The present invention provides a method for detecting structural variations (SV) within genomes of single cells or
population of single cells by integrating a three-layered information of sequencing read depth, read strand orientation and
haplotype phase. The method of the invention can detect deletions, duplications,
polyploidies, translocations, inversions, and copy number neutral loss of heterozygosity (CNN-LOH), and more. The method of the invention can fully
karyotype a
genome comprehensively, and may be applied in research and clinical approaches. For example, the methods of the invention are useful for analysing cellular samples of patients for diagnosing or aiding a diagnosis, in
reproductive medicine to detect embryonic abnormalities, or during therapeutic approaches based on cellular therapies to
quality control genetically engineered cells, such as in adoptive
T cell therapy and others. The method of the invention may further be applied in research to
decipher the karyotypes of cellular models (
cell lines), patient samples, or to further unravel genetic and mechanistic pathways leading to the generation of any SV within genomes.