7
$\begingroup$

I have been analyzing TCGA Ovary Cancer data. In Somatic Mutation data, there is data of mutations in all the chromosomes (1-22 and X), but amazingly, I have found one (just one) row of Y Chromosome mutation as well. What can it mean?

For Reference, I have pasted that row below:

icgc_mutation_id icgc_donor_id project_code chromosome chromosome_start 
MU42454          DO28056       OV-US        Y          13500742         

chromosome_end chromosome_strand mutation_type            
13500742       1                 single base substitution 

reference_genome_allele mutated_from_allele mutated_to_allele 
G                       G                   A                 

consequence_type aa_mutation cds_mutation gene_affected   transcript_affected 
stop_gained      R194*       580C>T       ENSG00000183704 ENST00000331172
Improve this question
$\endgroup$
6
  • 1
    $\begingroup$ In just one individual you mean? It means that there was a rare recombination event I guess in the father (or grand-father or grand-grand...-father) $\endgroup$
    – Remi.b
    Commented Apr 23, 2015 at 1:03
  • $\begingroup$ Yeah it is for one individual and only one entry: Individual is a 76yo female (deceased) $\endgroup$
    – Failed Scientist
    Commented Apr 23, 2015 at 1:05
  • 2
    $\begingroup$ Does it correspond to a region the is close to the PAR? $\endgroup$
    – Remi.b
    Commented Apr 23, 2015 at 1:06
  • 1
    $\begingroup$ Just to expand on what @Remi.b said, there is the possibility that at some point in the past, in a male ancestor, a rare event occurred where a portion of the Y chromosome somehow ended up grafted to an X chromosome (or possibly any one of the others), but didn't cause enough issues/abnormalities to be an issue, or at least noted. $\endgroup$
    – MattDMo
    Commented Apr 23, 2015 at 1:08
  • 1
    $\begingroup$ Its not in PAR of either X or Y $\endgroup$
    – Failed Scientist
    Commented Apr 23, 2015 at 2:28

1 Answer 1

Reset to default
2
$\begingroup$

This question was asked more than six years ago. Since then, the dataset in question has been updated. I accessed the OV-US project dataset from the ICGC Data Portal, specifically simple_somatic_mutation.open.OV-US.tsv.gz. The 9th field of this file is chromosome. Counting the occurrence of each chromosome, we see that Y is not represented:

awk -F$'\t' '{print $9}' simple_somatic_mutation.open.OV-US.tsv | sed '1d' | sort -n | uniq -c

  13171 X
  39564 1
  31363 2
  24657 3
  11021 4
  16849 5
  18643 6
  19492 7
  13067 8
  11133 9
  12090 10
  24980 11
  25608 12
   3947 13
  12728 14
  12123 15
  17554 16
  30315 17
   5669 18
  29571 19
   9054 20
   3639 21
   7084 22

Note that icgc_mutation_id MU42454 is only associated with acute myeloid leukaemia in a single donor. Moreover, the search scheme "Donor IS DO28056 AND Mutation Location IS ChrY" yields zero results from the ICGC data browser.

So, it seems that the inclusion of a Y chromosome mutation in the TCGA Ovary Cancer data was a mistake that has since been corrected.

Improve this answer
$\endgroup$
1
  • $\begingroup$ Nice to see the correction $\endgroup$
    – Failed Scientist
    Commented Jul 30, 2021 at 16:11

You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .