Nonsynonymous coding single-nucleotide polymorphisms spanning the genome in relation to glioblastoma survival and age at diagnosis.
OBJECTIVE
Our aim was to discover possible inherited factors associated with glioblastoma age at diagnosis and survival. Although new genotyping technologies allow greatly expanded exploration of such factors, they pose many challenges.


METHODS
In this pilot study, we (a) genotyped 112 newly diagnosed glioblastoma patients ascertained through a population-based study (group 1) with the ParAllele assay panel of approximately 10,000 nonsynonymous coding single-nucleotide polymorphisms (SNP), (b) used several statistical and bioinformatic techniques to identify 17 SNPs potentially related to either glioblastoma age at diagnosis or survival, and (c) genotyped 16 of these SNPs using conventional PCR methods in an independent group of 195 glioblastoma patients (group 2).


RESULTS
In group 2, only one of the 16 SNPs, rs8057643 (located on 16p13.2), was significantly associated with glioblastoma age at diagnosis (nominal P = 0.0017; Bonferroni corrected P = 0.054). Median ages at diagnosis for those with 0, 1, or 2 T alleles were 66, 57, and 59 years in group 1 and 64, 57, and 55 years in group 2 (combined P = 0.001). Furthermore, Cox regression analyses of time to death with number of T alleles adjusted for gender and patient group yielded a hazard ratio of 0.82 (95% confidence interval, 0.68-0.98; P = 0.03).


CONCLUSIONS
Although limited by a relatively small sample size, this pilot study, using well-characterized, unambiguous disease characteristics, illustrates the necessity of independent replication owing to the likelihood of false positives. Several other challenges are discussed, including attempts to incorporate information on the potential functional importance of SNPs in genome-disease association studies.
Wrensch
Margaret
M
Division of Neuroepidemiology, Department of Neurological Surgery, School of Medicine, University of California at San Francisco, 94102, USA. margaret.wrensch@ucsf.edu
McMillan
Alex
A
Wiencke
John
J
Wiemels
Joe
J
Kelsey
Karl
K
Patoka
Joe
J
Jones
Hywel
H
Carlton
Victoria
V
Miike
Rei
R
Sison
Jennette
J
Moghadassi
Michelle
M
Prados
Michael
M
D000367:Age Factors; D017668:Age of Onset; D000368:Aged; D000483:Alleles; D003062:Codon; D018388:Codon, Terminator; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D016678:Genome; D005838:Genotype; D005909:Glioblastoma / Q000235:genetics* / Q000401:mortality / Q000473:pathology*; D006801:Humans; D008297:Male; D008875:Middle Aged; D010865:Pilot Projects; D020641:Polymorphism, Single Nucleotide; D016896:Treatment Outcome
D003062:Codon; D018388:Codon, Terminator