Table 3: Description of data files deposited in the AMP-AD Knowledge Portal.

From: Human whole genome genotype and transcriptome data for Alzheimer’s and other neurodegenerative diseases

Study Name doi Data Type File Name doi File Type File Column Headers Definitions Reference
A. Mayo LOAD GWAS (Data Citation 2: Synapse http://dx.doi.org/10.7303/syn2910256) 10.7303/syn2910256 Genotype and Covariate MayoLOADGWAS_SNPGenotypes_covariates.csv 10.7303/syn3205821.6 Covariate information for subjects included in Mayo LOAD GWAS, comma delimited text file FID=Family ID; IID=Individual ID; RSGWAS=‘1’ indicates if sample is part of Mayo Clinic Rochester Antemortem Cohort; AUTGWAS=‘1’ indicates if sample is part of Mayo Clinic Brain Bank Postmortem Cohort; AgeOver60=number of years beyond the age of 60 for age at death (Mayo Clinic Brain Bank Postmortem Cohort) or age at diagnosis (Mayo Clinic Rochester and Jacksonville Antemortem Cohorts); Sex=1 if Male; APOE4_Dose (+/−)=‘1’ indicates carriers of at least one copy of the APOEε4 allele; APOE4_dosage (0,1,2)= number of APOEε4 alleles ; APOE_Genotype=APOE genotype calls. For all columns ‘−9’ indicates missing data. Carrasquillo et al., 1, Nature Genetics
MayoLOADGWAS_SNPGenotypes.bed 10.7303/syn3205812.4 LOAD GWAS binary ped file (PLINK format), genotype information Binary File, No Column Headers.
MayoLOADGWAS_SNPGenotypes.bim 10.7303/syn3205814.4 LOAD GWAS binary map file (PLINK format), variant information Binary File, No Column Headers.
MayoLOADGWAS_SNPGenotypes.fam 10.7303/syn3205816.4 LOAD GWAS fam file (PLINK format), pedigree and phenotype information Six columns: Column 1=Family ID; Column 2= Individual ID; Column 3=Paternal ID; Column 4=Maternal ID; Column 5=Sex (1=male; 2=female); Column 6=Phenotype (1=control; 2= AD case)
B. Mayo eGWAS (Data Citation 3: Synapse http://dx.doi.org/10.7303/syn3157225,Data Citation 4: Synapse http://dx.doi.org/10.7303/syn3157249) 10.7303/syn3157225 Array Expression and Covariate (Data Citation 3: Synapse http://dx.doi.org/10.7303/syn3157225) MayoEGWAS_arrayExpression_CBE_covariates.csv 10.7303/syn3256502.1 Covariate information for subjects with cerebellum expression measures, comma delimited text file. Dxn=Diagnosis (0=Non-AD, 1=AD); Sex=1 if female and 0 if male; Age=Age at Death; E4dose=Number of APOEε4 alleles; plate1-plate4 (cerebellum) or plate 2-plate 5 (temporal cortex)=PCR plate - technical covariate; RIN=RNA intergrity number - a numerical assessment of the integrity of RNA; RINsqAdj=(RIN-RINmean)^2 - a statistical adjustment of the RIN. Zou et al., 10, PLoS Genetics
MayoEGWAS_arrayExpression_TCX_covariates.csv 10.7303/syn3617056.1 Covariate information for subjects with temporal cortex expression measures, comma delimited text file.
MayoEGWAS_arrayExpression_CBE.csv 10.7303/syn3256501.1 Gene expression phenotypes from cerebellum tissue samples, comma delimited text file. FID=Family ID; IID=Individual ID; ILMN_1762337 to ILMN_2137536=WG-DASL Illumina Probe ID.
MayoEGWAS_arrayExpression_TCX.csv 10.7303/syn3617054.1 Gene expression phenotypes from temporal cortex tissue samples, comma delimited text file.
10.7303/syn3157249 eSNP Results (Data Citation 4: Synapse http://dx.doi.org/10.7303/syn3157249) MayoEGWAS_analysis_eQTL_CBE_results_AD.gz 10.7303/syn3207163.3 Brain expression GWAS (eGWAS) results obtained using Hap300 genotypes in the cerebellar samples of the AD subjects, text file with 444,372 rows. CHR=Chromosome; SNP=SNP rs number; BP=Physical position (base-pair) according to NCBI Ref Seq, Build 36.2; A1=Tested Allele; TEST=The ‘additive’ SNP genotype test; NMISS=Number of non-missing individuals included in analysis; BETA=Regression coefficient. Based on the SNP minor allele using an additive model; STAT=Coefficient t-statistic; P=Asymptotic p-value for t-statistic (uncorrected); PROBE=WG-DASL Illumina Probe ID; txStart=Starting base pair for the RefSeq gene the brain level of which is tested for associations. (Based on Build 36.2); txEnd=Ending base pair for the RefSeq gene the brain level of which is tested for associations. (Based on Build 36.2); SYMBOL=Gene symbol for the RefSeq gene tested in the eGWAS; hasSNP=If the probe sequence harbors ≥1 SNPs, then this is shown as ‘TRUE’ under the ‘SNP-In-Probe’ column, and ‘FALSE’, otherwise.
MayoEGWAS_analysis_eQTL_CBE_results_nonAD.gz 10.7303/syn3207167.3 Brain expression GWAS (eGWAS) results obtained using Hap300 genotypes in the cerebellar samples of the non-AD subjects, text file with 443,171 rows
MayoEGWAS_analysis_eQTL_CBE_results.gz 10.7303/syn3207165.3 Brain expression GWAS (eGWAS) results obtained using Hap300 genotypes in the cerebellar samples of the combined AD and non-AD subjects, text file with 443,784 rows
MayoEGWAS_analysis_eQTL_TCX_results_AD.gz 10.7303/syn3207169.3 Brain expression GWAS (eGWAS) results obtained using Hap300 genotypes in the temporal cortex samples of the AD subjects, text file with 450,813 rows.
MayoEGWAS_analysis_eQTL_TCX_results_nonAD.gz 10.7303/syn3207175.3 Brain expression GWAS (eGWAS) results obtained using Hap300 genotypes in the temporal cortex samples of the non-AD subjects, text file with 440,065 rows.
MayoEGWAS_analysis_eQTL_TCX_results.gz 10.7303/syn3207173.3 Brain expression GWAS (eGWAS) results obtained using Hap300 genotypes in the temporal cortex samples of the combined AD and non-AD subjects, text file with 445,356 rows.
MayoEGWAS_analysis_eQTL_CBE_imputedResults_AD.gz 10.7303/syn3207177.3 Brain expression GWAS (eGWAS) results obtained using HapMap2 imputed genotypes in the cerebellar samples of the AD subjects, text file with 4,427,924 rows. CHR=Chromosome; SNP=SNP rs number; BP=Physical position (base-pair) according to NCBI Ref Seq, Build 36.2; A1=Tested Allele; TEST=The ‘additive’ SNP genotype test; NMISS=Number of non-missing individuals included in analysis; BETA=Regression coefficient. Based on the SNP minor allele using an additive model; STAT=Coefficient t-statistic; P=Asymptotic p-value for t-statistic (uncorrected); PROBE=WG-DASL Illumina Probe ID; txStart=Starting base pair for the RefSeq gene the brain level of which is tested for associations. (Based on Build 36.2); txEnd=Ending base pair for the RefSeq gene the brain level of which is tested for associations. (Based on Build 36.2); SYMBOL=Gene symbol for the RefSeq gene tested in the eGWAS; hasSNP=If the probe sequence harbors ≥1 SNPs, then this is shown as ‘TRUE’ under the ‘SNP-In-Probe’ column, and ‘FALSE’, otherwise. We also calculated for each probe within each analytic group, percent detection rate above background. Probes that are detected in >12.5%, >25%, >50% and >75% of the subjects in each analytic group are annotated by four separate columns labeled respectively and indicated with ‘TRUE’ and ‘FALSE’ statetments.
MayoEGWAS_analysis_eQTL_CBE_imputedResults_nonAD.gz 10.7303/syn3207181.3 Brain expression GWAS (eGWAS) results obtained using HapMap2 imputed genotypes in the cerebellar samples of the non-AD subjects, text file with 4,419,055 rows
MayoEGWAS_analysis_eQTL_CBE_imputedResults.gz 10.7303/syn3207179.3 Brain expression GWAS (eGWAS) results obtained using HapMap2 imputed genotypes in the cerebellar samples of the combined AD and non-AD subjects, text file with 4,483,512 rows
MayoEGWAS_analysis_eQTL_TCX_imputedResults_AD.gz 10.7303/syn3207183.3 Brain expression GWAS (eGWAS) results obtained using HapMap2 imputed genotypes in the temporal cortex samples of the AD subjects, text file with 4,426,363 rows.
MayoEGWAS_analysis_eQTL_TCX_imputedResults_nonAD.gz 10.7303/syn3207187.3 Brain expression GWAS (eGWAS) results obtained using HapMap2 imputed genotypes in the temporal cortex samples of the non-AD subjects, text file with 4,425,955 rows.
MayoEGWAS_analysis_eQTL_TCX_imputedResults.gz 10.7303/syn3207185.3 Brain expression GWAS (eGWAS) results obtained using HapMap2 imputed genotypes in the temporal cortex samples of the combined AD and non-AD subjects, text file with 4,484,344 rows.
C. Mayo Pilot RNAseq (Data Citation 5: Synapse http://dx.doi.org/10.7303/syn3157268) 10.7303/syn3157268 RNA-seq Alignment, Expression and Covariate MayoPilotRNAseq Alzheimers Disease RNAseq BAMs 10.7303/syn5580964 Folder of BAM alignment files, 1 file per sample. Sample ID (IID) for each subject is provided in the first 12 digits of each file name. NA Allen et al., 18, Neurology:Genetics
MayoPilotRNAseq Progressive Supranuclear Palsy RNAseq BAMs 10.7303/syn5584594 Folder of BAM alignment files, 1 file per sample. Sample ID (IID) for each subject is provided in the first 12 digits of each file name.
MayoPilotRNAseq_RNAseq_TCX_AD_covariates.csv 10.7303/syn3607480.2 Covariate information for AD subjects with temporal cortex expression measures, comma delimited text file. IlluminaSampleID=Individual ID (matches corresponding IID in Mayo LOAD GWAS files); Sex=M if Male and F if Female; Age at death; RIN=RNA intergrity number - a numerical assessment of the integrity of RNA; RINsqAdj=(RIN-RINmean)^2 - a statistical adjustment of the RIN; Library Batch=RNAseq library preparation batch; FCC1MR9ACXX - FCD1LUUACXX (AD) or FCD1GH3ACXX -FCC1CDJACXX (PSP)=‘1’ indicates sample was on sequencing flowcell - technical covariate; Flowcell=sequencing flowcell name.
MayoPilotRNAseq_RNAseq_TCX_PSP_covariates.csv 10.7303/syn3607506.1 Covariate information for PSP subjects with temporal cortex expression measures, comma delimited text file.
MayoPilotRNAseq_RNAseq_TCX_AD_geneCounts.tsv 10.7303/syn3607482.2 Gene expression phenotypes from AD temporal cortex tissue samples, space delimited text file with 64,254 rows. Column 1=Ensemble Gene IDs; 1823480105_B - 1796012340_B=Illumina Sample ID's (matches corresponding IID in Mayo LOAD GWAS files).
MayoPilotRNAseq_RNAseq_TCX_AD_geneCounts_normalized.tsv 10.7303/syn3607497.1 Normalized gene expression phenotypes from AD temporal cortex tissue samples, tab delimited text file with 64,254 rows
MayoPilotRNAseq_RNAseq_TCX_AD_transcriptCounts.tsv 10.7303/syn3607485.2 Transcript expression phenotypes from AD temporal cortex tissue samples, space delimited text file with 208,245 rows. Column 1=Ensemble Transcript IDs; 1823480105_B - 1796012340_B=Illumina Sample ID's (matches corresponding IID in Mayo LOAD GWAS files).
MayoPilotRNAseq_RNAseq_TCX_AD_transcriptCounts_normalized.tsv 10.7303/syn3607502.1 Normalized transcript expression phenotypes from AD temporal cortex tissue samples, tab delimited text file with 208,245 rows.
MayoPilotRNAseq_RNAseq_TCX_PSP_geneCounts.tsv 10.7303/syn3607487.2 Gene expression phenotypes from PSP temporal cortex tissue samples, space delimited text file with 64,254 rows Column 1=Ensemble Gene IDs; 1811024586_A - 1811024534_A=Illumina Sample ID's (matches corresponding IID in Mayo LOAD GWAS files).
MayoPilotRNAseq_RNAseq_TCX_PSP_geneCounts_normalized.tsv 10.7303/syn3607513.1 Normalized gene expression phenotypes from PSP temporal cortex tissue samples, tab delimited text file with 64,254 rows
MayoPilotRNAseq_RNAseq_TCX_PSP_transcriptCounts.tsv 10.7303/syn3607489.2 Transcript expression phenotypes from PSP temporal cortex tissue samples, space delimited text file with 208,245 rows. Column 1=Ensemble Transcript IDs; 1811024586_A - 1811024534_A=Illumina Sample ID's (matches corresponding IID in Mayo LOAD GWAS files).
MayoPilotRNAseq_RNAseq_TCX_PSP_transcriptCounts_normalized.tsv 10.7303/syn3607519.1 Normalized transcript expression phenotypes from PSP temporal cortex tissue samples, tab delimited text file with 208,245 rows.
D. Mayo RNAseq (Data Citation 6: Synapse http://dx.doi.org/10.7303/syn3163039,Data Citation 7: Synapse http://dx.doi.org/10.7303/syn5049298) 10.7303/syn3163039 TCX RNA-seq Alignment, Expression and Covariate (Data Citation 6: Synapse http://dx.doi.org/10.7303/syn3163039) MayoRNAseq Temporal Cortex BAMs 10.7303/syn4894912 Folder of BAM alignment files, 1 file per sample. Sample ID (IID) for each subject is provided in the first 6 to 8 digits of each file name. NA NA
MayoRNAseq_RNAseq_TCX_covariates.csv 10.7303/syn3817650.5 Covariate information for subjects with temporal cortex expression measures, comma delimited text file. Sample ID=3 to 5 digit unique sample identifier followed by _TCX; Source=Pathology lab that provided the tissue; Tissue=Brain region sampled; RIN=RNA intergrity number - a numerical assessment of the integrity of RNA; Diagnosis=Pathological diagnosis at time of death (AD=Alzheimer's Disease; PSP=Progressive Supranuclear Palsy; Pathologic Aging; Control); Sex=M if Male, F if Female; AgeAtDeath; Flowcell=sequencing flowcell.
MayoRNAseq_RNAseq_TCX_geneCounts.tsv 10.7303/syn4650257.8 Gene expression phenotypes, temporal cortex tissue samples, space delimited text file with 64,254 rows Column 1=Ensemble Gene IDs; 11344_TCX to 1047_TCX etc.=Sample ID's (matches corresponding SampleID in Covariate file).
MayoRNAseq_RNAseq_TCX_geneCounts_normalized.tsv 10.7303/syn4650265.4 Normalized gene expression phenotypes, temporal cortex tissue samples, tab delimited text file with 64,254 rows
MayoRNAseq_RNAseq_TCX_transcriptCounts.tsv 10.7303/syn5600752.2 Transcript expression phenotypes, temporal cortex tissue samples, space delimited text file with 208,245 rows Column 1=Ensemble Transcript IDs; 11344_TCX to 1047_TCX etc.=Sample ID's (matches corresponding SampleID in Covariate file).
MayoRNAseq_RNAseq_TCX_transcriptCounts_normalized.tsv 10.7303/syn5600755.2 Normalized Transcript expression phenotypes, temporal cortex tissue samples, tab delimited text file with 208,245 rows
10.7303/syn5049298 CER RNA-seq Alignment, Expression and Covariate (Data Citation 7: Synapse http://dx.doi.org/10.7303/syn5049298) MayoRNAseq Cerebellum BAMs 10.7303/syn5049322 Folder of BAM alignment files, 1 file per sample. Sample ID for each subject is provided in the first 6 to 8 digits of each file name. NA
MayoRNAseq_RNAseq_CBE_covariates.csv 10.7303/syn5223705.2 Covariate information for subjects with cerebellum expression measures, comma delimited text file. Sample ID=3 to 5 digit unique sample identifier followed by _CER; Source=Pathology lab that provided the tissue; Tissue=Brain region sampled; RIN=RNA intergrity number - a numerical assessment of the integrity of RNA; Diagnosis=Pathological diagnosis at time of death (AD=Alzheimer's Disease; PSP=Progressive Supranuclear Palsy; Pathologic Aging; Control); Sex=M if Male, F if Female; AgeAtDeath; ApoE=APOE genotype; Flowcell=sequencing flowcell.
MayoRNAseq_RNAseq_CBE_geneCounts.tsv 10.7303/syn5201012.4 Gene expression phenotypes, cerebellum tissue samples, tab delimited text file with 64,254 rows Column 1=Ensemble Gene IDs; 1000_CER to 991_CER= Sample ID's (matches corresponding SampleID in Covariate file).
MayoRNAseq_RNAseq_CBE_geneCounts_normalized.tsv 10.7303/syn5201007.4 Normalized gene expression phenotypes, cerebellum tissue samples, tab delimited text file with 64,254 rows
MayoRNAseq_RNAseq_CBE_transcriptCounts.tsv 10.7303/syn5600773.2 Transcript expression phenotypes, cerebellum tissue samples, space delimited text file with 208,245 rows Column 1=Ensemble Transcript IDs; 1000_CER to 991_CER=Sample ID's (matches corresponding SampleID in Covariate file).
MayoRNAseq_RNAseq_CBE_transcriptCounts_normalized.tsv 10.7303/syn5600772.2 Normalized Transcript expression phenotypes, cerebellum tissue samples, tab delimited text file with 208,245 rows
  1. The Genotype and Covariate data from the Mayo LOAD GWAS study (A) and the eSNP results under the Mayo eGWAS study (B) were previously made available through the NIAGADS respository: https://www.niagads.org/datasets/ng00043 and https://www.niagads.org/datasets/ng00025 respectively.