Comparing genome results from 23andMe and deCODEme
Antonio C B Oliveira
acbolive
at sloan.mit.edu
April 2008
In order to determine the accuracy of the
genome profile provided by 23andMe and deCODEme I arranged to be genotyped by both
companies and wrote a computer program to compare
the results.
The downloaded files contains
576105 snips
in the case of 23andMe and 1013349 snips
for deCODE.
After
removing the no-call and
matching the two files by SNP identification, 560299
snips were present in both files.
The comparisson revealed
23 cases in which the
results do not agree.
The discrepancy by chromosome is summarized in the following table.
|
|
||||
Chrm |
equal |
not equal |
|||
1 |
42060 |
2 |
rs4660646 |
rs1934496 |
|
2 |
45328 |
1 |
rs10933181 |
||
3 |
37637 |
1 |
rs9881405 |
||
4 |
33557 |
3 |
rs1064205 |
rs312330 |
rs11100437 |
5 |
34530 |
0 |
|||
6 |
36742 |
1 |
rs4458717 |
||
7 |
30199 |
0 |
|||
8 |
31736 |
1 |
rs2955195 |
||
9 |
26745 |
3 |
rs7033246 |
rs1536928 |
rs10793963 |
10 |
29187 |
0 |
|||
11 |
27367 |
3 |
rs10894749 |
rs3921012 |
rs510978 |
12 |
27092 |
1 |
rs12296276 |
||
13 |
20766 |
0 |
|||
14 |
18356 |
0 |
|||
15 |
16630 |
2 |
rs754499 |
rs4965862 |
|
16 |
16863 |
1 |
rs11149566 |
||
17 |
14391 |
1 |
rs2290505 |
||
18 |
16799 |
1 |
rs12960185 |
||
19 |
9512 |
0 |
|||
20 |
14240 |
1 |
rs4814138 |
||
21 |
8193 |
0 |
|||
22 |
8443 |
0 |
|||
MT |
0 |
0 |
|||
X |
13793 |
1 |
rs6615048 |
||
Y |
110 |
0 |
|||
Total |
560276 |
23 |
This error rate seems to me to
be quite acceptable and I wonder if this is the rate expected in scientific studies
using the same technology.
www.barbosadeoliveira.com/comparing