Performance of conventional cytogenetic analysis on chorionic villi when only one cell layer, cytotrophoblast or mesenchyme alone, is analyzed.

OBJECTIVE: To provide an estimation of the probability of error when chorionic villi (CV) cytogenetic analysis is limited to a single placental layer; either a direct preparation (Dir) or long-term culture (LTC). METHODS: We retrospectively reviewed cytogenetic studies on 81,593 consecutive CV samples in which both Dir and LTC were analyzed. All mosaic cases received amniocentesis. The false omission and false discovery rates were calculated by assessing the results that would have been reported when analysis was limited to either Dir or LTC. RESULTS: For all abnormalities combined, the proportion of normal Dir or LTC only reports that would have been inconsistent with a subsequent amniocentesis was 0.09% and 0.03%, respectively (false omissions). Among abnormal reports based on Dir or LTC alone, 8.01% and 3.17%, respectively, would be inconsistent with a subsequent amniocentesis result (false discoveries). Differences are present for individual abnormalities. CONCLUSIONS: From the perspective of identifying all abnormalities of potential clinical significance, the analysis of both placental layers is optimal. LTC alone is the preferred approach if only one layer of placenta is to be analyzed. Although rare, it is important to acknowledge that one cell layer analysis alone can cause misdiagnosis due to undetected mosaicism.

Molecular Technologies in the Clinical Diagnostic Laboratory.

BACKGROUND: New technologies for molecular analysis are increasing our ability to diagnose cancer. METHODS: Several molecular analysis technologies are reviewed and their use in the clinical laboratory is discussed. RESULTS: Select key technologies, including polymerase chain reaction and next-generation sequencing, are helping transform our ability to analyze cancer specimens. As these technological advances become more and more incorporated into routine diagnostic testing, our classification systems are likely to be impacted and our approach to treatment transformed. The routine use of such technology also brings challenges for analysis and reimbursement. CONCLUSION: These advances in technology will change the way we diagnose, monitor, and treat patients with cancer.

Tips and tricks for preparing lampbrush chromosome spreads from Xenopus tropicalis oocytes.

Due to their large size and fine organization, lampbrush chromosomes (LBCs) of amphibian oocytes have been for decades one of the favorite tools of biologists for the analysis of transcriptional and post-transcriptional processes at the cytological level. The emergence of the diploid Xenopus tropicalis amphibian as a model organism for vertebrate developmental genetics and the accumulation of sequence data made available by its recent genomic sequencing, strongly revive the interest of LBCs as a powerful tool to study genes expressed during oogenesis. We describe here a detailed protocol for preparing LBCs from X. tropicalis oocyte and give practical advice to encourage a large number of researchers to become familiar with these chromosomes.

Stimulus-Responsive Microfluidic Interface Enables Efficient Enrichment and Cytogenetic Profiling of Circulating Myeloma Cells.

Minimal residual disease (MRD) provides an independent prognostic factor for multiple myeloma (MM) patients. However, clinical MRD assays suffer from highly invasive sampling, insufficient detection sensitivity, and high cost. Herein, a stiMulus-Responsive ligand-Decorated microfluidic chip (MRD-Chip) was developed for efficient capture and controlled release of circulating myeloma cells (CMCs) in the peripheral blood for noninvasive myeloma evaluation. The CD138 antibody-decorated herringbone chip with a disulfide linker was designed to enhance the collision probability between blood cells and capture antibodies, leading to high capture efficiency of CMCs. More importantly, the captured CMCs can be nondestructively released via a thiol-exchange reaction, allowing them to be used for subsequent cellular and molecular analysis. By fluorescence in situ hybridization assay, we successfully identified the cytogenetic abnormalities (chromosome 1q21 amplification and p53 deletion) of CMCs in clinical samples. Overall, with the merits of noninvasive sampling, high capture efficiency (70.93%), high throughput (1.5 mL/h), and nondestructive release of target cells (over 90% viability) for downstream analysis, our strategy provides new opportunities for myeloma evaluation, such as prognosis assessment, efficacy monitoring, and mechanism research of disease relapse and drug resistance.

Metaphase FISH on a chip: miniaturized microfluidic device for fluorescence in situ hybridization.

Fluorescence in situ Hybridization (FISH) is a major cytogenetic technique for clinical genetic diagnosis of both inherited and acquired chromosomal abnormalities. Although FISH techniques have evolved and are often used together with other cytogenetic methods like CGH, PRINS and PNA-FISH, the process continues to be a manual, labour intensive, expensive and time consuming technique, often taking over 3 5 days, even in dedicated labs. We have developed a novel microFISH device to perform metaphase FISH on a chip which overcomes many shortcomings of the current laboratory protocols. This work also introduces a novel splashing device for preparing metaphase spreads on a microscope glass slide, followed by a rapid adhesive tape-based bonding protocol leading to rapid fabrication of the microFISH device. The microFISH device allows for an optimized metaphase FISH protocol on a chip with over a 20-fold reduction in the reagent volume. This is the first demonstration of metaphase FISH on a microfluidic device and offers a possibility of automation and significant cost reduction of many routine diagnostic tests of genetic anomalies.

Microfluidic Device for On-Chip Immunophenotyping and Cytogenetic Analysis of Rare Biological Cells.

The role of circulating plasma cells (CPCs) and circulating leukemic cells (CLCs) as biomarkers for several blood cancers, such as multiple myeloma and leukemia, respectively, have recently been reported. These markers can be attractive due to the minimally invasive nature of their acquisition through a blood draw (i.e., liquid biopsy), negating the need for painful bone marrow biopsies. CPCs or CLCs can be used for cellular/molecular analyses as well, such as immunophenotyping or fluorescence in situ hybridization (FISH). FISH, which is typically carried out on slides involving complex workflows, becomes problematic when operating on CLCs or CPCs due to their relatively modest numbers. Here, we present a microfluidic device for characterizing CPCs and CLCs using immunofluorescence or FISH that have been enriched from peripheral blood using a different microfluidic device. The microfluidic possessed an array of cross-channels (2-4 µm in depth and width) that interconnected a series of input and output fluidic channels. Placing a cover plate over the device formed microtraps, the size of which was defined by the width and depth of the cross-channels. This microfluidic chip allowed for automation of immunofluorescence and FISH, requiring the use of small volumes of reagents, such as antibodies and probes, as compared to slide-based immunophenotyping and FISH. In addition, the device could secure FISH results in <4 h compared to 2-3 days for conventional FISH.

CABAS: a freely available PC program for fitting calibration curves in chromosome aberration dosimetry.

The aim of biological dosimetry is to estimate the dose and the associated uncertainty to which an accident victim was exposed. This process requires the use of the maximum-likelihood method for fitting a calibration curve, a procedure that is not implemented in most statistical computer programs. Several laboratories have produced their own programs, but these are frequently not user-friendly and not available to outside users. We developed a software for fitting a linear-quadratic dose-response relationship by the method of maximum-likelihood and for estimating a dose from the number of aberrations observed. The program called as CABAS consists of the main curve-fitting and dose estimating module and modules for calculating the dose in cases of partial body exposure, for estimating the minimum number of cells necessary to detect a given dose of radiation and for calculating the dose in the case of a protracted exposure. The program is freely available at http://www.pu.kielce.pl/ibiol/cabas.

Medical applications of array CGH and the transformation of clinical cytogenetics.

Microarray-based comparative genomic hybridization (array CGH) merges molecular diagnostics with traditional chromosome analysis and is transforming the field of cytogenetics. Prospective studies of individuals with developmental delay and dysmorphic features have demonstrated that array CGH has the ability to detect any genomic imbalance including deletions, duplications, aneuploidies and amplifications. Detection rates for chromosome abnormalities with array CGH range from 5-17% in individuals with normal results from prior routine cytogenetic testing. In addition, copy number variants (CNVs) were identified in all studies. These CNVs may include large-scale variation and can confound the diagnostic interpretations. Although cytogeneticists will require additional training and laboratories must become appropriately equipped, array CGH holds the promise of being the initial diagnostic tool in the identification of visible and submicroscopic chromosome abnormalities in mental retardation and other developmental disabilities.

[The need of regulation of production of components for forensic-medical molecular-genetic technologies and improvement of legal basis of forensic-medical molecular-genetic expert examinations in the Russian Federation].

Of late, Ministry of Health of Russian Federation has developed instructions concerning forensic-medical molecular genetic methods of analysis promoting creation of standardized forensic-medical genetic service. However, some legal uncertainty exists in respect to design and production of the materials for forensic-medical molecular-genetic technologies, unification and standardization of molecular-genetic kits and methods. It is thought necessary to regulate legally forensic medical molecular-genetic technologies from foreign countries and production and use of domestic components for forensic medical molecular-genetic expert examinations.

[Cytogenetic effect of the pulse reactor BARS-6 continuous or one-time irradiation with ultrahigh dose rate on human lymphocytes].

The results of the comparative study of radiation effects of the pulse reactor BARS-6 either in single pulse or continuos irradiation mode on human G0 lymphocytes are presented. Under identical doses the cytogenetic efficiency was observed to be higher for continuous irradiation (1 hour) than for single pulse irradiation with ultrahigh dose rate (0.5-3) x 106 Gy/minutes (pulse duration 65 x 10(-6) s). The difference averaged about 37% on total aberration frequency and 27% on the sum of dicentrics and centric rings. The influence of the dose rate and of the mixed gamma-neutron irradiation on the obtained results is discussed.

High-throughput sample processing and sample management; the functional evolution of classical cytogenetic assay towards automation.

High-throughput individual diagnostic dose assessment is essential for medical management of radiation-exposed subjects after a mass casualty. Cytogenetic assays such as the Dicentric Chromosome Assay (DCA) are recognized as the gold standard by international regulatory authorities. DCA is a multi-step and multi-day bioassay. DCA, as described in the IAEA manual, can be used to assess dose up to 4-6 weeks post-exposure quite accurately but throughput is still a major issue and automation is very essential. The throughput is limited, both in terms of sample preparation as well as analysis of chromosome aberrations. Thus, there is a need to design and develop novel solutions that could utilize extensive laboratory automation for sample preparation, and bioinformatics approaches for chromosome-aberration analysis to overcome throughput issues. We have transitioned the bench-based cytogenetic DCA to a coherent process performing high-throughput automated biodosimetry for individual dose assessment ensuring quality control (QC) and quality assurance (QA) aspects in accordance with international harmonized protocols. A Laboratory Information Management System (LIMS) is designed, implemented and adapted to manage increased sample processing capacity, develop and maintain standard operating procedures (SOP) for robotic instruments, avoid data transcription errors during processing, and automate analysis of chromosome-aberrations using an image analysis platform. Our efforts described in this paper intend to bridge the current technological gaps and enhance the potential application of DCA for a dose-based stratification of subjects following a mass casualty. This paper describes one such potential integrated automated laboratory system and functional evolution of the classical DCA towards increasing critically needed throughput.

New developments in automated cytogenetic imaging: unattended scoring of dicentric chromosomes, micronuclei, single cell gel electrophoresis, and fluorescence signals.

The quantification of DNA damage, both in vivo and in vitro, can be very time consuming, since large amounts of samples need to be scored. Additional uncertainties may arise due to the lack of documentation or by scoring biases. Image analysis automation is a possible strategy to cope with these difficulties and to generate a new quality of reproducibility. In this communication we collected some recent results obtained with the automated scanning platform Metafer, covering applications that are being used in radiation research, biological dosimetry, DNA repair research and environmental mutagenesis studies. We can show that the automated scoring for dicentric chromosomes, for micronuclei, and for Comet assay cells produce reliable and reproducible results, which prove the usability of automated scanning in the above mentioned research fields.

[Laser-assisted microdissection and molecular analysis at the cellular level]. / Lasermicrodissectie en moleculaire analyse op celniveau.

Developments of molecular biological techniques have allowed the analysis of small tissue samples. In order to obtain optimal results it is essential to work with pure cell populations. The procurement of pure samples has, however, been one of the main limiting factors in biomedical research. Recently developed systems for laser-assisted microdissection now allow the isolation of pure cell populations from tissue sections, even at a single cell level, that are suitable for subsequent molecular analyses. Since morphological features can be directly related to molecular characteristics, studies concerning molecular genetic backgrounds underlying disease can be performed more easily and accurately. By future combined use of laser microdissection and new molecular analysis methods, the applications for laser-micro-dissection will increase further.

An extended fluorescence in situ hybridization approach for the cytogenetic study of cholangiocarcinoma on endoscopic retrograde cholangiopancreatography brushing cytology preparations.

The cytological diagnosis of cholangiocarcinoma has been significantly aided by applying a 4-probe fluorescence in situ hybridization system on endoscopic retrograde cholangiopancreatography brushing smears, aiming mainly at the detection of hyperdiploidy. However, this approach adds little to our understanding of the genetic background of the disease. With the prospect of obtaining additional data on chromosomal aberrations, we have extended the fluorescence in situ hybridization study, with the application of 4 independent 2-probe systems in 35 patients with documented cholangiocarcinoma. Fluorescence in situ hybridization assays were performed on endoscopic retrograde cholangiopancreatography brushing smears, with probes for the 7q31, 11q13 (CCND1), 17p53 (TP53), and 9p21 (INK4 locus) bands, together with the respective centromeric probe. Hyperdiploidy, involving at least 2 of the 4 chromosomes targeted, was found in 31 patients. 17p13 deletion was detected in 3, and 9p21 deletion, in 5 of the hyperdiploid cases, with the 2 aberrations concurrent in 1. CCND1 amplification was found in 1 case as the sole abnormality and in another together with hyperdiploidy, but in apparently unrelated clones. This work indicates that interphase fluorescence in situ hybridization is a practical and useful tool for the cytogenetic study of cholangiocarcinoma on endoscopic retrograde cholangiopancreatography brushing smears, which is often the only available tissue specimen of the tumor. Apart from hyperdiploidy, it provides additional data on the genetic profile of cholangiocarcinoma, especially regarding structural chromosomal aberrations and clonal diversity. This line of investigation may prove useful in the delineation of oncogenesis and the interpretation of the diverse clinical features of the disease.

Comorbilidades en personas con síndrome de Down, habitantes de La Paz - Bolivia, 2015 / Comorbidities in down's syndrome people, residents of La Paz-Bolivia, 2015

El Síndrome de Down (SD), es una condición genética debida a la trisomía 21, caracterizada por afección multisistémica con principal daño neurobiológico. Se presenta con una frecuencia de 1/700 recién nacidos vivos (RNV) dependiendo de la población estudiada. Conlleva un efecto de exceso de dosis y genes, que desempeña un rol importante en la patogénesis las distintas comorbilidades del SD, tales como cardiopatías congénitas, disgenesia tiroidea, errores de refracción, alteraciones hematológicas, entre otras. El objetivo del estudio fue determinar la frecuencia de comorbilidades en personas con SD habitantes de ciudad de La Paz- Bolivia, por medio de un estudio descriptivo, de corte transversal, con evaluaciones multidisciplinarias e interinstitucionales. La mayor parte de las comorbilidades observadas están dentro de los parámetros reportados por estudios en otras poblaciones, sin embargo llama la atención una elevada frecuencia de hipertensión arterial pulmonar (93%), hipoplasia de glándula tiroidea (90%), errores de refracción (90%), pieloectasia renal (30%) y eritrocitosis (10%), como hallazgos propios de nuestra población (carga genética, condiciones ambientales y culturales). La prevalencia de patología médica en personas con SD repercute negativamente en su calidad y esperanza de vida. Sin embargo, existen estrategias médicas, educativas y sociales para las persona con SD, en busca de la prevención y seguimiento para mejorar su calidad y cantidad de vida.

Down syndrome (DS) is a genetic condition caused by 21 chromosome trisomy, characterized by multisystemic disease with main neurobiological damage. The frequency is 1/700 live births. It entails an effect of gene dose excess that plays an important role in the pathogenesis of various comorbidities in DS such as congenital heart disease, thyroid dysgenesis, refractive errors, hematological disorders, etc. The study's objective was determine the comorbidities frequency in people with DS from La Paz city in Bolivia through a descriptive cross-sectional survey with multidisciplinary and interinstitutional assessments. Most of observed comorbidities are in parameters reported in other population studies, however striking a high frequency of pulmonary arterial hypertension (93%), thyroid gland hypoplasia (90%), refractive errors (90 %), kidney pieloectasy (30%) and eritrocitosis (10%), as our population findings regarding the genetic and environmental conditions ( high altitude over the sea level). The prevalence of medical conditions in people with SD affects negatively their life quality and expectancy. However, there are medical, educational and social strategies for DS persons, searching for prevention and monitoring to improve their life quality and quantity.

Testing hygrometers used in cytogenetics laboratories for metaphase preparation.

This protocol describes procedures for checking small laboratory hygrometers for accuracy at three relative humidity (rh) levels. The work arose out of the need to provide laboratory assessors with documentary evidence that the hygrometer used to monitor humidity in the vicinity of the laboratory where medical cytogenetics testing slides are prepared and dried in the ambient environment is reproducible and sufficiently accurate. The procedure is based upon the physicochemical principle that when water or certain saturated salt solutions are placed into a sealed environment, the humidity will equilibrate to well defined levels. We choose to check our hygrometers at three points: 95%, 75%, and 33% rh, using distilled water, saturated sodium chloride solution, and saturated magnesium chloride solution, respectively. Our results have demonstrated that the procedure is convenient and of sufficient accuracy to be fit for this annual hygrometer validation purpose. The procedure takes 24 hr per relative humidity point checked.

Checking the foundation: recent radiobiology and the linear no-threshold theory.

The linear no-threshold (LNT) theory has been adopted as the foundation of radiation protection standards and risk estimation for several decades. The "microdosimetric argument" has been offered in support of the LNT theory. This argument postulates that energy is deposited in critical cellular targets by radiation in a linear fashion across all doses down to zero, and that this in turn implies a linear relationship between dose and biological effect across all doses. This paper examines whether the microdosimetric argument holds at the lowest levels of biological organization following low dose, low dose-rate exposures to ionizing radiation. The assumptions of the microdosimetric argument are evaluated in light of recent radiobiological studies on radiation damage in biological molecules and cellular and tissue level responses to radiation damage. There is strong evidence that radiation initially deposits energy in biological molecules (e.g., DNA) in a linear fashion, and that this energy deposition results in various forms of prompt DNA damage that may be produced in a pattern that is distinct from endogenous (e.g., oxidative) damage. However, a large and rapidly growing body of radiobiological evidence indicates that cell and tissue level responses to this damage, particularly at low doses and/or dose-rates, are nonlinear and may exhibit thresholds. To the extent that responses observed at lower levels of biological organization in vitro are predictive of carcinogenesis observed in vivo, this evidence directly contradicts the assumptions upon which the microdosimetric argument is based.

FISH and chips: chromosomal analysis on microfluidic platforms.

Interphase fluorescence in situ hybridisation (FISH) is a sensitive diagnostic tool used for the detection of alterations in the genome on cell-by-cell basis. However, the cost-per-test and the technical complexity of current FISH protocols have slowed its widespread utilisation in clinical settings. For many cancers, the lack of a cost-effective and informative diagnostic method has compromised the quality of life for patients. We present the first demonstration of a microchip-based FISH protocol, coupled with a novel method to immobilise peripheral blood mononuclear cells inside microfluidic channels. These first on-chip implementations of FISH allow several chromosomal abnormalities associated with multiple myeloma to be detected with a ten-fold higher throughput and 1/10-th the reagent consumption of the traditional slide-based method. Moreover, the chip test is performed within hours whereas the conventional protocol required days. In addition, two on-chip methods to enhance the hybridisation aspects of FISH have been examined: mechanical and electrokinetic pumping. Similar agitation methods have led to significant improvements in hybridisation efficiency with DNA microarray work, but with this cell-based method the benefits were moderate. On-chip FISH technology holds promise for sophisticated and cost-effective screening of cancer patients at every clinic visit.

Sister chromatid exchange.

Sister chromatid exchange (SCE) refers to the interchange of DNA between replication products. The technique for detecting such exchanges takes advantage of the semiconservative nature of DNA synthesis. 5'-bromodeoxyuridine (BrdU) is incorporated into the newly synthesized DNA. Using standard culturing techniques, Colcemid is added to the culture and conventional cytogenetic preparations are made. Differential staining with Hoechst dye and Giemsa allows the newly synthesized DNA within a chromatid to be recognized, since BrdU incorporation results in much weaker staining. SCEs represent a point of DNA template exchange during strand synthesis, visualized as asymmetric chromatid staining or "harlequin" chromosomes.