The human Y chromosome provides a fertile
ground for structural rearrangements owing to its haploidy
and high content of repeated sequences. The methodologies
used for copy number variation (CNV) studies have developed
over the years. Low-throughput techniques based
on direct observation of rearrangements were developed
early on, and are still used, often to complement arraybased
or sequencing approaches which have limited power
in regions with high repeat content and specifcally in the
presence of long, identical repeats, such as those found in
human sex chromosomes. Some specifc rearrangements
have been investigated for decades; because of their effects
on fertility, or their outstanding evolutionary features, the
interest in these has not diminished. However, following
the fourishing of large-scale genomics, several studies
have investigated CNVs across the whole chromosome.
These studies sometimes employ data generated within
large genomic projects such as the DDD study or the 1000
Genomes Project, and often survey large samples of healthy
individuals without any prior selection. Novel technologies
based on sequencing long molecules and combinations of
technologies, promise to stimulate the study of Y-CNVs in
the immediate future.