Special Programs Day

This forum will discuss genetic testing reference materials availability and needs (for test validation, quality control, and proficiency testing). Speakers will present a variety of current reference material development projects for molecular testing of inherited and somatic genetic disorders and infectious diseases, followed by group discussion. We also want to hear your thoughts and facilitate active discussions to formulate a fuller understanding of your reference material needs for particular disorders, specific molecular methods, or specific genes. These may include inherited disorders, molecular oncology, infectious diseases and others.

NGS technology underpins several clinical molecular diagnostics assays, yet the steps between the instrument and the signed-out report remain a black box. This hands-on workshop opens that box. The session starts by providing a practical orientation to DNA and RNA sequencing platforms and chemistries, the convergent data they produce, and what a bioinformatics pipeline actually is — from FASTQ to VCF to clinical report — including the options and resources required to build, buy, or outsource one.

In the second portion of the session, participants work through a complete pipeline themselves: FASTQ processing and QC, alignment and BAM generation, variant calling, normalization and annotation, and clinical report generation. The workshop concludes with two case studies from routine oncology practice: an AML with FLT3-ITD, where conventional callers fall short and specialized detection and VAF interpretation become essential, and a BRAF V600E at low allelic fraction, raising questions of limit of detection and caller threshold adjustment.

A closing discussion addresses what it genuinely takes to perform tumor NGS in your own laboratory, and the tradeoffs of outsourcing bioinformatics.

The University of Michigan Department of Pathology is an academic institution dedicated to excellence in patient care, education, and research. MLabs, our national reference laboratory, partners with hospitals and laboratories to deliver cutting-edge diagnostic testing nationally. The Division of Diagnostic Genetics and Genomics (DGG) integrates molecular genetics, cytogenetics, and genomics to provide comprehensive, state-of-the-art diagnostic services for oncology and constitutional conditions. Through continuous innovation, DGG serves as a hub for validating and deploying emerging genomic methodologies that drive precision medicine.

This 1.5-hour educational session is designed to offer three 30 minutes each targeted, in-depth lectures focusing on collaborative methodologies within molecular and cytogenetics. Highlighting innovative work in both constitutional and cancer diagnostics, this session complements the core AMP Annual Meeting program by providing actionable insights into advanced testing platforms, including methylation microarray, OGM, MS-MLPA, and WGS. To ensure an engaging learning environment, the session will be highly interactive, combining expert lectures with live audience questions polling to evaluate real-time comprehension and application.

Cytology specimens have become increasingly important substrates for molecular diagnostics, particularly as minimally invasive sampling techniques continue to expand across oncology practice. Advances in molecular techniques now position cytology specimens as critical resources for comprehensive biomarker testing, disease monitoring, and precision medicine.

This companion session will explore novel cytology-based testing strategies, including the use of substrates such as cytology supernatants, residual cytology materials, and liquid biopsy analytes such as circulating tumor DNA (ctDNA) that maximize the molecular utility of cytology specimens. Presentations will highlight recent advances in next-generation sequencing, biomarker testing, and pre-analytical optimization strategies that improve molecular testing success rates and better utilize cytology specimens.

Through multidisciplinary perspectives from cytopathologists and molecular pathologists, attendees will gain practical insights into integrating cytology-based molecular testing into routine clinical workflows. The session will emphasize how innovative utilization of cytology specimens can expand patient access to actionable molecular information, accelerate therapeutic decision-making, reduce repeat procedures, and ultimately improve patient outcomes.

Patients may miss the opportunity to receive precision oncology care because of problems between tumor biopsy, biomarker testing, reporting, and treatment selection. This 90-minute CAP companion program will examine how laboratory evidence can be used to address those problems. Faculty will present findings from CAP proficiency testing and practice studies involving neoplastic cellularity, NGS performance and troubleshooting, genomic reporting, and laboratory assay selection. The program will also describe how CAP applies these findings through laboratory improvement activities, Biomarker OneSource, accreditation, and advocacy.