Did you get your eyes from your mother? Nose from your father? Well, there is now a technique that can delve deeper than your features and identify which parts of your genome came from which biological parent. The new study, yet to be peer-reviewed, is published on the preprint service bioRxiv.
This type of technology could have greater medical implications, as it could be used in evaluating disease risks – when a patient’s risk depends on which gene they inherited from their parent. Another possible use is when doctors need to identify other family members that need to consider screening for the gene.
Typically, most cells in the body have two copies of each autosomal chromosome plus sex chromosomes (XX or XY), these cells are called diploid. The exceptions are sperm or egg cells (gametes), which are haploid, meaning they have one copy of each autosome chromosome and one sex chromosome. In our bodies, we have sets of genes that are so close together that they are unlikely to be split up during meiosis (which is a type of cell division that reduces the number of chromosomes in a gamete). These sets of genes are called haplotypes and can come exclusively from one biological parent.
The team developed the new methodology using DNA sequence data from the genomes of five people. These genomes had already been analyzed before in previous studies, and the genomes of each biological parent were available and accessible so the developed methodology could be validated.
All the genomes that were tested contained 22 pairs of autosomes – the typical number of human non-sex chromosomes. With autosome pairs, one comes from the biological mother and the other from the biological father. Before this research, it was often difficult to determine the parent of origin for these autosomes.
An existing technique called “Strand-seq” was applied to the datasets. Strand-seq is a genome library preparation method that can capture parental DNA template strands in daughter cells. This technique can be used as a scaffold for other techniques, to determine whether an autosome is maternally or paternally inherited, without parental sequence data.
Then, to identify which autosome came from which parent, the scientists looked for epigenetic marker evidence. The type of marker that was examined was DNA methylation, which is a biological process where methyl groups are added to the DNA molecule. It is important as it can change the activity of the DNA molecule without changing the sequence. DNA methylation patterns can be inherited from biological parents.
DNA methylation was examined in nearly 200 regions of the DNA, and these are well-known sites that could be used for identifying parent-specific methylation. These sites were then used as a guide to predict which biological parent was the source of a particular autosome – this indicated that only two or three parent-specific methylation sites were needed to identify the origin. The results were confirmed by looking at the genomes of the biological parents.
In the future, this method could become a routine component in genomic analysis.
"We predict that it will improve the diagnosis and management of many genetic diseases," the authors write in their paper.
[H/T: New Scientist]