Comment[ArrayExpressAccession]	E-MTAB-1794
MAGE-TAB Version	1.1
Investigation Title	Amplicon sequencing of different regions of metastatic melanomas
Comment[Submitted Name]	Amplicon sequencing of different regions of metastatic melanomas
Experiment Description	Genetic heterogeneity can provide tumors with opportunities for therapy evasion, however the degree of genetic heterogeneity within metastatic melanomas has not been thoroughly investigated. We therefore isolated DNA from different regions of formalin fixed paraffin embedded metastatic melanoma tissue samples and subjected them to amplicon sequencing-based profiling of mutations in a panel of well known cancer genes using the Ion Ampliseq Cancer Panel.
Experimental Design	disease state design	ex_vivo_design	genotype design
Comment[AEExperimentType]	genotyping by high throughput sequencing
Comment[AEExperimentDisplayName]	Amplicon sequencing-based profiling of formalin fixed paraffin embedded metastatic melanoma tissue samples
Experimental Factor Name	individual
Experimental Factor Type	individual
Public Release Date	2013-09-08
Person Last Name	Anaka
Person First Name	Matthew
Person Mid Initials	R
Person Email	matthew.anaka@ludwig.edu.au
Person Phone	+613 9496 5726
Person Address	Ludwig Institute For Cancer Research Ltd, Austin Hospital, Level 5, Olivia Newton-John Cancer & Wellness Centre, Studley Road, Heidelberg, Victoria, 3084, Australia
Person Affiliation	Ludwig Institute For Cancer Research
Person Roles	submitter
PubMed ID	24119551
Publication Author List	Anaka M, Hudson C, Lo PH, Do H, Caballero OL, Davis ID, Dobrovic A, Cebon J, Behren A.
Publication Title	Intratumoral genetic heterogeneity in metastatic melanoma is accompanied by variation in malignant behaviors.
Publication Status
Protocol Name	P-MTAB-33971	P-MTAB-33972	P-MTAB-33973	P-MTAB-33974	P-MTAB-33975
Protocol Type	treatment protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	high throughput sequence alignment protocol
Protocol Description	Three mm cores were removed from formalin fixed paraffin embedded tissue blocks, and the top 2mm removed with a sterile scalpel blade.	DNA was extracted from tissue core fragments using a 24 hour proteinase K digestion (Arcturus Picopure DNA Extraction kit), follwed by clean up using DNEasy columns (Qiagen).	Libraries were prepared using the Ion Ampliseq Cancer Panel kit (Life Technologies) and the Ion AmpliSeq Library Kit, after which individual libraries were barcoded using the Ion Xpress Barcode Adaptor Kit (Life Technologies)	Eight barcoded libraries were pooled for each run, and sequenced on Ion 318 chips	Reads were aligned to HG19 using TMAP. Variants were identified using the Ion Variant Caller plug-in; all settings default with the exception of a SNP QV minimum of 14.
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO
Protocol Hardware				454 GS
Term Source Name	EFO
Term Source File	http://www.ebi.ac.uk/efo
Comment[SecondaryAccession]	ERP003689
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/ERR319076-ERR319091
SDRF File	E-MTAB-1794.sdrf.txt
Publication DOI	10.1186/1755-8794-6-40