Join us to learn more about current topics in science focused in the NGS area. All webinars are recorded and accessible through the links provided below. As the list of offering expands, please visit our Events section for a full listing.
We welcome your comments and suggestions; contact us or call +1.734.677.4845.
“NGS Library Preparation with Unique Molecular Tags Simplified with ThruPLEX® Tag-seq,” September 14, 2016 10:00 AM EST
- How UMTs are incorporated into the libraries using ThruPLEX technology
- Specific features of the ThruPLEX Tag-seq kit
- Data analysis using Curio bioinformatics platform
- Performance of ThruPLEX Tag-seq in detecting low-frequency variants when paired with hybrid capture technologies
“The Use of Cell-free DNA in Monitoring Prostate Cancer,” May 19th, 2016 10:00 AM EST
Join Dr. Liang Wang from the Medical College of Wisconsin as he discusses the potential clinical use of cell-free (cfDNA) from urine in predicting treatment response and monitoring disease progression in prostate cancer patients. Using cfDNA libraries created with ThruPLEX® DNA-seq, Dr. Wang has identified tumor-associated CNVs and developed an algorithm to estimate tumor burden in cancer patients.
• The technology behind ThruPLEX
• Performance and workflow advantages of ThruPLEX DNA-seq
• The use of urine to detect CNVs in advanced prostate cancer patients
Presented by Dr. Liang Wang, Medical College of Wisconsin
“Single-cell Sequencing to Study Somatic Mosaicism in the Human Brain using PicoPLEX DNA-seq Kit,” March 23rd, 2016 1:00 PM EST
Join Dr. Mike McConnell from the University of Virginia School of Medicine as he discusses how his lab uses single-cell genomic approaches to map DNA copy number variation (CNV) in neurons. Using these approaches he has identified aneuploidies and subchromosomal CNVs in neurons, and has found that mosaic copy number variation is abundant in human neurons.
- The technology behind PicoPLEX
- Performance and workflow advantages of PicoPLEX DNA-seq
- The use of single-cell sequencing to investigate the effects of genetic differences in individual brain cells
- Application of PicoPLEX DNA-seq to examine somatic mosaicism in the human brain
Presented by Dr. Mike McConnell, University of Virginia School of Medicine
“An Introduction to Cell-free DNA libraries created with ThruPLEX Plasma-seq,” September 17th, 2015, 1:00 PM EST
Liquid biopsies contain cell-free DNA (cfDNA) that is found circulating in blood and isolated to the plasma component. It has been the subject of renewed attention in the scientific community recently due to easy access to genetic information that can be obtained by next generation sequencing. Two areas where cfDNA sequencing is being used are oncology and NIPT. Circulating tumor DNA (ctDNA) derived from malignant tumors is often found within the cfDNA, and changes in quantity and composition during progression, treatment, and development of drug resistance. Sequencing of cfDNA is now being evaluated as a way to monitor the genetic evolution of metastatic cancers in response to therapy. Another use of cfDNA involves detecting fetal chromosomal aneuploidy and other abnormalities in the plasma isolated from pregnant women. Development of assays utilizing cfDNA could eliminate more invasive procedures such as amniocentesis.
Rubicon Genomics has recently developed a library preparation kit, ThruPLEX® Plasma-seq, that is optimized specifically for cfDNA at input levels from less than 1 ng to 30 ng. This new member of the ThruPLEX product line is capable of transforming cfDNA into high complexity libraries for Illumina® NGS platforms. The three-step single-tube workflow yields indexed libraries from purified cfDNA within 2 hours.
- The use of cell-free DNA in research involving oncology and the fetal fraction of maternal plasma
- ThruPLEX technology and changes that impacted performance with cfDNA
- Creation of a library with ThruPLEX Plasma-seq
- Target enrichment with ThruPLEX Plasma-seq libraries
Presented by Dr. Kamran Shazand, Director of Applications at Rubicon Genomics
“The Use of ThruPLEX® DNA-seq Kit for ChIP-seq from Small Numbers of Cells,” March 11, 2015, 12:00 PM EST
The most informative tool for studying DNA-protein interactions genome-wide with high resolution is chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq). This method typically requires a large number of cells (1-20 million) as starting material, preventing its application in samples where a large number of cells is unobtainable, such as with mammalian preimplantation embryos. Dr. Pablo Ross has recently used ThruPLEX® DNA-seq Kit to perform ChIP-seq from low cell numbers (10,000 bovine fibroblast). This low cell number protocol was compared to ChIP-seq performed under standard conditions (10 million bovine fibroblasts). Results demonstrating the potential of ThruPLEX DNA-seq Kit for epigenetic profiling of challenging samples will be shown.
- Properties of ThruPLEX DNA-seq Kit
- ChIP-seq protocol with low cell numbers
- Application of technology with bovine preimplantation embryo cells
Presented by Dr. Pablo Ross, Assistant Professor of Animal Science at UC Davis
“Enrichment of cfDNA from Plasma for Next Generation Sequencing,” November 18, 2014, 10:00 AM EST
Cell-free (cf) DNA, found in plasma, is associated with various medical conditions and has been proposed as a non-invasive diagnostic tool. Recent publications* have provided proof of principle of valuable ways in which cfDNA can be used as a research tool for cancer screening and management. Since the amount of cfDNA in plasma is limited, efficient protocols for creation of the NGS libraries and enrichment for coding sequences are critical.
In this webinar, we will demonstrate how to create high quality WES libraries from as little as sub-nanogram amounts of patient plasma DNA.
- Purification of cfDNA from plasma
- Creation of libraries with ThruPLEX® DNA-seq kit from the purified cfDNA
- Protocols adapted for enriching coding sequences from ThruPLEX libraries
- Results obtained from sequencing the libraries
Presented by Dr. J.P. Jerome, Applications Scientist, Rubicon Genomics
To request a copy of the presentation slides click here.
“Target Enrichment for Illumina NGS Platforms,” May 6th, 2014
As exome capture emerges as one of the most widely used application in NGS, Rubicon Genomics is pleased to present a webinar on the basics of the application and detail how to use libraries prepared with ThruPLEX®-FD Prep Kits with several enrichment technologies.
• ThruPLEX technology
• Basics of target enrichment
• Enrichment technologies and protocols:
Roche Nimblegen® SeqCap®
• ThruPLEX-FD libraries for target enrichment:
Comparative sequencing data
Presented by Dr. Kamran Shazand, Director of Applications, Rubicon Genomics.
Protocols for enrichment are available here.
“PicoPLEX™ DNA-seq: Single Cell Sequencing, Theory and Applications,” February 19, 2014
PicoPLEX™ WGA has become the gold standard for preimplantation genetic screening and diagnostics (PGS/PGD) to detect aneuploidy and single-gene disorders of single human reproductive cells using microarray and PCR assays. Rubicon Genomics now introduces the PicoPLEX™ DNA-seq single cell library preparation kit for Illumina NGS platforms. This kit is the fastest and most reproducible method to sequence single reproductive or tumor cells for aneuploidy and CNV detection. In addition, PicoPLEX DNA-seq has found applications in de novo sequencing of single microdissected chromosomes.
- Advantages in performance and workflow of PicoPLEX DNA-seq
- Applications of PicoPLEX DNA-seq for de novo sequencing of single amphibian chromosomes by Jeramiah Smith, Ph.D.
- Applications of PicoPLEX DNA-seq for aneuploidy, CNV, and STR testing of single human cancer and reproductive cells by John Langmore
Presented by Dr. Jeramiah Smith, Assistant Professor of Biology at the University of Kentucky with Dr. John Langmore, Co-Founder and Chief Scientific Officer, Rubicon Genomics.
“Pan-Microbial Diagnosis & Discovery Using Next-Generation Sequencing,” October 9, 2013
Unbiased next-generation sequencing (NGS) of clinical research samples is a powerful tool for pathogen detection and discovery, with numerous applications including: direct infectious disease diagnosis, blood bank surveillance, unknown outbreak investigation, and pathogen discovery. Short reads from clinical samples can be identified and assembled to diagnose the presence of known pathogens. In addition, this “open,” primer-independent technology enables discovery and reconstruction of novel infectious agents. Because all microbes except prions contain DNA and/or RNA, the full spectrum of disease-causing viruses, bacteria, fungi, and parasites can be readily identified in a single assay.
- Development and validation of a real-time NGS assay for pan-microbial diagnosis with sensitivity to 10-100 viral copies per mL with less than 24 hour turnaround from sample to answer
- Rapid data analysis with the use of cloud-compatible bioinformatics pipelines
- Examples of the impact of NGS for microbial identification in clinical and public health settings
Presented by Dr. Charles Chiu, Asst. Professor of Laboratory Medicine & Medicine, Infectious Diseases, UCSF; Director of the UCSF-Abbott Viral Diagnostics & Discovery Center, UCSF China Basin; and Associate Director, USCF Clinical Microbiology Laboratory.
“RNA-Seq and Microarray Libraries for Expression Analysis of FFPE and Frozen Tissues,” July 30, 2013.
The Rubicon TransPLEX® WTA Kit is used for ultra-sensitive and robust expression analysis of fresh and frozen tissue in research and clinical testing using arrays and PCR. The ThruPLEX™-FD Kit for Illumina Next Gen library construction is used for WGS, WES, ChIP and other DNA-seq applications, specifically for low input DNA amounts as well as challenging samples such as FFPE tissue. We will show how to simplify the RNA-seq process using two products that are geared towards sensitivity: Rubicon’s ThruPLEX technologies and Clontech’s SMARTer® cDNA synthesis kits for NGS.
- Key features of TransPLEX for expression analysis
- Key features of ThruPLEX for DNA-seq of fragmented DNA
- Principles of using ThruPLEX for RNA-seq
- Clontech SMARTer technology products optimized for maximum performance of RNA-seq from low input samples
The audience will gain a better understanding of a range of improved expression analysis tools for array and NGS applications.
Presented by Dr. John P. Langmore, Co-Founder and Chief Scientific Officer, Rubicon Genomics with special guest, Dr. Magnolia Bostick, Scientist in Molecular Biology, Clontech Laboratories.
“Advancing Gold Standard for Single-Cell Aneuploidy, CNV and Mutations into the Next-Gen Era,” May 1, 2013.
PicoPLEX-WGA has become the gold standard for diagnostic aneuploidy and mutation testing of single human sperm, polar bodies, and blastomeres, and is now deployed worldwide in 90% of IVF genetic testing. Rubicon is developing PicoPLEX-scD, which is designed to make single-cell NGS libraries for the Illumina and LifeTechnologies platforms.
- Tools available for single-cell genomic DNA analysis
- Challenges for single cell testing
- Genetic analytes for single-cell preimplantation, prenatal, and cancer testing
- The clinical record of PicoPLEX WGA in detection of aneuploidy and single-gene disorders in IVF cases
- Preliminary NGS results using PicoPLEX-scD for single cell genetic studies.
Audience members will gain a better understanding of the rapidly changing challenges and solutions to single-cell genetics.
Presented by Dr. John P. Langmore, Co-Founder and Chief Scientific Officer, Rubicon Genomics
“What’s Next in Next-Generation Sequencing?”
Hosted by The Scientist and sponsored by Rubicon, March 5, 2013.
The advent of next-generation sequencing is considered the most disruptive technological advance, as it has resulted in the doubling of sequence data almost every 5 months and the precipitous drop in the cost of sequencing a DNA base. The first webinar to be conducted in March will track the evolution of next-generation sequencing (NGS) and what the future holds in terms of the technology and its applications. Following brief presentations given by our panel of experts, there will be a live Q&A session where attendees can ask questions and discuss NGS-related challenges they are facing in their laboratories.
• How NGS has evolved over the years
• Current limitations with the technology
• Challenges with data storage and analysis
• What the future holds for NGS
The Future of NGS for Open Access Genome and Trait Data
- Dr. George Church, Professor, Department of Genetics, Harvard Medical School
Next-Generation Microbiology and Infectious Disease Research
- Dr. George Weinstock, Professor of Genetics and Molecular Microbiology, Washington University
The Future of NGS for Systems Medicine and Multiscale Biology
- Dr. Joel Dudley, Assistant Professor of Genetics and Genomic Sciences and Director of Biomedical Informatics, Mount Sinai School of Medicine
“Challenges and Solutions for Sequencing Clinical Samples” October 30, 2012.
NGS has dramatically reduced the time and cost of sequencing DNA, creating an explosion of new research and clinical applications that depend on sequencing. In spite of this success, clinical samples such as FFPE, plasma, and single cell DNA are difficult to prepare for NGS. This webinar presentation will explain why these samples are challenging, identify the shortcomings of the first-generation NGS preps, and discuss how new technologies are removing the NGS sample preparation barrier.
Presented by Dr. John P. Langmore, Co-Founder and Chief Scientific Officer, Rubicon Genomics