Computationally Efficient Whole-Genome Signal Region Detection for Quantitative and Binary Traits

TL;DR

This paper introduces a distributed, covariate-adjusted version of the BiRS algorithm, called dBiRS, which efficiently detects genetic signal regions in whole-genome data for both binary and continuous traits, with theoretical error control.

Contribution

The paper presents dBiRS, a scalable, parallelizable algorithm that extends BiRS to handle covariates and various outcome types, improving computational efficiency and statistical power.

Findings

Validated dBiRS on UK Biobank data for cognitive traits.

Identified novel rare variants near new genes.

Confirmed previous genetic associations.

Abstract

The identification of genetic signal regions in the human genome is critical for understanding the genetic architecture of complex traits and diseases. Numerous methods based on scan algorithms (i.e. QSCAN, SCANG, SCANG-STARR) have been developed to allow dynamic window sizes in whole-genome association studies. Beyond scan algorithms, we have recently developed the binary and re-search (BiRS) algorithm, which is more computationally efficient than scan-based methods and exhibits superior statistical power. However, the BiRS algorithm is based on two-sample mean test for binary traits, not accounting for multidimensional covariates or handling test statistics for non-binary outcomes. In this work, we present a distributed version of the BiRS algorithm (dBiRS) that incorporate a new infinity-norm test statistic based on summary statistics computed from a generalized linear model. The dBiRS algorithm accommodates regression-based statistics, allowing for the adjustment of covariates and the testing of both continuous and binary outcomes. This new framework enables parallel computing of block-wise results by aggregation through a central machine to ensure both detection accuracy and computational efficiency, and has theoretical guarantees for controlling family-wise error rates and false discovery rates while maintaining the power advantages of the original algorithm. Applying dBiRS to detect genetic regions associated with fluid intelligence and prospective memory using whole-exome sequencing data from the UK Biobank, we validate previous findings and identify numerous novel rare variants near newly implicated genes. These discoveries offer valuable insights into the genetic basis of cognitive performance and neurodegenerative disorders, highlighting the potential of dBiRS as a scalable and powerful tool for whole-genome signal region detection.