
Investigation Title	Analysis of TCGA HNSC
Experimental Design	individual_genetic_characteristics_design
Experimental Design Term Source REF	MGED Ontology
Experimental Factor Name	HNSC Tumor vs. Normal
Experimental Factor Type	disease state

Person Last Name	Gabriel
Person First Name	Stacey
Person Mid Initials
Person Email	gdac@broadinstitute.org
Person Address	415 Main Street, Cambridge, MA 02142, USA
Person Affiliation	Broad Institute
Person Roles	Investigator

PubMed ID	TBD
Publication Author List	TBD
Publication Title	TBD
Publication Status	TBD
Experiment Description	Firehose pipeline: Round Up TCGA MAF Archive Files job number 62995222

Protocol Name	broad.mit.edu:library_preparation:IlluminaGA_DNASeq:01	broad.mit.edu:sequencing:IlluminaGA_DNASeq:01	broad.mit.edu:alignment:IlluminaGA_DNASeq:01	broad.mit.edu:variant_calling:IlluminaGA_DNASeq:01	broad.mit.edu:MAF_Generation:IlluminaGA_DNASeq:01
Protocol Type
Protocol Description	Agilent SureSelect Human All Exon v2 kit	Paired-end Sequencing on Illumina HiSeq2000	BWA	Production Analysis 1.3 (Somatic Variant Calling Pipeline: ContEst FHv107, MuTect v1.1.6, Indelocator FHv77) job number: 62995222	Production Analysis 1.3 (Oncotator v.1.2.7.0) job number: 62995222
Protocol Term Source REF	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology
Protocol Parameters

SDRF Files	broad.mit.edu_HNSC.IlluminaGA_DNASeq_curated.Level_2.1.6.0.tar.gz.sdrf.txt

Term Source Name	MGED Ontology
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php
Term Source Version	1.3.1.1
