23Andme Genotype For X Chromosome: Some Have Two Bases, Others Have One

Question

[jeff.hammerbacher]

I've downloaded my raw data from 23andMe. I'm a male. For most loci on the X chromosome, there is a single base in the "genotype" column. However, at the beginning and end of the chromosome, for a few hundred loci, there are two bases in the "genotype" column.

I've looked at my wife's 23andMe data, and her X chromosome has two bases for every loci on the X chromosome.

Where can I learn more about which loci in the X chromosome have one base versus two bases in a male? In particular, can I determine from the position number whether there will be one or two bases? Clearly I can come up with a decision rule based on manual inspection of the 23andMe data, but I'm curious if there's a rule that covers genomic loci that 23andMe does not yet measure.

Answer 1

[Pierre Lindenbaum]

These loci might be localized in the PAR regions http://en.wikipedia.org/wiki/Pseudoautosomal_region

from: http://www.genenames.org/genefamilies/PAR

At either end of the X and Y chromosomes are homologous regions known as the pseudoautosomal regions (PARs). These two regions pair regularly at male meiosis and undergo recombination. PAR1 is at the tip of the short 'p' arms (Xp22 and Yp11) and PAR2 is at the tip of the long 'q' arms (Xq28 and Yq12).

[jeff.hammerbacher]

Thanks! FYI, I found the locations of the PAR regions for the 23andMe reference genome at ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37.p10/par.txt