This tab shows an overview of the selected study/paper [more details]
Reference

Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer.

Paper Id
COSP28835
Authors
Barbieri CE,Baca SC,Lawrence MS,Demichelis F,Blattner M,Theurillat JP,White TA,Stojanov P,Van Allen E,Stransky N,Nickerson E,Chae SS,Boysen G,Auclair D,Onofrio RC,Park K,Kitabayashi N,Macdonald TY,Sheikh K,Vuong T,Guiducci C,Cibulskis K,Sivachenko A,Carter SL,Saksena G,Voet D,Hussain WM,Ramos AH,Winckler W,Redman MC,Ardlie K,Tewari AK,Mosquera JM,Rupp N,Wild PJ,Moch H,Morrissey C,Nelson PS,Kantoff PW,Gabriel SB,Golub TR,Meyerson M,Lander ES,Getz G,Rubin MA and Garraway LA
Affiliation
1] Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA. [2] Department of Urology, Weill Cornell Medical College, New York, New York, USA. [3].
Journal
Nature genetics 2012;44(6):685-9
ISSN:1546-1718
PUBMED:22610119
Abstract
Prostate cancer is the second most common cancer in men worldwide and causes over 250,000 deaths each year. Overtreatment of indolent disease also results in significant morbidity. Common genetic alterations in prostate cancer include losses of NKX3.1 (8p21) and PTEN (10q23), gains of AR (the androgen receptor gene) and fusion of ETS family transcription factor genes with androgen-responsive promoters. Recurrent somatic base-pair substitutions are believed to be less contributory in prostate tumorigenesis but have not been systematically analyzed in large cohorts. Here, we sequenced the exomes of 112 prostate tumor and normal tissue pairs. New recurrent mutations were identified in multiple genes, including MED12 and FOXA1. SPOP was the most frequently mutated gene, with mutations involving the SPOP substrate-binding cleft in 6-15% of tumors across multiple independent cohorts. Prostate cancers with mutant SPOP lacked ETS family gene rearrangements and showed a distinct pattern of genomic alterations. Thus, SPOP mutations may define a new molecular subtype of prostate cancer.
Paper Status
Curated
Genes Analysed
4710
Mutated Samples
124
Total No. of Samples
153
This tab shows genes with mutations in the selected study/paper [more details]
Genes Samples CDS Mutation AA Mutation
This tab shows genes without mutations in the selected study/paper [more details]
Non-Mutant Genes Gene Id (COSG)
This tab shows samples without mutations in the selected study/paper [more details]
Non-Mutant Samples Sample Id (COSS)
This tab shows mutated samples in the selected study/paper [more details]
Sample Name Mutation Count
This tab shows non coding variant in the selected study/paper [more details]
Sample ID Sample Name ID NCV Annotation Zygosity Chromosome Genome start Genome stop Genome version Strand WT seq Mut seq
This tab shows the gene expression and copy number variation data for this study. [more details]

Table Information

Hide

The table currently shows only high value (numeric) copy number data. Copy number segments are excluded if the total copy number and minor allele values are unknown.

Click here to include all copy number data. For more detailed information about copy number data and gain/loss definitions click here.

Sample Gene Expression Expr Level (Z-Score)

Over Expressed; Z-Score > 2.0

Under Expressed; Z-Score < -2.0

Normal; Z-Score within the range -2.0 to 2.0

CN Type Minor Allele Copy Number CN Segment Posn. Average Ploidy

1. N/A represents cases where the average ploidy value is not available( mostly ICGC samples). For some TCGA samples where the minor allele information is not available the average ploidy value could not be calculated.

2. For TCGA samples, the ASCAT algorithm was used to calculate the average ploidy.

3. For CGP samples, the PICNIC algorithm was used to calculate the average ploidy.

CNV
This tab shows a summary table with counts (number of samples) for CNV gain/loss and under/over expression for all genes. [more details]

The results shown in this table are derived from all copy number data. This includes non-numeric data with descriptive definitions of gain/loss.

  Copy Number Expression
Gene Gain Loss Tested Over Under Tested
This tab shows the fusion mutations observed in this sample [more details]
Gene Sample Name Id Sample(COSS) CDS Mutation Somatic status Zygosity Validated Type