Use Of Chromosomal Microarray Research Articles

Genetic Testing Guidelines Impact Care in Newborns with Congenital Heart Defects

To evaluate genetic evaluation practices in newborns with the most common birth defect, congenital heart defects (CHD), we determined the prevalence and the yield of genetic evaluation across time and across patient subtypes, before and after implementation of institutional genetic testing guidelines. This was a retrospective, cross-sectional study of 664 hospitalized newborns with CHD using multivariate analyses of genetic evaluation practices across time and patient subtypes. Genetic testing guidelines for hospitalized newborns with CHD were implemented in 2014, and subsequently genetic testing increased (40% in 2013 and 75% in 2018, OR 5.02, 95% CI 2.84-8.88, P<.001) as did medical geneticists' involvement (24% in 2013 and 64% in 2018, P<.001). In 2018, there was an increased use of chromosomal microarray (P<.001), gene panels (P=.016), and exome sequencing (P=.001). The testing yield was high (42%) and consistent across years and patient subtypes analyzed. Increased testing prevalence (P<.001) concomitant with consistent testing yield (P=.139) added an estimated 10 additional genetic diagnoses per year, reflecting a 29% increase. In patients with CHD, yield of genetic testing was high. After implementing guidelines, genetic testing increased significantly and shifted to newer sequence-based methods. Increased use of genetic testing identified more patients with clinically important results with potential to impact patient care.

Psychiatric genetic counseling for people with copy number variants associated with psychiatric conditions.

22q11.2 deletion is one of the most well-known copy number variants (CNVs) associated with developing a psychiatric condition (e.g., schizophrenia), but there is a growing list of other CNVs which also confer substantial risk for developing psychiatric conditions. With increased use of chromosome microarray and exome sequencing, the frequency with which these CNVs are detected is increasing. While individuals with such CNVs often receive genetic counseling, research shows that associated psychiatric conditions are less often addressed-clinicians tend to focus on the nonpsychiatric manifestations of the CNV. This represents an important service gap for people with these CNVs and their families, as research shows that not only do these families want genetic counseling about psychiatric illness, it can also produce meaningful positive outcomes for people, including increases in empowerment, and self-efficacy. Therefore, there is a need to ensure that individuals with psychiatric condition-associated CNVs are being counseled about these manifestations of their condition in a way that can promote the best outcomes. In this paper we describe the process of providing genetic counseling in two clinical scenarios in which a psychiatric susceptibility CNV is identified: (1) in an individual who has not been diagnosed with a psychiatric condition and (2) in an individual with an established psychiatric condition.

Prenatal diagnosis for fetuses with isolated and non-isolated congenital heart defects using chromosomal microarray and exome sequencing.

To investigate the use of chromosomal microarray (CMA) and Exome sequencing (ES) in fetuses with congenital heart disease (CHD). The Fetal Medicine Unit of Shanghai First Maternity and Infant Hospital records were reviewed to ascertain all cases diagnosed with CHD by level 2 ultrasound examination between 2016 and 2019. Cases were categorized as isolated or associated with other abnormalities or fetal growth restriction. CMA was offered to all cases as a first-line genetic test followed by ES when CMA was non-diagnostic. Of the 586 ascertained, 84 (14.3%) had causative CMA abnormality, of which 8.8% (35/400) were in fetuses with isolated CHD and 26.3% (49/186) in those with other abnormalities. ES was performed in 47 cases with a negative CMA. Causative variants were identified in two (10.5%, 2/19) isolated cases and four(14.3%, 4/28) with other abnormalities. Invasive procedures with CMA should be offered in pregnancies complicated by both non-isolated and isolated cardiac abnormalities. When CMA is not diagnostic, ES can add diagnostic value in both groups and should be considered even for fetuses with an isolated CHD.

Rare genetic causes of complex kidney and urological diseases.

Although often considered a single-entity, chronic kidney disease (CKD) comprises many pathophysiologically distinct disorders that result in persistently abnormal kidney structure and/or function, and encompass both monogenic and polygenic aetiologies. Rare inherited forms of CKD frequently span diverse phenotypes, reflecting genetic phenomena including pleiotropy, incomplete penetrance and variable expressivity. Use of chromosomal microarray and massively parallel sequencing technologies has revealed that genomic disorders and monogenic aetiologies contribute meaningfully to seemingly complex forms of CKD across different clinically defined subgroups and are characterized by high genetic and phenotypic heterogeneity. Investigations of prevalent genomic disorders in CKD have integrated genetic, bioinformatic and functional studies to pinpoint the genetic drivers underlying their renal and extra-renal manifestations, revealing both monogenic and polygenic mechanisms. Similarly, massively parallel sequencing-based analyses have identified gene- and allele-level variation that contribute to the clinically diverse phenotypes observed for many monogenic forms of nephropathy. Genome-wide sequencing studies suggest that dual genetic diagnoses are found in at least 5% of patients in whom a genetic cause of disease is identified, highlighting the fact that complex phenotypes can also arise from multilocus variation. A multifaceted approach that incorporates genetic and phenotypic data from large, diverse cohorts will help to elucidate the complex relationships between genotype and phenotype for different forms of CKD, supporting personalized medicine for individuals with kidney disease.

A case of de novo microdeletion with combination of 1q21.1 and 14q32.2q32.31

Background: Chromosomal microarray is considered as the first-line diagnostic genetic test in all individuals with intellectual disability (ID) and attention-deficit disorders. In recent years, the use of chromosomal microarrays routinely for this purpose has resulted in the identification of many new microdeletion and microduplication regions connected with these clinical situations, including the 1q21.1 and 14q32.2q32.31 microdeletions. Case Presentation: A 5-year-old male patient came to the clinic because of ID, hyperactivity, growth retardation, and speaking difficulty. We determined strabismus on both the eyes, and he was myopic. He had a high palate, little, and sparse teeth. On the right hand, there was a simian line. Both undescended testes were brought down with surgery. In addition, he had got an inward penis head. He had joint laxity in most of the joints. He had pes planus and talipes valgus. Therefore, we decided to make array-comparative genomic hybridization analysis and the result came 1368.001 kb deletion on 1q21.1 between chr1: 146023922 and 147391923 nucleotides and 992.003 kb deletion on 14q32.2q32.31 between chr14: 100453009 and 101445012 nucleotides according to �Human Genome Build 37� (The result was confirmed by a fluorescent in situ hybridization method performed to determine the particular deleted regions). Conclusion: Here, we report the first case presented with ID, hyperactivity, growth retardation, and speaking difficulty with other findings and has a combination of de novo 1q21.1 and 14q32.2q32.31 microdeletions. Although several research groups have reported similar results with similar regions separately, this study is the first of its kind revealing the effects of this combination to clinical outcome.

Polymicrogyria associated with 17p13.3p13.2 duplication: Case report and review of the literature

We present the case of a male infant with bilateral perisylvian polymicrogyria associated with a de novo duplication of chromosome region 17p13.3p13.2. To our knowledge, this is the first report of polymicrogyria associated with the 17p13.3 contiguous gene duplication syndrome. Testing for known monogenic causes of polymicrogyria was negative and there was no clinical evidence of an acquired prenatal cause. Given the critical, dose-sensitive role that the 17p13.3 region plays in brain development, we suggest that the chromosome duplication is the most likely explanation for the polymicrogyria. Clinical and functional studies have demonstrated deleterious effects of increased LIS1 expression on the developing brain and the contribution of YWHAE to the brain phenotype of the 17p13 duplication syndrome. There is also evidence that CRK, the other candidate gene in this region, via interaction with LIS1, plays a critical role in cortical development. In addition to LIS1, YWHAE and CRK, our patient's chromosome duplication involves at least 100 other genes, less than half of which are annotated at the time of writing. It is expected that the ongoing use of chromosome microarray and next-generation sequencing to investigate the genetic causes of brain malformations will continue to extend our understanding of the 17p13 region and of the contributions of the genes in this region to cortical development.

Chromosomal microarray analysis in fetuses with an isolated congenital heart defect: A retrospective, nationwide, multicenter study in France.

Congenital heart defects (CHDs) may be isolated or associated with other malformations. The use of chromosome microarray (CMA) can increase the genetic diagnostic yield for CHDs by between 4% and 10%. The objective of this study was to evaluate the value of CMA after the prenatal diagnosis of an isolated CHD. In a retrospective, nationwide study performed in France, we collected data on all cases of isolated CHD that had been explored using CMAs in 2015. A total of 239 fetuses were included and 33 copy number variations (CNVs) were reported; 19 were considered to be pathogenic, six were variants of unknown significance, and eight were benign variants. The anomaly detection rate was 10.4% overall but ranged from 0% to 16.7% as a function of the isolated CHD in question. The known CNVs were 22q11.21 deletions (n=10), 22q11.21 duplications (n=2), 8p23 deletions (n=2), an Alagille syndrome (n=1), and a Kleefstra syndrome (n=1). The additional diagnostic yield was clinically significant (3.1%), even when anomalies in the 22q11.21 region were not taken into account. Hence, patients with a suspected isolated CHD and a normal karyotype must be screened for chromosome anomalies other than 22q11.21 duplications and deletions.

Contemporary prenatal aneuploidy screening practice in Australia: Frequently asked questions in the cell-free DNA era.

Cell-free DNA screening has quickly become established in Australia as an accurate - albeit costly - prenatal screening test for trisomy 21, 18 and 13. It is also commonly used for the detection of sex chromosome abnormalities. The increasing number of prenatal screening pathways available to women has increased the complexity of pretest counselling. Concurrent advances in diagnostic testing with the widespread use of chromosomal microarrays create further challenges for the continuing education of clinicians and health consumers. This article aims to answer common clinical questions in this rapidly evolving field and complements the recently updated Royal Australian and New Zealand College of Obstetricians and Gynaecologists Statement on Prenatal Screening for Fetal Chromosome and Genetic Conditions.

Interstitial microdeletion of the 1p34.3p34.2 region.

BackgroundInterstitial microdeletions of chromosome 1p34.3p34.2 are rare, but are continuing to be identified by the use of chromosome microarray. There have been fewer than 10 individuals identified who have deletions of the 1p34.3p34.2 region; all of these previously described individuals have deletions of the AGO1, AGO3, GRIK3, SLC2A1, or RIMS3 genes. Haploinsufficiency of these genes has been associated with neurodevelopmental delays.MethodsChromosome microarray, quantitative PCR, and fluorescence in situ hybridization were performed with DNA extracted from peripheral blood.ResultsChromosome microarray identified a 2.3 Mb 1p34.3p34.2 one copy deletion in our patient with global developmental delay, mild intellectual disability, delayed bone age, bilateral vesicoureteral reflux, vocal cord paralysis, right aberrant subclavian artery, kyphoscoliosis, bilateral metatarsus adductus, and valgus knee deformity. This deletion was confirmed by quantitative PCR and does not include the AGO1, AGO3, GRIK3, SLC2A1, or RIMS3 genes. Subsequent FISH testing of the parents was negative.ConclusionHaploinsufficiency of the 1p34.3p34.2 region, including the SNIP1 gene and excluding the five genes listed above, is responsible for the neurocognitive delays and other symptoms as identified in our patient.

Current use of chromosomal microarray by Australian paediatricians and implications for the implementation of next generation sequencing.

Chromosomal microarray (CMA) is an important diagnostic test for children with multiple congenital anomalies or certain developmental behavioural problems suggestive of an underlying genetic diagnosis. However, there are medical and ethical complexities to its use and few Australian policies to guide practice. We aimed to describe the current practice of Australian paediatricians in relation to CMA testing. We hypothesised that there are knowledge gaps in their use of CMA. Online survey completed between September 2015 and January 2016 by paediatricians in secondary care settings. Participants were members of the Australian Paediatric Research Network. One hundred and sixty five (43%) of 383 active members responded. Our main outcome measures comprised: (i) the indications for which paediatricians request CMA; (ii) their approach to consent; (iii) their interpretation of results; and (iv) their understanding of the impact on patient management. A significant proportion of paediatricians (21-52%) did not regularly use CMA for conditions with established evidence of diagnostic yield. Paediatricians under-estimated the potential for CMA findings to alter patient management. There was wide variability in paediatricians' approach to consent, and low use of consent forms and fact sheets. Paediatricians reported difficulties interpreting CMA results, with high rates of referral to clinical genetics services. The reported practice of Australian paediatricians is not consistent with international standards on CMA. Australian practice could be improved by a standardised approach to ordering CMA, consenting patients and interpreting results. We provide resources for CMA ordering and make recommendations about preparation for next generation sequencing.

Genetic Evaluation and Use of Chromosome Microarray in Patients with Isolated Heart Defects: Benefits and Challenges of a New Model in Cardiovascular Care.

Congenital heart defects (CHDs) are common birth defects and result in significant morbidity and global economic impact. Genetic factors play a role in most CHDs; however, identification of these factors has been historically slow due to technological limitations and incomplete understanding of the impact of human genomic variation on normal and abnormal cardiovascular development. The advent of chromosome microarray (CMA) brought tremendous gains in identifying chromosome abnormalities in a variety of human disorders and is now considered part of a standard evaluation for individuals with multiple congenital anomalies and/or neurodevelopmental disorders. Several studies investigating use of CMA found that this technology can identify pathogenic copy-number variations (CNVs) in up to 15–20% of patients with CHDs with other congenital anomalies. However, there have been fewer studies exploring the use of CMA for patients with isolated CHDs. Recent studies have shown that the diagnostic yield of CMA in individuals with seemingly isolated CHD is lower than in individuals with CHDs and additional anomalies. Nevertheless, positive CMA testing in this group supports chromosome variation as one mechanism underlying the development of isolated, non-syndromic CHD – either as a causative or risk-influencing genetic factor. CMA has also identified novel genomic variation in CHDs, shedding light on candidate genes and pathways involved in cardiac development and malformations. Additional studies are needed to further address this issue. Early genetic diagnosis can enhance the medical management of patients and potentially provide crucial information about recurrence. This information is critical for genetic counseling of patients and family members. In this review, we review CMA for the non-genetics cardiology provider, offer a summary of CNV in isolated CHDs, and advocate for the use of CMA as part of the cardiovascular genetics evaluation of patients with isolated CHDs. We also provide perspective regarding the benefits and challenges that lie ahead for this model in the clinical setting.

Survey of the use of chromosomal microarray by Australian paediatricians

Survey of the use of chromosomal microarray by Australian paediatricians

Chromosomal microarray as first‐tier approach in low‐risk pregnancies: detection rate should not be the only criterion for its application

We read with interest the paper by Hillman et al.1 concerning the use of chromosomal microarray (CMA) in prenatal diagnosis. Presented datasets included: a prospective cohort of pregnant women with ultrasound abnormalities and a systematic review and meta-analysis of studies on prenatal cases referred for any indication, fetal ultrasound abnormalities included. The authors corroborated the usefulness of CMA in pregnancies with ultrasound abnormalities, and reported an additional detection rate of abnormalities by CMA compared with karyotyping of 4.1% in their cohort and of 10% in the whole meta-analysis. These different figures were likely due to the different analytical sensitivity of the CMA platforms used (i.e. bacterial artificial chromosome (BAC) vs oligoarray). A BAC platform comparable to that utilized in the Hillman study has been tested by other groups2, 3, who claimed higher detection rates, by also incorporating into their results large imbalances detectable by means of good-quality chromosomal preparations. Accordingly, Hillman et al. emphasize the relevance of high-quality laboratory practices to compare CMA and karyotyping results in order to avoid a significant bias in any conclusion. Furthermore, copy number variations (CNVs) such as the PMP22 deletion, classified as a ‘positive’ result, should be regarded as incidental findings1, 2 and should not be considered in the detection rate estimation of CMA when comparing with karyotyping; moreover, such results are unlikely to address the particular concerns the couple may have when seeking prenatal diagnosis for abnormal ultrasound findings. However, the results reported by Hillman et al. agree with published guidelines and statements indicating that pregnancies with ultrasound abnormalities would benefit from CMA. Subanalysis of the pregnancies referred for ‘any indication’ disclosed highly heterogeneous results, with the additional detection rate of abnormalities by CMA compared with karyotyping ranging from 0.4 to 50%, while the detection rate of VOUS (variants of unknown significance) was 1.4%. Therefore, given the heterogeneity and increasing resolution over the years of CMA platforms and the merging of low- and high-risk populations, it is difficult to draw any final conclusion, particularly regarding CMA use in low-risk pregnancies. A recent report has indeed shown that when advanced maternal age or anxiety were the only or main indications for referral, the detection gain by CMA ranged from 1.0% and 0.6%, respectively4. These figures are evidently low compared with the VOUS detection rate. In our opinion, the higher diagnostic capacity of CMA should not be the only criterion for updating health policy committee statements; such decisions should be planned only after careful assessment of the large-scale application of CMA to unselected populations. In this perspective, several crucial issues await resolution, including the appropriate array design, assessment of the clinical relevance of a CNV with variable penetrance and expressivity, consensus on reporting VOUS and the related emotional burden of such findings. In order to assess comprehensively the large-scale application of CMA in low-risk pregnancies, we reiterate the advocacy for a model such as ACCE5, which is formulated based on the main criteria for evaluation of a genetic test (analytical validity, clinical validity and clinical utility) but which also consciously considers ethical, legal and social implications. The latter considerations are of particular importance when proposing genetic testing in a prenatal setting. We think that to better balance the costs and benefits of CMA application in prenatal diagnosis without specific indications, teamwork between geneticists, obstetricians and public health methodologists should be established, with partnership of the non-scientific stakeholders (i.e. pregnant couples/family and patient support organizations). A. Baroncini†, L. Sinibaldi*‡, L. Bernardini‡, P. Cavalli§, F. Faravelli¶, M. Gentile**, M. Lituania††, P. Volpe‡‡, L. Camurri§§, A. Novelli‡, and B. Dallapiccola¶¶ †ASL di Imola, Italy, UOC di Genetica Medica, Dip. Materno-Infantile, Imola, Italy; ‡IRCCS Fondazione Casa Sollievo della Sofferenza, Laboratorio Mendel, San Giovanni Rotondo, Italy; §Azienda Istituti Ospitalieri di Cremona, Servizio di Genetica, Cremona, Italy; ¶IRCCS Ospedali Galliera, SSD Genetica Medica Genova, Genova, Italy; **Ospedale di Venere, ASL di Bari, UOC Genetica Medica, Bari, Italy; ††IRCCS Ospedali Galliera, SSD Fisiopatologia Preconcezionale e Prenatale, Genova, Italy; ‡‡Ospedale di Venere, ASL di Bari, UOC Medicina Fetale, Bari, Italy; §§RDI Rete Diagnostica Italiana, Genetica Medica, Padova, Italy; ¶¶IRCCS Ospedale Pediatrico Bambino Gesù, Roma, Italy *Correspondence. (e-mail: [email protected])

THE MATERNAL-FETAL MEDICINE: AN UPDATE

The development of Maternal-Fetal Medicine is contributing to an improvement of maternal well-being and of neonatal health, introducing a number of new and useful technologies. Advances in genomics in the field of prenatal screening and diagnosis allowed the discovery of fragments of cell-free fetal DNA in the maternal circulation and the use of chromosomal microarrays, which can test for microdeletions and microduplications in addition to aneuploidies. Color Doppler applications during pregnancy are expanding exponentially and Doppler flow velocity waveforms indices have provided important information from maternal, placental and fetal circulation with clinical implications. Ultrasound monitoring of fetal growth represents a fundamental tool to evaluate fetal wellbeing and several methods have been developed to improve fetal weight estimation accuracy. The combination of new biophysical and biochemical markers is enriching Maternal-Fetal Medicine and more research will allow to improve pregnancy outcome.

THE MATERNAL-FETAL MEDICINE: AN UPDATE

The development of Maternal-Fetal Medicine is contributing to an improvement of maternal well-being and of neonatal health, introducing a number of new and useful technologies. Advances in genomics in the field of prenatal screening and diagnosis allowed the discovery of fragments of cell-free fetal DNA in the maternal circulation and the use of chromosomal microarrays, which can test for microdeletions and microduplications in addition to aneuploidies. Color Doppler applications during pregnancy are expanding exponentially and Doppler flow velocity waveforms indices have provided important information from maternal, placental and fetal circulation with clinical implications. Ultrasound monitoring of fetal growth represents a fundamental tool to evaluate fetal wellbeing and several methods have been developed to improve fetal weight estimation accuracy. The combination of new biophysical and biochemical markers is enriching Maternal-Fetal Medicine and more research will allow to improve pregnancy outcome.

Identification of Small Exonic CNV from Whole-Exome Sequence Data and Application to Autism Spectrum Disorder

Copy number variation (CNV) is an important determinant of human diversity and plays important roles in susceptibility to disease. Most studies of CNV carried out to date have made use of chromosome microarray and have had a lower size limit for detection of about 30 kilobases (kb). With the emergence of whole-exome sequencing studies, we asked whether such data could be used to reliably call rare exonic CNV in the size range of 1-30 kilobases (kb), making use of the eXome Hidden Markov Model (XHMM) program. By using both transmission information and validation by molecular methods, we confirmed that small CNV encompassing as few as three exons can bereliably called from whole-exome data. We applied this approach to an autism case-control sample (n = 811, mean per-target read depth = 161) and observed a significant increase in the burden of rare (MAF ≤1%) 1-30 kb CNV, 1-30 kb deletions, and 1-10 kb deletions in ASD. CNV in the 1-30 kb range frequently hit just a single gene, and we were therefore able to carry out enrichment and pathway analyses, where we observed enrichment for disruption of genes in cytoskeletal and autophagy pathways in ASD. In summary, our results showed that XHMM provided an effective means to assess small exonic CNV from whole-exome data, indicated that rare 1-30kb exonic deletions could contribute to risk in up to 7% of individuals with ASD, and implicated a candidate pathway in developmental delay syndromes.

Key Informants’ Perspectives of Implementing Chromosomal Microarrays Into Clinical Practice in Australia

High-resolution genomic tests have the potential to revolutionize healthcare by vastly improving mutation detection. The use of chromosomal microarray (CMA) represents one of the earliest examples of these new genomic tests being introduced and disseminated in the clinic. While CMA has clear advantages over traditional karyotyping in terms of mutation detection, little research has investigated the process by which CMA was implemented in clinical settings. Fifteen key informants, six clinicians, and nine laboratory scientists from four Australian states were interviewed about their experiences during and in the time since CMA was adopted for clinical use. Participants discussed challenges such as result interpretation and communication. Strengths were also highlighted, including the collaborative approaches of some centers. Clinical experiences and opinions can inform larger studies with a range of stakeholders, including patients. The historical perspectives from this retrospective study can be helpful in guiding the implementation of future genomic technologies such as whole exome/genome sequencing.