OpenLB
Open Library of Bioscience
Advanced Search
Nucleic acids research
Jan 05, 2024;52 (D1): D871-D881.

COLOCdb: a comprehensive resource for multi-model colocalization of complex traits.

Siyu Pan, Hongen Kang, Xinxuan Liu, Shuhua Li, Peng Yang, Mingqiu Wu, Na Yuan, Shiqi Lin, Qiwen Zheng, Peilin Jia
Author Information
  1. Siyu Pan: CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China. ORCID
  2. Hongen Kang: CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China. ORCID
  3. Xinxuan Liu: CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China. ORCID
  4. Shuhua Li: CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  5. Peng Yang: CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  6. Mingqiu Wu: CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  7. Na Yuan: CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China. ORCID
  8. Shiqi Lin: CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  9. Qiwen Zheng: CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  10. Peilin Jia: CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China. ORCID
PMID: 37941154 DOI: 10.1093/nar/gkad939

Abstract

Large-scale genome-wide association studies (GWAS) have provided profound insights into complex traits and diseases. Yet, deciphering the fine-scale molecular mechanisms of how genetic variants manifest to cause the phenotypes remains a daunting task. Here, we present COLOCdb (https://ngdc.cncb.ac.cn/colocdb), a comprehensive genetic colocalization database by integrating more than 3000 GWAS summary statistics and 13 types of xQTL to date. By employing two representative approaches for the colocalization analysis, COLOCdb deposits results from three key components: (i) GWAS-xQTL, pair-wise colocalization between GWAS loci and different types of xQTL, (ii) GWAS-GWAS, pair-wise colocalization between the trait-associated genetic loci from GWASs and (iii) xQTL-xQTL, pair-wise colocalization between the genetic loci associated with molecular phenotypes in xQTLs. These results together represent the most comprehensive colocalization analysis, which also greatly expands the list of shared variants with genetic pleiotropy. We expect that COLOCdb can serve as a unique and useful resource in advancing the discovery of new biological mechanisms and benefit future functional studies.

References

  1. Genome Biol. 2021 Jan 13;22(1):32 [PMID: 33441155]
  2. Nat Neurosci. 2018 Sep;21(9):1161-1170 [PMID: 30150663]
  3. Nat Neurosci. 2022 Apr;25(4):421-432 [PMID: 35383335]
  4. Nat Commun. 2022 Nov 4;13(1):6642 [PMID: 36333282]
  5. Genome Med. 2021 Aug 26;13(1):136 [PMID: 34446064]
  6. Nucleic Acids Res. 2020 Jan 8;48(D1):D807-D816 [PMID: 31691819]
  7. Transl Psychiatry. 2016 Mar 29;6:e769 [PMID: 27023175]
  8. Nat Genet. 2019 Feb;51(2):245-257 [PMID: 30643258]
  9. Bioinformatics. 2012 Feb 1;28(3):451-2 [PMID: 22171328]
  10. Nat Genet. 2022 Apr;54(4):508-517 [PMID: 35393594]
  11. Nat Genet. 2019 Dec;51(12):1749-1755 [PMID: 31768069]
  12. Nat Genet. 2016 May;48(5):481-7 [PMID: 27019110]
  13. Mol Psychiatry. 2018 Mar;23(3):609-620 [PMID: 28194004]
  14. Genome Biol. 2023 May 30;24(1):130 [PMID: 37254169]
  15. Nucleic Acids Res. 2021 Jan 8;49(D1):D1311-D1320 [PMID: 33045747]
  16. Nat Commun. 2020 Sep 30;11(1):4912 [PMID: 32999275]
  17. Behav Genet. 2016 Mar;46(2):170-82 [PMID: 26362575]
  18. Bioinformatics. 2022 Sep 15;38(18):4409-4411 [PMID: 35894642]
  19. Nucleic Acids Res. 2022 Jan 7;50(D1):D1123-D1130 [PMID: 34669946]
  20. Nat Genet. 2013 Oct;45(10):1238-1243 [PMID: 24013639]
  21. Am J Hum Genet. 2023 Feb 2;110(2):179-194 [PMID: 36634672]
  22. Mol Psychiatry. 2021 Jun;26(6):2056-2069 [PMID: 32393786]
  23. Genome Biol. 2020 Jun 8;21(1):135 [PMID: 32513244]
  24. Nat Rev Rheumatol. 2022 Jan;18(1):1-2 [PMID: 34686856]
  25. PLoS Genet. 2014 May 15;10(5):e1004383 [PMID: 24830394]
  26. OMICS. 2016 Jul;20(7):400-14 [PMID: 27428252]
  27. Nat Commun. 2017 Feb 27;8:14357 [PMID: 28240269]
  28. Nature. 2023 Jan;613(7944):508-518 [PMID: 36653562]
  29. Genomics Proteomics Bioinformatics. 2022 Jun;20(3):541-548 [PMID: 35643189]
  30. Nat Genet. 2019 May;51(5):768-769 [PMID: 31043754]
  31. Nucleic Acids Res. 2019 Jan 8;47(D1):D1005-D1012 [PMID: 30445434]
  32. Nucleic Acids Res. 2022 Jan 7;50(D1):D1115-D1122 [PMID: 34718705]
  33. Cell. 2020 Sep 3;182(5):1198-1213.e14 [PMID: 32888493]
  34. Nature. 2015 Feb 19;518(7539):337-43 [PMID: 25363779]
  35. Nat Genet. 2024 May;56(5):846-860 [PMID: 38641644]
  36. Science. 2019 Sep 27;365(6460): [PMID: 31604244]
  37. Am J Psychiatry. 2018 Jan 1;175(1):15-27 [PMID: 28969442]
  38. Nucleic Acids Res. 2023 Jan 6;51(D1):D835-D844 [PMID: 36243988]
  39. Nat Commun. 2015 Mar 20;6:6601 [PMID: 25791433]
  40. Genome Res. 2014 May;24(5):850-9 [PMID: 24482540]
  41. Hum Mol Genet. 2022 Jun 4;31(11):1806-1820 [PMID: 34919704]
  42. Nat Genet. 2018 Apr;50(4):524-537 [PMID: 29531354]
  43. Nat Genet. 2019 Feb;51(2):237-244 [PMID: 30643251]
  44. Nucleic Acids Res. 2020 Jan 8;48(D1):D983-D991 [PMID: 31598699]
  45. Nat Genet. 2021 Nov;53(11):1616-1621 [PMID: 34737426]
  46. Am J Hum Genet. 2016 Dec 1;99(6):1245-1260 [PMID: 27866706]
  47. JAMA Psychiatry. 2017 Dec 1;74(12):1242-1250 [PMID: 28979981]

Grants

  1. XDB38010400/Strategic Priority Research Program of the Chinese Academy of Sciences
  2. 32270706/National Natural Science Foundation of China
  3. 232016009/Startup Research Fund of Henan Academy of Sciences

MeSH Term

Genome-Wide Association Study
Multifactorial Inheritance
Quantitative Trait Loci
Phenotype
Genetic Pleiotropy
Polymorphism, Single Nucleotide
Journal Article

Links to CNCB-NGDC Resources

Database Commons: DBC009324 (COLOCdb)
Article has an altmetric score of 2

Word Cloud

Created with Highcharts 10.0.0colocalizationgeneticGWASCOLOCdbcomprehensivepair-wiselocistudiescomplextraitsmolecularmechanismsvariantsphenotypestypesxQTLanalysisresultsresourceLarge-scalegenome-wideassociationprovidedprofoundinsightsdiseasesYetdecipheringfine-scalemanifestcauseremainsdauntingtaskpresenthttps://ngdccncbaccn/colocdbdatabaseintegrating3000summarystatistics13dateemployingtworepresentativeapproachesdepositsthreekeycomponents:GWAS-xQTLdifferentiiGWAS-GWAStrait-associatedGWASsiiixQTL-xQTLassociatedxQTLstogetherrepresentalsogreatlyexpandslistsharedpleiotropyexpectcanserveuniqueusefuladvancingdiscoverynewbiologicalbenefitfuturefunctionalCOLOCdb:multi-model

Similar Articles

Cited By