Table 2.
Examples of the application of NGS in cancer research
| Author and published data | Cancer | Sample source | The number of sequencing sample | Platform | The significant of result in PPPM |
|---|---|---|---|---|---|
| Marchetti et al. 2014 [49] | Non-small-cell lung cancer (NSCLC) | DNA from blood circulating tumor cells (CTCs) | 59 (37 NSCLC with EGFR mutation, 10 breast cancer without EGFR mutation and 12 healthy donors) | Roche 454 GS junior | Analysis of CTCs based on CellSearch System and NGS is a reliable method to detect EGFR mutation, which have important significance in stratifying patients |
| Vignot et al. 2013 [7] | NSCLC | DNA from archived surgical samples | 30 (15 pairs of primary matched metastatic tumor tissues) | HiSeq2000 (Illumina, San Diego, CA) | Genomic somatic alternations of primary tumor tissue may provide much of the relevant information required to guide treatment on recurrence |
| Hagemann et al. 2014 [50] | NSCLC | DNA from formalin-fixed, paraffin-embedded (FFPE) tumor tissue | 209 (147 adenocarcinoma, 4 large cell neuroendocrine, 9 poorly differentiated, 6 sarcomatoid, 36 squamous cells) | Illumina HiSeq 2000, MiSeq, HiSeq 2500 | Based on NGS well-chosen FFPE tissue can provide relevant genomic information such as potential actionable mutations |
| Beltran et al. 2012 [51] | Advanced prostate cancer (PCa) | DNA from formalin-fixed, paraffin-embedded (FFPE) tumor tissue | 45 (25 metastatic castration resistant PCa, 4 metastatic hormone-naive PCas, and 16 primary localized PCas) | HiSeq2000® (Illumina-Solexa) | Based on NGS, comprehensively genomics information derived from FFPE tissue has the potential to select appropriate targeted therapy patients, discover new biomarkers, drug targets |
| Berger et al. 2011 [52] | PCa | DNA from tumor tissue | 14 (7 tumor/normal tissue pairs) | Illumina GA II sequencer | The first whole genome sequencing analysis of human prostate cancer promising to establish genomics criterion to stratify patients, uncover mechanisms of carcinogenesis and identifies novel targets for therapeutic intervention |
| Weisman et al. 2016 [53] | Breast cancer | DNA from triple negative breast cancer tissue | 78 (39 tumor/normal tissue pairs) | HiSeq2000® (Illumina-Solexa) | This study identified the triple negative breast cancers with apocrine differentiation as a distinct subset, which elevate the precision treatment of triple negative breast cancer |
| Janku et al. 2014 [54] | Hepatocelluar carcinoma(HCC) | DNA from archived surgical samples | 14 (4 liver biopsy, 3 liver resection, 1 liver transplant, 4 metastatic lesion, 2 not available) | HiSeq2000® (Illumina-Solexa) | This study provide a comprehensive genomic profiling of advanced HCC and the result of targeted therapy and highlight the important role of NGS based genomics in cancer research |
| Ross et al. 2014 [55] | Intrahepatic cholangiocarcinomas (ICC) | DNA from formalin-fixed, paraffin-embedded (FFPE) tumor tissue | 28 (16 liver biopsies, 10 liver resections, 1 in lymph node metastasis, 1 in lung metastasis) | (Illumina HiSEquation 2000 (Illumina Inc., San Diego, CA) | This study provide a comprehensive genomic profiling of ICC, in which genomic alternations have the potential to determine the personal therapies and discover novel druggable target |
| Ward et al. 2016 [56] | Bladder cancer | DNA from urine cell pellets | 231 (120 primary bladder cancer, 20 non-cancer, 91 bladder cancer patients post-TURBT) | Illumina MiSeq | This non-invasion method detecting reported bladder cancer mutations based on sequencing of DNA from urine cell pellets has 70% sensitivity and 97% specificity |
| Liang et al. 2012 [57] | Pancreatic adenocarcinoma (PA) | DNA from tumor tissue and peripheral blood mononuclear cells (control) | 6 (3 paired tumor/normal samples) | Illumina HiSeq 2000 | The whole genome sequencing generated comprehensive genomic information of 3 PA patients provide individually potential tumorigenic mechanisms and visibe therapeutic targets |
| Kim et al. 2014 [58] | Bladder cancer | DNA from tumor tissue and peripheral blood mononuclear cells (control) | 218 (109 patients with tumor tissue and germline blood) | Illumina HiSeq 2000/2500 | This study demonstrated the relationship between genomic mutations and treatment outcomes, and genomic markers can guide personal treatment and elevate the therapy efficiency |