Clinical validation of the Tempus xO assay

Beaubier, Nike; Tell, Robert; Huether, Robert; Bontrager, Martin; Bush, Stephen J.; Parsons, Jerod; Shah, Kaanan P.; Baker, Tim; Selkov, Gene; Taxter, Timothy J.; Thomas, Amber; Bettis, Sam; Khan, Aly A.; Lau, Denise; Lee, Christina; Barber, Matthew D.; Cieślik, Marcin; Frankenberger, Casey; Franzen, Amy; Weiner, Ali; Palmer, Gary A.; Lonigro, Robert J.; Robinson, Dan R.; Wu, Yi-Mi; Cao, Xuhong; Lefkofsky, Eric; Chinnaiyan, Arul M.; White, Kevin P.

doi:10.18632/oncotarget.25381

Cited by 46 publications

(50 citation statements)

References 23 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…RNA data were used for fusion validation and differential expression. 16,17 Paired normal samples were used when they were available. Through Tempus bioinformatic pipelines, single nucleotide polymorphism and indel mutations were called as low as 3% allele frequency.…”

Section: Genomic Sequencing and Analysismentioning

confidence: 99%

BRAF fusion Spitz neoplasms; clinical morphological, and genomic findings in six cases

et al. 2020

View full text Add to dashboard Cite

Background: Fusions involving the BRAF gene are responsible for 5% of Spitz neoplasms. To better characterize them, we report the clinical, morphological, and genomic findings of six BRAF fusion Spitz tumors. Methods: The morphological, clinical, and molecular findings of six BRAF fusion Spitz neoplasms assessed by next generation sequencing (NGS) were compared to a control set of Spitz without BRAF fusions. Results: BRAF fusion Spitz tumors had frequent predominance of epithelioid morphology (4/6 cases), frequent high-grade nuclear atypia and pleomorphism (5/6 cases), and a frequent desmoplastic base (3/6 cases). Five of six cases were diagnosed as atypical Spitz tumor and one as Spitz nevus. All cases had uneventful clinical follow-up. There were five different fusion partners, with CLIP2 being the most frequent. Secondary pathogenic mutations were frequent and chromosomal copy number changes were seen in three of six cases by an NGS platform. Conclusions: BRAF fusions Spitz usually have epithelioid morphology, high-grade nuclear atypia, and desmoplasia. Chromosomal copy number changes are not infrequent. While our cases had uneventful follow-up, a meta-analysis of the literature suggests that among the fusion subtypes associated with Spitz tumors, they are among the subgroups more likely to develop distant metastasis.

show abstract

Section: Genomic Sequencing and Analysismentioning

confidence: 99%

BRAF fusion Spitz neoplasms; clinical morphological, and genomic findings in six cases

et al. 2020

View full text Add to dashboard Cite

show abstract

“…The Tempus xO Assay (performed at Tempus Labs) consists of a 1714-gene-targeted somatic and germline DNA sequencing panel and whole-transcriptome RNA sequencing to detect germline and somatic single-nucleotide polymorphisms, insertions/ deletions, copy number alterations, and gene rearrangements causing chimeric messenger RNA transcript expression in a wide array of tumor types. 17 The assay used formalin-fixed paraffin-embedded tumor samples and matched blood or saliva samples. Samples with low tumor percentage were macrodissected prior to RNA extraction.…”

mentioning

confidence: 99%

Tumor mutational burden and other predictive immunotherapy markers in histiocytic neoplasms

Goyal

Lau

Nagle

et al. 2019

Blood

Self Cite

View full text Add to dashboard Cite

“…In order to determine assay sensitivity for single nucleotide variants (SNVs) in solid tumors, a panel of formalin-fixed, paraffin-embedded (FFPE) clinical tumor samples were sequenced and compared against previously reported results from the Tempus xO assay [8]. There were 487 unique SNVs previously detected in the tumor samples, with variant allele fractions (VAFs) from 5% to 100% (median 25.9%).…”

Section: Resultsmentioning

confidence: 99%

“…The assay is designed to assess 21 gene rearrangement targets by DNA-seq (Table 2), in addition to comprehensive fusion detection by RNA-seq as previously reported [8]. The reportable range for gene rearrangements by DNA-seq is limited to fusions occurring in the specific regions listed in Table 2.…”

Section: Resultsmentioning

confidence: 99%

“…We previously presented the Tempus xO assay, a next generation sequencing (NGS)-based oncology assay that interrogates 1,711 cancer-related genes in matched tumor and normal tissue with whole transcriptome RNA sequencing (RNA-seq) for gene rearrangement detection [8]. We now present the Tempus xT assay, a more focused targeted oncology panel using hybrid capture NGS to interrogate a refined list of 595 genes (Table 1), including solid tumor and hematologic malignancy targets selected through extensive review of recent literature and oncogenic pathway analysis (see Methods).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Clinical validation of the tempus xT next-generation targeted oncology sequencing assay

et al. 2019

Self Cite

View full text Add to dashboard Cite

We developed and clinically validated a hybrid capture next generation sequencing assay to detect somatic alterations and microsatellite instability in solid tumors and hematologic malignancies. This targeted oncology assay utilizes tumor-normal matched samples for highly accurate somatic alteration calling and whole transcriptome RNA sequencing for unbiased identification of gene fusion events. The assay was validated with a combination of clinical specimens and cell lines, and recorded a sensitivity of 99.1% for single nucleotide variants, 98.1% for indels, 99.9% for gene rearrangements, 98.4% for copy number variations, and 99.9% for microsatellite instability detection. This assay presents a wide array of data for clinical management and clinical trial enrollment while conserving limited tissue.

show abstract

Clinical validation of the Tempus xO assay

Cited by 46 publications

References 23 publications

BRAF fusion Spitz neoplasms; clinical morphological, and genomic findings in six cases

BRAF fusion Spitz neoplasms; clinical morphological, and genomic findings in six cases

Tumor mutational burden and other predictive immunotherapy markers in histiocytic neoplasms

Clinical validation of the tempus xT next-generation targeted oncology sequencing assay

Contact Info

Product

Resources

About