Bladder cancer biorepositories in the "-omics" era: integrating quality tissue specimens with comprehensive clinical annotation.
Advances in genomic platforms have led to the need for well-characterized, high quality biospecimens for research. Bladder cancer, despite being a major epidemiological concern, has been under-represented in genomic programs due to unique challenges in collection of clinical informatics and tissues. Currently no targeted therapy exists for management of the disease. We report our experiences and lessons learnt in establishing an integrated model of bladder cancer that uses a dedicated bladder cancer team and relational databases. It streamlines both clinical activity and serial harvesting of biospecimens to obtain tissue that is consistently suitable for high-throughput genomic research. Fresh tissue, blood, and urine samples were prospectively collected and stored. RNA and DNA were extracted simultaneously, quality control was performed, and whole transcriptome sequencing also performed using the illumina series of platforms. Over a 15-month period, urine was banked for 209 patients, plasma and whole blood for 185 patients, and tissue for 71 patients. The collections included normal mucosa from patients with and without bladder cancer and cancer tissue across the entire histopathogical spectrum of bladder cancer from low-grade noninvasive cancers to metastatic lymph nodes. We used a relational database to link clinical information to tumor inventory and provide access to richly annotated specimens and matched clinical informatics. We found that tumor tissue was successfully banked more often in patients who had macroscopic papillary disease compared to those without. We also show that the median RNA integrity number (RIN) scores are significantly higher in patients whose tissues were banked using cold-cup biopsies compared to those banked using electrocautery. Transcriptome sequencing of all samples banked using cold-cup biopsies passed bioinformatics quality assessment and had a mean Q30 quality score well over the illumina quality control benchmark. Such an infrastructure will allow genomic profiling of bladder cancer to help us understand the "global picture" in bladder cancer pathogenesis.
1 Department of Urology and Surgery, University of Melbourne , Royal Melbourne Hospital, Parkville, Australia .
Nikhil
N
Sapre
Matthew K H
MK
Hong
James G
JG
Huang
John
J
Pedersen
Andrew
A
Ryan
Paul
P
Anderson
Anthony J
AJ
Costello
Niall M
NM
Corcoran
Christopher M
CM
Hovens
D000368:Aged; D018070:Biological Specimen Banks / Q000941:ethics* / Q000639:trends*; D004247:DNA / Q000032:analysis; D005260:Female; D023281:Genomics; D006801:Humans; D008297:Male; D008490:Medical Informatics / Q000379:methods*; D008499:Medical Records; D008875:Middle Aged; D011446:Prospective Studies; D011786:Quality Control; D012313:RNA / Q000032:analysis; D013048:Specimen Handling / Q000379:methods*; D001749:Urinary Bladder Neoplasms / Q000097:blood / Q000473:pathology / Q000652:urine
D012313:RNA; D004247:DNA