LASER

LASER estimates individual genetic ancestry directly from genome-wide short-read sequencing data to enable ancestry inference without genotype calling.

Key Features:

• Direct analysis from off-target reads: Utilizes off-target sequence reads to perform ancestry estimation without relying on genotype calls.
• Genotype-free inference: Circumvents the need for traditional genotype calling when deriving ancestry information from sequencing data.
• Low-coverage performance: Infers worldwide continental ancestry accurately at whole-genome shotgun coverages as low as 0.001× and provides fine-scale European estimates at 0.1× coverage.
• Fine-scale resolution: Discriminates between individuals from different provinces within Finland using exome sequencing data.
• Input data: Operates on genome-wide short-read sequencing data and exome sequencing reads.
• Implementation: Implemented in C++.

Scientific Applications:

• Genetic association studies: Provides individual ancestry estimates to control for population structure and reduce false positive signals in association analyses.
• Case-control matching: Improves matching of cases and controls by accounting for fine-scale and continental ancestry differences.

Methodology:

Implemented in C++ and using off-target sequence reads from genome-wide short-read and exome sequencing to estimate ancestry without genotype calling; validated on simulated and empirical datasets.