Structural variation on the human Y chromosome from population-scale resequencing

Area of Science:

• Genomics
• Human Genetics
• Population Genetics

Background:

• Structural variants (SVs) on the Y chromosome are crucial for male health and reproduction.
• Understanding Y-chromosome SVs in diverse populations is essential for genetic studies.

Purpose of the Study:

• To assess the feasibility of detecting Y-chromosome structural variants (SVs) using low-coverage whole-genome sequencing.
• To characterize Y-SVs in a general population sample.

Main Methods:

• Analysis of 70 individuals from Africa, Europe, and East Asia using 1000 Genomes Pilot project data.
• Application of read-depth and read-pair methods for Y-SV discovery.
• Validation of candidate Y-SVs through literature, independent datasets, and PCR.

Main Results:

• Validated 19 Y-SVs, including 2 novel variants.
• Observed Y-SV allele counts ranging from 1 to 64.
• Identified variation hotspots in heterochromatic, ampliconic, X-transposed, and X-degenerate regions; 5 gene families showed copy number variation.

Conclusions:

• Low-coverage sequencing effectively detects Y-SVs.
• Y-SVs are abundant in the human Y chromosome.
• Novel common and rare Y-SVs were identified and characterized.