A community effort to create standards for evaluating tumor subclonal reconstruction Journal Article
| Authors: | Salcedo, A.; Tarabichi, M.; Espiritu, S. M. G.; Deshwar, A. G.; David, M.; Wilson, N. M.; Dentro, S.; Wintersinger, J. A.; Liu, L. Y.; Ko, M.; Sivanandan, S.; Zhang, H.; Zhu, K.; Yang, T. H. O.; Chilton, J. M.; Buchanan, A.; Lalansingh, C. M.; P’ng, C.; Anghel, C. V.; Umar, I.; Lo, B.; Zou, W.; DREAM SMC-Het Participants; Simpson, J. T.; Stuart, J. M.; Anastassiou, D.; Guan, Y.; Ewing, A. D.; Ellrott, K.; Wedge, D. C.; Morris, Q.; Van Loo, P.; Boutros, P. C. |
| Contributor: | Vázquez-García, I. |
| Article Title: | A community effort to create standards for evaluating tumor subclonal reconstruction |
| Abstract: | Tumor DNA sequencing data can be interpreted by computational methods that analyze genomic heterogeneity to infer evolutionary dynamics. A growing number of studies have used these approaches to link cancer evolution with clinical progression and response to therapy. Although the inference of tumor phylogenies is rapidly becoming standard practice in cancer genome analyses, standards for evaluating them are lacking. To address this need, we systematically assess methods for reconstructing tumor subclonality. First, we elucidate the main algorithmic problems in subclonal reconstruction and develop quantitative metrics for evaluating them. Then we simulate realistic tumor genomes that harbor all known clonal and subclonal mutation types and processes. Finally, we benchmark 580 tumor reconstructions, varying tumor read depth, tumor type and somatic variant detection. Our analysis provides a baseline for the establishment of gold-standard methods to analyze tumor heterogeneity. © 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. |
| Keywords: | single nucleotide polymorphism; somatic mutation; gold standard; neoplasm; genotype; simulation; genome analysis; tumors; quantitative analysis; dna sequence; evolutionary dynamics; diseases; gene encoding; dna sequences; genetic heterogeneity; phylogeny; cancer genome; tumor heterogeneity; dna sequencing; human; priority journal; article; gold standards; algorithmic problems; quantitative metrics; standard practices; reconstruction algorithm |
| Journal Title: | Nature Biotechnology |
| Volume: | 38 |
| ISSN: | 1087-0156 |
| Publisher: | Nature Publishing Group |
| Date Published: | 2020-01-09 |
| Start Page: | 97 |
| End Page: | 107 |
| Language: | English |
| DOI: | 10.1038/s41587-019-0364-z |
| PUBMED: | 31919445 |
| PROVIDER: | scopus |
| PMCID: | PMC6956735 |
| DOI/URL: | |
| Notes: | Article -- Export Date: 3 February 2020 -- Source: Scopus |
