Identifying Carriers of Duplication in PAR1

One sperm donor (man 20) was previously identified as carrying a duplication of the X chromosome that encompassed the canonical PAR1 boundary and extended at least 12 kb proximal to this (S1 Fig). Twenty-three Y-STRs were typed in 81 donors, including man 20, using the PowerPlex Y23 kit (Promega). Y-chromosome haplogroups were predicted from the resulting STR haplotypes using a Bayesian Allele Frequency approach (http://www.nevgen.org/). Man 20 and man 53 were predicted to carry the haplogroup I2a-L233 sublineage. Two further unrelated ePAR carriers were found by surveying PowerPlex Y23 data to predict haplogroup I2a Y chromosomes among laboratory collections of DNA samples. A first-generation male from CEPH family 1334 (NA12146) was identified as another candidate carrier; he was reported to have an apparent duplication of X-linked SNPs in the vicinity of the ePAR1 (hg19 chrX:2694151–2808548; hg38 chrX:2776110–2890507) in DGV (http://dgv.tcag.ca/dgv/app/home), and predicted to belong to the same I2a sub-haplogroup based on his Y-STR profile (data kindly provided by C.Tyler-Smith, Wellcome Trust Sanger Institute). We also typed two Hungarian males known from sequencing of 3.4Mb of their male specific Y to have the most distantly related I2a sublineage (I2a-M423) [66 (link)] to determine whether all males within I2a possessed an ePAR.