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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.