Breast+Cancer+Materials+and+Methods

__ Articles Used __:

 * Review Article: "Analysis of Circulating Tumor DNA to Monitor Metastatic Breast Cancer" was used as an introduction to the most current works in breast cancer and genomics.
 * Primary Articles:
 * 1) " Genomic Approaches in Breast Cancer Research" was used for explanation of genomic classifications, gene expression profiling, and background information about the process of histologic grading of tumors.
 * 2) "Genomic Subtypes in Choosing Adjuvant Therapy for Breast Cancer//"// gave a good overview of what adjuvant therapies were and discussed how multi-gene tests and gene expression profiling help diagnose breast cancer.
 * 3) "Combining Functional Genomics Strategies Identifies Modular Heterogeneity of Breast Cancer Intrinsic Subtypes" broke down the intrinsic subtypes of breast cancer and gave great detail of biologic function regarding heterogeneity of breast cancer
 * 4) "Single Cell Mutational Analysis of PIK3CA in Circulating Tumor Cells and Metastases in Breast Cancer Reveals Heterogeneity, Discordance, and Mutation Persistence in Cultured Disseminated Tumor Cells From Bone Marrow" was a very current research study regarding the gene PIK3CA and its role in breast cancer. The article shows the newest techniques being performed and tested to determine gene mutations faster to better diagnose and treat.
 * 5) "Mining Genome Sequencing Data to Identify the Genomic Features Linked to Breast Cancer Histopathology" showed to positive attributes to large-scale genome sequencing projects and the future work that can come from the databases. Many correlations in this article to the others used (above).

__ Website Tools __:
**UCSC Genome Browser**-This tool was used to find the location of the specific gene of interest within the genome. UCSC Genome Browser can be used to look at a gene in a high amount of detail and compare it to various species genes, as well as find specific sequences of importance within that gene/section of a chromosome.
 * Accessed UCSC Genome Browser between February and April 2016
 * Species: Human Dec. 2013 (GRCh38/hg38) Assembly
 * Used same Species parameters for gene PIK3CA and gene TOP2A.
 * "Default Tracks: ON", "Default Order: ON", "Base Position: Dense", "GENCODE v22: full", RefSeq Genes: pack", OMIM AV SNPs: pack", "ENCODE Regulation: show", "Conservation: full" for both PIK3CA and TOP2A.
 * Only difference was with TOP2A: automatically defaulted for "RepeatMasker: full".

**RCSB Protein Data Bank**-this tool was used to examine the 3D structure of the protein of interest, 4FM9. This protein is in the family for the gene TOP2A. PDB uses various resources and databases to provide information about 3D shapes of proteins and nucleic acids. The website also provides extensive information on protein function, biological processes, and disease pathways. <span style="font-family: 'Calibri',sans-serif; font-size: 14.6667px;">Within Search box: TOP2A <span style="font-family: 'Calibri',sans-serif; font-size: 14.6667px;">Results: 4 results for proteins that are known to be associated with gene TOP2A.

Landmark or Region:PIK3CA Data Source: HapMap Data Rel 28 Phase II+III, on August10, on NCBI B36 assembly, db SNP b126 Reports and Analysis: Highlights and SNP Properties Scroll/Zoom: Show 86.19bp Overview (All checked on): gt'd SNPs/500Km, GWA Studies (NHGRI Catalog), Ideogram, NT contigs, OMIM disease associations. Region (All checked on): Copy Number Variation, Entrez genes, gt'd SNPs/20Kb Genes (All checked on): Ensemble genes, Entrez genes Genetic Associations-Genome Wide Association Studies (NHGRI catalog) Pathways-Reactome pathways Show Grid-Image width 800 Cache Tracks-alphabetic Highlight Feature-NM__006218@yellow Region Size-2Mbp
 * HapMap**- This tool was used to visualize the structure of the PIK3CA gene.


 * PharmGKB**- The PharmGKB is a pharmacogenomics an interactive collection of drug responses and associations between genotype-phenotype relationships. The site has many functions, including literature reviews of known genetic variants and their interactions between specific drug categories.

In this project, the effect of gene PIK3CA on the epidermal growth factor receptor was reviewed. Under "Search PharmGKB: PIK3CA", select "Pathways" tab, select #2 "EGFR Inhibitor Pathway, Pharmacodynamics"

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