Comparison of Fresh Frozen Tissue With Formalin-Fixed Paraffin-Embedded Tissue for Mutation Analysis Using a Multi-Gene Panel in Patients With Colorectal Cancer

Xian, Gao; Li, Juan; Gong, Hai Feng; Yu, Guo; Liu, Peng; Hao, Li Qiang; Liu, Lianjie; Bai, Chen; Zhang, Wei

doi:10.3389/fonc.2020.00310

Cited by 56 publications

(50 citation statements)

References 27 publications

(44 reference statements)

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“…On the other hand, frozen tissues allow Fig. 3 Sensitivity analysis showing the impact of exclusion of any study on the summary effect better DNA preservation, but require constant lowtemperature maintenance [50]. In the present study, the HPV detection rate was slightly higher when frozen tissues were used.…”

Section: Publication Biasmentioning

confidence: 59%

Prevalence of human papillomavirus detection in ovarian cancer: a meta-analysis

Cherif

Thies

Taube

et al. 2021

Eur J Clin Microbiol Infect Dis

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We conducted a meta-analysis of published data to update and estimate the prevalence of HPV in ovarian cancer. A comprehensive literature search was performed according to the PRISMA guidelines. Eligible articles published from 1989 until 2020 by searching Web of Sciences, Pubmed, Embase, and the Cochrane Library Central databases were gathered. A pooled estimation of HPV prevalence with a 95% confidence interval (CI) was calculated based on a random effect model. Quantitative assessment of heterogeneity was explored using Cochrane test and I2. Additionally, publication bias, sensitivity, meta-regression, and subgroup analyses were also performed. Twenty-nine studies involving 2280 patients with ovarian cancer were included. The statistical heterogeneity was high (I2 = 88%, P<0.0001). The pooled prevalence of HPV in ovarian cancer cases was 15.9% (95% CI, 11–22). In subgroup analyses, the highest prevalence of HPV was reported by studies from Asia (30.9%; 95% CI, 20–44) and Eastern Europe (29.3%; 95% CI, 4.4–78). Furthermore, the most frequently detected HPV genotype was HPV16 (54%; 95% CI, 27.9–55), followed by HPV18 (23.2%; 95% CI, 18.8–28.2). Our meta-analysis suggests a great difference in the prevalence of HPV detected in ovarian cancer by different studies, which is not seen in strongly HPV-associated cancers such as cervical cancer. However, the prevalence varied markedly by geographic region. Considering the substantial heterogeneity found, more studies with control groups and precise assays measuring HPV mRNA expression are needed to further evaluate the link and causative aetiology between HPV and ovarian cancer.

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Section: Publication Biasmentioning

confidence: 59%

Prevalence of human papillomavirus detection in ovarian cancer: a meta-analysis

Cherif

Thies

Taube

et al. 2021

Eur J Clin Microbiol Infect Dis

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“…Secondly, the samples were in FFPE form and were not fresh frozen tissue (FFT). Quality of PCR might be slightly higher in FFT samples compared to FFPE; however, the difference is trivial and non-significant in many cases [35,36]. For instance a previous study declared the superiority of fresh tissue samples over FFPE [27].…”

Section: Discussionmentioning

confidence: 96%

Association of human papilloma virus (HPV) infection with oncological outcomes in urothelial bladder cancer

Moghadam

Mansori

Nowroozi

et al. 2020

Infect Agents Cancer

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Background: Bladder cancer is one of the leading causes of cancer death in adults worldwide. There are various risk factors described for the bladder cancer development including genetic background as well as environmental exposure. Currently, infectious agents such as human papilloma virus (HPV) has also been linked to bladder cancer risk. The current study aimed to evaluate the potential correlation between HPV infection and the oncological outcome in urothelial bladder cancer. Methods: Totally 106 tissue samples of histopathologically confirmed transitional cell carcinoma (TCC) of the urinary bladder were included in this study. The presence of high risk (types 16 and 18) and low risk (types 11 and 6) types of HPV was evaluated using polymerase chain reaction (PCR) followed by in situ hybridization. Results: Out of 106 bladder cancer patients, a total of 24 cases (22.6%) were positive HPV infection. The most common type of HPV detected was type 16 followed by types 11 and 18, and 6. According to independent T-test results, there was a significant association between mean age and HPV infection (P = 0.015). Moreover, our findings showed a significant relation between infection with HPV and tumor stage, tumor grade, muscle invasion of the tumor, as well as tumor recurrence. The results of Chi-square Test indicated that there is significant statistical association between types of HPV and tumor grade (P-Value = 0.044). Conclusion: Our findings indicated that a family history of cancer and HPV infection can be potential independent predictive factors for tumor recurrence in bladder cancer. Overall, the results of this study strongly indicate a significant relationship between HPV infection and an aggravated outcome of the disease and a higher risk of recurrence in patients with bladder cancer.

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“…In a cohort of 10 paired metastatic liver CRC specimens, a high mutational concordance was observed when 212 amplicon regions in 48 cancer-related genes were sequenced, revealing 21 identical mutation calls and only two differing mutations [ 33 ]. Furthermore, Gao et al conducted an extensive study using a 22-gene panel detecting 103 hotspot mutations in paired FFPE and fresh-frozen primary CRC tissues from 118 patients [ 34 ]. The investigators identified a concordance rate ranging from 73.8% to 100% and highlighted that important differences exist between the two tissue types.…”

Section: Discussionmentioning

confidence: 99%

The Mutational Concordance of Fixed Formalin Paraffin Embedded and Fresh Frozen Gastro-Oesophageal Tumours Using Whole Exome Sequencing

Chong

Starling

Rust

et al. 2021

JCM

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1. Background: The application of massively parallel sequencing has led to the identification of aberrant druggable pathways and somatic mutations within therapeutically relevant genes in gastro-oesophageal cancer. Given the widespread use of formalin-fixed paraffin-embedded (FFPE) samples in the study of this disease, it would be beneficial, especially for the purposes of biomarker evaluation, to assess the concordance between comprehensive exome-wide sequencing data from archival FFPE samples originating from a prospective clinical study and those derived from fresh-frozen material. 2. Methods: We analysed whole-exome sequencing data to define the mutational concordance of 16 matched fresh-frozen and FFPE gastro-oesophageal tumours (N = 32) from a prospective clinical study. We assessed DNA integrity prior to sequencing and then identified coding mutations in genes that have previously been implicated in other cancers. In addition, we calculated the mutant-allele heterogeneity (MATH) for these samples. 3. Results: Although there was increased degradation of DNA in FFPE samples compared with frozen samples, sequencing data from only two FFPE samples failed to reach an adequate mapping quality threshold. Using a filtering threshold of mutant read counts of at least ten and a minimum of 5% variant allele frequency (VAF) we found that there was a high median mutational concordance of 97% (range 80.1–98.68%) between fresh-frozen and FFPE gastro-oesophageal tumour-derived exomes. However, the majority of FFPE tumours had higher mutant-allele heterogeneity (MATH) scores when compared with corresponding frozen tumours (p < 0.001), suggesting that FFPE-based exome sequencing is likely to over-represent tumour heterogeneity in FFPE samples compared to fresh-frozen samples. Furthermore, we identified coding mutations in 120 cancer-related genes, including those associated with chromatin remodelling and Wnt/β-catenin and Receptor Tyrosine Kinase signalling. 4. Conclusions: These data suggest that comprehensive genomic data can be generated from exome sequencing of selected DNA samples extracted from archival FFPE gastro-oesophageal tumour tissues within the context of prospective clinical trials.

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Comparison of Fresh Frozen Tissue With Formalin-Fixed Paraffin-Embedded Tissue for Mutation Analysis Using a Multi-Gene Panel in Patients With Colorectal Cancer

Cited by 56 publications

References 27 publications

Prevalence of human papillomavirus detection in ovarian cancer: a meta-analysis

Prevalence of human papillomavirus detection in ovarian cancer: a meta-analysis

Association of human papilloma virus (HPV) infection with oncological outcomes in urothelial bladder cancer

The Mutational Concordance of Fixed Formalin Paraffin Embedded and Fresh Frozen Gastro-Oesophageal Tumours Using Whole Exome Sequencing

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