High-resolution Chromosomal Microarray Research Articles

Genetic diagnosis of fetal microcephaly at a single tertiary center in China.

Background: Microcephaly is common in patients with neuropsychiatric problems, and it is usually closely related to genetic causes. However, studies on chromosomal abnormalities and single-gene disorders associated with fetal microcephaly are limited. Objective: We investigated the cytogenetic and monogenic risks of fetal microcephaly and evaluated their pregnancy outcomes. Methods: We performed a clinical evaluation, high-resolution chromosomal microarray analysis (CMA), and trio exome sequencing (ES) on 224 fetuses with prenatal microcephaly and closely followed the pregnancy outcome and prognosis. Results: Among 224 cases of prenatal fetal microcephaly, the diagnosis rate was 3.74% (7/187) for CMA and 19.14% (31/162) for trio-ES. Exome sequencing identified 31 pathogenic or likely pathogenic (P/LP) single nucleotide variants (SNVs) in 25 genes associated with fetal structural abnormalities in 37 microcephaly fetuses; 19 (61.29%) of which occurred de novo. Variants of unknown significance (VUS) was found in 33/162 (20.3%) fetuses. The gene variant involved included the single gene MPCH 2 and MPCH 11, which is associated with human microcephaly, and HDAC8, TUBGCP6, NIPBL, FANCI, PDHA1, UBE3A, CASK, TUBB2A, PEX1, PPFIBP1, KNL1, SLC26A4, SKIV2L, COL1A2, EBP, ANKRD11, MYO18B, OSGEP, ZEB2, TRIO, CLCN5, CASK, and LAGE3. The live birth rate of fetal microcephaly in the syndromic microcephaly group was significantly higher than that in the primary microcephaly group [62.9% (117/186) vs 31.56% (12/38), p = 0.000]. Conclusion: We conducted a prenatal study by conducting CMA and ES for the genetic analysis of fetal microcephaly cases. CMA and ES had a high diagnostic rate for the genetic causes of fetal microcephaly cases. In this study, we also identified 14 novel variants, which expanded the disease spectrum of microcephaly-related genes.

Chromosomal Microarray Study in Prader-Willi Syndrome.

A high-resolution chromosome microarray analysis was performed on 154 consecutive individuals enrolled in the DESTINY PWS clinical trial for Prader-Willi syndrome (PWS). Of these 154 PWS individuals, 87 (56.5%) showed the typical 15q11-q13 deletion subtypes, 62 (40.3%) showed non-deletion maternal disomy 15 and five individuals (3.2%) had separate unexpected microarray findings. For example, one PWS male had Klinefelter syndrome with segmental isodisomy identified in both chromosomes 15 and X. Thirty-five (40.2%) of 87 individuals showed typical larger 15q11-q13 Type I deletion and 52 individuals (59.8%) showed typical smaller Type II deletion. Twenty-four (38.7%) of 62 PWS individuals showed microarray patterns indicating either maternal heterodisomy 15 subclass or a rare non-deletion (epimutation) imprinting center defect. Segmental isodisomy 15 was seen in 34 PWS subjects (54.8%) with 15q26.3, 15q14 and 15q26.1 bands most commonly involved and total isodisomy 15 seen in four individuals (6.5%). In summary, we report on PWS participants consecutively enrolled internationally in a single clinical trial with high-resolution chromosome microarray analysis to determine and describe an unbiased estimate of the frequencies and types of genetic defects and address potential at-risk genetic disorders in those with maternal disomy 15 subclasses in the largest PWS cohort studied to date.

Prenatal diagnosis and genetic analysis of three fetuses with paternal chromosomal simplex 3q microduplication syndrome

To explore the phenotypic characteristics of paternal chromosomal simplex 3q microduplication syndrome. Amniotic fluid samples of 3 fetuses from a same couple were subjected to prenatal diagnosis through combined high-resolution chromosomal G-banding karyotyping and chromosomal microarray analysis (CMA). Peripheral blood samples were also collected the couple for the determination of parental origin. The karyotypes of all three fetuses were 46,XN,dup(3)(q25q26.1), and their CMA results were arr[hg19]3q25.33q26.1(159 336 333-166 924 969)×3. The duplication in the three fetuses have all derived from their father. No anomaly with found with the mother by CMA . Through combined G-banded chromosomal karyotyping and CMA assay, a paternally derived 3q25.33-q26.1 microduplication has been identified, which has enabled genetic counseling for this couple.

EP317: Comparative benchmarking of optical genome mapping and chromosomal microarray reveals high technological concordance in CNV identification and structural variant refinement

Children with developmental delays and/or congenital anomalies with suspected genetic etiology are often tested for structural variations (SVs) by chromosomal microarray (CMA), karyotype, fragile X testing, and sequencing. Because copy number variation (CNV) and structural variation are often found to be causative, CMA is recommended as first tier testing for many indications. Optical genome mapping (OGM) is an accurate technique for enabling the detection of CNVs similar to a high-resolution CMA, and also balanced rearrangements which cannot be detected by CMA.

Disruption and deletion of the proximal part of TCF4 are associated with mild intellectual disability: About three new patients

TCF4 gene (18q21.1) encodes for a transcription factor with multiple isoforms playing a critical role during neurodevelopment. Molecular alterations of this gene are associated with Pitt-Hopkins syndrome, a severe condition characterized by intellectual disability, specific facial features and autonomic nervous system dysfunction.We report here three patients presenting with structural variations of the proximal part of TCF4 associated with a mild phenotype. The first patient is a six-years-old girl carrier of a pericentric inversion of chromosome 18, 46,XX,inv(18)(p11.2q21.1). Whole genome sequencing (WGS) characterized the breakpoint at the base-pair level at chr18:1262334_1262336 and chr18:53254747_53254751 (hg19). This latter breakpoint disrupted the proximal promotor region of TCF4 in the first intron of the gene. The second and third patients are a son and his mother, carrier of a 46 kb deletion characterized by high-resolution chromosomal micro-array and WGS (chr:18:53243454_53287927, hg19) encompassing the first three exon of TCF4 gene and including the proximal promotor region. Expression studies on blood lymphocytes in these patients showed a marked decrease of mRNA level for long isoforms of TCF4 and an increased level for shorter isoforms.The patients described here, together with previously reported patients with proximal structural alterations of TCF4, help to delineate a phenotype of mild ID with non-specific facial dysmorphism without characteristic features of PTHS. It also suggests a gradient of phenotypic severity inversely correlated with the number of intact TCF4 promotor regions, with expression of short isoforms compensating in part the loss of longer isoforms.

Lessons learnt from multifaceted diagnostic approaches to the first 150 families in Victoria’s Undiagnosed Diseases Program

BackgroundClinical exome sequencing typically achieves diagnostic yields of 30%–57.5% in individuals with monogenic rare diseases. Undiagnosed diseases programmes implement strategies to improve diagnostic outcomes for these individuals.AimWe share the lessons...

35. Frequencies of Turner syndrome abnormalities as detected by high resolution chromosomal microarray in products of conception and postnatal blood samples

Turner syndrome, which results from a complete or partial loss of chromosome X, occurs in 1 of 2,500 live female births. Despite the relatively mild postnatal phenotype, most cases result in miscarriage. This discrepancy in clinical outcome is not fully understood but may be explained by mosaicism and genetic alteration type. Previous studies of genetic abnormalities in Turner syndrome utilized standard cytogenetic techniques, which are limited in their capability to detect mosaicism. Here, we describe the types and frequencies of Turner syndrome abnormalities as detected by high resolution chromosomal microarray in products of conception (POCs) and postnatal blood samples.

Omphaloceles Associated with Chromosomal Segmental Alterations Carry a Poor Prognosis

Abstract Introduction/Objective Omphaloceles are frequently associated with chromosomal abnormalities, including aneuploidy and segmental alterations. High resolution chromosomal microarray analysis (CMA) can detect segmental alterations < 5 Mb, which is not detectable by G-banding. However, the prognostic significance of the segmental alteration in infant with omphalocele is not elucidated. Methods To identify omphalocele cases with genetic studies, a CoPath database search (1/2000 - 7/2017) was performed with key words “omphalocele” and “genetic”. From 1/2000 to 12/2008, only G-banding was performed. From 1/2009 to 7/2017, omphalocele cases were screened with karyotyping. Cases with normal karyotype were reflexed to CMA. Copy number gains/losses and corresponding genes were analyzed by the Affymetrix Chromosome Analysis Suite. Results Follow-up data are available in 75% (67/89) cases. There is no significant difference of the overall survival rate of male and female patients (80.5% vs 76.9%; χ 2, p = 0.7645). There are 16.9% (15/89) omphaloceles with aneuploidy, 10.1% (9/89) cases with segmental alterations by CMA, and 73.0% (65/89) cases with normal CMA and/or normal karyotype. Although patients with segmental alterations have a significantly higher survival rate than those with aneuploidy (44.4% vs 0%, χ2, p = 0.0119), their overall survival rate is significantly lower than infant with normal CMA and/or normal karyotype (44.4% vs 82.8%; χ2, p < 0.0001). Infants with segmental alterations carry a significantly worse prognosis than infants with normal genetic study. Conclusion To date, this is the first study of the prognostic significance of segmental alteration in infants with omphalocele. Our data demonstrated that omphaloceles with segmental alterations carry a significantly worse prognosis than those with normal CMA and/or karyotype. It is crucial to convey the prognosis to the parents with a fetus carrying segmental alterations; so the family could make an informed decision and get ready for an infant with special needs.

Coffin-Siris Syndrome 4-Related Spectrum in a Young Woman Caused by a Heterozygous SMARCA4 Deletion Detected by High-Resolution aCGH

Coffin-Siris Syndrome 4 is an autosomal dominant congenital malformation syndrome caused by heterozygous mutations in the SMARCA4 gene with its main features being intellectual disability, developmental delay, behavioral abnormalities, and hypoplastic or absent fifth fingernails and fifth distal phalanges. Here, we report a young woman with developmental delay, moderate intellectual disability, and bilateral sensorineural hearing loss, referred for genetic testing. High-resolution chromosomal microarray analysis identified a 428-kb deletion in chromosome 19 which included the SMARCA4 gene. We conclude that haploinsufficiency of SMARCA4 may be a valid pathophysiological mechanism leading to milder Coffin-Siris syndrome phenotypes.

High-resolution chromosomal microarrayanalysis for copy-number variations in high-functioning autism reveals large aberration typical for intellectual disability.

Copy-number variants (CNVs), in particular rare, small and large ones (< 1% frequency) and those encompassing brain-related genes, have been shown to be associated with neurodevelopmental disorders like autism spectrum disorders (ASDs), attention deficit hyperactivity disorder (ADHD), and intellectual disability (ID). However, the vast majority of CNV findings lack specificity with respect to autistic or developmental-delay phenotypes. Therefore, the aim of the study was to investigate the size and frequency of CNVs in high-functioning ASD (HFA) without ID compared with a random population sample and with published findings in ASD and ID. To investigate the role of CNVs for the "core symptoms" of high-functioning autism, we included in the present exploratory study only patients with HFA without ID. The aim was to test whether HFA have similar large rare (> 1Mb) CNVs as reported in ASD and ID. We performed high-resolution chromosomal microarray analysis in 108 children and adolescents with HFA without ID. There was no significant difference in the overall number of rare CNVs compared to 124 random population samples. However, patients with HFA carried significantly more frequently CNVs containing brain-related genes. Surprisingly, six HFA patients carried very large CNVs known to be typically present in ID. Our findings provide new evidence that not only small, but also large CNVs affecting several key genes contribute to the genetic etiology/risk of HFA without affecting their intellectual ability.

Exon-Level Genomic Abnormalities Are Frequent in Cytogenetically Normal Patients with Philadelphia-Chromosome Negative Myeloproliferative Neoplasms (MPNs)

Polycythemia vera (PV) and essential thrombocythemia (ET) exhibit an abnormal karyotype in 10%-28% of patients (pts) while the frequency increases in up to 90% of pts with advanced forms of myelofibrosis (PMF) and MPN accelerated/blast phase. Similarly, Klampfl et al. (Blood,118(1) 167-176) demonstrated that an increase in the number of genomic abnormalities detected by chromosomal microarrays (CMA) is associated with disease progression. Although genomic aberrations in cytogenetically normal pts with MPN have been previously reported, this study focused on identifying cryptic genomic alterations with exon-level precision to genomically characterize pts with MPN that were karyotypically normal at the time of CMA analysis. We prospectively evaluated a cohort of 151 cytogenetically normal pts (23% PV, 35% ET, 21% PMF, and 21% post PV/ET MF) using a high-resolution chromosomal microarray (CMA) platform that detects both regions of copy-neutral loss of heterozygosity (cnLOH) and copy number alterations (CNAs) with exon-level resolution (Agilent's cancer-specific 2x400k aCGH+SNP). In order to uncover regions harboring genes that may have biological and/or clinical implications, we identified the minimal overlapping regions (MORs) containing CMA abnormalities occurring in at least 4 pts, using the "GRanges" package (Bioconductor). Genomic aberrations were documented in 69% (n=104) of pts. Of the 238 CMA abnormalities identified, 52 were gains, 38 were losses, and 148 were regions of cnLOH. Next-generation sequencing (NGS) was performed in 97% of these pts and 65% had JAK2, 15% had CALR, and 2% had MPL mutations. The remaining pts (n=25) were triple-negative, and 12 pts harbored other non-driver gene mutations. Only CMA lesions were identified in 6 pts (4%) and both NGS and CMA could not genomically detect abnormalities in 7 pts (5%). The most frequent MOR mapping to a single gene harbored JAK2 cnLOH which occurred in 25% of pts, consistent with previous reports. A statistical difference in the JAK2V617F variant allele frequency (VAF) in pts with 9p cnLOH (VAF=80%) and without 9p cnLOH (VAF=18%) (p&lt;0.001) was observed. In pts with PV, a high JAK2 allele burden is associated with an aggressive phenotype (Vannucchi et al. Therapeutic Advances in Hematology 2010 2, 21-32). Alterations of 1q32.1 involving MDM4, a negative regulator of TP53, was the second most frequent MOR occurring in 14% of pts. We have recently demonstrated that gain of 1q results in overexpression of MDM4 and is associated with advanced forms of MPN (Marcellino et al, Blood Advances, 2018 2(24), 3581-3589). Four other recurrent MORs harboring a single gene, TAF15, RASA3, RHOC, and NCOR2 occurred in 8%, 5%, 4%, and 3% of pts, respectively. Each had intragenic gains. We previously reported alterations in these genes in the spleens of pts with MF (Zimran et al., Haematologica, 2018 (10)103). Our current results indicate that these same alterations are present in the bone marrow cells of cytogenetically normal MPN pts. Since these abnormalities are present in pts with advanced forms of MPN, alterations of these genes may represent markers for disease progression. Of the MORs harboring multiple genes, 3 regions involved 1p, 17q, and 18q in 4%, 3%, and 6% of pts, respectively. All pts had cnLOH of these regions and each harbored relevant genes that may be implicated in MPN; CDKN2C (1p), PPM1D (17q), and ASXL3(18q). Our results demonstrated that CMA abnormalities were present in 51% of pts with ET, 66% with PV, 87% with PMF, and 70%-100% with post ET/PV MF. CMA lesions were the sole alteration in 4% while 5% of chromosomally normal pts with an initial diagnosis of ET had neither somatic mutations nor CMA abnormalities. We provided evidence that recurrent genomic alterations can be identified in regions associated with disease progression, as well as novel regions harboring genes with potential pathobiological implications. We conclude that CMA is a vital tool in identifying cryptic genomic aberrations in cytogenetically normal pts with chronic phase MPN. Disclosures Hoffman: Merus: Research Funding. Ozbek:Viracor: Patents &amp; Royalties: Biomarker Patent. Mascarenhas:Pharmaessentia: Consultancy, Membership on an entity's Board of Directors or advisory committees; Merus: Research Funding; Promedior: Research Funding; Janssen: Research Funding; CTI Biopharma: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Incyte: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Novartis: Research Funding; Roche: Consultancy, Research Funding; Merck: Research Funding. Kremyanskaya:La Jolla: Consultancy; Incyte, Celgene, Constellation, Protagonist.: Research Funding.

Elucidation of the phenotypic spectrum and genetic landscape in primary and secondary microcephaly

PurposeMicrocephaly is a sign of many genetic conditions but has been rarely systematically evaluated. We therefore comprehensively studied the clinical and genetic landscape of an unselected cohort of patients with microcephaly. MethodsWe performed clinical assessment, high-resolution chromosomal microarray analysis, exome sequencing, and functional studies in 62 patients (58% with primary microcephaly [PM], 27% with secondary microcephaly [SM], and 15% of unknown onset). ResultsWe found severity of developmental delay/intellectual disability correlating with severity of microcephaly in PM, but not SM. We detected causative variants in 48.4% of patients and found divergent inheritance and variant pattern for PM (mainly recessive and likely gene-disrupting [LGD]) versus SM (all dominant de novo and evenly LGD or missense). While centrosome-related pathways were solely identified in PM, transcriptional regulation was the most frequently affected pathway in both SM and PM. Unexpectedly, we found causative variants in different mitochondria-related genes accounting for ~5% of patients, which emphasizes their role even in syndromic PM. Additionally, we delineated novel candidate genes involved in centrosome-related pathway (SPAG5, TEDC1), Wnt signaling (VPS26A, ZNRF3), and RNA trafficking (DDX1). ConclusionOur findings enable improved evaluation and genetic counseling of PM and SM patients and further elucidate microcephaly pathways.

The role of recessive inheritance in early-onset epileptic encephalopathies: a combined whole-exome sequencing and copy number study

Early-onset epileptic encephalopathy (EE) and combined developmental and epileptic encephalopathies (DEE) are clinically and genetically heterogeneous severely devastating conditions. Recent studies emphasized de novo variants as major underlying cause suggesting a generally low-recurrence risk. In order to better understand the full genetic landscape of EE and DEE, we performed high-resolution chromosomal microarray analysis in combination with whole-exome sequencing in 63 deeply phenotyped independent patients. After bioinformatic filtering for rare variants, diagnostic yield was improved for recessive disorders by manual data curation as well as molecular modeling of missense variants and untargeted plasma-metabolomics in selected patients. In total, we yielded a diagnosis in ∼42% of cases with causative copy number variants in 6 patients (∼10%) and causative sequence variants in 16 established disease genes in 20 patients (∼32%), including compound heterozygosity for causative sequence and copy number variants in one patient. In total, 38% of diagnosed cases were caused by recessive genes, of which two cases escaped automatic calling due to one allele occurring de novo. Notably, we found the recessive gene SPATA5 causative in as much as 3% of our cohort, indicating that it may have been underdiagnosed in previous studies. We further support candidacy for neurodevelopmental disorders of four previously described genes (PIK3AP1, GTF3C3, UFC1, and WRAP53), three of which also followed a recessive inheritance pattern. Our results therefore confirm the importance of de novo causative gene variants in EE/DEE, but additionally illustrate the major role of mostly compound heterozygous or hemizygous recessive inheritance and consequently high-recurrence risk.

Chromosomal microarray analysis of patients with Duane retraction syndrome.

Duane retraction syndrome (DS) is a rare congenital strabismus with genetic heterogeneity. The genetic causes of DS are not always of monogenic origin; various chromosomal copy number variations (CNVs) have also been reported. The objective of our study was to characterize the CNVs, including gains and losses detected by high-resolution chromosomal microarray in patients with DS. Twenty patients with DS were investigated using high-resolution chromosomal microarray analysis (CMA) (Affymetrix CytoScan Array 750K). Conventional cytogenetic analysis was also performed. All samples revealed normal karyotype by cytogenetic analysis. However, in all our patients, multiple CNVs, including gains and losses, were detected using the high-resolution CMA method. Chromosomal loci 1q21.2, 2p11.2-q11.1, 2q21.1-q21.2, 4p16.1, 7p11.2-q11.21, 14q32.33, 17p11.2-q11.1 and 20p11.1-q11.21 were the most frequently affected regions. This study emphasized that CNVs in several chromosomal regions are known to be involved in DS. We also underscore the genetic heterogeneity of DS. Our suggestion is that genes located in the most frequently affected regions should be focused on in the following candidate gene studies.

Autism: A Different Vision

Genomic analysis has emphasized the enormous genetic contribution to autism spectrum disorders, with over 80% of patients having changes demonstrable by high resolution chromosome (microarray) analysis or whole exome sequencing. An overview of these genetic changes demonstrates the expected role of synaptic transmission in autism and, together with clinical observations, emphasizes the importance of visual input on developing sensory systems and social responses. Neonatal recognition of autism predisposition through genetic analysis could allow sensory stimulation therapies during periods of neuroplasticity, an approach analogous to strabismus correction before the cortical dissociation of the deviant eye.

Chromosomal microarray analysis of Bulgarian patients with epilepsy and intellectual disability

High resolution chromosomal microarray analysis (CMA) has facilitated the identification of small chromosomal rearrangements throughout the genome, associated with various neurodevelopmental phenotypes, including ID/DD. Recently, it became evident that intellectual disability (ID)/developmental delay (DD) can occur with associated co-morbidities like epileptic seizures, autism and additional congenital anomalies. These observations require whole genome approach in order to detect the genetic causes of these complex disorders. In this study, we examined 92 patients of Bulgarian origin at age between 1 and 22 years with ID, generalized epilepsy, autistic signs and congenital anomalies. CMA was carried out using SurePrint G3 Human CGH Microarray Kit, 4 × 180 K and SurePrint G3 Unrestricted CGH ISCA v2, 4 × 180 K oligo platforms. Referral indications for selection of the patients were the presence of generalized refractory seizures disorders and co-morbid ID. Clearly pathogenic copy number variations (CNVs) were detected in eight patients (8.7%) from our cohort. Additionally, possibly pathogenic rearrangements of unclear clinical significance were detected in six individuals (6.5%), which make for an overall diagnostic yield of 15.2% among our cohort of patients.We report here the patients with clearly pathogenic CNVs, discuss the potential causality of the possibly pathogenic CNVs and make genotype - phenotype correlations. One novel possibly pathogenic heterozygous deletion in 15q22.31 region was detected in a case with ID/DD. Additionally, whole APBA2 gene duplication in 15q13.1 was found in three generations of a family with epilepsy, ID and psychiatric abnormalities. The results from this study allow us to define the genetic diagnosis in a subset of Bulgarian patients and improve the genetic counseling of the affected families. To our knowledge, this is the first aCGH evaluation of a Bulgarian cohort of children with epilepsy and ID so far.

Prenatal diagnosis of posterior fossa anomalies: Additional value of chromosomal microarray analysis in fetuses with cerebellar hypoplasia.

To elucidate the relationship between copy number variations (CNVs) detected by high-resolution chromosomal microarray analysis (CMA) and the type of prenatal posterior fossa anomalies (PFAs), especially cerebellar hypoplasia (CH). This study involved 77 pregnancies with PFAs who underwent CMA. Chromosomal aberrations including pathogenic CNVs and variants of unknown significance were detected in 31.2% (24/77) of all cases by CMA and in 18.5% (12/65) in fetuses with normal karyotypes. The high detection rate of clinically significant CNVs was evident in fetuses with cerebellar hypoplasia (54.6%, 6/11), vermis hypoplasia (33.3%, 1/3), and Dandy-Walker malformation (25.0%, 3/12). Compare with fetuses without other anomalies, cases with CH and additional malformations had the higher CMA detection rate (33.3% vs 88.9%). Three cases of isolated unilateral CH with intact vermis and normal CMA result had normal outcomes. The deletion of 5p15, 6q terminal deletion, and X chromosome aberrations were the most frequent genetic defects associated with cerebellar hypoplasia. Among fetuses with PFA, those with cerebellar hypoplasia, vermis hypoplasia, or Dandy-Walker malformation are at the highest risk of clinically significant CNVs. Chromosomal microarray analysis revealed the most frequent chromosomal aberrations associated with CH.

High resolution chromosomal microarray analysis in paediatric obsessive-compulsive disorder

BackgroundObsessive-Compulsive Disorder (OCD) is a common and chronic disorder in which a person has uncontrollable, reoccurring thoughts and behaviours. It is a complex genetic condition and, in case of early onset (EO), the patients manifest a more severe phenotype, and an increased heritability. Large (>500 kb) copy number variations (CNVs) previously associated with autism and schizophrenia have been reported in OCD. Recently, rare CNVs smaller than 500 kb overlapping risk loci for other neurodevelopmental conditions have also been reported in OCD, stressing the importance of examining CNVs of any size range. The aim of this study was to further investigate the role of rare and small CNVs in the aetiology of EO-OCD.MethodsWe performed high-resolution chromosomal microarray analysis in 121 paediatric OCD patients and in 124 random controls to identify rare CNVs (>50 kb) which might contribute to EO-OCD.ResultsThe frequencies and the size of the observed rare CNVs in the patients did not differ from the controls. However, we observed a significantly higher frequency of rare CNVs affecting brain related genes, especially deletions, in the patients (OR = 1.98, 95% CI 1.02–3.84; OR = 3.61, 95% CI 1.14–11.41, respectively). Similarly, enrichment-analysis of CNVs gene content, performed with three independent methods, confirmed significant clustering of predefined genes involved in synaptic/brain related functional pathways in the patients but not in the controls. In two patients we detected de-novo CNVs encompassing genes previously associated with different neurodevelopmental disorders (NRXN1, ANKS1B, UHRF1BP1).ConclusionsOur results further strengthen the role of small rare CNVs, particularly deletions, as susceptibility factors for paediatric OCD.

OC21.04: Chromosomal microarray as a primary diagnostic genomic tool for pregnancies defined as being at increased risk within a population‐based combined first trimester screening program

Objective To evaluate the impact of using high-resolution chromosomal microarray (CMA) as the standard diagnostic approach to examine for genomic imbalances in pregnancies with increased risk (≥1 in 300) defined through combined first trimester screening (cFTS). Methods A cohort of 575 consecutive pregnancies that had cFTS risk ≥1:300 through a publicly funded population based screening program in the Central and Northern Regions of Denmark between September 2015 and September 2016. Women with an NT ≥3.5 mm or opting for NIPT were excluded. Comparative genomic hybridization was performed using a 180 K oligonucleotide array on DNA extracted directly from samples. Genomic outcomes are reported in relation to cFTS findings. Results 22 cases (22/575, 3.8%; 95% CI: 2.5-5.7%) of trisomy 21, 18 and 13 were detected. A further 14 cases (14/575, 2.4%; 95% CI: 1.4-4.0%) of other types of aneuploidy were detected as well as 15 (15/575, 2.6%: 95% CI: 1.5-4.3%) cases with a pathogenic or likely pathogenic copy number variant (CNV). Reducing the cFTS risk threshold for invasive diagnostic testing to 1 in 100 or 1 in 50 would have led, respectively, to 60% or 100% of the pathogenic CNVs being missed. Conclusion CMA is a valuable diagnostic technique that can identify an increased number of genomic aberrations in pregnancies at increased risk after cFTS. Limiting diagnostic testing to pregnancies with a risk above 1:100 or 1:50, as proposed in contingent NIPT/invasive testing models, will lead to a significant proportion of pathogenic CNVs being missed at first trimester screening.

Evaluation of three read-depth based CNV detection tools using whole-exome sequencing data

BackgroundWhole exome sequencing (WES) has been widely accepted as a robust and cost-effective approach for clinical genetic testing of small sequence variants. Detection of copy number variants (CNV) within WES data have become possible through the development of various algorithms and software programs that utilize read-depth as the main information. The aim of this study was to evaluate three commonly used, WES read-depth based CNV detection programs using high-resolution chromosomal microarray analysis (CMA) as a standard.MethodsPaired CMA and WES data were acquired for 45 samples. A total of 219 CNVs (size ranged from 2.3 kb – 35 mb) identified on three CMA platforms (Affymetrix, Agilent and Illumina) were used as standards. CNVs were called from WES data using XHMM, CoNIFER, and CNVnator with modified settings.ResultsAll three software packages detected an elevated proportion of small variants (< 20 kb) compared to CMA. XHMM and CoNIFER had poor detection sensitivity (22.2 and 14.6%), which correlated with the number of capturing probes involved. CNVnator detected most variants and had better sensitivity (87.7%); however, suffered from an overwhelming detection of small CNVs below 20 kb, which required further confirmation. Size estimation of variants was exaggerated by CNVnator and understated by XHMM and CoNIFER.ConclusionLow concordances of CNV, detected by three different read-depth based programs, indicate the immature status of WES-based CNV detection. Low sensitivity and uncertain specificity of WES-based CNV detection in comparison with CMA based CNV detection suggests that CMA will continue to play an important role in detecting clinical grade CNV in the NGS era, which is largely based on WES.