Table 2. Number of samples per validated variants in the targeted gene panel.
| Locus | Ref | Var | Gene | Variant type | Status (1=novel, 0=known) | AA-Normal Het (30) | AA-Normal Hom (30) | AA-Adenoma Het (21) | AA-Adenoma Hom (21) | AA-Ad. Adenoma Het (33) | AA-Ad. Adenoma Hom (33) | AA-CRC Het (56) | AA-CRC Hom (56) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 63409685 | C | T | AMER1 | intronic | 1 | 2 | 0 | 1 | 0 | 1 | 0 | 1 | 0 |
| 63410110 | T | C | AMER1 | synonymous SNV | 0 | 8 | 16 | 10 | 9 | 9 | 13 | 8 | 33 |
| 63412291 | C | G | AMER1 | non-synonymous SNV | 0 | 2 | 1 | 3 | 0 | 0 | 0 | 4 | 1 |
| 63412690 | A | C | AMER1 | non-synonymous SNV | 0 | 13 | 6 | 9 | 2 | 13 | 2 | 27 | 10 |
| 112043384 | T | G | APC | intronic | 0 | 6 | 0 | 3 | 0 | 7 | 1 | 12 | 0 |
| 112103015 | C | A | APC | stopgain | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| 112116592 | C | T | APC | stopgain | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 |
| 112128191 | C | T | APC | stopgain | 0 | 0 | 0 | 1 | 0 | 2 | 0 | 2 | 0 |
| 112136947 | A | T | APC | intronic | 0 | 3 | 0 | 2 | 0 | 3 | 0 | 3 | 0 |
| 112151261 | C | T | APC | stopgain | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 0 |
| 112154942 | C | T | APC | stopgain | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 1 | 0 |
| 112154980 | T | A | APC | stopgain | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| 112157658 | G | T | APC | stopgain | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| 112162854 | T | C | APC | synonymous SNV | 0 | 11 | 1 | 7 | 2 | 14 | 2 | 17 | 6 |
| 112164561 | G | A | APC | synonymous SNV | 0 | 16 | 5 | 14 | 6 | 20 | 7 | 27 | 16 |
| 112173553 | T | G | APC | synonymous SNV | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| 112173899 | C | T | APC | non-synonymous SNV | 0 | 1 | 0 | 1 | 0 | 2 | 0 | 3 | 0 |
| 112174096 | C | A | APC | stopgain | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| 112174763 | A | T | APC | stopgain | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| 112175023 | A | G | APC | synonymous SNV | 0 | 3 | 0 | 2 | 0 | 4 | 0 | 3 | 0 |
| 112175030 | G | A | APC | non-synonymous SNV | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 0 |
| 112175069 | C | T | APC | stopgain | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 2 | 0 |
| 112175207 | G | T | APC | stopgain | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 |
| 112175399 | A | T | APC | stopgain | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 1 | 0 |
| 112175576 | C | T | APC | stopgain | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0 | 0 |
| 112175639 | C | T | APC | stopgain | 0 | 0 | 0 | 2 | 0 | 4 | 0 | 2 | 0 |
| 112175770 | G | A | APC | synonymous SNV | 0 | 17 | 5 | 13 | 7 | 20 | 8 | 26 | 14 |
| 112176325 | G | A | APC | synonymous SNV | 0 | 19 | 4 | 14 | 6 | 21 | 6 | 26 | 17 |
| 112176541 | C | G | APC | synonymous SNV | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 2 | 0 |
| 112176559 | T | G | APC | synonymous SNV | 0 | 18 | 4 | 13 | 7 | 19 | 8 | 26 | 17 |
| 112176756 | T | A | APC | non-synonymous SNV | 0 | 3 | 26 | 4 | 17 | 8 | 24 | 4 | 50 |
| 112176918 | G | C | APC | non-synonymous SNV | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| 112177171 | G | A | APC | synonymous SNV | 0 | 16 | 5 | 14 | 6 | 21 | 7 | 31 | 15 |
| 112178492 | C | T | APC | synonymous SNV | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 0 |
| 112178795 | G | A | APC | non-synonymous SNV | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 0 |
| 112178995 | A | G | APC | synonymous SNV | 0 | 7 | 0 | 3 | 0 | 6 | 0 | 6 | 2 |
| 112179909 | C | A | APC | intronic | 0 | 9 | 1 | 9 | 1 | 12 | 0 | 20 | 3 |
| 27057621 | A | C | ARID1A | intronic | 0 | 3 | 0 | 0 | 0 | 8 | 0 | 0 | 0 |
| 27089446 | G | C | ARID1A | intronic | 0 | 2 | 0 | 0 | 0 | 5 | 1 | 1 | 0 |
| 27089585 | C | A | ARID1A | synonymous SNV | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 |
| 27101278 | C | T | ARID1A | synonymous SNV | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| 27102075 | G | A | ARID1A | synonymous SNV | 0 | 2 | 0 | 2 | 0 | 0 | 0 | 2 | 0 |
| 27102188 | A | G | ARID1A | non-synonymous SNV | 0 | 1 | 0 | 4 | 0 | 7 | 0 | 7 | 0 |
| 27105676 | G | T | ARID1A | stopgain | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| 27106323 | C | T | ARID1A | synonymous SNV | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 4 | 0 |
| 140434597 | G | A | BRAF | intronic | 0 | 7 | 0 | 4 | 0 | 6 | 0 | 5 | 0 |
| 140449071 | C | G | BRAF | intronic | 0 | 7 | 15 | 9 | 7 | 20 | 8 | 28 | 18 |
| 140449150 | T | C | BRAF | synonymous SNV | 0 | 10 | 13 | 11 | 5 | 20 | 8 | 30 | 18 |
| 140481511 | A | C | BRAF | intronic | 0 | 2 | 0 | 2 | 0 | 0 | 0 | 3 | 0 |
| 140487360 | G | A | BRAF | non-synonymous SNV | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| 79950497 | C | T | DHFR,MSH3 | intronic | 0 | 6 | 4 | 6 | 2 | 3 | 2 | 14 | 5 |
| 79950508 | C | T | DHFR,MSH3 | intronic | 0 | 4 | 0 | 1 | 0 | 3 | 0 | 5 | 0 |
| 79950512 | A | G | DHFR,MSH3 | intronic | 0 | 5 | 14 | 1 | 8 | 3 | 8 | 13 | 26 |
| 153245446 | G | A | FBXW7 | non-synonymous SNV | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| 153247138 | G | T | FBXW7 | intronic | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| 153247289 | G | A | FBXW7 | non-synonymous SNV | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 2 | 0 |
| 153247366 | C | T | FBXW7 | non-synonymous SNV | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| 153303509 | C | T | FBXW7 | intronic | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 0 |
| 25362854 | C | T | KRAS | intronic | 0 | 11 | 3 | 12 | 0 | 10 | 0 | 24 | 5 |
| 25368462 | C | T | KRAS | synonymous SNV | 0 | 0 | 29 | 0 | 21 | 1 | 32 | 1 | 53 |
| 25398255 | G | T | KRAS | non-synonymous SNV | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| 25398281 | C | T | KRAS | non-synonymous SNV | 0 | 0 | 0 | 3 | 0 | 5 | 0 | 9 | 0 |
| 25398284 | C | T | KRAS | non-synonymous SNV | 0 | 0 | 0 | 3 | 0 | 2 | 0 | 12 | 0 |
| 25398285 | C | A | KRAS | non-synonymous SNV | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 1 | 0 |
| 25398285 | C | T | KRAS | non-synonymous SNV | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 2 | 0 |
| 79960955 | G | A | MSH3 | intronic | 0 | 11 | 5 | 10 | 4 | 16 | 1 | 24 | 7 |
| 79966029 | G | A | MSH3 | synonymous SNV | 0 | 6 | 1 | 11 | 0 | 5 | 2 | 16 | 0 |
| 79966197 | G | A | MSH3 | intronic | 0 | 11 | 5 | 11 | 4 | 19 | 1 | 26 | 5 |
| 79968496 | C | T | MSH3 | intronic | 0 | 5 | 3 | 3 | 3 | 11 | 1 | 13 | 3 |
| 80024685 | C | A | MSH3 | non-synonymous SNV | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 |
| 80024738 | A | G | MSH3 | non-synonymous SNV | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 |
| 80024783 | G | A | MSH3 | non-synonymous SNV | 0 | 1 | 0 | 0 | 0 | 5 | 0 | 2 | 0 |
| 80083459 | G | A | MSH3 | synonymous SNV | 0 | 1 | 0 | 0 | 0 | 2 | 0 | 1 | 0 |
| 80149981 | A | G | MSH3 | non-synonymous SNV | 0 | 2 | 27 | 4 | 16 | 7 | 23 | 5 | 48 |
| 80160610 | T | A | MSH3 | intronic | 0 | 5 | 2 | 4 | 0 | 4 | 1 | 12 | 1 |
| 80168937 | G | A | MSH3 | non-synonymous SNV | 0 | 11 | 15 | 10 | 8 | 19 | 10 | 22 | 30 |
| 48022981 | G | T | MSH6 | intronic | 0 | 10 | 3 | 12 | 1 | 11 | 1 | 23 | 4 |
| 48023115 | T | C | MSH6 | synonymous SNV | 0 | 9 | 1 | 5 | 1 | 7 | 1 | 14 | 1 |
| 48026286 | C | T | MSH6 | synonymous SNV | 0 | 4 | 0 | 2 | 0 | 4 | 0 | 7 | 0 |
| 48027375 | T | C | MSH6 | synonymous SNV | 0 | 4 | 0 | 2 | 0 | 7 | 0 | 5 | 1 |
| 48030692 | T | A | MSH6 | synonymous SNV | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| 48030838 | A | T | MSH6 | intronic | 0 | 10 | 2 | 12 | 0 | 8 | 1 | 17 | 2 |
| 48032908 | A | G | MSH6 | intronic | 1 | 1 | 0 | 1 | 0 | 0 | 0 | 2 | 0 |
| 48032937 | T | C | MSH6 | intronic | 0 | 4 | 25 | 4 | 17 | 9 | 21 | 12 | 40 |
| 48033514 | T | C | MSH6 | intronic | 0 | 0 | 0 | 2 | 0 | 2 | 0 | 1 | 0 |
| 48033545 | A | C | MSH6 | intronic | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| 48033551 | C | G | MSH6 | intronic | 0 | 4 | 20 | 3 | 11 | 8 | 9 | 13 | 34 |
| 48033700 | G | A | MSH6 | non-synonymous SNV | 0 | 1 | 0 | 2 | 0 | 0 | 0 | 2 | 0 |
| 178917005 | A | G | PIK3CA | intronic | 0 | 8 | 7 | 11 | 2 | 16 | 3 | 28 | 7 |
| 178921639 | C | A | PIK3CA | intronic | 0 | 12 | 16 | 11 | 9 | 15 | 14 | 24 | 25 |
| 178922274 | C | A | PIK3CA | intronic | 0 | 6 | 17 | 11 | 9 | 8 | 14 | 14 | 26 |
| 178927345 | T | C | PIK3CA | intronic | 0 | 5 | 1 | 5 | 0 | 5 | 0 | 9 | 1 |
| 178927410 | A | G | PIK3CA | non-synonymous SNV | 0 | 4 | 2 | 7 | 0 | 12 | 2 | 23 | 1 |
| 178947985 | C | G | PIK3CA | intronic | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| 178948196 | A | G | PIK3CA | intronic | 0 | 6 | 0 | 4 | 1 | 4 | 0 | 6 | 0 |
| 48575700 | T | C | SMAD4 | intronic | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| 48584420 | G | A | SMAD4 | intronic | 0 | 3 | 0 | 1 | 0 | 1 | 0 | 3 | 0 |
| 48584624 | T | C | SMAD4 | intronic | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| 48591762 | G | A | SMAD4 | intronic | 0 | 1 | 0 | 9 | 1 | 7 | 0 | 9 | 0 |
| 48592020 | T | C | SMAD4 | intronic | 0 | 2 | 0 | 1 | 0 | 1 | 0 | 3 | 0 |
| 48602941 | G | C | SMAD4 | intronic | 0 | 1 | 0 | 4 | 0 | 0 | 0 | 1 | 0 |
| 70117450 | G | A | SOX9 | intronic | 0 | 3 | 0 | 1 | 0 | 0 | 1 | 3 | 1 |
| 70118935 | C | T | SOX9 | synonymous SNV | 0 | 10 | 0 | 3 | 0 | 3 | 0 | 16 | 1 |
| 70120551 | A | C | SOX9 | intronic | 0 | 13 | 1 | 8 | 0 | 11 | 3 | 19 | 0 |
| 114912081 | G | A | TCF7L2 | intronic | 0 | 1 | 0 | 2 | 0 | 2 | 0 | 4 | 0 |
| 114920452 | T | C | TCF7L2 | intronic | 1 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 |
| 30686414 | A | G | TGFBR2 | intronic | 0 | 11 | 4 | 10 | 3 | 16 | 4 | 23 | 5 |
| 30713126 | T | A | TGFBR2 | intronic | 0 | 6 | 0 | 10 | 0 | 12 | 0 | 13 | 1 |
| 30713619 | C | T | TGFBR2 | non-synonymous SNV | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 |
| 30713674 | A | G | TGFBR2 | synonymous SNV | 0 | 6 | 0 | 3 | 0 | 3 | 0 | 10 | 0 |
| 30713842 | C | T | TGFBR2 | synonymous SNV | 0 | 2 | 0 | 1 | 0 | 2 | 0 | 2 | 0 |
| 30729931 | C | T | TGFBR2 | synonymous SNV | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 2 | 0 |
| 7574003 | G | A | TP53 | stopgain | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 0 |
| 7576501 | G | A | TP53 | intronic | 0 | 1 | 0 | 0 | 0 | 2 | 0 | 5 | 0 |
| 7577120 | C | T | TP53 | non-synonymous SNV | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 2 | 0 |
| 7578210 | T | C | TP53 | synonymous SNV | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 |
| 7578212 | G | A | TP53 | stopgain | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 0 |
| 7578406 | C | T | TP53 | non-synonymous SNV | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | 0 |
| 7579311 | C | A | TP53 | intronic | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| 7579472 | G | C | TP53 | non-synonymous SNV | 0 | 21 | 0 | 14 | 0 | 22 | 0 | 34 | 0 |
| 7579801 | G | C | TP53 | intronic | 0 | 23 | 0 | 12 | 1 | 20 | 0 | 36 | 0 |