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Chunk #34 — Materials and methods — Sample preparation — Cancer specimen description

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Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing.
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Human primary tumors and whole blood were collected under the UC San Diego IRB-approved protocol with prospective consent. The participants were enrolled in accordance with the Helsinki Declaration and to local legislation and gave informed consent. The breast cancer corresponds to a primary metaplasmic carcinoma from a 62-year-old patient (T2, N0, M0) untreated at sampling. The sample was negative for progesterone receptor, HER2 and focally positive (< 5%) for estrogen receptor as estimated by immunohistochemistry. The colon cancer corresponds to an enteric adenocarcinoma from a 65-year-old patient (T3, N0, M0) untreated at sampling. The sample was positive for MLH1, PMS2 and CD20, and in a few cells for MSH2, and negative for MSH6 by immunohistochemistry. The ovarian cancer corresponds to a serous adenocarcinoma of enteric type from a 64-year-old patient (T3b, N0, M0) treated with three cycles of idarubacin and paclitaxol before sampling. The sarcoma sample corresponds to a small intestine pleomorphic sarcoma identified in a 59-year-old patient (metastasis M1) from recurrent disease following chemotherapy and 3 years after initial diagnosis.