introduction: Digital RNAseq Webinar Part 1QIAGEN
QIAseq RNA is a revolutionary turnkey solution for digital gene expression analysis by NGS. From 10 genes to 1000, from one sample to 100, QIAseq RNA delivers precise results on both ION and Illumina sequencing platforms. The data from QIAseq RNA is directly comparable to expression analysis derived from whole transcriptome sequencing or by qRTPCR, only better, cheaper, faster, and more flexible. This webinar will describe the principles of digital expression analysis by NGS, and review the features and benefits of the QIAseq system, options available, and the integrated data analysis package.
Apac distributor training series 3 swift product for cancer studySwift Biosciences
This document provides an overview of Swift Biosciences' product training series for their APAC distributors on using Swift products for cancer studies. It summarizes different Swift library preparation and sequencing kits that can be used for various cancer applications, including genomic sequencing, RNA sequencing, amplicon panels, hybridization capture, and DNA methylation. The document also reviews types of mutations found in cancer, considerations for cancer clinical workflows, and provides an example of using Swift's 2S Turbo kit for targeted sequencing of formalin-fixed, paraffin-embedded tissue samples.
Moving Towards a Validated High Throughput Sequencing Solution for Human Iden...Thermo Fisher Scientific
Presented by Jennifer D. Churchill, PhD during a special Lunch and Learn session during the American Academy of Forensic Sciences (AAFS) 67th annual conference, February 2015. / Conclusions
• Robust panels of identity and ancestry SNPs
• Robust STR panel
• Whole genome mtDNA sequencing
• Highly informative
• Sensitive
• Quantitative – scaling comparison
• Low density chip is not necessarily a bad chip
• Wide range of density can still yield high quality data
• Based on results continue development and validation
The document discusses GeneRead DNAseq Targeted Exon Enrichment and GeneRead Library Quantification System for Next Generation Sequencing. It provides an overview of the targeted enrichment workflow and principles, pathway-focused analysis tools, library quantification workflow, and performance data. The targeted enrichment panels allow users to focus sequencing on genes of interest, improve detection of low prevalence mutations from poor quality samples. The library quantification system uses qPCR to accurately quantify sequencing libraries and assess sample quality before NGS runs.
Analysis and Interpretation of Cell-free DNAQIAGEN
Identification and monitoring of cancer mutations from cell free DNA-Seq data is a key application in liquid biopsy. In this part of the webinar we will show how mutations can be best identified from this type of data and how they can be interpreted. Furthermore, potential challenges when analyzing this type of data will be discussed together with relevant strategies.
Digital RNAseq for Gene Expression Profiling: Digital RNAseq Webinar Part 2QIAGEN
Traditional RNA sequencing (RNA-Seq) is a powerful tool for expression profiling, but is hindered by PCR amplification bias and inaccuracy at low expressing genes. QIAseq RNA is a flexible and precise tool developed for mitigating these complications, allowing digital gene expression analysis. In this webinar we will cover, in depth, the sample requirements, experimental design, NGS platform specific challenges, and workflow for gene enrichment, library prep and sequencing. The applications of QIASeq RNA Panels in cancer research, stem cell differentiation and elucidating the effects small molecules on signaling pathways will be highlighted.
The document discusses exome sequencing and compares the performance of the xGen Exome Research Panel to other commercial exome sequencing panels. Key points:
1) An independent study directly compared the xGen panel to 3 other commercial exome panels and found that the xGen panel had a higher on-target rate and more uniform coverage than the other panels.
2) When deeply sequenced, the xGen panel was able to achieve greater than 20x coverage of over 94% of bases in the RefSeq database with only 40 million reads, which is 2.5-4 times fewer reads than the other panels tested.
3) The coverage profile produced by the xGen panel more closely resembled whole genome sequencing
A full picture of -omics cellular networks of regulation brings researchers closer to a realistic and reliable understanding of complex conditions. For more information, please visit: http://tbioinfopb.pine-biotech.com/
The document describes QIAGEN's GeneRead DNAseq Targeted Exon Enrichment and GeneRead Library Quantification System for next generation sequencing. It discusses targeted enrichment workflow and principles, data analysis, pathway content of panels, performance data and application examples. It also covers the library quantification workflow, using qPCR to quantify sequencing libraries, and a DNAseq library quantification array to assess sample quality. The document is aimed at promoting these NGS sample preparation and analysis solutions to potential customers.
Advanced NGS Library Prep for Challenging SamplesQIAGEN
This document discusses advanced next-generation sequencing (NGS) library preparation methods for challenging samples. It introduces NGS applications using various sample types and sizes. Standard NGS library preparation kits have input requirements that cannot accommodate many sample types and quantities. New techniques optimized for sub-nanogram inputs can construct high-quality libraries from as little as 10 picograms of DNA. These methods show consistent conversion across a wide input range and enable applications like ancient DNA analysis and circulating tumor DNA detection from blood. The document focuses on cell-free DNA library preparation challenges and solutions like the QIAGEN cfDNA library kits.
Presentation carried out by Sergi Beltran Agulló, from the CNAG, at the course: Identification and analysis of sequence variants in sequencing projects: fundamentals and tools .
Developing a Rapid Clinical Sequencing System to Classify Meningioma: Meet th...QIAGEN
Meningioma’s display a broad spectrum of clinical, histological and cytogenetic features even within the same WHO grade often posing a challenge for classification and prognostic stratification. In this webinar, we will describe our experience of using targeted amplicon sequencing to develop rapid clinical sequencing system to identify and confirm the meningioma genotype in just two weeks. In addition the details of the three meningioma categories and the genes involved will be discussed.
This document summarizes trends in DNA sequencing methods and applications. It discusses the purpose and historical methods of DNA sequencing, including the Maxam-Gilbert and Sanger methods. Next generation sequencing methods like Roche 454, Illumina, SOLiD, Ion Torrent, and PacBio are described. Applications of sequencing include analyzing gene structure, detecting mutations, microbial identification, and whole genome sequencing. The document provides details on sequencing techniques, platforms, yields, and error rates.
Forensic Genetics in the 21st century – meeting the challenges of biological ...Thermo Fisher Scientific
"Forensic Genetics in the 21st century – meeting the challenges of biological evidence
Presented by Peter M. Schneider, Institute of Legal Medicine
University of Cologne, Germany Human Identification Solutions Conference – Madrid, Spain
March 4, 2015 CO014206"
Innovative NGS Library Construction TechnologyQIAGEN
Next-generation sequencing (NGS) is a driving force for numerous new and exciting applications, including cancer research, stem cell research, metagenomics, population genetics, medical research and single cell analysis. While NGS technology is continuously improving, library preparation remains one of the biggest bottlenecks in the NGS workflow and includes several time-consuming steps that can result in considerable sample loss and the potential to introduce handling errors. Moreover, conducting single-cell genomic analysis using NGS methods has traditionally been challenging since the amount of genomic DNA present in a single cell is very limited.
Accelerate Your Discovery with QIAGEN Service Solutions for Biomarker Researc...QIAGEN
This slidedeck will highlight QIAGEN’s service capabilities in sample isolation, microarray and NGS-sequencing, qPCR panel and custom assay development and bioinformatics as we look at the identification of potential biomarkers and gene signatures. The applications of QIAGEN Service Core in microRNA discovery for toxicology markers in serum and plasma and in identification of RNA signatures for tumor stratification are featured. Learn how you can accelerate your research with QIAGEN service solutions.
The document discusses the development of a new microarray called the CytoSure ISCA UPD array that allows for the fast and easy detection of both copy number variations (CNVs) and uniparental disomy (UPD) from a single experiment. Key steps in the development included selecting informative SNPs from the human genome, designing probes to target each SNP allele, validating the array's ability to detect various forms of UPD compared to known samples, and developing software to analyze and visualize the SNP and CNV data to identify regions of homozygosity indicative of UPD. The array and accompanying analysis software provide a complete solution for cytogenetics laboratories to reliably detect CNVs and UPD with a standardized, high
This document discusses clinical and consumer applications of microarrays and genotyping technologies. It provides an overview of genotyping and different technologies like PCR microarrays and SNP microarrays. It describes how microarrays are still useful despite the rise of sequencing due to their low cost, high throughput, and ability to test millions of markers. The document outlines several applications of microarrays like direct-to-consumer testing, pharmacogenetics, and clinical sequencing. It also discusses challenges and trends in these areas like global initiatives to increase genomic data sharing.
Illumina is a global leader in genomic technologies that provides sequencing and microarray solutions. Their portfolio includes the MiSeq, NextSeq 500, HiSeq 2500, and HiSeq X Ten sequencing platforms. Illumina serves customers in human health, research, reproductive health, forensics, cancer, agriculture and more. Their reproductive and genetic health portfolio addresses the continuum from preconception to pregnancy to genetic conditions. Products highlighted include VeriSeq PGS for embryo screening, Karyomapping for inherited disorder screening, and their non-invasive prenatal testing solution in development. The NextSeq 550 was also introduced as a platform that enables both sequencing and array scanning applications on a single system.
IDT provides a range of solutions for targeted next generation sequencing. Labs processing hundreds to thousands of samples can create highly uniform, custom panels using xGen® Lockdown Probes. The new xGen Acute Myeloid Leukemia (AML) panel is a predesigned set of Lockdown Probes that captures 260 genes identified by whole genome and exome sequencing of 200 patient samples. The AML panel can be used as stand-alone or customized with additional probes to detect other targets of interest.
The document discusses various topics related to molecular profiling and personalized medicine. It describes first generation molecular profiling techniques like gene sequencing, microarrays, and PCR. It then covers next generation sequencing technologies like Roche 454, Illumina, and ABI SOLID. It also discusses second generation techniques for DNA and RNA profiling including exome sequencing, ChIP-seq, and RNA-seq. Finally, it briefly mentions third generation sequencing and epigenetic profiling.
Dr. Ben Hause - Next Generation Sequencing to Identify Viruses Associated wit...John Blue
Next Generation Sequencing to Identify Viruses Associated with Bovine Respiratory Disease - Dr. Ben Hause, Clinical Assistant Professor, Kansas State University, from the 2016 NIAA Annual Conference: From Farm to Table - Food System Biosecurity for Animal Agriculture, April 4-7, 2016, Kansas City, MO, USA.
More presentations at http://www.trufflemedia.com/agmedia/conference/2016_niaa_farm_table_food_system_biosecurity
Digital RNAseq Technology Introduction: Digital RNAseq Webinar Part 1QIAGEN
QIAseq RNA is a revolutionary turnkey solution for digital gene expression analysis by NGS. From 10 genes to 1000, from one sample to 100, QIAseq RNA delivers precise results on both ION and Illumina sequencing platforms. The data from QIAseq RNA is directly comparable to expression analysis derived from whole transcriptome sequencing or by qRTPCR, only better, cheaper, faster, and more flexible. This webinar will describe the principles of digital expression analysis by NGS, and review the features and benefits of the QIAseq system, options available, and the integrated data analysis package.
Apac distributor training series 3 swift product for cancer studySwift Biosciences
This document provides an overview of Swift Biosciences' product training series for their APAC distributors on using Swift products for cancer studies. It summarizes different Swift library preparation and sequencing kits that can be used for various cancer applications, including genomic sequencing, RNA sequencing, amplicon panels, hybridization capture, and DNA methylation. The document also reviews types of mutations found in cancer, considerations for cancer clinical workflows, and provides an example of using Swift's 2S Turbo kit for targeted sequencing of formalin-fixed, paraffin-embedded tissue samples.
Moving Towards a Validated High Throughput Sequencing Solution for Human Iden...Thermo Fisher Scientific
Presented by Jennifer D. Churchill, PhD during a special Lunch and Learn session during the American Academy of Forensic Sciences (AAFS) 67th annual conference, February 2015. / Conclusions
• Robust panels of identity and ancestry SNPs
• Robust STR panel
• Whole genome mtDNA sequencing
• Highly informative
• Sensitive
• Quantitative – scaling comparison
• Low density chip is not necessarily a bad chip
• Wide range of density can still yield high quality data
• Based on results continue development and validation
The document discusses GeneRead DNAseq Targeted Exon Enrichment and GeneRead Library Quantification System for Next Generation Sequencing. It provides an overview of the targeted enrichment workflow and principles, pathway-focused analysis tools, library quantification workflow, and performance data. The targeted enrichment panels allow users to focus sequencing on genes of interest, improve detection of low prevalence mutations from poor quality samples. The library quantification system uses qPCR to accurately quantify sequencing libraries and assess sample quality before NGS runs.
Analysis and Interpretation of Cell-free DNAQIAGEN
Identification and monitoring of cancer mutations from cell free DNA-Seq data is a key application in liquid biopsy. In this part of the webinar we will show how mutations can be best identified from this type of data and how they can be interpreted. Furthermore, potential challenges when analyzing this type of data will be discussed together with relevant strategies.
Digital RNAseq for Gene Expression Profiling: Digital RNAseq Webinar Part 2QIAGEN
Traditional RNA sequencing (RNA-Seq) is a powerful tool for expression profiling, but is hindered by PCR amplification bias and inaccuracy at low expressing genes. QIAseq RNA is a flexible and precise tool developed for mitigating these complications, allowing digital gene expression analysis. In this webinar we will cover, in depth, the sample requirements, experimental design, NGS platform specific challenges, and workflow for gene enrichment, library prep and sequencing. The applications of QIASeq RNA Panels in cancer research, stem cell differentiation and elucidating the effects small molecules on signaling pathways will be highlighted.
The document discusses exome sequencing and compares the performance of the xGen Exome Research Panel to other commercial exome sequencing panels. Key points:
1) An independent study directly compared the xGen panel to 3 other commercial exome panels and found that the xGen panel had a higher on-target rate and more uniform coverage than the other panels.
2) When deeply sequenced, the xGen panel was able to achieve greater than 20x coverage of over 94% of bases in the RefSeq database with only 40 million reads, which is 2.5-4 times fewer reads than the other panels tested.
3) The coverage profile produced by the xGen panel more closely resembled whole genome sequencing
A full picture of -omics cellular networks of regulation brings researchers closer to a realistic and reliable understanding of complex conditions. For more information, please visit: http://tbioinfopb.pine-biotech.com/
The document describes QIAGEN's GeneRead DNAseq Targeted Exon Enrichment and GeneRead Library Quantification System for next generation sequencing. It discusses targeted enrichment workflow and principles, data analysis, pathway content of panels, performance data and application examples. It also covers the library quantification workflow, using qPCR to quantify sequencing libraries, and a DNAseq library quantification array to assess sample quality. The document is aimed at promoting these NGS sample preparation and analysis solutions to potential customers.
Advanced NGS Library Prep for Challenging SamplesQIAGEN
This document discusses advanced next-generation sequencing (NGS) library preparation methods for challenging samples. It introduces NGS applications using various sample types and sizes. Standard NGS library preparation kits have input requirements that cannot accommodate many sample types and quantities. New techniques optimized for sub-nanogram inputs can construct high-quality libraries from as little as 10 picograms of DNA. These methods show consistent conversion across a wide input range and enable applications like ancient DNA analysis and circulating tumor DNA detection from blood. The document focuses on cell-free DNA library preparation challenges and solutions like the QIAGEN cfDNA library kits.
Presentation carried out by Sergi Beltran Agulló, from the CNAG, at the course: Identification and analysis of sequence variants in sequencing projects: fundamentals and tools .
Developing a Rapid Clinical Sequencing System to Classify Meningioma: Meet th...QIAGEN
Meningioma’s display a broad spectrum of clinical, histological and cytogenetic features even within the same WHO grade often posing a challenge for classification and prognostic stratification. In this webinar, we will describe our experience of using targeted amplicon sequencing to develop rapid clinical sequencing system to identify and confirm the meningioma genotype in just two weeks. In addition the details of the three meningioma categories and the genes involved will be discussed.
This document summarizes trends in DNA sequencing methods and applications. It discusses the purpose and historical methods of DNA sequencing, including the Maxam-Gilbert and Sanger methods. Next generation sequencing methods like Roche 454, Illumina, SOLiD, Ion Torrent, and PacBio are described. Applications of sequencing include analyzing gene structure, detecting mutations, microbial identification, and whole genome sequencing. The document provides details on sequencing techniques, platforms, yields, and error rates.
Forensic Genetics in the 21st century – meeting the challenges of biological ...Thermo Fisher Scientific
"Forensic Genetics in the 21st century – meeting the challenges of biological evidence
Presented by Peter M. Schneider, Institute of Legal Medicine
University of Cologne, Germany Human Identification Solutions Conference – Madrid, Spain
March 4, 2015 CO014206"
Innovative NGS Library Construction TechnologyQIAGEN
Next-generation sequencing (NGS) is a driving force for numerous new and exciting applications, including cancer research, stem cell research, metagenomics, population genetics, medical research and single cell analysis. While NGS technology is continuously improving, library preparation remains one of the biggest bottlenecks in the NGS workflow and includes several time-consuming steps that can result in considerable sample loss and the potential to introduce handling errors. Moreover, conducting single-cell genomic analysis using NGS methods has traditionally been challenging since the amount of genomic DNA present in a single cell is very limited.
Accelerate Your Discovery with QIAGEN Service Solutions for Biomarker Researc...QIAGEN
This slidedeck will highlight QIAGEN’s service capabilities in sample isolation, microarray and NGS-sequencing, qPCR panel and custom assay development and bioinformatics as we look at the identification of potential biomarkers and gene signatures. The applications of QIAGEN Service Core in microRNA discovery for toxicology markers in serum and plasma and in identification of RNA signatures for tumor stratification are featured. Learn how you can accelerate your research with QIAGEN service solutions.
The document discusses the development of a new microarray called the CytoSure ISCA UPD array that allows for the fast and easy detection of both copy number variations (CNVs) and uniparental disomy (UPD) from a single experiment. Key steps in the development included selecting informative SNPs from the human genome, designing probes to target each SNP allele, validating the array's ability to detect various forms of UPD compared to known samples, and developing software to analyze and visualize the SNP and CNV data to identify regions of homozygosity indicative of UPD. The array and accompanying analysis software provide a complete solution for cytogenetics laboratories to reliably detect CNVs and UPD with a standardized, high
This document discusses clinical and consumer applications of microarrays and genotyping technologies. It provides an overview of genotyping and different technologies like PCR microarrays and SNP microarrays. It describes how microarrays are still useful despite the rise of sequencing due to their low cost, high throughput, and ability to test millions of markers. The document outlines several applications of microarrays like direct-to-consumer testing, pharmacogenetics, and clinical sequencing. It also discusses challenges and trends in these areas like global initiatives to increase genomic data sharing.
VarSeq 2.6.0: Advancing Pharmacogenomics and Genomic AnalysisGolden Helix
In the rapidly evolving field of genomic analysis, staying current with the latest research, data sources, and test advancements is crucial. In this webinar, we review how VarSeq addresses the needs to stay on top of the latest with the release of VarSeq 2.6.0.
This release features an exome-optimized workflow for LOH and CNV calling as well as the introduction of VSPGx to produce pharmacogenomic reports for gene panels as well as exomes and genomes. With the recent release of gnomAD v4, we have had many requests for the integration of this large update to the most population frequency source. With VarSeq 2.6.0, the latest version of gnomAD has been integrated into VSClinical and the updated tracks spans beyond variants to cover CNVs and gene scores to update all your workflows to the latest data.
In this webcast, we will cover.
Improved VS-CNV performance and updated exome analysis workflows.
Pharmacogenomics in action: Utilizing VSPGx for exome and genome assessments.
gnomAD v4 in practice: Updated automated and manual variant interpretation workflows.
Join us for an insightful session on the latest VarSeq 2.6.0 features, bringing you the most up-to-date data and workflows for your genomic analysis.
Target enrichment enables researchers to focus their next generation sequencing (NGS) efforts on regions of interest, allowing them to obtain more sequencing data relevant to their study. In-solution target capture is a method of enrichment using oligonucleotide probes directed to specific regions within a genome. Target capture can be used to enrich multiple samples simultaneously, reducing the cost per sample, while using individually synthesized probes allows researchers to construct gene panels that can be optimized over time.
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.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.1- Next Generation Sequencing. Technologies and Applications. Part I: NGS Introduction and Technology Overview.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
VarSeq provides powerful annotation capabilities for variant analysis including gene tracks, assemblies, variant functions, frequency tracks, functional predictions, and transcript annotations. It integrates information from over 20 public databases and sources and updates annotations monthly to provide the most current clinically relevant information for researchers. By centralizing variant annotations from disparate sources, VarSeq saves customers significant time and resources compared to manual curation of this data.
A microarray is a laboratory tool used to detect the expression of thousands of genes at the same time. DNA microarrays are microscope slides that are printed with thousands of tiny spots in defined positions, with each spot containing a known DNA sequence or gene.
Axiom® Genome-Wide AFR 1 Array World Array 3Affymetrix
The document describes the Axiom Genome-Wide AFR 1 Array, which provides high coverage of genetic variants associated with disease in African and African American populations. It was designed to maximize coverage of common and rare variants down to a minor allele frequency of 1% in specific gene regions and disease-associated areas. The array contains over 893,000 SNPs selected from genome-wide association studies and databases of disease-associated variants. It enables genome-wide association studies, replication, and fine mapping with one experiment.
RT2 Profiler PCR Arrays are a real-time PCR technology that allows researchers to study gene expression patterns across biological pathways and processes. The arrays contain pre-designed primer assays for 84 relevant genes as well as controls on a single plate in a 96-well format. The gene content of the arrays is selected based on biological relevance and published associations with relevant pathways. The primer assays on the arrays undergo extensive validation for sensitivity, specificity, reproducibility, and amplification efficiency. The PCR Array system also includes optimized components for RNA isolation, cDNA synthesis, and real-time PCR to provide a complete validated workflow for gene expression analysis from sample to results.
This document discusses oncogenomics and cancer genomics technologies. It provides an overview of oncogenomics, the types of DNA biomarkers studied including mutations, and experimental strategies used for cancer genomics research. Key techniques discussed are next-generation sequencing, quantitative PCR (qPCR), and mass spectrometry. The document compares different technologies for mutation detection and profiling and their sensitivities. It also outlines the specifications and pipeline for developing a qPCR-based somatic mutation assay.
Next generation sequencing & microarray-- Genotypic TechnologyGenotypic Technology
Greetings from Genotypic Technology, Bangalore (www.genotypic.co.in). We are a 13 year old genomics and bioinformatics company ( 65+ employees, Service. Products and R & D) based in Bangalore, India, primarily working on applications of Microarrays and Next Generation Sequencing in Human Health and Disease, including in Molecular Diagnostics, Prognosis, Therapeutics, Vaccine Research, Basic Science Research, Veterinary Science, Agriculture, Industrial Biotechnology, Microbial Genetics and more.
Our major strength is in customized genomics solutions, particularly in your field, we can develop panel of markers for specific diseases, optimize, validate and help commercialize on open platforms or specific instrument platforms- in microarrays and sequencing based methods/ assays. We can also use genomic markers to aid in treatment of specific disease using personalized medicine approaches. All this can be done on a comprehensive end-to-end manner in our company as we have a very good blend of molecular biology and bioinformatics with totally 6 Ph.Ds. We work closely with Agilent's R &D as their partner.
The document discusses various applications and techniques of DNA microarrays, including summarizing key points about Affymetrix GeneChips, spotted microarrays, experimental design, data analysis, and several case studies on various topics like ovarian cancer, Sjogren's syndrome, wine yeast genomics, and norovirus genotyping. Microarrays allow analysis of gene expression patterns and copy number variations across genomes through comparative hybridization experiments. The document provides an overview of microarray technology and applications in genomic and biomedical research.
Bio-chips, also known as lab-on-a-chip devices, can provide portable, low-cost, and low-power platforms for integrating sensors and other components. DNA microarrays allow high-throughput screening by placing probes for thousands of genes on a single chip. mRNA is extracted from experimental and control samples, converted to fluorescent cDNA, and hybridized on the chip. The fluorescent intensities indicate gene expression levels. Protein microarrays similarly attach thousands of proteins to a chip and detect binding with probes to study protein interactions, expression levels, and functions.
Bio-chips, also known as lab-on-a-chip devices, can provide portable, low-cost, and low-power platforms for integrating sensors and other components. DNA microarrays allow high-throughput screening by placing probes for thousands of genes on a single chip. mRNA is extracted from experimental and control samples, converted to fluorescent cDNA, and hybridized on the chip. The resulting colors indicate gene expression levels. Protein microarrays similarly attach thousands of proteins to a chip and use probes to study protein interactions, expression profiles, and biochemical functions through detection of reaction products. Technical challenges include maintaining protein activity and structure during immobilization and detection.
This document summarizes the Genome in a Bottle (GIAB) Consortium's efforts to characterize structural variants in human genomes to serve as benchmarks. The GIAB Consortium has generated structural variant calls for 7 human genomes using diverse data types and analysis methods. The document describes the GIAB Consortium's process for integrating these data to identify high-confidence structural variant calls to include in version 0.6 of the structural variant benchmark set. It provides examples of different types of structural variants characterized and evaluates the trustworthiness of the benchmark calls based on independent validation. The document also discusses ongoing efforts to further improve structural variant characterization using emerging long-read technologies.
Protein microarrays allow the immobilization and detection of large numbers of proteins on small surfaces. Three key steps in the protein microarray workflow are printing, surface selection, and imaging. Optimizing the printing process is important to minimize contamination between samples. The Omnigrid and Microgrid systems can print contact-style onto 3D substrates with controls to reduce surface damage. Multiplexed protein microarrays on plates allow high-throughput screening by testing many samples in parallel. NovaRay imaging supports multiple array formats and wavelengths for detection. An example experiment showed specific and reproducible detection of target proteins in individual wells of a multiplexed plate with no carryover between wells.
This document discusses GeneRead DNAseq Targeted Exon Enrichment and the GeneRead Library Quantification System for next generation sequencing. It begins with an introduction and agenda, then discusses targeted enrichment including the workflow, principles, data analysis, pathway content, performance data, and an application example. It also discusses library quantification including the workflow and an application example. In summary, the document presents Qiagen's GeneRead DNAseq and Library Quant systems as targeted enrichment and library quantification solutions for next generation sequencing applications.
The document discusses different strategies for next generation sequencing in clinical practice, including PCR-based and hybridization-based capture methods. It compares methods such as Raindance, Fluidigm, and Agilent SureSelect custom capture on various disease panels. It finds that hybridization-based capture provides more even coverage and reliable allele ratios than PCR-based methods. It recommends Illumina's TruSeq Custom Amplicon sequencing for high-throughput clinical tests due to reduced sample preparation time and cost.
Targeted RNAseq for Gene Expression Using Unique Molecular Indexes (UMIs): In...QIAGEN
Traditional RNA sequencing (RNA-Seq) is a powerful tool for expression profiling, but is hindered by PCR amplification bias and inaccuracy at low expressing genes. QIAseq RNA is a flexible and precise tool developed for mitigating these complications, allowing digital gene expression analysis. This in-depth webinar will cover sample requirements, experimental design, NGS platform-specific challenges and workflow for gene enrichment, library prep and sequencing. The applications of QIASeq RNA Panels in cancer research, stem cell differentiation and elucidating the effects small molecules on signaling pathways will be highlighted.
Similar to Next Generation Diagnostics: Potential Clinical Applications of Illumina’sTechnology (20)
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Understanding User Needs and Satisfying ThemAggregage
https://www.productmanagementtoday.com/frs/26903918/understanding-user-needs-and-satisfying-them
We know we want to create products which our customers find to be valuable. Whether we label it as customer-centric or product-led depends on how long we've been doing product management. There are three challenges we face when doing this. The obvious challenge is figuring out what our users need; the non-obvious challenges are in creating a shared understanding of those needs and in sensing if what we're doing is meeting those needs.
In this webinar, we won't focus on the research methods for discovering user-needs. We will focus on synthesis of the needs we discover, communication and alignment tools, and how we operationalize addressing those needs.
Industry expert Scott Sehlhorst will:
• Introduce a taxonomy for user goals with real world examples
• Present the Onion Diagram, a tool for contextualizing task-level goals
• Illustrate how customer journey maps capture activity-level and task-level goals
• Demonstrate the best approach to selection and prioritization of user-goals to address
• Highlight the crucial benchmarks, observable changes, in ensuring fulfillment of customer needs
Implicitly or explicitly all competing businesses employ a strategy to select a mix
of marketing resources. Formulating such competitive strategies fundamentally
involves recognizing relationships between elements of the marketing mix (e.g.,
price and product quality), as well as assessing competitive and market conditions
(i.e., industry structure in the language of economics).
Part 2 Deep Dive: Navigating the 2024 Slowdownjeffkluth1
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The global retail industry has weathered numerous storms, with the financial crisis of 2008 serving as a poignant reminder of the sector's resilience and adaptability. However, as we navigate the complex landscape of 2024, retailers face a unique set of challenges that demand innovative strategies and a fundamental shift in mindset. This white paper contrasts the impact of the 2008 recession on the retail sector with the current headwinds retailers are grappling with, while offering a comprehensive roadmap for success in this new paradigm.
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The Evolution and Impact of OTT Platforms: A Deep Dive into the Future of Ent...ABHILASH DUTTA
This presentation provides a thorough examination of Over-the-Top (OTT) platforms, focusing on their development and substantial influence on the entertainment industry, with a particular emphasis on the Indian market.We begin with an introduction to OTT platforms, defining them as streaming services that deliver content directly over the internet, bypassing traditional broadcast channels. These platforms offer a variety of content, including movies, TV shows, and original productions, allowing users to access content on-demand across multiple devices.The historical context covers the early days of streaming, starting with Netflix's inception in 1997 as a DVD rental service and its transition to streaming in 2007. The presentation also highlights India's television journey, from the launch of Doordarshan in 1959 to the introduction of Direct-to-Home (DTH) satellite television in 2000, which expanded viewing choices and set the stage for the rise of OTT platforms like Big Flix, Ditto TV, Sony LIV, Hotstar, and Netflix. The business models of OTT platforms are explored in detail. Subscription Video on Demand (SVOD) models, exemplified by Netflix and Amazon Prime Video, offer unlimited content access for a monthly fee. Transactional Video on Demand (TVOD) models, like iTunes and Sky Box Office, allow users to pay for individual pieces of content. Advertising-Based Video on Demand (AVOD) models, such as YouTube and Facebook Watch, provide free content supported by advertisements. Hybrid models combine elements of SVOD and AVOD, offering flexibility to cater to diverse audience preferences.
Content acquisition strategies are also discussed, highlighting the dual approach of purchasing broadcasting rights for existing films and TV shows and investing in original content production. This section underscores the importance of a robust content library in attracting and retaining subscribers.The presentation addresses the challenges faced by OTT platforms, including the unpredictability of content acquisition and audience preferences. It emphasizes the difficulty of balancing content investment with returns in a competitive market, the high costs associated with marketing, and the need for continuous innovation and adaptation to stay relevant.
The impact of OTT platforms on the Bollywood film industry is significant. The competition for viewers has led to a decrease in cinema ticket sales, affecting the revenue of Bollywood films that traditionally rely on theatrical releases. Additionally, OTT platforms now pay less for film rights due to the uncertain success of films in cinemas.
Looking ahead, the future of OTT in India appears promising. The market is expected to grow by 20% annually, reaching a value of ₹1200 billion by the end of the decade. The increasing availability of affordable smartphones and internet access will drive this growth, making OTT platforms a primary source of entertainment for many viewers.
Company Valuation webinar series - Tuesday, 4 June 2024FelixPerez547899
This session provided an update as to the latest valuation data in the UK and then delved into a discussion on the upcoming election and the impacts on valuation. We finished, as always with a Q&A
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Building Your Employer Brand with Social MediaLuanWise
Presented at The Global HR Summit, 6th June 2024
In this keynote, Luan Wise will provide invaluable insights to elevate your employer brand on social media platforms including LinkedIn, Facebook, Instagram, X (formerly Twitter) and TikTok. You'll learn how compelling content can authentically showcase your company culture, values, and employee experiences to support your talent acquisition and retention objectives. Additionally, you'll understand the power of employee advocacy to amplify reach and engagement – helping to position your organization as an employer of choice in today's competitive talent landscape.
2. 2
HiScanSQ
Unique
combination
of
sequencing
and arrays
Provider of Genomic Analysis Tools
That Advance the Understanding of Genetics and Health
From Genome-Wide Discovery to Targeted Validation and Screening
Sequencing Arrays qPCR
HiSeq
1000
Powerful,
Flexible,
Scalable
12. 12
HumanCytoSNP-12 BeadChip:
Optimized for Efficient Cytogenetic Analysis
► Streamlined, most informative set of targeted and whole-
genome SNP and non-polymorphic markers
► Uniform picket fence of entire genome (including ~92% of
RefSeq genes)
– 300,000 markers, mostly SNPs
– 6.2kb median marker spacing yields ~30kb resolution
► Higher density in cyto high-value regions (~250 for ~40% of
genome)
– All pericentromeres and subtelomeres
– Sex chromosomes
– Common regions of interest (e.g., associated with known
syndromes)
– Regions contain ~9000 genes
► Higher density in ~400 “disease genes”
For Research Use Only
13. 13
BeadArrayTM Technology
Oligo Mfg 2 μm Silica
~18-fold Redundancy Decoding = 100% QC
Bead Identifier
(30base nt)
Specific Probe
(50 base nt)
Population in wells
14. 14
The Infinium HD Assay
► Unconstrained Marker Design
– Freedom to select the best, most
informative SNPs then fill-in with
intensity-only probes
► Well-proven
– High reproducibility (> 99.9%)
– High call rates (> 99%)
► Streamlined, automatable
► PCR-free protocol
► No need to run a reference
sample
► High locus selectivity and allele
specificity
– Two-step enzymatic
discrimination
15. 15
Copy-Neutral Cytogenetic Aberrations
Forms of copy-neutral cytogenetic aberrations
► Uniparental disomy
– Case in which individual receives two copies of a chromosomal region from one
parent, none from the other
► Copy-neutral loss of heterozygosity (or “acquired uniparental disomy”)
– Case in which one allele of a gene in a heterozygote is already inactivated and
the second, “good” allele is lost without a net change in copy number. This can
occur through a gene conversion event in which the chromosome region
containing the inactivated allele is used as a template to repair a gap occurring
in the corresponding region of the other chromosome
In either case, the absence a functional allele leaves the individual
vulnerable to phenotypes that may be associated to the effected gene(s)
For Research Use Only
16. 16
SNPs Provide More Information to Detect Copy Number
► Also can detect:
– Amplification
– Unbalanced aberration
– Aneuploidy
– Mosaicism
Normal (diploid)
Deletion (loss of one copy)
Duplication (gain of one copy)
Genotypes
Copy-Neutral LOH (UPD)
Log R Ratio B Allele Frequency
Intensity
For Research Use Only
17. 17
B allele frequency data
(AAB genotype)
A shift in the LogR value is
detectible, but the integration
of B allele data improves the
signal to noise ratio
Detected duplication
A profile of chromosome 3 of a cell line derived
from a breast tumor.
SNP-based Detection Provides More Information and
Enables Better Characterization of Chromosomal
Aberrations
For Research Use Only
20. 20
KaryoStudioDx Features Highlights
► Accepts data from any Infinium HD array*
► Automated data importation
► Automated scanning for aberrations
► User permissions and authentication
– Input validation
► Mosaic detection
► Inheritance confirmation (non‐paternity)
► UPD parent of origin / inheritance calculation
► % consanguinity
► Quality metric: Pass or Fail
► Integrated Chromosome Browser
► Ability to filter CNV polymorphisms
► Cross‐matching capabilities to the most popular cytogenetic databases
* Certain computer requirements must be met
25. 25
Load
MiSeq –
Finally a sequencer designed with Dx customers in mind
Go
Workflow
Fully integrated system
On-board cluster generation and data visualization
Preloaded reagent cartridge
1 flow cell lane per run
Performance
Up to 5M clusters
2 x 150 bp in under 28 hours
RFID reagent & flow cell tracking
Auto flow cell positioning
Walk-away automation
26. 26
MiSeq – Prep, Run, Analyze
Sample to Data in as Little as Eight Hours*
08:00:00
MiSeq is the Only Personal Sequencing System Capable of
an 8 Hour Sample to Data Workflow
Amplicons
Clones
gDNA
*1x36bp run – 3 hr sequencing
28. 28
► Rapid & Economical
– Up to 384 amplicons per sample, 96 samples per
plate (36,864 reactions)
– Plate based processing
– <8 hrs from DNA to sequencing‐ready library
– No gels, no fragmentation – uses standard lab equipment
► Fully customized target probes and capture
– Extension and ligation based assay
► Interactive probe design and ordering
– Personalized and easy to use design tool
– Rapid design turnaround – as little as 10 days from
design to assay shipment
►
Coming soon! TruSeq Custom Amplicon Sequencing
Unprecedented amplicon and sample multiplexing
29. 29
Assay
Biochemistry
TruSeq Custom Amplicon Assay Time
96 samples & 384 targets: from DNA to called variants in ~2 days
8am – Day 1
Hybridization
Setup
Oligos,
universal
reagents
Extension &
Ligation, PCR
with index
Library
Normalization
Create pooled
library,
normalize
Cluster Gen &
Sequencing
Pre-kitted
sequencing
reagents
Real-time
Analysis
Alignments,
variant calling
2pm – Day 1 5pm – Day 2
<8 hr assay with <3 hr hands-on time
No fragmentation required
No gel purification steps
No additional hardware
30. 30
► Coverage Uniformity spec: >80% bases covered at 0.2x mean coverage
– e.g. if mean coverage is 100x, then >80% bases covered at 20x
► Users need to carefully plan how many samples are sequenced together
based on number of amplicons, to achieve desired coverage
TSCA throughput and coverage on MiSeq
How many samples can be run together?
31. 31
MiSeq - Comparison to CE Sequencing
Example: TruSeq Custom Amplicon with 96 Samples x 384 TargetsTSCA
Assay
biochemistry
CE
One plate of gDNA+oligos
for all 384 amplicons
Quant
96 x 384 well
plates
3730xl
5-6 weeks
~$3/amplicon
96-wellplate
TruSeq Custom
Amplicon
•Highly multiplexed
•Integrated sample indexing
•Standard lab equipment
Dispense, PCR, Cleanup
Assay Biochemistry Pool Libraries and
Sequence
Dye-terminator sequencing,
cleanup
96 x 384 well
plates
MiSeq
4 days
<$0.75/amplicon
32. 32
MiSeq Applications
A huge variety of applications can be done on MiSeq*
Application Read Length Kit Config. Sample Prep Kit
TruSeq Custom Amplicon 2 x 150 300PE TSCA
Nextera Amplicon 1 x 36 50PE NXT
Standard Amplicon 2 x 150 300PE TS DNA or HB
Small Genome - De Novo 2 x 150 300PE TS DNA
Small Genome - Reseq., plasmids 1 x 36, 2 x 150 50PE / 300PE TS DNA or NXT
16S Metagenomics (amplicon) 2 x 150 300PE TS DNA, NXT, HB
Library QC 2 x 25 50PE Open
Small RNA 1 x 36 50PE TS smRNA
RNA-Seq (human, mammalian) 2 x 50 50PE TS RNA
RNA-Seq (bacterial, viral) 2 x 150 300PE RZ + TS RNA
TruSeq Custom Enrichment 2 x 50 300PE TS DNA
ChIP-Seq 1 x 50 50PE TS DNA
TSCA = TruSeq Custom Amplicon TS DNA = TruSeq DNA Sample Prep NXT = Nextera
TS RNA = TruSeq RNA Sample Prep TS smRNA = TruSeq Small RNA Sample Prep HB = Homebrew
RZ + TS RNA = RiboZero + TruSeq RNA Sample Prep
*Applications can be performed, but MiSeq platform may not be the most optimal solution for a particular application. There will be situations where
HiSeq, GA or HiScan SQ are better suited to a particular application.
33. 33
MiSeq
Characterization of Genetic Variations in Tumor Tissues
► Deep sequencing of cancer samples to
detect somatic mutations, gene
amplifications and germline variants
that influence patient treatment
decisions
► Genes under consideration include
AKT1, ALK, BRCA1, BRCA2, BRAF,
COMT, CYP17A1, CYP2A6, CYP2C8,
CYP2D6, CYP3A4, DPYD, EGFR,
ERBB2, FGFR2, GNAQ, KIT, KRAS,
MET, MTHFR, NRAS, PDGFRA,
PDGFRB, PIK3CA, PTEN, TP53,
TPMT, TYMS, UGT1A1, VEGFA,
VEGFR
34. 34
MiSeq FFPE Amplicon Data
KRAS Exon 2 – 76 Base Amplicon
1.1% variant in
normal adjacent
tissue > Assay
LOD of 0.5%
Rectal
Normal
Ovarian
Tumor
Gastric
Tumor
No-FFPE
Control
Gastric
Normal
Rectal
Tumor
Sample
Coverage 178667 X151695 X 176530 X 179630 X 161866 X 178900 X
27.5% G C
variant at Chr12:
25398284 in rectal
tumour
51. 51
How to Start a MiSeq Run
The MiSeq Control Software (MCS) is a streamlined push-button user
interface designed to quickly start a sequencing & analysis run
► Minimal user input required to start a run
► A sample sheet is required to initiate a run
► User has the option to save data locally or to a BaseSpace (cloud) account
53. 53
[OPTIONAL] Log on to BaseSpace
BaseSpace is a cloud option to store, analyse, and share your MiSeq data.
54. 54
[OPTIONAL] First Time BaseSpace User
If this is the first time user is using BaseSpace, they must agree the to terms &
conditions of BaseSpace use.
57. 57
Sample Sheet Required for MiSeq Run
Sample Sheet is required for each MiSeq run
► Contains instructions on how to perform sequencing chemistry
► Also contains instructions on how to perform bioinformatics secondary
analysis:
– Resequencing
– amplicon resequencing
– de novo
– small RNA
– Metagenomics
– library QC
► By default, MiSeq will use the Sample Sheet (in Sample Sheet repository)
that matches the reagent cartridge RFID
► User may override MCS to select a user-specified Sample Sheet
59. 59
Review of MiSeq Run
User has opportunity to review parameters of run before submitting
60. 60
MiSeq Performs Pre-Run Check
MCS checks for dependencies to ensure run success
Click here
to start run
61. 61
MiSeq Performs Sequencing Run
Current status
of run
Output to current
BaseSpace
account
Name of run
Realtime run
metrics
Connectivity status
With BaseSpace
62. 62
MiSeq Reporter
► MiSeq Reporter (MSR) is the onboard bioinformatics engine that
automatically processes MiSeq primary analysis (image and basecall) data.
► At launch, MSR supports the following reports:
– Resequencing
– Amplicon resequencing
– de novo assembly (using Velvet)
– Small RNA
– 16S metagenomics
– Library QC
► MSR contains a webserver so users may point browser to MiSeq
instrument to view reports.
► MSR outputs may be stored on the instrument or on network folders.
83. 83
• A patient treated with Erlotinib but lung
metastases are unresponsive
• Whole genome and transcriptome
sequencing of the cancer on the GA
reveals that
• The drug target was mutated, hence the
unresponsiveness
• 17 genetic disruptions of a key cancer
pathway
• A target for the alternative FDA
approved drug sunitinib was over-
expressed
• Sunitinib treatment was successful and
the tumours regressed.
Jones et al. Genome Biology 2010, 11:R82
http://genomebiology.com/2010/11/8/R82
Sequencing Informs Therapy
84. 84
Acute Promyelocytic Leukemia (APL)
Most APL patients have a characteristic translocation between
chromosomes 15 and 17 that fuses the PML1 and RARA genes
– These patients respond well to treatment with ATRA but treatment requires prior
demonstration of the translocation or fusion gene
► A targeted PCR test of the patient’s DNA did not reveal the characteristic
fusion gene
► Whole genome sequencing (in just 1 week) revealed a novel 77 kb insertion
that recapitulates the translocation
► Rearrangement event confirmed by PCR
► ATRA treatment prescribed
Mardis, E, Wilson R et al. unpublished
85. 85
Nextera DNA Sample Prep
Sequencing’s fastest and easiest sample prep
► 90 min sample prep
► No Covaris required
► High throughput
► Super low 50ng input unlocks access
to precious samples
► Enables a range of CE applications:
amplicons, plasmids, small genomes
~1.5 hours
~12 hours
Enables effective use of single
36bp reads
86. 86
Overall positioning of Targeted Resequencing on MiSeq
PCR amplicons through TruSeq Custom Enrichment
Application
Target
Sequence
Number samples
/ project
Price / sample
(Prep and Seq)
Key Benefit
CE +
Amplicons
< 10 kb <100 $50
Small sample/content
projects
Nextera +
Amplicons
< 20 kb 100s $80
Long contiguous
amplicons and speed
TSCA 10 – 96 kb 100s – 1000s $50 - 300
Multiplexing and
speed
TSCE 700 kb – 2 Mb 100s – 1000s $260 - 800 More target content
88. 88
Nextera and MiSeq
Sequencing’s fastest time to answer for rapid variant analysis
08:00:00
15:00:00
*Based on 1 x 36 bp reads
1 – 8 samples
1 – 96 samples
89. 89
Ovarian Cancer
Deadly
Incurable
Difficult Dx
Patients present with a suspicious/palpable mass
Less than 40% are cured
204,449 New cases annually; 124,860 deaths
Early Dx is Key
Five year survival is good if diagnosed early,
but most patients are diagnosed late stage
Illumina Solution
Develop a diagnostic assay which will diagnose
ovarian cancer at an early stage
19%
22%
30%
33%
37%
40%
47%
54%
72%
100%
92%
85%
82%
69%
56%
51%
39%
26%
17%
12%
-10%
10%
30%
50%
70%
90%
110%
Ia Ib Ic Iia Iib Iic IIIa IIIb IIIc IV
Cum % of Cases
5 Yr Survival
90. 90
TruSeq Targeted Resequencing
A broad suite of tools for discovery or validation experiments
Option
Amount of
sequence
Best for Availability
TruSeq Exome
Enrichment
~62 Mb
Mendelian disease:
case-control exome studies, rarer
variants, causal variants
exome-wide linkage analysis
Now!
TruSeq Custom
Enrichment
~1 to ~10 Mb
GWAS follow-up: validation of
variants, variant discovery, pathways
Now!
TruSeq Custom
Amplicon
Sub-500 Kb
Amplicon sequencing: high-
throughput CE experiments, ultra
deep seq, variant disc, screening
2H2011
Nextera + PCR
Amplicons
100’s of bp
targets
Amplicon sequencing: ultra-deep
sequencing, validation, screening, CE
replacement
Now!
93. 93
Options for Targeted Resequencing with Illumina
From specific, customized regions of interest to the complete coding region
Option
Amount of
sequence
Best for Availability
TruSeq Exome
Enrichment
~62 Mb
Mendelian disease:
case-control studies, rarer variants,
causal variants, linkage analysis
Now!
TruSeq Custom
Enrichment
~700Kb to ~15
Mb
GWAS follow-up: validation of variants,
variant discovery, pathways
Now!
Nextera + PCR
Amplicons
100’s of bp
targets
Amplicon sequencing: ultra-deep seq,
validation, screening, CE replacement
Now!
TruSeq Custom
Amplicon
~100 Kb
Amplicon seq: high-throughput CE,
ultra deep seq, variant disc, screening
2H2011
The only company with the complete end-to-end TRS workflow solution.
94. 94
Simplest Sequencing Workflow
Integrated workflow from sample to analyzed data
TruSeq Chemistry
Clustering & Sequencing
TruSeq DNA
Simple, scalable and cost
effective
TruSeq RNA
Optimized, gel-fee, low input
TruSeq Small RNA
Hi throughput miRNA
discovery & profiling
TruSeq Exome
Lowest cost and most
scalable exome sequencing
95. 95
MiSeq Workflow Guide
Pre-defined data analysis workflows
Targeted
Resequencing
TruSeq Custom
Amplicon
Nextera PCR
Amplicon
Metagenomics
16S rRNA
Clone Checking
TruSeq Custom
Enrichment
ChIP-Seq
Small Genome
Sequencing
De novo
Resequencing
Plasmids
RNA
Sequencing
Small RNA
RNA-Seq
Library QC
Library QC
Primary
workflows
Secondary
workflows
Automated
Semi-Automated
96. 96
MiSeq Applications
A huge variety of applications can be done on MiSeq*
Application Read Length Kit Config. Sample Prep Kit
TruSeq Custom Amplicon 2 x 150 300PE TSCA
Nextera Amplicon 1 x 36 50PE NXT
Standard Amplicon 2 x 150 300PE TS DNA or HB
Small Genome - De Novo 2 x 150 300PE TS DNA
Small Genome - Reseq., plasmids 1 x 36, 2 x 150 50PE / 300PE TS DNA or NXT
16S Metagenomics (amplicon) 2 x 150 300PE TS DNA, NXT, HB
Library QC 2 x 25 50PE Open
Small RNA 1 x 36 50PE TS smRNA
RNA-Seq (human, mammalian) 2 x 50 50PE TS RNA
RNA-Seq (bacterial, viral) 2 x 150 300PE RZ + TS RNA
TruSeq Custom Enrichment 2 x 50 300PE TS DNA
ChIP-Seq 1 x 50 50PE TS DNA
TSCA = TruSeq Custom Amplicon TS DNA = TruSeq DNA Sample Prep NXT = Nextera
TS RNA = TruSeq RNA Sample Prep TS smRNA = TruSeq Small RNA Sample Prep HB = Homebrew
RZ + TS RNA = RiboZero + TruSeq RNA Sample Prep
*Applications can be performed, but MiSeq platform may not be the most optimal solution for a particular application. There will be situations where
HiSeq, GA or HiScan SQ are better suited to a particular application.
98. 98
Illumina’s First FDA Cleared In-Vitro Diagnostic Device
► The BeadXpress System is an FDA 510(k) cleared In-Vitro Diagnostic
Device
► FDA Cleared BeadXpress System includes:
– BeadXpress Reader
– VeraScan Software
► The Intended Use Statement:
– The BeadXpress® System is an In-Vitro Diagnostic
Device intended for the simultaneous detection
of multiple analytes in a DNA sample utilizing
VeraCode holographic microbead technology.
The BeadXpress System consists of the
BeadXpress Reader and VeraScan software.
– It is cleared for use only with FDA cleared
VeraCode tests.
BeadXpress Reader and
VeraScan Software
99. 99
Comprehensive VeraCode product portfolio
Research
Use Only
VeraCode ADME
Core Panel
VeraCode Universal
Capture & Carboxyl
Beads
Custom GoldenGate
Genotyping,
48, 96, 144, 192 &
384-plex
DASL Custom Gene
Expression,
32 to 384-plex
Custom GoldenGate
Methylation,
48 to 384-plex
Regulated
Products
VeraCode GPR
Universal Capture
Beads
VeraCode GPR
Carboxyl Beads
VeraCode PGx Panel
(in development)
VeraCode GI Panel
(in development)
101. 101
Sequencing Services
Illumina Clinical Services Lab
Somatic Mutation Panel
Somatic Mutation Panel launch Q4 11
Content will include genes with proven/anticipated clinical utility:
KRAS EGFR BRAF TP53 VEGF-A
ERBB2 ESR1 PGR TYMS UGT1A1
TPMT COMT CYP2D6 NRAS EML4/ALK
WGS
30+ Whole genomes sequenced Q4 10
First clinical case reimbursed Q4 10
Cancer, genetic diseases, SCID cases
Infrastucture
CLIA certified for high complexity molecular diagnostics Q1 09
CAP Accredited Q2 09
CA State CLS training program Q1 10
102. 102
Individual Genome Sequencing: Workflow
o Initial discussion & genetic counseling
o Informed Consent and Service Agreement
o Saliva and blood sample taken (DNA possible)
o Cooling-off period (7+ days); order confirmed
o Barcode samples for confidentiality
o Saliva and blood genotype for ID match
o Whole genome sequencing of blood DNA
o Analyze and QC sequence and called variants
o Check sequence and genotype ID match
o Archive full dataset
Physician orders IGS for patient
Genome sequencing and QC
Clinical lab delivers data to physician
104. 104
► Summary Report
► Consensus sequence with quality scores of calls
► SNPs report, with dbSNP designation or novel
► All individual reads, aligned to the human genome reference sequence
► GenomeStudio genome browser installed on an encrypted hard drive with variants
annotated
Delivery of Individual Genome Sequence
105. 105
Illumina Sequencing Workflow
Fragment DNA
Repair ends
Add A overhang
Ligate adapters
Purify
Library Preparation1
Cluster Generation Hybridize to flow cell
Extend hybridized template
Perform bridge amplification
Prepare flow cell for sequencing
2
Sequencing
Perform sequencing
Generate base calls
3
Data Analysis
Images
Intensities
Reads
Alignments
4
107. 107
DNA
(0.1-1.0 ug)
Sample
preparation Cluster growth
5’
5’3’
G
T
C
A
G
T
C
A
G
T
C
A
C
A
G
T
C
A
T
C
A
C
C
T
A
G
C
G
T
A
G
T
Illumina Sequencing Technology
Robust Reversible Terminator Chemistry Foundation
Sequencing
109. 109
MiSeq FFPE Cancer Sequencing
Summary
• MiSeq and SBS Chemistry is capable of generating high depth of
coverage sufficient enough to detect rare variants even in highly
degraded DNA
• The limit of detection for these types of assays is approximately
0.5%, MiSeq was able to easily detect a variant close to the limit of
detection
• MiSeq has the bandwidth to cover 48 amplicons from 48 samples
at an average coverage depth of over 2000x
110. 110
Competitive Environment
TruSeq Custom
Amplicon
Fluidigm Access
Array
HaloPlex PCR PCR/Homebrew
Number of Amplicons 48 – 384 48 ‐ 480[1] < 2,000 1 ‐ 5
Target Genomic
Sequence
< 96 kb < 120 kb < 400 kb < 3 kb
Panel Design DesignStudio FLDM service Design Wizard Primer3/Manual
Total Assay Time
(hands on)
7 hr (2.5 hr) 5 hr (<1 hr) 24 hr (2.5 hr est) 2 hr (0.5 hr)
Manual Batch Size
(samples)
192 48 48 < 384
Order to Ship Time 10 days 3 weeks < 3 weeks[2] < 5 days
Special Hardware None $75K ??? ‐
Price per amplicon < $1.00 $0.50 ‐ 0.70 $0.50 – 1.10 $0.50 – 1.00
Input DNA 0.25 µg 0.05 µg 0.9 µg < 0.25 µg
End to end solution Yes No No No
llumina supported
assay
Yes No No No
[1] Promising 10‐plex PCR [2] Estimated