Background
Methods
Subjects
Targeted resequencing
Probe design
Gene |
PTPN11
|
SOS1
|
BRAF
|
RAF1
|
KRAS
|
NRAS
|
HRAS
|
SHOC2
|
MAP2K1
|
MAP2K2
|
CBL
|
---|---|---|---|---|---|---|---|---|---|---|---|
Number of exons uploaded into DS
| 15 | 23 | 18 | 16 | 5 | 4 | 5 | 8 | 11 | 11 | 16 |
Number of exons entirely covered by DS with predicted success score >60%
| 14 | 23 | 18 | 16 | 5 | 3 | 5 | 8 | 11 | 11 | 16 |
Total exons covered by DS/ total exons uploaded into DS (%)
| 98.5 | ||||||||||
Number of exons successfully sequenced with coverage > 30
| 13 | 22 | 16 | 16 | 5 | 3 | 5 | 8 | 9 | 9 | 14 |
Total exons successfully sequenced/ total exons covered by DS (%)
| 92.4% |
Library preparation and sequencing
Data analysis
Sanger sequencing validation
Results
TSCA performance
Validation set
Patient ID | Gene | Mutation | Allele state | Mutation detected by TSCA sequencing | Coverage | Qscore |
---|---|---|---|---|---|---|
1
|
PTPN11
| Y63C | het | Y63C | 374 | 38 |
2
|
PTPN11
| N308D | het | N308D | 519 | 39 |
3
|
PTPN11
| T468M | het | T468M | 525 | 40 |
4
|
SOS1
| M279R | het | M279R | 390 | 39 |
5
|
SOS1
| I733N | het | I733N | 78 | 37 |
6
|
HRAS
| G12A | het | G12A | 20 | 37 |
Training set
Case | Phenotype | Gene | Mutation | Protein substitution | Allele state | Variant frequency | Coverage | Qscore | Reference |
---|---|---|---|---|---|---|---|---|---|
1
| NS |
PTPN11
| c.184 T > G | Y62D | het | 0.448 | 460 | 39 | [30] |
2
| NS |
PTPN11
| c.188A > G | Y63C | het | 0.521 | 190 | 39 | [9] |
3
| NS |
PTPN11
| c.188A > G | Y63C | het | 0.54 | 512 | 39 | [9] |
4
| NS |
PTPN11
| c.188A > G | Y63C | het | 0.481 | 1046 | 38 | [9] |
5
| NS |
PTPN11
| c.317A > C | D106A | het | 0.495 | 632 | 39 | [31] |
6
| NS |
PTPN11
| c.328G > A | E110K | het | 0.486 | 702 | 36 | [31] |
7
| NS |
PTPN11
| c.417 G > C | E139D | het | 0.498 | 406 | 38 | [30] |
8
| NS |
PTPN11
| c.661A > G | I221V | het | 0.482 | 737 | 39 |
p.s
|
9
| NS |
PTPN11
| c.767A > G | Q256R | het | 0.514 | 290 | 36 |
p.s
|
10
| NS |
PTPN11
| c.854 T > C | F285S | het | 0.406 | 64 | 39 | [30] |
11
| NS |
PTPN11
| c.922 A > G | N308D | het | 0.526 | 812 | 38 | [9] |
12
| NS |
PTPN11
| c.922 A > G | N308D | het | 0.508 | 1174 | 39 | [9] |
13
| NS |
PTPN11
| c.922 A > G | N308D | het | 0.505 | 3126 | 39 | [9] |
14
| NS |
PTPN11
| c.922 A > G | N308D | het | 0.486 | 3111 | 39 | [9] |
15
| NS |
PTPN11
| c.923 A > G | N308S | het | 0.555 | 119 | 40 | [30] |
16
| NS |
PTPN11
| c.1183G > T | D395Y | het | 0.556 | 561 | 38 |
p.s
|
16
| NS |
PTPN11
| c.1186 T > C | Y396H | het | 0.557 | 560 | 37 |
p.s
|
17
| NS |
PTPN11
| c.1226G > C | G409A | het | 0.444 | 178 | 38 | [32] |
18
| NS |
PTPN11
| c.1282G > T | V428L | het | 0.502 | 416 | 38 |
p.s
|
19
| LS |
PTPN11
| c.1403C > T | T468M | het | 0.467 | 319 | 40 | [20] |
20
| LS |
PTPN11
| c.1492 C > T | R498W | het | 0.573 | 185 | 35 | [33] |
21
| LS |
PTPN11
| c.1492 C > T | R498W | het | 0.521 | 142 | 38 | [33] |
22
| NS |
SOS1
| c.755 T > C | I252T | het | 0.528 | 212 | 39 | [34] |
23
| NS |
SOS1
| c.806 T > G | M269R | het | 0.564 | 140 | 38 | [34] |
24
| NS |
SOS1
| c.806 T > G | M269R | het | 0.496 | 391 | 38 | [34] |
25
| NS |
SOS1
| c.1310 T > A | I437N | het | 0.46 | 302 | 40 | [34] |
26
| NS |
SOS1
| c.1649 T > C | L550P | het | 0.516 | 275 | 39 | [34] |
27
| NS |
SOS1
| c.1649 T > C | L550P | het | 0.428 | 428 | 39 | [34] |
28
| NS |
SOS1
| c.2104 T > C | Y702H | het | 0.52 | 421 | 37 | [34] |
29
| NS |
SOS1
| c.2371C > A | L791I | het | 0.576 | 363 | 37 |
p.s
|
30
| NS |
SOS1
| c.2371C > A | L791I | het | 0.546 | 108 | 39 |
p.s
|
31
| NS/CFCS |
BRAF
| c.1694A > G | D565G | het | 0.463 | 341 | 39 |
p.s
|
32
| CFCS |
BRAF
| c.1802A > T | K601I | het | 0.538 | 1120 | 37 | [17] |
33
| CFC |
MEK2
| c.326C > T | A110 T | het | 0.505 | 299 | 37 |
p.s
|
34
| CFC |
MEK2
| c. 395 T > G | G132D | het | 0.533 | 227 | 38 | [35] |
35
| NS |
RAF1
| c.785 A > T | N262I | het | 0.504 | 135 | 39 |
p.s
|
36
| NS |
RAF1
| c.781C > T | P261S | het | 0.524 | 143 | 39 | [13] |
37
| NS |
CBL
| c.2350G > A | V784M | het | 0.428 | 173 | 36 |
p.s
|
Reproducibility
Discussion
Case n°8 | Case n°9 | Case n°10 | Case n°16 | Father case n°16 | Case n°18 | Mother case n°18 | |
---|---|---|---|---|---|---|---|
Sex
| |||||||
Short stature
| |||||||
Macrocephaly
| + | - | + | - | - | ||
Hypertelorism
| |||||||
Downslanting palpebral fissures
| |||||||
Palpebral ptosis
| - | - | + | - | + | + | + |
Epicanthal folds
| + | + | - | + | - | ||
Short broad nose
| + | + | - | + | - | - | |
Deeply grooved philtrum
| + | + | + | + | + | ||
High wide peaks of the vermilion
| + | + | + | + | + | + | + |
Micrognathia
| - | + | - | ||||
Low-set and/or posteriorly angulated ears with thick helices
| |||||||
Low posterior hairline
| - | + | + | - | - | + | - |
Thorax anomalies
| - | + | + | - | - | + | - |
Cardiac defect
| + | + | - | - | - | ||
- PVS
| - | + | + | - | - | - | - |
- ASD
| - | - | - | ||||
- VSD
| - | - | - | - | - | ||
- PDA
| - | + | - | - | - | ||
Arrhythmia
| - | - | - | - | - | WPW | - |
Renal anomaly
| - | - | - | - | - | - | - |
Cryptorchidism
| NA | - | - | + | NA | ||
Developmental delay or cognitive deficit
| |||||||
Alopecia
| - | - | + | + | - | ||
Pancreatic cyst
| + | - | - | - | - | ||
Angioma
| - | - | - | - | - | ||
Inheritance
| NT | pat | NT | mat | NT |