Dataset Information

Diversity analysis of US Canola core collection

ABSTRACT: The study was done to analyze the genetic diversity, identify SNPs and genes associated to specific traits and optimize genomic selection models in a Canola core collection.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Brassica Napus

SUBMITTER: North Dakota State University

PROVIDER: PRJEB42419 | EVA | 2021-01-13

REPOSITORIES: EVA

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Source:

			Action	DRS
	Canola_variants.accessioned.vcf.gz	Vcf
	Canola_variants.vcf.gz	Vcf
	Canola_variants.vcf.gz.tbi	Vcf

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Project description:Systematic collection of fresh tissues for research at the time of diagnostic image-guided breast biopsy has the potential to fuel a wide variety of innovative studies. Here we report the initial experience, including safety, feasibility and laboratory proof-of-principle, with the collection and analysis of research specimens obtained via breast core needle biopsy immediately following routine clinical biopsy at a single institution over a 14-month period. Study eligibility criteria consisted of patients age 18 or older who were undergoing a clinical breast needle biopsy. Patients providing informed consent underwent one or two additional core biopsies following collection of all necessary clinical specimens. In total, 395 patients were approached and 270 consented to the research study, yielding a 68.4% consent rate. Among consenting patients, 238 lesions were biopsied for research, resulting in 446 research specimens collected. No immediate complications were observed. During the same period, zero complications were reported among the non-research procedures (1622 breast biopsy procedures). Representative research core specimens showed high diagnostic concordance with clinical core biopsies. Flow cytometry demonstrated consistent recovery of hundreds to thousands of viable cells per research core. Among a group of HER2+ tumor research specimens, HER2 assessment by flow cytometry correlated highly with immunohistochemistry (IHC) staining, and in addition revealed extensive inter- and intra-tumoral variation in HER2 levels of potential clinical relevance. Suitability for single-cell transcriptomic analysis was demonstrated for a triple-negative tumor core biopsy, revealing substantial cellular diversity in the tumor immune microenvironment, including a prognostically relevant T cell subpopulation. Thus, collection of fresh tissues for research purposes at the time of diagnostic breast biopsy is safe, feasible and efficient, and may provide a high-yield mechanism to generate a rich tissue repository for a wide variety of cross-disciplinary research.

Dataset Information

Diversity analysis of US Canola core collection

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