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Genome-wide association and targeted analysis of copy number variants with psoriatic arthritis in German patients.

Abstract Psoriatic Arthritis (PsA) is a chronic inflammatory disease of the joints. PsA is etiologically complex, and 11 susceptibility loci have been identified so far. Most of these overlap with loci associated with psoriasis vulgaris (PsV), the most common psoriatic skin manifestation which is also frequently seen in PsA patients. In addition, two copy number variants (CNVs) are associated with PsV, one of which, located within the LCE3 gene cluster, is also associated with PsA. Finally, an intergenic deletion has been reported as a PsA-specific CNV.
PMID
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Authors

Mayor MeshTerms
Keywords

Copy number variant

Genome-wide association study

Psoriasis susceptibility loci

Psoriatic arthritis

SNP arrays

TRB

Journal Title bmc medical genetics
Publication Year Start




PMID- 28835222
OWN - NLM
STAT- In-Process
DA  - 20170824
LR  - 20170824
IS  - 1471-2350 (Electronic)
IS  - 1471-2350 (Linking)
VI  - 18
IP  - 1
DP  - 2017 Aug 23
TI  - Genome-wide association and targeted analysis of copy number variants with
      psoriatic arthritis in German patients.
PG  - 92
LID - 10.1186/s12881-017-0447-y [doi]
AB  - BACKGROUND: Psoriatic Arthritis (PsA) is a chronic inflammatory disease of the
      joints. PsA is etiologically complex, and 11 susceptibility loci have been
      identified so far. Most of these overlap with loci associated with psoriasis
      vulgaris (PsV), the most common psoriatic skin manifestation which is also
      frequently seen in PsA patients. In addition, two copy number variants (CNVs) are
      associated with PsV, one of which, located within the LCE3 gene cluster, is also 
      associated with PsA. Finally, an intergenic deletion has been reported as a
      PsA-specific CNV. METHODS: We performed a genome-wide association study (GWAS) of
      CNVs in PsA and assessed the contribution to disease risk by CNVs at known
      psoriasis susceptibility loci. RESULTS: After stringent quality assessment and
      validation of CNVs of the GWAS with an alternative quantitative method, two
      significantly associated CNVs remained, one near UXS1, the other one at the TRB
      locus. However, MLPA analysis did not confirm the CN state in ~1/3 of
      individuals, and an analysis of an independent case-control-study failed to
      confirm the initial associations. Furthermore, detailed PCR-based analysis of the
      sequence at TRB revealed the existence of a more complex genomic sequence most
      accurately represented by freeze hg18 which accordingly failed to confirm the
      hg19 sequence. Only rare CNVs were detected at psoriasis susceptibility loci. At 
      three of 12 susceptibility loci with CNVs (CSMD1, IL12B, RYR2), CN variability
      was confirmed independently by MLPA. Overall, the rate of CNV confirmation by
      MLPA was strongly dependent upon CNV type, CNV size and the number of array
      markers involved in a CNV. CONCLUSION: Although we identified PsA associations at
      several loci and confirmed that the common CNVs at these sites were real, ~1/3 of
      the common CNV states could not be reproduced. Furthermore, replication analysis 
      failed to confirm the original association. Furthermore, SNP array-based analyses
      of CNVs were found to be more reliable for deletions than duplications,
      independent of the respective CNV allele frequency. CNVs are thus good candidate 
      disease variants, while the methods to detect them should be applied cautiously
      and reproduced by an independent method.
FAU - Uebe, Steffen
AU  - Uebe S
AD  - Institute of Human Genetics, Friedrich-Alexander-Universitat Erlangen-Nurnberg
      (FAU), Schwabachanlage 10, 91054, Erlangen, Germany.
FAU - Ehrlicher, Maria
AU  - Ehrlicher M
AD  - Institute of Human Genetics, Friedrich-Alexander-Universitat Erlangen-Nurnberg
      (FAU), Schwabachanlage 10, 91054, Erlangen, Germany.
FAU - Ekici, Arif Bulent
AU  - Ekici AB
AD  - Institute of Human Genetics, Friedrich-Alexander-Universitat Erlangen-Nurnberg
      (FAU), Schwabachanlage 10, 91054, Erlangen, Germany.
FAU - Behrens, Frank
AU  - Behrens F
AD  - Division of Rheumatology and IME Fraunhofer Project Group Translational Medicine 
      & Pharmacology, Goethe University, Frankfurt/Main, Germany.
FAU - Bohm, Beate
AU  - Bohm B
AD  - Division of Rheumatology and IME Fraunhofer Project Group Translational Medicine 
      & Pharmacology, Goethe University, Frankfurt/Main, Germany.
FAU - Homuth, Georg
AU  - Homuth G
AD  - Interfaculty Institute for Genetics and Functional Genomics, University Medicine 
      and Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany.
FAU - Schurmann, Claudia
AU  - Schurmann C
AD  - Interfaculty Institute for Genetics and Functional Genomics, University Medicine 
      and Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany.
FAU - Volker, Uwe
AU  - Volker U
AD  - Interfaculty Institute for Genetics and Functional Genomics, University Medicine 
      and Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany.
FAU - Junger, Michael
AU  - Junger M
AD  - Clinic of Dermatology, University of Greifswald, Greifswald, Germany.
FAU - Nauck, Matthias
AU  - Nauck M
AD  - Institute of Clinical Chemistry and Laboratory Medicine, University of
      Greifswald, Greifswald, Germany.
FAU - Volzke, Henry
AU  - Volzke H
AD  - Institute for Community Medicine, University of Greifswald, Greifswald, Germany.
FAU - Traupe, Heiko
AU  - Traupe H
AD  - Department of Dermatology, University of Munster, Munster, Germany.
FAU - Krawczak, Michael
AU  - Krawczak M
AD  - Institute for Medical Informatics and Statistics, Christian-Albrechts University 
      Kiel, Kiel, Germany.
FAU - Burkhardt, Harald
AU  - Burkhardt H
AD  - Division of Rheumatology and IME Fraunhofer Project Group Translational Medicine 
      & Pharmacology, Goethe University, Frankfurt/Main, Germany.
FAU - Reis, Andre
AU  - Reis A
AD  - Institute of Human Genetics, Friedrich-Alexander-Universitat Erlangen-Nurnberg
      (FAU), Schwabachanlage 10, 91054, Erlangen, Germany.
FAU - Huffmeier, Ulrike
AU  - Huffmeier U
AUID- ORCID: http://orcid.org/0000-0001-6448-4671
AD  - Institute of Human Genetics, Friedrich-Alexander-Universitat Erlangen-Nurnberg
      (FAU), Schwabachanlage 10, 91054, Erlangen, Germany.
      [email protected]
LA  - eng
PT  - Journal Article
DEP - 20170823
PL  - England
TA  - BMC Med Genet
JT  - BMC medical genetics
JID - 100968552
OTO - NOTNLM
OT  - Copy number variant
OT  - Genome-wide association study
OT  - Psoriasis susceptibility loci
OT  - Psoriatic arthritis
OT  - SNP arrays
OT  - TRB
EDAT- 2017/08/25 06:00
MHDA- 2017/08/25 06:00
CRDT- 2017/08/25 06:00
PHST- 2016/03/04 [received]
PHST- 2017/07/31 [accepted]
AID - 10.1186/s12881-017-0447-y [doi]
AID - 10.1186/s12881-017-0447-y [pii]
PST - epublish
SO  - BMC Med Genet. 2017 Aug 23;18(1):92. doi: 10.1186/s12881-017-0447-y.