Investigation Title	Comprehensive molecular characterization of human colon and rectal cancer
Experimental Design	individual_genetic_characteristics_design
Experimental Design Term Source REF	MGED Ontology

Experimental Factor Name	Tumor versus normal	Call variants by individual
Experimental Factor Type	disease_state	individual

Person Last Name	Wheeler	Drummond	Chang	Xi	Hale	Kalra
Person First Name	David	Jennifer	Kyle	Liu	Walker	Divya
Person Mid Initials	A	A				
Person Email	david.wheeler@bcm.edu	jenn@bcm.edu	kylec@bcm.edu	lxi@bcm.edu	hale@bcm.edu	divyak@bcm.edu
Person Address	1 Baylor Plaza Houston TX 77030	1 Baylor Plaza Houston TX 77030	1 Baylor Plaza Houston TX 77030	1 Baylor Plaza Houston TX 77030	1 Baylor Plaza Houston TX 77030	1 Baylor Plaza Houston TX 77030
Person Affiliation	Baylor College of Medicine	Baylor College of Medicine	Baylor College of Medicine	Baylor College of Medicine	Baylor College of Medicine	Baylor College of Medicine
Person Roles	investigator	data_analyst	data_analyst	data_analyst;submitter	submitter	submitter

PubMed ID	22810696
Publication Author List	The Cancer Genome Atlas Research Network
Publication Title	Comprehensive molecular characterization of human colon and rectal cancer
Publication Status	published online Nature 487: 330 (08 July 2012)

Experiment Description	Whole exome sequencing data was produced and analyzed by Baylor Human Genome Sequencing Center as part of the TCGA effort towards comprehensive genomic characterization of multiple tumor types.  Massively parallel sequencing exome capture was performed on untreated rectal adenocarcinoma samples using NimbleGen (custom designed) arrays according the manufacturer’s instructions. All exome sequencing was performed on the ABS SOLiD and Illumina HiSeq platforms. Basic alignment and initial sequence analysis were carried out using the Mercury analysis pipeline.

Protocol Name	hgsc.bcm.edu:library_preparation:illumina:01	genome.wustl.edu:library_preparation:imported:01	genome.wustl.edu:dna_sequencing:imported:01	hgsc.bcm.edu:dna_sequencing:illumina:16	hgsc.bcm.edu:mapping_wxs:illumina:10	genome.wustl.edu:mapping_wxs:imported:01	broad.mit.edu:variant_calling:imported:01	hgsc.bcm.edu:maf_generation:na:99
Protocol Type								
Protocol Description	Libraries were constructed into Illumina paired end pre capture libraries according to the manufacturer’s protocol (Illumina Multiplexing_SamplePrep_Guide_1005361_D) using Invitrogen enzyme mix with modifications. Libraries were prepared using Beckman robotic workstations (Biomek FX and FXp models).  The complete protocol and oligonucleotide sequences are accessible from the HGSC website https://www.hgsc.bcm.edu/sites/default/files/documents/Illumina_Barcoded_Paired-End_Capture_Library_Preparation.pdf			instrument=Illumina HiSeq 2000, lane design=multiplexed, read length 200, alignment program=Casava V1.7	Phred+64 to Phred+33 conversion --> bwa v0.5.8 --> bcm java app v1.36 --> picard v1.36 -> bcm java app v1.36		variant calling performed by Broad Institute of MIT and Harvard (broadinstitute.org)	Variant calling performed by Broad Institute were curated by a cross institutional collaborative analysis working group. Refer to TCGA Colorectal publication for details. PubMed ID 22810696.
Protocol Parameters	Vendor;Catalog Name;Catalog Number;Annotation URL;Product URL;Target File URL;Target File Format;Target File Format Version;Probe File URL;Probe File Format;Probe File Format Version;Target Reference Accession	Vendor;Catalog Name;Catalog Number;Annotation URL;Product URL;Target File URL;Target File Format;Target File Format Version;Probe File URL;Probe File Format;Probe File Format Version;Target Reference Accession			Protocol Min Base Quality;Protocol Min Map Quality;Protocol Min Tumor Coverage;Protocol Min Normal Coverage	Protocol Min Base Quality;Protocol Min Map Quality;Protocol Min Tumor Coverage;Protocol Min Normal Coverage		
Protocol Term Source REF								

SDRF Files	hgsc.bcm.edu_READ.IlluminaGA_DNASeq.Level_2.1.1.0.sdrf.txt

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