Analytical validation of the Oncomine Pan-Cancer Cell-Free Assay in a CLIA- and CAP-regulated laboratory for detection of solid tumor-derived variants in blood plasma.

Solano, Luis; Yuki, Akemi; Burkhart, Vanessa D.; Chitwood, James L.; Cao, Ran; Schageman, Jeoffrey; Saunders, Hannah; Cheng, Angie; Ha, Thomas; Ojcius, Cecilia; White, Roxana; McCall, Kimberly; Salazar, Suzanne; Bramlett, Kelli; Tian, Huan; Ramsamooj, Rajendra

doi:10.1200/jco.2019.37.15_suppl.e14614

Cited by 8 publications

(6 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The previous study using the Oncomine Lung Cell-Free DNA Assay, the same platform with the different assay, demonstrated a sensitivity of 81% with <20 ng of cfDNA at a VAF of 0.1%, whereas our data showed a sensitivity of 50% under the same condition [21]. In the report by the manufacturer, the same assay in the present study showed a sensitivity of 80% at a VAF of 0.1% for SNV [22]. In the present study, most of the analytical performance tests were conducted using reference materials and clinical samples containing only EGFR mutations.…”

Section: Discussionsupporting

confidence: 50%

Analytical Validation of a Pan-Cancer Panel for Cell-Free Assay for the Detection of EGFR Mutations

Park

Kim

et al. 2021

Diagnostics

View full text Add to dashboard Cite

Liquid biopsies have increasingly shown clinical utility. Although next-generation sequencing has been widely used for the detection of somatic mutations from plasma, performance characteristics vary by platform. Therefore, thorough validation is mandatory for clinical use. This study aimed to evaluate the analytical validity of the Oncomine Pan-Cancer Cell-Free Assay. A massively parallel sequencing for the assay was performed using the Ion S5 XL System with Ion 540 kit. The analytical sensitivity and precision were evaluated using pre-characterized reference materials. The specificity was evaluated using plasma from healthy subjects. A comparison with the Cobas EGFR Mutation Test v2 was performed using reference materials and plasma from lung cancer patients. For SNVs and short indels, the analytical sensitivities at variant allele frequencies (VAFs) of 0.1%, 0.5%, and 1% were 50%, 93.4%, and 100% with 20 ng of input, respectively. The overall precision of the true positive variants was 98% at a VAF of 1% with 20 ng input. The assay showed a similar sensitivity to that of the Cobas EGFR Mutation Test v2 at a VAF of 0.5% with 20 ng of input and 100% concordance on clinical samples. The Pan-Cancer Cell-Free Assay can be applied to detect EGFR mutations in advanced lung cancer patients, although follow-up studies will be needed to evaluate the analytical validity for other types of genes and aberrations using clinical samples.

show abstract

Section: Discussionsupporting

confidence: 50%

Analytical Validation of a Pan-Cancer Panel for Cell-Free Assay for the Detection of EGFR Mutations

Park

Kim

et al. 2021

Diagnostics

View full text Add to dashboard Cite

show abstract

“…In turn, this enables interrogation of limiting amounts of ctDNA (as in low tumor burden samples), and enriches the density of informative sequencing reads which are on-target. Analytical sensitivities of amplicon-based methods are reportedly superior [25,26] compared to hybrid capture-based methods [15,24] for single nucleotide variants (SNVs) and insertion/deletion events (INDELs), in the biologically relevant sub-1% ctDNA range. While multiple analytical and post-analytical factors differ between individual methods, including variant calling algorithms, better sensitivity can at least be partially attributed to the superior on-target capture rate of amplicon-based enrichment methods.…”

Section: Introductionmentioning

confidence: 99%

Analytical and clinical validation of an amplicon-based next generation sequencing assay for ultrasensitive detection of circulating tumor DNA

Poh¹,

Ngeow²,

Pek³

et al. 2022

PLoS ONE

View full text Add to dashboard Cite

Next-generation sequencing of circulating tumor DNA presents a promising approach to cancer diagnostics, complementing conventional tissue-based diagnostic testing by enabling minimally invasive serial testing and broad genomic coverage through a simple blood draw to maximize therapeutic benefit to patients. LiquidHALLMARK® is an amplicon-based next-generation sequencing assay developed for the genomic profiling of plasma-derived cell-free DNA (cfDNA). The comprehensive 80-gene panel profiles point mutations, insertions/deletions, copy number alterations, and gene fusions, and further detects oncogenic viruses (Epstein-Barr virus (EBV) and hepatitis B virus (HBV)) and microsatellite instability (MSI). Here, the analytical and clinical validation of the assay is reported. Analytical validation using reference genetic materials demonstrated a sensitivity of 99.38% for point mutations and 95.83% for insertions/deletions at 0.1% variant allele frequency (VAF), and a sensitivity of 91.67% for gene fusions at 0.5% VAF. In non-cancer samples, a high specificity (≥99.9999% per-base) was observed. The limit of detection for copy number alterations, EBV, HBV, and MSI were also empirically determined. Orthogonal comparison of epidermal growth factor receptor (EGFR) variant calls made by LiquidHALLMARK and a reference allele-specific polymerase chain reaction (AS-PCR) method for 355 lung cancer specimens revealed an overall concordance of 93.80%, while external validation with cobas® EGFR Mutation Test v2 for 50 lung cancer specimens demonstrated an overall concordance of 84.00%, with a 100% concordance rate for EGFR variants above 0.4% VAF. Clinical application of LiquidHALLMARK in 1,592 consecutive patients demonstrated a high detection rate (74.8% circulating tumor DNA (ctDNA)-positive in cancer samples) and broad actionability (50.0% of cancer samples harboring alterations with biological evidence for actionability). Among ctDNA-positive lung cancers, 72.5% harbored at least one biomarker with a guideline-approved drug indication. These results establish the high sensitivity, specificity, accuracy, and precision of the LiquidHALLMARK assay and supports its clinical application for blood-based genomic testing.

show abstract

“…Somatic alterations were identified in tumor tissues by either hybrid capture-based targeted DNA sequencing in using FoundationOne CDx (15) or PCR-amplicon-based target capture using Oncomine (16). Somatic alterations in cell-free DNA (cfDNA) were detected by Oncomine (17) and Guardant360 (18). Lollipop figures were created using the visualize data feature by cBioPortal (19,20) and annotation of the biologic and oncogenic effects and prognostic and predictive significance of somatic molecular alterations were extracted from the OncoKB knowledge base (21).…”

Section: Somatic Alteration Identification and Annotationmentioning

confidence: 99%

Molecular Profiling of Metastatic Bladder Cancer Early-Phase Clinical Trial Participants Predicts Patient Outcomes

Alhalabi

Hahn

Msaouel

et al. 2021

Molecular Cancer Research

View full text Add to dashboard Cite

Prognosis for patients with metastatic bladder carcinoma (mBC) remains limited and in need of novel therapies. We retrospectively analyzed medical records of 43 patients with platinum-refractory metastatic bladder cancer (mBC) who participated in one or more phase I trials of various investigational therapies. Patients' tumors or circulating tumor DNA were analyzed by next-generation sequencing. The median progression-free survival was 4.2 months, the median overall survival was 9.6 months, and the overall response rate was 17.5%. TP53, ERBB2, PI3KCA, FGFR3, and ARID1A alterations were detected in 66%, 29%, 27%, 24%, and 22% of all patients, respectively. Alterations in FGFR3 were almost mutually exclusive of TP53. More than half (64%) of patients with an FGFR alt received an FGFR inhibitor, 67% of which achieved disease control. Among patients with urothelial carcinoma histology, those harboring a TP53 alteration had a shorter median progression-free survival (PFS) compared with those whose tumors carry wild-type TP53. The reverse relationship was observed in patients harboring an FGFR alteration. Implications: Patients with platinum-refractory mBC derive clinical benefit from participating in early-phase clinical trials and their survival outcomes correlate with the genetic profile of the tumor. Visual Overview: http://mcr.aacrjournals.org/content/molcanres/19/3/395/F1.large.jpg.

show abstract

Analytical validation of the Oncomine Pan-Cancer Cell-Free Assay in a CLIA- and CAP-regulated laboratory for detection of solid tumor-derived variants in blood plasma.

Cited by 8 publications

References 0 publications

Analytical Validation of a Pan-Cancer Panel for Cell-Free Assay for the Detection of EGFR Mutations

Analytical Validation of a Pan-Cancer Panel for Cell-Free Assay for the Detection of EGFR Mutations

Analytical and clinical validation of an amplicon-based next generation sequencing assay for ultrasensitive detection of circulating tumor DNA

Molecular Profiling of Metastatic Bladder Cancer Early-Phase Clinical Trial Participants Predicts Patient Outcomes

Contact Info

Product

Resources

About