The DOI matches its Crossref record; 48 of the 48 references it cites were found in a registry or an index.
Validation and Implementation of Targeted Capture and Sequencing for the Detection of Actionable Mutation, Copy Number Variation, and Gene Rearrangement in Clinical Cancer Specimens
Open accessAbstract
Recent years have seen development and implementation of anticancer therapies targeted to particular gene mutations, but methods to assay clinical cancer specimens in a comprehensive way for the critical mutations remain underdeveloped. We have developed UW-OncoPlex, a clinical molecular diagnostic assay to provide simultaneous deep-sequencing information, based on >500× average coverage, for all classes of mutations in 194 clinically relevant genes. To validate UW-OncoPlex, we tested 98 previously characterized clinical tumor specimens from 10 different cancer types, including 41 formalin-fixed paraffin-embedded tissue samples. Mixing studies indicated reliable mutation detection in samples with ≥ 10% tumor cells. In clinical samples with ≥ 10% tumor cells, UW-OncoPlex correctly identified 129 of 130 known mutations [sensitivity 99.2%, (95% CI, 95.8%-99.9%)], including single nucleotide variants, small insertions and deletions, internal tandem duplications, gene copy number gains and amplifications, gene copy losses, chromosomal gains and losses, and actionable genomic rearrangements, including ALK-EML4, ROS1, PML-RARA, and BCR-ABL. In the same samples, the assay also identified actionable point mutations in genes not previously analyzed and novel gene rearrangements of MLL and GRIK4 in melanoma, and of ASXL1, PIK3R1, and SGCZ in acute myeloid leukemia. To best guide existing and emerging treatment regimens and facilitate integration of genomic testing with patient care, we developed a framework for data analysis, decision support, and reporting clinically actionable results.
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The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
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ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
Wang, K., Li, M., & Hakonarson, H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq603 · Cited by 14,621
ggplot2: Elegant Graphics for Data Analysis
Wickham, H. (2009) · doi:10.1007/978-0-387-98141-3 · Cited by 14,447
Comprehensive molecular portraits of human breast tumours
The Cancer Genome Atlas Network (2012) · Nature · doi:10.1038/nature11412 · Cited by 12,129
Fast and accurate long-read alignment with Burrows-Wheeler transform.
Li, H., & Durbin, R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp698 · Cited by 12,063
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A framework for variation discovery and genotyping using next-generation DNA sequencing data
DePristo, M. A., Banks, E., Poplin, R., Garimella, K. V., Maguire, J. R., Hartl, C., Philippakis, A. A., del Angel, G., Rivas, M. A., Hanna, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.806 · Cited by 11,456
Cited by
Comprehensive Characterization of Cancer Driver Genes and Mutations
Bailey, M. H., Tokheim, C., Porta-Pardo, E., Sengupta, S., Bertrand, D., Weerasinghe, A., Colaprico, A., Wendl, M. C., Kim, J., Reardon, B., et al. (2018) · Cell · doi:10.1016/j.cell.2018.02.060 · Cited by 2,256
Self-citationMemorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT)
Cheng, D. T., Mitchell, T. N., Zehir, A., Shah, R. H., Benayed, R., Syed, A., Chandramohan, R., Liu, Z. Y., Won, H. H., Scott, S. N., et al. (2015) · The Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2014.12.006 · Cited by 2,119
Age-related mutations associated with clonal hematopoietic expansion and malignancies
Xie, M., Lu, C., Wang, J., McLellan, M. D., Johnson, K. J., Wendl, M. C., McMichael, J. F., Schmidt, H. K., Yellapantula, V., Miller, C. A., et al. (2014) · Nature Medicine · doi:10.1038/nm.3733 · Cited by 1,874
Inherited DNA-Repair Gene Mutations in Men with Metastatic Prostate Cancer
Pritchard, C. C., Mateo, J., Walsh, M. F., De Sarkar, N., Abida, W., Beltran, H., Garofalo, A., Gulati, R., Carreira, S., Eeles, R., et al. (2016) · New England Journal of Medicine · doi:10.1056/nejmoa1603144 · Cited by 1,680
Self-citationPennington, K. P., Walsh, T., Harrell, M. I., Lee, M. K., Pennil, C. C., Rendi, M. H., Thornton, A., Norquist, B. M., Casadei, S., Nord, A. S., et al. (2014) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-13-2287 · Cited by 1,051
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Metadata
- Authors
- Pritchard, C. C., Salipante, S. J., Koehler, K., Smith, C., Scroggins, S., Wood, B., Wu, D., Lee, M. K., Dintzis, S., Adey, A., Liu, Y., Eaton, K. D., Martins, R., Stricker, K., Margolin, K. A., Hoffman, N., Churpek, J. E., Tait, J. F., King, M.-C., & Walsh, T.
- Venue
- The Journal of Molecular Diagnostics
- Publisher
- Elsevier BV
- Published
- 2014-01
- Volume
- 16
- Issue
- 1
- Pages
- 56-67
- ISSN
- 1525-1578 (ISSN-L)
- OpenAlex
- W2044060805
- Cited by
- 273
- References
- 48
- FWCI
- 11.28
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Pritchard, C. C., Salipante, S. J., Koehler, K., Smith, C., Scroggins, S., Wood, B., Wu, D., Lee, M. K., Dintzis, S., Adey, A., Liu, Y., Eaton, K. D., Martins, R., Stricker, K., Margolin, K. A., Hoffman, N., Churpek, J. E., Tait, J. F., King, M.-C., & Walsh, T. (2014). Validation and Implementation of Targeted Capture and Sequencing for the Detection of Actionable Mutation, Copy Number Variation, and Gene Rearrangement in Clinical Cancer Specimens. The Journal of Molecular Diagnostics. https://doi.org/10.1016/j.jmoldx.2013.08.004
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
