General
| Acronym/Abbreviation | Definition |
|---|---|
| ACL | Access Control List |
| BAM | Bidirectional Associative Memory |
| BCR | Biospecimen Core Resource |
| CNV | Copy Number Variation |
| DCC | Data Coordinating Center |
| eRA | Electronic Research Administration |
| MAGE-TAB | Microarray Gene Expression - Tabular format |
| PHI | Proctected Health Information |
| TARGET | Therapeutically Applicable Research to Generate Effective Treatments |
| t-SNE | t-distributed stochastic neighbor embedding |
| TSV | Tab Separated Values |
| VCFS | Version Controlled File System |
File Types
| Acronym/Abbreviation | Definition |
|---|---|
| csv | Comma Separated Values |
| fastq | Text-based format for storing both a biological sequence and corresponding quality score |
| json | JavaScript Object Notation |
| maf | Mutation Annotation Format |
| rds | Ray Dream Studio (contains three-dimensional objects and animation settings) |
| tsv | Tab separated value |
| txt | Text |
| xml | Extensible Markup Language |
Scientific Assays
| Acronym/Abbreviation | Definition |
|---|---|
| CyCIF | Cyclic Immunofluorescence |
| CyTOF | Cytometry by time of flight |
| DLP+ | DNA transposition single-cell library preparation |
| FACS | Fluorescence-activated cell sorting |
| FISH | Fluorescence in Situ Hybridization |
| H&E | Hematoxylin and eosin stain |
| IHC | Immunohistochemistry |
| inferCNV | Inferred copy number variation |
| scDNA | Single cell DNA sequencing |
| scRNA | Single cell RNA sequencing |
| scWGS | Single cell whole genome sequencing |
| t-CYCIF | Tissue-based cyclic immunofluorescence |
| TMAs | Tissue Microarrays |
Breast Cancer Specific Words
| Acronym/Abbreviation | Definition |
|---|---|
| AV | Alveolar Cells |
| BA | Basal Cells |
| BL | Borderline (both basal and luminal) |
| BRCA 1/2 | Breast Cancer Type 1, 2 |
| Cas9 | Clustered regularly interspaced short palindromic repeats (CRISPR) associated protein 9 |
| CNA | Copy Number Alteration |
| DCIS | Ductal carcinoma in situ |
| FFPE | Formalin-fixed, paraffin-embedded |
| HS | Hormone Sensing Cells |
| LOH | Loss of Heterozygosity |
| LP | Luminal Progenitors |
| LUM | Subset within ER+ mature luminal cells enriched in BRCA2 mutations |
| MECs | Mammary Epithelial Cell |
| ML | Mature Luminal |
| RNAi | RNA interference |
| ROS | Reactive Oxygen Species |
| SNV | Single nucleotide variant |
| TNBC | Triple Negative Breast Cancer |
| WOO | Window of opportunity clinical trials |
| WT | Wildtype |
Web Applications
| Acronym/Abbreviation | Definition |
|---|---|
| API | Application Programming Interface |
| CI/CD | Continuous integration/continuous delivery |
| DCA | Data Curator App |
| HTTP | Hypertext Transfer Protocol |
| REST | Representational State Transfer |
| URL | Universal Resource Locator |
| UUID | Universally Unique Identifier |
Related Research Organizations
| Acronym/Abbreviation | Definition |
|---|---|
| GDC | Genomic Data Commons |
| HTAN | Human Tumor Atlast Network |
| NCI | National Cancer Institute |
| NIH | National Institutes of Health |
| TCGA | The Cancer Genome Atlas |