Roche at the 13th Annual CGC Meeting

St. Louis, MO

July 31st - Aug 3rd

 

Roche at the 13th Annual CGC Meeting

We are looking forward to meeting you in St. Louis for the CGC 2022 Annual Meeting. It's been a while since we have been able to meet in person, and we can't wait to show you what we've added to our NGS workflow.  We'll be featuring a talk on our AVENIO Tumor Tissue CGP kit, posters featuring our KAPA HyperPETE workflow and NGS automation methods. Stop by our booth to learn about our new solutions or to let us know what you've been working on.

Conference Location: Marriott St. Louis Grand Hotel, St. Louis, MO

Conference Dates: July 31st - Aug 3rd, 2022

Roche Booth: 14

Booth Hours: 

  • Sun, July 31: 3:50 – 4:30pm & 7:00 – 9:00pm

  • Mon, August 1: 10:30 – 11:15am,  12:50 – 1:45pm, 4:00 – 4:40pm & 6:15 – 7:45pm

  • Tues, August 2: 10:30 – 11:15am, 12:50 – 2:00pm & 4:00 – 4:45pm

  • Wed, August 3: 10:45 – 11:30am

25 Minute Vendor Showcase | General Session

Evaluation of the AVENIO Tumor Tissue Comprehensive Genomic Profiling (CGP) Kit

Date:          Wednesday, August 3rd
Time:          11:35am - 12:00pm
Duration:    25 minutes

This presentation will include:

  • Introduction to AVENIO Tumor Tissue CGP Kit
  • Study overview and methodology
  • Review of agreement results between AVENIO Tumor Tissue CGP Kit and FoundationOne®CDx (F1CDx)

Speaker: Stephanie Yaung, PhD
Director, Bioinformatics
Roche Sequencing Solutions

Scientific Poster

Authors: ENitya Furtado¹*, Florence Crary-Dooley¹*, Mingyang Cai¹*, Brian Godwin¹, Liu Xi¹, Jimmy Tu¹, Liesl Joubert², Marius Snyman², Mariana Fitarelli-Kiehl³, Spencer Debenport³, and Jingchuan Li¹

¹ Roche Sequencing Solutions, Pleasanton, CA 94588, ² Roche Sequencing Solutions, Cape Town, South Africa 7925, ³ Roche Sequencing & Life Science, Wilmington, MA, USA, *co-first authors


Abstract:  
KAPAHyperPETE (Primer Extension Target Enrichment) is a novel target enrichment solution newly launched by Roche, which employs primer extension reactions to specifically capture and release target library molecules for sequencing. It offers the simplicity and speed of amplicon-based workflows and the high performance of hybridization-based capture. KAPA HyperPETE is a single day workflow that demonstrates high coverage uniformity and detects all major somatic variant types (SNV, InDel, CNV, MSI status, and novel fusion transcript partners).

Pre-capture multiplex pooling is an established approach in capture-based target enrichment methods to decrease the number of sample reaction tubes handled during enrichment steps. While pre-capture multiplex pooling reduces the reagent cost and hands-on time when processing many samples, it is understood that enrichment performance can be impacted. These performance losses are usually minimal when detecting heterozygous and homozygous SNPs or InDels while using high quality genomic DNA, but can potentially be problematic when detecting somatic variants of less than 5% allele frequency. This can be compounded by the use of low quality and/or low nucleic acid input amounts commonly derived from oncology samples. 

We optimized pre-capture multiplexing conditions for oncology samples in the Tissue DNA, Tissue RNA, and Plasma cfDNA enrichment workflows. The results demonstrate sequencing performance metrics and variant calling results comparable to single-plex capture. KAPA HyperPETE Workflow with pre-capture multiplexing improves turnaround time, optimizes cost, and increases the number of samples that can be processed simultaneously while retaining high performance.

The KAPA HyperPETE pre-capture multiplexing is not yet an officially supported protocol in somatic oncology research applications.

Presenter: Emma White, Automation Scientist NGS, Roche Diagnostics, Wilmington, MA 01887
Co-Authors: Joshua Tjokrosurjo1*, Marsha McMakin1, Rachel Kasinskas1, Nicole Madamba2, Dawn Obermoeller2
1Roche Diagnostics, 200 Ballardvale St #250, Wilmington, MA 01887 
2Perkin Elmer, Inc. 940 Winter Street, Waltham, MA 02451 USA
*Author no longer employee of Roche

Abstract: Genomes hold an abundance of information, both invaluable and inscrutable. Whole-genome sequencing with Next-Generation Sequencing (NGS) technology has driven a wide diversity of investigations and applications, especially in the field of human health. Technological advances have improved throughput capacity and decreased cost-per-base, thereby increasing the feasibility of large-scale studies and sequencing-based diagnostic tools. Even so, the financial and computational costs of sequencing remain non-trivial. NGS can be economized by limiting the sequencing libraries to specific genomic regions during preparation in a process called target enrichment. Using a target enrichment approach allows for higher throughput and more replicates for equivalent sequencing and computational resources.

Expanding the scope and scale of sequencing-based experiments through targeted enrichment adds logistical complexity to sample preparation. Larger sample sizes impose greater labor demands, longer processing time, and more opportunities for errors. Automating sample preparations on liquid handling instruments resolves many of these issues. Standardized NGS liquid handling platforms, such as the Sciclone G3 NGSx and NGSx iQ workstations from Perkin Elmer, expedite implementation of NGS workflows by offering out-of-the box solutions for many popular reagent kits, including the Roche KAPA NGS workflows. The KAPA HyperCap v3 workflow is a protocol for high-quality, automation-friendly library preparation and target enrichment and has been implemented on both the Sciclone G3 NGSx and NGSx iQ systems. Sequencing libraries are constructed by using either the KAPA HyperPrep Kit or the KAPA HyperPlus Kit, ligation-based preparations with an optional upfront enzymatic fragmentation step in the KAPA HyperPlus Kit. Libraries are then enriched using the KAPA Target Enrichment Kit, an in-solution probe hybridization process compatible with the KAPA HyperExome human exome probe panel or other custom probe panels.

The automated workflow was demonstrated on the Sciclone G3 NGSx workstation with 96 replicates of 100 ng of intact human gDNA, using the KAPA HyperPlus Kit. The pre-capture sequencing libraries were combined into pools of 8 libraries each for target enrichment using the KAPA HyperExome panel. The libraries were assessed for quantity and fragment distribution before and after target enrichment, demonstrating consistent yields and expected fragment.

Featured Products

Bring the Power of Foundation Medicine®
and Roche into Your Lab

The AVENIO Tumor Tissue CGP Kit is an in-house next-generation sequencing (NGS) research assay that provides comprehensive genomic profiling of solid tumors from formalin-fixed paraffin-embedded (FFPE) tissue samples. Designed to match the content of the 324-gene FoundationOne® CDx panel, the kit leverages the proven technology of Foundation Medicine and Roche’s expertise to help your lab obtain reliable genomic insights.

Learn more

A true walk-away experience with AVENIO Edge System*

AVENIO Edge System is Roche’s fully automated system for library preparation, target enrichment, library QC and pooling.  It is designed for users at any level of automation experience, providing the freedom to walk away and work away—with confidence and trust.  The AVENIO Edge System's intuitive software provides step-by-step on-screen instruction without a need for special training, and its reagents are all barcoded and ready-to-load—further simplifying the user experience.

Learn more about AVENIO Edge System
Picture of a DNA strand in blue and green colors

KAPA HyperPETE Target Enrichment Portfolio for NGS

Combine the performance of hybrid-capture with the simplicity and short turnaround time of amplicon-based workflows with primer extension target enrichment (PETE) technology. KAPA HyperPETE is optimized to detect all major somatic variants in cfDNA, FFPE, and RNA samples, including SNVs, short indels, CNVs, MSI, and fusion transcripts (novel and known).

  • Interrogate difficult regions by leveraging Roche’s expertise in panel content and design
  • Save valuable time and resources with single-day, automatable workflows
  • Increase analysis efficiency with focused, high-uniformity panel design—without the need for primer trimming
  • Preserve precious samples and improve sensitivity by avoiding the need to split panels
Learn More

KAPA HyperCap Probes for hybrid capture target enrichment

  • KAPA HyperChoice and KAPA HyperExplore, custom panels for targeting regions specific to your cancer research
  • KAPA HyperExome, a comprehensive-yet-compact panel for sensitive, reliable exome sequencing; includes 387 sample-tracking SNPs
  • KAPA HyperCap Workflow v3, a fast, automation-friendly targeted NGS library preparation workflow that includes KAPA HyperPrep or KAPA HyperPlus Library Preparation Kits

 

Learn More

KAPA Library Prep (RNA, DNA and custom kits)

 

  • KAPA DNA Library Preparation Kits provide efficient, time-saving solutions optimized to preserve the unique mutation signature of samples across a wide range of sample inputs, sequencing applications, and throughput strategies.  Ask us about our custom solutions!
  • 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. Choose solutions for mRNA enrichment and for the depletion of rRNA, globin mRNA, and/or user-defined targets.

 

Learn More

Introducing the Digital LightCycler® System*

The Digital LightCycler® System is designed to enable laboratory flexibility specific to your application of focus. This new instrument enables you to simultaneously perform thousands of PCR reactions from a single sample, and achieve increased specificity and sensitivity with flexible batch sizes all with a simplified workflow. 

Key differentiators:

  • Trusted LightCycler® brand 
  • 3 nanowell plate types
  • 6 detection channels
  • 5x concentration of DNA and RNA Master Mix Reagents
Contact us for more information