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Genes 2014, 5(2), 366-384; doi:10.3390/genes5020366
Article

Characterization of the Genomic Architecture and Mutational Spectrum of a Small Cell Prostate Carcinoma

1,* , 1
, 1
, 2
, 1
 and 3,†
Received: 17 February 2014; in revised form: 1 April 2014 / Accepted: 15 April 2014 / Published: 12 May 2014
(This article belongs to the Special Issue Grand Celebration: 10th Anniversary of the Human Genome Project)
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Abstract: We present the use of a series of laboratory, analytical and interpretation methods to investigate personalized cancer care for a case of small cell prostate carcinoma (SCPC), a rare and aggressive tumor with poor prognosis, for which the underlying genomic architecture and mutational spectrum has not been well characterized. We performed both SNP genotyping and exome sequencing of a Virchow node metastasis from a patient with SCPC. A variety of methods were used to analyze and interpret the tumor genome for copy number variation, loss of heterozygosity (LOH), somatic mosaicism and mutations in genes from known cancer pathways. The combination of genotyping and exome sequencing approaches provided more information than either technique alone. The results showed widespread evidence of copy number changes involving most chromosomes including the possible loss of both alleles of CDKN1B (p27/Kip1). LOH was observed for the regions encompassing the tumor suppressors TP53, RB1, and CHD1. Predicted damaging somatic mutations were observed in the retained TP53 and RB1 alleles. Mutations in other genes that may be functionally relevant were noted, especially the recently reported high confidence cancer drivers FOXA1 and CCAR1. The disruption of multiple cancer drivers underscores why SCPC may be such a difficult cancer to manage.
Keywords: small cell prostate cancer (SCPC); exome sequencing; Illumina SNP array; Ingenuity; NGS (next generation sequencing) small cell prostate cancer (SCPC); exome sequencing; Illumina SNP array; Ingenuity; NGS (next generation sequencing)
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Scott, A.F.; Mohr, D.W.; Ling, H.; Scharpf, R.B.; Zhang, P.; Liptak, G.S. Characterization of the Genomic Architecture and Mutational Spectrum of a Small Cell Prostate Carcinoma. Genes 2014, 5, 366-384.

AMA Style

Scott AF, Mohr DW, Ling H, Scharpf RB, Zhang P, Liptak GS. Characterization of the Genomic Architecture and Mutational Spectrum of a Small Cell Prostate Carcinoma. Genes. 2014; 5(2):366-384.

Chicago/Turabian Style

Scott, Alan F.; Mohr, David W.; Ling, Hua; Scharpf, Robert B.; Zhang, Peng; Liptak, Gregory S. 2014. "Characterization of the Genomic Architecture and Mutational Spectrum of a Small Cell Prostate Carcinoma." Genes 5, no. 2: 366-384.



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