Sample 39
Homo sapiens
Protocols: Formalin-fixed, paraffin-embedded (FFPE) tissue samples of 65 vulvar lesions were retrieved from the pathology archives of the Departments of Pathology of the VU University Medical Center (n=26), the Academic Medical Center (n=25), and the Netherlands Cancer Institute / Antoni van Leeuwenhoek Hospital (n=4), Amsterdam, The Netherlands. These included 24 VSCC and 41 high-grade VIN, including 10 pairs of VIN-VSCC (i.e. meaning that both VIN and VSCC were from the same woman). Of the 41 VIN, 14 VIN were of women who did not develop VSCC during a follow-up period of at least 10 years (VIN without VSCC) and 27 VIN were of women with associated VSCC (VIN with VSCC). The mean age of women included in this study was 70 (range 37-95) for carcinomas and 53 (range 21-88) for VIN. Collection, storage and use of archival tissue were performed in compliance with the Code for Proper Secondary Use of Human Tissue in the Netherlands (www.federa.org). DNA from VIN lesions was isolated following either macro- or microdissection of dysplastic regions. For VSCC, whole tissue sections were used. All isolates contained > 70% dysplastic cells. Micro-dissection was performed using the Leica LMD6500 (Leica Microsystems, Wetzlar, Germany) as described before (Wilting et al. 2009, Cancer Res 69:647-655; Weiss et al. 1999, Mol Pathol 52:243-251), with a few modifications (Voorham et al. 2012, Clin Cancer Res 18:4560-4569). Eight micrometer thick sections were cut and mounted on PEN MembraneSlides (Leica). Sections were hydrated, stained with Mayers Hematoxylin and completely dehydrated. Genomic DNA of micro-dissected tissue was extracted after a 5-day incubation period with lysis buffer (ATL buffer, QIAamp DNA microkit [Qiagen, Hilden, Germany]) and daily freshly added proteinase K (200 ng) (Voorham et al. 2012, Clin Cancer Res 18:4560-4569). For macrodissected VIN lesions and VSCC, DNA was isolated using the QIAamp DNA FFPE tissue kit (Qiagen). Concentrations and purity was measured using the Qubit dsDNA BR assay kit (Thermo Fisher Scientific, Waltham, MA, USA) on the Qubit 2.0 Fluorometer (Thermo Fisher Scientific). Samples were prepared using the TruSeq Nano DNA Library Prep Kit (Illumina San Diego, CA, USA) according to the manufacturers instructions
ENA first public
2018-01-01
ENA last update
2017-10-05
External Id
SAMEA104336212
INSDC center alias
Cancer Center Amsterdam, department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
INSDC center name
Cancer Center Amsterdam, department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
INSDC first public
2018-01-01T17:01:43Z
INSDC last update
2017-10-05T14:20:19Z
INSDC status
public
Submitter Id
E-MTAB-6113:Sample 39
age
60
broker name
ArrayExpress
common name
human
disease
Vulvar Squamous Cell Carcinoma
individual
63
infect
Human papillomavirus
organism part
mammalian vulva
sample name
E-MTAB-6113:Sample 39
sex
female
tumor grading
moderately-differentiated