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Multiple-testing corrections in case-control studies using identity-by-descent segments.

Seth D Temple1, Nicola H Chapman2, Seung Hoan Choi3

  • 1Department of Statistics, University of Washington, Seattle, WA, USA; Department of Statistics, University of Michigan, Ann Arbor, MI, USA; Michigan Institute for Data and AI in Society, University of Michigan, Ann Arbor, MI, USA.

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Summary
This summary is machine-generated.

We developed a novel Identity-by-descent (IBD) mapping method to identify Alzheimer's disease (AD) risk loci. This approach complements genome-wide association studies (GWASs) and successfully detected six significant AD risk signals.

Keywords:
Alzheimer diseasebinary traitshaplotypesidentity by descentmean-reverting processesmultiple testing

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Area of Science:

  • Genetics
  • Genomic analysis
  • Statistical genetics

Background:

  • Genome-wide association studies (GWASs) may miss complex genetic signals from multiple causal variants.
  • Identity-by-descent (IBD) mapping offers complementary insights into disease genetics.

Purpose of the Study:

  • To introduce a novel IBD mapping statistic and hypothesis testing framework for identifying disease risk loci.
  • To develop a scalable and reproducible computational workflow for IBD mapping.
  • To apply the method to discover Alzheimer's disease (AD) risk loci.

Main Methods:

  • Proposed a statistic based on the difference between affected-affected and control-control IBD rates.
  • Utilized a computationally efficient stochastic process approach for genome-wide significance testing controlling the family-wise error rate (FWER).
  • Integrated IBD mapping with selection scans and phenotype randomization for confounding assessment.
  • Developed automated workflows for haplotype phasing and local ancestry probability calling.

Main Results:

  • Whole-genome simulations confirmed conservative control of the FWER.
  • Identified six genome-wide significant AD risk loci in the Alzheimer's Disease Sequencing Project (ADSP) data.
  • Detected signals in samples of African, European, and Amish ancestries.
  • Found previously associated variants and nominated therapeutic target genes within identified loci.

Conclusions:

  • The developed IBD mapping approach is a scalable and effective tool for discovering disease risk loci, particularly for complex genetic architectures.
  • This method enhances the utility of large genomic consortia data for understanding disease mechanisms.
  • The identified AD risk loci provide further targets for therapeutic intervention and research.