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Chunk #90 — Online Methods — Determination of tumor purity via pathology review

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Absolute quantification of somatic DNA alterations in human cancer.
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Frozen ovarian serous cystadenocarcinoma specimens were collected from multiple hospital tissue banks and maintained frozen in liquid nitrogen vapors. A tissue portion was created with two flanking H&E slides (arbitrarily named top and bottom) as follows: tissues were mounted in optimal cutting temperature media (OCT) and brought to -20°C. A 4μm frozen section (top slide) was cut with a cryostat (Leica Microsystems, Wetzlar, Germany). A specimen for molecular extraction was created by shaving 100 mg of tumor tissue from the tissue face with a scalpel, then a second 4μm frozen section was cut (bottom slide). An H&E stain was conducted on both slide tissue sections using an Autostainer XL with integrated coverslipper (Leica). Digital images of slides were created at 20× resolution using a Scanscope XT (Aperio, Vista, CA, USA). Board-certified pathologists conducted the pathology review remotely via ImageScope software (Aperio). Pathologists initially reviewed each slide at low magnification to determine low power microscopic morphology, then increased magnification to 20× and reviewed 10 representative high power fields on each slide. Diagnosis of ovarian serous cystadenocarcinoma was verified, and tumor purity