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  • gender check using sequencing data

    Hi All,

    I have exome sequencing data from siblings and would like to confirm their gender and relationship using genetics to make sure they are in fact siblings. I also want to confirm that the gender information is correct. Are there tools out there that can do this using exome seq data?


  • #2
    To verify pedigree this post might help:

    The Center for Public Health Genomics at UVA is focused on translational and personalized medicine — moving gene discovery into the delivery of health care.

    To check gender, may be you could check the number of aligned reads to Y chromsome?


    • #3
      I would second that -- map reads against a panel of Y-chromosome genes/exons.


      • #4
        But I have pure female reads that can map a lot Y?


        • #5
          The average sequencing depth of chrY and chrX


          • #6
            in plink there is an option to check sex using X chr, I hope you are looking for this..
            plink --bfile data --impute-sex --make-bed --out newfile


            • #7
              I also use the average depth of X and Y


              • #8
                Testing sex determination with CCLE samples

                I've tried using [num reads mapped to chrX] / [num reads mapped to chrY]
                to determine sex in some CCLE exome-seq samples. The ratios turned out to be:

                9.4 -- s1
                304.6 -- s2
                272.9 -- s3
                168.3 -- s4
                220.6 -- s5
                297.8 -- s6
                226.1 -- s7
                257.1 -- s8
                241.9 -- s9
                287.0 -- s10
                278.6 -- s11
                260.3 -- s12
                9.7 -- s13
                8.7 -- s14
                261.2 -- s15
                279.3 -- s16
                9.0 -- s17
                8.5 -- s18
                260.7 -- s19
                297.4 -- s20
                8.7 -- s21
                261.8 -- s22
                189.0 -- s23
                147.4 -- s24
                291.2 -- s25
                So it looks like the difference is pretty wide -
                [num reads mapped to chrX] / [num reads mapped to chrY] is < 10 for all male samples and > 100 for all female samples.

                Still, I'm not sure whether these thresholds are stable across exome-seq kits, gene panels, etc. I wonder if there's a more robust way to determine sex.
                Last edited by bw.; 02-13-2014, 11:07 AM.


                • #9
                  How about using % heterozygosity on X (without the pseudoautosomal regions (X:60000-2699520 and X:154931043-155260560). In our lab, male = < 30 % and female = > 50 %.


                  • #10
                    Gender = biological sex + culture. You don't care about people's gender, you care about their sex. (And even the biology is not black and white 100% of the time)


                    • #11
                      @swbarnes2 cool. never realized there was a difference.

                      @oyvindbusk thanks, I also tried this and ended up with similar thresholds (male < 40% and female > 50%). I didn't try to filter out pseudoautosomal regions since their coordinates differ across species and assembly versions (based on PAR coordinates at:


                      Looking at 322 CCLE samples, 233 were called Male, 73 Female, and 10 Unknown (which is >= 40% and <= 50%). Out of the 233 Male, only 5 would have been called differently with your thresholds. I will see if I can check the thresholds against a different approach. Also, a lot of the CCLE cells have copy number amplifications / deletions, so these results might be skewed by that.

                      Here is the distribution of nHet / nHomo for chrX in CCLE samples (I used this instead of nHet/(nHet+nHomo)). The 2 vertical blue lines are equivalent to 40% and 50% thresholds, and the 30% threshold is the red line.

                      Last edited by bw.; 02-12-2014, 11:48 PM.


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