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Infinium Assay for Large-scale SNP Genotyping Applications
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Extent to which array genotyping and imputation with large reference panels approximate deep whole-genome sequencing.

Sarah C Hanks1, Lukas Forer2, Sebastian Schönherr2

  • 1Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI, USA.

American Journal of Human Genetics
|August 18, 2022
PubMed
Summary

Array genotyping with genotype imputation can approximate whole-genome sequencing (WGS) for identifying genetic variants. Imputation accuracy varies by ancestry, array type, and genomic region, but tools like RsqBrowser can assess quality.

Keywords:
genotype imputationgenotyping arraywhole-genome sequencing

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Area of Science:

  • Genetics
  • Bioinformatics
  • Population Genetics

Background:

  • Accurate identification and genotyping of genetic variants are crucial for understanding human diseases and traits.
  • Deep whole-genome sequencing (WGS) is the gold standard but remains prohibitively expensive for large-scale studies.
  • Array genotyping followed by genotype imputation offers a cost-effective alternative to WGS.

Purpose of the Study:

  • To quantify how well array genotyping and imputation can approximate WGS across diverse ancestries.
  • To evaluate the impact of different imputation reference panels and genotype arrays on imputation quality.
  • To identify factors influencing imputation accuracy, including ancestry and genomic location.

Main Methods:

  • Genotype imputation was performed using variants from Illumina Core, OmniExpress, MEGA, and Omni 2.5M arrays.
  • Imputation utilized the 1000G, HRC, and TOPMed reference panels.
  • Imputation quality was assessed using r-squared values down to minor-allele frequencies (MAFs) of 0.14-0.85% across ancestries.

Main Results:

  • Using the Omni 2.5M array and TOPMed panel, ≥90% of bi-allelic single-nucleotide variants (SNVs) were well imputed (r² > 0.8) down to low MAFs (0.11-0.85%).
  • Imputation quality showed minimal differences among arrays with >700k variants when using the TOPMed panel.
  • Imputation quality varied significantly across individuals, US studies, and specific genomic regions, with some regions showing poor imputation even for common variants.

Conclusions:

  • Array genotyping and imputation can effectively approximate WGS, but quality is contingent on the reference panel, genotype array, sample ancestry, and genomic region.
  • The RsqBrowser tool, available on the Michigan Imputation Server, allows querying imputation quality by variant or genomic region.
  • These findings have implications for cost-effective genetic studies across diverse populations.