Reference Samples to Compare Next-Generation Sequencing Test Performance for Oncology Therapeutics and Diagnostics

SPOT/Dx Pilot Reanalysis and College of American Pathologists Proficiency Testing for KRAS and NRAS Demonstrate Excellent Laboratory Performance

CONTEXT.—

The Sustainable Predictive Oncology Therapeutics and Diagnostics quality assurance pilot study (SPOT/Dx pilot) on molecular oncology next-generation sequencing (NGS) reportedly demonstrated performance limitations of NGS laboratory-developed tests, including discrepancies with a US Food and Drug Administration-approved companion diagnostic. The SPOT/Dx pilot methods differ from those used in proficiency testing (PT) programs.

OBJECTIVE.—

To reanalyze SPOT/Dx pilot data using PT program methods and compare to PT program data.Also see p. 136.

DESIGN.—

The College of American Pathologists (CAP) Molecular Oncology Committee reanalyzed SPOT/Dx pilot data applying PT program methods, adjusting for confounding conditions, and compared them to CAP NGS PT program performance (2019-2022).

RESULTS.—

Overall detection rates of KRAS and NRAS single-nucleotide variants (SNVs) and multinucleotide variants (MNVs) by SPOT/Dx pilot laboratories were 96.8% (716 of 740) and 81.1% (129 of 159), respectively. In CAP PT programs, the overall detection rates for the same SNVs and MNVs were 97.2% (2671 of 2748) and 91.8% (1853 of 2019), respectively. In 2022, the overall detection rate for 5 KRAS and NRAS MNVs in CAP PT programs was 97.3% (1161 of 1193).

CONCLUSIONS.—

CAP PT program data demonstrate that laboratories consistently have high detection rates for KRAS and NRAS variants. The SPOT/Dx pilot has multiple design and analytic differences with established PT programs. Reanalyzed pilot data that adjust for confounding conditions demonstrate that laboratories proficiently detect SNVs and less successfully detect rare to never-observed MNVs. The SPOT/Dx pilot results are not generalizable to all molecular oncology testing and should not be used to market products or change policy affecting all molecular oncology testing.

Genomic Data Heterogeneity across Molecular Diagnostic Laboratories: A Real-World Connect Myeloid Disease Registry Perspective on Variabilities in Genomic Assay Methodology and Reporting

Genomic data variability from laboratory reports can impact clinical decisions and population-level analyses; however, the extent of this variability and the impact on the data's value are not well characterized. This pilot study used anonymized genetic and genomic test reports from the Connect Myeloid Disease Registry (NCT01688011), a multicenter, prospective, observational cohort study of patients with newly diagnosed myelodysplastic syndromes, acute myeloid leukemia, or idiopathic cytopenia of undetermined significance, to analyze laboratory test variabilities and limitations. Results for 56 randomly selected patients enrolled in the Registry were independently extracted and evaluated (data cutoff, January 2020). Ninety-five reports describing 113 assay results from these 56 patients were analyzed for discrepancies. Almost all assay results [101 (89%)] identified the sequencing technology applied, and 94 (83%) described the test limitations; 95 (84%) described the limits of detection, but none described the limit of blank for detecting false positives. RNA transcript identifiers were not provided for 20 (43%) variants analyzed by next-generation sequencing and reported by the same laboratory. Of 42 variants with variant allele frequencies ≥30%, 16 (38%) of the variants did not have report text indicating that the variants might be germline. Variabilities and lack of standardization present challenges for incorporating this information into clinical care and render data collation ineffective and unreliable for large-scale use in centralized databases for therapeutic discovery.

Reforms Needed to Modernize the US Food and Drug Administration's Oversight of Dietary Supplements, Cosmetics, and Diagnostic Tests

This JAMA Forum discusses long-awaited reforms that could modernize the US Food and Drug Administration’s regulatory processes, promote innovation, and provide US consumers greater assurance that the products they use are safe and reliable.

Missing Companion Diagnostic for US Food and Drug Administration-Approved Hematological and Oncological Drugs

Within hematology and oncology, companion diagnostics (CDxs) play an increasing role in securing an optimal therapy for individual patients, and the US Food and Drug Administration (FDA) consider this type of assay essential for the safe and effective use of a corresponding therapeutic product. Most CDxs are developed prospectively using the drug-diagnostic codevelopment model, which normally secures the simultaneous approval of both drugs and diagnostics. A CDx assay is an important treatment decision tool that needs to be available simultaneously with the drug. However, within the past few years, several targeted drugs and new indications have been approved by the FDA without a CDx, despite the use of a predictive biomarker assay for patient selection during clinical development. A missing analytical and clinically validated CDx assay could affect the correct use of these drugs and ultimately patient safety. An alternative to FDA-approved or FDA-cleared CDxs could be to use a laboratory-developed test, which will normally miss documentation on the clinical validity. On the basis of the information available from different publicly available FDA databases, this article briefly discusses the issue of missing CDx assays in relation to the approval of hematological and oncological drugs and new indications.