Enhanced retrieval of DNA from human fecal samples results in improved performance of colorectal cancer screening test.
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.
Whitney
Duncan
D
Applied Research Group, EXACT Sciences Corporation, 100 Campus Drive, Marlborough, MA, USA.
Skoletsky
Joel
J
Moore
Kent
K
Boynton
Kevin
K
Kann
Lisa
L
Brand
Randall
R
Syngal
Sapna
S
Lawson
Michael
M
Shuber
Anthony
A
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
D004273:DNA, Neoplasm; D020106:Acrylamide; D004247:DNA