Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA.
Plasma of cancer patients contains cell-free tumor DNA that carries information on tumor mutations and tumor burden. Individual mutations have been probed using allele-specific assays, but sequencing of entire genes to detect cancer mutations in circulating DNA has not been demonstrated. We developed a method for tagged-amplicon deep sequencing (TAm-Seq) and screened 5995 genomic bases for low-frequency mutations. Using this method, we identified cancer mutations present in circulating DNA at allele frequencies as low as 2%, with sensitivity and specificity of >97%. We identified mutations throughout the tumor suppressor gene TP53 in circulating DNA from 46 plasma samples of advanced ovarian cancer patients. We demonstrated use of TAm-Seq to noninvasively identify the origin of metastatic relapse in a patient with multiple primary tumors. In another case, we identified in plasma an EGFR mutation not found in an initial ovarian biopsy. We further used TAm-Seq to monitor tumor dynamics, and tracked 10 concomitant mutations in plasma of a metastatic breast cancer patient over 16 months. This low-cost, high-throughput method could facilitate analysis of circulating DNA as a noninvasive "liquid biopsy" for personalized cancer genomics.
Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
Tim
T
Forshew
Muhammed
M
Murtaza
Christine
C
Parkinson
Davina
D
Gale
Dana W Y
DW
Tsui
Fiona
F
Kaper
Sarah-Jane
SJ
Dawson
Anna M
AM
Piskorz
Mercedes
M
Jimenez-Linan
David
D
Bentley
James
J
Hadfield
Andrew P
AP
May
Carlos
C
Caldas
James D
JD
Brenton
Nitzan
N
Rosenfeld
D004247:DNA / Q000097:blood* / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009369:Neoplasms / Q000097:blood* / Q000175:diagnosis* / Q000235:genetics
D004247:DNA