Cold Formalin Fixation Guarantees DNA Integrity in Formalin Fixed Paraffin Embedded Tissues: Premises for a Better Quality of Diagnostic and Experimental Pathology With a Specific Impact on Breast Cancer

Berrino, Enrico; Annaratone, Laura; Miglio, Umberto; Maldi, Elena; Piccinelli, Chiara; Peano, Erica; Balmativola, Davide; Cassoni, Paola; Pisacane, Alberto; Sarotto, Ivana; Venesio, Tiziana; Sapino, Anna; Marchiò, Caterina

doi:10.3389/fonc.2020.00173

Cited by 24 publications

(15 citation statements)

References 22 publications

(25 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These trends have been previously reported [ 19 , 22 , 23 ]; however, these differences were not observed in the FFPE samples, for which we had the largest sample size and the most recent mean collection date. This discrepancy may have occurred because storage conditions were different for the FFPE samples (room temperature versus cold temperature), and there may be disadvantages to using DNA extracted from FFPE samples stored at room temperature (as our samples were) relative to cooler temperatures [ 67 , 68 ]. In addition, a previous study on the extraction of HPV DNA concluded that the extraction protocol used for FFPE samples can significantly affect the results, and different HPV primers may be preferable to the GP5 + /6 + primers used in this study [ 69 ].…”

Section: Discussionmentioning

confidence: 99%

HPV genotyping by L1 amplicon sequencing of archived invasive cervical cancer samples: a pilot study

Warden

Cholli

Qin

et al. 2022

Infect Agents Cancer

View full text Add to dashboard Cite

Background Human papillomavirus (HPV) is the primary cause of invasive cervical cancer (ICC). The prevalence of various HPV genotypes, ranging from oncogenically low- to high-risk, may be influenced by geographic and demographic factors, which could have critical implications for the screening and prevention of HPV infection and ICC incidence. However, many technical factors may influence the identification of high-risk genotypes associated with ICC in different populations. Methods We used high-throughput sequencing of a single amplicon within the HPV L1 gene to assess the influence of patient age, race/ethnicity, histological subtype, sample type, collection date, experimental factors, and computational parameters on the prevalence of HPV genotypes detected in archived DNA (n = 34), frozen tissue (n = 44), and formalin-fixed paraffin-embedded (FFPE) tissue (n = 57) samples collected in the Los Angeles metropolitan area. Results We found that the percentage of off-target human reads and the concentration of DNA amplified from each sample varied by HPV genotype and by archive type. After accounting for the percentage of human reads and excluding samples with especially low levels of amplified DNA, the HPV prevalence was 95% across all ICC samples: HPV16 was the most common genotype (in 56% of all ICC samples), followed by HPV18 (in 21%). Depending upon the genotyping parameters, the prevalence of HPV58 varied up to twofold in our cohort. In archived DNA and frozen tissue samples, we detected previously established differences in HPV16 and HPV18 frequencies based on histological subtype, but we could not reproduce those findings using our FFPE samples. Conclusions In this pilot study, we demonstrate that sample collection, preparation, and analysis methods can influence the detection of certain HPV genotypes and must be carefully considered when drawing any biological conclusions based on HPV genotyping data from ICC samples.

show abstract

Section: Discussionmentioning

confidence: 99%

HPV genotyping by L1 amplicon sequencing of archived invasive cervical cancer samples: a pilot study

Warden

Cholli

Qin

et al. 2022

Infect Agents Cancer

View full text Add to dashboard Cite

show abstract

“…The surgical material should be managed according to ministerial guidelines regarding the traceability, collection, transport, and storage of cells and tissues for diagnostic investigations of Pathological Anatomy Laboratories 18 , 26-28 . In particular, the cold ischemic time (i.e.…”

Section: Pathological Evaluation After Neoadjuvant Therapymentioning

confidence: 99%

Pathological examination of breast cancer samples before and after neoadjuvant therapy: recommendations from the Italian Group for the Study of Breast Pathology - Italian Society of Pathology (GIPaM-SIAPeC)

et al. 2022

Self Cite

View full text Add to dashboard Cite

Summary Neoadjuvant therapy (NAT) in breast cancer is administered to downstage the tumor, de-escalate surgery, and provide prognostic information that can be used to tailor subsequent adjuvant therapy. In this respect, the pathological evaluation of both pre-NAT biopsies and post-NAT surgical specimens is crucial to precisely assess the treatment response. With the increasing possibilities of NAT protocols and the rising number of eligible patients, it has become extremely important to standardize the pathological response assessment. Here, we provide an update on the recommendations of the Italian Group for the Study of Breast Pathology - the Italian Society of Pathology (GIPaM-SIAPeC) for the analysis of breast cancer samples before and after NAT.

show abstract

“…In this respect, for FFPE tissue samples, the time of fixation is also important since formalin fixation impacts DNA/RNA fragmentation and therefore affects the success of downstream molecular analyses. Recently, the temperature of formalin fixation has been shown to matter [54,55], and cold fixation can be considered when aiming to obtain a lesser degree of nucleic acid degradation [54][55][56][57][58].…”

Section: A Focus On Cancer-oriented Biobanksmentioning

confidence: 99%

Basic principles of biobanking: from biological samples to precision medicine for patients

et al. 2021

Self Cite

View full text Add to dashboard Cite

The term “biobanking” is often misapplied to any collection of human biological materials (biospecimens) regardless of requirements related to ethical and legal issues or the standardization of different processes involved in tissue collection. A proper definition of biobanks is large collections of biospecimens linked to relevant personal and health information (health records, family history, lifestyle, genetic information) that are held predominantly for use in health and medical research. In addition, the International Organization for Standardization, in illustrating the requirements for biobanking (ISO 20387:2018), stresses the concept of biobanks being legal entities driving the process of acquisition and storage together with some or all of the activities related to collection, preparation, preservation, testing, analysing and distributing defined biological material as well as related information and data. In this review article, we aim to discuss the basic principles of biobanking, spanning from definitions to classification systems, standardization processes and documents, sustainability and ethical and legal requirements. We also deal with emerging specimens that are currently being generated and shaping the so-called next-generation biobanking, and we provide pragmatic examples of cancer-associated biobanking by discussing the process behind the construction of a biobank and the infrastructures supporting the implementation of biobanking in scientific research.

show abstract

Cold Formalin Fixation Guarantees DNA Integrity in Formalin Fixed Paraffin Embedded Tissues: Premises for a Better Quality of Diagnostic and Experimental Pathology With a Specific Impact on Breast Cancer

Cited by 24 publications

References 22 publications

HPV genotyping by L1 amplicon sequencing of archived invasive cervical cancer samples: a pilot study

HPV genotyping by L1 amplicon sequencing of archived invasive cervical cancer samples: a pilot study

Pathological examination of breast cancer samples before and after neoadjuvant therapy: recommendations from the Italian Group for the Study of Breast Pathology - Italian Society of Pathology (GIPaM-SIAPeC)

Basic principles of biobanking: from biological samples to precision medicine for patients

Contact Info

Product

Resources

About