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Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function.

Publication ,  Journal Article
Chasman, DI; Fuchsberger, C; Pattaro, C; Teumer, A; Böger, CA; Endlich, K; Olden, M; Chen, M-H; Tin, A; Taliun, D; Li, M; Gao, X; Gorski, M ...
Published in: Hum Mol Genet
December 15, 2012

In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P = 5.6 × 10(-9)) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 × 10(-4)-2.2 × 10(-7). Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in general.

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Published In

Hum Mol Genet

DOI

EISSN

1460-2083

Publication Date

December 15, 2012

Volume

21

Issue

24

Start / End Page

5329 / 5343

Location

England

Related Subject Headings

  • Polymorphism, Single Nucleotide
  • Membrane Proteins
  • Low Density Lipoprotein Receptor-Related Protein-2
  • Intracellular Signaling Peptides and Proteins
  • Inhibin-beta Subunits
  • Humans
  • Glomerular Filtration Rate
  • Genome-Wide Association Study
  • Genetics & Heredity
  • Genetic Predisposition to Disease
 

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Chasman, D. I., Fuchsberger, C., Pattaro, C., Teumer, A., Böger, C. A., Endlich, K., … Köttgen, A. (2012). Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function. Hum Mol Genet, 21(24), 5329–5343. https://doi.org/10.1093/hmg/dds369
Chasman, Daniel I., Christian Fuchsberger, Cristian Pattaro, Alexander Teumer, Carsten A. Böger, Karlhans Endlich, Matthias Olden, et al. “Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function.Hum Mol Genet 21, no. 24 (December 15, 2012): 5329–43. https://doi.org/10.1093/hmg/dds369.
Chasman DI, Fuchsberger C, Pattaro C, Teumer A, Böger CA, Endlich K, et al. Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function. Hum Mol Genet. 2012 Dec 15;21(24):5329–43.
Chasman, Daniel I., et al. “Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function.Hum Mol Genet, vol. 21, no. 24, Dec. 2012, pp. 5329–43. Pubmed, doi:10.1093/hmg/dds369.
Chasman DI, Fuchsberger C, Pattaro C, Teumer A, Böger CA, Endlich K, Olden M, Chen M-H, Tin A, Taliun D, Li M, Gao X, Gorski M, Yang Q, Hundertmark C, Foster MC, O’Seaghdha CM, Glazer N, Isaacs A, Liu C-T, Smith AV, O’Connell JR, Struchalin M, Tanaka T, Li G, Johnson AD, Gierman HJ, Feitosa MF, Hwang S-J, Atkinson EJ, Lohman K, Cornelis MC, Johansson A, Tönjes A, Dehghan A, Lambert J-C, Holliday EG, Sorice R, Kutalik Z, Lehtimäki T, Esko T, Deshmukh H, Ulivi S, Chu AY, Murgia F, Trompet S, Imboden M, Coassin S, Pistis G, CARDIoGRAM Consortium, ICBP Consortium, CARe Consortium, WTCCC2, Harris TB, Launer LJ, Aspelund T, Eiriksdottir G, Mitchell BD, Boerwinkle E, Schmidt H, Cavalieri M, Rao M, Hu F, Demirkan A, Oostra BA, de Andrade M, Turner ST, Ding J, Andrews JS, Freedman BI, Giulianini F, Koenig W, Illig T, Meisinger C, Gieger C, Zgaga L, Zemunik T, Boban M, Minelli C, Wheeler HE, Igl W, Zaboli G, Wild SH, Wright AF, Campbell H, Ellinghaus D, Nöthlings U, Jacobs G, Biffar R, Ernst F, Homuth G, Kroemer HK, Nauck M, Stracke S, Völker U, Völzke H, Kovacs P, Stumvoll M, Mägi R, Hofman A, Uitterlinden AG, Rivadeneira F, Aulchenko YS, Polasek O, Hastie N, Vitart V, Helmer C, Wang JJ, Stengel B, Ruggiero D, Bergmann S, Kähönen M, Viikari J, Nikopensius T, Province M, Ketkar S, Colhoun H, Doney A, Robino A, Krämer BK, Portas L, Ford I, Buckley BM, Adam M, Thun G-A, Paulweber B, Haun M, Sala C, Mitchell P, Ciullo M, Kim SK, Vollenweider P, Raitakari O, Metspalu A, Palmer C, Gasparini P, Pirastu M, Jukema JW, Probst-Hensch NM, Kronenberg F, Toniolo D, Gudnason V, Shuldiner AR, Coresh J, Schmidt R, Ferrucci L, Siscovick DS, van Duijn CM, Borecki IB, Kardia SLR, Liu Y, Curhan GC, Rudan I, Gyllensten U, Wilson JF, Franke A, Pramstaller PP, Rettig R, Prokopenko I, Witteman J, Hayward C, Ridker PM, Parsa A, Bochud M, Heid IM, Kao WHL, Fox CS, Köttgen A. Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function. Hum Mol Genet. 2012 Dec 15;21(24):5329–5343.
Journal cover image

Published In

Hum Mol Genet

DOI

EISSN

1460-2083

Publication Date

December 15, 2012

Volume

21

Issue

24

Start / End Page

5329 / 5343

Location

England

Related Subject Headings

  • Polymorphism, Single Nucleotide
  • Membrane Proteins
  • Low Density Lipoprotein Receptor-Related Protein-2
  • Intracellular Signaling Peptides and Proteins
  • Inhibin-beta Subunits
  • Humans
  • Glomerular Filtration Rate
  • Genome-Wide Association Study
  • Genetics & Heredity
  • Genetic Predisposition to Disease