Sequence variant discovery in DNA repair genes from radiosensitive and radiotolerant prostate brachytherapy patients.
OBJECTIVE
The presence of intrinsic radiosensitivity within prostate cancer patients may be an important factor contributing to development of radiation toxicity. We investigated whether variants in genes responsible for detecting and repairing DNA damage independently contribute to toxicity following prostate brachytherapy.


METHODS
Genomic DNA was extracted from blood samples of 41 prostate brachytherapy patients, 21 with high and 20 with low late toxicity scores. For each patient, 242 PCR amplicons were generated containing 173 exons of eight candidate genes: ATM, BRCA1, ERCC2, H2AFX, LIG4, MDC1, MRE11A, and RAD50. These amplicons were sequenced and all sequence variants were subjected to statistical analysis to identify those associated with late radiation toxicity.


RESULTS
Across 41 patients, 239 sites differed from the human genome reference sequence; 170 of these corresponded to known polymorphisms. Sixty variants, 14 of them novel, affected protein coding regions and 43 of these were missense mutations. In our patient population, the high toxicity group was enriched for individuals with at least one LIG4 coding variant (P = 0.028). One synonymous variant in MDC1, rs28986317, was associated with increased radiosensitivity (P = 0.048). A missense variant in ATM, rs1800057, associated with increased prostate cancer risk, was found exclusively in two high toxicity patients but did not reach statistical significance for association with radiosensitivity (P = 0.488).


CONCLUSIONS
Our data revealed new germ-line sequence variants, indicating that existing sequence databases do not fully represent the full extent of sequence variation. Variants in three DNA repair genes were linked to increased radiosensitivity but require validation in larger populations.
Pugh
Trevor J
TJ
Genome Sciences Centre, Provincial Prostate Brachytherapy Program, and Medical Biophysics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.
Keyes
Mira
M
Barclay
Lorena
L
Delaney
Allen
A
Krzywinski
Martin
M
Thomas
Dallas
D
Novik
Karen
K
Yang
Cindy
C
Agranovich
Alexander
A
McKenzie
Michael
M
Morris
W Jim
WJ
Olive
Peggy L
PL
Marra
Marco A
MA
Moore
Richard A
RA
D001918:Brachytherapy / Q000009:adverse effects*; D004260:DNA Repair / Q000235:genetics*; D005091:Exons / Q000235:genetics; D006801:Humans; D008297:Male; D020125:Mutation, Missense; D020641:Polymorphism, Single Nucleotide; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000532:radiotherapy*; D011836:Radiation Tolerance / Q000235:genetics*