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Table 1 Overview of predictor consistency and best performing data processing pipelines

From: Significant variation in the performance of DNA methylation predictors across data preprocessing and normalization strategies

Predictor information

Reliability (ICC statistics)

Name

Phenotype

Array

Probes

Median

Min

Max

Best analytical pipeline

GrimAge [15]

Mortality

EPIC/450 K

1030

0.990

0.921

0.994

ENmix: bg = oob, dye = mean, norm = q3, probe = rcp

ZhangAge [8]

Chronological age

EPIC/450 K

514

0.991

0.987

0.992

ENmix: bg = neg, dye = mean, norm = q2, probe = rcp

TIMP_1 [15]

TIMP-1 serum protein

EPIC/450 K

42

0.988

0.973

0.992

ENmix: bg = oob, dye = relic, norm = q2, probe = rcp

Bcell [5]

B-lymphocyte cell fraction

EPIC

50

0.980

0.881

0.988

Minfi: no bg correction with control normalization

Neu [5]

Neutrophil cell fraction

EPIC

50

0.984

0.973

0.987

ENmix: bg = oob, dye = mean, norm = q2, probe = rcp

B2M [15]

B2M serum protein

EPIC/450 K

91

0.973

0.759

0.985

ENmix: bg = oob, dye = relic, norm = q1, probe = rcp

SkinBloodAge [9]

Chronological age

EPIC/450 K

391

0.979

0.908

0.982

ENmix: bg = neg, dye = relic, norm = q1, probe = rcp

Smoking_Lu [15]

Smoking pack years

EPIC/450 K

172

0.971

0.889

0.981

ENmix: bg = oob, dye = no, norm = no, probe = rcp

Smoking_McCartney [20]

Smoking pack years

EPIC

233

0.975

0.942

0.979

Minfi: noob with dye correction

HannumAge [7]

Chronological age

450 K

71

0.972

0.834

0.978

ENmix: bg = est, dye = relic, norm = no, probe = rcp

CD8T [5]

CD8 + T-cell fraction

EPIC

50

0.969

0.881

0.978

ENmix: bg = neg, dye = mean, norm = q1, probe = rcp

NK [5]

Natural killer cell fraction

EPIC

50

0.952

0.883

0.977

ENmix: bg = neg, dye = relic, norm = q3, probe = rcp

BioAge4HAStatic [17]

Chronological age

450 K

-

0.966

0.826

0.975

ENmix: bg = oob, dye = relic, norm = no, probe = rcp

Cystatin_C [15]

Cystatin-C serum protein

EPIC/450 K

87

0.954

0.829

0.973

ENmix: bg = oob, dye = no, norm = q2, probe = rcp

PhenoAge [14]

Mortality

EPIC/450 K/27 K

513

0.954

0.926

0.97

ENmix: bg = neg, dye = relic, norm = q1, probe = rcp

Mono [5]

Monocyte cell fraction

EPIC

50

0.953

0.865

0.968

Minfi: illumine bg correction with control normalization

DNAmTL [12]

Telomere length

EPIC/450 K

140

0.952

0.912

0.965

ENmix: bg = oob, dye = relic, norm = q1, probe = rcp

HorvathAge [6]

Chronological age

450 K/27 K

353

0.950

0.867

0.964

WateRmelon: naten

CD4T [5]

CD4 + T-cell fraction

EPIC

50

0.959

0.951

0.964

ENmix: bg = neg, dye = no, norm = no, probe = rcp

epiTOC [18]

Mitotic divisions

450 K

385

0.911

0.498

0.962

ENmix: bg = oob, dye = mean, norm = q2, probe = rcp

Leptin [15]

Leptin serum protein

EPIC/450 K

187

0.896

0.447

0.953

ENmix: bg = oob, dye = relic, norm = q3, probe = rcp

VidalBraloAge [13]

Chronological age

27 K

8

0.945

0.922

0.952

ENmix: bg = neg, dye = mean, norm = no, probe = rcp

MiAge [19]

Mitotic divisions

450 K

268

0.884

0.348

0.947

WateRmelon: nanes

LinAge [10]

Chronological age

450 K

99

0.930

0.878

0.939

ENmix: bg = est, dye = relic, norm = no, probe = no_rcp

ADM [15]

ADM serum protein

EPIC/450 K

186

0.900

0.756

0.938

ENmix: bg = neg, dye = mean, norm = q3, probe = rcp

WHR [20]

Waist-to-hip ratio

EPIC

226

0.878

0.634

0.925

ENmix: bg = oob, dye = relic, norm = q2, probe = rcp

ZhangMortality [16]

Mortality

450 K

10

0.877

0.807

0.92

Minfi: no bg correction with control normalization

BodyFat [20]

Body fat

EPIC

968

0.893

0.843

0.918

ENmix: bg = est, dye = relic, norm = no, probe = rcp

Cholesterol [20]

Total cholesterol

EPIC

204

0.888

0.762

0.917

ENmix: bg = oob, dye = no, norm = q2, probe = rcp

BMI [20]

BMI

EPIC

1109

0.904

0.877

0.914

ENmix: bg = neg, dye = mean, norm = no, probe = rcp

GDF_15 [20]

GDF-15 serum protein

EPIC/450 K

137

0.819

0.502

0.903

ENmix: bg = est, dye = mean, norm = q1, probe = rcp

LDL [20]

LDL

EPIC

233

0.846

0.732

0.901

ENmix: bg = oob, dye = relic, norm = no, probe = rcp

HDLratio [20]

Total to HDL cholesterol ratio

EPIC

412

0.848

0.643

0.890

ENmix: bg = oob, dye = relic, norm = q1, probe = rcp

Alcohol [20]

Alcohol

EPIC

450

0.807

0.551

0.878

ENmix: bg = neg, dye = relic, norm = no, probe = rcp

WeidnerAge [11]

Chronological age

27 K

3

0.826

0.583

0.865

ENmix: bg = neg, dye = relic, norm = no, probe = rcp

Education [20]

Educational attainment

EPIC

373

0.774

0.506

0.865

Cross: noob with dye correction + BMIQ

HDL [20]

HDL cholesterol

EPIC

737

0.835

0.694

0.853

ENmix: bg = est, dye = relic, norm = q1, probe = rcp

CD8pCD28nCD45Ran [6]

Specific T-cell fraction

27 K

-

0.814

0.756

0.845

ENmix: bg = oob, dye = relic, norm = no, probe = rcp

PlasmaBlast [6]

Plasma B cell fraction

27 K

-

0.718

0.638

0.840

Cross: noob with dye correction + BMIQ

PAI_1 [15]

PAI-1 serum protein

EPIC/450 K

211

0.744

0.22

0.838

ENmix: bg = neg, dye = relic, norm = q3, probe = rcp

CD8naive [6]

CD8 T-cell fraction

27 K

-

0.777

0.659

0.830

WateRmelon: danen

  1. Shown is general information on each DNAm-based predictor alongside their corresponding ICC statistics. The name of the predictor, the phenotype it is trained on, the array platform it can be applied on, and the number of predictor probes (if available) are listed on the left side of the table. ICC statistics are listed on the right side of the table. The ICC quantifies the degree of absolute agreement between estimator values of a pair of technical replicates. For each predictor, across 101 pipelines, the median, minimum, and maximum ICC are listed. Predictors are ranked by the maximum ICC. The final column reports methodological details of the best performing data processing pipelines (i.e., the pipeline with the highest consistency). Bg background correction, dye dye-bias correction, norm normalization method, probe probe-type bias correction. Full details on analytical pipelines and how they were implemented are available in Additional file 4.
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Genome Biology

ISSN: 1474-760X

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