This document discusses bladder cancer and different types (T1NP and T1P), which are differentiated by whether the disease progresses to become muscle-invasive or metastatic. RNA sequencing was used to analyze gene expression differences between the two types. The sequencing was done using the Illumina Genome Analyzer II, and the resulting reads were analyzed using CASAVA, TopHat, and Cufflinks software. CASAVA aligns reads and detects variants, TopHat identifies splice junctions, and Cufflinks assembles transcripts and tests for differential expression. Biomarkers identified through this analysis may help predict cancer progression using archived samples.

1. Bladder Cancer
USD Bioinformatics

2. Bladder Cancer
Bladder Cancer
 T1NP: T1 non progressive cancer
 Patients have multiples recurrences of the disease without
developing muscle-invasive tumors
 T1P: T1 progressive cancer
 Patient’s disease develops into muscle invasive tumors and
becomes metastatic.
 Once metastatic, cancer survival is around 5.4% at 5 years.

3. Through RNA Seq
 Different gene expressions appeared between
Nonprogressive and Progressive bladder cancer.
 Biomarkers that were identified in the future could also
help predict the pace of progression of muscle invasive
tumors using Formalin-Fixed and Paraffin-Embedded
samples.

4. How to achieve these result?
 cDNA samples were sequenced on Illumina Genome
Analyzer II.
 Sequences attained from Illumina were given by
CASAVA software
 Reads attained were compared to the human
genome using Tophat
 Reads were done using Cufflinks

5. Workflow of Reads
 Quality Assessment
 Alignment
 Variant Identification
 Variant Annotation
 Visualization

6. CASAVA
 Stands for Consensus Assessment of Sequence and
Variation software
 Aligns reads, calls SNPs, and detects INDELs in
RNA sequencing data
 Analyzes reads in 3 stages:
 FASTQ file generation and simplify
 Alignment to a reference genome
 Variant detection and counting

7. TopHat
 Fast splice junction mapper for RNA-Seq reads.
 Aligns reads using Bowtie
 Then analyzes the mapping results to identify splice
junctions between exons

8. Cufflink
 Assembles transcripts
 Estimates their abundances
 Tests for differential expression and regulation

9. Conclusion
 Tools work together to help clinicians analyze the
patient
 Helps in making not precise but more accurate
predictions and diagnosis

10. Works Cited
"CASAVA." Support. Illumina, n.d. Web. 27 June 2014.
<http://support.illumina.com/sequencing/sequencing_software/casava.ilmn>.
"CASAVA | Align reads, call SNPs and detect indels in DNA sequencing data |
Illumina." CASAVA | Align reads, call SNPs and detect indels in DNA
sequencing data | Illumina. Illumina, n.d. Web. 27 June 2014.
<http://www.illumina.com/informatics/sequencing-microarray-data-
analysis/casava.ilmn>.
Pachter, Lior, Steven Salzberg, and Barbara Wold. "Cufflinks." - Transcript assembly,
differential expression, and differential regulation for RNA-Seq. N.p., 26 Sept.
2009. Web. 27 June 2014. <http://cufflinks.cbcb.umd.edu/>.
Trapnell, Cole, Daehwan Kim, and Steven Salzberg. "TopHat." :: Center for
Bioinformatics and Computational Biology. John Hopkins University, 27 Oct.
2008. Web. 25 June 2014. <http://ccb.jhu.edu/software/tophat/index.shtml>.

11. Works Cited
Sharron Lin, Xuanhui, et al. "Differentiating Progressive From Nonprogressive T1 Bladder Cancer By
Gene Expression Profiling: Applying RNA-Sequencing Analysis On Archived
Specimens." Urologic Oncology 32.3 (2014): 327-336. Academic Search Premier. Web. 23
June 2014.