Prior to alignment, BAM files that were submitted to the GDC are split by read groups and converted to FASTQ format.
An aggregation pipeline incorporates variants from all cases in one project into a MAF file for each pipeline.ĭNA-Seq analysis is implemented across six main procedures: Somatic-caller-identified variants are then annotated.
Four different variant calling pipelines are then implemented separately to identify somatic mutations. The first pipeline starts with a reference alignment step followed by co-cleaning to increase the alignment quality. Somatic variants are identified by comparing allele frequencies in normal and tumor sample alignments, annotating each mutation, and aggregating mutations from multiple cases into one project file. The GDC DNA-Seq analysis pipeline identifies somatic variants within whole exome sequencing (WXS) and whole genome sequencing (WGS) data.
#NUCLEOTIDE SEQUENCE ANALYSIS PDF#
Whole Genome Sequencing Variant Callingīioinformatics Pipeline: Copy Number Variation Analysisīioinformatics Pipeline: Methylation Analysis Pipelineīioinformatics Pipeline: Protein Expressionįa-file-text Download PDF /Data/PDF/Data_UG.pdf.Tumor-Only Variant Call Command-Line Parameters.DNA-Seq Co-Cleaning Command Line Parameters.DNA-Seq Alignment Command Line Parameters.fa-file-text Download PDF /Data/PDF/Data_UG.pdfīioinformatics Pipeline: DNA-Seq Analysis.Bioinformatics Pipeline: Protein Expression.Bioinformatics Pipeline: Methylation Analysis Pipeline.Bioinformatics Pipeline: Copy Number Variation Analysis.Bioinformatics Pipeline: miRNA Analysis.Bioinformatics Pipeline: DNA-Seq Analysis.fa-file-text Download PDF /Data_Transfer_Tool/PDF/Data_Transfer_Tool_UG.pdf.Data Transfer Tool Command Line Documentation.fa-file-text Download PDF /Data_Submission_Portal/PDF/Data_Submission_Portal_UG.pdf.Before Submitting Data to the GDC Portal.
fa-file-text Download PDF /Data_Portal/PDF/Data_Portal_UG.pdf.fa-file-text Download PDF /API/PDF/API_UG.pdf.Appendix C: Format of Submission Queries and Responses.It has been widely used for the prediction of bone metastases in patients with breast cancer. ĬA15-3, a high molecular weight glycoprotein (300-450 kDa), is produced by the epithelial ducts and acinic breast cells and is then secreted in milk normally. Together, ERRα binds to DNA, in complex with PGC-1α, to regulate the activity of genes such as FNDC5. ERRα and ERα could compete with each other to bind to similar DNA elements.
ERRα interacts with a canonical sequence of the estrogen response elements (ERRE). The ERRα structure is similar to that of the estrogen receptor alpha (ERα), but this receptor does not bind to natural estrogens. One of them allows the interaction with DNA, and the second one with a ligand. ERRα is encoded by the ESRRA gene and is an orphan nuclear receptor, which has two domains. Studies indicated that the estrogen-related receptor alpha (ERRα) could be a factor that plays a role in PGC-1α binding to DNA. PGC-1α is a transcriptional co-activator which does not bind directly to DNA. Irisin is encoded by the FNDC5 gene, whose expression is controlled by the peroxi- some proliferator activated receptor gamma coactivator 1 alpha (PGC-1α). Its incidence is increasing but mortality has decreased in a considerable way due to the combined effect of early detection and improvement in treatment. Why Should I Register and Submit Results?īreast cancer is the most frequent cancer in women worldwide.
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