Analytical validation of clinical whole-genome and transcriptome sequencing of patient-derived tumors for reporting targetable variants in cancer Journal Article
| Authors: | Wrzeszczynski, K. O.; Felice, V.; Abhyankar, A.; Kozon, L.; Geiger, H.; Manaa, D.; London, F.; Robinson, D.; Fang, X.; Lin, D.; Lamendola-Essel, M. F.; Khaira, D.; Dikoglu, E.; Emde, A. K.; Robine, N.; Shah, M.; Arora, K.; Basturk, O.; Bhanot, U.; Kentsis, A.; Mansukhani, M. M.; Bhagat, G.; Jobanputra, V. |
| Article Title: | Analytical validation of clinical whole-genome and transcriptome sequencing of patient-derived tumors for reporting targetable variants in cancer |
| Abstract: | We developed and validated a clinical whole-genome and transcriptome sequencing (WGTS) assay that provides a comprehensive genomic profile of a patient's tumor. The ability to fully capture the mappable genome with sufficient sequencing coverage to precisely call DNA somatic single nucleotide variants, insertions/deletions, copy number variants, structural variants, and RNA gene fusions was analyzed. New York State's Department of Health next-generation DNA sequencing guidelines were expanded for establishing performance validation applicable to whole-genome and transcriptome sequencing. Whole-genome sequencing laboratory protocols were validated for the Illumina HiSeq X Ten platform and RNA sequencing for Illumina HiSeq2500 platform for fresh or frozen and formalin-fixed, paraffin-embedded tumor samples. Various bioinformatics tools were also tested, and CIs for sensitivity and specificity thresholds in calling clinically significant somatic aberrations were determined. The validation was performed on a set of 125 tumor normal pairs. RNA sequencing was performed to call fusions and to confirm the DNA variants or exonic alterations. Here, we present our results and WGTS standards for variant allele frequency, reproducibility, analytical sensitivity, and present limit of detection analysis for single nucleotide variant calling, copy number identification, and structural variants. We show that The New York Genome Center WGTS clinical assay can provide a comprehensive patient variant discovery approach suitable for directed oncologic therapeutic applications. © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology |
| Keywords: | controlled study; leukemia; single nucleotide polymorphism; pancreas cancer; reproducibility; multiple myeloma; ovary cancer; breast cancer; skin cancer; gene frequency; lung cancer; transcriptomics; sarcoma; colon cancer; human genome; uterine cervix cancer; lymphoma; liver cancer; dna sequence; brain cancer; kidney cancer; bioinformatics; false positive result; transcriptome; genomic dna; bone cancer; rna sequence; appendix cancer; copy number variation; limit of detection; next generation sequencing; human; article; whole genome sequencing; malignant neoplasm |
| Journal Title: | Journal of Molecular Diagnostics |
| Volume: | 20 |
| Issue: | 6 |
| ISSN: | 1525-1578 |
| Publisher: | Elsevier Science, Inc. |
| Date Published: | 2018-11-01 |
| Start Page: | 822 |
| End Page: | 835 |
| Language: | English |
| DOI: | 10.1016/j.jmoldx.2018.06.007 |
| PUBMED: | 30138725 |
| PROVIDER: | scopus |
| PMCID: | PMC6198246 |
| DOI/URL: | |
| Notes: | Article -- Export Date: 1 November 2018 -- Source: Scopus |
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