SCHOOL: Software for Clinical Health in Oncology for Omics Laboratories
Bioinformatics analysis is a key element in the development of in-house next-generation sequencing assays for tumor genetic profiling that can include both tumor DNA and RNA with comparisons to matched-normal DNA in select cases. Bioinformatics analysis encompasses a computationally heavy component...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Journal of Pathology Informatics |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S215335392200757X |
| _version_ | 1797976975599468544 |
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| author | Chelsea K. Raulerson Erika C. Villa Jeremy A. Mathews Benjamin Wakeland Yan Xu Jeffrey Gagan Brandi L. Cantarel |
| author_facet | Chelsea K. Raulerson Erika C. Villa Jeremy A. Mathews Benjamin Wakeland Yan Xu Jeffrey Gagan Brandi L. Cantarel |
| author_sort | Chelsea K. Raulerson |
| collection | DOAJ |
| description | Bioinformatics analysis is a key element in the development of in-house next-generation sequencing assays for tumor genetic profiling that can include both tumor DNA and RNA with comparisons to matched-normal DNA in select cases. Bioinformatics analysis encompasses a computationally heavy component that requires a high-performance computing component and an assay-dependent quality assessment, aggregation, and data cleaning component. Although there are free, open-source solutions and fee-for-use commercial services for the computationally heavy component, these solutions and services can lack the options commonly utilized in increasingly complex genomic assays. Additionally, the cost to purchase commercial solutions or implement and maintain open-source solutions can be out of reach for many small clinical laboratories. Here, we present Software for Clinical Health in Oncology for Omics Laboratories (SCHOOL), a collection of genomics analysis workflows that (i) can be easily installed on any platform; (ii) run on the cloud with a user-friendly interface; and (iii) include the detection of single nucleotide variants, insertions/deletions, copy number variants (CNVs), and translocations from RNA and DNA sequencing. These workflows contain elements for customization based on target panel and assay design, including somatic mutational analysis with a matched-normal, microsatellite stability analysis, and CNV analysis with a single nucleotide polymorphism backbone. All of the features of SCHOOL have been designed to run on any computer system, where software dependencies have been containerized. SCHOOL has been built into apps with workflows that can be run on a cloud platform such as DNANexus using their point-and-click graphical interface, which could be automated for high-throughput laboratories. |
| first_indexed | 2024-04-11T04:59:35Z |
| format | Article |
| id | doaj.art-2b79772af1f64605ac2df7ef0a0d566a |
| institution | Directory Open Access Journal |
| issn | 2153-3539 |
| language | English |
| last_indexed | 2024-04-11T04:59:35Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Pathology Informatics |
| spelling | doaj.art-2b79772af1f64605ac2df7ef0a0d566a2022-12-26T04:09:05ZengElsevierJournal of Pathology Informatics2153-35392022-01-0113100163SCHOOL: Software for Clinical Health in Oncology for Omics LaboratoriesChelsea K. Raulerson0Erika C. Villa1Jeremy A. Mathews2Benjamin Wakeland3Yan Xu4Jeffrey Gagan5Brandi L. Cantarel6Bioinformatics Core Facility, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USABioinformatics Core Facility, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USABioinformatics Core Facility, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USABioinformatics Core Facility, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USADepartment of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USADepartment of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USABioinformatics Core Facility, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Corresponding author at: Bioinformatics Core Facility, Department of Bioinformatics, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, EB3.212, MC 9365, Dallas, TX 75390-9365, USA.Bioinformatics analysis is a key element in the development of in-house next-generation sequencing assays for tumor genetic profiling that can include both tumor DNA and RNA with comparisons to matched-normal DNA in select cases. Bioinformatics analysis encompasses a computationally heavy component that requires a high-performance computing component and an assay-dependent quality assessment, aggregation, and data cleaning component. Although there are free, open-source solutions and fee-for-use commercial services for the computationally heavy component, these solutions and services can lack the options commonly utilized in increasingly complex genomic assays. Additionally, the cost to purchase commercial solutions or implement and maintain open-source solutions can be out of reach for many small clinical laboratories. Here, we present Software for Clinical Health in Oncology for Omics Laboratories (SCHOOL), a collection of genomics analysis workflows that (i) can be easily installed on any platform; (ii) run on the cloud with a user-friendly interface; and (iii) include the detection of single nucleotide variants, insertions/deletions, copy number variants (CNVs), and translocations from RNA and DNA sequencing. These workflows contain elements for customization based on target panel and assay design, including somatic mutational analysis with a matched-normal, microsatellite stability analysis, and CNV analysis with a single nucleotide polymorphism backbone. All of the features of SCHOOL have been designed to run on any computer system, where software dependencies have been containerized. SCHOOL has been built into apps with workflows that can be run on a cloud platform such as DNANexus using their point-and-click graphical interface, which could be automated for high-throughput laboratories.http://www.sciencedirect.com/science/article/pii/S215335392200757XBioinformaticscancerNGS |
| spellingShingle | Chelsea K. Raulerson Erika C. Villa Jeremy A. Mathews Benjamin Wakeland Yan Xu Jeffrey Gagan Brandi L. Cantarel SCHOOL: Software for Clinical Health in Oncology for Omics Laboratories Journal of Pathology Informatics Bioinformatics cancer NGS |
| title | SCHOOL: Software for Clinical Health in Oncology for Omics Laboratories |
| title_full | SCHOOL: Software for Clinical Health in Oncology for Omics Laboratories |
| title_fullStr | SCHOOL: Software for Clinical Health in Oncology for Omics Laboratories |
| title_full_unstemmed | SCHOOL: Software for Clinical Health in Oncology for Omics Laboratories |
| title_short | SCHOOL: Software for Clinical Health in Oncology for Omics Laboratories |
| title_sort | school software for clinical health in oncology for omics laboratories |
| topic | Bioinformatics cancer NGS |
| url | http://www.sciencedirect.com/science/article/pii/S215335392200757X |
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