Colorectal cancer accounts for more than 10% of all cancer deaths but is curable, if detected early. We reported previously on a stool-based screening test in which DNA from stool samples is subjected to genome analysis; sensitivity of the test has been limited in part by inefficiency of retrieving DNA from stool. Our aim was to test the impact of a new purification method that would increase the yield of human DNA from stool. DNA from 86 cancer and 100 non-cancer subjects (diagnosed by colonoscopy) were purified from stool with a new method for DNA recovery based on sequence-specific capture with acrylamide gel immobilized capture probes as well as with a previously developed magnetic bead-capture procedure. The new purification method gives an average 5.4-fold increase in the quantity of human DNA that can routinely be retrieved from fecal samples. The increased recovery of DNA corresponds with an increase in assay sensitivity from 53% (CI: 42 to 64%) to 70% (CI: 59 to 79%); P ؍ Colorectal cancer (CRC) is curable in more than 90% of cases when caught in the earliest stages. Current colorectal cancer screening guidelines include a variety of options. Colonoscopy may be the most sensitive screening test, 1 however its invasiveness (including bowel preparation and the procedure itself) present major barriers to its implementation for large-scale, nationwide screening.2 An improved non-invasive screening option could address many of the issues associated with colonoscopy. Non-invasive screening is available today through assessment of occult blood in fecal samples, but this test has relatively low sensitivity, especially for early stage cancer, limiting its impact on cancer mortality. However, analysis of DNA from stool provides an attractive, alternative, non-invasive means for CRC screening if scalable, sensitive, and specific tests can be developed.We have previously described 3 a stool-based screening test for early detection of colorectal cancers. The multi-target nucleic acid assay consists of a panel of 21 specific mutations in adenomatous polyposis coli (APC), 4 p53 5,6 , and K-ras 7 genes, a microsatellite instability marker (BAT-26), 8 and a marker for genomic integrity (DNA Integrity assay; DIA). 9 As reported in separate studies, 3,10,11,12 the multi-target assay has an aggregate sensitivity of 67% (95% CI: 60.3 to 73.9%) and specificity of 97% (95% CI: 92.9 to 99.2%), a major improvement to the current screening methods of the fecal occult blood test (25 to 40% sensitivity). 13,14 In the multi-target assay studies human DNA was recovered and purified using streptavidin-bound magnetic beads. 3,15 We have reported on the use of separate components of this multi-target test elsewhere. 9,11,16,17,18 The mutation panel portion of the multi-target assay relies on detecting mutations in several well-documented colorectal cancer-associated genes. 19,20 The DNA integrity portion of the test consists of a set of markers that serve as surrogate markers for the presence of long DNA fragments. The principles and...