title: Next-generation prostate cancer biobanking: toward a processing protocol amenable for the International Cancer Genome Consortium.
abstract: Next-generation DNA and RNA sequencing requires intact nucleic acids from high-quality human tissue samples to better elucidate the molecular basis of cancer. We have developed a prostate biobanking protocol to acquire suitable samples for sequencing without compromising the accuracy of clinical diagnosis. To assess the clinical implications of implementing this protocol, we evaluated 105 consecutive radical prostatectomy specimens from November 2008 to February 2009. Alternating levels of prostate samples were submitted to Surgical Pathology as formalin-fixed, paraffin-embedded blocks and to the institutional biobank as frozen blocks. Differences in reported pathologic characteristics between clinical and procured specimens were compared. Clinical staging and grading were not affected by the biobank protocol. Tumor foci on frozen hematoxylin and eosin slides were identified and high-density tumor foci were scored and processed for DNA and RNA extractions for sequencing. Both DNA and RNA were extracted from 22 cases of 44 with high-density tumor foci. Eighty-two percent (18/22) of the samples passed rigorous quality control steps for DNA and RNA sequencing. To date, DNA extracted from 7 cases has undergone whole-genome sequencing, and RNA from 18 cases has been RNA sequenced. This protocol provides prostate tissue for high-throughput biomedical research and confirms the feasibility of actively integrating prostate cancer into The Cancer Genome Atlas Program, a member of the International Cancer Genome Consortium.
authors.affiliation: Departments of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065, USA.
authors.forename: Raquel
authors.initials: R
authors.lastname: Esgueva
authors.forename: Kyung
authors.initials: K
authors.lastname: Park
authors.forename: Robert
authors.initials: R
authors.lastname: Kim
authors.forename: Naoki
authors.initials: N
authors.lastname: Kitabayashi
authors.forename: Christopher E
authors.initials: CE
authors.lastname: Barbieri
authors.forename: Philip J
authors.initials: PJ
authors.lastname: Dorsey
authors.forename: Cyril
authors.initials: C
authors.lastname: Abraham
authors.forename: Samprit
authors.initials: S
authors.lastname: Banerjee
authors.forename: Robert A
authors.initials: RA
authors.lastname: Leung
authors.forename: Ashutosh K
authors.initials: AK
authors.lastname: Tewari
authors.forename: Stéphane
authors.initials: S
authors.lastname: Terry
authors.forename: Maria M
authors.initials: MM
authors.lastname: Shevchuk
authors.forename: David S
authors.initials: DS
authors.lastname: Rickman
authors.forename: Mark A
authors.initials: MA
authors.lastname: Rubin
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D004247:DNA / Q000302:isolation & purification; D052138:Genes, Neoplasm; D015894:Genome, Human; D006801:Humans; D007391:International Cooperation; D008297:Male; D008875:Middle Aged; D011467:Prostate / Q000473:pathology*; D011468:Prostatectomy; D011471:Prostatic Neoplasms / Q000235:genetics / Q000473:pathology* / Q000601:surgery; D012313:RNA / Q000302:isolation & purification; D017423:Sequence Analysis, RNA; D013048:Specimen Handling; D014015:Tissue Banks
chemical_list: D012313:RNA; D004247:DNA