Hot Topics in Medicine, Genetics and Biology 2020
by Susan Mahler Zneimer Ph.D. (Author)
Biological science, and in particular genetics, is expanding rapidly in its research and development, and with its progress into medicine, has the ability to touch people’s lives in the most profound ways. Much of what we know in medicine today has been learned in just the last 50 to 100 years. Biological research and medicine have helped us cope with the burgeoning list of diseases for which we are at risk, and yet the list of diseases seems to keep growing. It is time we understand more about how biology and genetics plays a role in our health and well-being and how we are diagnosed and treated for different disease in our world.
Cytogenetic Abnormalities: Chromosomal, FISH and Microarray-Based Clinical Reporting
by Susan Mahler Zneimer Ph.D. (Author)
Cytogenetics is the study of the structure and function of chromosomes in relation to phenotypic expression.Chromosomal abnormalities underlie the development of a wide variety of diseases and disorders ranging from Down syndrome to cancer, and are of widespread interest in both basic and clinical research.
Cytogenetic Abnormalities: Chromosomal, FISH, and Microarray-Based Clinical Reporting is a practical guide that describes cytogenetic abnormalities, their clinical implications and how best to report and communicate laboratory findings in research and clinical settings. The text first examines chromosomal, FISH, and microarray-based analyses in constitutional disorders. Using these same methodologies, the book's focus shifts to acquired abnormalities in cancers. Both sections provide illustrative examples of cytogenetic abnormalities and how to communicate these findings in standardized laboratory reports.
Providing both a wealth of cytogenetic information, as well as practical guidance on how best to communicate findings to fellow research and medical professionals, Cytogenetic Abnormalities will be an essential resource for cytogeneticists, laboratory personnel, clinicians, research scientists, and students in the field.
Cytogenetic Laboratory Management, Chromosomal, FISH and Microarray-based Best Practices and Procedures
by Susan Mahler Zneimer Ph.D. (Author)
Cytogenetic Laboratory Management: Chromosomal, FISH and Microarray-Based Best Practices and Procedures is a practical guide that describes how to develop and implement best practice processes and procedures in the genetic laboratory setting. The text first describes good laboratory practices, including quality management, design control of tests and FDA guidelines for laboratory developed tests, and pre-clinical validation study designs. The second focus of the book describes best practices for staffing and training, including cost of testing, staffing requirements, process improvement using Six Sigma techniques, training and competency guidelines and complete training programs for cytogenetic and molecular genetic technologists. The third part of the text provides step-wise standard operating procedures for chromosomal, FISH and microarray-based tests, including pre-analytic, analytic and post-analytic steps in testing, and divided into categories by specimen type, and test-type.
All three sections of the book include example worksheets, procedures, and other illustrative examples that can be downloaded from the Wiley website to be used directly without having to develop prototypes in your laboratory.
Providing both a wealth of information on laboratory management and molecular and cytogenetic testing, Cytogenetic Laboratory Management will be an essential tool for laboratorians world-wide in the field of laboratory testing and genetics testing in particular.
Incidence of X and Y Chromosomal Aneuploidy in a Large Child Bearing Population
Samango-Sprouse, C., Zneimer, S.M., et al., (2016) Incidence of X and Y Chromosomal Aneuploidy in a Large Child Bearing Population. PLOS ONE DOI:10.1371/journal.pone. 0161045 August 11, 2016.
Background: X&Y chromosomal aneuploidies are among the most common human whole-chromosomal copy number changes, but the population-based incidence and prevalence in the child-bearing population is unclear.
A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis.
Bik, E, Zneimer, S. et. al., (2019) A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis. PLOS ONE PONE-D-18-10359R2. May 2019.
Abstract: The composition of the vaginal microbiome, including both the presence of pathogens involved in sexually transmitted infections (STI) as well as commensal microbiota, has been shown to have important associations for a woman’s reproductive and general health. Currently, healthcare providers cannot offer comprehensive vaginal microbiome screening, but are limited to the detection of individual pathogens, such as high-risk human papillomavirus (hrHPV), the predominant cause of cervical cancer. There is no single test on the market that combines HPV, STI, and microbiome screening. Here, we describe a novel inclusive vaginal health assay that combines self-sampling with sequencing-based HPV detection and genotyping, vaginal microbiome analysis, and STI-associated pathogen detection. The assay includes genotyping and detection of 14 hrHPV types, 5 low-risk HPV types (lrHPV), as well as the relative abundance of 31 bacterial taxa of clinical importance, including Lactobacillus, Sneathia, Gardnerella, and 3 pathogens involved in STI, with high sensitivity, specificity, and reproducibility. For each of these taxa, reference ranges were determined in a group of 50 self-reported healthy women. The HPV sequencing portion of the test was evaluated against the digene High-Risk HPV HC2 DNA test. For hrHPV genotyping, agreement was 95.3% with a kappa of 0.804 (601 samples); after removal of samples in which the digene hrHPV probe showed cross-reactivity with lrHPV types, the sensitivity and specificity of the hrHPV genotyping assay were 94.5% and 96.6%, respectively, with a kappa of 0.841. For lrHPV genotyping, agreement was 93.9% with a kappa of 0.788 (148 samples), while sensitivity and specificity were 100% and 92.9%, respectively. This novel assay could be used to complement conventional cervical cancer screening, because its self-sampling format can expand access among women who would otherwise not participate, and because of its additional information about the composition of the vaginal microbiome and the presence of pathogens.
Self-sampling for HPV testing: Increased cervical cancer screening participation and incorporation in international screening programs.
Gupta S, Zneimer S, et al. (2018) Self-sampling for HPV testing: Increased cervical cancer screening participation and incorporation in international screening programs. Front. Public Health doi: 10.3389/fpubh.2018.00077. March 2018.
Abstract: In most industrialized countries, screening programs for cervical cancer have shifted from cytology (Pap smear or ThinPrep) alone on clinician-obtained samples to the addition of screening for human papillomavirus (HPV), its main causative agent. For HPV testing, self-sampling instead of clinician-sampling has proven to be equally accurate, in particular for assays that use nucleic acid amplification techniques. In addition, HPV testing of self-collected samples in combination with a follow-up Pap smear in case of a positive result is more effective in detecting precancerous lesions than a Pap smear alone. Self-sampling for HPV testing has already been adopted by some countries, while others have started trials to evaluate its incorporation into national cervical cancer screening programs. Self-sampling may result in more individuals willing to participate in cervical cancer screening, because it removes many of the barriers that prevent women, especially those in low socioeconomic and minority populations, from participating in regular screening programs. Several studies have shown that the majority of women who have been underscreened but who tested HPV-positive in a self-obtained sample will visit a clinic for follow-up diagnosis and management. In addition, a self-collected sample can also be used for vaginal microbiome analysis, which can provide additional information about HPV infection persistence as well as vaginal health in general.
Validation of Fluorescence in Situ Hybridization (FISH) for Clinical Testing
Zneimer, S. M. (2020). Validation of Fluorescence In Situ Hybridization (FISH) for Clinical Testing. Current Protocols in Human Genetics, e96. doi: 10.1002/cphg.96.
Abstract: In order to comply with regulations set by established local, state, and federal agencies and other regulatory organizations, such as the College of American Pathologists and the International Organization for Standardization, a clinical laboratory needs to develop procedures for the processes of validating laboratory‐developed tests (LDTs) and establishing performance specifications for these assays prior to use in clinical testing. This is applicable to all fluorescence in situ hybridization (FISH) assays. Even Food and Drug Administration–approved FISH assays must undergo some form of verification before implementation in the clinical laboratory. The process of validating an assay as an LDT must include a plan, a procedure, and a report. The validation studies described here include metaphase and interphase FISH methodology for identification of the LSI EGR1/D5S23, D5S721 dual‐color probe, which labels distinct biomarkers consistent with myeloid hematologic disorders, including myelodysplasias and acute myeloid leukemia.