Genotyping data comes from four groups of subjects, 622 high grade astrocytic glioma cases and 602 controls from AGS, 3390 controls from Illumina controls (iControls), and 70 glioblastoma cases from TCGA 4 (link) (Supplementary Table 1a) that passed quality control measures described below, including checks for relatedness and European ancestry. Details of subject recruitment for AGS have been provided previously 20 ,21 (link). Briefly, cases aged 20 or older, diagnosed with histologically confirmed incident gliomas (International Classification of Diseases for Oncology, morphology codes 9380–9481) were recruited from the local population based registry, the Northern California Rapid Case Ascertainment program and the University of California, San Francisco Neuro-oncology clinic between 1997 and 2006. Additional pathology reviews were conducted by specialty trained neuropathologists including Kenneth Aldape and Tarik Tihan. Glioblastoma, which is the diagnosis for the large majority (84%) of cases, is a diagnosis with good concordance between pathologists 22 (link). Although survival bias is a concern for studies of glioblastoma, we obtained blood from subjects within a median of 80 days from diagnosis. Nevertheless, the results may not apply to those with the most rapidly fatal forms of this disease. AGS controls aged 20 years or older from the same residential area as cases were identified using random digit dialing and were frequency matched to cases on age, gender and ethnicity. Consenting participants provided blood and/or buccal specimens and information during an in-person or telephone interview. Because of the large scale genotyping platform used, only subjects who provided blood specimens were included in the present analysis. We initially only included individuals who self-identified as white in the genotyping, but then used methods described below to verify European ancestry.
We also assembled an independent control genotype dataset of 3390 non-redundant white controls from Illumina iControlDB (Illumina, Inc., San Diego, CA). The subjects are anonymous, with information only on their age, gender and ethnicity. The iControl data also included 262 HapMap samples [30 CEU parent-child trios (Utah residents with ancestry from northern and western Europe), 84 YRI (Yoruba in Ibadan, Nigeria) and 88 Chinese or Japanese] that we used to identify and remove subjects with evidence of non-European ancestry from our analysis. We checked for evidence of non-European ancestry (Supplementary Figure 2) and sample duplicates or related subjects (IBS > 1.6; Supplementary Figure 3) among AGS samples, TCGA, and iControls by performing Multi-dimensional scaling (MDS) analysis on 20 bootstrap samples of 1000 random autosomal bi-allelic SNPs. Following these quality assessment measures, we obtained a total of 3390 white controls from three different Illumina panels with up to 306,154 autosomal SNPs overlapping the HumanHap370duo panel used for the AGS subjects: Illumina HumanHap300 (n=336 subjects), HumanHap550v1 (n=1519), and HumanHap550v3 (n=1552).
We downloaded HumanHap550 platform genotyping data from blood specimen DNA and demographic data for 89 glioblastoma cases from the Cancer Genome Atlas (TCGA; http://cancergenome.nih.gov/)4 (link). Although 72 were identified as whites, our analyses showed that one had non-European ancestry (Supplementary Figure 3) and another appeared to duplicate an AGS case, leaving 70 TCGA cases.