Abstract
The Type I Diabetes Genetics Consortium (T1DGC) Rapid Response Workshop was established to evaluate published candidate gene associations in a large collection of affected sib-pair (ASP) families. We report on our quality control (QC) and preliminary family-based association analyses. A random sample of blind duplicates was analyzed for QC. Quality checks, including examination of plate-panel yield, marker yield, Hardy–Weinberg equilibrium, mismatch error rate, Mendelian error rate, and allele distribution across plates, were performed. Genotypes from 2324 families within nine cohorts were obtained from a panel of 21 candidate genes, including 384 single-nucleotide polymorphisms on two genotyping platforms performed at the Broad Institute Center for Genotyping and Analysis (Cambridge, MA, USA). The T1DGC Rapid Response project, following rigorous QC procedures, resulted in a 2297 family, 9688 genotyped individual database on a single-candidate gene panel. The available data include 9005 individuals with genotype data from both platforms and 683 individuals genotyped (276 in Illumina; 407 in Sequenom) on only one platform.
Keywords: type I diabetes, candidate gene, SNP, quality control, association
Introduction
The Type I Diabetes Genetics Consortium (T1DGC; http://www.t1dgc.org) is an international effort to identify genes that determine an individual’s risk of type I diabetes (T1D). The creation of a resource base of well-characterized affected sib-pair (ASP) families and other collections has been implemented that will facilitate the localization and characterization of T1D genes that determine disease risk. The aim of the T1DGC Rapid Response project was to explore candidate genes previously reported to be associated with T1D (for example INS,1 CTLA4,2 PTPN22,3 SUMO44). Confirmation of candidate genes for T1D has been difficult for some but not for others. Although many of the initial studies were underpowered, some genes appeared to exhibit their association only in certain populations or ethnic groups.
In the T1DGC Rapid Response experiment, a series of candidate genes were chosen for evaluation in a large collection of Caucasian ASP families. The candidate genes had been published earlier with identified polymorphisms that suggested association and may (or may not) have been replicated in other studies. In a separate component of the project, candidate genes that emerged from recent genome-wide association scans for T1D, type II diabetes, and other autoimmune diseases were included for follow-up. This report provides the background of the quality control (QC) procedures in the first Rapid Response experiment, whose objectives were to (1) establish evidence of replication of published candidate genes and (2) test hypotheses of population heterogeneity, the impact of stratification, potential genetic interaction on risk, and other modifying factors on T1D risk.
Results
The T1DGC Rapid Response project had three data-set releases. The second and third data-set releases resulted in modified, updated, and more complete versions of the earlier Rapid Response data. The main modifications for each release were incorporation of re-called markers and resolution of problematic families. As major histocompatibility complex (MHC) fine mapping and genome-wide linkage scans were being performed on the same families, these additional data provided more specific relationship information to help resolve pedigree structure problems. All datasets were securely maintained in the T1DGC web site (http://www.t1dgc.org) with password-protected access. These and other T1DGC datasets are now available (https://www.t1dgc.org/views/vw_databases.cfm).
The initial data release (2007.03.RR) consisted of 2317 families from 9 cohorts with genotype data on 21 candidate genes as well as a set of DNA fingerprinting markers. For this release, seven families were removed because of high levels of Mendelian inconsistencies. In addition, 135 individuals had either a pedigree change (that is classified new parent, sample switch, or gender reclassification) or were considered unrelated to other family members. The number of single-nucleotide polymorphisms (SNPs) genotyped per candidate gene ranged from 1 to 66. There were 357 SNPs released that were genotyped using the Illumina GoldenGate assay and 375 SNPs that were genotyped using the Sequenom platform; 334 SNPs were common to the two platforms. The Sequenom genotyping resulted in a slightly higher number of inconsistencies within families. Two SNPs were eliminated in the Illumina panel, as they resulted in problems in >20% of the families. Four SNPs were set to missing in the Sequenom panel that resulted in problems in >10% of the families. In addition, eight SNPs genotyped with the Illumina assay and two SNPs genotyped with the Sequenom assay were missing because of <80% call rate.
The second data release (2007.12.RR) were generated on 2297 families from 9 cohorts on 21 candidate genes and included DNA fingerprinting markers and re-genotyped data for seven SNPs on the Sequenom platform. These seven SNPs (INS rs1003483; PTPN22 rs1746860; IL13 rs1881457; IL12B rs2569253; IL4R rs3024613; IL2RA rs4147359; VDR rs7975232) had their data re-scored based on significant deviation from Hardy–Weinberg equilibrium assumptions. It was also determined that these seven SNPs had a low genotyping concordance compared with that observed on the Illumina panel. Thus, these SNPs were determined to have erroneously scored genotypes. The repeated scoring resulted in releasing 377 markers on the Sequenom platform and increasing the number to 336 SNPs that were scored on both platforms.
Earlier, the datasets that were released included all SNPs (regardless of genotyping status), three families whose Mendelian inconsistencies were resolved, elimination of one member from a pair of monozygotic twins, and removal of 23 duplicate families. This dataset incorporated 137 individuals who had either a pedigree change (that is classified new parent, sample switch, or gender reclassification), were members of a family who were determined to be unrelated, or were a duplicate sample and, therefore, had their genotype dataset to ‘missing.’
The third and final data release (2008.07.RR) consisted of 2297 families from 9 cohorts with genotype data on 21 candidate genes and a set of DNA fingerprinting markers (Table 1). For this release, the raw genotype data generated from the Sequenom platform were scored using the new Typer 4.0 software. A comparison of scoring 10 SNPs that were considered ‘poor performing’ markers and a second comparison of 20 SNPs using Typer 4.0 software suggested that well-called SNPs remained so, whereas poorly called SNPs improved when scored with the Typer 4.0 software. The Sequenom assay for TCF7 rs5742913 was originally designed to detect C and T alleles in dbSNP using ss65832708 (http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=5742913). This assay resulted in the SNP appearing monomorphic for the C allele; however, earlier data5,6 reported that the correct alleles are C and A (not T) as defined by ss93257904. By virtue of the Sequenom iPLEX chemistry use of four mass-distinct chain-terminating nucleotides, a re-definition by the Typer 4.0 software to identify and measure the mass peak corresponding to the A-extended primer (earlier attempting to detect the absent T-extended primer) permitted the accurate re-call of genotypes. To provide consistent data, all SNPs in the Sequenom dataset were recalled using Typer 4.0 software. These data were then subjected to standard QC procedures. The Illumina data were unchanged from the earlier release (2007.12.RR).
Table 1.
Description of T1DGC Rapid Response data following QC procedures
| T1DGC | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2008.07.RR | |||||||||||
| Data characteristics | |||||||||||
| Family summary: post-modification | |||||||||||
| Contributor | Families in dataset | Families with genotype data | Families (n (%)) with |
||||||||
| Parents |
Affected full siblings |
||||||||||
| 0 | 1 | 2 | 0 | 1 | 2 | 3 | 4+ | Half sib | |||
| Asia-Pacific | 191 | 191 | 27 | 53 | 111 | 1 | 11 | 168 | 8 | 1 | 2 |
| BDA | 417 | 417 | 6 | 71 | 340 | 6 | 63 | 347 | 1 | 0 | 0 |
| Danish | 146 | 146 | 17 | 41 | 88 | 1 | 18 | 115 | 12 | 0 | 0 |
| Europe | 475 | 475 | 51 | 114 | 310 | 0 | 30 | 420 | 22 | 1 | 2 |
| HBDI | 431 | 431 | 1 | 40 | 390 | 0 | 24 | 365 | 35 | 6 | 1 |
| North America | 334 | 334 | 38 | 103 | 193 | 0 | 28 | 293 | 10 | 0 | 3 |
| United Kingdom | 114 | 114 | 5 | 24 | 85 | 0 | 6 | 104 | 3 | 1 | 0 |
| Joslin | 112 | 111 | 38 | 24 | 49 | 1 | 12 | 90 | 5 | 0 | 3 |
| Sardinian | 78 | 78 | 4 | 22 | 52 | 0 | 8 | 70 | 0 | 0 | 0 |
| All | 2298 | 2297 | 187 | 492 | 1618 | 9 | 200 | 1972 | 96 | 9 | 11 |
Abbreviations: BDA, British Dietetic Association; HBDI, Human Biological Data Interchange; QC, quality control; TIDGC, Type I Diabetes Genetics Consortium.
Discussion
The T1DGC Rapid Response project resulted in a dataset containing 9688 individuals from 2297 ASP families with family members genotyped for 21 T1D candidate genes on two genotype platforms. Five of the candidate genes were ‘fully investigated,’ in that the structure of the gene was evaluated using tagging SNPs. Sixteen of the genes were subjected to genotyping using only the reported SNPs that exhibited the strongest association with T1D (for more detail, see Julier et al.,7 this volume). In this dataset, there are 9005 individuals with genotype data derived from both platforms. There are 683 individuals genotyped only on one platform (276 in Illumina; 407 in Sequenom).
There are two important aspects of the Rapid Response project. The first was that a majority of the families were included in a genome-wide linkage scan panel (6000 SNPs).8,9 Second, all families were included in the MHC Fine Mapping project.10 As a result of the additional genetic information, the T1DGC Coordinating Center was able to better resolve QC issues (such as questionable family structure) within the Rapid Response dataset. The T1DGC Rapid Response project permitted the creation of a valuable resource of well-characterized families from multiple geographic sites that showed the localization and characterization of T1D genes.
Materials and methods
Genotyping
The T1DGC Molecular Technology Subcommittee established a list of genes for investigation at the Rapid Response Laboratory (Broad Institute of Harvard/Massachusetts Institute of Technology). An initial set of published candidate genes and associated SNPs was selected, based on a literature search. Two lists of candidate genes were constructed for consideration in the experiment. List 1 included those genes (INS, PTPN22, CTLA4, IL2R/CD25, and SUMO4) that had been confirmed or replicated, excluding those in the MHC. List 2 included those genes (IL12B, IL4R, IL4, IL13, OAS1, VDR, SDF1, PAX4, FOXP3, IRS1, TCF7, IFIH1, EFHB, CAPSL, Q7Z4C4(5Q), and CEACAM21) that had not been replicated earlier.
From the initial set of candidate genes, a panel of 384 SNPs was identified using the ‘Tagger’ algorithm11 such that all observed SNPs in HapMap-CEU with minor allele frequency >3% were captured with a perfect proxy (r2 = 1) for genes on List 1, or with a tagging SNP at r2≥0.8 for genes on List 2. SNPs were preferentially chosen with high-design scores for the Illumina GoldenGate assay.
The panel of 384 SNPs was genotyped on two platforms, using the Illumina GoldenGate assay and the Sequenom MALDI-TOF assay. A preliminary round of design and assay testing using the HapMap CEU sample panel was performed on both platforms. For genotyping using the Sequenom platform, 19 SNPs were not included because of an inability to design robust assays. The 19 excluded SNPs were replaced with 16 SNPs potentially useful for sample tracking for Affymetrix whole-genome genotyping. The 381 SNPs genotyped using the Sequenom iPLEX technology were distributed among 20 iPLEX pools (13–21 SNPs/pool; median pool size 19). The SNPs were part of 21 candidate genes: 5 fully investigated (158 SNPs) and 16 replicated (226 SNPs). The number of SNPs genotyped for each gene ranged from 1 to 69 SNPs. Four genes contained a single SNP; 3 genes contained 5–6 SNPs; 7 genes contained 10–16 SNPs; 4 genes contained 21–28 SNPs; 3 genes contained 37–42 SNPs; and one gene contained 69 SNPs.
In the Illumina assay, 367 SNPs were adequately genotyped, whereas the remaining 17 SNPs could not be accurately called and were considered ‘missing.’ For the Sequenom assay, all 381 SNPs were genotyped. For the genotyped SNPs, 8 in the Illumina panel and 2 in the Sequenom panel had <80% call rate and were set to ‘missing.’ Using strand information, genotypes were examined and calls were adjusted on the Sequenom panel to reflect the strand order of the Illumina panel. This procedure required ‘flipping’ genotype calls.
For the original release of the Rapid Response data, the Sequenom platform used Typer 3.0 software (http://www.sequenom.com (software no longer available)) to call genotypes. The Sequenom genotype data were later re-called using Typer 4.0 software (http://sequenom.com/Genetic-Analysis/Applications/iPLEX-Genotyping/iPLEX-Literature). This version of the Sequenom genotype calling software allows the simultaneous viewing and consistent clustering of multiple production plates of data, ensuring that genotype class definitions are stable across plates. (For a complete list of SNPs, see Appendix A)
Appendix A.
Rapid Response reference SNP list
| Study | Chromosome | Gene | Marker | Physical position | Illumina | Sequenom |
|---|---|---|---|---|---|---|
| Full | 1 | PTPN22 | rs3827733 | 114050631 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs3789602 | 114051793 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs1217379 | 114056125 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs6537798 | 114063748 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs3789607 | 114078476 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs2476600 | 114081776 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs1217395 | 114086477 | Genotyped | Ungenotyped |
| Full | 1 | PTPN22 | rs1970559 | 114089190 | Genotyped | Ungenotyped |
| Full | 1 | PTPN22 | rs2476601 | 114089610 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs1775759 | 114100846 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs3765598 | 114106505 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs11582409 | 114111475 | Ungenotyped | Genotyped |
| Full | 1 | PTPN22 | rs1217418 | 114113273 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs1217414 | 114124709 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs17510162 | 114125773 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs2488457 | 114127410 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs1235005 | 114129479 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs6665194 | 114129885 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs1217384 | 114131802 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs12566340 | 114132370 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs7529353 | 114132504 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs7524200 | 114138866 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs1217423 | 114139335 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs1746860 | 114141382 | Ungenotyped | Genotyped |
| Full | 1 | PTPN22 | rs2358994 | 114141503 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs1539438 | 114142398 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs1217394 | 114145701 | Genotyped | Genotyped |
| Full | 1 | PTPN22 | rs1217393 | 114145988 | Genotyped | Ungenotyped |
| Full | 2 | CTLA4 | rs231811 | 204539397 | Genotyped | Genotyped |
| Full | 2 | CTLA4 | rs6741283 | 204540316 | Genotyped | Genotyped |
| Full | 2 | CTLA4 | rs11571293 | 204543219 | Genotyped | Genotyped |
| Full | 2 | CTLA4 | rs2162610 | 204544235 | Genotyped | Genotyped |
| Full | 2 | CTLA4 | rs926169 | 204548258 | Genotyped | Genotyped |
| Full | 2 | CTLA4 | rs11571290 | 204548647 | Genotyped | Genotyped |
| Full | 2 | CTLA4 | rs231770 | 204554659 | Genotyped | Genotyped |
| Full | 2 | CTLA4 | rs733618 | 204556450 | Genotyped | Genotyped |
| Full | 2 | CTLA4 | rs11571316 | 204556595 | Genotyped | Genotyped |
| Full | 2 | CTLA4 | rs16840252 | 204557025 | Genotyped | Genotyped |
| Full | 2 | CTLA4 | rs11571317 | 204557514 | Genotyped | Genotyped |
| Full | 2 | CTLA4 | rs5742909 | 204557853 | Genotyped | Genotyped |
| Full | 2 | CTLA4 | rs231777 | 204559094 | Genotyped | Genotyped |
| Full | 2 | CTLA4 | rs231779 | 204559993 | Genotyped | Genotyped |
| Full | 2 | CTLA4 | rs3087243 | 204564425 | Genotyped | Ungenotyped |
| Full | 2 | CTLA4 | rs1427676 | 204566672 | Genotyped | Genotyped |
| Full | 2 | CTLA4 | rs231727 | 204567056 | Genotyped | Genotyped |
| Full | 2 | CTLA4 | rs231731 | 204570036 | Genotyped | Genotyped |
| Full | 2 | CTLA4 | rs11571300 | 204572273 | Genotyped | Genotyped |
| Full | 2 | CTLA4 | rs960792 | 204574756 | Ungenotyped | Ungenotyped |
| Full | 2 | CTLA4 | rs1365965 | 204577376 | Genotyped | Genotyped |
| Full | 2 | CTLA4 | rs231757 | 204578993 | Genotyped | Genotyped |
| Full | 2 | CTLA4 | rs231755 | 204579075 | Genotyped | Genotyped |
| Full | 2 | CTLA4 | rs7600322 | 204579859 | Genotyped | Ungenotyped |
| Full | 2 | CTLA4 | rs6748358 | 204582411 | Genotyped | Genotyped |
| Full | 6 | SUMO4 | rs12204461 | 149743228 | Genotyped | Genotyped |
| Full | 6 | SUMO4 | rs7742990 | 149746219 | Genotyped | Genotyped |
| Full | 6 | SUMO4 | rs9373589 | 149748981 | Genotyped | Genotyped |
| Full | 6 | SUMO4 | rs9404034 | 149753676 | Genotyped | Genotyped |
| Full | 6 | SUMO4 | rs2789490 | 149756012 | Genotyped | Genotyped |
| Full | 6 | SUMO4 | rs237032 | 149757865 | Genotyped | Genotyped |
| Full | 6 | SUMO4 | rs237025 | 149763383 | Genotyped | Genotyped |
| Full | 6 | SUMO4 | rs2789488 | 149766983 | Genotyped | Genotyped |
| Full | 6 | SUMO4 | rs2789489 | 149769038 | Genotyped | Genotyped |
| Full | 6 | SUMO4 | rs652921 | 149772539 | Genotyped | Genotyped |
| Full | 6 | SUMO4 | rs366905 | 149776790 | Genotyped | Genotyped |
| Full | 6 | SUMO4 | rs480034 | 149777123 | Genotyped | Genotyped |
| Full | 6 | SUMO4 | rs236999 | 149781068 | Genotyped | Genotyped |
| Full | 6 | SUMO4 | rs513923 | 149782364 | Genotyped | Genotyped |
| Full | 6 | SUMO4 | rs9485389 | 149782907 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs6602363 | 6076150 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs7898880 | 6077559 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs7911500 | 6077732 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs17147986 | 6078484 | Ungenotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs6602364 | 6078859 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs1323653 | 6079064 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs7477011 | 6080600 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs10795731 | 6082040 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs17322780 | 6082478 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs10795733 | 6083484 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs764851 | 6087950 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs10795737 | 6089350 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs12359875 | 6091113 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs12722608 | 6092847 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs12722605 | 6093169 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs12244380 | 6093380 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs12722598 | 6095156 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs9663421 | 6095610 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs12722596 | 6096300 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs2386841 | 6097738 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs7899538 | 6099904 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs12722588 | 6100439 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs2274037 | 6102114 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs2076846 | 6103259 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs7093069 | 6103325 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs11596355 | 6104187 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs12722574 | 6106468 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs2031229 | 6106574 | Genotyped | Ungenotyped |
| Full | 10 | IL2R/CD25 | rs2025345 | 6107694 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs12722561 | 6109899 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs7910961 | 6117802 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs6602391 | 6118038 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs12722521 | 6118802 | Genotyped | Ungenotyped |
| Full | 10 | IL2R/CD25 | rs11256448 | 6119485 | Ungenotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs7072398 | 6119852 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs12722518 | 6120643 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs11256456 | 6120718 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs12722516 | 6121223 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs4749924 | 6122402 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs6602398 | 6122959 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs4749926 | 6125318 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs10905656 | 6126099 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs942201 | 6126298 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs706780 | 6127032 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs1107345 | 6127301 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs11256497 | 6127800 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs791587 | 6128705 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs791589 | 6129577 | Genotyped | Ungenotyped |
| Full | 10 | IL2R/CD25 | rs791590 | 6130328 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs10905669 | 6132099 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs1323658 | 6134360 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs2476491 | 6135416 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs2256774 | 6137171 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs706779 | 6138830 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs706778 | 6138955 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs2104286 | 6139051 | Genotyped | Ungenotyped |
| Full | 10 | IL2R/CD25 | rs3134883 | 6140731 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs3118470 | 6141719 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs12722486 | 6143768 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs7072793 | 6146272 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs7073236 | 6146558 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs4147359 | 6148445 | Ungenotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs7089861 | 6150332 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs7090512 | 6150835 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs1887027 | 6153788 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs4749955 | 6158972 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs11594656 | 6162015 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs12251307 | 6163501 | Genotyped | Genotyped |
| Full | 10 | IL2R/CD25 | rs7100400 | 6164086 | Genotyped | Genotyped |
| Full | 11 | INS | rs4244808 | 2119686 | Genotyped | Ungenotyped |
| Full | 11 | INS | rs1003483 | 2124119 | Genotyped | Genotyped |
| Full | 11 | INS | rs3741208 | 2126350 | Ungenotyped | Genotyped |
| Full | 11 | INS | rs1004446 | 2126719 | Genotyped | Genotyped |
| Full | 11 | INS | rs4320932 | 2128177 | Genotyped | Genotyped |
| Full | 11 | INS | rs7924316 | 2130023 | Genotyped | Genotyped |
| Full | 11 | INS | rs3842753 | 2137636 | Ungenotyped | Genotyped |
| Full | 11 | INS | rs3842748 | 2137971 | Genotyped | Genotyped |
| Full | 11 | INS | rs2070762 | 2142911 | Genotyped | Genotyped |
| Full | 11 | INS | rs6356 | 2147527 | Genotyped | Genotyped |
| Full | 11 | INS | rs10840490 | 2150393 | Ungenotyped | Genotyped |
| Full | 11 | INS | rs10743149 | 2150751 | Genotyped | Genotyped |
| Full | 11 | INS | rs10840491 | 2150966 | Genotyped | Ungenotyped |
| Full | 11 | INS | rs7119275 | 2151386 | Genotyped | Genotyped |
| Full | 11 | INS | rs10840495 | 2152413 | Genotyped | Ungenotyped |
| Full | 11 | INS | rs4930046 | 2153724 | Genotyped | Ungenotyped |
| Full | 11 | INS | rs4929966 | 2154012 | Genotyped | Genotyped |
| Full | 11 | INS | rs11042978 | 2154994 | Genotyped | Genotyped |
| Full | 11 | INS | rs11564710 | 2156905 | Genotyped | Genotyped |
| Full | 11 | INS | rs6578993 | 2157739 | Genotyped | Genotyped |
| Full | 11 | INS | rs11564709 | 2157914 | Genotyped | Genotyped |
| Replication | 2 | IFIH1 | rs2111485 | 162936043 | Genotyped | Genotyped |
| Replication | 2 | IFIH1 | rs1990760 | 162949558 | Genotyped | Genotyped |
| Replication | 2 | IFIH1 | rs3747517 | 162954331 | Genotyped | Genotyped |
| Replication | 2 | IFIH1 | rs3788964 | 163032987 | Genotyped | Genotyped |
| Replication | 2 | IFIH1 | rs984971 | 163050028 | Genotyped | Genotyped |
| Replication | 2 | IFIH1 | rs2068330 | 163062897 | Genotyped | Genotyped |
| Replication | 2 | IRS1 | rs16822551 | 227407085 | Genotyped | Genotyped |
| Replication | 2 | IRS1 | rs11683087 | 227412111 | Genotyped | Genotyped |
| Replication | 2 | IRS1 | rs2251692 | 227415285 | Genotyped | Ungenotyped |
| Replication | 2 | IRS1 | rs17208239 | 227423202 | Genotyped | Genotyped |
| Replication | 2 | IRS1 | rs17208470 | 227429410 | Genotyped | Genotyped |
| Replication | 2 | IRS1 | rs2435185 | 227461928 | Genotyped | Genotyped |
| Replication | 2 | IRS1 | rs4675095 | 227477472 | Genotyped | Genotyped |
| Replication | 2 | IRS1 | rs1801278 | 227486049 | Genotyped | Genotyped |
| Replication | 2 | IRS1 | rs1801123 | 227486548 | Genotyped | Genotyped |
| Replication | 2 | IRS1 | rs6725330 | 227492362 | Genotyped | Genotyped |
| Replication | 2 | IRS1 | rs6725556 | 227492497 | Genotyped | Genotyped |
| Replication | 2 | IRS1 | rs13018009 | 227493906 | Genotyped | Genotyped |
| Replication | 2 | IRS1 | rs4675096 | 227494446 | Genotyped | Genotyped |
| Replication | 2 | IRS1 | rs956115 | 227500069 | Genotyped | Ungenotyped |
| Replication | 2 | IRS1 | rs957797 | 227502248 | Genotyped | Genotyped |
| Replication | 2 | IRS1 | rs13417106 | 227509333 | Genotyped | Genotyped |
| Replication | 3 | EFHB | rs2929366 | 19934760 | Genotyped | Genotyped |
| Replication | 5 | CAPSL | rs1445898 | 35946286 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs7730126 | 158662525 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs1549922 | 158664126 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs4921466 | 158665350 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs6859018 | 158669570 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs17875325 | 158673108 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs3181225 | 158673201 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs17875324 | 158673428 | Ungenotyped | Genotyped |
| Replication | 5 | IL12B | rs3212227 | 158675528 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs2853696 | 158677238 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs919766 | 158680142 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs2853694 | 158681666 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs2569253 | 158683571 | Genotyped | Ungenotyped |
| Replication | 5 | IL12B | rs3181219 | 158684717 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs17875303 | 158685556 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs1433048 | 158688423 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs2546893 | 158688538 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs2546890 | 158692478 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs10052709 | 158693055 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs7709212 | 158696755 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs6868898 | 158696998 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs17056704 | 158700244 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs13188370 | 158701707 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs17056705 | 158701831 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs17056706 | 158703333 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs953861 | 158705160 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs4244437 | 158705695 | Genotyped | Genotyped |
| Replication | 5 | IL12B | rs11747112 | 158707187 | Genotyped | Genotyped |
| Replication | 5 | IL13 | rs2240032 | 132005026 | Ungenotyped | Genotyped |
| Replication | 5 | IL13 | rs1881457 | 132020308 | Ungenotyped | Genotyped |
| Replication | 5 | IL13 | rs1800925 | 132020708 | Genotyped | Genotyped |
| Replication | 5 | IL13 | rs1295686 | 132023742 | Genotyped | Genotyped |
| Replication | 5 | IL13 | rs20541 | 132023863 | Genotyped | Genotyped |
| Replication | 5 | IL4 | rs848 | 132024399 | Genotyped | Genotyped |
| Replication | 5 | IL4 | rs1295683 | 132026775 | Genotyped | Genotyped |
| Replication | 5 | IL4 | rs2243210 | 132029285 | Genotyped | Genotyped |
| Replication | 5 | IL4 | rs2243248 | 132036543 | Genotyped | Genotyped |
| Replication | 5 | IL4 | rs2243250 | 132037053 | Genotyped | Genotyped |
| Replication | 5 | IL4 | rs2227284 | 132040624 | Genotyped | Genotyped |
| Replication | 5 | IL4 | rs2243263 | 132041198 | Genotyped | Genotyped |
| Replication | 5 | IL4 | rs2243274 | 132042731 | Genotyped | Genotyped |
| Replication | 5 | IL4 | rs11242122 | 132052607 | Genotyped | Genotyped |
| Replication | 5 | IL4 | rs1468216 | 132064151 | Genotyped | Genotyped |
| Replication | 5 | Q7Z4C4(5Q) | rs9127 | 96397921 | Genotyped | Genotyped |
| Replication | 5 | TCF7 | rs30503 | 133465245 | Genotyped | Genotyped |
| Replication | 5 | TCF7 | rs30500 | 133467775 | Genotyped | Genotyped |
| Replication | 5 | TCF7 | rs30499 | 133469625 | Genotyped | Genotyped |
| Replication | 5 | TCF7 | rs244948 | 133472960 | Genotyped | Genotyped |
| Replication | 5 | TCF7 | rs5742913 | 133479582 | Ungenotyped | Genotyped |
| Replication | 5 | TCF7 | rs244692 | 133480434 | Genotyped | Genotyped |
| Replication | 5 | TCF7 | rs151822 | 133483860 | Genotyped | Genotyped |
| Replication | 5 | TCF7 | rs152404 | 133486613 | Genotyped | Genotyped |
| Replication | 5 | TCF7 | rs152406 | 133489485 | Genotyped | Genotyped |
| Replication | 5 | TCF7 | rs249611 | 133492556 | Ungenotyped | Genotyped |
| Replication | 5 | TCF7 | rs17653687 | 133495899 | Genotyped | Genotyped |
| Replication | 7 | PAX4 | rs3779536 | 126827928 | Genotyped | Genotyped |
| Replication | 7 | PAX4 | rs806213 | 126828941 | Genotyped | Genotyped |
| Replication | 7 | PAX4 | rs3735640 | 126830289 | Genotyped | Genotyped |
| Replication | 7 | PAX4 | rs806216 | 126831813 | Genotyped | Genotyped |
| Replication | 7 | PAX4 | rs3824006 | 126835931 | Genotyped | Genotyped |
| Replication | 7 | PAX4 | rs10229583 | 126840854 | Genotyped | Genotyped |
| Replication | 7 | PAX4 | rs712701 | 126845139 | Genotyped | Genotyped |
| Replication | 7 | PAX4 | rs327518 | 126845743 | Genotyped | Genotyped |
| Replication | 7 | PAX4 | rs7801118 | 126857837 | Genotyped | Genotyped |
| Replication | 7 | PAX4 | rs806187 | 126863590 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs731336 | 44159260 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs1147882 | 44166437 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs266109 | 44170430 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs1147879 | 44170656 | Ungenotyped | Genotyped |
| Replication | 10 | CXCL12 | rs266108 | 44172126 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs266105 | 44175669 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs11595588 | 44175746 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs17391002 | 44175933 | Ungenotyped | Genotyped |
| Replication | 10 | CXCL12 | rs4948876 | 44176752 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs11239011 | 44176969 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs185545 | 44178846 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs17156191 | 44179353 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs266098 | 44181674 | Genotyped | Ungenotyped |
| Replication | 10 | CXCL12 | rs10900029 | 44182226 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs266093 | 44186214 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs266092 | 44186281 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs1801157 | 44188263 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs197452 | 44190246 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs266087 | 44191068 | Ungenotyped | Genotyped |
| Replication | 10 | CXCL12 | rs2297630 | 44191554 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs2839693 | 44194573 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs4948878 | 44194827 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs2839689 | 44195465 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs3780891 | 44198719 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs2839685 | 44201644 | Ungenotyped | Genotyped |
| Replication | 10 | CXCL12 | rs1413519 | 44202567 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs2861442 | 44204965 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs754617 | 44206348 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs7088285 | 44207935 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs6593412 | 44208136 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs1855531 | 44209658 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs11595460 | 44211083 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs1023264 | 44213762 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs1023262 | 44213870 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs1779384 | 44214449 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs4948881 | 44216041 | Genotyped | Genotyped |
| Replication | 10 | CXCL12 | rs1761325 | 44216995 | Genotyped | Genotyped |
| Replication | 12 | OAS1 | rs3741982 | 111791701 | Genotyped | Genotyped |
| Replication | 12 | OAS1 | rs12177 | 111798145 | Genotyped | Genotyped |
| Replication | 12 | OAS1 | rs2240193 | 111798381 | Genotyped | Genotyped |
| Replication | 12 | OAS1 | rs2240191 | 111798451 | Genotyped | Genotyped |
| Replication | 12 | OAS1 | rs12309946 | 111798975 | Genotyped | Genotyped |
| Replication | 12 | OAS1 | rs4766662 | 111808419 | Genotyped | Genotyped |
| Replication | 12 | OAS1 | rs3741981 | 111811590 | Genotyped | Genotyped |
| Replication | 12 | OAS1 | rs10774671 | 111819913 | Genotyped | Genotyped |
| Replication | 12 | OAS1 | rs7135579 | 111829602 | Genotyped | Genotyped |
| Replication | 12 | OAS1 | rs3803057 | 111831454 | Genotyped | Genotyped |
| Replication | 12 | OAS1 | rs7967461 | 111832479 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs1859281 | 46502016 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs2544028 | 46502697 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs10747524 | 46509741 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs11608702 | 46515035 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs12721364 | 46517697 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs7968585 | 46518360 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs6580639 | 46518439 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs731236 | 46525024 | Ungenotyped | Genotyped |
| Replication | 12 | VDR | rs7975232 | 46525104 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs11574113 | 46525167 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs1544410 | 46526102 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs11574085 | 46537061 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs11168267 | 46537809 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs11574077 | 46539194 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs2239182 | 46541678 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs2107301 | 46541837 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs2239180 | 46542313 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs2239179 | 46544033 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs11574066 | 46544902 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs12717991 | 46545393 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs886441 | 46549231 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs2189480 | 46550095 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs3819545 | 46551273 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs3782905 | 46552434 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs2239186 | 46555677 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs10735810 | 46559162 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs2254210 | 46559981 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs2238136 | 46563980 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs2853564 | 46564754 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs4760648 | 46566932 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs11168287 | 46571681 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs4328262 | 46571915 | Ungenotyped | Ungenotyped |
| Replication | 12 | VDR | rs4237855 | 46573470 | Ungenotyped | Genotyped |
| Replication | 12 | VDR | rs11574027 | 46573640 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs11574026 | 46574513 | Genotyped | Ungenotyped |
| Replication | 12 | VDR | rs10875695 | 46579304 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs11168292 | 46579872 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs12721377 | 46581618 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs10783219 | 46581755 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs7299460 | 46582535 | Genotyped | Genotyped |
| Replication | 12 | VDR | rs4760658 | 46582753 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs2057768 | 27229596 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs2107356 | 27230905 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs6498012 | 27239475 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs1110470 | 27243928 | Ungenotyped | Genotyped |
| Replication | 16 | IL4R | rs4787948 | 27248560 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs2283563 | 27253855 | Ungenotyped | Genotyped |
| Replication | 16 | IL4R | rs3024530 | 27258188 | Genotyped | Ungenotyped |
| Replication | 16 | IL4R | rs3024537 | 27260320 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs1805010 | 27263704 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs3024560 | 27264168 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs3024571 | 27265428 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs2301807 | 27265599 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs3024578 | 27265852 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs2239347 | 27266522 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs3116578 | 27267337 | Ungenotyped | Genotyped |
| Replication | 16 | IL4R | rs3024613 | 27271754 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs3024614 | 27271846 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs3024622 | 27272954 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs4787423 | 27274835 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs3024668 | 27279450 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs2234897 | 27281113 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs1805011 | 27281373 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs1805012 | 27281465 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs1805015 | 27281681 | Genotyped | Ungenotyped |
| Replication | 16 | IL4R | rs1801275 | 27281901 | Ungenotyped | Genotyped |
| Replication | 16 | IL4R | rs1805016 | 27282428 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs1805014 | 27282530 | Genotyped | Ungenotyped |
| Replication | 16 | IL4R | rs2074570 | 27282658 | Ungenotyped | Genotyped |
| Replication | 16 | IL4R | rs8832 | 27283288 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs3024685 | 27284411 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs12102586 | 27285554 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs4787956 | 27285750 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs16976728 | 27289213 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs4787426 | 27292232 | Ungenotyped | Genotyped |
| Replication | 16 | IL4R | rs12445135 | 27293007 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs4787427 | 27293895 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs7191188 | 27296912 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs6498015 | 27299125 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs6498016 | 27299289 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs2382722 | 27300127 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs9944340 | 27301092 | Genotyped | Genotyped |
| Replication | 16 | IL4R | rs6498017 | 27302359 | Genotyped | Genotyped |
| Replication | 19 | CEACAM21 | rs2302188 | 46777713 | Genotyped | Genotyped |
| Replication | X | FOXP3 | rs11796927 | 48844942 | Genotyped | Genotyped |
| Replication | X | FOXP3 | rs2294016 | 48849899 | Genotyped | Genotyped |
| Replication | X | FOXP3 | rs5952519 | 48851586 | Genotyped | Genotyped |
| Replication | X | FOXP3 | rs3761548 | 48874612 | Genotyped | Genotyped |
| Replication | X | FOXP3 | rs4824747 | 48885394 | Genotyped | Genotyped |
| Replication | X | FOXP3 | rs5906761 | 48887202 | Genotyped | Genotyped |
| 3 | FINGERPRINT | rs11130795 | 60873474 | Ungenotyped | Genotyped | |
| 3 | FINGERPRINT | rs39639 | 124861224 | Ungenotyped | Genotyped | |
| 4 | FINGERPRINT | rs6834736 | 57035453 | Ungenotyped | Genotyped | |
| 4 | FINGERPRINT | rs6841061 | 186374692 | Ungenotyped | Genotyped | |
| 6 | FINGERPRINT | rs4870405 | 156367804 | Ungenotyped | Genotyped | |
| 8 | FINGERPRINT | rs2014286 | 16951496 | Ungenotyped | Genotyped | |
| 8 | FINGERPRINT | rs1367972 | 62166007 | Ungenotyped | Genotyped | |
| 9 | FINGERPRINT | rs12682834 | 87292377 | Ungenotyped | Genotyped | |
| 11 | FINGERPRINT | rs1025412 | 14202872 | Ungenotyped | Genotyped | |
| 12 | FINGERPRINT | rs10748087 | 66481362 | Ungenotyped | Genotyped | |
| 13 | FINGERPRINT | rs1408229 | 36702353 | Ungenotyped | Genotyped | |
| 13 | FINGERPRINT | rs2639486 | 82495935 | Ungenotyped | Genotyped | |
| 15 | FINGERPRINT | rs12909691 | 91645766 | Ungenotyped | Genotyped | |
| 16 | FINGERPRINT | rs8045964 | 80374234 | Ungenotyped | Genotyped | |
| 20 | FINGERPRINT | rs6038115 | 5209132 | Ungenotyped | Genotyped | |
| 20 | FINGERPRINT | rs6512586 | 47734553 | Ungenotyped | Genotyped |
Samples
DNA samples from members of 2324 ASP families obtained from nine cohorts were used for genotyping. The families selected consisted primarily of nuclear families with an ASP with T1D. A total of 9982 DNA samples were shipped. A total of 9985 samples were used in the genotyping on both platforms: 9982 production samples (including 339 QC duplicate samples) and 3 CEPH control samples. For the Illumina platform, 9479 of the production samples and 322 QC samples genotyped with >90% call rate on 367 SNPs. For the Sequenom platform, 9581 production samples and 315 QC samples genotyped at >90% call rate on 380 SNPs.
The initial QC procedure of the Coordinating Center consisted of reviewing the failed status of the SNPs and samples, based on reports from the genotyping facility. Using the production and duplicate QC samples, concordance rates were generated between the pairs. This rate was based on both samples having a called genotype for a given SNP. The total number of concordant SNPs was divided by the total number of SNPs where both samples had a called genotyped. ‘Missingness’ was also examined between the two samples. Samples that were discordant (that is concordance rate <96%) were reviewed within families to identify the sample with Mendelian consistency. For concordant samples, the sample that had the greatest number of called genotypes was preserved for analysis. If a production sample or QC sample failed genotyping, the sample that passed evaluation was preserved for analysis.
Genotypes from each of the two marker panels (Illumina and Sequenom) were reviewed initially as separate datasets. The results of each QC procedure were then compared across both analyses to detect similar (or different) problems. In each genotyping platform, there were 339 QC samples. In both panels, two (different) samples failed for both the production and QC genotyping. For the Illumina panel, nine samples failed the production sample but passed for the QC sample. For the Sequenom panel, 16 samples failed QC genotyping but passed for the production sample. Four failed samples were common to the two platforms. For the Illumina panel, 15 samples failed QC genotyping but passed the production sample. For the Sequenom panel, 21 samples failed QC genotyping but passed for the production sample.
The overall concordance rate in the Illumina platform between the production sample and QC sample was 98.6%. There were 10 samples with concordance <96%. Only one of these 10 samples had >80% of total SNPs genotyped. In the Sequenom platform, there were seven samples with concordance rate <96%. Three of these samples had >80% of total SNPs genotyped. Once the production and QC sample concordance and comparison estimates were made, family structures and genotypic data were used to check for Mendelian inconsistency, relationship misclassification, and existence of duplicate samples.
Families were examined for Mendelian inconsistencies to detect relationship misclassification using the Ped-Check12 software. After summarizing PedCheck results, the Coordinating Center enumerated ‘Mendelian Inconsistency Errors’ (MIE) within each family. If the total number of inconsistencies was >2% of the total number of SNPs, the family was considered to be problematic and individually reviewed. From these in-depth reviews, pedigrees were re-arranged, restructured, or individuals coded as missing all SNP genotypes. Results from both genotyping datasets were reviewed. As part of this QC procedure, individual SNPs were independently checked for excess MIE. If an SNP had MIE in >20% of families, the SNP was considered to be problematic and the entire set of SNP genotypes was coded as missing. SNPs with MIE counts of 10–20% were reviewed on an individual basis. To aid in detection of family structure problems for the MHC data, we used the PREST13 results from the T1DGC genome-wide linkage scans.6,8
The Coordinating Center reviewed pairwise comparisons within families and between families to detect potential duplicate samples. The identical by state (IBS) statistics for pairwise individuals were obtained using Graphical Relationship Representation software.14 For pairs of relatives that had IBS > 1.98, the data were reviewed to determine whether they were within families (that is twins or duplicate samples) or between families (that is same person belonging to two distinct families, multiple individuals common between two distinct families, or duplicate sample between families). In combination with the IBS information, MIE results were used to determine whether a sample switch or a duplicate sample had occurred. The Coordinating Center examined individuals and families across all genotyping datasets released earlier. Using these data, the Coordinating Center decided whether there were sample switches, relatedness issues, gender discrepancies, or duplicate samples (that is within families, across families, or twins). After all issues were resolved, datasets were assembled for final MIE checks and families were re-examined. Families that continued to exhibit high-MIE rates were removed from the dataset. The remaining families were deemed to have random MIE. A family that was deemed problematic and a reasonable solution was not available was completely removed from the analysis dataset. Once families were considered ‘clean,’ the family was included the final analysis data file (Table 2).
Table 2.
Description of the T1DGC Rapid Response genetic data
| T1DGC | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2008.07.RR | |||||||||||||
| Pedigree summary | |||||||||||||
| Data characteristics and preparation | |||||||||||||
| Source | DNA | Filtered ILMN | Filtered SQNM | Modifications |
|||||||||
| Pedigree changes |
Genotypes dropped |
||||||||||||
| New relationship | Added members | Samples switched | Sex difference | Ungenotyped | Problematic families removed | Duplicate families removed | Within family duplicates removed | Valid marker count ILMN | Valid marker count SQNM | ||||
| Asia-Pacific | 782 | 763 (97.6) | 756 (96.7) | 2 | 3 | 1 | 0 | 3 | 0 | 0 | 0 | 357 | 376 |
| BDA | 1808 | 1668 (92.3) | 1646 (91.0) | 5 | 2 | 2 | 3 | 50 | 3 | 5 | 1 | 357 | 377 |
| Danish | 686 | 678 (98.8) | 636 (92.7) | 4 | 1 | 1 | 0 | 6 | 1 | 0 | 0 | 357 | 377 |
| Europe | 1953 | 1941 (99.4) | 1898 (97.2) | 2 | 2 | 3 | 0 | 11 | 0 | 0 | 4 | 357 | 377 |
| HBDI | 2143 | 1959 (91.4) | 2042 (95.3) | 1 | 1 | 3 | 0 | 7 | 0 | 7 | 2 | 357 | 377 |
| North America | 1376 | 1323 (96.1) | 1301 (94.5) | 1 | 1 | 4 | 1 | 8 | 0 | 4 | 4 | 357 | 377 |
| United Kingdom | 484 | 442 (91.3) | 459 (94.8) | 0 | 0 | 0 | 2 | 8 | 0 | 2 | 6 | 357 | 377 |
| Joslin | 386 | 368 (95.3) | 335 (86.8) | 2 | 2 | 1 | 0 | 4 | 1 | 5 | 0 | 357 | 377 |
| Sardinian | 364 | 337 (92.6) | 339 (93.1) | 0 | 0 | 0 | 0 | 8 | 0 | 0 | 1 | 357 | 377 |
| Total | 9982 | 9479 (95.0) | 9412 (94.3) | 17 | 12 | 15 | 6 | 105 | 5 | 23 | 18 | ||
Abbreviations: BDA, British Dietetic Association; HBDI, Human Biological Data Interchange; TIDGC, Type I Diabetes Genetics Consortium.
Summary
The Coordinating Center for the T1DGC performed QC and initial family-based association analyses on data from two genotyping platforms (Illumina Golden Gate and Sequenom iPLEX) for the T1DGC Rapid Response project. A random sample of blind duplicates was evaluated for QC. DNA samples collected from participants were shipped to the genotyping laboratory from several T1DGC DNA Repository sites. Quality checks, including examination of plate-panel yield, marker yield, Hardy–Weinberg equilibrium, mismatch error rate, Mendelian error rate, and allele distribution across plates, were performed. Genotypes from 2324 families within nine cohorts were genotyped for 21 candidate genes (384 SNPs). The final data consisted of genotypes from 2297 families (9688 individuals) that enabled robust estimation of candidate gene effects on T1D risk.
Acknowledgments
This research uses resources provided by the Type I Diabetes Genetics Consortium, a collaborative clinical study sponsored by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), the National Institute of Allergy and Infectious Diseases (NIAID), the National Human Genome Research Institute (NHGRI), the National Institute of Child Health and Human Development (NICHD), and the Juvenile Diabetes Research Foundation International (JDRF), and supported by U01 DK062418. We appreciate the technical assistance of the entire CGA Illumina team as led by Jamie Moore, and of the Sequenom team (led by LZ), with particular thanks to Rob Borkowski and Cherylyn Smith. Genotyping was performed at the Broad Institute Center for Genotyping and Analysis is supported by grant U54 RR020278 from the National Center for Research Resources.
Footnotes
Conflict of interest
The authors declare no conflict of interest.
References
- 1.Davies JL, Kawaguchi Y, Bennett ST, Copeman JB, Cordell HJ, Pritchard LE, et al. A genome-wide search for human type 1 diabetes susceptibility genes. Nature. 1994;371:130–136. doi: 10.1038/371130a0. [DOI] [PubMed] [Google Scholar]
- 2.Ueda H, Howson JM, Esposito L, Heward J, Snook H, Chamberlain G, et al. Association of the T-cell regulatory gene CTLA4 with susceptibility to autoimmune disease. Nature. 2003;423:506–511. doi: 10.1038/nature01621. [DOI] [PubMed] [Google Scholar]
- 3.Bottini N, Musumeci L, Alonso A, Rahmouni S, Nika K, Rostamkhani M, et al. A functional variant of lymphoid tyrosine phosphatase is associated with type I diabetes. Nat Genet. 2004;36:337–338. doi: 10.1038/ng1323. [DOI] [PubMed] [Google Scholar]
- 4.Guo D, Li M, Zhang Y, Yang P, Eckenrode S, Hopkins D, et al. A functional variant of SUMO4, a new I kappa B alpha modifier, is associated with type 1 diabetes. Nat Genet. 2004;36:837–841. doi: 10.1038/ng1391. [DOI] [PubMed] [Google Scholar]
- 5.Noble JA, White AM, Lazzeroni LC, Valdes AM, Mirel DB, Reynolds R, et al. A polymorphism in the TCF7 gene, C883A, is associated with type 1 diabetes. Diabetes. 2003;52:1579–1582. doi: 10.2337/diabetes.52.6.1579. [DOI] [PubMed] [Google Scholar]
- 6.Cooper JD, Smyth DJ, Bailey R, Payne F, Downes K, Godfrey LM, et al. The candidate genes TAF5 L, TCF7, PDCD1, IL6 and ICAM1 cannot be excluded from having effects in type 1 diabetes. BMC Med Genet. 2007;8:71–85. doi: 10.1186/1471-2350-8-71. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Julier C, Akolkar B, Concannon P, Morahan G, Nierras C. Pugliese A and the Type I Diabetes Genetics Consortium. The Type I Diabetes Genetics Consortium ‘Rapid Response’ family-based candidate gene study: strategy, genes selection, and main outcome. Genes Immun. 2009;10(Suppl 1):S121–S127. doi: 10.1038/gene.2009.99. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Concannon P, Erlich HA, Julier C, Morahan G, Nerup J, Pociot F, et al. Type 1 diabetes: evidence for susceptibility loci from four genome-wide linkage scans in 1,435 multiplex families. Diabetes. 2005;54:2995–3001. doi: 10.2337/diabetes.54.10.2995. [DOI] [PubMed] [Google Scholar]
- 9.Concannon P, Chen WM, Julier C, Morahan G, Akolkar B, Erlich HA, et al. Genome-wide scan for linkage to type 1 diabetes in 2,496 multiplex families from the Type 1 Diabetes Genetics Consortium. Diabetes. 2009;58:1018–1022. doi: 10.2337/db08-1551. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Fine Mapping of the MHC Region for Type 1 Diabetes Genes. Proceedings of the Type 1 Diabetes Genetics Consortium MHC Fine Mapping Workshop; Washington, DC. 27–28 August 2007. . [Google Scholar]; Diabetes Obes Metab. 2009;11(Suppl 1):1–109. doi: 10.1111/j.1463-1326.2008.00996.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.de Bakker PIW, Yelensky R, Pe’er I, Gabriel SB, Daly MJ, Altshuler D. Efficiency and power in genetic association studies. Nat Genet. 2005;37:1217–1223. doi: 10.1038/ng1669. [DOI] [PubMed] [Google Scholar]
- 12.O’Connell JR, Weeks DE. PedCheck: a program for identifying marker typing incompatibilities in linkage analysis. Am J Hum Genet. 1998;63:259–266. doi: 10.1086/301904. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.McPeek MS, Sun L. Statistical tests for detection of misspecified relationships by use of genome-screen data. Am J Hum Genet. 2000;66:1076–1094. doi: 10.1086/302800. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Abecasis GR, Cherny SS, Cookson WO, Cardon LR. GRR: graphical representation of relationship errors. Bioinformatics. 2001;17:742–743. doi: 10.1093/bioinformatics/17.8.742. [DOI] [PubMed] [Google Scholar]