Abstract
The characterization of Y chromosome haplogroups is currently done by genotyping SNPs and a few InDels. However, InDels are increasingly gaining importance, so the aim of this work was to create an InDel PCR multiplex allowing a fast, simple and straightforward characterization of the main Y-haplogroups. For this, we have selected the InDels already accepted by the Y Chromosome Consortium. However, due to their position in the Y chromosome phylogenetic tree, they only allow classifying chromosomes from 6 of the 20 main Y haplogroups. Thus, we have extended the search to already described and validated InDels in dbSNP and MGS. All 154 InDels retrieved from that search were subjected to multiple screenings and just 10 were found to be new, potentially polymorphic and Y specific. Their typing in samples for 13 distinct haplogroups confirmed only 2 polymorphisms (named M2 and M14). M2 is polymorphic in R haplogroup but it also shows a reversion within the R1b1b2 sub-haplogroup. Therefore, it is not recommended for the characterization and distinction between R and the other haplogroups. M14 shows variation in R and Q and so it can be used to identify samples belonging to the paragroup P, which was not possible before using the InDels in the phylogenetic tree of the Y Chromosome Consortium. The detailed analysis of all the available information allowed us to conclude that the creation of the aimed multiplex will only be possible with the detection and phylogenetic characterization of new InDels.
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call