WCX2CytoSure - visualization of structural variants in prenatal samples

Advancements in non-invasive prenatal testing (NIPT) allow for early detection of aberrations in a restricted set of chromosomes through Illumina short-read sequencing of cell-free fetal DNA present in maternal blood. The fraction of fetal cell-free DNA in maternal blood is referred to as the fetal fraction. This project aims to enhance the interpretation of NIPT data by visualizing the sequencing coverage - i.e., the number of sequencing reads aligning to a genomic region, graphically in the CytoSure Interpret Software. Furthermore, this project aims to investigate whether the visualization can aid in detecting small copy number variants in prenatal samples. Visualization was enabled by creating a Python script named “WCX2CytoSure” and integrating it into the current pipeline - Fluffy, that processes NIPT data at Karolinska universitetssjukhuset. Initial testing was done with two known trisomy cases. Two NIPT batches containing 46 samples each were then processed. Results show that coverage patterns successfully can be viewed in CytoSure Interpret Software and trisomies on test chromosomes could be visualized. Regarding the visualization of smaller copy number variants, bootstrap resampling showed that a 5Mb duplication significantly can be distinguished from background noise when the sample displays a fetal fraction of 5-8%. A 1Mb deletion can be visualized when the sample displays a fetal fraction of 12%. In conclusion, the visualization of NIPT data in CytoSure is successful in terms of what the analysis needs currently. However, challenges remain in visualizing copy number variants. This challenge is due to the high variability of the coverage data.