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Saldivar JS, Harris J, Ayash E, Hong M, Tandon P, Sinha S, Hebron PM, Houghton EE, Thorne K, Goodman LJ, Li C, Marfatia TR, Anderson J, Morra M, Lyle J, Bartha G, Chen R. Analytic validation of NeXT Dx™, a comprehensive genomic profiling assay. Oncotarget 2023; 14:789-806. [PMID: 37646774 PMCID: PMC10467627 DOI: 10.18632/oncotarget.28490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/19/2023] [Indexed: 09/01/2023] Open
Abstract
We describe the analytic validation of NeXT Dx, a comprehensive genomic profiling assay to aid therapy and clinical trial selection for patients diagnosed with solid tumor cancers. Proprietary methods were utilized to perform whole exome and whole transcriptome sequencing for detection of single nucleotide variants (SNVs), insertions/deletions (indels), copy number alterations (CNAs), and gene fusions, and determination of tumor mutation burden and microsatellite instability. Variant calling is enhanced by sequencing a patient-specific normal sample from, for example, a blood specimen. This provides highly accurate somatic variant calls as well as the incidental reporting of pathogenic and likely pathogenic germline alterations. Fusion detection via RNA sequencing provides more extensive and accurate fusion calling compared to DNA-based tests. NeXT Dx features the proprietary Accuracy and Content Enhanced technology, developed to optimize sequencing and provide more uniform coverage across the exome. The exome was validated at a median sequencing depth of >500x. While variants from 401 cancer-associated genes are currently reported from the assay, the exome/transcriptome assay is broadly validated to enable reporting of additional variants as they become clinically relevant. NeXT Dx demonstrated analytic sensitivities as follows: SNVs (99.4%), indels (98.2%), CNAs (98.0%), and fusions (95.8%). The overall analytic specificity was >99.0%.
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Affiliation(s)
| | - Jason Harris
- Personalis, Inc., Fremont, CA 94555, USA
- These authors contributed equally to this work
| | - Erin Ayash
- Personalis, Inc., Fremont, CA 94555, USA
| | | | | | | | | | | | | | | | - Conan Li
- Personalis, Inc., Fremont, CA 94555, USA
| | | | | | | | - John Lyle
- Personalis, Inc., Fremont, CA 94555, USA
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Quiggle AM, Goodwin ZA, Marfatia TR, Kumar MG, Ciliberto H, Bayliss SJ, de Guzman Strong C. Low filaggrin monomer repeats in African American pediatric patients with moderate to severe atopic dermatitis. JAMA Dermatol 2015; 151:557-9. [PMID: 25564772 DOI: 10.1001/jamadermatol.2014.4916] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Ashley M Quiggle
- Center for Pharmacogenomics, Center for the Study of Itch, Division of Dermatology, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Zane A Goodwin
- Center for Pharmacogenomics, Center for the Study of Itch, Division of Dermatology, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Twinkal R Marfatia
- Center for Pharmacogenomics, Center for the Study of Itch, Division of Dermatology, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Monique G Kumar
- Center for Pharmacogenomics, Center for the Study of Itch, Division of Dermatology, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Heather Ciliberto
- Center for Pharmacogenomics, Center for the Study of Itch, Division of Dermatology, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Susan J Bayliss
- Center for Pharmacogenomics, Center for the Study of Itch, Division of Dermatology, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri
| | - Cristina de Guzman Strong
- Center for Pharmacogenomics, Center for the Study of Itch, Division of Dermatology, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri
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