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|Interface||Command line interface|
|Restrictions to use||None|
|Operating system||Unix/Linux, Mac OS, Windows|
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- person_outline Karen Messer
Publication for AbsCN-seq
The Clinical Significance and Molecular Features of the Spatial Tumor Shapes in Breast Cancers
[…] e 41 patients, two showed poor quality in exome sequencing data, and the final exome analysis was done in 39 patients. Absolute copy numbers based on copy-number variations of samples are inferred by absCN-seq , and clonality analysis is performed by sciClone . Somatic mutations are calculated by VarScan v2.3.6 and variants are annotated by in-house annotation pipeline. […]
Mutational Profiling Can Establish Clonal or Independent Origin in Synchronous Bilateral Breast and Other Tumors
[…] n to both tumors (, upper panel). There was an additional deletion in the distal end of 6q (6q25.1-6q27) apparent only in the TN tumor (, lower panel), covering the entire ESR1 locus. We then applied absCN-seq to estimate the absolute copy numbers for the ESR1 region () and found that the HR+ tumor has two copies and the TN tumor only one copy for this region. Thus a plausible evolutionary sequenc […]
BACOM2.0 facilitates absolute normalization and quantification of somatic copy number alterations in heterogeneous tumor
[…] eotide variants but not original sequence reads. The formulation does not explicitly consider effects of copy number gains/losses and may bias tumor purity estimation. Moreover, PuriryEst, THetA, and AbsCN-seq rely on next-generation sequencing data, thus may not be applicable to existing copy number data acquired using more classic methods such as SNP arrays.Since BACOM2.0 is supported by a well- […]
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