Comment[ArrayExpressAccession]	E-GEOD-14353
Investigation Title	Liver tumor/normal pairs
Comment[Submitted Name]	Liver tumor/normal pairs
Publication Title	High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays.
Publication Author List	Wang Y, Carlton VE, Karlin-Neumann G, Sapolsky R, Zhang L, Moorhead M, Wang ZC, Richardson AL, Warren R, Walther A, Bondy M, Sahin A, Krahe R, Tuna M, Thompson PA, Spellman PT, Gray JW, Mills GB, Faham M
Publication DOI	
PubMed ID	19228381
Experimental Design	comparative genomic hybridization by array
Experimental Design Term Source REF	EFO
Public Release Date	2009-01-22
Experiment Description	A major challenge to the study of tumor DNA copy number (CN) in clinical specimens is the lack of appropriate fresh frozen samples and thus a dependence on Formalin-Fixed Paraffin Embedded (FFPE) banked samples, which typically have more extensive clinical follow up information.  However, on most high density CN platforms, DNA from FFPE tissues generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking.  Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from DNA isolated from cell lines and frozen tumor samples.  Since the MIP probes require only a small (~40 bp) target binding site, we reasoned they may be well suited to assess FFPE samples.  In this study, we successfully applied MIP technology with a panel of 50,000 markers to CN determination in FFPE samples.  Using an input of 37 ng genomic DNA, we demonstrated high quality CN data with MIP technology from 93 FFPE samples from seven diverse collections.  We found that the performance of FFPE DNA for CN determination was comparable to that of DNA obtained from matched frozen tumor, with only a modest loss in performance of DNA.  Tumor FFPE were analyzed using matched normal FFPE as the reference. Tumor and normal pairs: 01-02, 12-13, 16-17, 08-09, 20-21, 24-25, 28-29, and 35-36.  Tumor 32 has no matched normal sample.																												
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Person Last Name	Wang	Wang	Carlton	Warren	Faham																								
Person First Name	Yuker	Yuker	Victoria	Robert	Malek																								
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Person Email	yuker_wang@affymetrix.com																												
Person Affiliation	Affymetrix																												
Person Phone	408-731-5703																												
Person Fax	408-481-0422																												
Person Address	Affymetrix, 3380 Central Expressway, Santa Clara, CA, USA																												
Person Roles	submitter																												
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Protocol Name	P-GSE14353-2	P-GSE14353-3	P-GSE14353-1	P-GSE14353-16	P-GSE14353-14	P-GSE14353-17	P-GSE14353-15	P-GSE14353-29	P-GSE14353-12	P-GSE14353-10	P-GSE14353-13	P-GSE14353-11	P-GSE14353-28	P-GSE14353-26	P-GSE14353-4	P-GSE14353-8	P-GSE14353-6	P-GSE14353-9	P-GSE14353-7	P-GSE14353-27	P-GSE14353-5	P-GSE14353-22	P-GSE14353-25	P-GSE14353-19	P-GSE14353-20	P-GSE14353-24	P-GSE14353-23	P-GSE14353-21	P-GSE14353-18
Protocol Description	ID_REF = <br>VALUE = copy number assessment	ID_REF = <br>VALUE = copy number	ID_REF = <br>VALUE = copy number assessment relative to paired normal sample	Molecular Inversion Probes and Universal Tag Arrays: Application to Highplex Targeted SNP Genotyping	George Karlin-Neumann, Marina Sedova, Ronald Sapolsky, Jonathan	p. 199 – 211; Cold Spring Harbor Lab’s “Genetic Variation: A Laboratory Manual”, edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007). 	Forman, Yuker Wang, Martin Moorhead, and Malek Faham	p. 199 – 211; Cold Spring Harbor Lab’s “Genetic Variation: A Laboratory Manual”, edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007).	Molecular Inversion Probes and Universal Tag Arrays: Application to Highplex Targeted SNP Genotyping	George Karlin-Neumann, Marina Sedova, Ronald Sapolsky, Jonathan	p. 199 – 211; Cold Spring Harbor Lab’s “Genetic Variation: A Laboratory Manual”, edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007). 	Forman, Yuker Wang, Martin Moorhead, and Malek Faham	p. 199 – 211; Cold Spring Harbor Lab’s “Genetic Variation: A Laboratory Manual”, edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007).	genomic DNA extracted from a FFPE block. It's a customer sample	genomic DNA extracted from a FFPE block.  It's a customer sample.	Molecular Inversion Probes and Universal Tag Arrays: Application to Highplex Targeted SNP Genotyping	George Karlin-Neumann, Marina Sedova, Ronald Sapolsky, Jonathan	p. 199 – 211; Cold Spring Harbor Lab’s “Genetic Variation: A Laboratory Manual”, edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007). 	Forman, Yuker Wang, Martin Moorhead, and Malek Faham	p. 199 – 211; Cold Spring Harbor Lab’s “Genetic Variation: A Laboratory Manual”, edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007).	MIP technology		Wang YK, Moorhead M, Karlin-Neumann G, Falkowski M, Chen C, Siddiqui F, Davis RW, Willis TD, Faham M.: Allele quantification using Molecular Inversion Probes (MIP). Nucleic Acids Res. 21:2528, 2005.	Yuker Wang, Martin Moorhead, and Malek Faham	Molecular Inversion Probe Targeted Genotyping: Application to Copy Number Determination	For more details, see Wang Y, Moorhead M, Karlin-Neumann G, Wang NJ, Ireland J, Lin S, Chen C, Heiser LM, Chin K, Esserman L, Gray JW, Spellman PT, Faham M.:    Analysis of molecular inversion probe performance for allele copy number determination.  Genome Biol. 2007;8(11):R246	Briefly, we used two chips per sample. For SNP A/B, one (xxxA.CEL) chip give signal / copy number of A allele, the other chip (xxxC.CEL) give that of B allele.  Copy number assessment of a given SNP is the sum of allele A and B.  We use normals as the reference for the test samples.  The copy number is a relative value between the test and normal references.	p. 249 – 252; Cold Spring Harbor Lab’s “Genetic Variation: A Laboratory Manual”, edited by M.P. Weiner, S.B. Gabriel & J.C. Stephens (2007).	George Karlin-Neumann, Marina Sedova, Ronald Sapolsky, Steven Lin,
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Protocol Type	bioassay_data_transformation	bioassay_data_transformation	bioassay_data_transformation	image_aquisition	image_aquisition	image_aquisition	image_aquisition	image_aquisition	hybridization	hybridization	hybridization	hybridization	hybridization	nucleic_acid_extraction	nucleic_acid_extraction	labeling	labeling	labeling	labeling	labeling	labeling	feature_extraction	feature_extraction	feature_extraction	feature_extraction	feature_extraction	feature_extraction	feature_extraction	feature_extraction
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Comment[SecondaryAccession]	GSE14353																												
Comment[GEOLastUpdateDate]	2009-03-04
Comment[GEOReleaseDate]	2009-01-23
Comment[ArrayExpressSubmissionDate]	2009-01-08
SDRF File	E-GEOD-14353.sdrf.txt