Roche Sequencing at the ABRF 2021 Virtual Annual Meeting

Roche Sequencing at the ABRF 2021 Virtual Annual Meeting

Our team is looking forward to virtually connecting with you at the ABRF Annual Meeting this year.  We will be featuring NGS workflow solutions for Library Preparation, including RNA-seq library prep automation, Target Enrichment and more:

Featured Workflow Solutions

  • Library preparation (DNA, RNA & custom kits)
  • Automation for RNA-seq library prep 
  • KAPA Target Enrichment (exome and custom)

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KAPA SARS-CoV-2 Target Enrichment Panel

  • Detect diverse variants during surveillance testing
  • Achieve 1X coverage of >97% of the SARS-CoV-2 genome down to 1000 viral copies
  • Further increase SARS-CoV-2 coverage by removing rRNA from input samples

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Scientific Poster

Check out our virtual poster in the ABRF poster hall:

Analyzing the SARS-CoV-2 genome with target enriched RNA-seq

Authors:
Sarah Trusiak1, Jonathan Nowacki1, Ranjit Kumar1, Spencer Debenport1
1Roche Sequencing & Life. Science, Wilmington, MA

Abstract:
Since the emergence of the SARS-CoV-2 and its resulting disease, COVID-19, over 30 million people have been infected worldwide and over 900,000 people have died. Many research programs have pivoted to studying the virus and understanding its health impacts and disease complications to develop treatments. RNA sequencing (RNA-seq) is a high-throughput method that enables research into the host’s transcriptional response to viral infection and the RNA genome of the virus itself; this is critical for understanding the impact of new viral mutations and emerging strains. Samples from infected hosts typically contain a single SARS-CoV-2 strain, while environmental samples like soil and sewage often contain a mixture of strains. When studying the RNA genome of viruses in mixed-RNA samples, such as total RNA from a human host, it is necessary to enrich for the viral RNA molecules above the much-more-abundant background RNA. Hybridization-based target enrichment (TE) using well-designed probes complementary to viral sequences has the potential to isolate and greatly enrich for viral reads of interest, and enable the capture of diverse viral strain mutations with a single TE panel, providing insights into the distribution and evolution of the virus. To enable hybridization capture RNA-seq for SARS-CoV-2 genome sequencing, we have developed a KAPA SARS-CoV-2 Target Enrichment Panel and workflow. Our probe panel covers 100% of the SARS-CoV-2 reference genome and >99.7% of 184 publicly available SARS-CoV-2 sequences (NCBI). Using this panel, we have developed a new target-enriched RNA-seq workflow that incorporates the KAPA SARS-CoV-2 Target Enrichment Panel into a modified version of the HyperCap Workflow v3 and includes the KAPA RNA HyperPrep Kit. In order to determine the lowest viral load that yields full coverage of the SARS-CoV-2 genome using this workflow, we tested varying levels of viral genome copies in different amounts of human total RNA. We show here that the KAPA SARS-CoV-2 Target Enrichment Panel detects mutations from six different strains of SARS-CoV-2 within a single target enrichment reaction. We also present a single-day target enrichment workflow with hybridization times as short as one hour. We conclude that this panel, when used with the modified HyperCap Workflow v3 adapted for RNA-seq, is a powerful tool for studying the SARS-CoV-2 genome in both infected host samples and samples containing mixed viral strains, and for distinguishing between multiple strains in a single sample.

Breakout Session

Short Talk: Analyzing the SARS-CoV-2 genome with target enriched RNA-seq

Date:          Thursday, March 11, 2021 
Time:          3:00 PM – 4:00 (EST)
Duration:   10-minute presentation
Session:    New Technologies in Genomics & Imaging

Abstract:   
RNA-seq with hybridization-based target enrichment (TE) enables high-throughput genome studies of RNA viruses such as SARS-CoV-2, which are critical for discovering new viral mutations and tracking strain transmission. We have developed a KAPA SARS-CoV-2 Target Enrichment Panel and workflow for SARS-CoV-2 genome sequencing. In this presentation, we discuss the performance of this panel on samples with varying levels of SARS-CoV-2 RNA in human total RNA. We also present a single-day target enrichment workflow with hybridization times as short as one hour. Finally, we will show that the KAPA SARS-CoV-2 Target Enrichment Panel can detect mutations from different strains of SARS-CoV-2 within a single reaction.

Sarah Trusiak, PhD
Senior Applications Scientist, Roche Sequencing and Life Science
Dr. Trusiak holds a Ph.D. in genetics and genomics from the University of Connecticut. She has spent the past ten years working in NGS, applying and developing NGS technology in academic and industry settings.

Featured Products

KAPA Library Prep (RNA, DNA and custom kits)

  • KAPA RNA HyperPrep Kit portfolio for RNA library prep provides single-day, single-tube library preparation, yielding high performance libraries even from low-input and degraded samples. The versatile portfolio includes solutions for mRNA enrichment, rRNA depletion, globin depletion, and custom depletion of other high-expressors.
  • KAPA HyperPrep Kit and HyperPlus Kit for DNA library prep offers high performance with whole-genome and targeted sequencing, PCR-free workflows with HyperPrep, and high-quality data, even from low-quality samples.
  • Solutions for custom library prep. If your moderate- to high-throughput library preparation workflows would be enhanced by library kit customization, reach out to our team of Genome Specialists so we can find the right solution to meet your needs.

Automate RNA-seq library preparation

Library prep automation improves results and saves time with:
  • Reduced hands-on time
  • Increased consistency of pipetting 
  • Greater opportunities for workflow standardization
Validated scripts are available for KAPA RNA HyperPrep Kits for many liquid handling instruments.
 
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Automate RNA-seq library preparation

KAPA Target Enrichment

  • KAPA Target Enrichment probes, produced using KAPA HiFi in a new manufacturing process but built on more than a decade's experience in probe design and deployment for hybrid capture
  • KAPA HyperExome, a comprehensive-yet-compact panel for sensitive, reliable exome sequencing; includes 387 sample-tracking SNPs
  • KAPA HyperChoice and KAPA HyperExplore, custom panels for targeting regions specific to your research
  • KAPA HyperCap Workflow v3, a fast, automation-friendly targeted NGS library preparation workflow

 

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