Immunochip analyses identify a novel risk locus for primary biliary cirrhosis at 13q14, multiple independent associations at four established risk loci and epistasis between 1p31 and 7q32 risk variants
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To further characterize the genetic basis of primary biliary cirrhosis (PBC), we genotyped 2426 PBC patients and 5731 unaffected controls from three independent cohorts using a single nucleotide polymorphism (SNP) array (Immunochip) enriched for autoimmune disease risk loci. Meta-analysis of the genotype data sets identified a novel disease-associated locus near the TNFSF11 gene at 13q14, provided evidence for association at six additional immune-related loci not previously implicated in PBC and confirmed associations at 19 of 22 established risk loci. Results of conditional analyses also provided evidence for multiple independent association signals at four risk loci, with haplotype analyses suggesting independent SNP effects at the 2q32 and 16p13 loci, but complex haplotype driven effects at the 3q25 and 6p21 loci. By imputing classical HLA alleles from this data set, four class II alleles independently contributing to the association signal from this region were identified. Imputation of genotypes at the non-HLA loci also provided additional associations, but none with stronger effects than the genotyped variants. An epistatic interaction between the IL12RB2 risk locus at 1p31and the IRF5 risk locus at 7q32 was also identified and suggests a complementary effect of these loci in predisposing to disease. These data expand the repertoire of genes with potential roles in PBC pathogenesis that need to be explored by follow-up biological studies.
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Genetic contribution to PBC is supported by higher monozygotic than dizygotic twin concordance and by HLA allele associations that vary by ethnicity.
“In addition to the high concordance among monozygotic twins compared with dizygotic twins with PBC (5) , the strong association with human leukocyte antigen alleles, which vary by ethnicity, supports a genetic cause of inherited risk.(12)(13)(14)(15)(16)(17)(18)(19)(20)”
From Primary Biliary Cholangitis: 2018 Practice Guidance from the American Association for the Study of Liver Diseases (2019) · cites this paper as [12]
The presence of genetic susceptibility is supported by the increased concordance rate in monozygotic twins and confirmed by the identification of significant numbers of associated genetic loci in GWAS and other large-scale genetic approaches.
“The presence of genetic susceptibility is supported by the increased concordance rate in monozygotic twins44 and confirmed by the identification of significant numbers of associated genetic loci in Genome Wide Association Studies (GWAS) and other large-scale, high-quality genetic approaches.45–54”
From The British Society of Gastroenterology/UK-PBC primary biliary cholangitis treatment and management guidelines (2018) · cites this paper as [50]
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- Authors
- Juran, B. D., Hirschfield, G. M., Invernizzi, P., Atkinson, E. J., Li, Y., Xie, G., Kosoy, R., Ransom, M., Sun, Y., Bianchi, I., Schlicht, E. M., Lleo, A., Coltescu, C., Bernuzzi, F., Podda, M., Lammert, C., Shigeta, R., Chan, L. L., Balschun, T., Marconi, M., Cusi, D., Heathcote, E. J., Mason, A. L., Myers, R. P., Milkiewicz, P., Odin, J. A., Luketic, V. A., Bacon, B. R., Bodenheimer, H. C., Liakina, V., Vincent, C., Levy, C., Franke, A., Gregersen, P. K., Bossa, F., Gershwin, M. E., deAndrade, M., Amos, C. I., Lazaridis, K. N., Seldin, M. F., & Siminovitch, K. A.
- Affiliations
- Mayo Clinic (US)
- University of Birmingham (GB)
- IRCCS Humanitas Research Hospital (IT)
- The University of Texas MD Anderson Cancer Center (US)
- University of California, Davis (US)
- University Health Network (CA)
- Christian-Albrechts-Universität zu Kiel (DE)
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico (IT)
- University of Milan (IT)
- University of Alberta (CA)
- University of Calgary (CA)
- Pomeranian Medical University (PL)
- Icahn School of Medicine at Mount Sinai (US)
- Virginia Commonwealth University (US)
- Saint Louis University (US)
- Albert Einstein College of Medicine (US)
- Vilnius University (LT)
- Hôpital Saint-Luc (CA)
- University of Miami (US)
- Northwell Health (US)
- Istituti di Ricovero e Cura a Carattere Scientifico (IT)
- Mount Sinai Hospital (CA)
- Corresponding author
- Siminovitch, Katherine A.
- ORCID
- Hirschfield, Gideon M.
- Invernizzi, Pietro
- Atkinson, Elizabeth J.
- Li, Yafang
- Kosoy, Roman
- Sun, Ye
- Bernuzzi, Francesca
- Podda, Mauro
- Lammert, Craig
- Chan, Landon L.
- Mason, Andrew L.
- Milkiewicz, Piotr
- Odin, Joseph A.
- Luketic, Velimir A.
- Liakina, Valentina
- Vincent, Catherine
- Levy, Cynthia
- Gregersen, Peter K.
- Bossa, Fabrizio
- Amos, Christopher I.
- Lazaridis, Konstantinos N.
- Siminovitch, Katherine A.
- Venue
- Human Molecular Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-08-29
- Volume
- 21
- Issue
- 23
- Pages
- 5209-5221
- ISSN
- 0964-6906 (ISSN-L)
- 1460-2083
- PMC
- PMC3490520
- OpenAlex
- W2122008473
- Cited by
- 150
- References
- 53
- Citations by year
- 2026: 1 · 2025: 6 · 2024: 7 · 2023: 3 · 2022: 8 · 2021: 9 · 2020: 10 · 2019: 11 · 2018: 20 · 2017: 10 · 2016: 8 · 2015: 17 · 2014: 22 · 2013: 17 · 2012: 1
- FWCI
- 2.28
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- public-domain
- Locations
- Human Molecular Genetics (publishedVersion, public-domain)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- CINECA IRIS Institutial research information system (University of Pisa) (submittedVersion)
- ArTS Archivio della ricerca di Trieste (University of Trieste https://www.units.it/) (submittedVersion)
- BOA (University of Milano-Bicocca) (submittedVersion)
- Archivio istituzionale della ricerca (Alma Mater Studiorum Università di Bologna) (submittedVersion)
- Florence Research (University of Florence) (submittedVersion)
- IRIS UNIMORE (University of Modena and Reggio Emilia) (submittedVersion, cc-by)
- IRIS Research product catalog (Sapienza University of Rome) (submittedVersion)
- Institutional Research Information System University of Turin (University of Turin) (submittedVersion)
- Università Politecnica delle Marche (Università Politecnica delle Marche) (submittedVersion)
- University of Birmingham Research Portal (University of Birmingham) (submittedVersion)
- Padua Research Archive (University of Padova) (submittedVersion, other-oa)
- Funders
- National Institutes of Health (UL1TR000058)
- Canadian Institutes of Health Research (MOP74621)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK080670, R01 DK 80670, R01DK056839, R01DK091823)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (R01AR044422, AR-44422)
- National Center for Advancing Translational Sciences
- Topics
- Health Sciences › Medicine › Hepatology › Liver Diseases and Immunity
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Inflammatory Bowel Disease
- Keywords
- primary biliary cirrhosis, genetic susceptibility, 13q14, TNFSF11, IL12RB2, IRF5, epistasis, haplotype analysis, HLA class II alleles, 6p21
- MeSH terms
- Alleles, Chromosomes, Human, Pair 1, Chromosomes, Human, Pair 13, Chromosomes, Human, Pair 7, Epistasis, Genetic, Gene Frequency, Genotype, HLA Antigens, Humans, Liver Cirrhosis, Biliary, Case-Control Studies, Genetic Predisposition to Disease, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Genetic Loci
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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