Allele-specific copy number analysis of tumors

By Peter Van Loo, Silje H. Nordgard, O. Lingjærde, H. Russnes, I. H. Rye, Wei Sun, V. Weigman, P. Marynen, A. Zetterberg, B. Naume and 3 more. Proceedings of the National Academy of Sciences of the United States of America, 2010

1,185 citations recorded by the source corpus.

Subfields: Cancer Research, Cell Biology, Genetics

View Paper: https://www.semanticscholar.org/paper/654ba9d2ae53224b630545defc303cf2359b57c1

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In Cancer Research

1. Charles Swanton
2. Nicholas McGranahan
3. Gad Getz
4. Peter J. Campbell
5. S. Nik-Zainal
6. David C. Wedge
7. Ludmil B. Alexandrov
8. Niko Beerenwinkel

In Cell Biology

1. Michael R. Stratton
2. Charles Swanton
3. Stephen J. Elledge
4. D. Pellman

In Genetics

1. Charles Swanton
2. Nicholas McGranahan
3. Elaine R. Mardis
4. Hui Shen
5. William T. Barry
6. Michael R. Stratton
7. Javier Herrero
8. Peter W. Laird

Citations in the corpus

• Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics (2013, methodology): “We confirmed that the observed heterogeneity was not the result of differences in normal contamination by demonstrating the absence of significant correlation between the estimated cellularity [using ASCAT (Allele Specific Copy number Analysis of Tumors) (20)] and the fraction of shared (Spearman’s ”
• Mutational Processes Molding the Genomes of 21 Breast Cancers (2012, methodology): “Copy number and allelic ratio profiles were statistically processed by using the ASCAT algorithm, version 2.0 (Van Loo et al., 2010).”
• Mutational signatures associated with tobacco smoking in human cancer (2016, methodology): “Each sample’s purity ρ and the copy number of the surrounding region in the tumor ψt was determined by ASCAT (46), the copy number in the normal ψn is assumed to be two, except for variants on sex chromosomes in male patients where it is set to one.”
• Absolute quantification of somatic DNA alterations in human cancer (2012, methodology): “Notably, we observed an apparent bias by ASCAT to underestimate cancer cell fraction (Fig.”
• Universal Patterns of Selection in Cancer and Somatic Tissues (2018, positive): “Copy number profiles for all tumor samples were then inferred from the corrected data using ASCAT version 2.4.2 (Van Loo et al., 2010).”
• Ploidy and large-scale genomic instability consistently identify basal-like breast carcinomas with BRCA1/2 inactivation. (2012, positive): “Second, SNP array analyses can be used to infer chromosome numbers and tumor ploidy status (23, 44).”
• Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition (2021, neutral): “…José Afonso Guerra-Assunção,5 Lucia Conde,5 Andrew J.S. Furness,6 Sunil Kumar Saini,7 Sine R. Hadrup,7 Javier Herrero,5 Se-Hoon Lee,8,9 Peter Van Loo,10 Tariq Enver,4 James Larkin,6 Matthew D. Hellmann,11 Samra Turajlic,6,12 Sergio A. Quezada, PhD,2,3,* Nicholas McGranahan,3,* and Charles…”
• The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma (2018, methodology): “[PubMed: 17145819] Van Loo P, Nordgard SH, Lingjærde OC, Russnes HG, Rye IH, Sun W, Weigman VJ, Marynen P, Zetterberg A, Naume B, et al. Allele-specific copy number analysis of tumors.”
• Subclonal diversification of primary breast cancer revealed by multiregion sequencing (2015, positive): “Segmental copy number information was derived for each of the 29 tumor samples for which we had whole genome NGS data using the ASCAT algorithm (allele-specific copy number analysis) of tumors as previously described 32 .”