| Item | Cancer Case Number | Cancer Percentage (%) | Noncancer Case Number | Noncancer Percentage (%) | Total Case Number | Total Percentage (%) |
|---|---|---|---|---|---|---|
| Sample types | ||||||
| Cancer cohort/other conditions | 10,060 | 18.7 | 25,013 | 46.4 | 35,073 | 65.0 |
| Non-cancer individuals | 18,844 | 35.0 | - | - | 18,844 | 35.0 |
| Total | 28,904 | 53.6 | 25,013 | 46.4 | 53,917 | 100.0 |
| Origins of samples | ||||||
| Mainland | 11,885 | 22.0 | 28,807 | 53.4 | 40,692 | 75.5 |
| Sigapore | 2,657 | 4.9 | 288 | 0.5 | 2,945 | 5.5 |
| Macau | 4,302 | 8.0 | - | - | 4,302 | 8.0 |
| Taiwan | - | - | 5,184 | 9.6 | 5,184 | 9.6 |
| Hong Kong | - | - | 696 | 1.3 | 696 | 1.3 |
| Malaysia | - | - | 98 | 0.2 | 98 | 0.2 |
| Total | 18,844 | 35.0 | 35,073 | 65.0 | 53,917 | 100.0 |
| Item | MLH1 | MSH2 | MSH6 | PMS2 | Total Case Number | Total Percentage (%) |
|---|---|---|---|---|---|---|
| Coding | 422 | 501 | 610 | 361 | 1,894 | 8.9 |
| Non-coding | 4,108 | 9,973 | 2,491 | 2,910 | 19,482 | 91.1 |
| Total | 4,530 | 10,474 | 3,101 | 3,271 | 21,376 | 100.0 |
| Clinical Impact | Variant Number | Frequency (%) |
|---|---|---|
| Pathogenic | 146 | 7.7 |
| Likely pathogenic | 38 | 2.0 |
| Uncertain significance | 652 | 34.4 |
| Likely benign | 287 | 15.2 |
| Benign | 82 | 4.3 |
| Unclassified | 584 | 30.8 |
| Conflicting interpretation | 105 | 5.5 |
| Total | 1,894 | 100.0 |
| Item | Case Number | Frequency (%) |
|---|---|---|
| Digestive system | ||
| Sub-total | 18,413 | 83.0 |
| LS/HNPCC | 4,788 | 21.6 |
| Colon cancer | 8,399 | 37.9 |
| Gastric cancer | 2,261 | 10.2 |
| HCC | 2,057 | 9.3 |
| Esophageal cancer | 665 | 3.0 |
| Neoplastic intestinal polyps | 240 | 1.1 |
| Familial adenomatous polyposis | 3 | 0.0 |
| Non-digestive system | ||
| Sub-total | 3,766 | 17.0 |
| Breast cancer | 2,417 | 10.9 |
| Lung cancer | 500 | 2.3 |
| Papillary thyroid cancer | 204 | 0.9 |
| Gliomas | 23 | 0.1 |
| Insulinomas | 16 | 0.1 |
| Ovarian cancer | 14 | 0.1 |
| Endometrial cancer | 5 | 0.0 |
| Others | 587 | 2.6 |
| Total | 22,179 | 100.0 |
| Mutation Type | Variant Number | Frequency (%) |
|---|---|---|
| Missense | 709 | 37.4 |
| Synonymous SNV | 282 | 14.9 |
| Splice site | 78 | 4.1 |
| Frameshift insertion | 77 | 4.1 |
| Frameshift deletion | 69 | 3.6 |
| Nonsynonymous SNV | 50 | 2.6 |
| Intron variant | 48 | 2.5 |
| Nonsense | 44 | 2.3 |
| Stopgain | 28 | 1.5 |
| Nonframeshift insertion | 11 | 0.6 |
| Nonframeshift deletion | 10 | 0.5 |
| UTR5 variant | 6 | 0.3 |
| Splice acceptor | 4 | 0.2 |
| Splice donor | 3 | 0.2 |
| Inframe variant | 2 | 0.1 |
| UTR3 variant | 2 | 0.1 |
| Frameshift variant | 1 | 0.1 |
| Nonframeshift substitution | 1 | 0.1 |
| Stoploss | 1 | 0.1 |
| Unclassified | 468 | 24.7 |
| Total | 1,894 | 100.0 |
| Variant ID | Gene | Exon | HGVS cDNA | HGVS Protein | Mutation Type | Variant Impact | Case Number | Carrier Number | Carrier Rate (%) |
|---|---|---|---|---|---|---|---|---|---|
| 1 | MLH1 | 14 | c.1588_1590delTTC | p.Phe530del | Inframe variant | Pathogenic | 158 | 5 | 3.2 |
| 2 | MLH1 | 12 | c.1163_1164insT | p.Arg389Profs | Frameshift insertion | Pathogenic | 127 | 4 | 3.1 |
| 3 | MLH1 | 3 | c.265G>T | p.Glu89Ter | Nonsense | Pathogenic | 429 | 13 | 3.0 |
| 4 | MLH1 | 3 | c.243_244insA|c.244dupA | p.Thr82Asnfs | Frameshift insertion | Pathogenic | 172 | 5 | 2.9 |
| 5 | MLH1 | 2 | c.199G>A | p.Gly67Arg | Missense | Pathogenic | 371 | 10 | 2.7 |
| 6 | MLH1 | 16 | c.1852delAAG/c.1852_1854delAAG | p.Lys618del | Inframe variant | Pathogenic | 315 | 8 | 2.5 |
| 7 | MLH1 | 19 | c.2157dupT | p.Val720Cysfs | Frameshift insertion | Pathogenic | 196 | 4 | 2.0 |
| 8 | MLH1 | 14 | c.1591_1592del|c.1592_1593delTG | p.Val531Glyfs | Frameshift deletion | Pathogenic | 245 | 3 | 1.2 |
| 9 | MLH1 | 13 | c.1459C>T | p.Arg487Ter | Nonsense | Pathogenic | 633 | 7 | 1.1 |
| 10 | MLH1 | 5 | c.453+1G>T | - | Splice site | Likely pathogenic | 188 | 2 | 1.1 |
| 11 | MLH1 | 1 | c.157_160delGAGG | p.Gly54Alafs | Frameshift deletion | Pathogenic | 196 | 2 | 1.0 |
| 12 | MSH2 | 6 | c.943-1G>A | - | Splice site | Likely pathogenic | 1,200 | 42 | 3.5 |
| 13 | MSH2 | 3 | c.595T>C | p.Cys199Arg | Missense | Pathogenic | 292 | 10 | 3.4 |
| 14 | MSH2 | 8 | c.1277-1G>A | - | Splice site | Likely pathogenic | 118 | 2 | 1.7 |
| 15 | MSH2 | 11 | c.1738G>T | p.Glu580Ter | Nonsense | Pathogenic | 316 | 5 | 1.6 |
| 16 | MSH2 | 12 | c.1760delG | p.Gly587Alafs | Frameshift deletion | Pathogenic | 316 | 5 | 1.6 |
| 17 | MSH2 | 11 | c.1664delA|c.1665delA | p.Lys555fs | Frameshift deletion | Pathogenic | 138 | 2 | 1.4 |
| 18 | MSH2 | 3 | c.513delG | p.Lys172Asnfs | Frameshift deletion | Pathogenic | 285 | 4 | 1.4 |
| 19 | MSH2 | 9 | c.1457_1460delATGA | p.Asn486Thrfs | Frameshift deletion | Pathogenic | 2,371 | 33 | 1.4 |
| 20 | MSH2 | 14 | c.2292G>A | p.Trp764Ter | Nonsense | Pathogenic | 245 | 3 | 1.2 |
| 21 | MSH2 | 13 | c.2038C>T | p.Arg680Ter | Nonsense | Pathogenic | 341 | 4 | 1.2 |
| 22 | MSH2 | 8 | c.1147C>T | p.Arg383Ter | Nonsense | Pathogenic | 279 | 3 | 1.1 |
| 23 | MSH2 | 14 | c.2211-2A>C | p.Thr8Arg | Splice site | Likely pathogenic | 492 | 5 | 1.0 |
| 24 | MSH6 | 4 | c.2684dup | p.Asn897Lysfs*3 | Frameshift insertion | Pathogenic | 465 | 6 | 1.3 |
| 25 | PMS2 | 5 | c.478C>A | p.Gln160Lys | Missense | Pathogenic | 156 | 10 | 6.4 |
| 26 | PMS2 | 2 | c.121G>A | p.Glu41Lys | Stopgain | Pathogenic | 156 | 8 | 5.1 |
| 27 | PMS2 | 6 | c.673G>T | p.Glu225Ter | Stopgain | Pathogenic | 10,611 | 2 | 2.2 |