Non-invasive Genetic Screening Research Articles

Noninvasive genetic screening: current advances in artificial intelligence for embryo ploidy prediction

This review discusses the use of artificial intelligence (AI) algorithms in noninvasive prediction of embryo ploidy status for preimplantation genetic testing in invitro fertilization procedures. The current gold standard, preimplantation genetic testing for aneuploidy, has limitations, such as an invasive biopsy, financial burden, delays in results reporting, and difficulty in results reporting, Noninvasive ploidy screening methods, including blastocoel fluid sampling, spent media testing, and AI algorithms using embryonic images and clinical parameters, are explored. Various AI models have been developed using different machine learning algorithms, such as random forest classifier and logistic regression, have shown variable performance in predicting euploidy. Static embryo imaging combined with AI algorithms have demonstrated good accuracy in ploidy prediction, with models such as Embryo Ranking Intelligent Classification Algorithm and STORK-A outperforming human grading. Time-lapse embryo imaging analyzed by AI algorithms has also shown promise in predicting ploidy status; however, the inclusion of clinical parameters is crucial to improving the predictive value of these models. Mosaicism, an important aspect of embryo classification, is often overlooked in AI algorithms and should be considered in future studies. The integration of AI algorithms into microscopy equipment and Embryoscope platforms will facilitate noninvasive genetic testing. Further development of algorithms that optimize clinical considerations and incorporate minimal-necessary covariates will also enhance the predictive value of AI in embryo selection. Artificial intelligence-based ploidy prediction has the potential to improve pregnancy rates and reduce costs in invitro fertilization cycles.

Oral cancer prediction by noninvasive genetic screening.

Oral squamous cell carcinomas (OSCCs) develop in genetically altered epithelium in the mucosal lining, also coined as fields, which are mostly not visible but occasionally present as white oral leukoplakia (OL) lesions. We developed a noninvasive genetic assay using next-generation sequencing (NGS) on brushed cells to detect the presence of genetically altered fields, including those that are not macroscopically visible. The assay demonstrated high accuracy in OL patients when brush samples were compared with biopsies as gold standard. In a cohort of Fanconi anemia patients, detection of mutations in prospectively collected oral brushes predicted oral cancer also when visible abnormalities were absent. We further provide insight in the molecular landscape of OL with frequent changes of TP53, FAT1 and NOTCH1. NGS analysis of noninvasively collected samples offers a highly accurate method to detect genetically altered fields in the oral cavity, and predicts development of OSCC in high-risk individuals. Noninvasive genetic screening can be employed to screen high-risk populations for cancer and precancer, map the extension of OL lesions beyond what is visible, map the oral cavity for precancerous changes even when visible abnormalities are absent, test accuracy of promising imaging modalities, monitor interventions and determine genetic progression as well as the natural history of the disease in the human patient.

THE HISTORY, OPPORTUNITIES AND PROSPECTS OF TIME-LAPSE TECHNOLOGIES IN THE STUDY OF EARLY HUMAN EMBRYONIC DEVELOPMENT

Despite advances in assisted reproductive technologies, the high failure rate of existing stimulation protocols remains a key industry challenge. One of the leading reasons for this is the limited ability to assess the biological potential of the embryo and its chances of implantation. Over the past ten years, the focus of attention in reproductive technologies has significantly shifted from the patient to the embryo, since the need to improve their effectiveness stimulates the need to understand the deep processes of early development of the embryo. In order to increase the effectiveness of in vitro fertilization procedures in clinical embryology, high-tech methods of culturing and evaluating embryos are being introduced and improved. The purpose of the review is to demonstrate the history, possibilities and prospects in the study of early human embryonic development of time-lapse imaging technology. The active study and use of the capabilities of the time-lapse slow-motion technology allowed not only to expand the understanding of the processes of early development of the embryo, but also at the current moment allows us to assess its potential from the point of view of both biological and clinical perspectives. The main advantages of this method are the possibility of morphological assessment during the continuous cultivation of embryos in closed-type incubators without their extraction, as well as the determination of the exact time intervals of key events of the stages of embryo development with special attention to those moments that are not available for observation and fixation under conditions of traditional cultivation. clinical practice. The main point of growth for the development of time-lapse imaging technology was the creation and validation of the so-called morphokinetic criteria and algorithms for assessing the quality of developing embryos. The key perspective of the method is its use in combination with elements of artificial intelligence in order to predict the most potential embryo for transfer into the uterine cavity. Modern directions of research using the method of time-lapse shooting are the continuation of the development of morphokinetic algorithms and their effective criteria, the introduction of the technology of self-learning computer programs and the adaptation of these tools in clinical practice, the search and assessment of possible factors influencing the morphokinetics of embryos, quality control of the work of embryological laboratories. The future development of such technologies is presented in combination not only with the capabilities of artificial intelligence, but also in combination with the use of non-invasive genetic screening, the assessment of metabolomics and proteomics of developing embryos.

DNA Extraction from Various Types of Prenatal Specimens.

A prenatal noninvasive genetic screening test that yields a positive result typically warrants further direct assessment of fetal DNA following an invasive procedure. The precious nature of these invasively acquired samples, combined with the time sensitive nature with which results should be reported, demands that the methodologies used for analysis be quick, efficient, and dependable.Prenatal diagnosis has been performed using DNA extracted from amniotic fluid and chorionic villi for several decades, and more recently methodologies have been developed to extract cell free fetal DNA from amniotic fluid. DNA extraction methodologies in these matrices should reliably and reproducibly isolate a sufficient quality and quantity of DNA for the intended downstream application, and make it possible to purify and concentrate samples that may arrive with suboptimal quality or quantity.Phenol-Chloroform extraction followed by DNA precipitation in ethanol has historically been used for prenatal samples, but this methodology is labor intensive, time consuming, and requires use of toxic chemicals. There are now commercially available, solid phase-based kits for rapid and reproducible DNA extraction and purification, enabling simultaneous extraction of a large number of samples. Commercial kits are available for a variety of sample matrices including all prenatal specimen types, although other methodologies including organic or inorganic liquid phase extraction may also be utilized.Here, we describe extraction using both commercially available kits for direct amniocytes and chorionic villi and cell free fetal DNA derived from amniotic fluid, as well as inorganic liquid phase extraction for tissue culture of amniocytes, CVS, and products of conception.

“I think we’ve got too many tests!”: Prenatal providers’ reflections on ethical and clinical challenges in the practice integration of cell-free DNA screening

The recent introduction of cell-free DNA-based non-invasive prenatal screening (cfDNA screening) into clinical practice was expected to revolutionize prenatal testing. cfDNA screening for fetal aneuploidy has demonstrated higher test sensitivity and specificity for some conditions than conventional serum screening and can be conducted early in the pregnancy. However, it is not clear whether and how clinical practices are assimilating this new type of testing into their informed consent and counselling processes. Since the introduction of cfDNA screening into practice in 2011, the uptake and scope have increased dramatically. Prenatal care providers are under pressure to stay up to date with rapidly changing cfDNA screening panels, manage increasing patient demands, and keep up with changing test costs, all while attempting to use the technology responsibly and ethically. While clinical literature on cfDNA screening has shown benefits for specific patient populations, it has also identified significant misunderstandings among providers and patients alike about the power of the technology. The unique features of cfDNA screening, in comparison to established prenatal testing technologies, have implications for informed decision-making and genetic counselling that must be addressed to ensure ethical practice. This study explored the experiences of prenatal care providers at the forefront of non-invasive genetic screening in the United States to understand how this testing changes the practice of prenatal medicine. We aimed to learn how the experience of providing and offering this testing differs from established prenatal testing methodologies. These differences may necessitate changes to patient education and consent procedures to maintain ethical practice. We used the online American Congress of Obstetricians and Gynecologists Physician Directory to identify a systematic sample of five prenatal care providers in each U.S. state and the District of Columbia. Beginning with the lowest zip code in each state, we took every fifth name from the directory, excluding providers who were retired, did not currently practice in the state in which they were listed, or were not involved in a prenatal specialty. After repeating this step twice and sending a total of 461 invitations, 37 providers expressed interest in participating, and we completed telephone interviews with 21 providers (4.6%). We developed a semi-structured interview guide including questions about providers' use of and attitudes toward cfDNA screening. A single interviewer conducted and audio-recorded all interviews by telephone, and the interviews lasted approximately 30 minutes each. We collaboratively developed a codebook through an iterative process of transcript review and code application, and a primary coder coded all transcripts. Prenatal care providers have varying perspectives on the advantages of cfDNA screening and express a range of concerns regarding the implementation of cfDNA screening in practice. While providers agreed on several advantages of cfDNA, including increased accuracy, earlier return of results, and decreased risk of complications, many expressed concern that there is not enough time to adequately counsel and educate patients on their prenatal screening and testing options. Providers also agreed that demand for cfDNA screening has increased and expressed a desire for more information from professional societies, labs, and publications. Providers disagreed about the healthcare implications and future of cfDNA screening. Some providers anticipated that cfDNA screening would decrease healthcare costs when implemented widely and expressed optimism for expanded cfDNA screening panels. Others were concerned that cfDNA screening would increase costs over time and questioned whether the expansion to include microdeletions could be done ethically. The perspectives and experiences of the providers in this study allow insight into the clinical benefit, burden on prenatal practice, and potential future of cfDNA screening in clinical practice. Given the likelihood that the scope and uptake of cfDNA screening will continue to increase, it is essential to consider how these changes will affect frontline prenatal care providers and, in turn, patients. Providers' requests for additional guidance and data as well as their concerns with the lack of time available to explain screening and testing options indicate significant potential issues with patient care. It is important to ensure that the clinical integration of cfDNA screening is managed responsibly and ethically before it expands further, exacerbating pre-existing issues. As prenatal screening evolves, so should informed consent and the resources available to women making decisions. The field must take steps to maximize the advantages of cfDNA screening and responsibly manage its ethical issues.

Congenital heart defects: is it time to explore maternal blood for a non-invasive genetic screening test?

Congenital heart defects: is it time to explore maternal blood for a non-invasive genetic screening test?

Molecular screening of oral precancer

Early detection and treatment of high risk premalignant mucosal changes of the oral cavity, will expectedly improve survival and reduce treatment-related morbidity. Aims of this study were to evaluate a non-invasive screening approach and to assess the value of molecular markers to identify patients at risk for oral cancer. Exfoliated cells and biopsies were obtained from oral leukoplakia lesions of 43 patients, of whom six developed oral cancer. All samples were investigated for loss of heterozygosity (LOH) at chromosomes 3p, 9p, 11q and 17p using microsatellite markers. On the biopsy specimen additional immunohistochemical staining for p53, TP53 mutation analysis and histopathological grading were performed. The analytical sensitivity of the non-invasive assay using exfoliated cells to detect genetic changes present in the lesions was 45% (9 of 20), the specificity was 100% (19 of 19), and the positive predictive value was also 100% (9 of 9). LOH was present in 20 of 39 (51%) of the biopsies with uniformly LOH at 9p. Mutated TP53 and LOH at 9p in the biopsy, as single markers and in combination, were significant risk factors for malignant progression of leukoplakia to oral cancer (Kaplan-Meier analysis, p<0.05). A non-invasive genetic screening approach using LOH in exfoliated cells has limited value for monitoring patients with leukoplakia. However, LOH at 9p, but also mutated TP53 in biopsies of oral leukoplakia have a significant association with malignant transformation and are promising candidate biomarkers to predict the risk for malignant progression.

Methylation pattern of SFRP1 promoter in stool sample is a potential marker for early detection of colorectal cancer

Background:To setup a non-invasive genetic screening method for colorectal cancer, we evaluated the promoter methylation status of secreted frizzled-related protein1 (sfrp1) in stool samples of colorectal cancer with respect to a series of healthy individuals, using methylation-specific polymerase chain reaction.Materials and Methods:In stool samples from 25 patients with colorectal cancer and 25 healthy control subjects, isolated DNA was treated with sodium bisulfite and analyzed by methylation-specific polymerase chain reaction with primers specific for methylated or unmethylated promoter sequences of the SFRP1 gene.Result:Methylation of the SFRP1 promoter was present in the stool DNA of patients with colorectal cancer. A sensitivity of 52% and specificity of 92% were achieved in the detection of colorectal neoplasia. The difference in methylation status of the SFRP1 promoter between the patients with colorectal neoplasia and the control group was statistically highly significant (P = 0.006).Conclusions:The results indicate that this DNA stool test of methylation of the SFRP1 promoter is a sensitive and specific method. It is assumed that the test is potentially useful for the early detection of colorectal cancer.

404 PERFORMANCE OF ACOUSTIC RADIATION FORCE IMPULSE IMAGING IN THE NONINVASIVE ASSESSMENT OF LIVER FIBROSIS, IN COMPARISON TO UNIDIMENSIONAL TRANSIENT ELASTOGRAPHY

Conclusions: The common PNPLA3 polymorphism confers an increased risk of liver fibrosis in patients with chronic liver diseases. This observation can be attributed to the additive harmful effects of hepatic fat accumulation and inflammation in response to chronic liver injury. Our findings point to a novel non-invasive genetic screening strategy to identify patients with chronic liver diseases at risk for cirrhosis.

Screening for Oral Precancer with Noninvasive Genetic Cytology

Oral squamous cell carcinomas develop in precancerous fields consisting of genetically altered mucosal epithelial cells. These precancerous fields may appear as clinically visible lesions, in particular, oral leukoplakia, but the large majority remains clinically undetectable. The aim of this study was to assess the potential value of a noninvasive screening approach to detect precancerous fields. As a first step, we developed a suitable assay and investigated 25 leukoplakia patients and 20 noncancer control subjects. Exfoliated cells were removed by a brush from multiple small areas of the oral mucosa, including the leukoplakia. Brushed samples were investigated for allelic imbalance (AI) at chromosomes 3p, 9p, 11q, and 17p using microsatellite markers known to show frequent alterations in oral precancer. AI was absent in all (137) of the samples of the 20 control subjects, yielding a specificity of 100%. AI was detected in exfoliated cell samples of 40% (10 of 25) of the leukoplakia lesions studied. Genetic changes were also found outside the leukoplakia lesions. Most frequent was AI at 9p (9 of 10). The noninvasive assay was validated against the biopsy results of the leukoplakia lesions yielding an estimate of sensitivity of 78% (7 of 9) and a positive predictive value of 100% (7 of 7). Altogether, these results show the feasibility of a noninvasive genetic screening approach for the detection and monitoring of oral precancer. This assay could therefore contribute to the secondary prevention of oral squamous cell carcinoma. The assay also shows promise for the detection of precancerous changes that are not macroscopically visible.

10:50: Noninvasive Genetic Screening Test for HNSCC

10:50: Noninvasive Genetic Screening Test for HNSCC

A noninvasive genetic screening test to detect oral preneoplastic lesions

Early diagnosis of oral squamous cell carcinoma (OSCC) may have a major impact on survival and quality of life. Recent studies have shown that the majority of OSCC is preceded by precursor lesions characterized by genetic alterations. The aim of this study was to develop and evaluate a noninvasive screening test for oral preneoplastic lesions, based on genetic alterations as marker. Various methods to obtain a high yield of cells by brushing a small area of the oral mucosa were compared. A novel genetic assay, multiplex ligation-dependent probe amplification (MLPA), was applied that enables the measurement of gains and losses at 40 different chromosomal locations in one PCR reaction using 150 ng DNA. MLPA was performed on DNA of normal and dysplastic oral mucosa as well as of OSCC with the intention to select a specific probe set for accurate detection of precursor lesions in the oral cavity. The assay was correlated to loss of heterozygosity analysis using microsatellite markers, and evaluated on noncancer subjects and patients with oral leukoplakia. A noninvasive sampling method was developed with DNA yields ranging from 150 to 600 ng. Using 120 probes, we could detect large differences with MLPA in the number of alterations between normal vs dysplastic and dysplastic vs tumor tissue with P-values <0.001. A significant correlation was found between the number of alterations as detected by MLPA and the analysis for allelic loss. The available data enabled the selection of a set of 42 MLPA probes, which had the power to optimally discriminate between normal and dysplastic tissue. Our data show that MLPA is a sensitive, reliable, high-throughput and easy-to-perform technique, enabling the detection of genetic alterations on small noninvasive samples and can be considered a promising method for population-based screening of preneoplastic lesions in the oral cavity.

PD.66 A non-invasive genetic screening test to detect oral preneoplastic lesions

PD.66 A non-invasive genetic screening test to detect oral preneoplastic lesions

Prenatal diagnosis using fetal cells from the maternal circulation.

Current prenatal diagnosis relies on invasive methods such as amniocentesis and chorionic villus sampling. Because these methods carry a low, but finite risk of pregnancy loss, noninvasive genetic screening techniques are the focus of intense research. Isolating fetal cells from maternal blood for genetic analysis is the least invasive method currently being investigated. We discuss the various methods that have been used to isolate these cells. Nucleated red blood cells have emerged as the ideal fetal cell type. This is because they have the DNA material necessary for genetic analysis, they are consistently present in maternal blood, they can be easily identified based on their morphology, and they have a definite gestational life span.