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

Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing.

Paper Id
COSP29744
Authors
Imielinski M,Berger AH,Hammerman PS,Hernandez B,Pugh TJ,Hodis E,Cho J,Suh J,Capelletti M,Sivachenko A,Sougnez C,Auclair D,Lawrence MS,Stojanov P,Cibulskis K,Choi K,de Waal L,Sharifnia T,Brooks A,Greulich H,Banerji S,Zander T,Seidel D,Leenders F,Ansén S,Ludwig C,Engel-Riedel W,Stoelben E,Wolf J,Goparju C,Thompson K,Winckler W,Kwiatkowski D,Johnson BE,Jänne PA,Miller VA,Pao W,Travis WD,Pass HI,Gabriel SB,Lander ES,Thomas RK,Garraway LA,Getz G and Meyerson M
Affiliation
Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA.
Journal
Cell 2012;150(6):1107-20
ISSN:1097-4172
PUBMED:22980975
Abstract
Lung adenocarcinoma, the most common subtype of non-small cell lung cancer, is responsible for more than 500,000 deaths per year worldwide. Here, we report exome and genome sequences of 183 lung adenocarcinoma tumor/normal DNA pairs. These analyses revealed a mean exonic somatic mutation rate of 12.0 events/megabase and identified the majority of genes previously reported as significantly mutated in lung adenocarcinoma. In addition, we identified statistically recurrent somatic mutations in the splicing factor gene U2AF1 and truncating mutations affecting RBM10 and ARID1A. Analysis of nucleotide context-specific mutation signatures grouped the sample set into distinct clusters that correlated with smoking history and alterations of reported lung adenocarcinoma genes. Whole-genome sequence analysis revealed frequent structural rearrangements, including in-frame exonic alterations within EGFR and SIK2 kinases. The candidate genes identified in this study are attractive targets for biological characterization and therapeutic targeting of lung adenocarcinoma.
Paper Status
Curated
Genes Analysed
16562
Mutated Samples
184
Total No. of Samples
185
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

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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