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Table 1 Rheumatic disease studies utilizing next-generation DNA sequencing methodologies

From: Use of next-generation DNA sequencing to analyze genetic variants in rheumatic disease

Disease Sequencing application Platform Study design Sample size sequenced Population Associated genes Reference
AS Targeted Illumina Case–control 50 cases and 50 controls; 846 cases and 1,308 controls Han Chinese/ European IL23R [8]
BD Exome Illumina Case–control 766 cases, 768 controls Japanese; Turkish IL23R, TLR4, MEFV [9]
  Exome Illumina Case–control 32 cases, 59 controls Korean KIR3DL3, MTHFR, MICA, KIR2KL4, FCGR3A, ICAM1, IFNAR1, KIR2DL4 [10]
IBD Exome Illumina Case–control 350 cases, 350 controls Caucasian NOD2, IL23R, CARD9, IL18RAP, CUL2, C1orf106, PTPN22, MUC19 [11]
  Sanger Applied Biosystems Case–control 528 cases, 549 controls Caucasian TNFRSF6B [12]
CU Whole genome/Sanger Illumina/Applied Biosystems Family 1 case; 27 cases Caucasian PLCG2 [13]
DDH Whole exome Illumina Family 4 cases Caucasian CX3CR1 [14]
FMS Whole exome Illumina Family 19 cases, 150 trios Caucasian ZNF77, KNG1, MMP8, STARD6, C14orf105, FAM81B, C11orf40 [15]
Gout Whole genome Illumina Case–control 457 cases Caucasian ALDH16A1 [16]
HUVS Whole exome/targeted exome Illumina Family 1 case; 3 cases, 9 unaffecteds Caucasian DNASE1L3 [17]
OA Sanger Applied Biosystems Case–control 992 cases, 944 controls Caucasian GDF5 [18],[19]
  Whole genome Illumina Case–control 623 cases, 69,153 controls Icelandic ALDH1A2 [20]
RA Targeted Beckman Coulter Case–control 34 cases, 74 controls Alaska Native MHC [21]
  Exome Illumina Case–control 500 cases, 650 controls Caucasian CD2, IL2RA, IL2RB [22]
  Whole exome Illumina Case–control 19 cases Japanese BTNL2 [23]
  Whole exome/ targeted exome Illumina Consanguineous family/case–control 4 cases; 1,088 cases, 1,088 controls Caucasian PLB1 [24]
SLE Targeted Illumina Case–control 74 cases, 100 controls Caucasian UBE2L3 [25]
  Targeted Illumina Case–control 100 cases, 100 controls Caucasian IKBKE, IFIH1 [26]
  Targeted Illumina Case–control 218 cases, 157 controls Caucasian; African-American; Hispanic TNIP1 [27]
  Targeted Illumina Case–control 7 cases Caucasian TNFAIP3 [28]
  Exome Sanger Case–control 191 cases, 96 controls Caucasian FAM167A; BLK [29]
  Whole exome/Sanger Life Technologies Family 1 case; 3 cases, 3 unaffecteds Caucasian PRKCD [30]
pSS Targeted Sanger Case–control 19 cases Caucasian TNFAIP3 [31]
  1. AS, ankylosing spondylitis; BD, Behçet’s disease; IBD, inflammatory bowel disease; CU, cold-induced urticaria; DDH, developmental dysplasia of the hip; FMS, fibromyalgia syndrome; HUVS, hypocomplementemic urticarial vasculitis syndrome; OA, osteoarthritis; RA, rheumatoid arthritis; SLE, systemic lupus erythematosus; pSS, primary Sjögren’s syndrome.