View source for Discovery of novel prostate cancer-associated genes

{{Projectproposal
|Contact person=Jaap Heringa
|Contact person2=Guido Jenster (Erasmus MC)
|Master areas=Bioinformatics
|Fulfilled=No
}}
Prostate cancer is one of the most common cancers in men, mostly occurring above the age of 50 with
its incidence rate increasing with age. Despite its wide spread in males, PCa tumors often remain
unnoticed and until metastasis occur. Therefore, testing for the presence of prostate specific antigen
(PSA test) is often performed. However, since PSA is not prostate cancer specific and does not offer
prognostic value, many patients with benign tumors undergo unnecessary treatment, as they cannot be
distinguished from aggressive forms. At the same time, modern medicine is unable to predict the
occurrence of metastasis and resistant disease.

Hence, our goal is to investigate novel genes and transcripts in prostate cancer that can address the need
for highly specific biomarkers and help in prognosis of tumor development.

==The project==
RNA- and DNA-sequencing of PCa patients offers a large source of clinical information that enables us
to search for aberrations within PCa on both genomic and transcriptomic level.
From Affymetrix exon arrays and RNA-Seq analyses, we discovered novel unannotated prostate cancer
specific transcripts that might be related to aggressive tumor types. We would like to extend this search
for novel genes using RNA-Seq data and perform assembly of the reads into the mature mRNA.
Analysis steps include sequence alignment, assembly of novel transcripts and subsequent abundance
estimation. Furthermore, PCa specific alternative splicing and promoter use are also of interest. In
order to do so, a fully functional pipeline should be developed which can involve already existing tools,
such as aligners (bowtie, BWA, GSNAP etc.). The resulting genes might play a crucial role in
development and progression of prostate cancer and are therefore potential biomarkers for PCa.

The Department of Urology of the Erasmus MC Rotterdam is offering student projects in the field of
bioinformatics for Bachelor and Master students. Our research questions focus on discovery of novel
genes for prostate cancer (PCa) by integration of several established high throughput technologies.

==The research group==
The group headed by Prof. Dr. Guido Jenster consists of about 20 scientists including postdocs, PhD
students, technicians, bioinformaticians and BSc and MSc students.

The research is focused on genes and pathways responsible for prostate
cancer initiation and progression. In addition, model systems and
biomarkers for this disease are being developed. The latest technologies
including in RNA-Seq and DNA-Seq are implemented to optimally
identify and validate genes and markers of interest.

==Contact details:==
* phone: +31-10-704 3672
* fax: +31-10-704 4661
* e-mail: g.jenster@erasmusmc.nl
[[Media:Bioinfo Student projects EMC.pdf|Further information]]