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Status
Public on Jul 07, 2013
Title
Affymetrix OncoScan™ FFPE Express V2 334K
Technology type
in situ oligonucleotide
Distribution
custom-commercial
Organism
Homo sapiens Manufacturer
Affymetrix
Manufacture protocol
See manufacturer's web site.
Catalog number
000798
Support
glass
Description
A platform that offers high-quality copy number, genotype, and somatic mutation data with whole-genome coverage and high resolution in cancer genes for FFPE samples. This array should be used together with the MIP (Molecular Inversion Probes) technology.
Web link
http://www.affymetrix.com/ Submission date
Jul 11, 2012
Last update date
Jul 22, 2014
Contact name
Markus Riester
E-mail(s)
markus@jimmy.harvard.edu Organization name
Dana-Farber Cancer Institute
Department
Biostatistics & Computational Biology
Lab
Michor
Street address
3 Blackfan Circle
City
Boston
State/province
MA
ZIP/Postal code
02115
Country
USA
Samples (213)
GSM959927 , GSM959928 , GSM959929 , GSM959930 , GSM959931 , GSM959932
GSM959933 ,
GSM959934 ,
GSM959935 ,
GSM959936 ,
GSM959937 ,
GSM959938 ,
GSM959939 ,
GSM959940 ,
GSM959941 ,
GSM959942 ,
GSM959943 ,
GSM959944 ,
GSM959945 ,
GSM959946 ,
GSM959947 ,
GSM959948 ,
GSM959949 ,
GSM959950 ,
GSM959951 ,
GSM959952 ,
GSM959953 ,
GSM959954 ,
GSM959955 ,
GSM959956 ,
GSM959957 ,
GSM959958 ,
GSM959959 ,
GSM959960 ,
GSM1220119 ,
GSM1220120 ,
GSM1220121 ,
GSM1220122 ,
GSM1220123 ,
GSM1220124 ,
GSM1220125 ,
GSM1220126 ,
GSM1220127 ,
GSM1220128 ,
GSM1220129 ,
GSM1220130 ,
GSM1220131 ,
GSM1220132 ,
GSM1220133 ,
GSM1220134 ,
GSM1220135 ,
GSM1220136 ,
GSM1220137 ,
GSM1220138 ,
GSM1220139 ,
GSM1220140 ,
GSM1220141 ,
GSM1220142 ,
GSM1220143 ,
GSM1220144 ,
GSM1220145 ,
GSM1220146 ,
GSM1220147 ,
GSM1220148 ,
GSM1220149 ,
GSM1220150 ,
GSM1220151 ,
GSM1220152 ,
GSM1220153 ,
GSM1220154 ,
GSM1220155 ,
GSM1220156 ,
GSM1220157 ,
GSM1220158 ,
GSM1220159 ,
GSM1220160 ,
GSM1220161 ,
GSM1220162 ,
GSM1220163 ,
GSM1220164 ,
GSM1220165 ,
GSM1220166 ,
GSM1220167 ,
GSM1220168 ,
GSM1220169 ,
GSM1220170 ,
GSM1220171 ,
GSM1220172 ,
GSM1220173 ,
GSM1220174 ,
GSM1220175 ,
GSM1220176 ,
GSM1220177 ,
GSM1220178 ,
GSM1220179 ,
GSM1220180 ,
GSM1220181 ,
GSM1220182 ,
GSM1220183 ,
GSM1220184 ,
GSM1220185 ,
GSM1220186 ,
GSM1220187 ,
GSM1220188 ,
GSM1220189 ,
GSM1502992 ,
GSM1502993 ,
GSM1502994 ,
GSM1502995 ,
GSM1502996 ,
GSM1502997 ,
GSM1502998 ,
GSM1502999 ,
GSM1503000 ,
GSM1503001 ,
GSM1503002 ,
GSM1503003 ,
GSM1503004 ,
GSM1503005 ,
GSM1503006 ,
GSM1503007 ,
GSM1503008 ,
GSM1503009 ,
GSM1503010 ,
GSM1503011 ,
GSM2256647 ,
GSM2256648 ,
GSM2354134 ,
GSM2354135 ,
GSM2354136 ,
GSM2354137 ,
GSM2354138 ,
GSM2354139 ,
GSM2354140 ,
GSM2354141 ,
GSM2354142 ,
GSM2354143 ,
GSM2354144 ,
GSM2354145 ,
GSM2354146 ,
GSM2354147 ,
GSM2354148 ,
GSM2354149 ,
GSM2354150 ,
GSM2354151 ,
GSM2354152 ,
GSM2354153 ,
GSM2354154 ,
GSM2354155 ,
GSM2354156 ,
GSM2354157 ,
GSM2354158 ,
GSM2354159 ,
GSM2354160 ,
GSM2354161 ,
GSM2354162 ,
GSM2354163 ,
GSM2354164 ,
GSM2354165 ,
GSM2354166 ,
GSM2354167 ,
GSM2354168 ,
GSM2354169 ,
GSM2354170 ,
GSM2354171 ,
GSM2354172 ,
GSM2354173 ,
GSM2354174 ,
GSM2354175 ,
GSM2354176 ,
GSM2354177 ,
GSM2354178 ,
GSM2354179 ,
GSM2354180 ,
GSM2354181 ,
GSM2354182 ,
GSM2354183 ,
GSM2354184 ,
GSM2354185 ,
GSM2354186 ,
GSM2354187 ,
GSM2354188 ,
GSM2354189 ,
GSM2354190 ,
GSM2354191 ,
GSM2354192 ,
GSM2354193 ,
GSM2354194 ,
GSM2354195 ,
GSM2354196 ,
GSM2354197 ,
GSM2354198 ,
GSM2354199 ,
GSM2354200 ,
GSM2354201 ,
GSM2354202 ,
GSM2354203 ,
GSM2354204 ,
GSM2354205 ,
GSM2354206 ,
GSM2354207 ,
GSM2354208 ,
GSM2354209 ,
GSM2354210 ,
GSM2354211 ,
GSM2354212 ,
GSM2354213 ,
GSM2354214 ,
GSM2354215 ,
GSM2354216 ,
GSM2354217 ,
GSM2354218 ,
GSM3763154 Series (9)
GSE39280 DNA copy number gain at 1q23.3 is associated with poor survival in metastatic bladder cancer [Affymetrix]
GSE39282 DNA copy number gain at 1q23.3 is associated with poor survival in metastatic bladder cancer
GSE50495 Somatic copy number variation profiling in matched brain and extracranial metastases of melanoma
GSE50496 Melanoma brain metastases and matched extracranial metastases
GSE60886 Molecular characterization of choroid plexus tumors reveals novel clinically relevant subgroups
GSE61363 Genome-wide copy number and allele-specific copy number analysis of choroid plexus tumors (II)
GSE85035 Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumour tissue
GSE88909 Oncoscan™ Affymetrix array for pure LCIS, LCIS associated with ILC (invLCIS) and ILC
GSE131087 The genetic architecture of breast papillary lesions as a predictor of progression to carcinoma
Data table header descriptions ID Unique identifier for the SNP or CNV probe set
dbSNP RS ID Public name of the genomic location for the assay. Usually this corresponds to the dbSNP rs # of the SNP. However some SNPs have other identifiers (for historical reasons) and also there are some genomic locations that do not correspond to SNPs, e.g. OncoScan locations are monomorphic.
Major Allele Most frequent allele seen in the normal (non-cancer) reference population.
Minor Allele Least frequent allele seen in the normal (non-cancer) reference population.
Chromosome Chromosome of the assay.
Chromosome_ACC NCBI RefSeq Accession for chromosome (NCBI build 36)
Physical Position (bp) Gene Gene name (if applicable).
ORF ORF Name
SPOT_ID
Data table ID dbSNP RS ID Major Allele Minor Allele Chromosome Chromosome_ACC Physical Position (bp) Gene ORF SPOT_ID amp184660
C
C
chr1
NC_000001.9
59369
OR4F5
OR4F5 copy numer probe: amp184660
amp947
rs6683466 C
G
chr1
NC_000001.9
524446
-
amp947
amp53303
C
C
chr1
NC_000001.9
552824
-
copy numer probe: amp53303
amp364886
C
C
chr1
NC_000001.9
683543
-
copy numer probe: amp364886
amp121615
rs3131968 C
T
chr1
NC_000001.9
744055
-
amp121615
amp288732
C
C
chr1
NC_000001.9
744264
-
copy numer probe: amp288732
amp358123
C
C
chr1
NC_000001.9
782468
-
copy numer probe: amp358123
amp70940
rs11240777 G
A
chr1
NC_000001.9
788822
-
amp70940
amp329597
rs4970405 T
C
chr1
NC_000001.9
1038818
C1orf159
C1orf159 amp329597
amp264443
rs3813199 C
T
chr1
NC_000001.9
1148140
SDF4
SDF4 amp264443
amp288493
rs2229831 T
A
chr1
NC_000001.9
1211299
SCNN1D
SCNN1D amp288493
tag101400
rs2649588 T
C
chr1
NC_000001.9
1303878
-
tag101400
amp950
rs11488464 T
C
chr1
NC_000001.9
1373870
-
amp950
amp302726
rs1887284 C
T
chr1
NC_000001.9
1476922
SSU72
SSU72 amp302726
amp268551
rs7366884 T
C
chr1
NC_000001.9
1479791
SSU72
SSU72 amp268551
amp340063
rs11260611 C
T
chr1
NC_000001.9
1488240
SSU72
SSU72 amp340063
amp143245
rs9439468 A
G
chr1
NC_000001.9
1489161
SSU72
SSU72 amp143245
amp253174
rs760926 C
T
chr1
NC_000001.9
1636517
CDC2L2
CDC2L2 amp253174
amp298357
rs2377221 T
C
chr1
NC_000001.9
1650247
-
amp298357
amp365288
C
C
chr1
NC_000001.9
1725825
GNB1
GNB1 copy numer probe: amp365288
334008 22353 Kbytes .Supplementary data files not provided
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