ArcherDX presents at the
XXXI International Congress of the IAP
and 28th Congress of the ESP

Cologne, Germany
September 25-29, 2016
Stand #40



NGS-based Diagnostics in Oncology Forum

Practical Insights and Experience

Tuesday, 27 September | 19:00 to 21:00 | Hotel Mondial am Dom
Address: Kurt-Hackenberg-Platz 1, Köln


Join us for an evening of scientific discussion, as leaders in moledular pathology provide insight into their experiences using NGS in clinical and translocational research.

This forum is provided to all ESP participants and is free of charge. Dinner and drinks will be provided for the first 100 registrants.


Register now to
reserve your spot.







Forum Presenters

Headshot of Volker Endris

Volker Endris, Ph.D.

Head, IPH
Center for Molecular Pathology
University Hospital Heidelberg

Headshot of Jason Christiansen

Jason Christiansen, Ph.D.

Vice President of Diagnostics
Ignyta

Headshot of Brian Kudlow

Brian Kudlow, Ph.D.

Vice President of R&D
ArcherDX


Presentations at the IAP/ESP Congress

Detection of all major classes of MET deregulation by Anchored Multiplex PCR-based next-generation sequencing

Josh Haimes, Marc Bessette, Namitha Manoj, Danielle Murphy, Robert Shoemaker, Laura M. Griffin, Josh Stahl, Brian Kudlow

ArcherDX, Inc., Boulder, CO, USA

Objective

Deregulation of the proto-oncogene, MET, confers an aggressive phenotype in a variety of cancers. MET deregulation can be driven be gene amplification, overexpression, single nucleotide variants (SNVs), exon 14 skipping and fusions. We developed target enrichment kits for next-generation sequencing (NGS) to sensitively detect all types of MET aberrations from low-input clinical sample types, such as FFPE samples.

Methods

VariantPlex™ and FusionPlex™ kits were developed based on Anchored Multiplex PCR (AMP™) to generate NGS libraries from DNA and RNA, respectively. Probes were designed to cover the MET gene and transcript, enabling detection of copy numbers and SNVs by VariantPlex, and fusions, exon skipping and expression by FusionPlex kits.

Results

VariantPlex and FusionPlex kits enabled detection of MET amplifications, confirmed by FISH, and the resulting overexpression in FFPE samples. Exon 14 skipping was also detected in FFPE and in cells, concomitant with splice site SNVs, and verified by RT-PCR. Lastly, we detected a GTF2I:MET fusion in an FFPE sample and a Y1253D activating point mutation in cells.

Conclusions

These results demonstrate the utility of Archer VariantPlex and FusionPlex kits to detect all types of MET mutations by NGS. Enhanced detection sensitivity enabled by AMP technology permits confident detection of mutations from low-input clinical samples.


Comprehensive thyroid and lung cancer profiling by Anchored Multiplex PCR- based next-generation sequencing

Josh Haimes, Laura Johnson, James Covino, Namitha Manoj, Marc Bessette, Elina Baravik, Abel Licon, Ryan D. Walters, Laura M. Griffin, Brady P. Culver, Joshua A. Stahl, Brian A. Kudlow

ArcherDX, Inc., Boulder, CO, USA

Objective

Thyroid and lung cancers are driven by multiple types of genetic aberrations, including single nucleotide variants (SNVs), insertions and deletions (indels), copy number variants (CNVs) and fusions. Next generation sequencing (NGS) of target-enriched libraries is a highly sensitive and scalable method to detect these mutations. Anchored Multiplex PCR (AMP™) is a target enrichment strategy that uses unidirectional gene-specific primers and molecular barcoded adapters ligated to DNA ends for amplification. This enables amplification of both known and unknown mutations within target regions and increases coverage of target regions.

Methods

We developed AMP-based comprehensive thyroid and lung (CTL) assays, VariantPlex™ and FusionPlex™ CTL, with probes covering relevant genes in thyroid and lung cancers.

Results

Our data show that parallel interrogation of DNA and RNA using VariantPlex and FusionPlex CTL assays, respectively, enables simultaneous detection of known and unknown SNVs, indels, CNVs and fusions from low-input clinical sample types. Furthermore, we show that characterization of gene expression, including detection of splice variants, expression imbalances and whole gene expression levels provides orthogonal verification of detected mutations.

Conclusion

These results demonstrate the utility of CTL assays to simultaneously and sensitively detect all types of mutations in clinically relevant genes in thyroid and lung cancer samples.


Sensitive detection of copy number variants from FFPE samples by Anchored Multiplex PCR-based next-generation sequencing

Josh D. Haimes, James Covino, Namitha Manoj, Elina Baravik, Laura Johnson, Laura M. Griffin, Joshua Stahl, Brady P. Culver, Brian Kudlow

ArcherDX, Inc., Boulder, CO, USA

Objective

Copy number variations (CNVs) impact more of the cancer genome than all other mutation types combined. Next-generation sequencing (NGS) is an invaluable tool to detect CNVs. However, routine formalin-fixed paraffin-embedded (FFPE) storage of clinical specimens severely damages DNA, limiting detection sensitivity. We developed a target enrichment strategy based on Anchored Multiplex PCR (AMP™) to enhance NGS-based detection sensitivity of CNVs.

Methods

AMP generates libraries for NGS by amplifying degraded DNA fragments, thereby increasing read coverage of target regions. We developed the Archer™ VariantPlex™ Solid Tumor kit with AMP probes to amplify 43 CNVs associated with a variety of carcinomas. We also developed the PreSeq™ DNA QC Assay to determine the integrity of genomic DNA prior to library preparation.

Results

By screening 139 FFPE samples, we show that NGS-based CNV detection sensitivity is primarily driven by the integrity of the input genomic DNA. Using optimal input amounts of genomic DNA, the VariantPlex Solid Tumor kit enabled detection of CNVs as low as 2-fold in FFPE samples and in samples with as low as 3% tumor cellularity.

Conclusions

These results demonstrate that AMP-based NGS accurately detects low-level CNVs in genomic DNA from low-input clinical samples and from samples with low tumor cellularity.

About ArcherDX

To address the existing bottlenecks of using NGS in translational research, we’ve created a robust platform that is purpose-built for clinical oncology research.

By combining revolutionary Anchored Multiplex PCR (AMP™) chemistry with an easy-to-use workflow and intuitive software, we are unleashing the power of translational NGS to enable accurate and scalable mutation detection.

How to contact us

Address

2477 55th Street, Suite 202

Boulder, CO 80301

Phone

Phone: (877) 771 1093

Phone: (303) 357 9001

All content © 2017 ArcherDX, Inc.

For Research Use Only. Not for use in diagnostic procedures. For Research Use Only. Not for use in diagnostic procedures.