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| Status |
Public on Oct 15, 2015 |
| Title |
Combination testing using a single MSH5 variant alongside HLA haplotypes improves coeliac disease risk prediction in the Polish population |
| Organism |
Homo sapiens |
| Experiment type |
SNP genotyping by SNP array
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| Summary |
Background. Assessment of non-HLA variants alongside standard HLA testing was previously shown to improve the identification of potential coeliac disease (CD) patients. We intended to identify new genetic variants associated with CD in the Polish population that would improve CD risk prediction when used alongside HLA haplotype analysis.
Results. Association analysis using four HLA-tagging SNPs showed that, as was found in other populations, positive predicting genotypes (HLA-DQ2.5/DQ2.5, HLA-DQ2.5/DQ2.2, and HLA-DQ2.5/DQ8) were found at higher frequencies in CD patients than in healthy control individuals in the Polish population. Both CD-associated SNPs discovered by GWAS were found in the CD susceptibility region, confirming the previously-determined association of the major histocompatibility (MHC) region with CD pathogenesis. The two most significant SNPs from the GWAS were rs9272346 (HLA-dependent; localized within 1 Kb of DQA1) and rs3130484 (HLA-independent; mapped to MSH5). Specificity of CD prediction using the four HLA-tagging SNPs achieved 92.9%, but sensitivity was only 45.5%. However, when a testing combination of the HLA-tagging SNPs and the MSH5 SNP was used, specificity decreased to 80%, and sensitivity increased to 74%.
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| Overall design |
DNA samples of 336 CD and 264 unrelated healthy controls were used to create DNA pools (9 and 6, respectively) for a genome wide association study (GWAS). GWAS findings were validated with individual HLA tag singlenucleotide polymorphism (SNP) typing of 473 patients and 714 healthy controls.
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| Contributor(s) |
Paziewska A, Cukrowska B, Dabrowska M, Goryca K, Piatkowska M, Kluska A, Mikula M, Karczmarski J, Oralewska B, Rybak A, Socha J, Balabas A, Zeber-Lubecka N, Ambrozkiewicz F, Konopka E, Trojanowska I, Zagroba M, Szperl M, Ostrowski J |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Jan 29, 2015 |
| Last update date |
Nov 27, 2018 |
| Contact name |
Krzysztof Goryca |
| Organization name |
Uniwersytet Warszawski
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| Department |
CeNT
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| Street address |
Banacha 2c
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| City |
Warszawa |
| ZIP/Postal code |
02-097 |
| Country |
Poland |
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| Platforms (1) |
| GPL6801 |
[GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array |
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| Samples (15)
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| Relations |
| BioProject |
PRJNA273961 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE65424_RAW.tar |
369.3 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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