SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization

Qiao, Yi; Quinlan, Aaron R.; Jazaeri, Amir A.; Wheeler, David A.; Marth, Gábor

doi:10.1186/preaccept-1691129011290725

Cited by 18 publications

(31 citation statements)

References 47 publications

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“…[43]. Cancer cell fractions were defined using ABSOLUTE [44] and clonal composition analysis was carried out using SubcloneSeeker [45] (Supplementary Methods). …”

Section: Methodsmentioning

confidence: 99%

“…Red solid arrows depict the divergence of a cell population from one lesion to another. Decomposition of genetically distinct clones and clonal evolution in lesions from case 9 and case 16 were performed using the results from ABSOLUTE [44] and SubcloneSeeker [45]. The percentages indicate the prevalence of each clone in each morphologically distinct component of each case.…”

Section: Figurementioning

confidence: 99%

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The repertoire of somatic genetic alterations of acinic cell carcinomas of the breast: an exploratory, hypothesis‐generating study

Guerini-Rocco

Hodi

Piscuoglio

et al. 2015

The Journal of Pathology

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Acinic cell carcinoma (ACC) of the breast is a rare form of triple-negative (that is, estrogen receptor-negative, progesterone receptor-negative, HER2-negative) salivary gland-type tumor displaying serous acinar differentiation. Despite its triple-negative phenotype, breast ACCs are reported to have an indolent clinical behavior. Here, we sought to define whether ACCs have a mutational repertoire distinct from that of other triple-negative breast cancers (TNBCs). DNA was extracted from microdissected formalin-fixed paraffin-embedded sections of tumor and normal tissue from two pure and six mixed breast ACCs. Each tumor component of the mixed cases was microdissected separately. Tumor and normal samples were subjected to targeted capture massively parallel sequencing targeting all exons of 254 genes, including genes most frequently mutated in breast cancer and related to DNA repair. Selected somatic mutations were validated by targeted amplicon resequencing and Sanger sequencing. Akin to other forms of TNBC, the most frequently mutated gene found in breast ACCs was TP53 (one pure and six mixed cases). Additional somatic mutations affecting breast cancer-related genes found in ACCs included PIK3CA, MTOR, CTNNB1, BRCA1, ERBB4, ERBB3, INPP4B and FGFR2. Copy number alteration analysis revealed complex patterns of gains and losses similar to those of common forms of TNBCs. Of the mixed cases analyzed, identical somatic mutations were found in the acinic and the high-grade non-acinic components in two out of four cases analyzed, providing evidence of their clonal relatedness. In conclusion, breast ACCs display the hallmark somatic genetic alterations found in high-grade forms of TNBC, including complex patterns of gene copy number alterations and recurrent TP53 mutations. Furthermore, we provide circumstantial genetic evidence to suggest that ACCs may constitute the substrate for the development of more aggressive forms of triple-negative disease.

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“…[43]. Cancer cell fractions were defined using ABSOLUTE [44] and clonal composition analysis was carried out using SubcloneSeeker [45] (Supplementary Methods). …”

Section: Methodsmentioning

confidence: 99%

Section: Figurementioning

confidence: 99%

The repertoire of somatic genetic alterations of acinic cell carcinomas of the breast: an exploratory, hypothesis‐generating study

Guerini-Rocco

Hodi

Piscuoglio

et al. 2015

The Journal of Pathology

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“…Given the variations in the rates and mechanisms of SNV versus CNV evolution, some methods have found particular power in combining data types, as is done by GRAFT 134 , PhyloWGS 135 , SPRUCE 136 , and Canopy 137 . The available methods also cover a range of models and algorithmic techniques, including various combinatorial (parsimony-like) character-based methods 130,131,134,138 , probabilistic character-based methods 133,135 , and distance-based minimum evolution 85 .…”

Section: Variations On Tumour Phylogeneticsmentioning

confidence: 99%

The evolution of tumour phylogenetics: principles and practice

2017

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Rapid advances in high-throughput sequencing and a growing realization of the importance of evolutionary theory to cancer genomics have led to a proliferation of phylogenetic studies of tumour progression. These studies have yielded not only new insights but also a plethora of experimental approaches, sometimes reaching conflicting or poorly supported conclusions. Here, we consider this body of work in light of the key computational principles underpinning phylogenetic inference, with the goal of providing practical guidance on the design and analysis of scientifically rigorous tumour phylogeny studies. We survey the range of methods and tools available to the researcher, their key applications, and the various unsolved problems, closing with a perspective on the prospects and broader implications of this field.

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“…These encompass next-generation sequencing methods for analyzing tumor and normal cell composition, the analysis of clonal populations in cancers (Qiao et al . [ 6 ]), and methods addressing epigenetic plasticity (Zheng et al . [ 7 ]).…”

Section: Methodological Approaches To Heterogeneitymentioning

confidence: 99%

Tumor heterogeneity: next-generation sequencing enhances the view from the pathologist's microscope

Aparicio

Mardis

2014

Genome Biol

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SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization

Cited by 18 publications

References 47 publications

The repertoire of somatic genetic alterations of acinic cell carcinomas of the breast: an exploratory, hypothesis‐generating study

The repertoire of somatic genetic alterations of acinic cell carcinomas of the breast: an exploratory, hypothesis‐generating study

The evolution of tumour phylogenetics: principles and practice

Tumor heterogeneity: next-generation sequencing enhances the view from the pathologist's microscope

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