Combined burden and functional impact tests for cancer driver discovery using DriverPower
| العنوان: | Combined burden and functional impact tests for cancer driver discovery using DriverPower |
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| المؤلفون: | Shuai S., Abascal F., Amin S. B., Bader G. D., Bandopadhayay P., Barenboim J., Beroukhim R., Bertl J., Boroevich K. A., Brunak S., Campbell P. J., Carlevaro-Fita J., Chakravarty D., Chan C. W. Y., Chen K., Choi J. K., Deu-Pons J., Dhingra P., Diamanti K., Feuerbach L., Fink J. L., Fonseca N. A., Frigola J., Gambacorti Passerini C., Garsed D. W., Gerstein M., Getz G., Guo Q., Gut I. G., Haan D., Hamilton M. P., Haradhvala N. J., Harmanci A. O., Helmy M., Herrmann C., Hess J. M., Hobolth A., Hodzic E., Hong C., Hornshoj H., Isaev K., Izarzugaza J. M. G., Johnson R., Johnson T. A., Juul M., Juul R. I., Kahles A., Kahraman A., Kellis M., Khurana E., Kim J., Kim J. K., Kim Y., Komorowski J., Korbel J. O., Kumar S., Lanzos A., Larsson E., Lawrence M. S., Lee D., Lehmann K. -V., Li S., Li X., Lin Z., Liu E. M., Lochovsky L., Lou S., Madsen T., Marchal K., Martincorena I., Martinez-Fundichely A., Maruvka Y. E., McGillivray P. D., Meyerson W., Muinos F., Mularoni L., Nakagawa H., Nielsen M. M., Paczkowska M., Park K., Pedersen J. S., Pons T., Pulido-Tamayo S., Raphael B. J., Reimand J., Reyes-Salazar I., Reyna M. A., Rheinbay E., Rubin M. A., Rubio-Perez C., Sahinalp S. C., Saksena G., Salichos L., Sander C., Schumacher S. E., Shackleton M., Shapira O., Shen C., Shrestha R., Sidiropoulos N., Sieverling L., Sinnott-Armstrong N., Stein L. D., Stuart J. M., Tamborero D., Tiao G., Tsunoda T., Umer H. M., Uuskula-Reimand L., Valencia A., Vazquez M., Verbeke L. P. C., Wadelius C., Wadi L., Wang J., Warrell J., Waszak S. M., Weischenfeldt J., Wheeler D. A., Wu G., Yu J., Zhang J., Zhang X., Zhang Y., Zhao Z., Zou L., von Mering C., Gallinger S., Stein L. |
| المساهمون: | Shuai, Shimin [0000-0002-9527-8018], Apollo - University of Cambridge Repository, Shuai, S, Abascal, F, Amin, S, Bader, G, Bandopadhayay, P, Barenboim, J, Beroukhim, R, Bertl, J, Boroevich, K, Brunak, S, Campbell, P, Carlevaro-Fita, J, Chakravarty, D, Chan, C, Chen, K, Choi, J, Deu-Pons, J, Dhingra, P, Diamanti, K, Feuerbach, L, Fink, J, Fonseca, N, Frigola, J, Gambacorti Passerini, C, Garsed, D, Gerstein, M, Getz, G, Guo, Q, Gut, I, Haan, D, Hamilton, M, Haradhvala, N, Harmanci, A, Helmy, M, Herrmann, C, Hess, J, Hobolth, A, Hodzic, E, Hong, C, Hornshoj, H, Isaev, K, Izarzugaza, J, Johnson, R, Johnson, T, Juul, M, Juul, R, Kahles, A, Kahraman, A, Kellis, M, Khurana, E, Kim, J, Kim, Y, Komorowski, J, Korbel, J, Kumar, S, Lanzos, A, Larsson, E, Lawrence, M, Lee, D, Lehmann, K, Li, S, Li, X, Lin, Z, Liu, E, Lochovsky, L, Lou, S, Madsen, T, Marchal, K, Martincorena, I, Martinez-Fundichely, A, Maruvka, Y, Mcgillivray, P, Meyerson, W, Muinos, F, Mularoni, L, Nakagawa, H, Nielsen, M, Paczkowska, M, Park, K, Pedersen, J, Pons, T, Pulido-Tamayo, S, Raphael, B, Reimand, J, Reyes-Salazar, I, Reyna, M, Rheinbay, E, Rubin, M, Rubio-Perez, C, Sahinalp, S, Saksena, G, Salichos, L, Sander, C, Schumacher, S, Shackleton, M, Shapira, O, Shen, C, Shrestha, R, Sidiropoulos, N, Sieverling, L, Sinnott-Armstrong, N, Stein, L, Stuart, J, Tamborero, D, Tiao, G, Tsunoda, T, Umer, H, Uuskula-Reimand, L, Valencia, A, Vazquez, M, Verbeke, L, Wadelius, C, Wadi, L, Wang, J, Warrell, J, Waszak, S, Weischenfeldt, J, Wheeler, D, Wu, G, Yu, J, Zhang, J, Zhang, X, Zhang, Y, Zhao, Z, Zou, L, von Mering, C, Gallinger, S |
| المصدر: | Nature Communications Nature Communications, Vol 11, Iss 1, Pp 1-12 (2020) Shuai, S, Abascal, F, Amin, S B, Bader, G D, Bandopadhayay, P, Barenboim, J, Beroukhim, R, Bertl, J, Boroevich, K A, Brunak, S, Campbell, P J, Carlevaro-Fita, J, Chakravarty, D, Chan, C W Y, Chen, K, Choi, J K, Deu-Pons, J, Dhingra, P, Diamanti, K, Feuerbach, L, Fink, J L, Fonseca, N A, Frigola, J, Gambacorti-Passerini, C, Garsed, D W, Gerstein, M, Getz, G, Guo, Q, Gut, I G, Haan, D, Hamilton, M P, Haradhvala, N J, Harmanci, A O, Helmy, M, Herrmann, C, Hess, J M, Hobolth, A, Hodzic, E, Hong, C, Hornshøj, H, Isaev, K, Izarzugaza, J M G, Johnson, R, Johnson, T A, Juul, M, Juul, R I, Kahles, A, Pedersen, J S, Sidiropoulos, N, Weischenfeldt, J, PCAWG Drivers and Functional Interpretation Working Group & PCAWG Consortium 2020, ' Combined burden and functional impact tests for cancer driver discovery using DriverPower ', Nature Communications, vol. 11, no. 1, 734 . https://doi.org/10.1038/s41467-019-13929-1Test Nature Communications, 11 (1) Nature Communications, 11 Nature Communications, 11, 1 Nature communications, vol 11, iss 1 Shuai, Shimin; Gallinger, Steven; Stein, Lincoln (2020). Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nature communications, 11(1), p. 734. Nature Publishing Group 10.1038/s41467-019-13929-1 <http://dx.doi.org/10.1038/s41467-019-13929-1Test> Shuai, S, PCAWG Drivers and Functional Interpretation Working Group, Gallinger, S, Stein, L & PCAWG Consortium 2020, ' Combined burden and functional impact tests for cancer driver discovery using DriverPower ', Nature Communications, vol. 11, no. 1, 734 . https://doi.org/10.1038/s41467-019-13929-1Test NATURE COMMUNICATIONS |
| بيانات النشر: | Nature Publishing Group UK, 2020. |
| سنة النشر: | 2020 |
| مصطلحات موضوعية: | 0301 basic medicine, Cancer genome sequencing, Mutation rate, Medizin, General Physics and Astronomy, VARIANTS, Genome, Receptors, G-Protein-Coupled, 0302 clinical medicine, Peptide Elongation Factor 1, PCAWG Drivers and Functional Interpretation Working Group, Mutation Rate, Neoplasms, BINDING, Receptors, Medicine and Health Sciences, HETEROGENEITY, RECURRENT, Càncer, lcsh:Science, 610 Medicine & health, Cancer, Multidisciplinary, Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17], MEF2 Transcription Factors, Genomics, Women's cancers Radboud Institute for Health Sciences [Radboudumc 17], 030220 oncology & carcinogenesis, F1 score, Medical Genetics, Medical genomics, Algorithms, Human, EXPRESSION, ACETYLATION, SOMATIC MUTATION, Science, Computational biology, Biology, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, G-Protein-Coupled, Germline mutation, Genetics, Humans, Genomes, MOF, Medicinsk genetik, Whole genome sequencing, Whole Genome Sequencing, Genome, Human, Human Genome, Biology and Life Sciences, PCAWG Consortium, General Chemistry, Oncogenes, 030104 developmental biology, Good Health and Well Being, Mutation, CHROMATIN ORGANIZATION, cancer genome sequencing, DriverPower, Software, MEF2 Transcription Factors, Neoplasms, Mutation Rate, lcsh:Q, PATHOGENICITY, Software, Coding (social sciences) |
| الوصف: | The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features derived from public sources, DriverPower’s background mutation model explains up to 93% of the regional variance in the mutation rate across multiple tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2583 cancer genomes from the PCAWG project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Working Group, DriverPower has the highest F1 score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery. Nature Communications, 11 (1) ISSN:2041-1723 |
| وصف الملف: | application/pdf; application/application/pdf; application/zip; text/xml |
| اللغة: | English |
| تدمد: | 2041-1723 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a66b76677d0b16adc338a5e2ae7f60b2Test http://europepmc.org/articles/PMC7002750Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....a66b76677d0b16adc338a5e2ae7f60b2 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 20411723 |
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