Table 4.
Confirmation of genotypes from 26 ambiguous variations calls
| |
European |
African |
Asian |
|
Huvariome |
|||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chromosome | Position | Reference base | Amino acid change | Gene | NA12156 | NA12878 | NA18507 | NA18517 | NA19129 | NA19240 | NA18555 | NA18956 | Change | European | African | Asian |
| 2 |
227829345 |
G |
ASP,TYR |
COL4A3 |
K |
G |
G |
G |
G |
G |
G |
G |
K |
G:T |
|
G:T |
| 6 |
71029714 |
T |
GLU,GLY |
COL9A1 |
Y |
T |
T |
T |
T |
T |
T |
T |
Y |
T:T |
T:T |
T:T |
| 14 |
70059717 |
T |
TYR,CYS |
ADAM20 |
Y |
T |
T |
T |
T |
T |
T |
T |
Y |
T:T |
T:T |
T:T |
| 16 |
28511156 |
T |
ASN,THR |
SULT1A2 |
K |
T |
T |
T |
T |
T |
T |
T |
K |
T:G |
T:G |
T:G |
| 9 |
100837151 |
C |
PRO,LEU |
COL15A1 |
C |
Y |
C |
C |
C |
C |
C |
C |
Y |
C:C |
|
|
| 14 |
69994396 |
T |
TYR,HIS |
ADAM21 |
T |
Y |
T |
T |
T |
T |
T |
T |
Y |
T:T |
T:T |
T:T |
| 16 |
28514697 |
G |
PRO,LEU |
SULT1A2 |
G |
R |
G |
G |
G |
G |
G |
G |
R |
G:A |
G:A |
|
| 2 |
227632472 |
G |
PRO,LEU |
COL4A4 |
G |
G |
R |
G |
G |
G |
G |
G |
R |
|
G:A |
|
| 2 |
237945216 |
G |
ARG,TRP |
COL6A3 |
G |
G |
R |
G |
G |
G |
G |
G |
R |
|
G:A |
|
| 6 |
32286548 |
C |
GLY,ARG |
NOTCH4 |
C |
C |
Y |
C |
C |
C |
C |
C |
Y |
|
C:T |
|
| 10 |
123233227 |
C |
ARG,GLN |
FGFR2 |
C |
C |
Y |
C |
C |
C |
C |
C |
Y |
C:C |
C:C |
C:C |
| 15 |
72802259 |
A |
ILE,THR |
CYP1A1 |
A |
A |
R |
A |
A |
A |
A |
A |
R |
|
A:G |
|
| 15 |
82491107 |
T |
MET,THR |
ADAMTSL3 |
T |
T |
Y |
T |
T |
T |
T |
T |
Y |
|
T:C |
|
| 19 |
46210061 |
T |
ILE,THR |
CYP2B6 |
T |
T |
Y |
T |
T |
T |
T |
T |
Y |
T:T |
T:T |
T:T |
| 4 |
73407648 |
C |
GLY,ARG |
ADAMTS3 |
C |
C |
C |
Y |
C |
C |
C |
C |
Y |
|
C:T |
|
| 6 |
46728211 |
C |
ARG,PRO |
CYP39A1 |
C |
C |
C |
S |
C |
C |
C |
C |
S |
C:G |
C:G |
|
| 7 |
99283117 |
G |
ARG,GLN |
CYP3A43 |
G |
G |
G |
R |
G |
G |
G |
G |
R |
|
G:A |
|
| 10 |
96474119 |
G |
VAL,LEU |
CYP2C18 |
G |
G |
G |
K |
G |
G |
G |
G |
K |
|
G:T |
|
| 10 |
96698964 |
A |
HIS,ARG |
CYP2C9 |
A |
A |
A |
R |
A |
A |
A |
A |
R |
|
A:G |
|
| 15 |
76845583 |
G |
PRO,LEU |
ADAMTS7 |
G |
G |
G |
R |
G |
G |
G |
G |
R |
|
G:A |
|
| 1 |
120269806 |
C |
GLY,ARG |
NOTCH2 |
C |
C |
C |
C |
C |
Y |
C |
C |
Y |
C:C |
C:C |
C:C |
| 8 |
24420887 |
C |
PRO,LEU |
ADAM7 |
C |
C |
C |
C |
C |
Y |
C |
C |
Y |
C:C |
C:C |
C:C |
| 17 |
38961570 |
G |
PRO,LEU |
ETV4 |
G |
G |
G |
G |
G |
G |
R |
G |
R |
|
|
G:A |
| 21 |
46365928 |
C |
PRO,THR |
COL6A2 |
C |
C |
C |
C |
C |
C |
M |
C |
M |
|
|
C:A |
| 2 |
189622367 |
G |
PRO,LEU |
COL5A2 |
G |
G |
G |
G |
G |
G |
G |
R |
R |
|
|
G:A |
| 5 | 129100767 | C | THR,ILE | ADAMTS19 | C | C | C | C | C | C | C | T | T | C:T | ||
Results from Huvariome analysis of 26 selected coding SNVs to disambiguate genetic variation determined by Ng et al. 2009 [24]. The first 7 columns display the normal variations and their proposed functional impact, determined by Ng et al. 2009. The base changes are presented as the IUPAC codes per sample (e.g. NA12156), which are grouped by populations, CEU (NA12156, NA12878), YRI (NA18507, NA18517, NA19129, NA19240), Asian (NA18555, NA18956), with the impacted bases denoted with bold letters, and in the column titled “change”. The last three columns contain the genotypes called for the three populations present in Huvariome Core and the Diversity Panel (European, African, and Asian). The Huvariome genotypes highlighted as bold demonstrate that Huvariome calls homozygous reference while the genotypes are heterozygous reference.