STATISTICS

Statistics for 3-cell-type analyses

    Table 1. Demographic and profile statistics.
    Monocytes CD4+ T cells Neutrophils
    Demographic characteristics of study subjects N 102 102 94

    Males, N

    (%)

    		 48 (47.1) 49 (48.0) 48 (51.1)

    Median age

    (range)

    		 62.5 (35–75) 62.0 (35–75) 58.0 (24–81)
    DNAm profiles

    Sequencing

    depth1

    		 31.1 ± 1.8 31.0 ± 1.6 54.7 ± 1.6

    # autosomal

    CpGs2

    		 23,941,821 24,037,518 25,483,031
    Gene expression profiles

    # sequencing

    reads1

    33,917,157

    ± 3,153,528

    35,175,996

    ± 1,275,575

    46,409,683

    ± 6,731,058
    # genes3 16,789 18,894 14,534
    SNV profiles # SNVs4 8,945,669 8,951,822 8,792,880

    1Average ± standard deviation

    2CpGs that were retained in ≥ 50% of subjects for each cell type

    3Genes that were expressed with a FPKM ≥ 0.1 in ≥ 50% of subjects for each cell type

    4SNVs with a MAC > 1 (MAC: minor allele count)

    Abbreviations: DNAm, DNA methylation; FPKM, fragments per kilobase of exon per million mapped fragments; SNV, single nucleotide variant.


    Table 2. Number of detected CpG sites per chromosome.
    #. CpGs with call rate >= 50%
    Chr Monocytes CD4+ T cells Neutrophils
    1 2,042,138 2,050,589 2,169,599
    2 1,924,655 1,934,169 2,061,342
    3 1,454,563 1,461,634 1,562,224
    4 1,275,761 1,283,597 1,390,178
    5 1,326,857 1,333,428 1,427,409
    6 1,321,901 1,328,810 1,417,880
    7 1,379,804 1,385,406 1,476,474
    8 1,158,964 1,163,948 1,238,085
    9 1,042,018 1,046,651 1,111,494
    10 1,213,368 1,218,112 1,285,846
    11 1,180,273 1,183,442 1,247,761
    12 1,161,284 1,166,091 1,236,094
    13 706,826 710,512 765,997
    14 779,218 779,549 827,813
    15 766,453 769,697 814,282
    16 987,665 990,124 1,034,331
    17 1,070,104 1,073,533 1,117,390
    18 610,896 613,615 652,750
    19 994,754 996,078 1,031,712
    20 675,502 677,115 703,058
    21 340,618 342,081 361,974
    22 528,199 529,337 549,338
    Autosomal 23,941,821 24,037,518 25,483,031


Statistics for 8-cell-population analyses

    Table 3. Demographic and profile statistics. Each cell population were isolated from the same 20 subjects.
    Neutrophils Monocytes CD4+ T cells CD8+ T cells
    Demographic characteristics N 20 20 20 20

    Males, N

    (%)

    		 10 (50) 10 (50) 10 (50) 10 (50)

    Median age

    (SD)

    		 48.5 (11.9) 48.5 (11.9) 48.5 (11.9) 48.5 (11.9)
    DNAm profiles

    Sequencing

    depth1

    		 7.2 ± 1.0 7.1 ± 0.7 6.8 ± 0.8 7.2 ± 0.8

    # autosomal

    CpGs2

    		 26,030,767 26,017,342 26,012,680 26,038,299
    Table 3. (continued)
    B cells NK cells PBMCs Leukocytes
    Demographic characteristics N 20 20 20 20

    Males, N

    (%)

    		 10 (50) 10 (50) 10 (50) 10 (50)

    Median age

    (SD)

    		 48.5 (11.9) 48.5 (11.9) 48.5 (11.9) 48.5 (11.9)
    DNAm profiles

    Sequencing

    depth1

    		 7.4 ± 0.8 7.2 ± 0.8 7.0 ± 0.8 7.0 ± 0.9

    # autosomal

    CpGs2

    		 24,311,000 26,023,559 26,032,316 26,033,709

    1Average ± standard deviation.

    2CpGs that were retained in ≥ 50% of subjects for each cell type.



Statistics for PBMC analyses (n=656)

    Table 4. Demographic and profile statistics.
    PBMC
    Demographic characteristics N 656

    Males, N (%)

    		 188 (28.7)

    Median age (SD)

    		 53 (14.3)
    DNAm profiles

    Read depth of CpGs1

    		 30.6 ± 25.4

    # autosomal CpGs

    		 5,029,453

    1Average ± standard deviation.



Statistics for 3-cell-type QTL analyses

    Table 5. Statistics of QTL analyses. The values given in parentheses are that obtained through new pipline with updated softwares.
    Monocytes CD4+ T cells Neutrophils
    eQTL analysis # test

    92,860,381

    (32,833,338)

    106,067,569

    (32,833,338)

    141,827,132

    (32,833,338)

    # eQTL1

    (SNV-Gene pair)

    463,082

    (185,997)

    472,190

    (76,659)

    3,294

    (79,779)
    eQTM analysis # test

    380,940,810

    (7,546,301)

    410,461,826

    (7,546,301)

    520,221,300

    (7,546,301)

    # eQTM1

    (CpG-Gene pair)

    5,730

    (634)

    2,609,764

    (4,189)

    238

    (2,944)
    mQTL analysis # test

    3,398,929,030

    (1,219,472,361)

    3,255,830,847

    (1,219,472,361)

    3,799,884,224

    (1,219,472,361)

    # mQTL1

    (SNV-CpG pair)

    44,032,528

    (1,085,948)

    72,594,605

    (3,151,144)

    83,464,257

    (3,254,887)

    1A significance threshold of q = 0.05 (FDR adjusted p value) was applied.



Statistics for PBMC QTL analyses (n=384)

    Table 6. Statistics of QTL analyses.
    PBMC
    eQTL analysis # test 4,354,557
    # eQTL (SNV-Gene pair)1 546,367
    eQTM analysis # test 826,987
    # eQTM (CpG-Gene pair)1 179,828
    mQTL analysis # test 17,471,105
    # mQTL (SNV-CpG pair)1 5,637,700

    1A significance threshold of q = 0.05 (FDR adjusted p value) was applied.



Statistics for kidney cancer EWAS samples

    Table 7. Statistics for kidney cancer EWAS saples. Agilent SureSelect Human Methyl-Seq Capture probe sets and custom designed probe sets (CDMVv3) were used for phase1 and phase2, respectively.

    Phase1

    Case

    Phase1

    Ctrl

    Phase2

    Case

    Phase2

    Ctrl

    Demographic

    characteristics

    		 n 50 50 48 48

    Male, N

    (%)

    		 38 (76.0) 38 (76.0) 37 (77.1) 37 (77.1)

    Mean age

    (SD)

    		 61.1 (12.3) 61.0 (12.4) 64.1 (10.7) 64.5 (10.4)

    DNAm

    profiles

    Sequencing

    depth1

    		 36.1 ± 2.2 36.8 ± 3.1 24.9 ± 1.7 23.9 ± 1.9

    # autosomal

    CpG2

    		 2,993,338 2,993,338 1,318,169 1,318,169

    1Average ± standard deviatio.

    2CpGs that were retained in >=50% call rate.



　　　　　　　　　　　
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