I.
General Information:
Date of README file: 05-01-2012
The following 12 files are the complete results from the brain expression
genome-wide association study (eGWAS) conducted at Mayo Clinic by ErtekinTaner and colleagues and described in full detail in the Zou et al. PloS Genetics,
2012 paper. The brief description of the file contents and their headings are
described in sections II and III, respectively. Please refer to the manuscript for a
complete description of the study including analytic details. Any remaining
inquiries can be forwarded to Dr. Ertekin-Taner’s e-mail as follows:
taner.nilufer@mayo.edu (taner dot nilufer at mayo dot edu).
Any publications that utilize parts or all of this dataset should cite the following
manuscript:
Zou F, Chai HS, Younkin CS, Allen M, Crook J, Pankratz VS, Carrasquillo MM,
Rowley CN, Nair AA, Middha S, Maharjan S, Nguyen T, Ma L, Malphrus KG,
Palusak R, Lincoln S, Bisceglio G, Georgescu C, Kouri N, Kolbert CP, Jen J,
Haines JL, Mayeux R, Pericak-Vance MA, Farrer LA, Schellenberg GD,
Alzheimer’s Disease Genetics Consortium, Petersen RC, Graff-Radford NR,
Dickson DW, Younkin SG, Ertekin-Taner N. (2012) Brain Expression GenomeWide Association Study (eGWAS) Identifies Human Disease-Associated
Variants. PLoS Genet 8(6): e1002707. doi:10.1371/journal.pgen.1002707.
The size of the complete dataset in compressed format is 815 Megabytes and
4.1 Gigabytes uncompressed.
II.
File Names and contents:
N.B. Each file has a header row. Therefore the total number of rows pertains to
the total number of data rows, excluding the header row.
Hap300_CER_AD.txt
Brain expression GWAS (eGWAS) results obtained in the cerebellar samples of
the AD subjects. The GWAS genotypes are obtained by the Illumina Hap300
platform. The total number of rows = 444372
Hap300_CER_All.txt
Brain expression GWAS (eGWAS) results obtained in the cerebellar samples of
the combined AD and non-AD subjects. The GWAS genotypes are obtained by
the Illumina Hap300 platform. The total number of rows = 443784
Hap300_CER_Control.txt
Brain expression GWAS (eGWAS) results obtained in the cerebellar samples of
the non-AD subjects. The GWAS genotypes are obtained by the Illumina Hap300
platform. The total number of rows = 443171
Hap300_TX_AD.txt
Brain expression GWAS (eGWAS) results obtained in the temporal cortex
samples of the AD subjects. The GWAS genotypes are obtained by the Illumina
Hap300 platform. The total number of rows = 450813
Hap300_TX_All.txt
Brain expression GWAS (eGWAS) results obtained in the temporal cortex
samples of the combined AD and non-AD subjects. The GWAS genotypes are
obtained by the Illumina Hap300 platform. The total number of rows = 445356
Hap300_TX_Control.txt
Brain expression GWAS (eGWAS) results obtained in the temporal cortex
samples of the non-AD subjects. The GWAS genotypes are obtained by the
Illumina Hap300 platform. The total number of rows = 440065
HapMap2_CER_AD.txt
Brain expression GWAS (eGWAS) results obtained in the cerebellar samples of
the AD subjects. The GWAS genotypes are the HapMap2 imputed genotypes.
The total number of rows = 4427924
HapMap2_CER_All.txt
Brain expression GWAS (eGWAS) results obtained in the cerebellar samples of
the combined AD and non-AD subjects. The GWAS genotypes are the
HapMap2 imputed genotypes. The total number of rows = 4483512
HapMap2_CER_Control.txt
Brain expression GWAS (eGWAS) results obtained in the cerebellar samples of
the non-AD subjects. The GWAS genotypes are the HapMap2 imputed
genotypes. The total number of rows = 4419055
HapMap2_TX_AD.txt
Brain expression GWAS (eGWAS) results obtained in the temporal cortex
samples of the AD subjects. The GWAS genotypes are the HapMap2 imputed
genotypes. The total number of rows = 4426363
HapMap2_TX_All.txt
Brain expression GWAS (eGWAS) results obtained in the temporal cortex
samples of the combined AD and non-AD subjects. The GWAS genotypes are
the HapMap2 imputed genotypes. The total number of rows = 4484344
HapMap2_TX_Control.txt
Brain expression GWAS (eGWAS) results obtained in the temporal cortex
samples of the non-AD subjects. The GWAS genotypes are the HapMap2
imputed genotypes. The total number of rows = 4425955
III.
Column names and definitions:
a. For the “Hap300” files:
CHR
SNP
BP
A1
TEST
NMISS
BETA
STAT
P
PROBE
txStart
txEnd
SYMBOL
hasSNP
Chromosome
SNP rs number
Physical position (base-pair) according to NCBI Ref Seq, Build 36.2
Tested allele (minor allele by default)
The "additive" SNP genotype test.
Number of non-missing individuals included in analysis
Regression coefficient. Based on the SNP minor allele using an
additive model.
Coefficient t-statistic
Asymptotic p-value for t-statistic (uncorrected)
WG-DASL Illumina Probe ID
Starting base pair for the RefSeq gene the brain level of which is
tested for associations. (Based on Build 36.2)
Ending base pair for the RefSeq gene the brain level of which is
tested for associations. (Based on Build 36.2)
Gene symbol for the RefSeq gene tested in the eGWAS.
If the probe sequence harbors ≥1 SNPs, then this is shown as
"TRUE" under the "SNP-In-Probe" column, and "FALSE",
otherwise.
b. For the “HapMap2” files:
CHR
SNP
BP
A1
TEST
NMISS
BETA
STAT
P
PROBE
txStart
Chromosome
SNP rs number
Physical position (base-pair) according to NCBI Ref Seq, Build 36.2
Tested allele (minor allele by default)
The "additive" SNP genotype test.
Number of non-missing individuals included in analysis
Regression coefficient. Based on the SNP minor allele using an
additive model.
Coefficient t-statistic
Asymptotic p-value for t-statistic (uncorrected)
WG-DASL Illumina Probe ID
Starting base pair for the RefSeq gene the brain level of which is
tested for associations. (Based on Build 36.2)
txEnd
Symbol
hasSNP
Ending base pair for the RefSeq gene the brain level of which is
tested for associations. (Based on Build 36.2)
Gene symbol for the RefSeq gene tested in the eGWAS.
If the probe sequence harbors ≥1 SNPs, then this is shown as
"TRUE" under the "SNP-In-Probe" column, and "FALSE",
otherwise.
[Tissue Region][DiagnosticGroup]12point5
Results are shown for the
[Tissue Region] eGWAS (i.e. either cerebellum or temporal cortex) using
HapMap2-imputed genotypes for the [DiagnosticGroup] dataset (i.e. AD, Control
or All), with transcripts detected in >12.5% of the subjects (TRUE=detected,
FALSE=not detected).
[Tissue Region][DiagnosticGroup]25
Results are shown for the
[Tissue Region] eGWAS (i.e. either cerebellum or temporal cortex) using
HapMap2-imputed genotypes for the [DiagnosticGroup] dataset (i.e. AD, Control
or All), with transcripts detected in >25% of the subjects (TRUE=detected,
FALSE=not detected).
[Tissue Region][DiagnosticGroup]50
Results are shown for the
[Tissue Region] eGWAS (i.e. either cerebellum or temporal cortex) using
HapMap2-imputed genotypes for the [DiagnosticGroup] dataset (i.e. AD, Control
or All), with transcripts detected in >50% of the subjects (TRUE=detected,
FALSE=not detected).
[Tissue Region][DiagnosticGroup]75
Results are shown for the
[Tissue Region] eGWAS (i.e. either cerebellum or temporal cortex) using
HapMap2-imputed genotypes for the [DiagnosticGroup] dataset (i.e. AD, Control
or All), with transcripts detected in >75% of the subjects (TRUE=detected,
FALSE=not detected).
Tissue Regions:
CER
Cerebellar eGWAS
TX
Temporal cortex eGWAS
Diagnostic Groups:
AD
Results for subjects with Alzheimer's disease pathology.
Control
Results for subjects with non-Alzheimer's disease pathology.
All
Results for the combined AD and Control samples.