Methods for use in the diagnosis of autoimmune diseases
This disclosure provides new genetic targets, diagnostic methods, and therapeutic treatment regimens for multiple autoimmune disorders, including pediatric autoimmune disorders that are co-inherited and genetically shared. The disclosure, for example, provides methods of diagnosing or determining a susceptibility for one or more autoimmune diseases and methods of determining treatment protocols for patients with one or more autoimmune diseases based on determining if the patients have genetic alterations in particular genes.
1. A method for detecting a T allele in a single nucleotide variation (SNV) in rs77150043 on 16q12.1 in ADCY7 in a Crohn's disease (CD) or psoriasis (PS or PSOR) human patient, the method comprising:
a) obtaining a biological sample from the human patient; and
b) detecting in a nucleic acid from the sample a T allele in SNV rs77150043 on 16q12.1 in ADCY7 by contacting the sample with a probe specific for said SNV and detecting binding between said probe and said SNV.
2. The method of claim 1 , wherein the method further comprises detecting an allele present in an SNV in one or more of IL23R, LPHN2, PTPN22, TNFSF18, CRB1, IL10, TSSC1, IL18R1, ATG16L1, GPR35, DAG1, CYTL1, IL21, TNM3, PTGER4, ANKRD55, ERAP2, IL5, IL12B, 8q24.23, JAK2, LURAP1L, TNFSF15, FNBP1, CARD9, IL2RA, ANKRD30A, ZNF365, ZMIZ1, NKX2-3, INS, LRRK2, SUOX, EFNB2, SMAD3, SBK1, ATXN2L, NOD2, IKZF3, TYK2, FUT2, TNFRSF6B, PSMG1, CD40LG, and RBMX, by contacting the sample with a probe specific for said SNV and detecting binding between said probe and said SNV, wherein said allele is
rs11580078
G allele
1p31.3
IL23R;
rs2066363
C allele
1p31.1
LPHN2;
rs6679677
A allele
1.13.2
PTPN22;
rs34884278
C allele
1q24.3
TNFSF18;
rs6689858
C allele
1q31.3
CRB1;
rs55705316
G allele
1q32.1
IL10;
rs114846446
A allele
2p25.3
TSSC1;
rs2075184
T allele
2q12.1
IL18R1;
rs36001488
C allele
2q37.1
ATG16L1;
rs4676410
A allele
2q37.3
GPR35;
rs4625
G allele
3p21.31
DAG1;
rs76772495
C allele
4p16.2
CYTL1;
rs62324212
A allele
4q27
IL21;
rs7660520
A allele
4q35.1
TNM3;
rs7725052
C allele
5p13.1
PTGER4;
rs7731626
A allele
5q11.2
ANKRD55;
rs4869313
T allele
5q15
ERAP2;
rs11741255
A allele
5q31.1
IL5;
rs755374
T allele
5q33.3
IL12B;
rs7831697
G allele
8q24.23;
rs36051895
T allele
9p24.1
JAK2;
rs7042370
T allele
9p23
LURAPIL;
rs4246905
T allele
9q32
TNFSF15;
rs10988542
C allele
9q34.11
FNBP1;
rs11145763
C allele
9q34.3
CARD9;
rs706778
T allele
10p15.1
IL2RA;
rs7100025
G allele
10p11.21
ANKRD30A;
rs10822050
C allele
10q21.2
ZNF365;
rs1250563
C allele
10q22.3
ZMIZ1;
rs1332099
T allele
10q24.2
NKX2-3;
rs1885785
T allele
11p15.5
INS;
rs17466626
G allele
12q12
LRRK2;
rs1689510
C allele
12q13.2
SOUX;
rs11839053
C allele
13q33.3
EFNB2;
rs72743477
G allele
15q22.33
SMAD3;
rs12598357
G allele
16p11.2
SBK1;
rs12928404
C allele
16p11.2
ATXN2L;
rs117372389
T allele
16q2.1
NOD2;
rs1223497
C allele
17q12
IKZF3;
rs62131887
T allele
19p13.2
TYK2;
rs602662
G allele
19q13.33
FUT2;
rs2738774
A allele
20q13.33
TNFRSF6B;
rs2836882
A allele
21q22.2
PSMG1;
rs2807264
C allele
Xq26.3
CD40LG; and
rs12863738
T allele
Xq26.3
RBMX.
3. The method of claim 1 , wherein the patient is a pediatric or an adult patient.
4. The method of 1 , wherein the method further comprises detecting an allele present in an SNV in one or more of IL23R, PTPN22, TNM3, DAG1, ATG16L1, SUOX, SBK1, IL2RA, and ZMIZ1, by contacting the sample with a probe specific for said SNV and detecting binding between said probe and said SNV, wherein said allele is
rs11580078
G allele
1p31.3
IL23R;
rs6679677
A allele
1.13.2
PTPN22;
rs7660520
A allele
4q35.1
TNM3;
rs4625
G allele
3p21.31
DAG1;
rs36001488
C allele
2q37.1
ATG16L1;
rs1689510
C allele
12q13.2
SOUX;
rs7725052
C allele
5p13.1
SBK1
rs706778
T allele
10p15.1
IL2RA; and
rs1250563
C allele
10q22.3
ZMIZ1.
5. The method of claim 1 , wherein the method further comprises detecting an allele present in an SNV in one or more of IL23R, DAG1, ATG16L1, PTGER4, ANKRD55, LRRK2, SBK1, ADCY7, IL2RA, TNFSF15, CD40LG, ZMIZ1, IL21, CARD9, and PSMG1 genes, by contacting the sample with a probe specific for said SNV and detecting binding between said probe and said SNV, wherein said allele is
rs11580078
G allele
1p31.3
IL23R;
rs36001488
C allele
2q37.1
ATG16L1;
rs4625
G allele
3p21.31
DAG1;
rs62324212
A allele
4q27
IL21;
rs7725052
C allele
5p13.1
PTGER4;
rs7731626
A allele
5q11.2
ANKRD55;
rs11741255
A allele
5q31.1
IL5;
rs755374
T allele
5q33.3
IL12B;
rs4246905
T allele
9q32
TNFSF15;
rs11145763
C allele
9q34.3
CARD9;
rs706778
T allele
10p15.1
IL2RA;
rs10822050
C allele
10q21.2
ZNF365;
rs1250563
C allele
10q22.3
ZMIZ1;
rs1332099
T allele
10q24.2
NKX2-3;
rs17466626
G allele
12q12
LRRK2;
rs1689510
C allele
12q13.2
SUOX;
rs72743477
G allele
15q22.33
SMAD3;
rs12598357
G allele
16p11.2
SBK1;
rs117372389
T allele
16q12.1
NOD2; and
rs2836882
A allele
21q22.2
PSMG1.
6. The method of claim 1 , wherein detecting at step b) further comprises the step of analyzing a polynucleotide sample to determine the presence of said genetic alteration by performing a process selected from the group consisting of detection of specific hybridization, measurement of allele size, restriction fragment length polymorphism analysis, allele-specific hybridization analysis, single base primer extension reaction, and sequencing of an amplified polynucleotide.
7. The method of claim 1 , wherein in the nucleic acid is DNA.
8. The method of claim 1 , wherein in the nucleic acid RNA.