In this OncomineWorld 2021 presentation, learn how next-generation sequencing is playing a crucial role in cancer research. To watch the full presentation, visit www.oncomine.com/events.
In this presentation we showcase the latest advancements in myeloid genomic profiling: The Ion Torrent Oncomine Myeloid Assay GX.
Learn how this solution addresses key challenges in myeloid molecular testing and see recent data from the University of Pennsylvania.
Learn more at www.oncomine.com/myeloid
The document summarizes the Oncomine Myeloid Assay GX, a one-day genomic profiling assay for myeloid samples. It provides automated specimen-to-report workflow including library preparation, sequencing, variant calling, and reporting. The assay can simultaneously interrogate DNA mutations and RNA fusion transcripts covering major myeloid disorders. It has high gene coverage, detects challenging targets, and provides an annotated variant report.
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.
HDx™ Reference Standards and Reference Materials for Next Generation Sequenci...Candy Smellie
This document summarizes a presentation about reference standards for next generation sequencing (NGS). Horizon Diagnostics has developed genomic DNA and formalin-fixed, paraffin-embedded (FFPE) reference standards containing defined mutations at known allelic frequencies to validate NGS workflows and monitor assay performance. Multiplex reference standards contain up to 40 mutations at low allelic frequencies down to 1.3% that can be quantified using digital PCR. Several laboratories demonstrated they could accurately detect the mutations in Horizon's reference standards using different NGS platforms. The standards help evaluate sensitivity, specificity, and limits of detection on NGS assays.
2016 Dal Human Genetics - Genomics in Medicine LectureDan Gaston
Genomic medicine aims to identify genetic variations that cause disease and inform treatment. While whole genome sequencing is technically possible for $1000, analysis costs remain high. Current clinical applications include diagnosing rare childhood disorders and guiding cancer treatment. Continued cost reductions and expanding biological knowledge databases will drive further innovation, though challenges around data interpretation and reporting remain. Large reference populations and functional studies are still needed to realize genomics' full potential in healthcare.
Next Generation Sequencing application in virologyEben Titus
Next Generation Sequencing (NGS) is a promising technique for virus diagnosis that provides several advantages over traditional Sanger sequencing. NGS workflows involve sample preparation, sequencing, and data analysis. NGS has various applications in virology including identifying viral quasispecies, detecting antiviral drug resistance mutations, discovering novel virus genotypes, and performing quality control of live vaccines. While NGS reduces costs and improves throughput over Sanger sequencing, analyzing large NGS datasets requires strong bioinformatics skills. Overall, NGS represents a significant improvement for virus research and diagnosis.
The OncoScan(TM) platform for analysis of copy number and somatic mutations i...Lawrence Greenfield
The OncoScan microarray offers high-quality copy number, genotype, and somatic mutation data with whole-genome coverage and high resolution in cancer genes for use with challenging FFPE samples.
In this OncomineWorld 2021 presentation, learn how next-generation sequencing is playing a crucial role in cancer research. To watch the full presentation, visit www.oncomine.com/events.
In this presentation we showcase the latest advancements in myeloid genomic profiling: The Ion Torrent Oncomine Myeloid Assay GX.
Learn how this solution addresses key challenges in myeloid molecular testing and see recent data from the University of Pennsylvania.
Learn more at www.oncomine.com/myeloid
The document summarizes the Oncomine Myeloid Assay GX, a one-day genomic profiling assay for myeloid samples. It provides automated specimen-to-report workflow including library preparation, sequencing, variant calling, and reporting. The assay can simultaneously interrogate DNA mutations and RNA fusion transcripts covering major myeloid disorders. It has high gene coverage, detects challenging targets, and provides an annotated variant report.
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.
HDx™ Reference Standards and Reference Materials for Next Generation Sequenci...Candy Smellie
This document summarizes a presentation about reference standards for next generation sequencing (NGS). Horizon Diagnostics has developed genomic DNA and formalin-fixed, paraffin-embedded (FFPE) reference standards containing defined mutations at known allelic frequencies to validate NGS workflows and monitor assay performance. Multiplex reference standards contain up to 40 mutations at low allelic frequencies down to 1.3% that can be quantified using digital PCR. Several laboratories demonstrated they could accurately detect the mutations in Horizon's reference standards using different NGS platforms. The standards help evaluate sensitivity, specificity, and limits of detection on NGS assays.
2016 Dal Human Genetics - Genomics in Medicine LectureDan Gaston
Genomic medicine aims to identify genetic variations that cause disease and inform treatment. While whole genome sequencing is technically possible for $1000, analysis costs remain high. Current clinical applications include diagnosing rare childhood disorders and guiding cancer treatment. Continued cost reductions and expanding biological knowledge databases will drive further innovation, though challenges around data interpretation and reporting remain. Large reference populations and functional studies are still needed to realize genomics' full potential in healthcare.
Next Generation Sequencing application in virologyEben Titus
Next Generation Sequencing (NGS) is a promising technique for virus diagnosis that provides several advantages over traditional Sanger sequencing. NGS workflows involve sample preparation, sequencing, and data analysis. NGS has various applications in virology including identifying viral quasispecies, detecting antiviral drug resistance mutations, discovering novel virus genotypes, and performing quality control of live vaccines. While NGS reduces costs and improves throughput over Sanger sequencing, analyzing large NGS datasets requires strong bioinformatics skills. Overall, NGS represents a significant improvement for virus research and diagnosis.
The OncoScan(TM) platform for analysis of copy number and somatic mutations i...Lawrence Greenfield
The OncoScan microarray offers high-quality copy number, genotype, and somatic mutation data with whole-genome coverage and high resolution in cancer genes for use with challenging FFPE samples.
Next generation sequencing in cancer treatment MarliaGan
Next-generation sequencing (NGS) provides several advantages over first generation sequencing methods. NGS allows large amounts of genomic information to be sequenced in parallel at a lower cost. NGS has various applications in cancer treatment including predicting cancer progression, identifying drug targets and resistance mutations, detecting minimal residual disease, and improving cancer classification. While powerful, NGS also faces limitations such as tissue heterogeneity, complexity of data analysis, and difficulties identifying driver mutations as cancers evolve with treatment.
This document discusses next-generation sequencing and its applications in genomics and pathology. It begins with an overview of common NGS terms and technologies. It then covers the typical NGS analysis workflow including quality control, mapping reads to a reference genome, variant calling and annotation. Challenges such as data storage, sharing and reporting are also addressed. The document concludes that clinical sequencing is becoming established but requires ongoing collaboration between pathologists, geneticists and bioinformaticians to realize its potential.
The Application of Next Generation Sequencing (NGS) in cancer treatmentPremadarshini Sai
Next-generation sequencing (NGS) has several advantages for cancer treatment including high throughput sequencing, screening of multiple genes simultaneously, and decreased costs. NGS faces challenges from complex data analysis and validation of new technologies. Key clinical applications of NGS include whole genome sequencing, transcriptome analysis via RNA-seq, and sequencing of cell-free DNA. Future areas of development include immunotherapy, epigenetics research, and using circulating tumor cells to detect early relapse. More research is still needed to fully realize the potential of NGS in personalized cancer treatment.
Affymetrix OncoScan®* data analysis with Nexus Copy Number™Affymetrix
This document discusses the analysis of Affymetrix OncoScan data using Nexus Copy Number software. It outlines researchers' needs such as visualizing data, identifying common aberrations, comparing sample populations, and predictive analysis. It then describes the data processing in Nexus, including algorithms for identifying significant aberrations and dealing with heterogeneity. Finally, it shows examples of data visualization, analysis features for survival, enrichment, and comparing groups that Nexus provides to help researchers analyze and understand OncoScan data.
Sequencing 60,000 Samples: An Innovative Large Cohort Study for Breast Cancer...QIAGEN
This slidedeck focuses on the design of a large cohort study for assessing breast cancer risk and how an innovative digital sequencing approach is able to solve the previously unmet challenges of this type of NGS study design. Our speaker, Dr. Fergus J. Couch of the Mayo Clinic, presents on the design of this NCI-funded project, which comprises the sequencing of 60,000 samples to assess the risk of breast cancer through association with targeted genes. The design and size of the study requires an accurate, robust and high-throughput sequencing method. The investigators are using a digital DNA sequencing approach from QIAGEN that incorporates molecular barcodes to tag and remove PCR duplicates and increase NGS assay sensitivity. The approach also uses proprietary chemistry that enables uniform sequencing to efficiently utilize sequencing power and deliver optimized results.
The clinical application development and validation of cell free dna assays -...Candy Smellie
What is the impact of assay failure in your laboratory and how do you monitor for it?
In cancer patients, cell-free DNA carries tumour-related genetic alterations that are relevant to cancer development, disease progression and response to therapy.
Cell-free DNA detection allows:
Early detection
Frequent sampling
Monitoring of disease progression
Measure response to therapy
Detection of resistance mutation
Non-invasive diagnostic tool development
This document provides an overview of next generation sequencing (NGS), including its history, key methods, applications and challenges. It discusses that NGS allows for massively parallel sequencing of thousands of DNA molecules simultaneously, providing exact sequences of genes. Some main NGS platforms and their sequencing methods are described, such as Illumina sequencing by synthesis. Applications of NGS discussed include cancer research, pharmacogenetics and preimplantation genetic diagnosis. Challenges associated with NGS like poor quality FFPE samples and large data analysis workflows are also outlined.
Join Fight CRC in a webinar about biomarkers. In this session, Dr. Chris Lieu will focus the discussion on the NTRK biomarker, in addition to ctDNA, and Next-Generation Sequencing.
High Sensitivity Detection of Tumor Gene Mutations-v3Michael Powell
This document summarizes a new method called QClamp PCR that can highly sensitively detect tumor gene mutations. QClamp uses synthetic XNA probes to selectively block amplification of wild-type DNA sequences, improving the sensitivity of PCR to detect mutations present in less than 0.1% of samples. This level of sensitivity allows detection of mutations from biopsy, tissue, or blood samples. The document discusses applications of QClamp PCR for detection of EGFR mutations in lung cancer patients and enriching samples for DNA sequencing. QClamp represents an improvement over other methods by reducing the excess of wild-type DNA that creates high background signals.
Next-Generation Sequencing Clinical Research Milestones InfographicQIAGEN
DNA mutations have been implicated in several diseases, particularly cancer. NGS presents an ideal technology to efficiently profile the multitude of mutations in a high throughput manner. In 2001 the first draft of human genome was published. Since then many major milestones have been reached. Do you know when PIK3CA was identified in colon cancer? When was Olaparib for ovarian cancer treatment? This infographic traces the major clinical research milestones starting from the first draft of the human genome.
1) The document describes QClamp XNA-PCR, a technology from DiaCarta that uses molecular "clamps" to highly sensitively detect low frequency and cell-free circulating mutant DNA.
2) It needs assays that can detect biomarkers present at low frequency in samples containing a high amount of normal DNA. Existing technologies are inadequate for this need.
3) QClamp assays can reliably detect all possible mutations in a gene region using a single reaction. They can achieve ultra-high sensitivity down to 0.01% from minimal sample input.
Analysis of Single-Cell Sequencing Data by CLC/Ingenuity: Single Cell Analysi...QIAGEN
Single-cell analysis is useful to study genetic heterogeneity between individual cells and can help in result interpretation by looking at the average behavior of a large number of cells. Applications include circulating tumor cells, cells from small biopsies and cells from in vitro fertilized embryos. In this slidedeck, we show how single cell next-generation sequencing data can be analyzed and what challenges needs to be overcome. One of the examples we use is single cell data from two colorectal cancer cell lines.
Challenges and Opportunities for Digital PCR in the CLIA Laboratory of the Mo...Kate Barlow
Anthony Magliocco, Chair of Anatomical Pathology, Moffitt Cancer Center, USA
The Moffit Cancer Center is one of the largest NCI designated comprehensive free-standing cancer centers in the USA. The center has developed one of the most advanced personalized cancer medicine treatment programs in the world. This program is supported by a comprehensive and advanced CLIA molecular diagnostics. Digital PCR assays are currently being developed for several clinical applications including TKI resistance monitoring in patients with advanced lung cancer. The challenges and opportunities in deploying digital PCR into clinical practice will be discussed.
This document discusses accelerating genetic variant calling using hardware. It motivates this by noting that identifying genetic variants can help diagnose diseases and recommend treatments, but current algorithms take too long. It describes workflows for identifying germline and somatic variants using pairwise alignment and explains that the Pairwise Haplotype Mapping (PairHMM) computation is the most intensive part. Profiling shows PairHMM takes 70% of runtime. It proposes implementing PairHMM in hardware to accelerate variant calling.
Circulating cell free DNA is a potential tumor marker in a non-invasive blood test for the treatment and evaluation of cancer and recurrence monitoring. As circulating tumor DNA is often present at low frequencies within circulating cell free DNA, targeted sequencing on the Ion Torrent™ platform is an optimal tool or mutation detection with very little sample input required. Here, we demonstrate a complete workflow from isolation through molecular characterization of circulating tumor DNA. We have optimized a protocol using magnetic beads to isolate circulating cell free DNA. This protocol is easily automated to process up to 192 samples a day. It is also easily scalable for any input volume and can elute in volumes down to 15 μL resulting in no loss of low frequency alleles. We demonstrate comparable performance between this bead based isolation and column based isolation. We have completed molecular characterization of circulating cell free DNA using the multiplexing capabilities of AmpliSeq™ and the Ion PGM™. With the Ion AmpliSeq™ Cancer Hotspot Panel v2, we performed targeted sequencing of 50 genes of interest, covering 2800 COSMIC mutations. We demonstrate good reproducibility of amplicon representation as well as allelic frequencies. Through saturation studies and subsampling, we have determined the limit of detection of hotspots circulating cell free DNA on the Ion PGM™ to be below 1%. We further demonstrate proof of principle of this workflow on circulating cell free DNA and matched FFPE samples. Our results verify the accuracy and ease of our workflow. This protocol, from isolation through targeted sequencing, will not only result in a simple sample preparation for circulating cell free DNA but also facilitate rapid mutation detection to advance cancer research.
Translational Genomics and Prostate Cancer: Meet the NGS Experts Series Part 2QIAGEN
Advanced prostate cancer is highly heterogeneous but this inter-patient heterogeneity has until recently not been understood. We have through an international research effort dissected the molecular landscape of advanced castration resistant prostate, elucidating key molecular targets in this group of diseases. We have also shown that PARP inhibitors have antitumor activity against a significant proportion of these cancers, mainly in men whose cancers harbor DNA repair defects.
This slidedeck details two comprehensive informatics solutions — the Biomedical Genomics Workbench and Ingenuity Knowledge Base Variant Analysis platforms. We show the intuitive user interface of CLC Cancer Research Workbench and demonstrate how the rich biological content from Ingenuity Knowledge Base helps you rapidly identify critical variants in your samples.
CTC Detection and Molecular Characterization – Challenges and SolutionsQIAGEN
Circulating Tumor Cells (CTCs) have been extensively explored as circulating biomarkers in various cancers. Due to their rarity, heterogeneity and stem cell-like properties, detecting and profiling CTCs from blood samples is very challenging. In this webinar, Dr. Siegfried Hauch will introduce the well-known AdnaTests, which uses the Combination of Combinations Principle (COCP) to enable enriching and detecting CTCs in whole blood with high specificity and sensitivity, and how to overcome challenges in CTC enrichment and detection. The AdnaTests combine an immunomagnetic capturing method that increases purity, and is followed by molecular profiling of the captured CTCs. In addition, leukocyte contamination is another issue in CTCs detection and may lead to false positive results due to illegitimate expression of target genes or false interpretation. The AdnaWash is developed to reduce leukocyte contamination to such a level that whole gene panels can be analyzed while maintaining the required specificity and sensitivity.
Invicta eshre-poster-pregnancy rate after frozen blastocystINVICTA GENETICS
Assessment of pregnancy rate after comprehensive chromosome screening using next-generation sequencing-based preimplantation genetic diagnosis (NGS PGD) of trophectoderm in frozen blastocyst transfer.
C2 Reimbursement Perspectives on Precision MedicineEmilie Adams
This document summarizes a presentation on reimbursement perspectives for precision medicine. It discusses:
1) The promise of precision medicine in tailoring treatments to a patient's specific biomarkers or genetic profile, leading to better outcomes. Examples are given of targeted therapies approved for lung cancer subtypes.
2) Best practices from other countries in implementing precision medicine, such as France's national network of molecular testing centers to ensure equal access. Challenges discussed include getting the right test to the right patient at the right time for the right price.
3) Recommendations to optimize precision medicine in the future, such as establishing molecular testing programs and guidelines to help integrate testing into clinical practice and minimize delays in treatment. Time
Update on the Adoption and Utilization of Emerging Precision Medicine Biomark...Andrew Aijian
In this 2nd wave of our precision oncology pulse survey, we explore how recent clinical, commercial, and regulatory events have impacted the adoption of emerging precision oncology biomarkers and diagnostic tools. We also examine the key technological trends likely to impact the landscape in the near-mid term.
Next generation sequencing in cancer treatment MarliaGan
Next-generation sequencing (NGS) provides several advantages over first generation sequencing methods. NGS allows large amounts of genomic information to be sequenced in parallel at a lower cost. NGS has various applications in cancer treatment including predicting cancer progression, identifying drug targets and resistance mutations, detecting minimal residual disease, and improving cancer classification. While powerful, NGS also faces limitations such as tissue heterogeneity, complexity of data analysis, and difficulties identifying driver mutations as cancers evolve with treatment.
This document discusses next-generation sequencing and its applications in genomics and pathology. It begins with an overview of common NGS terms and technologies. It then covers the typical NGS analysis workflow including quality control, mapping reads to a reference genome, variant calling and annotation. Challenges such as data storage, sharing and reporting are also addressed. The document concludes that clinical sequencing is becoming established but requires ongoing collaboration between pathologists, geneticists and bioinformaticians to realize its potential.
The Application of Next Generation Sequencing (NGS) in cancer treatmentPremadarshini Sai
Next-generation sequencing (NGS) has several advantages for cancer treatment including high throughput sequencing, screening of multiple genes simultaneously, and decreased costs. NGS faces challenges from complex data analysis and validation of new technologies. Key clinical applications of NGS include whole genome sequencing, transcriptome analysis via RNA-seq, and sequencing of cell-free DNA. Future areas of development include immunotherapy, epigenetics research, and using circulating tumor cells to detect early relapse. More research is still needed to fully realize the potential of NGS in personalized cancer treatment.
Affymetrix OncoScan®* data analysis with Nexus Copy Number™Affymetrix
This document discusses the analysis of Affymetrix OncoScan data using Nexus Copy Number software. It outlines researchers' needs such as visualizing data, identifying common aberrations, comparing sample populations, and predictive analysis. It then describes the data processing in Nexus, including algorithms for identifying significant aberrations and dealing with heterogeneity. Finally, it shows examples of data visualization, analysis features for survival, enrichment, and comparing groups that Nexus provides to help researchers analyze and understand OncoScan data.
Sequencing 60,000 Samples: An Innovative Large Cohort Study for Breast Cancer...QIAGEN
This slidedeck focuses on the design of a large cohort study for assessing breast cancer risk and how an innovative digital sequencing approach is able to solve the previously unmet challenges of this type of NGS study design. Our speaker, Dr. Fergus J. Couch of the Mayo Clinic, presents on the design of this NCI-funded project, which comprises the sequencing of 60,000 samples to assess the risk of breast cancer through association with targeted genes. The design and size of the study requires an accurate, robust and high-throughput sequencing method. The investigators are using a digital DNA sequencing approach from QIAGEN that incorporates molecular barcodes to tag and remove PCR duplicates and increase NGS assay sensitivity. The approach also uses proprietary chemistry that enables uniform sequencing to efficiently utilize sequencing power and deliver optimized results.
The clinical application development and validation of cell free dna assays -...Candy Smellie
What is the impact of assay failure in your laboratory and how do you monitor for it?
In cancer patients, cell-free DNA carries tumour-related genetic alterations that are relevant to cancer development, disease progression and response to therapy.
Cell-free DNA detection allows:
Early detection
Frequent sampling
Monitoring of disease progression
Measure response to therapy
Detection of resistance mutation
Non-invasive diagnostic tool development
This document provides an overview of next generation sequencing (NGS), including its history, key methods, applications and challenges. It discusses that NGS allows for massively parallel sequencing of thousands of DNA molecules simultaneously, providing exact sequences of genes. Some main NGS platforms and their sequencing methods are described, such as Illumina sequencing by synthesis. Applications of NGS discussed include cancer research, pharmacogenetics and preimplantation genetic diagnosis. Challenges associated with NGS like poor quality FFPE samples and large data analysis workflows are also outlined.
Join Fight CRC in a webinar about biomarkers. In this session, Dr. Chris Lieu will focus the discussion on the NTRK biomarker, in addition to ctDNA, and Next-Generation Sequencing.
High Sensitivity Detection of Tumor Gene Mutations-v3Michael Powell
This document summarizes a new method called QClamp PCR that can highly sensitively detect tumor gene mutations. QClamp uses synthetic XNA probes to selectively block amplification of wild-type DNA sequences, improving the sensitivity of PCR to detect mutations present in less than 0.1% of samples. This level of sensitivity allows detection of mutations from biopsy, tissue, or blood samples. The document discusses applications of QClamp PCR for detection of EGFR mutations in lung cancer patients and enriching samples for DNA sequencing. QClamp represents an improvement over other methods by reducing the excess of wild-type DNA that creates high background signals.
Next-Generation Sequencing Clinical Research Milestones InfographicQIAGEN
DNA mutations have been implicated in several diseases, particularly cancer. NGS presents an ideal technology to efficiently profile the multitude of mutations in a high throughput manner. In 2001 the first draft of human genome was published. Since then many major milestones have been reached. Do you know when PIK3CA was identified in colon cancer? When was Olaparib for ovarian cancer treatment? This infographic traces the major clinical research milestones starting from the first draft of the human genome.
1) The document describes QClamp XNA-PCR, a technology from DiaCarta that uses molecular "clamps" to highly sensitively detect low frequency and cell-free circulating mutant DNA.
2) It needs assays that can detect biomarkers present at low frequency in samples containing a high amount of normal DNA. Existing technologies are inadequate for this need.
3) QClamp assays can reliably detect all possible mutations in a gene region using a single reaction. They can achieve ultra-high sensitivity down to 0.01% from minimal sample input.
Analysis of Single-Cell Sequencing Data by CLC/Ingenuity: Single Cell Analysi...QIAGEN
Single-cell analysis is useful to study genetic heterogeneity between individual cells and can help in result interpretation by looking at the average behavior of a large number of cells. Applications include circulating tumor cells, cells from small biopsies and cells from in vitro fertilized embryos. In this slidedeck, we show how single cell next-generation sequencing data can be analyzed and what challenges needs to be overcome. One of the examples we use is single cell data from two colorectal cancer cell lines.
Challenges and Opportunities for Digital PCR in the CLIA Laboratory of the Mo...Kate Barlow
Anthony Magliocco, Chair of Anatomical Pathology, Moffitt Cancer Center, USA
The Moffit Cancer Center is one of the largest NCI designated comprehensive free-standing cancer centers in the USA. The center has developed one of the most advanced personalized cancer medicine treatment programs in the world. This program is supported by a comprehensive and advanced CLIA molecular diagnostics. Digital PCR assays are currently being developed for several clinical applications including TKI resistance monitoring in patients with advanced lung cancer. The challenges and opportunities in deploying digital PCR into clinical practice will be discussed.
This document discusses accelerating genetic variant calling using hardware. It motivates this by noting that identifying genetic variants can help diagnose diseases and recommend treatments, but current algorithms take too long. It describes workflows for identifying germline and somatic variants using pairwise alignment and explains that the Pairwise Haplotype Mapping (PairHMM) computation is the most intensive part. Profiling shows PairHMM takes 70% of runtime. It proposes implementing PairHMM in hardware to accelerate variant calling.
Circulating cell free DNA is a potential tumor marker in a non-invasive blood test for the treatment and evaluation of cancer and recurrence monitoring. As circulating tumor DNA is often present at low frequencies within circulating cell free DNA, targeted sequencing on the Ion Torrent™ platform is an optimal tool or mutation detection with very little sample input required. Here, we demonstrate a complete workflow from isolation through molecular characterization of circulating tumor DNA. We have optimized a protocol using magnetic beads to isolate circulating cell free DNA. This protocol is easily automated to process up to 192 samples a day. It is also easily scalable for any input volume and can elute in volumes down to 15 μL resulting in no loss of low frequency alleles. We demonstrate comparable performance between this bead based isolation and column based isolation. We have completed molecular characterization of circulating cell free DNA using the multiplexing capabilities of AmpliSeq™ and the Ion PGM™. With the Ion AmpliSeq™ Cancer Hotspot Panel v2, we performed targeted sequencing of 50 genes of interest, covering 2800 COSMIC mutations. We demonstrate good reproducibility of amplicon representation as well as allelic frequencies. Through saturation studies and subsampling, we have determined the limit of detection of hotspots circulating cell free DNA on the Ion PGM™ to be below 1%. We further demonstrate proof of principle of this workflow on circulating cell free DNA and matched FFPE samples. Our results verify the accuracy and ease of our workflow. This protocol, from isolation through targeted sequencing, will not only result in a simple sample preparation for circulating cell free DNA but also facilitate rapid mutation detection to advance cancer research.
Translational Genomics and Prostate Cancer: Meet the NGS Experts Series Part 2QIAGEN
Advanced prostate cancer is highly heterogeneous but this inter-patient heterogeneity has until recently not been understood. We have through an international research effort dissected the molecular landscape of advanced castration resistant prostate, elucidating key molecular targets in this group of diseases. We have also shown that PARP inhibitors have antitumor activity against a significant proportion of these cancers, mainly in men whose cancers harbor DNA repair defects.
This slidedeck details two comprehensive informatics solutions — the Biomedical Genomics Workbench and Ingenuity Knowledge Base Variant Analysis platforms. We show the intuitive user interface of CLC Cancer Research Workbench and demonstrate how the rich biological content from Ingenuity Knowledge Base helps you rapidly identify critical variants in your samples.
CTC Detection and Molecular Characterization – Challenges and SolutionsQIAGEN
Circulating Tumor Cells (CTCs) have been extensively explored as circulating biomarkers in various cancers. Due to their rarity, heterogeneity and stem cell-like properties, detecting and profiling CTCs from blood samples is very challenging. In this webinar, Dr. Siegfried Hauch will introduce the well-known AdnaTests, which uses the Combination of Combinations Principle (COCP) to enable enriching and detecting CTCs in whole blood with high specificity and sensitivity, and how to overcome challenges in CTC enrichment and detection. The AdnaTests combine an immunomagnetic capturing method that increases purity, and is followed by molecular profiling of the captured CTCs. In addition, leukocyte contamination is another issue in CTCs detection and may lead to false positive results due to illegitimate expression of target genes or false interpretation. The AdnaWash is developed to reduce leukocyte contamination to such a level that whole gene panels can be analyzed while maintaining the required specificity and sensitivity.
Invicta eshre-poster-pregnancy rate after frozen blastocystINVICTA GENETICS
Assessment of pregnancy rate after comprehensive chromosome screening using next-generation sequencing-based preimplantation genetic diagnosis (NGS PGD) of trophectoderm in frozen blastocyst transfer.
C2 Reimbursement Perspectives on Precision MedicineEmilie Adams
This document summarizes a presentation on reimbursement perspectives for precision medicine. It discusses:
1) The promise of precision medicine in tailoring treatments to a patient's specific biomarkers or genetic profile, leading to better outcomes. Examples are given of targeted therapies approved for lung cancer subtypes.
2) Best practices from other countries in implementing precision medicine, such as France's national network of molecular testing centers to ensure equal access. Challenges discussed include getting the right test to the right patient at the right time for the right price.
3) Recommendations to optimize precision medicine in the future, such as establishing molecular testing programs and guidelines to help integrate testing into clinical practice and minimize delays in treatment. Time
Update on the Adoption and Utilization of Emerging Precision Medicine Biomark...Andrew Aijian
In this 2nd wave of our precision oncology pulse survey, we explore how recent clinical, commercial, and regulatory events have impacted the adoption of emerging precision oncology biomarkers and diagnostic tools. We also examine the key technological trends likely to impact the landscape in the near-mid term.
Personalized Medicine Through Tumor SequencingGolden Helix
One of the main recent advances in cancer therapy is the identification of medications that target specific gene mutations. In 2001 Gleevec was approved to treat patients with the BCR-ABL fusion in chronic myelogenous leukemia (CML), but since then many more drugs have been developed. Currently, there are numerous ongoing trials to identify tumor drivers that can be attacked by a drug. In order to identify the mutations driving a tumor, the tumor needs to be sequenced. There are a range of different approaches for sequencing tumors ranging from the sequencing of a few genes in the tumor up to paired whole-exome sequencing in both the tumor and adjacent normal tissue. Each type of sequencing has benefits and drawbacks and a balance needs to be made between cost and usability of the results. We have developed a clinical workflow for a 50 gene panel that identifies mutations in hotspots in known cancer genes. This workflow uses BaseSpace, VarSeq and N-Of-One to provide insight for our physicians and patients.
Jeffrey Rosenfeld described his work using tumor sequencing to personalize cancer treatment. His lab uses a targeted sequencing panel to identify driver mutations in tumors, then filters variants using software like VarSeq. Potentially actionable mutations are evaluated using databases like N-Of-One and discussed at molecular tumor boards to guide treatment. Integrating sequencing results into clinical decision making and research databases allows improving outcomes for patients.
Mapping Treatment and Diagnostic Costs of key tumour types and positioning of...Dhaval Vaghela
The document provides an overview of a presentation mapping treatment and diagnostic costs for various tumor types and positioning of a Cancer Genomics Test. It discusses objectives to evaluate if the Cancer Genomics test can replace conventional diagnostic tests and study associated cost benefits. It outlines tumor types covered, current diagnostic scenario, methodology for collecting treatment cost and diagnostic test cost data from Mumbai hospitals, insights from doctors, costs of cytogenetic and chemotherapy regimens, details of the Cancer Genomics Test, recommendations and data/tables presented.
Next Generation Companion Diagnostics; Adoption, Drivers, and Moderators of N...Andrew Aijian
Analysis and synthesis of a pulse survey conducted across >140 oncologists, pathologists, and lab directors regarding current adoption and trends associated with emerging oncology biomarkers and companion diagnostics (CDx), with an emphasis on next-generation sequencing (NGS)-based CDx.
Ομιλία - Παρουσίαση: “Βιοδείκτες: Η Κλινική τους Αξία και η Σχέση τους με τον ΕΟΠΥΥ”
Νικόλαος Τσούλος, MSc, MBA, Βιοχημικός, Διευθύνων Σύμβουλος GeneKor Medical SA
Development and Clinical Validation of Liquid ddPCR Tests for Actionable Soma...Kate Barlow
We have developed and validated blood-based variant specific ddPCR tests for EGFR, KRAS, BRAF, EML4-ALK, ROS1 and RET variants. These tests are intended for use in patients diagnosed with Non-Small Cell Lung Cancer (NSCLC). The tests have been on the market as ”the GeneStrat® test” since 2015; and in that time, has been utilized to analyze over 80,000 individual variants. Greater than 90% of tests have been delivered in less than 72 hours from receipt at the testing Laboratory. We will report on factors critical to the development, validation and on-market support of these tests. In this talk we will cover:
• Learning how Droplet Digital ™ PCR technology is being used for liquid biopsy testing in the clinical setting
• Reviewing development and validation case studies for cfDNA testing using ddPCR
• Reviewing performance data and quality metrics from on-market experiences
Gary Pestano, Vice President, Development and Operations, Biodesix
A biomarker strategy aims to answer key clinical questions to support drug development through identifying and testing biomarkers. Developing a robust biomarker strategy can mitigate risks and inform clinical study design by generating testable hypotheses to bridge pre-clinical and clinical research. Effective biomarker strategies consider assay suitability, study design, and sample availability to reliably detect biomarkers and provide statistically meaningful results. Emerging technologies allow deeper interrogation of drugs and disease through multiplexed readouts to enhance biomarker discovery and clinical development.
This document discusses specimen handling and biomarker testing for non-small cell lung cancer. It emphasizes the importance of proper specimen handling and fixation to ensure accurate biomarker results. Key drivers of lung adenocarcinoma are discussed, including mutations in KRAS, EGFR, ALK, and other genes. The biomarker testing process requires multidisciplinary collaboration between pulmonologists, pathologists, oncologists, and other specialists to ensure timely and successful testing that guides personalized treatment selection.
What can we learn from oncologists? A survey of molecular testing patternsThermo Fisher Scientific
Oncologists are increasingly incorporating NGS testing to guide targeted and immuno-oncology therapies1. Most clinical NGS testing is confined to large academic institutions and reference labs, despite the fact that most cancer patients are treated in the community settings. We therefore sought to examine molecular testing selection patterns directly from oncologists in order to better identify perceived gaps in testing and treatment paradigms
Chair, Alexander Drilon, MD, prepared useful Practice Aids pertaining to NSCLC for this CME/MOC/NCPD/AAPA activity titled “Selective, Potent, Different: How to Enhance Clinical Benefits With Next-Generation ROS1 and TRK Inhibition in Treatment-Naïve and Pretreated NSCLC and Other Tumors.” For the full presentation, downloadable Practice Aids, and complete CME/MOC/NCPD/AAPA information, and to apply for credit, please visit us at https://bit.ly/44fbxRs. CME/MOC/NCPD/AAPA credit will be available until August 8, 2024.
di Pier Giuseppe Pelicci, MD-PhD, Istituto Europeo di Oncologia IEO, Università degli Studi di Milano.
Slide per l'intervento tenuto in Fondazione Giannino Bassetti in occasione del primo incontro del ciclo "La medicina di precisione", primo progetto dalla convenzione tra Università di Pavia e Fondazione Bassetti.
12 marzo 2018
Alexander Drilon, MD, and Benjamin Levy, MD, prepared useful practice aids pertaining to precision management of lung cancer for this CME/MOC/CC/CNE activity titled, "Improving Outcomes in Patients With Molecularly Altered NSCLC Through Broad Implementation of Precision Testing and Treatment: Latest Evidence and Practical Guidance in the Context of a Changing Targeted Therapy Landscape." For the full presentation, monograph, complete CME/MOC/CC/CNE information, and to apply for credit, please visit us at http://bit.ly/2ZX2KTt. CME/MOC/CC/CNE credit will be available until April 29, 2021.
Chair, Nathan A. Pennell, MD, PhD, FASCO, and Laura J. Tafe, MD, prepared useful Practice Aids pertaining to NSCLC for this CME/MOC/CC/NCPD/CPE/IPCE activity titled “Fine-Tuning Biomarker Testing to Identify and Target RET Fusions as Uncommon But Actionable Genomic Alterations in NSCLC.” For the full presentation, downloadable Practice Aids, and complete CME/MOC/CC/NCPD/CPE/IPCE information, and to apply for credit, please visit us at https://bit.ly/3fwhuok. CME/MOC/CC/NCPD/CPE/IPCE credit will be available until January 29, 2024.
multi-sDNA versus faecal immunochemical testingRamezAntakia1
This study compared the performance of a multitarget stool DNA test (MT-sDNA) versus a fecal immunochemical test (FIT) for colorectal cancer screening in an average-risk population. MT-sDNA had higher sensitivity than FIT for detecting colorectal cancer and advanced precancerous lesions, but lower specificity. Using a fixed specificity of 95%, MT-sDNA sensitivity was higher than FIT for detecting cancers and advanced lesions. While neither test was more sensitive for detecting specific lesion characteristics, MT-sDNA and FIT may provide complementary benefits when used together for colorectal cancer screening.
Biomarkers and biomarker testing are changing the way some colorectal cancer is treated and knowing your biomarkers can help your doctors identify your best treatment options and help you in making well informed decisions about how your cancer will be treated allowing you to be your own best advocate.
Join in on this informative webinar with guest Dr. Christopher Lieu from the University of Colorado Cancer Center, as he discusses everything you need to know about biomarkers.
Question of Quality Conference 2016 - Personalized Cancer MedicineHCA Healthcare UK
This document summarizes a presentation on personalized cancer medicine. It discusses:
1. A brief history of precision oncology, from identifying the Philadelphia chromosome in 1960 to recent advances in immunotherapy.
2. The concept of driver mutations that directly or indirectly confer growth advantages to cancer cells and have clinical implications for diagnosis, prognosis, or targeted therapies.
3. How next-generation sequencing can best identify all four classes of genomic alterations that drive tumor growth by sequencing both DNA and RNA.
4. Some case histories where genomic profiling identified targetable alterations and patients benefited from matched targeted therapies.
5. Concluding thoughts on the complexity of the cancer genome and how comprehensive genomic profiling is enabling evidence-based
Tariq Mughal discusses personalized cancer medicine and highlights some key points:
1. Precision medicine has evolved greatly over the past few decades from basic cytogenetics and hormone therapies to comprehensive genomic profiling and immunotherapy. Targeted therapies are revolutionizing cancer treatment.
2. Driver mutations directly or indirectly confer a growth advantage to cancer cells and have clinical implications for diagnosis, prognosis, and targeted therapies. Comprehensive genomic profiling using next-generation sequencing can best identify all classes of driver mutations.
3. Case histories demonstrate how genomic profiling can identify targetable genomic alterations like ERBB2 mutations, ALK fusions, and FBXW7 mutations and guide treatment with targeted therapies, often with dramatic responses
This document summarizes the story of Ted Taylor, a glioblastoma patient who was given a terminal diagnosis but found an effective targeted therapy called Vitrakvi after extensive research. Vitrakvi targets NTRK fusions and Ted tested positive for this biomarker. He worked with his oncologists to gain access to Vitrakvi from Canada and the US. While on Vitrakvi, Ted has experienced significant tumor shrinkage with minimal side effects compared to standard chemotherapy. He hopes to help other patients advocate for themselves to find effective targeted therapies.
Similar to Benefits of Genomic Profiling Infographic (20)
Local Advanced Lung Cancer: Artificial Intelligence, Synergetics, Complex Sys...Oleg Kshivets
Overall life span (LS) was 1671.7±1721.6 days and cumulative 5YS reached 62.4%, 10 years – 50.4%, 20 years – 44.6%. 94 LCP lived more than 5 years without cancer (LS=2958.6±1723.6 days), 22 – more than 10 years (LS=5571±1841.8 days). 67 LCP died because of LC (LS=471.9±344 days). AT significantly improved 5YS (68% vs. 53.7%) (P=0.028 by log-rank test). Cox modeling displayed that 5YS of LCP significantly depended on: N0-N12, T3-4, blood cell circuit, cell ratio factors (ratio between cancer cells-CC and blood cells subpopulations), LC cell dynamics, recalcification time, heparin tolerance, prothrombin index, protein, AT, procedure type (P=0.000-0.031). Neural networks, genetic algorithm selection and bootstrap simulation revealed relationships between 5YS and N0-12 (rank=1), thrombocytes/CC (rank=2), segmented neutrophils/CC (3), eosinophils/CC (4), erythrocytes/CC (5), healthy cells/CC (6), lymphocytes/CC (7), stick neutrophils/CC (8), leucocytes/CC (9), monocytes/CC (10). Correct prediction of 5YS was 100% by neural networks computing (error=0.000; area under ROC curve=1.0).
Cell Therapy Expansion and Challenges in Autoimmune DiseaseHealth Advances
There is increasing confidence that cell therapies will soon play a role in the treatment of autoimmune disorders, but the extent of this impact remains to be seen. Early readouts on autologous CAR-Ts in lupus are encouraging, but manufacturing and cost limitations are likely to restrict access to highly refractory patients. Allogeneic CAR-Ts have the potential to broaden access to earlier lines of treatment due to their inherent cost benefits, however they will need to demonstrate comparable or improved efficacy to established modalities.
In addition to infrastructure and capacity constraints, CAR-Ts face a very different risk-benefit dynamic in autoimmune compared to oncology, highlighting the need for tolerable therapies with low adverse event risk. CAR-NK and Treg-based therapies are also being developed in certain autoimmune disorders and may demonstrate favorable safety profiles. Several novel non-cell therapies such as bispecific antibodies, nanobodies, and RNAi drugs, may also offer future alternative competitive solutions with variable value propositions.
Widespread adoption of cell therapies will not only require strong efficacy and safety data, but also adapted pricing and access strategies. At oncology-based price points, CAR-Ts are unlikely to achieve broad market access in autoimmune disorders, with eligible patient populations that are potentially orders of magnitude greater than the number of currently addressable cancer patients. Developers have made strides towards reducing cell therapy COGS while improving manufacturing efficiency, but payors will inevitably restrict access until more sustainable pricing is achieved.
Despite these headwinds, industry leaders and investors remain confident that cell therapies are poised to address significant unmet need in patients suffering from autoimmune disorders. However, the extent of this impact on the treatment landscape remains to be seen, as the industry rapidly approaches an inflection point.
Integrating Ayurveda into Parkinson’s Management: A Holistic ApproachAyurveda ForAll
Explore the benefits of combining Ayurveda with conventional Parkinson's treatments. Learn how a holistic approach can manage symptoms, enhance well-being, and balance body energies. Discover the steps to safely integrate Ayurvedic practices into your Parkinson’s care plan, including expert guidance on diet, herbal remedies, and lifestyle modifications.
Muktapishti is a traditional Ayurvedic preparation made from Shoditha Mukta (Purified Pearl), is believed to help regulate thyroid function and reduce symptoms of hyperthyroidism due to its cooling and balancing properties. Clinical evidence on its efficacy remains limited, necessitating further research to validate its therapeutic benefits.
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Our backs are like superheroes, holding us up and helping us move around. But sometimes, even superheroes can get hurt. That’s where slip discs come in.
- Video recording of this lecture in English language: https://youtu.be/kqbnxVAZs-0
- Video recording of this lecture in Arabic language: https://youtu.be/SINlygW1Mpc
- Link to download the book free: https://nephrotube.blogspot.com/p/nephrotube-nephrology-books.html
- Link to NephroTube website: www.NephroTube.com
- Link to NephroTube social media accounts: https://nephrotube.blogspot.com/p/join-nephrotube-on-social-media.html
One health condition that is becoming more common day by day is diabetes.
According to research conducted by the National Family Health Survey of India, diabetic cases show a projection which might increase to 10.4% by 2030.
Osteoporosis - Definition , Evaluation and Management .pdfJim Jacob Roy
Osteoporosis is an increasing cause of morbidity among the elderly.
In this document , a brief outline of osteoporosis is given , including the risk factors of osteoporosis fractures , the indications for testing bone mineral density and the management of osteoporosis
Adhd Medication Shortage Uk - trinexpharmacy.comreignlana06
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