Abstract 2227: An automatic pipeline to find and annotate rare subclonal somatic variants in a paired tumor/normal sample
| العنوان: | Abstract 2227: An automatic pipeline to find and annotate rare subclonal somatic variants in a paired tumor/normal sample |
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| المؤلفون: | Nathan Pearson, Thomas Knudsen, Anika Joecker, Bodil Oster, Dan Richards, Roald Forsberg, Anne-Mette K. Hein, Naomi Thomson, Anne Arens, Bjarne Knudsen, Cecilie Boysen |
| المصدر: | Cancer Research. 74:2227-2227 |
| بيانات النشر: | American Association for Cancer Research (AACR), 2014. |
| سنة النشر: | 2014 |
| مصطلحات موضوعية: | Whole genome sequencing, Genetics, Cancer Research, education.field_of_study, media_common.quotation_subject, Population, Cancer, Biology, medicine.disease, Phenotype, Primary tumor, Annotation, Ingenuity, Oncology, medicine, education, Allele frequency, media_common |
| الوصف: | Identifying and characterizing somatic variants in deep genome sequence data from tumor samples remains challenging and time-consuming. Of special interest in cancer research and diagnostics is the detection and annotation of rare subclonal somatic variants found only in a small proportion of primary tumor cells. Such variants can drive tumor spread and recurrence, but are often neglected in choosing treatments. Currently, few tools reliably distinguish such rare subclonal variants from sequencing errors. And even among real somatic variants, drivers (of tumor growth, spread, or resistance) are hard to distinguish from passengers. Doing so entails integrating diverse information on variants, genes, pathways, cancer-relevant phenotypes, and treatments (including insights on population allele frequencies and broader evolutionary conservation; known/likely effects on gene product structure, function, expression, and interaction; and relations among gene products, phenotypes, and drugs). Software for effectively integrating such data in light of genomic variation in samples, to highlight relevant findings through clear visualization, has been a pressing need. Here we present an end-to-end analysis workflow for finding and functionally characterizing rare subclonal variants, using the newly developed CLC Cancer Research Workbench to feed the interpretive platform of Ingenuity Variant Analysis, to identify cancer driver mutations in paired tumor/normal samples. We will show new interesting results from this analysis, which were not shown beforehand on this publicly available cancer dataset (Case Reports in Oncological Medicine, Volume 2013 (2013), Article ID 270362) from a patient with massive acinic cell carcinoma. Citation Format: Anika Joecker, Nathan Pearson, Cecilie Boysen, Naomi Thomson, Anne-Mette Hein, Bodil Oster, Anne Arens, Bjarne Knudsen, Thomas Knudsen, Dan Richards, Roald Forsberg. An automatic pipeline to find and annotate rare subclonal somatic variants in a paired tumor/normal sample. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2227. doi:10.1158/1538-7445.AM2014-2227 |
| تدمد: | 1538-7445 0008-5472 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_________::80fc1db9e380daeca8d8c0672cb13e65 https://doi.org/10.1158/1538-7445.am2014-2227 |
| رقم الأكسشن: | edsair.doi...........80fc1db9e380daeca8d8c0672cb13e65 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 15387445 00085472 |
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