Biospecimen repositories and cytopathology

Biobanks as an Indispensable Tool in the "Era" of Precision Medicine: Key Role in the Management of Complex Diseases, Such as Melanoma

In recent years, medicine has undergone profound changes, strongly entering a new phase defined as the "era of precision medicine". In this context, patient clinical management involves various scientific approaches that allow for a comprehensive pathology evaluation: from preventive processes (where applicable) to genetic and diagnostic studies. In this scenario, biobanks play an important role and, over the years, have gained increasing prestige, moving from small deposits to large collections of samples of various natures. Disease-oriented biobanks are rapidly developing as they provide useful information for the management of complex diseases, such as melanoma. Indeed, melanoma, given its highly heterogeneous characteristics, is one of the oncologic diseases with the greatest clinical and therapeutic management complexity. So, the possibility of extrapolating tissue, genetic and imaging data from dedicated biobanks could result in more selective study approaches. In this review, we specifically analyze the several biobank types to evaluate their role in technology development, patient monitoring and research of new biomarkers, especially in the melanoma context.

Storage, Retention, and Use of Leftover Pathology Specimens: The Underestimated Treasures

The proper regulations for storage, retention, and use of archived specimens in pathology laboratories and academic institutions are yet to be established. These specimens could be used appropriately for research purposes. Ideal storage and retention in a controlled environment is necessary, and there is a lack of established rules regarding the ownership of the tissue specimens, paraffin blocks, and slides. Though there are numerous uses of formalin-fixed tissue specimens, blocks, and slides, there are also problems in archiving them that hinder their use. This review article addresses the above issues and proposes simple guidelines for the effective use of archived specimens.

The Role of Electronic Health Records in Advancing Genomic Medicine

Recent advances in genomic technology and widespread adoption of electronic health records (EHRs) have accelerated the development of genomic medicine, bringing promising research findings from genome science into clinical practice. Genomic and phenomic data, accrued across large populations through biobanks linked to EHRs, have enabled the study of genetic variation at a phenome-wide scale. Through new quantitative techniques, pleiotropy can be explored with phenome-wide association studies, the occurrence of common complex diseases can be predicted using the cumulative influence of many genetic variants (polygenic risk scores), and undiagnosed Mendelian syndromes can be identified using EHR-based phenotypic signatures (phenotype risk scores). In this review, we trace the role of EHRs from the development of genome-wide analytic techniques to translational efforts to test these new interventions to the clinic. Throughout, we describe the challenges that remain when combining EHRs with genetics to improve clinical care.

Comparison of Automated and Manual DNA Isolation Methods of Liquid-Based Cytology Samples

Liquid-based cytology (LBC) has been used as a diagnostic tool for cervical cancer for years and is now being adopted for other gynecological cancers. LBC represents an important challenge to ensure that the process yields representative biospecimens for quality control (QC) of diagnostic procedures. In this study, we compare QC parameters (integrity, yield and purity, and polymerase chain reaction [PCR] amplification) of DNA isolated from LBC (N = 296) using two different nucleic acid isolation methods, manual (n = 233) or automated (n = 63). We also evaluated two different types of cytological brushes for sampling from the cervix. Our results suggest that manual isolation (yield 22.81 ± 1.92 μg) resulted in increased DNA recovery when compared with automated isolation (yield 9.96 ± 1.11 μg) from LBC samples, with a p-value of <0.0003. We estimated that 98% (53/54) of the samples preserved the integrity of DNA and were suitable for standard molecular biology analyses. The β-globin gene was amplified in 100% (296/296) of the DNA samples by endpoint PCR. We found no significant difference between the performance of the cytological brushes (p value of <0.6711) in a general overview. However, when looking at the results from using each brush individually, the manual isolation method was statistically superior to the automated method. Our work illustrates the impact of good QC of preanalytic conditions, which will be important for the application of LBC for developing early detection methods for gynecological cancers.

Management of cytological material, pre-analytical procedures and bio-banking in effusion cytopathology

Serous effusion fluid is one of the most commonly encountered specimens in routine cytopathology practice. It provides invaluable information about the patient and the clinical status; but to get the most of it, specimen handling and processing must be carried out properly. Cytomorphology is the basis of a successful analysis which should complemented by ancillary tests when needed. A wide spectrum of ancillary techniques - ranging from immunocytochemistry and flow cytometry to different assays of molecular pathology - can be applied to serous effusions. This article describes the acquisition and management of serous effusion fluids, methods for preservation and transportation, different techniques of cytopreparation, application of immunocytochemistry, flow cytometry, and fluorescence in-situ hybridization (FISH), as well as DNA extraction for polymerase chain reaction (PCR) and next generation sequencing (NGS). Principles of bio-banking of effusion samples are also discussed which is getting more important in correlation with the developments in personalized medicine.

An Introduction to Starting a Biobank

The purpose of a biobank is to process, organize, and maintain various types of biospecimens that are to be utilized for both clinical and research-based services. There are different types of biobanks, so the goals of the biobank should be delineated at the outset of forming a biobank. The startup of a biobank benefits from accreditation and stringent adherence to standards of practice. Fundamental to these practices is the protection of privacy and informed consent. A budget must be developed, and sources of funding should be obtained to properly equip the designated space and personnel. The appropriate space for freezers and for biospecimen processing should be identified. Information technology is also a critical part of the biobank and effort should be expended to ensure that this aspect is effective and secure. Given the ethical concerns surrounding biospecimens, engagement with the public is also highly valuable.

Integrated morphologic and molecular analysis of Trichomonas vaginalis, Mycoplasma hominis, and human papillomavirus using cytologic smear preparations

Pathogenic microbes may colonize the female genital tract via sexual transmission and cause health issues like inflammation or malignancy, summarized as sexually transmitted disease (STD). A major representative of such pathogens is Trichomonas vaginalis (T.v.), whose role in the etiology of cervical cancer remains elusive. Traditional morphologic screening of cervical smears is able to detect T.v., although its identification may be complicated by look-alikes such as degenerated granulocytes and basal cells. In addition, the parasite's endosymbiont Mycoplasma hominis (M.h.) cannot be detected in the Pap test. This investigation was aimed at designing a PCR-based method to detect specific pathogenic germs by using cervical cytology slides to overcome morphologic uncertainty and increase diagnostic accuracy. To test our molecular screening method on T.v., M.h., and HPV in archival smears, we elaborated a multiplex PCR approach based on microdissection. This assay was applied to a minute quantity of starting material which harbored or was suspected to harbor T.v.; the resulting isolated DNA was used for subsequent molecular analyses of T.v., M.h., and HPV. We clarified the diagnosis of genital T.v. infection in 88 and 1.8% of morphologically suspicious and T.v.-negative cases, respectively. We also revealed a tendency of M.h. co-infection in high-risk HPV cases. In conclusion, a microdissection-based approach to detect pathogenic microbes such as T.v., HPV, and M.h. is a molecular tool easy to implement and may help to better understand the interactivity of these germs with respect to pathogenesis.