Table 1.
Summary of NGS approaches applied to study MSI or MMR-D in solid cancers in the past 5 years
| Year | Cancer type | No. of patients | No. positive for MMR-D/MSI | Sequencing approach | Platform | Sensitivity | Specificity | Ref |
|---|---|---|---|---|---|---|---|---|
| 2015 | CRC | 50 | 34% | TS | Illumina MiSeq | 100% | 100% | [31] |
| 2015 | CRC | 142 | 20.4% | TS by AmpliSeq Cancer Hotspot Panel | Personal Genome Machine | ND | ND | [63] |
| 2015 | CRC | 78 | ND | ES, TS | MSIplus | 97% | 100% | [40] |
| 2016 | CRC | 224 | 13% | ES, selective introns for 410-gene panel | MSK-IMPACT assay | 100% | 100% | [35] |
| 2016 | CRC | 243 | 11.7% | ES, RNAseq | Illumina HiSeq 2500 | 91-92% | 98-100% | [64] |
| 2017 | CRC | 138 | 1.4% | ES, introns | Foundation One (Foundation Medicine) | ND | ND | [65] |
| 2017 | CRC | 91 | ND | TS by ColonCore NGS panel | MSI-ColonCore | 97.9% | 100% | [36] |
| 2017 | CRC | 68 | 48.5% | TS by 111 loci smMIP panel | Illumina NextSeq 500 | 100% | 100% | [66] |
| Prostate | 33 | 33.3% | 100% | 100% | ||||
| EC | 43 | 55.8% | 95.8% | 100% | ||||
| 2014 | GC | 295 | 22% | WGS, RNA sequencing | Six platforms | ND | ND | [67] |
| 2018 | COUP | 389 | 1.8% | 592-gene panel | Illumina NextSeq | ND | ND | [68] |
| 2018 | Pancreatic cancer | 833 | 0.8% | ES, selective introns for 468-gene panel | MSK-IMPACT assay | ND | ND | [69] |
| 2018 | Prostate cancer | 91 | 29.7% | TS | mSINGS, MSIplus, large-panel NGS | 96.6% (MSIplus) | 100% (MSIplus) | [41] |
| 93.1% (large-panel NGS) | 98.4% (large-panel NGS) | |||||||
| 2014 | EC | 242 | 28.9% | ES | MSIsensor | ND | ND | [30] |
| 2014 | BC | 656 | ND | ES | NA | 88.4% | 77.1% | [70] |
| 2017 | BC | 640 | 1.7% | WGS | Illumina GAIIx, HiSeq 2000, or 2500 | ND | ND | [48] |
| 2013 | Across cancer types | 551 | 5.8% | TS | NA | ND | ND | [71] |
| 2014 | Across cancer types | 324 | ND | ES, TGS | mSINGS, ColoSeq, UW-OncoPlex | 97.8% | 98.32% | [28] |
| 2014 | Across cancer types | ND | ND | WGS | Complete Genomics Illumina short-read sequencing | 98% | 99% | [72] |
| 2016 | 23 cancer types | 7197 | ND | WGS, ES | Sputnik algorithm | ND | ND | [47] |
| 2016 | 18 cancer types | ND | EC 30% | ES | MISA, mSINGS, MOSAIC classifier | 95.8% | 97.6% | [9] |
| CRC 19% | ||||||||
| GC 19% | ||||||||
| 2017 | 6 cancer types | 458 | ND | WES | MANTIS | 97.18% | 99.68% | [29] |
| 2018 | 26 cancer types | 11348 | 3% | 592-gene NGS panel | Illumina NextSeq | 95.8% (compared to PCR) | 99.4% (compared to PCR) | [34] |
| 87.1% (compared to IHC) | 99.6% (compared to IHC) |
Note: BC, Breast cancer; CRC, Colorectal cancer; GC, Gastric cancer; EC, Endometrial cancer; COUP, Cancer of unknown primary; WGS, Whole-genome sequencing; ES, Exome sequencing; TS, Targeted sequencing; NA, not applicable; ND, not determined.