Cohorts
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ALS_Batch1
Origin UK Postnormalization QC M se 0.054594454262859 Normalisation method Dasen Tissue whole blood ProbeQC methylation detection P; nbead Cellcounts reference houseman M value 0.28452698398239 Imputation reference 1000G phase 3 Covariates Sex;Age;Slide Normalisation software wateRmelon Genotype array Average age 62.26 Nsnp 8564845 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 483644 Lambda nocisadj 0.989147446 M sd 0.96433032935449 Phase 2 Cohort type ALS case control cohort Imputation software Minimac3 Lambda cisadj 1.001408242 SampleQC methylation intensity; gender mismatch; duplicate samples; SNP consordance; bisufite conversion; detection P value Samplesize 702 Proportion male 0.57 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK ALS_Batch2
Origin UK Postnormalization QC M se 0.051029364604781 Normalisation method Dasen Tissue whole blood ProbeQC methylation detection P; nbead Cellcounts reference houseman M value 0.014542331665728 Imputation reference 1000G phase 3 Covariates Sex;Age;Slide Normalisation software wateRmelon Genotype array Average age 62.33 Nsnp 8564845 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 484241 Lambda nocisadj 0.991381212 M sd 0.90280161955209 Phase 2 Cohort type ALS case control cohort Imputation software Minimac3 Lambda cisadj 1.006677127 SampleQC methylation intensity; gender mismatch; duplicate samples; SNP consordance; bisufite conversion; detection P value Samplesize 619 Proportion male 0.56 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK ARIES
Origin UK Postnormalization QC PCA; t-test and F-tests to identify batch variables M se 0.052160890531098 Normalisation method Functional normalization Tissue whitecells/PBLs ProbeQC methylation detection P; nbeads Cellcounts reference houseman M value -0.42333739595015 Imputation reference 1000G phase I-version3 (December 2013) Covariates Age;Sex;Slide Normalisation software meffil Genotype array Illumina HumanHap 550k Average age 31.68 Nsnp 8262539 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 482855 Lambda nocisadj 1.078357969 M sd 0.90043657927539 Phase 1 Cohort type Population/Birth cohort Imputation software IMPUTE v2 Lambda cisadj 0.92878622 SampleQC methylation gender mismatch; detection score; nbeads; dyebias; SNP concordance (methylation array vs GWA) per indiv; SNP concordance mum-kid; PCA; ratio methylated/unmethylated; control probes check; PCA Samplesize 1774 Proportion male 0.25 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK BAMSE
Origin Sweden Postnormalization QC M se 0.073197419601221 Normalisation method Dasen Tissue whole blood ProbeQC methylation detection P; nbeads Cellcounts reference houseman M value 0.32767988259894 Imputation reference 1000 GP phase I Covariates Sex;Age;Slide Normalisation software wateRmelon Genotype array Illumina Human610-Quad Average age 8.32 Nsnp 7292333 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 438713 Lambda nocisadj 1.040788343 M sd 1.1268599513683 Phase 1 Cohort type Birth cohort Imputation software Minimac (release stamp 2012-11-16 Lambda cisadj 1.011944524 SampleQC methylation gender mismatch; detection p-value Samplesize 459 Proportion male 0.56 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK BASICMAR
Origin Spain Postnormalization QC M se 0.056740546946247 Normalisation method functional normalisation Tissue whole blood ProbeQC methylation detection P; nbeads; missingness; PCA Cellcounts reference houseman M value -0.084090938117563 Imputation reference 1000Genomes Phase I integrated variant set release (v3) reference Covariates Sex;Age;Slide;Batch Normalisation software meffil Genotype array Illumina HumanOmni5PlusExome BeadChip; HumanCoreExome-12v1-1_a Average age 74.75 Nsnp 9081881 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 484072 Lambda nocisadj 1.031038172 M sd 0.97620128132303 Phase 1 Cohort type hospital patient cohort Imputation software IMPUTE v2.3.0 Lambda cisadj 1.011944524 SampleQC methylation gender mismatch; detection score; nbeads; dyebias; SNP concordance (methylation array vs GWA) per indiv; ratio methylated/unmethylated; control probes check Samplesize 511 Proportion male 0.54 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK BorninBradford
Origin UK Postnormalization QC PCA M se 0.075912570127988 Normalisation method Functional normalisation Tissue cord ProbeQC methylation Cellcounts reference houseman M value -0.25241870769335 Imputation reference 1000G phase 3 Covariates Slide;Age;Sex Normalisation software meffil Genotype array HumanCoreExome Average age 13.48 Nsnp 8095975 Methylation array Infinium MethylationEPIC BeadChip Ncpg 860529 Lambda nocisadj 0.984920868 M sd 0.9511817773904 Phase 2 Cohort type Birth cohort Imputation software Sanger Imputation Service (EAGLE2 and impute) Lambda cisadj 0.913233339 SampleQC methylation Gender; Detection p-value; Genotype mismatch; Control probe (bisulfite1); Control probe (bisulfite2) Samplesize 861 Proportion male 0.26 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK BSGS
Origin Australia Postnormalization QC outlier removal M se 0.058604779580776 Normalisation method glm Tissue whole blood ProbeQC methylation detection P; nbeads Cellcounts reference houseman M value 0.49343478822116 Imputation reference 1000G phase 3 Covariates Sex;Age;Slide Normalisation software Genotype array Illumina Quad610 Average age 21.38 Nsnp 7704504 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 484973 Lambda nocisadj 0.968565953 M sd 0.93216608391262 Phase 1 Cohort type Families with adolescent twins Imputation software IMPUTE v2 Lambda cisadj 0.758422543 SampleQC methylation gender; detection p-value; dye intensity outliers and ratio Samplesize 601 Proportion male 0.51 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK DunedinAge26
Origin New Zealand Postnormalization QC M se 0.064721816474944 Normalisation method default Tissue whole blood ProbeQC methylation Cellcounts reference houseman M value 0.40510398251785 Imputation reference 1000G phase 3 Covariates Sex;Age;Slide Normalisation software methylumi (v2.14.0) Genotype array Illumina OmniExpress 12v1.1 BeadChip Average age 26 Nsnp 5066915 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 482421 Lambda nocisadj 0.99794562 M sd 0.84138361417428 Phase 1 Cohort type Birth cohort Imputation software IMPUTE v2.3.1 Lambda cisadj 1.01448402 SampleQC methylation gender mismatch; detection p-value >= 0.001 Samplesize 758 Proportion male 0.52 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK DunedinAge38
Origin New Zealand Postnormalization QC M se 0 Normalisation method default Tissue whole blood ProbeQC methylation Cellcounts reference houseman M value 0 Imputation reference 1000G phase 3 Covariates Sex;Age;Slide Normalisation software methylumi (v2.14.0) Genotype array Illumina OmniExpress 12v1.1 BeadChip Average age 38.33 Nsnp 4962994 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 482421 Lambda nocisadj 0.99786265 M sd 0 Phase 1 Cohort type Birth cohort Imputation software IMPUTE v2.3.1 Lambda cisadj 0 SampleQC methylation gender mismatch; detection p-value >= 0.001 Samplesize 0 Proportion male 0.5 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK EGC_asthma
Origin Estonia Postnormalization QC PCA M se 0.055200680613818 Normalisation method Functional normalization Tissue whole blood ProbeQC methylation detection P; nbeads Cellcounts reference houseman M value -0.25099451531965 Imputation reference 1000G phase 3 Covariates Sex;Age;Slide;Row Normalisation software meffil Genotype array Illumina HumanOmniExpress BeadChip Average age 26.16 Nsnp 8902920 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 484893 Lambda nocisadj 1.006032035 M sd 0.91872242480705 Phase 2 Cohort type Asthma case control study Imputation software IMPUTE v2 Lambda cisadj 1.006679211 SampleQC methylation Methylated vs Unmethylated; X-Y ratio outlier; Low bead numbers; Detection p-value; Sex mismatch; Genotype mismatch; Control probe (bisulfite1); Control probe (bisulfite2) Samplesize 105 Proportion male 0.37 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK EGC_CTG
Origin Estonia Postnormalization QC PCA M se 0.057462628352598 Normalisation method Functional normalization Tissue whole blood ProbeQC methylation detection P; nbeads Cellcounts reference houseman M value 0.11942568899113 Imputation reference 1000G phase 3 Covariates Sex;Age;Slide;Row Normalisation software meffil Genotype array Illumina HumanOmniExpress BeadChip Average age 50.14 Nsnp 8948535 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 485100 Lambda nocisadj 0.983933198 M sd 1.0068265852454 Phase 2 Cohort type Population cohort Imputation software IMPUTE v2 Lambda cisadj 0.983855091 SampleQC methylation Methylated vs Unmethylated; X-Y ratio outlier; Low bead numbers; Detection p-value; Sex mismatch; Genotype mismatch; Control probe (bisulfite1); Control probe (bisulfite2) Samplesize 305 Proportion male 0.5 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK EPICOR
Origin Italy Postnormalization QC control pcs=1:10; Control probe scree plots; PCAplots of control probes; PCAplots of normalized betas. M se 0.056098428724175 Normalisation method Functional normalisation (Normalised methylation data -> Option 1 in pipeline pre-requisites step) Tissue whole blood ProbeQC methylation beadnum.samples.threshold= 0.1; detectionp.samples.threshold= 0.1; detectionp.cpgs.threshold= 0.1; beadnum.cpgs.threshold= 0.1; sex.outlier.sd= 5; snp.concordance.threshold= 0.95; sample.genotype.concordance.threshold= 0.8 Cellcounts reference houseman M value -0.17256714556832 Imputation reference 1000G phase 3 Covariates Sex;Age Normalisation software meffil Genotype array Illumina OmniExpressExome BeadChip Average age 52.77 Nsnp 7680624 Methylation array Infinium HumanMethylation450 Beadchip Ncpg 484683 Lambda nocisadj 0.997827794 M sd 0.88699403962504 Phase 1 Cohort type Nested case-control study Imputation software IMPUTE v2.3.1 Lambda cisadj 0.997897577 SampleQC methylation Control probe (dye.bias); Methylated vs Unmethylated; X-Y ratio outlier; Low bead numbers; Detection p-value; Sex mismatch; Genotype mismatch Samplesize 556 Proportion male 0.65 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK EPIC_Norfolk
Origin UK Postnormalization QC PCA; t-test and F-tests to identify batch variables M se 0.047863307029784 Normalisation method Functional normalization Tissue whole blood ProbeQC methylation detection P;nbeads Cellcounts reference houseman M value -0.44940515487348 Imputation reference 1000G phase 3 Covariates Sex;Age;Plate;Slide Normalisation software meffil Genotype array Affymetrix UK Biobank chip Average age 60.34 Nsnp 9181292 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 479880 Lambda nocisadj 1.081457487 M sd 0.86419450825826 Phase 1 Cohort type Diabetes case cohort study Imputation software IMPUTE v2.3.1 Lambda cisadj 0.993184596 SampleQC methylation gender mismatch; detection score; nbeads; dyebias; SNP concordance (methylation array vs GWA) per indiv; SNP concordance mum-kid; PCA; ratio methylated/unmethylated; control probes check; PCA Samplesize 1088 Proportion male 0.51 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK Erisk
Origin UK Postnormalization QC M se 0.05309203796955 Normalisation method dasen Tissue whole blood ProbeQC methylation detection P; nbead Cellcounts reference houseman M value 0.056621261717065 Imputation reference 1000G phase 3 Covariates Sex;Age;Slide Normalisation software wateRmelon Genotype array Illumina OmniExpress 24v1.1 BeadChip Average age 18.31 Nsnp 6173986 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 430802 Lambda nocisadj 1.00442043 M sd 0.80518062198791 Phase 2 Cohort type Twin birth cohort Imputation software IMPUTE v2.3.1 Lambda cisadj 0.79485531 SampleQC methylation intensity; gender mismatch; duplicate samples; SNP consordance; bisufite conversion; detection P value; ckecl twin zygosity Samplesize 1501 Proportion male 0.51 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK Factor_V_Leiden_Fami
Origin France/Canada Postnormalization QC M se 0 Normalisation method Tissue whole blood ProbeQC methylation Cellcounts reference houseman M value 0 Imputation reference 1000G phase 1 Covariates Sex;Age;Slide Normalisation software Genotype array Illumina Human660W-Quad BeadChip Average age 39.8 Nsnp 7585404 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 480518 Lambda nocisadj 0.924909854 M sd 0 Phase 2 Cohort type Thrombophilia Family study Imputation software SHAPEIT2/IMPUTE2 Lambda cisadj 1.426929801 SampleQC methylation Samplesize 212 Proportion male 0.48 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK FTC
Origin Finland Postnormalization QC M se 0.057823703684437 Normalisation method Functional normalization Tissue whole blood ProbeQC methylation detection P; nbeads Cellcounts reference houseman M value 0.14780319251384 Imputation reference 1000Genomes Phase 3 Covariates Sex;Age;Slide Normalisation software meffil Genotype array Human670-QuadCustom Illumina BeadChip; Illumina HumanCoreExome chip Average age 33.76 Nsnp 8644202 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 485378 Lambda nocisadj 0.999238734 M sd 0.98470219115112 Phase 1 Cohort type Twin cohort Imputation software IMPUTE v2.1.0 Lambda cisadj 0.83793127 SampleQC methylation gender mismatch; detection p-value; Low bead numbers and dye intensity outliers and ratio Samplesize 1177 Proportion male 0.4 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK GenerationR_Study
Origin The Netherlands Postnormalization QC None M se 0.073028023976489 Normalisation method CPACOR Tissue cord ProbeQC methylation detection p-value Cellcounts reference bakulski M value -0.11287864077158 Imputation reference 1000G Phase 3 Covariates Sex;Age; Plate Normalisation software R; minfi Genotype array Illumina Human610-Quad and 660 Average age 0 Nsnp 8902467 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 468940 Lambda nocisadj 1.001880677 M sd 1.1147244065764 Phase 2 Cohort type Population/Birth cohort Imputation software Minimac/MACH Lambda cisadj 1.007553928 SampleQC methylation gender mismatch; bisulfite conversion; hybridization; extension; sample call rate >95% Samplesize 1251 Proportion male 0.51 Cellcounts Bcell;CD4T;CD8T;Gran;Mono;NK; nRBC GLAKU
Origin Finland Postnormalization QC M se 0.057539959812156 Normalisation method Functional normalization Tissue whole blood ProbeQC methylation probes that are also a SNP excluded; X; Y chr and non-specific binding probes were excluded; probes with detection p value >0.01 in > 50% of the samples were excluded; probes located within 10 bp from a SNP with MAF≥0.05 excluded Cellcounts reference houseman M value 0.13166803064228 Imputation reference 1000G phase 3 Covariates Sex;Age;Slide;Column;Row Normalisation software meffil Genotype array Illumina OmniExpressExome 1.2 Average age 11.78 Nsnp 9689995 Methylation array Infinium MethylationEPIC BeadChip Ncpg 410460 Lambda nocisadj 0.985500413 M sd 0.98492546100152 Phase 2 Cohort type Birth cohort Imputation software IMPUTE v2 Lambda cisadj 0.999544788 SampleQC methylation exclusion of samples with gender mismatch/low intensities Samplesize 231 Proportion male 0.49 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK GOYA
Origin Denmark Postnormalization QC MDS plots of normalised data.Betas M se 0.07797127819721 Normalisation method Functional normalization Tissue cord ProbeQC methylation detection P Cellcounts reference bakulski M value 0.20253374200289 Imputation reference 1000G phase3 Covariates Sex;Age;Slide;Sliderow Normalisation software meffil Genotype array Illumina HumanCoreExome chip version 1.0 Average age 0 Nsnp 7455343 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 485013 Lambda nocisadj 1.064380279 M sd 1.1643594848184 Phase 1 Cohort type Offspring sample from mother-child pairs Imputation software SHAPEIT/IMPUTE2 Lambda cisadj 1.004874257 SampleQC methylation detection p-value; plots of control probes and several batches to identify outliers. Samplesize 888 Proportion male 0.52 Cellcounts Bcell;CD4T;CD8T;Gran;Mono;NK;nRBC GSK
Origin Caucasian Postnormalization QC None M se 0.056477208414374 Normalisation method Functional normalization Tissue whole blood ProbeQC methylation probes that are also a SNP excluded; X; Y chr and non-specific binding probes were excluded; probes with detection p value >0.01 in > 50% of the samples were excluded; probes located within 10 bp from a SNP with MAF≥0.05 excluded Cellcounts reference houseman M value -0.45058382427578 Imputation reference 1000G phase3 Covariates Sex;Age;Slide;SmokingScore Normalisation software minfi Genotype array Illumina HumanHap 550k Average age 51.16 Nsnp 8718785 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 424958 Lambda nocisadj 1.001617015 M sd 0.9830928472403 Phase 1 Cohort type Case-control study for unipolar depressive disorder Imputation software IMPUTE v2 Lambda cisadj 1.000968759 SampleQC methylation exclusion of samples with gender mismatch/low intensities Samplesize 248 Proportion male 0.37 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK INMA
Origin Spain Postnormalization QC None M se 0.05340960585559 Normalisation method Functional normalization Tissue cord ProbeQC methylation None Cellcounts reference cord M value -0.83103426520163 Imputation reference 1000G phase 1v3 Covariates Sex;Batch;Age;Smoking Normalisation software meffil Genotype array Illumina HumanOmni1-Quad BeadChip Average age 0 Nsnp 8060251 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 484998 Lambda nocisadj 0.990308004 M sd 0.89530813988231 Phase 1 Cohort type Population/Birth cohort Imputation software IMPUTE v2 Lambda cisadj 0.994226611 SampleQC methylation gender mismatch; detection score; nbeads; dyebias; SNP concordance (methylation array vs GWA) per indiv; ratio methylated/unmethylated; control probes check Samplesize 320 Proportion male 0.5 Cellcounts Bcell;CD3T;CD4T;CD8T;Gran;Mono;NK IOW F2
Origin UK Postnormalization QC None M se 0.064463499800015 Normalisation method Functional normalization Tissue cord ProbeQC methylation Detection P-value Cellcounts reference cord M value -0.20156690918428 Imputation reference 1000G phase 1v3 Covariates Sex;Age;Slide Normalisation software meffil Genotype array Illumina Infinium OmniExpressExome-8 Kit Average age 0 Nsnp 8015356 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 485004 Lambda nocisadj 0.992172659 M sd 1.0670607897266 Phase 1 Cohort type Parent-triad study Imputation software IMPUTE v2 Lambda cisadj 0.992620221 SampleQC methylation gender mismatch; detection score; nbeads; dyebias; control probes check Samplesize 111 Proportion male 0.52 Cellcounts Bcell;CD3T;CD4T;CD8T;Gran;Mono;NK LBC21
Origin Scotland Postnormalization QC outlier removal M se 0.065489279696104 Normalisation method glm Tissue whole blood ProbeQC methylation detection P; nbeads Cellcounts reference houseman M value -0.017573762054145 Imputation reference 1000G phase 3 Covariates Sex;Age;Slide Normalisation software Genotype array Illumina Quad610 Average age 79.14 Nsnp 6920489 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 477057 Lambda nocisadj 0.991259961 M sd 0.9353740075731 Phase 1 Cohort type Birth cohort Imputation software IMPUTE v2 Lambda cisadj 0.991889379 SampleQC methylation gender; detection p-value; dye intensity outliers and ratio Samplesize 435 Proportion male 0.39 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK LBC36
Origin Scotland Postnormalization QC outlier removal M se 0.062354111048949 Normalisation method glm Tissue whole blood ProbeQC methylation detection P; nbeads Cellcounts reference houseman M value -0.22133366623231 Imputation reference 1000G phase 3 Covariates Sex;Age;Slide Normalisation software Genotype array Illumina Quad610 Average age 69.59 Nsnp 7189799 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 470707 Lambda nocisadj 1.067680327 M sd 0.96397116365814 Phase 1 Cohort type Birth cohort Imputation software IMPUTE v2 Lambda cisadj 0.999724471 SampleQC methylation gender; detection p-value; dye intensity outliers and ratio Samplesize 905 Proportion male 0.51 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK Leiden_Longevity_Stu
Origin The Netherlands Postnormalization QC None M se 0.055791163835319 Normalisation method Functional normalization Tissue whole blood ProbeQC methylation Detection p-val; nbeads Cellcounts reference houseman M value 0.30270513548706 Imputation reference 1000G phase 1 Covariates Sex;Age;Slide;Plate Normalisation software meffil Genotype array Illumina Human660-Quad; Illumina OmniExpress Average age 58.98 Nsnp 6728884 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 484899 Lambda nocisadj 1.06163266 M sd 0.81233160714395 Phase 1 Cohort type Offspring sample Imputation software IMPUTE v2 Lambda cisadj 1.014010463 SampleQC methylation Detection p-val; nbeads; ratio methylated/unmethylated Samplesize 718 Proportion male 0.48 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK MARS
Origin Germany Postnormalization QC None M se 0 Normalisation method Functional normalization Tissue ProbeQC methylation meffil default qc; additional exclusion: non-specific binding probes; Probes located within 10bp from SNP with MAF >= 0.05; samples with gender mismatch/low intensities Cellcounts reference houseman M value 0 Imputation reference 1000G phase 3 Covariates Sex;Age;Slide;Column;Row Normalisation software Genotype array Illumina 300K; 610K and OmniExpress Average age 46.26 Nsnp 4726159 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 436241 Lambda nocisadj 0.997808843 M sd 0 Phase 2 Cohort type Depression case control study Imputation software IMPUTE v2 Lambda cisadj 0.99870477 SampleQC methylation exclusion of samples with gender mismatch/low intensities Samplesize 111 Proportion male 0.49 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK MARTHA
Origin France Postnormalization QC M se 0.069041071617487 Normalisation method SWAN Tissue whole blood ProbeQC methylation detection P; cross reactivity Cellcounts reference houseman M value 0.33688485013494 Imputation reference 1000 Genomes 2012-02-14 Covariates Sex;Age;Slide;Chip Normalisation software Genotype array Illumina Human 610/660 Average age 44.29 Nsnp 7044254 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 388120 Lambda nocisadj 1.018318618 M sd 0.8895319829186 Phase 1 Cohort type Hospital based patient cohort Imputation software Minimac Lambda cisadj 0.994310559 SampleQC methylation gender mismatch Samplesize 344 Proportion male 0.21 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK MinE
Origin The Netherlands Postnormalization QC None M se 0.055758701161466 Normalisation method Functional normalization Tissue whole blood ProbeQC methylation detection P; nbeads Cellcounts reference houseman M value -0.10889070920238 Imputation reference 1000G phase 1v3 Covariates Sex;Smoked;Age;sentrix_col;DNA_row;Slide;DNA_col Normalisation software meffil Genotype array Illumina 2.5M Average age 63.5 Nsnp 7086169 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 485405 Lambda nocisadj 0.990372563 M sd 0.83451982431088 Phase 2 Cohort type Controls from ALS control project Imputation software IMPUTE v2 Lambda cisadj 1.002531106 SampleQC methylation gendermismatch; detection p-value; nbeads; dye intensity outliers; ratio methylated/unmethylated. Samplesize 486 Proportion male 0.57 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK NTR
Origin The Netherlands Postnormalization QC godmc QC pipeline M se 0.049068953005794 Normalisation method Functional normalization Tissue whole blood ProbeQC methylation godmc QC pipeline Cellcounts reference houseman M value 0.60596511715122 Imputation reference 1000G phase 3 Covariates Sex;Age;samplesource;plate;scanner;sentrixbarcode;sentrix_row;sentrix_col Normalisation software meffil Genotype array Affymetrix6; Illumina Human660-Quad Average age 36.64 Nsnp 7817352 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 485031 Lambda nocisadj 0.996154898 M sd 0.81075216108263 Phase 1 Cohort type Twin cohort Imputation software IMPUTE v2 Lambda cisadj 0.664955653 SampleQC methylation godmc QC pipeline Samplesize 2757 Proportion male 0.34 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK Phase1_SCZ
Origin UK Postnormalization QC M se 0.08505719876703 Normalisation method Dasen Tissue whole blood ProbeQC methylation detection P; nbeads Cellcounts reference houseman M value -0.17970706273989 Imputation reference 1000G phase 3 Covariates Sex;Age;Slide Normalisation software wateRmelon Genotype array Affy 5/6? Average age 40.4 Nsnp 4849145 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 483571 Lambda nocisadj 1.011990966 M sd 0.86323628711708 Phase 1 Cohort type Schizophrenia case control study Imputation software Minimac Lambda cisadj 1.001644027 SampleQC methylation probe intensities; gender mismatch; pvalue detection; mismatch genotypes data; PC outliers Samplesize 608 Proportion male 0.6 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK Phase2_SCZ
Origin UK Postnormalization QC M se 0.079599054314934 Normalisation method Dasen Tissue whole blood ProbeQC methylation detection P; nbeads Cellcounts reference houseman M value 0.2213760585213 Imputation reference 1000G phase 4 Covariates Sex;Age;Slide Normalisation software wateRmelon Genotype array Affy 5/6? Average age 44.61 Nsnp 5947837 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 420374 Lambda nocisadj 1.007828639 M sd 0.93507716462376 Phase 1 Cohort type Schizophrenia case control study Imputation software Minimac Lambda cisadj 0.996426067 SampleQC methylation probe intensities; gender mismatch; pvalue detection; mismatch genotypes data; PC outliers Samplesize 665 Proportion male 0.72 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK PIAMA
Origin The Netherlands Postnormalization QC M se 0.062874087925855 Normalisation method Functional normalization Tissue whole blood ProbeQC methylation decection P; nbeads Cellcounts reference houseman M value 0.22071981568298 Imputation reference 1000G phase 3 Covariates Sex;Age;Slide Normalisation software meffil Genotype array Illumina Human 610K;Illumina HumanOmniExpress; Illumina Human Omni Express Exome Array Average age 16.35 Nsnp 6687384 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 484020 Lambda nocisadj 0.98875139 M sd 0.92191509939324 Phase 2 Cohort type Birth cohort Imputation software Minimac Lambda cisadj 0.993292307 SampleQC methylation gender mismatch; detection pvalue; SNP concordance (methylation array vs GWAS) Samplesize 509 Proportion male 0.49 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK PRECISESADS
Origin Spain Postnormalization QC M se 0.10660353665074 Normalisation method Functional normalization Tissue whole blood ProbeQC methylation detection P Cellcounts reference houseman M value 0.47888551288678 Imputation reference 1000G phase 3 Covariates Sex;Age;Slide Normalisation software meffil Genotype array Illumina Human Core-12 v1 microarray Average age 51.94 Nsnp 2259093 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 484965 Lambda nocisadj 0.981961676 M sd 0.71511826377882 Phase 2 Cohort type autoimmune case control study Imputation software IMPUTE v2 Lambda cisadj 0.982280439 SampleQC methylation gender mismatch; detection pvalue; ratio methylated/unmethylated Samplesize 493 Proportion male 0.14 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK PREDO
Origin Finland Postnormalization QC M se 0.06582347095153 Normalisation method Functional normalization Tissue cord ProbeQC methylation probes that are also a SNP excluded; X; Y chr and non-specific binding probes were excluded; probes with detection p value >0.01 in > 50% of the samples were excluded; probes located within 10 bp from a SNP with MAF≥0.05 excluded Cellcounts reference houseman M value -0.4753938946604 Imputation reference 1000G phase 3 Covariates Sex;Age;Slide;Column;Row Normalisation software meffil Genotype array Illumina HumanOmniExpress Average age 0 Nsnp 9289276 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 404649 Lambda nocisadj 0.990870857 M sd 1.1286374185111 Phase 2 Cohort type Birth cohort Imputation software IMPUTE v2 Lambda cisadj 0.999150614 SampleQC methylation exclusion of samples with gender mismatch/low intensities Samplesize 885 Proportion male 0.53 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK Raine
Origin Australia Postnormalization QC none M se 0.057612337648043 Normalisation method BMIQ Tissue whole blood ProbeQC methylation intentional SNP probes; sex chromosome probes; probes with detectable p-value greater than 0.05; probes with low bead counts (bead counts less than three in more than 5% of samples) Cellcounts reference houseman M value 0.43147677350074 Imputation reference 1000GP Phase3 Covariates Sex;Age Normalisation software meffil Genotype array Illumina Human660W Quad BeadChip Average age 17.03 Nsnp 7782690 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 474481 Lambda nocisadj 1.067269832 M sd 0.93786090869441 Phase 2 Cohort type Population cohort Imputation software Minimac Lambda cisadj 1.033648727 SampleQC methylation gender mismatch; outlier due to batch effects identified using shinyMethyl and MethylAid; contaminated sample among sample ran in duplicate or triplicate checked using RnBeads Samplesize 718 Proportion male 0.51 Cellcounts Bcell;CD4T;CD8T;Eos;Neu;Mono;NK Rotterdam_Study
Origin The Netherlands Postnormalization QC M se 0.060604136562395 Normalisation method Quantile normalization for each of the six probe type categories separately: type I methylated red/green; type I unmethylated red/green and type II red/green. Beta values were calculated as proportion of methylated intensity value on the sum of methylated Tissue whole blood ProbeQC methylation Probes that had a detection p-value above background (based on sum of methylated and unmethylated intensity values) ≥ 1E-16 in >5% of the samples were removed. (Lehne B; et al.; Genome Biology; 2015). Cellcounts reference houseman M value 0.03546141731389 Imputation reference 1000G Phase 3 Covariates Sex;Age;Slide Normalisation software CPACOR workflow Genotype array Illumina HapMap 550k Average age 64.26 Nsnp 7847483 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 473682 Lambda nocisadj 0.992952808 M sd 0.98842355496716 Phase 2 Cohort type Population cohort Imputation software MACH/Minimac Lambda cisadj 0.996338703 SampleQC methylation Samples with observed technical problems during steps like bisulfite conversion; hybridization; extension or specificity; as well as samples with mismatch between sex of the proband and sex determined by the chr X and Y probe intensities were removed from Samplesize 1472 Proportion male 0.45 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK SABRE
Origin UK Postnormalization QC None M se 0.053444157567481 Normalisation method Functional normalization Tissue whole blood ProbeQC methylation Detection P value; nbeads Cellcounts reference houseman M value -0.19499313759373 Imputation reference HRC imputation Covariates Sex;Age;Slide Normalisation software meffil Genotype array UCL druggable target array (Illumina Human Core Bead Chip (~240k genome wide markers)+200k druggable target) Average age 53.48 Nsnp 6912559 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 484781 Lambda nocisadj 0.996824581 M sd 0.88788102916719 Phase 2 Cohort type Tri-ethnic population based study Imputation software Minimac3 Lambda cisadj 0.996290136 SampleQC methylation gender mismatch; nbeads; dyebias; ratio methylated/unmethylated; detection P Samplesize 722 Proportion male 1 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK SYS
Origin French-Canadian Postnormalization QC M se 0 Normalisation method Illumina normalization (background correction and control normalization) and SWAN Tissue whole blood ProbeQC methylation detection P Cellcounts reference houseman M value 0 Imputation reference 1000G phase1_v3 Covariates Age;Sex;Slide;Plate;Parent Normalisation software minfi Genotype array Illumina Human610-Quad BeadChip;Illumina HumanOmniExpress BeadChip Average age 35.35 Nsnp 7123728 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 484792 Lambda nocisadj 1.017496163 M sd 0 Phase 1 Cohort type Prospective study Imputation software IMPUTE v2 Lambda cisadj 0 SampleQC methylation gender mismatch Samplesize 0 Proportion male 0.51 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK TwinsUK
Origin UK Postnormalization QC outlier removal M se 0.052324763812449 Normalisation method Functional normalization Tissue whole blood ProbeQC methylation detection P; missingness Cellcounts reference houseman M value 0.078923500658167 Imputation reference 1000G phase1_v3 (Sept2013 Haplotype Reference Panel release) Covariates Sex;Age;Slide;Batch Normalisation software meffil Genotype array Illumina HumanHap300; HumanHap610Q Average age 57.99 Nsnp 8014768 Methylation array Infinium HumanMethylation450k Beadchip Ncpg 484942 Lambda nocisadj 1.025863288 M sd 0.88334368101445 Phase 1 Cohort type Twin cohort Imputation software IMPUTE v2 Lambda cisadj 0.652919214 SampleQC methylation detection score; SNP concordance (methylation array vs GWAS); PCA Samplesize 843 Proportion male 0.04 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK UnderstandingSociety
Origin UK Postnormalization QC M se 0.057800035411266 Normalisation method Dasen Tissue whole blood ProbeQC methylation detection P; nbead Cellcounts reference houseman M value -0.079116874887201 Imputation reference 1000G phase 3 Covariates Sex;Age;Slide;Batch1;Batch2 Normalisation software wateRmelon Genotype array Illumina HumanCoreExome Average age 57.96 Nsnp 6513638 Methylation array Infinium MethylationEPIC BeadChip Ncpg 856359 Lambda nocisadj 1.000247797 M sd 0.79251415734118 Phase 2 Cohort type Household longitudinal study Imputation software Minimac3 Lambda cisadj 1.001319946 SampleQC methylation intensity; gender mismatch; duplicate samples; SNP consordance; bisufite conversion; detection P value Samplesize 1124 Proportion male 0.42 Cellcounts Bcell;CD4T;CD8T;Eos;Mono;Neu;NK