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Investigation of Inversion Polymorphisms in the Human Genome Using Principal Components Analysis

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  • Jianzhong Ma
  • Christopher I Amos

Abstract

Despite the significant advances made over the last few years in mapping inversions with the advent of paired-end sequencing approaches, our understanding of the prevalence and spectrum of inversions in the human genome has lagged behind other types of structural variants, mainly due to the lack of a cost-efficient method applicable to large-scale samples. We propose a novel method based on principal components analysis (PCA) to characterize inversion polymorphisms using high-density SNP genotype data. Our method applies to non-recurrent inversions for which recombination between the inverted and non-inverted segments in inversion heterozygotes is suppressed due to the loss of unbalanced gametes. Inside such an inversion region, an effect similar to population substructure is thus created: two distinct “populations” of inversion homozygotes of different orientations and their 1∶1 admixture, namely the inversion heterozygotes. This kind of substructure can be readily detected by performing PCA locally in the inversion regions. Using simulations, we demonstrated that the proposed method can be used to detect and genotype inversion polymorphisms using unphased genotype data. We applied our method to the phase III HapMap data and inferred the inversion genotypes of known inversion polymorphisms at 8p23.1 and 17q21.31. These inversion genotypes were validated by comparing with literature results and by checking Mendelian consistency using the family data whenever available. Based on the PCA-approach, we also performed a preliminary genome-wide scan for inversions using the HapMap data, which resulted in 2040 candidate inversions, 169 of which overlapped with previously reported inversions. Our method can be readily applied to the abundant SNP data, and is expected to play an important role in developing human genome maps of inversions and exploring associations between inversions and susceptibility of diseases.

Suggested Citation

  • Jianzhong Ma & Christopher I Amos, 2012. "Investigation of Inversion Polymorphisms in the Human Genome Using Principal Components Analysis," PLOS ONE, Public Library of Science, vol. 7(7), pages 1-12, July.
  • Handle: RePEc:plo:pone00:0040224
    DOI: 10.1371/journal.pone.0040224
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    References listed on IDEAS

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    2. Chao Tian & Robert M Plenge & Michael Ransom & Annette Lee & Pablo Villoslada & Carlo Selmi & Lars Klareskog & Ann E Pulver & Lihong Qi & Peter K Gregersen & Michael F Seldin, 2008. "Analysis and Application of European Genetic Substructure Using 300 K SNP Information," PLOS Genetics, Public Library of Science, vol. 4(1), pages 1-11, January.
    3. Nick Patterson & Alkes L Price & David Reich, 2006. "Population Structure and Eigenanalysis," PLOS Genetics, Public Library of Science, vol. 2(12), pages 1-20, December.
    4. Jianzhong Ma & Christopher I Amos, 2010. "Theoretical Formulation of Principal Components Analysis to Detect and Correct for Population Stratification," PLOS ONE, Public Library of Science, vol. 5(9), pages 1-14, September.
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    1. Bahram Namjou & Yizhao Ni & Isaac T W Harley & Iouri Chepelev & Beth Cobb & Leah C Kottyan & Patrick M Gaffney & Joel M Guthridge & Kenneth Kaufman & John B Harley, 2014. "The Effect of Inversion at 8p23 on BLK Association with Lupus in Caucasian Population," PLOS ONE, Public Library of Science, vol. 9(12), pages 1-13, December.
    2. Ronald J Nowling & Krystal R Manke & Scott J Emrich, 2020. "Detecting inversions with PCA in the presence of population structure," PLOS ONE, Public Library of Science, vol. 15(10), pages 1-20, October.

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