IGSP: Integrated Gene Signal Processing

Rare variants of major effect play an important role in human complex diseases and can be discovered by sequencing-based genome-wide association studies. IGSP combines the rare variant association test with gene network and phenotype information to identify risk genes implicated by rare variants for human complex diseases. This data integration can significantly improve the identification of disease risk genes with marginal association signals. IGSP follows a 'discovery-driven' strategy without relying on prior knowledge about the disease and thus maintains the unbiased character of genome-wide association studies.

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Citation

Lin, J.R., et al. (2017) Integrated rare variant-based risk gene prioritization in disease case-control sequencing studies. PLOS Genet, 13, e1007142.


Application

Input file (required; example):

Method: Network + Phenotype (full integration) Network

Risk gene percentage: 1 2 3 4 5 %



Source codes

The source codes for this work are available at Zenodo
  • Source codes for IGSP
  • Source codes for obtaining CHD gene association P-values


  • References

    Guo, T., et al (2015) Histone Modifier Genes Alter Conotruncal Heart Phenotypes in 22q11.2 Deletion Syndrome. Am J Hum Genet, 97, 869-77.

    Sifrim, A., et al (2016) Distinct genetic architectures for syndromic and nonsyndromic congenital heart defects identified by exome sequencing. Nat Genet, 48, 1060-5.