We tested 250 primary cancer samples spanning 26 human malignancies, which included: lung cancer (n = 87), breast cancer (n = 33), colorectal cancer (n = 30), pancreatic cancer (n = 23), prostate cancer (n = 20), melanoma (n = 11), chronic myeloproliferative disease (n = 10), cholangiocarcinoma (n = 6), gastric cancer (n = 4), ovarian cancer (n = 3), salivary gland cancer (n = 3) and thyroid cancer (n = 3) among others. Sixty-two of these primary tumour samples were evaluated for official clinical testing, and included 52 lung adenocarcinomas, most of them small core biopsies with very limited tissue. For haematopoietic malignancies, spare DNA that had been previously extracted from patient blood for clinical testing was obtained from the Massachusetts General Hospital (MGH) Molecular Diagnostics Laboratory. For solid tumours, formalin-fixed paraffin-embedded (FFPE) tumour blocks were obtained from the MGH archives. All samples were collected with institutional review board approval. Histological examination of haematoxylin and eosin-stained slides derived from FFPE samples was performed by a pathologist (AJI) and assessed for the presence of tumour. Available tumour tissue was manually macrodissected from serial 5 µm unstained sections, or cored from the paraffin block using a 1.5 mm dermal punch. Total nucleic acid was extracted from FFPE material using a modified FormaPure System (Agencourt Bioscience Corporation, Beverly, MA) on a custom Beckman Coulter Biomek NXP workstation. Blood-derived DNA was extracted using the QIAamp Blood kit (Qiagen, Inc., Valencia, CA).