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Biology subjects

Barnell, E. K.

Publications and source records attributed to Barnell, E. K..

2 recordsLinked to original sources

Spontaneous aggressive ERα+ mammary tumor model is driven by Kras activation

The NRL-PRL murine model, defined by mammary-selective transgenic rat prolactin ligand rPrl expression, establishes spontaneous ER+ mammary tumors, mimicking the association between elevated prolactin (PRL) and risk for development of ER+ breast cancer in postmenopausal women. Whole genome and exome sequencing in a discovery cohort (n=5) of end stage tumors revealed canonical activating mutations and copy number amplifications of Kras. The frequent mutations in this pathway were validated in an extension cohort, identifying activating Ras alterations in 79% (23/29) of tumors. Transcriptome analyses over the course of oncogenesis revealed marked alterations associated with Ras activity in established tumors, compared to preneoplastic tissues, in cell-intrinsic processes associated with mitosis, cell adhesion and invasion, as well as in the tumor microenvironment, including immune activity. These genomic analyses suggest that PRL induces a selective bottleneck for spontaneous Ras-driven tumors which may model a subset of aggressive clinical ER+ breast cancers.

cancer biology

Standard operating procedure for somatic variant refinement of tumor sequencing data

PurposeManual review of aligned sequencing reads is required to develop a high-quality list of somatic variants from massively parallel sequencing data (MPS). Despite widespread use in analyzing MPS data, there has been little attempt to describe methods for manual review, resulting in high inter- and intra-lab variability in somatic variant detection and characterization of tumors.\n\nMethodsOpen source software was used to develop an optimal method for manual review setup. We also developed a systemic approach to visually inspect each variant during manual review.\n\nResultsWe present a standard operating procedures for somatic variant refinement for use by manual reviewers. The approach is enhanced through representative examples of 4 different manual review categories that indicate a reviewers confidence in the somatic variant call and 19 annotation tags that contextualize commonly observed sequencing patterns during manual review. Representative examples provide detailed instructions on how to classify variants during manual review to rectify lack of confidence in automated somatic variant detection.\n\nConclusionStandardization of somatic variant refinement through systematization of manual review will improve the consistency and reproducibility of identifying true somatic variants after automated variant calling.

genetics