Trans-ancestral studies fine map the SLE-susceptibility locus TNFSF4.
We previously established an 80 kb haplotype upstream of TNFSF4 as a susceptibility locus in the autoimmune disease SLE. SLE-associated alleles at this locus are associated with inflammatory disorders, including atherosclerosis and ischaemic stroke. In Europeans, the TNFSF4 causal variants have rema...
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2013-01-01
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| Series: | PLoS Genetics |
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| author | Harinder Manku Carl D Langefeld Sandra G Guerra Talat H Malik Marta Alarcon-Riquelme Juan-Manuel Anaya Sang-Cheol Bae Susan A Boackle Elizabeth E Brown Lindsey A Criswell Barry I Freedman Patrick M Gaffney Peter A Gregersen Joel M Guthridge Sang-Hoon Han John B Harley Chaim O Jacob Judith A James Diane L Kamen Kenneth M Kaufman Jennifer A Kelly Javier Martin Joan T Merrill Kathy L Moser Timothy B Niewold So-Yeon Park Bernardo A Pons-Estel Amr H Sawalha R Hal Scofield Nan Shen Anne M Stevens Celi Sun Gary S Gilkeson Jeff C Edberg Robert P Kimberly Swapan K Nath Betty P Tsao Tim J Vyse |
| author_facet | Harinder Manku Carl D Langefeld Sandra G Guerra Talat H Malik Marta Alarcon-Riquelme Juan-Manuel Anaya Sang-Cheol Bae Susan A Boackle Elizabeth E Brown Lindsey A Criswell Barry I Freedman Patrick M Gaffney Peter A Gregersen Joel M Guthridge Sang-Hoon Han John B Harley Chaim O Jacob Judith A James Diane L Kamen Kenneth M Kaufman Jennifer A Kelly Javier Martin Joan T Merrill Kathy L Moser Timothy B Niewold So-Yeon Park Bernardo A Pons-Estel Amr H Sawalha R Hal Scofield Nan Shen Anne M Stevens Celi Sun Gary S Gilkeson Jeff C Edberg Robert P Kimberly Swapan K Nath Betty P Tsao Tim J Vyse |
| author_sort | Harinder Manku |
| collection | DOAJ |
| description | We previously established an 80 kb haplotype upstream of TNFSF4 as a susceptibility locus in the autoimmune disease SLE. SLE-associated alleles at this locus are associated with inflammatory disorders, including atherosclerosis and ischaemic stroke. In Europeans, the TNFSF4 causal variants have remained elusive due to strong linkage disequilibrium exhibited by alleles spanning the region. Using a trans-ancestral approach to fine-map the locus, utilising 17,900 SLE and control subjects including Amerindian/Hispanics (1348 cases, 717 controls), African-Americans (AA) (1529, 2048) and better powered cohorts of Europeans and East Asians, we find strong association of risk alleles in all ethnicities; the AA association replicates in African-American Gullah (152,122). The best evidence of association comes from two adjacent markers: rs2205960-T (P=1.71 × 10(-34) , OR=1.43[1.26-1.60]) and rs1234317-T (P=1.16 × 10(-28) , OR=1.38[1.24-1.54]). Inference of fine-scale recombination rates for all populations tested finds the 80 kb risk and non-risk haplotypes in all except African-Americans. In this population the decay of recombination equates to an 11 kb risk haplotype, anchored in the 5' region proximal to TNFSF4 and tagged by rs2205960-T after 1000 Genomes phase 1 (v3) imputation. Conditional regression analyses delineate the 5' risk signal to rs2205960-T and the independent non-risk signal to rs1234314-C. Our case-only and SLE-control cohorts demonstrate robust association of rs2205960-T with autoantibody production. The rs2205960-T is predicted to form part of a decameric motif which binds NF-κBp65 with increased affinity compared to rs2205960-G. ChIP-seq data also indicate NF-κB interaction with the DNA sequence at this position in LCL cells. Our research suggests association of rs2205960-T with SLE across multiple groups and an independent non-risk signal at rs1234314-C. rs2205960-T is associated with autoantibody production and lymphopenia. Our data confirm a global signal at TNFSF4 and a role for the expressed product at multiple stages of lymphocyte dysregulation during SLE pathogenesis. We confirm the validity of trans-ancestral mapping in a complex trait. |
| format | Article |
| id | doaj-art-b2196afc1ed34573a4882b40747d22a9 |
| institution | OA Journals |
| issn | 1553-7390 1553-7404 |
| language | English |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
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| series | PLoS Genetics |
| spelling | doaj-art-b2196afc1ed34573a4882b40747d22a92025-08-20T02:30:39ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042013-01-0197e100355410.1371/journal.pgen.1003554Trans-ancestral studies fine map the SLE-susceptibility locus TNFSF4.Harinder MankuCarl D LangefeldSandra G GuerraTalat H MalikMarta Alarcon-RiquelmeJuan-Manuel AnayaSang-Cheol BaeSusan A BoackleElizabeth E BrownLindsey A CriswellBarry I FreedmanPatrick M GaffneyPeter A GregersenJoel M GuthridgeSang-Hoon HanJohn B HarleyChaim O JacobJudith A JamesDiane L KamenKenneth M KaufmanJennifer A KellyJavier MartinJoan T MerrillKathy L MoserTimothy B NiewoldSo-Yeon ParkBernardo A Pons-EstelAmr H SawalhaR Hal ScofieldNan ShenAnne M StevensCeli SunGary S GilkesonJeff C EdbergRobert P KimberlySwapan K NathBetty P TsaoTim J VyseWe previously established an 80 kb haplotype upstream of TNFSF4 as a susceptibility locus in the autoimmune disease SLE. SLE-associated alleles at this locus are associated with inflammatory disorders, including atherosclerosis and ischaemic stroke. In Europeans, the TNFSF4 causal variants have remained elusive due to strong linkage disequilibrium exhibited by alleles spanning the region. Using a trans-ancestral approach to fine-map the locus, utilising 17,900 SLE and control subjects including Amerindian/Hispanics (1348 cases, 717 controls), African-Americans (AA) (1529, 2048) and better powered cohorts of Europeans and East Asians, we find strong association of risk alleles in all ethnicities; the AA association replicates in African-American Gullah (152,122). The best evidence of association comes from two adjacent markers: rs2205960-T (P=1.71 × 10(-34) , OR=1.43[1.26-1.60]) and rs1234317-T (P=1.16 × 10(-28) , OR=1.38[1.24-1.54]). Inference of fine-scale recombination rates for all populations tested finds the 80 kb risk and non-risk haplotypes in all except African-Americans. In this population the decay of recombination equates to an 11 kb risk haplotype, anchored in the 5' region proximal to TNFSF4 and tagged by rs2205960-T after 1000 Genomes phase 1 (v3) imputation. Conditional regression analyses delineate the 5' risk signal to rs2205960-T and the independent non-risk signal to rs1234314-C. Our case-only and SLE-control cohorts demonstrate robust association of rs2205960-T with autoantibody production. The rs2205960-T is predicted to form part of a decameric motif which binds NF-κBp65 with increased affinity compared to rs2205960-G. ChIP-seq data also indicate NF-κB interaction with the DNA sequence at this position in LCL cells. Our research suggests association of rs2205960-T with SLE across multiple groups and an independent non-risk signal at rs1234314-C. rs2205960-T is associated with autoantibody production and lymphopenia. Our data confirm a global signal at TNFSF4 and a role for the expressed product at multiple stages of lymphocyte dysregulation during SLE pathogenesis. We confirm the validity of trans-ancestral mapping in a complex trait.https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1003554&type=printable |
| spellingShingle | Harinder Manku Carl D Langefeld Sandra G Guerra Talat H Malik Marta Alarcon-Riquelme Juan-Manuel Anaya Sang-Cheol Bae Susan A Boackle Elizabeth E Brown Lindsey A Criswell Barry I Freedman Patrick M Gaffney Peter A Gregersen Joel M Guthridge Sang-Hoon Han John B Harley Chaim O Jacob Judith A James Diane L Kamen Kenneth M Kaufman Jennifer A Kelly Javier Martin Joan T Merrill Kathy L Moser Timothy B Niewold So-Yeon Park Bernardo A Pons-Estel Amr H Sawalha R Hal Scofield Nan Shen Anne M Stevens Celi Sun Gary S Gilkeson Jeff C Edberg Robert P Kimberly Swapan K Nath Betty P Tsao Tim J Vyse Trans-ancestral studies fine map the SLE-susceptibility locus TNFSF4. PLoS Genetics |
| title | Trans-ancestral studies fine map the SLE-susceptibility locus TNFSF4. |
| title_full | Trans-ancestral studies fine map the SLE-susceptibility locus TNFSF4. |
| title_fullStr | Trans-ancestral studies fine map the SLE-susceptibility locus TNFSF4. |
| title_full_unstemmed | Trans-ancestral studies fine map the SLE-susceptibility locus TNFSF4. |
| title_short | Trans-ancestral studies fine map the SLE-susceptibility locus TNFSF4. |
| title_sort | trans ancestral studies fine map the sle susceptibility locus tnfsf4 |
| url | https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1003554&type=printable |
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