Comprehensive Genomic Profiling of Solid Tumors

After expert pathologist assessment, solid tumor genomic DNA was isolated from formalin-fixed, paraffin-embedded tumor samples. DNA libraries were prepared using the KAPA Hyper Prep Kit, hybridized to the xT probe set, and amplified with the KAPA HiFi HotStart ReadyMix. The amplified target-captured DNA tumor libraries were sequenced to an average target depth of 500 × on an Illumina HiSeq 4000 using the Tempus xT (Tempus labs Chicago, IL, USA) gene panel. The panel analyzes single nucleotide variants (SNVs), indels, and copy number variants in 596 genes and genomic rearrangements in 21 genes with an average coverage of 500x^{28 (link)}. Variants were called using Freebayes (version 1.0.2). Clinically relevant mutations were identified using the Cancer Genome Interpretor^{29 (link)} and ClinVar^{30 (link)}. Data was graphed using Microsoft Excel 2016.

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Baschnagel A.M., Kaushik S., Durmaz A., Goldstein S., Ong I.M., Abel L., Clark P.A., Gurel Z., Leal T., Buehler D., Iyer G., Scott J.G, & Kimple R.J. (2021). Development and characterization of patient-derived xenografts from non-small cell lung cancer brain metastases. Scientific Reports, 11, 2520.

Publication 2021

Hyper Prep Kit HiFi HotStart ReadyMix

Cancer Dna libraries Embedded paraffin Formalin Gene Genes rearrangements Genome Indels Mutations Nucleotide Pathologist Tumor Tumor dna

Corresponding Organization : University of Wisconsin–Madison

Other organizations : Case Western Reserve University, University of Wisconsin Carbone Cancer Center, Cleveland Clinic

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Variable analysis

independent variables

Solid tumor genomic DNA was isolated from formalin-fixed, paraffin-embedded tumor samples.

dependent variables

Sequencing the amplified target-captured DNA tumor libraries to an average target depth of 500 × on an Illumina HiSeq 4000 using the Tempus xT (Tempus labs Chicago, IL, USA) gene panel.
Analyzing single nucleotide variants (SNVs), indels, and copy number variants in 596 genes and genomic rearrangements in 21 genes.
Identifying clinically relevant mutations using the Cancer Genome Interpretor and ClinVar.

control variables

The xT probe set used for hybridization.
The KAPA Hyper Prep Kit used for DNA library preparation.
The KAPA HiFi HotStart ReadyMix used for amplification.

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