Abstract
Deletions of chromosome 1p36 are common in malignancies; however, there is limited information regarding the biological and prognostic implications of 1p36 in cancer. Steroid Receptor–Associated and Regulated Protein (SRARP) is a tumor suppressor on chromosome 1p36.13 that its inactivation predicts poor cancer outcome, indicating that the 1p36.13 segment requires further studies. Therefore, a comprehensive multi-omics analysis of The Cancer Genome Atlas (TCGA), the Pan-Cancer Analysis of Whole Genomes (PCAWD), the International Cancer Genome Consortium (ICGC), and the Genomic Data Commons (GDC) Pan-Cancer datasets was conducted to investigate the prognostic implications of 1p36.13 in malignancies. This study revealed that expression and DNA methylation of multiple genes on 1p36.13 are significantly associated with survival in primary tumors and normal adjacent tissues. In addition, copy-number loss in every gene on 1p36.13 predicts poor cancer outcome. Importantly, copy-number loss and somatic mutations of chromosome 1p36.13 segment are associated with worse survival in primary tumors, and DNA hypermethylation of 1p36.13 predicts poor outcome in normal adjacent tissues. Therefore, genomic and epigenetic aberrations of chromosome 1p36.13 have promising prognostic implications in cancer.
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Abbreviations
- SRARP:
-
Steroid Receptor–Associated and Regulated Protein
- AR:
-
Androgen receptor
- Mb:
-
Megabases
- TCGA:
-
The Cancer Genome Atlas
- RNAseq:
-
RNA sequencing
- RSEM:
-
RNA Seq by Expectation Maximization
- PCAWG:
-
The Pan-Cancer Analysis of Whole Genomes
- GDC:
-
The Genomic Data Commons
- FPKM-UQ:
-
Fragments per kilobase of transcript per million mapped reads upper quartile
- ICGC:
-
International Cancer Genome Consortium
- CNV:
-
Copy-number variation
- FDR:
-
False discovery rate
- DNA-VAF:
-
DNA-variant allele frequency.
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AN conceived the study, carried out the bioinformatics and biostatistics analyses of datasets, interpreted the analyzed data, and drafted the manuscript.
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Naderi, A. Genomic and epigenetic aberrations of chromosome 1p36.13 have prognostic implications in malignancies. Chromosome Res 28, 307–330 (2020). https://doi.org/10.1007/s10577-020-09638-x
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DOI: https://doi.org/10.1007/s10577-020-09638-x