title: Enhanced retrieval of DNA from human fecal samples results in improved performance of colorectal cancer screening test.
abstract: 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 = 0.0005 (by McNemar's test), with no change in specificity. The newly developed sample preparation method mitigates a major problem in detecting rare cancer-associated genetic changes in heterogeneous clinical samples such as stool.
authors.affiliation: Applied Research Group, EXACT Sciences Corporation, 100 Campus Drive, Marlborough, MA, USA.
authors.forename: Duncan
authors.initials: D
authors.lastname: Whitney
authors.forename: Joel
authors.initials: J
authors.lastname: Skoletsky
authors.forename: Kent
authors.initials: K
authors.lastname: Moore
authors.forename: Kevin
authors.initials: K
authors.lastname: Boynton
authors.forename: Lisa
authors.initials: L
authors.lastname: Kann
authors.forename: Randall
authors.initials: R
authors.lastname: Brand
authors.forename: Sapna
authors.initials: S
authors.lastname: Syngal
authors.forename: Michael
authors.initials: M
authors.lastname: Lawson
authors.forename: Anthony
authors.initials: A
authors.lastname: Shuber
mesh_terms: D020106:Acrylamide / Q000737:chemistry; D015179:Colorectal Neoplasms / Q000175:diagnosis* / Q000473:pathology*; D004247:DNA / Q000378:metabolism; D004252:DNA Mutational Analysis; D004273:DNA, Neoplasm / Q000032:analysis / Q000302:isolation & purification; D005243:Feces / Q000737:chemistry*; D016678:Genome; D006801:Humans; D008280:Magnetics; D008403:Mass Screening; D025202:Molecular Diagnostic Techniques; D009154:Mutation; D009369:Neoplasms / Q000378:metabolism; D012680:Sensitivity and Specificity
chemical_list: D004273:DNA, Neoplasm; D020106:Acrylamide; D004247:DNA