Prenatal array comparative genomic hybridization in a well-defined cohort of high-risk pregnancies. A 3-year implementation results in a public tertiary academic referral hospital.

OBJECTIVE: To find out whether the diagnostic yield of prenatal array comparative genomic hybridization (aCGH) can be improved by targeting preselected high-risk pregnancies. METHOD: All the in-house arrays ordered by the Fetomaternal Medical Center from February 2016 until December 2018 were retrospectively analyzed. The indications for array analysis included fetal structural abnormalities, increased nuchal translucency ≥3.5 mm and a chromosomal abnormality in a parent or a sibling. Common aneuploidies were excluded. RESULTS: Diagnostic yield was 15.1% in the entire patient cohort and as high as 20% in fetuses with multiple structural anomalies. The diagnostic yield was lowest in the group with isolated growth retardation. A total of 76 copy number variants (CNVs) were reported from a total of 65 samples, including 16 CNVs associated with a well-described microdeletion/microduplication syndrome, six autosomal trisomies in mosaic form, and three pathogenic single-gene deletions with dominant inheritance and 12 CNVs known to be risk factors for eg developmental delay. CONCLUSION: The diagnostic yield of aCGH was higher than what has previously been reported in less defined patient cohorts. However, the number of CNVs with unclear correlation to the fetal ultrasound findings was still relatively high. The importance of adequate pre- and posttest counseling must therefore be emphasized.

Chromosomal microarray analysis in fetuses with central nervous system anomalies: An 8-year long observational study from a tertiary care university hospital.

OBJECTIVES: To evaluate the prevalence of DNA copy number variants (CNVs) detected with array comparative genomic hybridization (CGH) in fetuses with central nervous system (CNS) anomalies. Secondary objectives were to describe the prevalence of CNV in specific CNS abnormalities, in isolated defects or associated with other malformations or fetal growth restriction (FGR). METHODS: Observational cohort study in 238 fetuses with CNS anomalies in which an array-CGH had been performed between January 2009 and December 2017. Pathogenic CNV and variants of unknown significance (VUS) were reported. RESULTS: Pathogenic CNVs were found in 16/238 cases (6.7%), VUS in 18/238 (7.6%), and normal result in 204/238 (85.7%) cases. Pathogenic CNVs were more frequent in posterior fossa anomalies (cerebellar hypoplasia 33%, megacisterna magna 20%), moderate ventriculomegaly (11%) and spina bifida (3.7%). Pathogenic CNVs and VUS were found in 7/182 (3.8%) and 14/182 (7.7%) cases of isolated anomalies, in 9/49 (18.4%) and 4/49 (8.2%) presenting another malformation, and in 0/7 and 0/7 cases with associated FGR (P = .001, P = .741, respectively). CONCLUSION: These results provide strong evidence toward performing array in fetuses with CNS anomalies, particular in cases of posterior fossa anomalies. The prevalence of pathogenic CNVs is higher in association with other malformations.

The utility of genome-wide cell-free DNA screening in the prenatal diagnosis of Pallister-Killian syndrome.

OBJECTIVE: To report genome-wide cell-free DNA (cfDNA) screening facilitating the diagnosis of Pallister-Killian syndrome (PKS). METHODS: This is a retrospective cohort analysis of positive genome-wide cfDNA screening results showing increased signal from chromosome 12 and the detection of PKS. The genome-wide cfDNA screening results and the subsequent investigations were reviewed. RESULTS: Three singleton pregnancies (3/29007) from 2016 to 2017 yielded positive results indicating large gains on the entire p-arm of chromosome 12. In two cases, multiple structural abnormalities were detected by prenatal ultrasound and the couples opted for termination of pregnancy. Chromosomal microarray performed on fetal skin tissues of the two abortuses detected mosaic tetrasomy 12p, consistent with PKS. In the third case, karyotype and chromosomal microarray performed on an amniotic fluid sample also showed mosaic tetrasomy 12p. In each of the three cases, genome-wide cfDNA screening revealed a large gain on chromosome 12p; subsequent prenatal or postnatal diagnostic testing confirmed the diagnosis of PKS. CONCLUSION: We report the ability of genome-wide cfDNA screening to provide early suspicion and facilitate the subsequent genetic diagnosis of PKS. As genome-wide cfDNA screening becomes increasingly available, incidental diagnosis of partial aneuploidies is expected to increase.

Monosomy of Chromosome 9 Is Associated With Higher Grade, Advanced Stage, and Adverse Outcome in Clear-cell Renal Cell Carcinoma.

BACKGROUND: Clear-cell renal cell carcinoma (ccRCC) is one of the most common malignancies in humans and is usually associated with poor outcomes. Cancers are considered to be genetic diseases. Therefore, a better understanding of genetic alterations that are related to disease progression or poor prognosis can help to more precisely identify high-risk patients and treat them more effectively. The aim of this study was to examine the frequency of whole chromosome 9 loss (monosomy of chromosome 9) and its prognostic value in patients with ccRCC. MATERIALS AND METHODS: Single nucleotide polymorphism-based chromosome microarray (CMA) analysis was performed on 103 resected specimens from patients with ccRCC who had undergone partial or radical nephrectomy between January 2002 and March 2017 at Fox Chase Cancer Center. Monosomy 9 was correlated with clinicopathologic parameters and recurrence-free survival. RESULTS: Chromosome 9 loss was detected in 31 (30%) of 103 tumors. Tumors with chromosome 9 loss had higher histologic grade (3 and 4; P < .001) and pathologic stage (P < .001). In 59 patients with non-metastatic ccRCC, chromosome 9 loss was also associated with higher recurrence rate and shorter recurrence-free survival (RFS) (12-month RFS, 77.8%; 95% confidence interval, 36.5%-93.9% for chromosome 9 loss vs. 95.7%; 95% confidence interval, 84.0%-98.9% for no loss; P = .002). CONCLUSIONS: Chromosome 9 loss was found in 30% of patients with ccRCC and correlated with higher grade, advanced stage, and shorter RFS in patients with Stage I to III ccRCC.

The epidemic of abnormal copy number variant cases missed because of reliance upon noninvasive prenatal screening.

OBJECTIVE: To assess the implications of increasing utilization of noninvasive prenatal screening (NIPS), which may reach 50% with the concomitant decrease in diagnostic procedures (DPs) for its impact on detection of chromosomal abnormalities. METHODS: We studied our program's statistics over 5 years for DPs and utilization of array comparative genomic hybridization (aCGH). We then modeled the implications in our program if DP had not fallen and nationally of a 50% DP and aCGH testing rate using well-vetted expectations for the diagnosis of abnormal copy number variants (CNVs). RESULTS: Our DP fell 40% from 2013-2017. Utilization of aCGH for DP nearly tripled. We detected 28 abnormal CNVs. If DP had not fallen, we likely would have detected 60. With 4 million US births per year, 2 million DPs would detect 30 000 abnormal CNVs and 4000 standard aneuploidies. At a 1/500 complication-pregnancy loss rate, the detection/complication ratio is 8.5/1. CONCLUSIONS: Noninvasive prenatal screening has significantly changed the practice of prenatal screening. However, while increasing the detection of Down syndrome, the concomitant decrease in DP and lack of aCGH results in missing many more abnormalities than the increase in Down syndrome and complications of DP combined. From a public health perspective, such represents a missed opportunity for overall health care delivery.

Pregnancy outcomes from more than 1,800 in vitro fertilization cycles with the use of 24-chromosome single-nucleotide polymorphism-based preimplantation genetic testing for aneuploidy.

OBJECTIVE: To measure in vitro fertilization (IVF) outcomes following 24-chromosome single‒nucleotide-polymorphism (SNP)-based preimplantation genetic testing for aneuploidy (PGT-A) and euploid embryo transfer. DESIGN: Retrospective. SETTING: Fertility clinics and laboratory. PATIENT(S): Women 20-46 years of age undergoing IVF treatment. INTERVENTION(S): Twenty-four-chromosome SNP-based PGT-A of day 5/6 embryo biopsies. MAIN OUTCOME MEASURE(S): Maternal age-stratified implantation, clinical pregnancy, and live birth rates per embryo transfer; miscarriage rates; and number of embryo transfers per patient needed to achieve a live birth. RESULT(S): An implantation rate of 69.9%, clinical pregnancy rate per transfer of 70.6%, and live birth rate per transfer of 64.5% were observed in 1,621 nondonor frozen cycles with the use of SNP-based PGT-A. In addition, SNP-based PGT-A outcomes, when measured per cycle with transfer, remained relatively constant across all maternal ages; when measured per cycle initiated, they decreased as maternal age increased. Miscarriage rates were ∼5% in women ≤40 years old. No statistically significant differences in pregnancy outcomes were found for single-embryo transfers (SET) versus double-embryo transfers with SNP-based PGT-A. On average, 1.38 embryo transfers per patient were needed to achieve a live birth in nondonor cycles. CONCLUSION(S): Our findings that SNP-based PGT-A can mitigate the negative effects of maternal age on IVF outcomes in cycles with transfer, and that pregnancy outcomes from SET cycles are not significantly different from those of double-embryo transfer cycles, support the use of SET when transfers are combined with SNP-based PGT-A.

Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression.

By integrating Haar wavelets with Hidden Markov Models, we achieve drastically reduced running times for Bayesian inference using Forward-Backward Gibbs sampling. We show that this improves detection of genomic copy number variants (CNV) in array CGH experiments compared to the state-of-the-art, including standard Gibbs sampling. The method concentrates computational effort on chromosomal segments which are difficult to call, by dynamically and adaptively recomputing consecutive blocks of observations likely to share a copy number. This makes routine diagnostic use and re-analysis of legacy data collections feasible; to this end, we also propose an effective automatic prior. An open source software implementation of our method is available at http://schlieplab.org/Software/HaMMLET/ (DOI: 10.5281/zenodo.46262). This paper was selected for oral presentation at RECOMB 2016, and an abstract is published in the conference proceedings.

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing.

Germline copy number variants (CNVs) and somatic copy number alterations (SCNAs) are of significant importance in syndromic conditions and cancer. Massively parallel sequencing is increasingly used to infer copy number information from variations in the read depth in sequencing data. However, this approach has limitations in the case of targeted re-sequencing, which leaves gaps in coverage between the regions chosen for enrichment and introduces biases related to the efficiency of target capture and library preparation. We present a method for copy number detection, implemented in the software package CNVkit, that uses both the targeted reads and the nonspecifically captured off-target reads to infer copy number evenly across the genome. This combination achieves both exon-level resolution in targeted regions and sufficient resolution in the larger intronic and intergenic regions to identify copy number changes. In particular, we successfully inferred copy number at equivalent to 100-kilobase resolution genome-wide from a platform targeting as few as 293 genes. After normalizing read counts to a pooled reference, we evaluated and corrected for three sources of bias that explain most of the extraneous variability in the sequencing read depth: GC content, target footprint size and spacing, and repetitive sequences. We compared the performance of CNVkit to copy number changes identified by array comparative genomic hybridization. We packaged the components of CNVkit so that it is straightforward to use and provides visualizations, detailed reporting of significant features, and export options for integration into existing analysis pipelines. CNVkit is freely available from https://github.com/etal/cnvkit.

Sequential model selection-based segmentation to detect DNA copy number variation.

Array-based CGH experiments are designed to detect genomic aberrations or regions of DNA copy-number variation that are associated with an outcome, typically a state of disease. Most of the existing statistical methods target on detecting DNA copy number variations in a single sample or array. We focus on the detection of group effect variation, through simultaneous study of multiple samples from multiple groups. Rather than using direct segmentation or smoothing techniques, as commonly seen in existing detection methods, we develop a sequential model selection procedure that is guided by a modified Bayesian information criterion. This approach improves detection accuracy by accumulatively utilizing information across contiguous clones, and has computational advantage over the existing popular detection methods. Our empirical investigation suggests that the performance of the proposed method is superior to that of the existing detection methods, in particular, in detecting small segments or separating neighboring segments with differential degrees of copy-number variation.

A Systems Biology Interpretation of Array Comparative Genomic Hybridization (aCGH) Data through Phylogenetics.

Array Comparative Genomic Hybridization (aCGH) is a rapid screening technique to detect gene deletions and duplications, providing an overview of chromosomal aberrations throughout the entire genome of a tumor, without the need for cell culturing. However, the heterogeneity of aCGH data obfuscates existing methods of data analysis. Analysis of aCGH data from a systems biology perspective or in the context of total aberrations is largely absent in the published literature. We present here a novel alternative to the functional analysis of aCGH data using the phylogenetic paradigm that is well-suited to high dimensional datasets of heterogeneous nature, but has not been widely adapted to aCGH data. Maximum parsimony phylogenetic analysis sorts out genetic data through the simplest presentation of the data on a cladogram, a graphical evolutionary tree, thus providing a powerful and efficient method for aCGH data analysis. For example, the cladogram models the multiphasic changes in the cancer genome and identifies shared early mutations in the disease progression, providing a simple yet powerful means of aCGH data interpretation. As such, applying maximum parsimony phylogenetic analysis to aCGH results allows for the differentiation between drivers and passenger genes aberrations in cancer specimens. In addition to offering a novel methodology to analyze aCGH results, we present here a crucial software suite that we wrote to carry out the analysis. In a broader context, we wish to underscore that phylogenetic analysis of aCGH data is a non-parametric method that circumvents the pitfalls and frustrations of standard analytical techniques that rely on parametric statistics. Organizing the data in a cladogram as explained in this research article provides insights into the disease common aberrations, as well as the disease subtypes and their shared aberrations (the synapomorphies) of each subtype. Hence, we report the method and make the software suite publicly and freely available at http://software.phylomcs.com so that researchers can test alternative and innovative approaches to the analysis of aCGH data.

Integrating Microarrays into Routine Prenatal Diagnosis: Determinants of Decision Making.

OBJECTIVES: The explosion in genetic technologies, including array comparative genomic hybridization (aCGH), has increased the complexity of genetic counseling. We now offer chorionic villus sampling (CVS) and aCGH to all first-trimester patients, as this allows the prenatal diagnosis of an additional 1% of anomalies not otherwise detectable and can detect genetic copy number variants at a much higher resolution than conventional cytogenetics. Here, we explored some of the determinants of how patients are deciding to use or not use this new technology and evaluate risk-benefit analyses for that decision. METHODS: This is a retrospective case-control study of singleton and multiples pregnancies at our center. Those having aCGH testing along with CVS were defined as 'testers' and those who declined aCGH but had the CVS were 'nontesters'. RESULTS: Demographic data of 181 educated women who chose CVS were compared. Among those carrying singletons (n = 144), older women, defined as over 35 years of age (or 'advanced maternal age'; AMA), were more likely to choose the aCGH than younger women. Further, women who had a prior history of genetic testing and who wanted to know the gender of the fetus were more likely to choose the aCGH test. In women carrying multiples (n = 37), AMA ceases to be a predictor of choice. Having had prior genetic counseling remains a strong predictor for choosing aCGH, as does wanting to know the gender of the fetus. Neither prior abortions nor having prior children were significant for women carrying singletons or multiples. CONCLUSION: Offering pregnant couples an individualized choice regarding aCGH seems an appropriate approach. There are discrete patterns associated with the choice of taking the aCGH that varied depending on whether the patient was carrying a singleton or multiples.

Array-Comparative Genomic Hybridization Analysis in Fetuses with Major Congenital Malformations Reveals that 24% of Cases Have Pathogenic Deletions/Duplications.

Karyotyping and aCGH are routinely used to identify genetic determinants of major congenital malformations (MCMs) in fetal deaths or terminations of pregnancy after prenatal diagnosis. Pathogenic rearrangements are found with a variable rate of 9-39% for aCGH. We collected 33 fetuses, 9 with a single MCM and 24 with MCMs involving 2-4 organ systems. aCGH revealed copy number variants in 14 out of 33 cases (42%). Eight were classified as pathogenic which account for a detection rate of 24% (8/33) considering fetuses with 1 or more MCMs and 33% (8/24) taking into account fetuses with multiple malformations only. Three of the pathogenic variants were known microdeletion syndromes (22q11.21 deletion, central chromosome 22q11.21 deletion, and TAR syndrome) and 5 were large rearrangements, adding up to >11 Mb per subject and comprising strong phenotype-related genes. One of those was a de novo complex rearrangement, and the remaining 4 duplications and 2 deletions were 130-900 kb in size, containing 1-7 genes, and were classified as variants of unknown clinical significance. Our study confirms aCGH as a powerful technique to ascertain the genetic etiology of fetal major congenital malformations.

High-Resolution Array Comparative Genomic Hybridization Utility in Polish Newborns with Isolated Cleft Lip and Palate.

Cleft lip with or without cleft palate is one of the most common birth defects of unknown etiology. A fraction of its genetic causes is attributable to copy number variations detected by array comparative genomic hybridization. The value of array comparative genomic hybridization screening as a first-tier test in the newborn population with multiple congenital anomalies has now been accepted. Due to unspecific clinical picture at this age, it can also be applied to neonates with isolated anomalies. Our purpose was to assess utility of array comparative genomic hybridization in the population of newborns with isolated cleft lip and palate. We conducted the study in a group of 52 Polish newborns with apparently isolated cleft lip and palate. In the study group, we found 8 rearrangements. Of these, 2 de novo events have been noted that potentially explain the phenotype. In addition, 2 novel candidate genes for cleft lip and palate, CHN2 and CDH19, are suggested. Given the high number of inherited potentially benign changes, we question the clinical utility of array comparative genomic hybridization in the newborn population with isolated cleft lip and palate, at the same time pointing to the need of skilled professional's clinical assessment at a later age. However, the value of this technology in searching for the cause of isolated anomalies cannot be underestimated.

Miscarriage chromosome testing: utility of comparative genomic hybridization with reflex microsatellite analysis in preserved miscarriage tissue.

OBJECTIVE: To assess the utility of comparative genomic hybridization (CGH) and reflex microsatellite analysis (MSA) for chromosome analysis of preserved miscarriage tissue. DESIGN: Observational study. SETTING: Academic recurrent pregnancy loss program. PATIENT(S): Patients with recurrent early pregnancy loss, defined as two or more miscarriages at <10 weeks, and at least one preserved miscarriage specimen sent for CGH. INTERVENTION(S): Preserved miscarriage specimens were sent for CGH. If results were euploid female (46,XX), reflex MSA was performed to assess if the result was of miscarriage or maternal origin. MAIN OUTCOME MEASURE(S): Results were recorded as either informative or uninformative. Uninformative results were classified as "CGH failed" or "maternal contamination." RESULT(S): Fifty-eight women with 77 miscarriage specimens met the criteria. CGH failed in nine of the preserved miscarriage specimens owing to minimal pregnancy tissue, and two owing to poor-quality DNA. Twenty-two of the 33 specimens reported as 46,XX by CGH were sent for MSA; maternal contamination was confirmed in 23% (5/22). CGH was therefore informative in 79% (61/77) of the specimens; 64% (39/61) were euploid, and 36% (22/61) were noneuploid, with a 46,XX/46,XY ratio of 2.5. CONCLUSION(S): CGH with reflex MSA is useful for obtaining chromosome results in preserved miscarriage specimens, although informative results were achieved in only 79% of specimens. Maternal contamination should be assessed after an initial diploid female result.

De novo small supernumerary marker chromosomes detected on 143,000 consecutive prenatal diagnoses: chromosomal distribution, frequencies, and characterization combining molecular cytogenetics approaches.

OBJECTIVE: The risk of clinical consequences in prenatal cases with de novo small supernumerary marker chromosomes (sSMC), often in mosaic conditions, is not easy to predict, which results in difficulties in genetic counseling. METHOD: In this study, we evaluated the frequency, the chromosomal origin, and the clinical indication of 104 de novo sSMC detected in a monocenter survey on the basis of 143,000 consecutive prenatal diagnoses, and we assessed the reliability of molecular cytogenetics technologies for sSMC characterization. RESULTS: We detected a de novo sSMC frequency of 0.072%. Its incidence in advanced maternal age group is statistically different from that found in maternal anxiety indication (<35 years old). A higher prevalence of mosaicism in chorionic villi sampling (CVS) than in amniotic fluids was also revealed related to confined placental mosaicisms. The risk of confirmation in amniotic fluids of mosaics previously revealed at CVS was 33.3%. No uniparental disomy conditions were found when imprinted chromosomes were involved in the occurrence of de novo sSMC. The majority of de novo sSMC were acrocentric derived-chromosomes, and a neocentromere formation was observed in one pregnancy. CONCLUSION: Our data support that array comparative genomic hybridization has improved sSMC characterization and demonstrate its utility in supporting genetic counseling. We propose a workflow for de novo sSMC characterization.

Comparative study of exome copy number variation estimation tools using array comparative genomic hybridization as control.

Exome sequencing using next-generation sequencing technologies is a cost-efficient approach to selectively sequencing coding regions of the human genome for detection of disease variants. One of the lesser known yet important applications of exome sequencing data is to identify copy number variation (CNV). There have been many exome CNV tools developed over the last few years, but the performance and accuracy of these programs have not been thoroughly evaluated. In this study, we systematically compared four popular exome CNV tools (CoNIFER, cn.MOPS, exomeCopy, and ExomeDepth) and evaluated their effectiveness against array comparative genome hybridization (array CGH) platforms. We found that exome CNV tools are capable of identifying CNVs, but they can have problems such as high false positives, low sensitivity, and duplication bias when compared to array CGH platforms. While exome CNV tools do serve their purpose for data mining, careful evaluation and additional validation is highly recommended. Based on all these results, we recommend CoNIFER and cn.MOPs for nonpaired exome CNV detection over the other two tools due to a low false-positive rate, although none of the four exome CNV tools performed at an outstanding level when compared to array CGH.

Diminished effect of maternal age on implantation after preimplantation genetic diagnosis with array comparative genomic hybridization.

OBJECTIVE: To assess the relationship between maternal age, chromosome abnormality, implantation, and pregnancy loss. DESIGN: Multicenter retrospective study. SETTING: IVF centers in the United States. PATIENT(S): IVF patients undergoing chromosome screening. INTERVENTION(S): Embryo biopsy on day 3 or day 5/6 with preimplantation genetic diagnosis (PGD) by array comparative genomic hybridization. MAIN OUTCOME MEASURE(S): Aneuploidy, implantation, pregnancy, and loss rates. RESULT(S): Aneuploidy rates increased with maternal age from 53% to 93% for day 3 biopsies and from 32% to 85% for blastocyst biopsies. Implantation rates for euploid embryos for ages <35-42 years did not decrease after PGD: ranges 44%-32% for day 3 and 51%-40% for blastocyst. Ongoing pregnancy rates per transfer did not decrease for maternal ages <42 years after PGD with day 3 biopsy (48.5%-38.1%) or blastocyst biopsy (64.4%-54.5%). Patients >42 years old had implantation rates of 23.3% (day 3), 27.7% (day 5/6), and the pregnancy rate with day 3 biopsy was 9.3% and with day 5 biopsy 10.3%. CONCLUSION(S): Selective transfer of euploid embryos showed that implantation and pregnancy rates were not significantly different between reproductively younger and older patients up to age 42 years. Some patients who start an IVF cycle planning to have chromosome screening do not have euploid embryos available for transfer, a situation that increases with advancing maternal age. Mounting data suggests that the dramatic decline in IVF treatment success rates with female age is primarily caused by aneuploidy.

FDR control with pseudo-gatekeeping based on a possibly data driven order of the hypotheses.

We propose a multiple testing procedure controlling the false discovery rate. The procedure is based on a possibly data driven ordering of the hypotheses, which are tested at the uncorrected level q until a suitable number is not rejected. When the order is data driven, larger effect sizes are considered first, therefore selecting more interesting hypotheses with larger probability. The proposed procedure is valid under independence for the test statistics. We also propose a modification which makes our procedure valid under arbitrary dependence. It is shown in simulation that we compare particularly well when the sample size is small. We conclude with an application to identification of molecular signatures of intracranial ependymoma. The methods are implemented in an R package (someMTP), freely available on CRAN.

Chromosomal microarray (CMA) analysis in infants with congenital anomalies: when is it really helpful?

BACKGROUND: Birth defects are very common, affecting two to three infants in every 100 births, and often represent a diagnostic and management challenge. The birth of a child with multiple malformations is the beginning of a complex diagnostic process, where the primary purpose is to determine a precise nosological definition. An accurate diagnosis is a key prerequisite in providing a care plan, a prognosis and genetic counselling. The poor specificity of birth defects, the aetiology and course of which can vary despite similar phenotypic patterns, often makes the diagnostic path problematic. The advent and application of high-resolution chromosomal microarray, encompassing array-based comparative genome hybridization and single-nucleotide polymorphism arrays, has led to the detection of genomic copy-number abnormalities in patients affected by multiple congenital anomalies, dysmorphisms, developmental delay and mental retardation, but who have a normal karyotype. AIM: We discuss current guidelines and recommendations for chromosomal microarray use and how its application can help clinicians make accurate diagnoses in order to appropriately manage and treat affected newborns. CONCLUSIONS: Current guidelines strongly support the application of chromosomal microarray analysis as a first-tier cytogenetic diagnostic test alternative to karyotyping for patients with multiple congenital anomalies, or developmental delay, intellectual disability and autism spectrum disorders.