Abnormal chromosomes identification using chromosomal microarray

In this study, we presented a case series to highlight the chromosomal microarray (CMA) in identifying chromosomal abnormalities which is undetectable by conventional karyotyping or known abnormal chromosomes without clear diagnosis. Extensive studies showed that CMA was gradually accepted as a prenatal invasive testing during pregnancy. The aim of this study was to evaluate the diagnostic effect of CMA for foetuses with abnormal chromosomes unrecognised by conventional karyotyping. Pregnant women who need prenatal diagnosis with all indications were enrolled in this study. For aberrant cytogenetic findings that cannot be defined by routine karyotyping, single nucleotide polymorphism array (SNP-array) was used. Six cases with abnormal karyotype were included in the study. With higher resolution of translocation breakpoints, CMA could detect smaller chromosomal imbalances that were undetectable by karyotyping. This study highlights the value of CMA for the detection of submicroscopic abnormalities in foetuses that cannot be detected by conventional karyotyping. Impact StatementWhat is already known on this subject? Chromosomal microarray (CMA) offers additional diagnostic benefits by revealing submicroscopic imbalances or copy number variations (CNVs) that are too small to be identified on a standard G-banded chromosome preparation.What do the results of this study add? We added a case series to highlight the CMA in identifying chromosomal abnormalities not detectable by conventional karyotyping or known abnormal chromosomes without clear diagnosis.What are the implications of these findings for clinical practice and/or further research? This study highlights the value of CMA in the case of associated foetuses with submicroscopic abnormalities that cannot detect by conventional karyotyping.

Disparities in the acceptance of chromosomal microarray at the time of prenatal genetic diagnosis

OBJECTIVE

Chromosomal microarray (CMA) increases the diagnostic yield of prenatal genetic diagnostic testing but is not universally performed. Our objective was to identify provider and patient characteristics associated with the acceptance of CMA at the time of prenatal genetic diagnostic testing.

METHODS

Retrospective cohort study of patients undergoing prenatal genetic diagnostic testing (chorionic villus sampling or amniocentesis) at a single institution between 2014 and 2020. Primary outcome was the acceptance of CMA based on the genetic counselor ,GC who saw the patient. Secondary analyses assessed patient characteristics associated with the acceptance of CMA.

RESULTS

2372 participants were included. Fifty-eight percent of participants accepted CMA. Acceptance of CMA varied significantly by GC, ranging from 31% to 90%. Patients with public insurance and those who identified as Black or Hispanic/Latina were less likely to have CMA performed (aOR 0.24, 95% CI 0.20-0.30, and 0.68, 95% CI 0.50-0.92). Even among those with a structural anomaly present, public insurance was associated with significantly lower odds of CMA being performed (aOR 0.39, 95% CI 0.25-0.61).

CONCLUSIONS

Acceptance of CMA at the time of prenatal genetic diagnostic testing varied based on the GC performing the counseling. Public insurance was associated with lower frequency of accepting CMA.

Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges-Systematic Review of the Literature and Meta-Analysis

Fetal malformations occur in 2-3% of pregnancies. They require invasive procedures for cytogenetics and molecular testing. "Structural anomalies" include non-transient anatomic alterations. "Soft markers" are often transient minor ultrasound findings. Anomalies not fitting these definitions are categorized as "dynamic". This meta-analysis aims to evaluate the diagnostic yield and the rates of variants of uncertain significance (VUSs) in fetuses undergoing molecular testing (chromosomal microarray (CMA), exome sequencing (ES), genome sequencing (WGS)) due to ultrasound findings. The CMA diagnostic yield was 2.15% in single soft markers (vs. 0.79% baseline risk), 3.44% in multiple soft markers, 3.66% in single structural anomalies and 8.57% in multiple structural anomalies. Rates for specific subcategories vary significantly. ES showed a diagnostic rate of 19.47%, reaching 27.47% in multiple structural anomalies. WGS data did not allow meta-analysis. In fetal structural anomalies, CMA is a first-tier test, but should be integrated with karyotype and parental segregations. In this class of fetuses, ES presents a very high incremental yield, with a significant VUSs burden, so we encourage its use in selected cases. Soft markers present heterogeneous CMA results from each other, some of them with risks comparable to structural anomalies, and would benefit from molecular analysis. The diagnostic rate of multiple soft markers poses a solid indication to CMA.

Utilization and uptake of clinical genetics services in high-income countries: A scoping review

Ongoing rapid growth in the need for genetic services has the potential to severely strain the capacity of the clinical genetics workforce to deliver this care. Unfortunately, assessments of the scale of this health policy challenge and potential solutions are hampered by the lack of a consolidated evidence base on the growth in genetic service utilization. To enable health policy research and strategic planning by health systems in this area, we conducted a scoping review of the literature on the utilization and uptake of clinical genetics services in high-income countries published between 2010 and 2018. One-hundred-and-ninety-five unique studies were included in the review. Most focused on cancer (85/195; 44%) and prenatal care (50/195; 26%), which are consistently the two areas with the greatest volume of genetic service utilization in both the United States and other high-income countries. Utilization and uptake rates varied considerably and were influenced by contextual factors including health system characteristics, provider knowledge, and patient preferences. Moreover, growth in genetic service utilization appears to be driven to a significant degree by technological advances and the integration of new tests into clinical care. Our review highlights both the policy challenge posed by the rapid growth in the utilization of genetic services and the variability in this trend across clinical indications and health systems.

Chromosomal microarray analysis in pregnancies at risk for a molecular disorder

Objective: The aim of this study was to evaluate the utility of chromosomal microarray (CMA) in patients who were solely referred for molecular diagnosis.Methods: During a 2-year period, CMA was the patients' choice, whether to opt for it or not, for those at risk for fetal hemoglobin Bart's disease or β-thalassemia major who were referred for invasive prenatal diagnosis and had a normal fetal genotype. CytoScan 750 K array (Affymetrix Inc., Santa Clara, CA) was used for CMA. The CMA testing results were collected.Results: There were 184 patients, who had a normal genotypic result, opting CMA testing without an obvious indication for fetal karyotyping. The median maternal age was 29 years (range, 17-34); the median gestational age was 13 weeks (range, 11-20). In two out of 184 (1.1%) cases unexpected de novo pathogenic microdeletions were found: a 3.2 Mb 22q11.21 microdeletion and a 0.8 Mb 16p11.2 microdeletion.Conclusions: Pregnancies at risk for thalassemia can also benefit from performing CMA. This information might be a part of the contents in comprehensive pretest counseling for those who are referred for diagnostic testing due to a molecular disorder.

How should costs and cost-effectiveness be considered in prenatal genetic testing?

In January 2017, a group of experts in prenatal genetics attended a workshop at the Society of Maternal-Fetal Medicine meeting to review the evidence behind the costs and cost-effectiveness of prenatal genetic testing. Over the past decade, prenatal genetic testing options have dramatically expanded to include additional options with cell-free DNA (cfDNA) screening, as well as increased diagnostic abilities through chromosomal microarray analysis (CMA), gene panels, whole exome sequencing, and other tests. With these expanding technologies, it is important to consider the options available as well as the cost effectiveness of their use. Other important considerations are the effects of movements toward value-based health care; the role of professional societies, commercial laboratories, and insurers; disparities that exist in prenatal genetic testing; and outcomes for both patients and health care systems. Workshop participants identified key areas of research to advance our understanding of the costs and cost-effectiveness of prenatal genetic testing, which include (1) understanding the short- and long-term costs to patients and to health care systems with prenatal genetic tests; (2) elucidating the short- and long-term health outcomes for parents and children that are important to consider when comparing one testing strategy to another; (3) understanding the value underlying prenatal genetic testing to individuals and health care systems; and (4) identifying disparities in prenatal genetic testing, reasons for these disparities, and how to minimize them.

Frequency of submicroscopic chromosomal aberrations in pregnancies without increased risk for structural chromosomal aberrations: systematic review and meta-analysis

OBJECTIVE

To establish, based on a systematic literature review, the frequency of pathogenic submicroscopic chromosomal aberrations in fetuses that are not at increased risk for unbalanced structural chromosomal aberrations, with the aim of determining whether high-resolution testing for submicroscopic aberrations is beneficial in a general pregnant population.

METHODS

EMBASE, PubMed, Web of Science and CENTRAL databases were searched systematically on 3 June 2016 for all relevant articles on the prevalence of pathogenic submicroscopic copy number variants (CNVs) in fetuses referred for prenatal invasive testing because of advanced maternal age (AMA) or parental anxiety (ANX). Relevant full-text articles were analyzed and the prevalence of submicroscopic CNVs was calculated based on the extracted data. Meta-analysis was conducted in a pooled cohort of 10 614 fetuses based on the 10 largest studies (n > 300) of a total of 19 that were relevant.

RESULTS

Pooled estimate analysis indicated that 0.84% (95% CI, 0.55-1.30%) of fetuses that had invasive testing because of AMA/ANX carried a pathogenic clinically significant submicroscopic aberration. The onset/penetrance of submicroscopic findings was studied in 10 314 fetuses reported in eight papers that presented aberrant cases with all necessary details to allow assessment of the findings. The pooled estimates resulting from meta-analysis of the data indicated that an early-onset syndromic disorder was detected in 0.37% (95% CI, 0.27-0.52%) of cases, a susceptibility CNV was found in 0.30% (95% CI, 0.14-0.67%) and late-onset diseases were reported in 0.11% (95% CI, 0.05%-0.21%). The prevalence of early-onset syndromic disorders caused by a submicroscopic aberration was calculated to be 1:270. When the risk for submicroscopic aberrations is added to the individual risk for microscopic chromosomal aberrations, all pregnant women have a risk of higher than 1 in 180 for a relevant chromosomal aberration, and pregnant women under 36 years of age have a higher risk for submicroscopic pathogenic aberrations than for Down syndrome.

CONCLUSION

This systematic review shows that a significant proportion of fetuses in a general pregnant population carry a submicroscopic pathogenic CNV. Based on these figures, all women should be informed on their individual risk for all pathogenic chromosomal aberrations and not only for common trisomies. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.

[Contribution of chromosomal microarray analysis by a multidisciplinary prenatal diagnosis center]

OBJECTIVE

Chromosomal analysis by array CGH is a cytogenetic technique that has opened its application to prenatal diagnosis in recent years. The main objective of the study was to analyze the contribution for couples using chromosomal analysis by array CGH in a CPDPN.

METHODS

A retrospective cohort study was conducted in 2015 in a CPDPN. All the patients with array CGH analysis were included in the study. The analysis indications were CN≥3.5mm, ultrasound signs, intra-uterine growth retardation and fetal deaths. Data were collected in the prenatal diagnosis and genetic records.

RESULTS

In total, 155 patients underwent analysis by array CGH, which corresponds to 36% of patients with invasive sampling indication. Fifteen CGH analysis were positive which represents 9.6% of indications. None of those diagnoses was possible with standard karyotype. These positive results have changed the outcome of pregnancy and what to do for a future pregnancy in 54% of cases.

CONCLUSION

Array CGH enables a diagnostic gain despite a delicate interpretation and changes taking care of patients in future pregnancies. These results should be confirmed in a prospective multicenter study.

Microarrays in prenatal diagnosis

In prenatal diagnosis, chromosomal microarray (CMA) has not yet fully replaced conventional karyotyping but has rapidly become the recommended test in pregnancies with ultrasound abnormalities. In this review, we provide an overview of the published data concerning this technology and the controversies concerning its use in the prenatal setting. There is abundant evidence indicating the added detection of pathogenic abnormalities with CMA in comparison to the traditional karyotyping, especially in fetuses with multiple or isolated ultrasound abnormalities such as congenital heart disease, increased nuchal translucency, or oral cleft. On the other hand, there is also a risk to detect variants of unknown significance, late-onset disorders, and variants in susceptibility loci. However, it has been shown that pregnant couples tend to prefer a maximum of information about the health of their unborn child. Taken together, CMA has considerable diagnostic and prognostic values during pregnancy and should therefore be the test of choice.