Traditional Chromosomal Analysis Research Articles

Prevalence and patterns of chromosomal abnormalities among Egyptian patients with infertility: a single institution\u2019s 5-year experience

BackgroundChromosomal abnormalities represent an important cause of human infertility. Little is known about the prevalence of chromosomal abnormalities among Egyptian couples with infertility. We estimated the cytogenetic profiles and semen analysis patterns among infertile couples. We analyzed data from medical archives of 2150 patients with infertility in Mansoura University Children’s Hospital, Egypt from 2015 to 2019. The data included karyotypes and semen analysis reports.ResultsChromosomal abnormalities were reported in 13.5% of infertile patients (290/2150); 150 out of 1290 (11.62%) males and 140 out of 860 (16.28%) females. Within the infertile males, the numerical chromosomal abnormalities were detected in 134/1290 (10.38%) males, and structural abnormalities were found in 16/1290 (1.24%) males. Within the infertile females, numerical sex chromosome abnormalities were detected in 75/860 (8.72%) females, structural sex chromosome abnormalities were found in 31/860 (3.6%) females, mosaicism of the sex chromosome was found in 22/860 (2.56%) females, and male pseudohermaphrodites were detected in 12/860 (1.39%) females.ConclusionsNumerical chromosomal aberrations are the most frequent patterns among infertile couples. Attention should be paid to the traditional chromosomal analysis as an important diagnostic step in the infertility work-up.

Horse Clinical Cytogenetics: Recurrent Themes and Novel Findings.

Simple SummaryHorse chromosomes have been studied for veterinary diagnostic purposes for over half a century. The findings show that changes in the chromosome number or structure are among the most common non-infectious causes of decreased fertility, infertility, and developmental abnormalities. Based on large-scale surveys, almost 30% of horses with reproductive or developmental problems have abnormal chromosomes. For a comparison, only 2–5% of horses in the general population have abnormal chromosomes. Most chromosome abnormalities are rare and found in one or a few animals. However, two conditions are recurrent: sterile mares with only one X chromosome, instead of two, and sterile mares with XY male sex chromosomes where the Y has lost the ‘maleness’ gene SRY. The two are signature features of chromosome abnormalities in the horse, being rare or absent in other domestic animals. The progress in horse genome sequencing and the development of molecular tools have improved the depth and quality of diagnostic chromosome analysis, allowing for an understanding of the underlying molecular mechanisms. Nevertheless, cutting-edge genomics tools are not about to entirely replace traditional chromosome analysis, which still is the most straightforward, cost-effective, and fastest approach for the initial evaluation of potential breeding animals and horses with reproductive or developmental disorders.Clinical cytogenetic studies in horses have been ongoing for over half a century and clearly demonstrate that chromosomal disorders are among the most common non-infectious causes of decreased fertility, infertility, and congenital defects. Large-scale cytogenetic surveys show that almost 30% of horses with reproductive or developmental problems have chromosome aberrations, whereas abnormal karyotypes are found in only 2–5% of the general population. Among the many chromosome abnormalities reported in the horse, most are unique or rare. However, all surveys agree that there are two recurrent conditions: X-monosomy and SRY-negative XY male-to-female sex reversal, making up approximately 35% and 11% of all chromosome abnormalities, respectively. The two are signature conditions for the horse and rare or absent in other domestic species. The progress in equine genomics and the development of molecular tools, have qualitatively improved clinical cytogenetics today, allowing for refined characterization of aberrations and understanding the underlying molecular mechanisms. While cutting-edge genomics tools promise further improvements in chromosome analysis, they will not entirely replace traditional cytogenetics, which still is the most straightforward, cost-effective, and fastest approach for the initial evaluation of potential breeding animals and horses with reproductive or developmental disorders.

Chromosomal abnormalities and copy number variations in fetal ventricular septal defects

BackgroundThis study aimed to evaluate the applicability of chromosomal microarray analysis (CMA), rather than traditional chromosome analysis, in prenatal diagnosis of ventricular septal defects (VSDs) for superior prenatal genetic counseling and to reveal a potential correlation between submicroscopic chromosomal aberrations and VSDs.ResultsAmong the 151 VSD cases, 79 (52.3%) had isolated defects and 72 (47.7%) had additional ultrasound anomalies. Karyotype analysis identified 16 chromosomal abnormalities. Besides the 14 cases of chromosome abnormalities consistent with karyotype analysis, CMA identified an additional 20 cases (13.2%) of abnormal copy number variations (CNVs), of which 13 were pathogenetic CNVs, 5 were variations of uncertain clinical significance (VOUS) and 2 were benign CNVs. The detection rate of pathogenic CNVs in non-isolated-VSDs was significantly higher than that in isolated-VSDs (36.1% (26/72) vs. 1.3% (1/79), p = 0.001). We also found that CMA results indicating pathogenic abnormalities affected the rate of pregnancy termination.ConclusionsThis study showed that CMA combined with cytogenetic analysis is particularly effective in identifying CNVs in fetuses with VSDs and can have an effect on obstetrical outcomes. The elucidation of the etiology of VSDs suggested that gene mutations or other factors may be implicated.

Contribution of genomic copy-number variations in prenatal oral clefts: a multicenter cohort study.

We sought to investigate the utility of chromosomal microarray analysis (CMA) for prenatal diagnosis of oral clefts, as compared with traditional chromosome analysis, for improved prenatal genetic counseling and discovery of a potential correlation between genotype and oral cleft. This retrospective analysis encompassed 270 prenatal oral cleft cases with documented detailed ultrasound findings and CMA results from four referral centers. Detection rates for pathogenic copy-number variants (CNVs) were calculated and compared with cases for which chromosome analysis was also performed. The overall detection rate was 14.8% (40/270) for pathogenic CNVs by CMA, 7.2% (9/125) for the nonsyndromic cases, and 21.4% (31/145) for the syndromic cases. Of the nonsyndromic cases with ultrasound soft markers, 20% (5/25) were identified with pathogenic CNVs. CMA showed an improved detection rate of 15.3% (29/190) compared with 10.5% (20/190) for chromosome analysis. This study not only highlights the improved detection of chromosomal defects by CMA in prenatal oral clefts but also deepens our understanding of oral clefts. The results suggest that CMA is highly recommended in prenatal invasive genetic testing not only for syndromic oral cleft cases but also for nonsyndromic cases with soft markers. Candidate genes including CRKL, AKAP8, SYDE1, BRD4 are worthy of further investigation regarding their role in human palatogenesis.Genet Med 18 10, 1052-1055.

The feasibility study of Ion Proton semiconductor sequencing platform in the non-invasive prenatal genetic diagnosis

Objective To evaluate the feasibility of apply Ion Proton semiconductor sequencing platform in non-invasive prenatal genetic diagnosis. Methods Totally 1 000 pregnant women with a singleton pregnancy of 12-32 weeks gestation were selected from the Third affiliated Hospital of Zhengzhou University from Jan to Dec 2013. Using noninvasive prenatal genetic diagnosis based on Ion Proton semiconductor sequencing platform to study their cffDNA. In parallel, 72 pregnant women received invasive prenatal diagnosis by traditional chromosomal analysis with amniocentesis chorionic villus sampling. Results It′s shown that 18 out of 1 000 (1.8%) pregnant women underwent the noninvasive prenatal genetic testing had a high risk for aneuploid chromosomes, including 7 cases of 21-trisomy, 4 cases of 18-trisomy, 2 cases of 13-trisomy, 4 cases of sex chromosomal abnormality, and 1 case of 15-trisomy. It demonstrated that the rate and accuracy of fetal 21-trisomy, 13-trisomy and 18-trisomy by non-invasive prenatal genetic testing were both 100% without misdiagnosis, the rate of detection for sex chromosomal abnormality was 2/2 with a false positive rate of 1/3. However, the 15-trisomy predicted by the non-invasive prenatal diagnosis in a woman was finally proved to be a false positive. Based on the results by karyotyping (55/55) as well as follow-ups (493/493), the specificity of the non-invasive prenatal diagnosis for detection of 21-trisomy, 18-trisomy and 13-trisomy was 100%. One Ion PITM chip could detect 12 to 15 samples in 1.5 h and the whole process of noninvasive detection could be completed in 1 to 1.5 days. Conclusions The non-invasive prenatal diagnosis by Ion Proton semiconductor sequencing platform could provide fast and accurate detection of fetal aneuploidy. The benchtop high-throughput sequencing platform has laid the foundation for the independent application in clinical settings for fetal aneuploidy detection. （Chin J Lab Med，2014,37：861-865） Key words: Prenatal diagnosis; Aneuploidy; Chromosome aberrations; Aneuploidy; Sequence analysis, DNA; High-throughput nucleotide sequencing; Feasibility studies

An Exploration of Genetic Counselors’ Needs and Experiences with Prenatal Chromosomal Microarray Testing

Because of the higher yield over traditional chromosomal analysis, chromosomal microarray analysis (CMA) is being used increasingly in prenatal diagnosis. Unfortunately, the clinical implication of many copy number variants found on prenatal CMA is uncertain, complicating genetic counseling. Recognizing that uncertain results will be encountered frequently as more of the genome is assayed prenatally, we set out to understand the experiences and needs of genetic counselors when counseling patients about uncertain prenatal microarray results, their comfort with various aspects of prenatal genetic counseling, and their interest in additional education and training about prenatal microarray testing. We first interviewed 10 genetic counselors about their experiences of providing pre- and post-test genetic counseling about prenatal CMA. Based on the findings from the counselor interviews, we developed items for a survey to assess the prevalence of genetic counselors' attitudes towards, experience and comfort with, and educational needs regarding prenatal CMA. Based on surveys completed by 193 prenatal genetic counselors, we found that when there is an uncertain CMA result, only 59% would be comfortable providing genetic counseling and only 43% would be comfortable helping a patient make a decision about pregnancy termination. Being less comfortable was associated with seeing fewer patients having prenatal CMA testing. Respondents expressed a high degree of interest in additional education about prenatal CMA and counseling about uncertain results. Further genetic counselor education and training aimed at improving counselors' personal comfort with uncertain results and communicating about them with patients is needed.

Karyotyping of Human Chromosomes Using M_FISH Images

Karyotyping is a technique used to align the chromosomes in the decreasing order of size so that the structural and numerical changes can be easily identified. Traditional chromosome analysis is simplified by the introduction of M_FISH (multiplex fluorescence in-situ hy-bridization), a combinatorial labeling technique in which each chromosomes appears in distinct color. In this paper, Bayes classification of M-FISH chromosome images using the features intensity in five channel as well as size of the chromosome is presented. Watershed transform is employed for segmentation . Also reclassification of small misclassified segments to the neighbor region is performed as post-processing to improve the performance. The classifier was trained and tested on a set of images from the dataset [2] and an overall accuracy of 91.09% was obtained.

Comparison of chromosome analysis and chromosomal microarray analysis: what is the value of chromosome analysis in today’s genomic array era?

Chromosomal microarray analysis enables the detection of microdeletions/duplications and has become the standard in clinical diagnostic testing for individuals with congenital anomalies and developmental disabilities. In the era of genomic arrays, the value of traditional chromosome analysis needs to be reassessed. We studied 3,710 unrelated patients by chromosomal microarray analysis and chromosome analysis simultaneously and compared the results. We found that chromosomal microarray analysis detected the chromosomal imbalances that were identified by chromosome analysis with the exception of six cases (0.16%) that had mosaic abnormalities. Of note, one case showed mosaicism for two abnormal cell lines, resulting in a balanced net effect and a normal chromosomal microarray analysis. Further structural abnormalities such as unbalanced translocations, rings, and complex rearrangements were subsequently clarified by chromosome analysis in 18% of the cases with abnormal chromosomal microarray analysis results. Apparently balanced rearrangements were detected by chromosome analysis in 30 cases (0.8%). Our data demonstrate that although chromosomal microarray analysis should be the first-tier test for clinical diagnosis of chromosome abnormalities, chromosome analysis remains valuable in the detection of mosaicism and delineation of chromosomal structural rearrangements.

ARRAY CGH AND ITS APPLICATIONS IN PRENTAL DIAGNOSIS

In prenatal diagnosis, array CGH has several advantages more than traditional chromosomal analysis. It can detect all of aneuploidies, deletions, duplications and unbalanced structural rearrangements of chromosomes with higher resolution, avoidance of culturing amniocytes or chorionic villi, automation, and faster turnaround times. But array CGH has high cost, inability to detect balanced inversions or translocations as well as polyploidy and mosaicism below 20%. Array CGH can identify marker chromosomes and copy number variants (CNVs) of chromosomes but many of them have uncertain clinical significance. So that in prenatal diagnosis array CGH is indicated in the following cases : (1) abnormal fetal ultrasound findings; (2) suspected chromosome imbalances; (3) had children with abnormal chromosomes (4) parents with chromosome balances; (5) advanced maternal age.

Detection of subtelomeric chromosomal rearrangements in idiopathic mental retardation

Subtelomeric regions of chromosomes are rich in genes; their rearrangements cannot be identified by traditional chromosome analysis. Since these subtelomeric aberrations are responsible for about 7% of cases with mental retardation, their detection is important both from the diagnostic point of view and to prevent recurrence in the family. Subtelomeric chromosomal alterations can be detected by fluorescence in situ hybridization. Based on international criteria, 35 out of 59 patients with mental retardation have been selected. Subtelomeric rearrangements were revealed in 6 patients (5 familial cases, 1 new onset) whereas the subtelomeric FISH result was normal in 29 cases. Deletion of 8pter and duplication of 12pter were detected in 2 patients, while a deletion of 21qter and duplication of the 10pter due to an unbalanced translocation were found in 3 other cases. Finally, a new onset deletion of 3qter was observed in 1 patient. In order to clarify the origin of chromosome aberrations, 12 healthy family members were also examined, 5 of them carried balanced translocations. We concluded that the phenotype is mostly influenced by the size of regions involved in deletion/duplication and - in case of translocations - by the associated chromosomal abnormalities.

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 present state and perspectives of micronucleus assay in radiation protection. A review

The occurrence of micronuclei proved to be a sensitive biological indicator of clastogenic effects of many chemical and physical agents. The possibility of using the micronucleus technique in radiation protection as an alternative to the traditional chromosomal analysis has recently been followed with increasing interest. This review outlines the main biological and practical aspects of the micronucleus assay and discusses its potential to serve as a rapid and reliable measure of radiation overexposures and hypersensitivities.