Best practices for improving alignment and variant calling on human sex chromosomes

Area of Science:

• Human genetics
• Genomic analysis
• Bioinformatics

Background:

• Sex chromosomes (X and Y) differ from autosomes in genomic processing.
• Shared sequence similarity exists between X and Y chromosomes in regions like PARs and XTR.
• Standard autosomal analysis methods may not be optimal for sex chromosomes.

Purpose of the Study:

• To evaluate the impact of sex chromosome complement (SCC)-informed alignment, variant calling, and filtering on sex chromosome variant detection.
• To compare standard autosomal strategies with SCC-aware approaches for accuracy and efficiency.

Main Methods:

• Simulation study assessing variant calling strategies.
• Comparison of autosomal versus SCC-informed alignment and variant calling.
• Analysis of false positives and false negatives in different scenarios.

Main Results:

• SCC-informed alignment increases true positives in PARs and XTR (XX samples).
• Masking XTR in XY samples significantly increases false positives.
• Haploid calling in XY samples reduces false positives without increasing false negatives.

Conclusions:

• SCC-informed reference genomes improve sex chromosome variant detection accuracy.
• Accurate ploidy calling is crucial for reliable variant identification.
• Optimized variant calling can identify disease-relevant variants for conditions like cardiomyopathy and Alzheimer disease.