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Many studies have shown that the spatial distribution of genes within a single chromosome
exhibits distinct patterns. However, little is known about the characteristics of inter-chromosomal distribution
of genes (including protein-coding genes, processed transcripts and pseudogenes) in different
genomes. In this study, we explored these issues using the available genomic data of both human and
model organisms. Moreover, we also analyzed the distribution pattern of protein-coding genes that
have been associated with 14 common diseases and the insert/deletion mutations and single nucleotide
polymorphisms detected by whole genome sequencing in an acute promyelocyte leukemia patient. We
obtained the following novel findings. Firstly, inter-chromosomal distribution of genes displays a nonstochastic
pattern and the gene densities in different chromosomes are heterogeneous. This kind of
heterogeneity is observed in genomes of both lower and higher species. Secondly, protein-coding
genes involved in certain biological processes tend to be enriched in one or a few chromosomes. Our
findings have added new insights into our understanding of the spatial distribution of genome and disease-
related genes across chromosomes. These results could be useful in improving the efficiency of
disease-associated gene screening studies by targeting specific chromosomes.