This workflow was successfully applied to the handling of 6,303 frozen tumor tissues and paired blood samples- from Mutographs’ biorepository containing over 11,000 tumor tissues- spanning eight cancer types across seven organs, for WGS. Biological material was collected in accordance with national and international regulations, following signed informed consent from patients enrolled in the project (^^BOX 1^^). Ethical approval was obtained from institutional review boards and the IARC ethics committee (IEC-17-10).
- OCT (Optimal Cutting Temperature) medium, NEG-50 OCT, Fisher Scientific^®, cat. no. 11912365.
- Ethanol (70%, 95%, 100% v/v), Emprove Expert, Merck^®, cat. no. 1.00983.1000, or VWR International.
- ! CAUTION: Ethanol is flammable. Store in sealed containers away from ignition sources.
- Hematoxylin, Masson’s alum, Merck^®, cat. no. 1.11487.0025.
- Erythrosine B, 0.1% solution, Merck^®, cat. no. 1.15936.0025.
- Xylene, VWR International, cat. no. 28973.363.
- ! CAUTION: Xylene is toxic, flammable, and irritant. Use in a fume hood with adequate ventilation. Store in a flammable cabinet. Wear protective gloves and clothing.
- Paraformaldehyde (PFA), 16% stock and 4% working solutions, Polysciences^®, cat. no. 18814.
- ! CAUTION: PFA is classified as a high-hazard chemical. Handle under a fume hood or in a well-ventilated area. Wear gloves, protective eyewear, and lab coat. Avoid inhalation and skin contact. Store sealed in a cool, dry place.
- Phosphate-buffered saline (PBS), Eurobio^®, cat. no. C3SP80S01-01.
- Mounting medium, PERTEX, Labelling^®, cat. no. PERTEX500.
- DNA Away, Dutscher, cat. no. 038188.
- RNase Away, M-Thermo, Fisher Scientific, cat. no. 11580095.
- Cresyl violet acetate (powder), Aldrich^®, cat. no. 86098-0.
- Ethanol (50% v/v), Emprove Expert, Merck^®, cat. no. 1.00983.1000, or VWR International.
- DNA Away, Dutscher, cat. no. 038188.
- Deep freezers, –80 °C and –20 °C, any institutional model.
- Cryostat (Institutional model): Microm HM550, Epedia, Thermo Fisher, cat. no. 956454D, equipped with:
o Multiple-size metal embedding cryomolds, Tissue-Tek cryomolds; Sakura Finetek.
o Multiple-size metal specimen chucks, Thermo Fisher, 30 mm.
o Built-in pre-cooled area (freezing stage).
- Digital slide scanner (Institutional model): Aperio GT450, ref. no. 23GT450; Leica Biosystems), or any equivalent scanner.
- Facilities for digital pathology, including computer and monitors.
- Label printer, e.g., Brady Bench i3300, serial no. PIG332134012022.
o NOTE: Used at IARC to print specimen identification barcodes on StainerBondz™ solvent-resistant labels for glass slides. Any institutional approach for secure identification of products is considered.
- Disposable microtome blades (high-profile and low-profile), Fisher Scientific, cat. no. 1291830.
- Sterile disposable surgical scalpels, cat. no. 3752021.
- Fume hood, e.g., Thermo Scientific Herasafe 2030i, cat. no. 51033051/42952033.
- Forceps, medium and small (fine) size, serrated and flat tips, Fisher Scientific, cat. no. 12-651-915, or equivalent.
- Fine paintbrush, e.g., M-M France, cat. no. F/PINCEAUA12.
- Cryotubes, 1.5–2.0 ml, with secure caps, Safelock tubes, Dutscher, cat. no. 033290.
- Superfrost™ Plus adhesion slides, Fisher Scientific, cat. no. 10149870.
- Polyethylene Naphthalate (PEN)-NF membrane slides, Zeiss SAS, cat. no. 415190-9081-000.
- Cryo-resistant deep freezer storage boxes, 136 x 136 x 50 mm, Grossroen, cat. no. 6.080130.
- Kimwipes or lint-free tissue, Paredes, cat. no. 484104.
- Staining station slide racks and staining jars, Myreva station, cat. no. SS30, or equivalent.
- Coplin (glass staining) jars, Fisher Scientific, cat. no. 12697696.
- Glass coverslips, 24 x 50 mm, Roth, cat. no. 1871.2.
- Personal protective equipment (PPE): laboratory coat, gloves, and eye protection, VWR International, or any institutional equivalent such as StarLab France.
**Part 4 (Steps 44 to 60)**
- Laser Capture Microdissection device, e.g., Zeiss PALM MicroBeam IV.
- Adhesive cap opaque 500 µl tube, Zeiss, cat. no. 415190-9201-000.
- Coplin (glass staining) jars, Fisher Scientific, cat. no. 12697696.
- Personal protective equipment (PPE): laboratory coat, gloves, and eye protection, VWR International.