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Idiopathic achalasia is a severe motility disorder of the esophagus and is characterized by a failure of the lower esophageal sphincter to relax due to a loss of neurons in the myenteric plexus. Most recently, we identified an eight-amino-acid insertion in the cytoplasmic tail of HLA-DQβ1 as strong achalasia risk factor in a sample set from Central Europe, Italy and Spain. Here, we tested whether the HLA-DQβ1 insertion also confers achalasia risk in the Polish and Swedish population. We could replicate the initial findings and the insertion shows strong achalasia association in both samples (Poland P=1.84 × 10−04, Sweden P=7.44 × 10−05). Combining all five European data sets – Central Europe, Italy, Spain, Poland and Sweden – the insertion is achalasia associated with Pcombined=1.67 × 10−35. In addition, we observe that the frequency of the insertion shows a geospatial north-south gradient. The insertion is less common in northern (around 6-7% in patients and 2% in controls from Sweden and Poland) compared with southern Europeans (~16% in patients and 8% in controls from Italy) and shows a stronger attributable risk in the southern European population. Our study provides evidence that the prevalence of achalasia may differ between populations.
The HLA-DQβ1 insertion is a strong achalasia risk factor and displays a geospatial north-south gradient among Europeans
Jessica Becker,1,2,32 Stephan L Haas,3,32 Anna Mokrowiecka,4,32 Justyna Wasielica-Berger,5 Zeeshan Ateeb,3 Jonna Bister,3 Peter Elbe,3 Marek Kowalski,4 Magdalena Gawron-Kiszka,6 Marek Majewski,7 Agata Mulak,8 Maria Janiak,9 Mira M Wouters,10 Till Schwammle,1,2 Timo Hess,1,2 Lothar Veits,11 Stefan Niebisch,12 Jose L Santiago,13 Antonio Ruiz de Leon,14 Julio Perez de la Serna,14 Elena Urcelay,13 Vito Annese,15 Anna Latiano,16 Uberto Fumagalli,17 Riccardo Rosati,18 Luigi Laghi,19 Rosario Cuomo,20 Frank Lenze,21 Giovanni Sarnelli,20 Michaela Muller,22 Burkhard HA von Rahden,23 Cisca Wijmenga,24 Hauke Lang,25 Kamila Czene,26 Per Hall,26 Paul IW de Bakker,27,28 Michael Vieth,11 Markus M Nothen,1,2 Henning G Schulz,29 Krystian Adrych,9 Anita Gasiorowska,4 Leszek Paradowski,8 Grzegorz Wallner,7 Guy E Boeckxstaens,10 Ines Gockel,12 Marek Hartleb,6 Srdjan Kostic,3 Anna Dziurkowska-Marek,6 Mats Lindblad,3 Magnus Nilsson,3 Michael Knapp,30 Anders Thorell,31 Tomasz Marek,6 Andrzej Dabrowski,5 Ewa Małecka-Panas,4,32 and Johannes Schumacher1,2,*,32
Alopecia areata (AA) is a common hair loss disorder, which is thought to be a tissue-specific autoimmune disease. Previous research has identified a few AA susceptibility genes, most of which are implicated in autoimmunity. To identify new genetic variants and further elucidate the genetic basis of AA, we performed a genome-wide association study using the strategy of pooled DNA genotyping (729 cases, 656 controls). The strongest association was for variants in the HLA region, which confirms the validity of the pooling strategy. The selected top 61 single-nucleotide polymorphisms (SNPs) were analyzed in an independent replication sample (454 cases, 1364 controls). Only one SNP outside of the HLA region (rs304650) showed significant association. This SNP was then analyzed in a second independent replication sample (537 cases, 657 controls). The finding was not replicated on a significant level, but showed the same tendency. A combined analysis of the two replication samples was then performed, and the SNP rs304650 showed significant association with P=3.43 × 10−4 (OR=1.24 (1.10-1.39)). This SNP maps to an intronic region of the SPATA5 (spermatogenesis-associated protein 5) gene on chromosome 4. The results therefore suggest the SPATA5 locus is a new susceptibility locus for AA.
alopecia areata, genome-wide association study, autoimmunity, hair loss
Genome-wide pooling approach identifies SPATA5 as a new susceptibility locus for alopecia areata
Lina M Forstbauer,1,20 Felix F Brockschmidt,1,2,20 Valentina Moskvina,3 Christine Herold,4 Silke Redler,1 Alexandra Herzog,1 Axel M Hillmer,5 Christian Meesters,4,6 Stefanie Heilmann,1,2 Florian Albert,1 Margrieta Alblas,1,2 Sandra Hanneken,7 Sibylle Eigelshoven,7 Kathrin A Giehl,8 Dagny Jagielska,1,9 Ulrike Blume-Peytavi,9 Natalie Garcia Bartels,9 Jennifer Kuhn,10,11,12 Hans Christian Hennies,10,11,12 Matthias Goebeler,13 Andreas Jung,13 Wiebke K Peitsch,14 Anne-Katrin Kortum,15 Ingrid Moll,15 Roland Kruse,16 Gerhard Lutz,17 Hans Wolff,7 Bettina Blaumeiser,18 Markus Bohm,19 George Kirov,3 Tim Becker,4,6 Markus M Nothen,1,2 and Regina C Betz1,*
We aimed at identifying transcripts whose expression is regulated by a SNP-SNP interaction. Out of 47 294 expression phenotypes we used 3107 transcripts that survived an extensive quality control and 86 613 linkage disequilibrium-pruned SNP markers that have been genotyped in 210 individuals. For each transcript we defined cis-SNPs, tested them for epistasis with all trans-SNPs, and corrected all observed cis-trans-regulated expression effects for multiple testing. We determined that the expression of about 15% of all included transcripts is regulated by a significant two-locus interaction, which is more than expected (P=2.86 × 10−144). Our findings suggest further that cis-markers with so called ‘marginal effects’ are more likely to be involved in two-locus gene regulation than expected (P=8.27 × 10−05), although the majority of interacting cis-markers showed no one-locus regulation. Furthermore, we found evidence that gene-mediated trans-effects are not a major source of epistasis, as no enrichment of genes has been found in close vicinity of trans-SNPs. In addition, our data support the notion that neither chromosomal regions nor cellular processes are enriched in epistatic interactions. Finally, some of the cis-trans regulated genes have been found in genome-wide association studies, which might be interesting for follow-up studies of the corresponding disorders. In summary, our results provide novel insights into the complex genome-transcriptome regulation.
eQTLs, epistasis, interaction, cis-regulation, trans-regulation
A systematic eQTL study of cis-trans epistasis in 210 HapMap individuals
Jessica Becker,1,2,4 Jens R Wendland,3,4 Britta Haenisch,1,2 Markus M Nothen,1,2 and Johannes Schumacher2,*