Supplemental Figure 1 IRF8:NM_002163:c.C602T IRF8:NM_002163:c.C671T Mother Son Brother Nephew Sister (deceased) Supplemental Figure 1. Confirmation of family member IRF8 variants by Sanger sequencing. The proband’s mother, son, brother and fraternal nephew were sequenced for the C602T (left traces) and C671T (right traces). DNA was extracted from material obtained from paraffin-embedded tissue from the now-deceased sister and the C671T variant was confirmed. Supplemental Figure 2 Healthy Donor CD14 CD141 CD123 HLA-DR A201V/P224L Lineage CD16 CD11c CD1c 0.015 0.4 8 A201V/P224L P224L/WT P224L/WT 0.3 6 + A201V/WT Control 1 14+% 0.010 Control 2 PB MC MC MC 0.2 4 PB PB % % 0.005 0.1 2 0.0 0 0.000 1c+ DC pDC 14+ Mono 141+ DC Supplemental Figure 2. DC cell phenotype of patients with IRF8 mutations. DC phenotypes of heterozygous, homozygous, and healthy donor were evaluated by multi-parametric FACS phenotyping as described in Methods with the panel shown in Supplemental Table 4. Frequencies are shown as a percentage of cells found within peripheral blood mononuclear cells. Supplementary Table 1: Candidate gene variants from whole exome sequencing of Patient 1 a a b c d f g g g Gene Coordinates Zygosity vR tR Type ESP5400 1000G ExAC ExAC PhyloP SIFT Polyphen2 LRT Mut e Count Tast Recessive model variants: ELK1 X:47498442_G>A Hemi 244 248 NS 0.0001 0 0.00009 1 0.95 T D N N IRF8 16:85952023_C>T Het 39 112 NS 0.002 0.0046 0.0025 0 0.23 n/a B N D IRF8 16:85952092_C>T Het 44 72 NS 0 0 0.000045 0 0.58 T B N N LRP2 2:169989127_A>G Het 27 73 NS 0.003 0.0005 0.0019 1 -1.42 T B N N LRP2 2:170103472_G>A Het 36 82 NS 0.002 0.0023 0.0037 5 0.80 T D D D SYNE2 14:64593458_C>T Het 34 65 NS 0.0006 0 0.0006 0 -0.08 T B N N SYNE2 14:64687305_G>A Het 32 60 NS 0.004 0.0023 0.0035 1 0.16 T P N N SYNE2 14:64688390_C>T Het 69 121 NS 0.003 0.0023 0.0034 1 1.56 D P N N Dominant model variants: Variants not shared with unaffected family members TRIP12 2:230632449_GATTCA>G Het 2 19 FS_del 0 0 0 0 0 n/a n/a n/a n/a TNRC18 7:5353412_TG>T Het 2 10 FS_del 0 0 0 0 0 n/a n/a n/a n/a BRCC3 X:154348318_CCT>C Het 2 19 FS_del 0 0 0 0 0 n/a n/a n/a n/a RGP1 9:35749729_T>C Het 27 62 Splicing 0.000001 0 0.000039 3 0 n/a n/a n/a n/a ADAMTS17 15:100649248_G>T Het 30 78 NS 0 0 0 0 -2.11 D D D D FSD2 15:83455641_C>T Het 56 110 NS 0.0002 0 0.0000083 1 2.38 T D N N TYW5 2:200797842_C>T Het 148 289 NS 0 0 0.000025 3 2.89 T D D D KCTD18 2:201369482_C>G Het 29 53 NS 0.00009 0 0 0 2.94 T D D N FAT1 4:187525601_G>C Het 32 65 NS 0 0 0.000017 2 1.01 T B N n/a SLC45A4 8:142228549_C>A Het 11 20 NS 0.00009 0 0.000017 2 0.01 T P N D 1 FPGS 9:130566811_G>A Het 53 115 NS 0 0 0.000033 4 0.57 T P N D F10 13:113777231_G>C Het 59 121 NS 0 0 0.000034 4 0.06 T B N N Variants shared with mother but not other unaffected family members (dominant incomplete penetrance model) RTBDN 19:12936746_G>T Het 8 21 Stopgain 0 0 0 0 0.25 D D N n/a FBXO47 17:37119112_A>T Het 4 8 Stopgain 0 0 0 0 1.94 T n/a D A ODF3L2 19:472393_C>T Het 49 93 Splicing 0 0 0 0 2.03 n/a n/a n/a n/a TRHDE 12:73046175_A>T Het 16 41 NS 0 0 0 0 2.02 T P D D MYO5B 18:47511133_C>T Het 71 122 NS 0 0 0.000017 2 2.58 T D D D PYGB 20:25276272_T>G Het 8 21 NS 0 0 0.0000083 1 2.09 D B N n/a LIMD1 3:45637006_C>T Het 48 76 NS 0 0 0.000033 4 -0.18 T B N N LOC402160 4:2438661_C>T Het 53 117 NS 0 0 n/a n/a 0 n/a n/a n/a n/a CEP78 9:80880802_A>G Het 29 67 NS 0 0 0.00009 2 2.15 T P n/a N HELZ 17:65105372_G>A Het 35 75 NS 0 0 0.000025 3 2.80 D P D N Footnotes: a vR, variant reads; tR, total reads b Minor allelic frequency in the ESP5400 database c Minor allelic frequency in the 1000 Genomes database d Minor allelic frequency in the ExAC database e For recessive model, number of homozygotes (hemizygotes for X chromosome variants) in the ExAC database; for dominant model, allele count in the ExAC database f PhyloP conservation score g Damage predictions by the SIFT, PolyPhen2, LRT, and Mutation Taster algorithms: A, allowed; B, benign; D, damaging; N, neutral; P, possibly damaging; T, tolerated Other abbreviations: FS_del, frameshift deletion; Hemi, hemizygous; het, heterozygous; n/a, not available; NS, nonsynonymous 2 Supplementary Table 2: Genes up- and down-regulated in Patient 1 relative to 3 healthy donors MEAN SD GENE ID GENE NAME Gene Ontology killer cell immunoglobulin-like receptor, two -39.67 8.57 NM_014511.3 KIR2DL1/KIR2DL3 domains, long cytoplasmic tail, 3 other -36.69 5.66 NM_032782.3 HAVCR2 hepatitis A virus cellular receptor 2 other -31.21 14.70 NM_005810.3 KLRG1 killer cell lectin like receptor G1 other -25.92 19.11 NM_001337.3 CX3CR1 chemokine (C-X3-C motif) receptor 1 G-protein coupled receptor -15.08 5.37 NM_016260.2 IKZF2 IKAROS family zinc finger 2 transcription regulator -12.92 4.59 NM_201563.4 FCGR2C Fc fragment of IgG receptor IIc (gene/pseudogene) transmembrane receptor -12.84 14.43 NM_002460.1 IRF4 interferon regulatory factor 4 transcription regulator -12.64 9.76 NM_002184.2 IL6ST interleukin 6 signal transducer transmembrane receptor -12.38 7.41 NM_001557.2 CXCR2 chemokine (C-X-C motif) receptor 2 G-protein coupled receptor -12.24 15.28 NM_002983.2 CCL3 chemokine (C-C motif) ligand 3 cytokine -12.05 5.30 NM_004072.1 CMKLR1 chemerin chemokine-like receptor 1 G-protein coupled receptor tumor necrosis factor receptor superfamily member -11.44 1.70 NM_003820.2 TNFRSF14 14 transmembrane receptor -11.23 2.85 NM_198157.1 UBE2L3 ubiquitin conjugating enzyme E2L 3 kinase -10.04 3.91 NM_002385.2 MBP myelin basic protein other -10.01 4.99 NM_001184714.1 SLAMF6 SLAM family member 6 transmembrane receptor -9.31 2.10 NM_005745.7 BCAP31 B-cell receptor-associated protein 31 transporter -9.20 0.53 NM_002880.2 RAF1 Raf-1 proto-oncogene, serine/threonine kinase transcription regulator -8.77 0.15 NM_002208.4 ITGAE integrin subunit alpha E other inhibitor of kappa light polypeptide gene enhancer -8.76 2.93 NM_014002.2 IKBKE in B-cells, kinase epsilon kinase -8.25 3.50 NM_198282.1 TMEM173 transmembrane protein 173 transmembrane receptor -8.08 2.33 NM_000570.4 FCGR3A/FCGR3B Fc fragment of IgG receptor IIIa transmembrane receptor Supplementary Table 2: Genes up- and down-regulated in Patient 1 relative to 3 healthy donors -7.88 3.59 NM_002609.3 PDGFRB platelet derived growth factor receptor beta growth factor tumor necrosis factor receptor superfamily member -7.77 1.11 NM_001066.2 TNFRSF1B 1B transmembrane receptor -7.68 2.99 NM_005384.2 NFIL3 nuclear factor, interleukin 3 regulated transcription regulator -7.17 2.34 NM_000873.3 ICAM2 intercellular adhesion molecule 2 other -6.71 1.09 NM_000022.2 ADA adenosine deaminase enzyme killer cell immunoglobulin-like receptor, three -6.55 7.87 NM_001083539.1 KIR3DS1 domains, short cytoplasmic tail, 1 other -6.18 1.15 NM_000215.2 JAK3 Janus kinase 3 kinase -6.15 0.77 NM_000175.2 GPI glucose-6-phosphate isomerase enzyme mitogen-activated protein kinase kinase kinase -6.08 2.39 NM_004579.2 MAP4K2 kinase 2 transcription regulator -6.01 2.51 NM_005903.5 SMAD5 SMAD family member 5 transcription regulator -5.71 1.20 NM_005041.3 PRF1 perforin 1 (pore forming protein) transcription regulator -5.37 1.56 NM_005356.2 LCK LCK proto-oncogene, Src family tyrosine kinase other -5.35 2.35 NM_080921.3 PTPRC protein tyrosine phosphatase, receptor type C phosphatase -5.18 0.37 NM_004131.3 GZMB granzyme B peptidase ABL proto-oncogene 1, non-receptor tyrosine -5.07 1.44 NM_005157.3 ABL1 kinase kinase -4.91 0.61 NM_005419.2 STAT2 signal transducer and activator of transcription 2 transcription regulator -4.76 0.86 NM_005535.1 IL12RB1 interleukin 12 receptor subunit beta 1 transmembrane receptor -4.65 0.24 NM_078481.2 ADGRE5 adhesion G protein-coupled receptor E5 G-protein coupled receptor -4.59 0.62 NM_021602.2 CD79B CD79b molecule transmembrane receptor nucleotide binding oligomerization domain -4.46 0.86 NM_006092.1 NOD1 containing 1 other -4.43 0.44 NM_000210.1 ITGA6 integrin subunit alpha 6 transmembrane receptor Supplementary Table 2: Genes up- and down-regulated in Patient 1 relative to 3 healthy donors -4.29 1.57 NM_001198.3 PRDM1 PR domain containing 1, with ZNF domain enzyme -4.06 0.59 NM_002468.3 MYD88 myeloid differentiation primary response 88 enzyme -3.92 0.58 NM_012448.3 STAT5B signal transducer and activator of transcription 5B transcription regulator -3.90 1.21 NM_014261.1 TICAM1 toll-like receptor adaptor molecule 1 other leukocyte-associated immunoglobulin-like receptor -3.86 1.41 NM_002287.3 LAIR1 1 transmembrane receptor -3.82 0.45 NM_019009.2 TOLLIP toll interacting protein cytokine -3.79 1.03 NM_001760.2 CCND3 cyclin D3 other -3.78 2.56 NM_001081637.1 LILRB1 leukocyte immunoglobulin like receptor B1 transmembrane receptor -3.72 0.57 NM_004849.2 ATG5 autophagy related 5 other -3.62 0.99 NM_002120.3 HLA-DOB major histocompatibility complex, class II, DO beta transmembrane receptor -3.56 1.10 NM_001131028.1 ATG10 autophagy related 10 enzyme -3.53 0.84 NM_002117.4 HLA-C major histocompatibility complex, class I, C other macrophage migration inhibitory factor -3.52 4.98 NM_002415.1 MIF (glycosylation-inhibiting factor) transporter -3.40 1.72 NM_002984.2 CCL4 chemokine (C-C motif) ligand 4 cytokine -3.38 0.43 NM_006060.3 IKZF1 IKAROS family zinc finger 1 transcription regulator -3.34 1.18 NM_002205.2 ITGA5 integrin subunit alpha 5 transmembrane receptor -3.31 0.42 NM_005531.1 IFI16 interferon, gamma-inducible protein 16 transcription regulator inhibitor of kappa light polypeptide gene enhancer -3.31 1.19 NM_003640.3 IKBKAP in B-cells, kinase complex-associated protein other -3.30 0.73 NM_005658.3 TRAF1 TNF receptor