Workshops and Poster Sessions at AMP16


Wednesday, November 9

12:00-12:45 pm

Defining the Standard of Care: FDA-Cleared, Clinically Proven CML Monitoring at the MR4.7 Level
Presented by: Christopher D. Watt, M.D., Ph.D. and Bernard F. Andruss, Ph.D.

This workshop will describe the new FDA cleared QuantideX® qPCR BCR-ABL IS Kit, a highly sensitive, reproducible and clinically proven assay that detects & quantifies major breakpoint fusions (e13a2 & e14a2) on the IS scale. Our speakers will focus on both the results obtained during the FDA clinical trials and their experience in using the assay in a clinical laboratory setting with specific focus on assay performance, ease-of-use and the implications of having an MR4.7 (0.002% IS) on improving patient care.

2:00-2:45 pm

Evaluation of an NGS Assay for Detecting RNA Fusions and Splicing Events in Lung Cancer
Presented by: Léon C. van Kempen, Ph.D. and Gary J. Latham, Ph.D.

This workshop discusses the evaluation of a new targeted panel for RNA sequencing of FFPE lung cancer samples. Dr. Léon van Kempen, Scientific Director of Dubrovsky Molecular Pathology Centre at Jewish General Hospital, will share his laboratory’s experience with the QuantideX® NGS RNA Lung Cancer Kit (RUO) for analysis of a cohort of 30 TNA isolates from FFPE residual tumor biopsies and cancer cell lines. The results of the evaluation yielded 100% agreement for fusion and splice variant calling across 16 negative and 14 diverse positive samples.



Friday, November 11

H54: BCR-ABL1 Molecular Responses at 12-18 Months Predict Long-Term Event-Free Survival in Patients With Tyrosine Inhibitor (TKI)-treated Chronic Myelogenous Leukemia (CML)
Author: Garrett Eickelberg

Describes the clinical outcome study performed for the first FDA-cleared BCR-ABL 1 monitoring assay for CML. This multi-center effort spanned 3 laboratories to validate clinical monitoring. Event-free survival (EFS) at 32-40 months against test results at 12-18 months on TKI was statistically significant between groups stratified as either <MR3 and >MR3.

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Solid Tumors
S86: A Novel RT-ddPCR Assay Enables Sensitive and Accurate Quantification of MET Exon 14 Skipping in Lung Adenocarcinomas
Author: Michael Dodge, Ph.D.

Presents a prototype droplet digital™ PCR assay that quantifies oncogenic exon-skipping MET transcripts. The poster results demonstrate analytical sensitivity to 1% skipped RNA with tolerance for low-quantity and low-quality FFPE tumor biopsies.

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Saturday, November 12
9:45-10:45 am

G25: A Streamlined PCR Assay for Rapid and Accurate Genotyping of Poly-T Length Polymorphisms at rs10524523 of the TOMM40 Gene
Author: Sarah Statt, Ph.D.

Poly-T polymorphisms at rs10524523 of the TOMM40 gene are known to influence the age of onset in late-onset Alzheimer’s Disease. This poster describes a rapid, simple, and accurate PCR research assay that reliably reports TOMM40 poly-T length at single-nucleotide resolution across all repeat categories with potential to improve risk assessments.

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G57: A Putative SNP in the Fragile X Gene Neither Affects PCR-based Genotyping nor is Verified by Sanger Sequencing: Practical Implications for Genome Database Accuracy
Author: Homero Rey, Ph.D.

The plethora of genome data available through next generation sequencing drives the identification and frequency of single nucleotide polymorphisms. This poster reconciles a putative SNP for FMR1 analysis and affirms the need for secondary testing of these rare events for their presence in the genome and impact on PCR-based assays.

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H31: BCR-ABL1 Monitoring on the IS Using a Clinically and Analytically Validated Multiplex Assay Directly Aligned to the WHO Primary Standards and that Unifies Reporting Formats
Author: Justin Brown, Ph.D.

Describes highlights of the analytical and clinical validation of the first FDA-cleared BCR-ABL1 monitoring assay for CML. The assay is directly traceable to the WHO Primary materials and simultaneously reports on continuous %IS and MR scales without conversion factors.

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Solid Tumors
S19: Independent Evaluation of a Fully-integrated Next-Generation Sequencing Technology for the Accurate Detection of Oncogenic RNA Fusions and Aberrant Splicing Events in Lung Cancer
Author: Richard Blidner, Ph.D.

Demonstrates the performance of a new targeted RNA-seq lung cancer assay* that covers 107 known oncogenic gene fusions, MET exon 14 skipping variants, 26 expression markers, and 5 imbalance markers for novel fusion detection using a streamlined, sample-to-answer workflow. Results from an assessment of residual clinical specimens by Jewish General Hospital in Montreal, Canada are described.

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S91: Modular Next Generation Sequencing Technology that Combines Targeted Enrichment and Bioinformatics Analyses to Reveal RNA Expression and DNA Mutations in Lung Cancer
Author: Brian Haynes, Ph.D.

Describes an efficient, Sample-Aware™ NGS workflow* that pinpoints diagnostically-relevant RNA and DNA markers in lung cancer. More than 200 NSCLC FFPE tumors were analyzed in collaboration with MD Anderson Cancer Center to reveal RNA fusions, exon skipping variants, and DNA mutation signatures that together provide a more comprehensive portrait of disease to advance clinical research.

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Technical Topics
TT43: Multi-site Evaluation of a Single-tube Long-read PCR Assay for the Reliable Detection and Characterization of C9orf72 Hexanucleotide Repeat Expansions
Author: EunRan Suh, Ph.D.

Presents an evaluation of more than 800 specimens using a novel repeat-primed PCR assay* relevant to ALS and FTD. This assay accurate resolves up to 145 hexanucleotide repeats by capillary electrophoresis, flags larger expansions irrespective of size, and provides an indication of size mosaicism and 3’ sequence variants.

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TT71: Performance Assessment of On-market Liquid Biopsy Nucleic Acid Isolation Technologies
Authors: Bradley Hall, Ph.D. and Jon Kemppainen

Compares and contrasts 8 circulating cell-free DNA isolation kits by quantifying the recovery of exogenous and endogenous targets and assessing fragment size bias, with implications for liquid biopsy precision medicine applications.

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

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