: A copy number clustering tool designed to refit and recalibrate the baseline region of tumors’ profiles
Tài liệu tham khảo
Beroukhim, 2010, The landscape of somatic copy-number alteration across human cancers, Nature, 10.1038/nature08822
Zack, 2013, Pan-cancer patterns of somatic copy number alteration, Nat Genet, 45, 1134, 10.1038/ng.2760
Cardona-Benavides, 2021, Genetic Abnormalities in Multiple Myeloma: Prognostic and Therapeutic Implications, Cells, 10, 336, 10.3390/cells10020336
Barwick, 2019, Cell of origin and genetic alterations in the pathogenesis of multiple myeloma, Front Immunol, 10.3389/fimmu.2019.01121
Bergamaschi, 2006, Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer, Genes Chromosom Cancer, 10.1002/gcc.20366
Pawlyn, 2017, Evolutionary biology of high-risk multiple myeloma, Nat Rev Cancer, 17, 543, 10.1038/nrc.2017.63
Palumbo, 2015, Revised international staging system for multiple myeloma: A report from international myeloma working group, J Clin Oncol, 10.1200/JCO.2015.61.2267
Hieronymus, 2018, Tumor copy number alteration burden is a pan-cancer prognostic factor associated with recurrence and death, eLife, 7, 1, 10.7554/eLife.37294
Smith, 2018, Systematic identification of mutations and copy number alterations associated with cancer patient prognosis, eLife, 7, 1, 10.7554/eLife.39217
Mayrhofer, 2016, Rawcopy: Improved copy number analysis with Affymetrix arrays, Sci Rep, 10.1038/srep36158
Carter, 2012, Absolute quantification of somatic DNA alterations in human cancer, Nat Biotechnol, 30, 413, 10.1038/nbt.2203
Van Loo, 2010, Allele-specific copy number analysis of tumors, Proc Natl Acad Sci USA, 107, 16910, 10.1073/pnas.1009843107
Translational Genomics Research Institute (TGen). tCoNut. Published 2016. https://github.com/tgen/tCoNuT.wiki.git.
Gao, 2020, Minimum error calibration and normalization for genomic copy number analysis, Genomics, 112, 3331, 10.1016/j.ygeno.2020.05.008
Keats, 2016
The Cancer Genome Atlas Program - National Cancer Institute. Accessed September 22, 2021. https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga.
Charrad M, Ghazzali N, Boiteau V, Niknafs A. NbClust : An R Package for Determining the. J Stat Softw. Published online 2014. Accessed January 14, 2022. https://www.jstatsoft.org/article/view/v061i06.
Poletti A, Mazzocchetti G, Solli V. BOBaFIT: Refitting diploid region profiles using a clustering procedure. Published 2021. Accessed January 11, 2022. https://bioconductor.org/packages/devel/bioc/html/BOBaFIT.html.
Avet-Loiseau, 2009, Prognostic significance of copy-number alterations in multiple myeloma, J Clin Oncol, 10.1200/JCO.2008.20.6136
Mikhael, 2013, Management of newly diagnosed symptomatic multiple myeloma: Updated mayo stratification of myeloma and risk-adapted therapy (msmart) consensus guidelines 2013, Mayo Clin Proc, 88, 360, 10.1016/j.mayocp.2013.01.019
Tarabichi, 2021, A practical guide to cancer subclonal reconstruction from DNA sequencing, Nat Methods, 18, 144, 10.1038/s41592-020-01013-2