Challenges of interpreting copy number variation in syndromic and non-syndromic congenital heart defects

Array comparative genomic hybridization (aCGH) has led to an increased detection of causal chromosomal imbalances in individuals with congenital heart defects (CHD). The introduction of aCGH as a diagnostic tool in a clinical cardiogenetic setting entails numerous challenges. Based on our own experience as well as those of others described in the literature, we outline the state of the art and attempt to answer a number of outstanding questions such as the detection frequency of causal imbalances in different patient populations, the added value of higher-resolution arrays, and the existence of predictive factors in syndromic cases. We introduce a step-by-step approach for clinical interpretation of copy number variants (CNV) detected in CHD, which is primarily based on gene content and overlap with known chromosomal syndromes, rather than on CNV inheritance and size. Based on this algorithm, we have reclassified the detected aberrations in aCGH studies for their causality for syndromic and non-syndromic CHD. From this literature overview, supplemented with own investigations in a cohort of 46 sporadic patients with severe non-syndromic CHD, it seems clear that the frequency of causal CNVs in non-syndromic CHD populations is lower than that in syndromic CNV populations (3.6 vs. 19%). Moreover, causal CNVs in non-syndromic CHD mostly involve imbalances with a moderate effect size and reduced penetrance, whereas the majority of causal imbalances in syndromic CHD consistently affects human development and significantly reduces reproductive fitness.     

Comparative mapping of the DiGeorge region in the dog and exclusion of linkage to inherited canine conotruncal heart defects.

Conotruncal defects (CTDs) of the heart are a frequent component of DiGeorge, velocardiofacial, or other syndromes caused by deletions of the human chromosome 22q11 region (HSA22q11). In addition, some human patients with isolated nonsyndromic CTDs have been reported to have deletions of this region. Taken together, these findings lead to the conclusion that deletions of an HSA22q11 locus or loci produce abnormalities in cardiac development leading to CTDs. A spontaneous model of isolated inherited conotruncal malformations occurs in the keeshond dog. We have previously shown in experimental matings that nonsyndromic CTDs in the keeshond are inherited in a manner consistent with a major underlying locus. In the studies described in this article we tested two hypotheses: (1) the region of HSA22q11 commonly deleted in DiGeorge and related syndromes is evolutionarily conserved in the dog, and (2) a locus in this region is linked to hereditary CTD in the keeshond. Two loci within the minimal DiGeorge critical region (MDGCR) and two loci that lie telomeric to the MDGCR, one of which is commonly deleted in DiGeorge patients, were mapped in the dog using a combination of linkage analysis and fluorescence in situ hybridization (FISH). The results confirm conserved synteny of the loci DGS-I, CTP, D22S788 (N41), and IGLC on the telomeric end of canine chromosome 26 (CFA26). The group of four syntenic gene loci, which spans a genetic distance of 2.5 cM is the first to be mapped to this small acrocentric canine chromosome and adds gene-associated polymorphic markers to the developing dog linkage map. Linkage of loci in this region to hereditary CTD in the keeshond was excluded.     

Association of assisted reproductive technology,germline de novo mutations and congenital heart defects in a prospective birth cohort study

Emerging evidence suggests that children conceived through assisted reproductive technology (ART) have a higher risk of congenital heart defects (CHDs) even when there is no family history. De novo mutation (DNM) is a well-known cause of sporadic congenital diseases; however, whether ART procedures increase the number of germline DNM (gDNM) has not yet been well studied. Here, we performed whole-genome sequencing of 1137 individuals from 160 families conceived through ART and 205 families conceived spontaneously. Children conceived via ART carried 4.59 more gDNMs than children conceived spontaneously, including 3.32 paternal and 1.26 maternal DNMs, after correcting for parental age at conception, cigarette smoking, alcohol drinking, and exercise behaviors. Paternal DNMs in offspring conceived via ART are characterized by C>T substitutions at CpG sites, which potentially affect protein-coding genes and are significantly associated with the increased risk of CHD. In addition, the accumulation of non-coding functional mutations was independently associated with CHD and 87.9% of the mutations were originated from the father. Among ART offspring, infertility of the father was associated with elevated paternal DNMs; usage of both recombinant and urinary follicle-stimulating hormone and high-dosage human chorionic gonadotropin trigger was associated with an increase of maternal DNMs. In sum, the increased gDNMs in offspring conceived by ART were primarily originated from fathers, indicating that ART itself may not be a major reason for the accumulation of gDNMs. Our findings emphasize the importance of evaluating the germline status of the fathers in families with the use of ART.Subject terms: Genomic analysis, Developmental biology     

A modified multiplex ligation-dependent probe amplification method for the detection of 22q11.2 copy number variations in patients with congenital heart disease

Background

Copy number variations (CNVs) of chromosomal region 22q11.2 are associated with a subset of patients with congenital heart disease (CHD). Accurate and efficient detection of CNV is important for genetic analysis of CHD. The aim of the study was to introduce a novel approach named CNVplex®, a high-throughput analysis technique designed for efficient detection of chromosomal CNVs, and to explore the prevalence of sub-chromosomal imbalances in 22q11.2 loci in patients with CHD from a single institute.

Results

We developed a novel technique, CNVplex®, for high-throughput detection of sub-chromosomal copy number aberrations. Modified from the multiplex ligation-dependent probe amplification (MLPA) method, it introduced a lengthening ligation system and four universal primer sets, which simplified the synthesis of probes and significantly improved the flexibility of the experiment. We used 110 samples, which were extensively characterized with chromosomal microarray analysis and MLPA, to validate the performance of the newly developed method. Furthermore, CNVplex® was used to screen for sub-chromosomal imbalances in 22q11.2 loci in 818 CHD patients consecutively enrolled from Shanghai Children’s Medical Center. In the methodology development phase, CNVplex® detected all copy number aberrations that were previously identified with both chromosomal microarray analysis and MLPA, demonstrating 100% sensitivity and specificity. In the validation phase, 22q11.2 deletion and 22q11.2 duplication were detected in 39 and 1 of 818 patients with CHD by CNVplex®, respectively. Our data demonstrated that the frequency of 22q11.2 deletion varied among sub-groups of CHD patients. Notably, 22q11.2 deletion was more commonly observed in cases with conotruncal defect (CTD) than in cases with non-CTD (P < 0.001). With higher resolution and more probes against selected chromosomal loci, CNVplex® also identified several individuals with small CNVs and alterations in other chromosomes.

Conclusions

CNVplex® is sensitive and specific in its detection of CNVs, and it is an alternative to MLPA for batch screening of pathogenetic CNVs in known genomic loci.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1590-5) contains supplementary material, which is available to authorized users.     

Thymic medullary structures: Microscopical picture of the thymic medullary structures in children with congenital heart defects

The aim of this work is to describe the structure of the thymus, especially its medullary part, in children with congenital heart defects. It is known that development of the thymus and the heart is also influenced by neural crest cells. During the early development of the heart and the thymus cells proliferate and migrate to their primordia. It is known that inadequate cephalic neural crest contribution during development of pharyngeal pouch derivatives results in defective organogenesis of the face, the thymus, parathyroid glands and also the heart. We studied the structure of the thymus in children with congenital heart defects from 0 to 12 years of life at light microscopic and electron-microscopic levels. Thymuses of the patients were surgically removed in the Children’s Cardiocenter in Bratislava. The results of our study confirmed the differences in the medullary structures of thymuses with chosen diagnoses. Hassall’s corpuscles in the thymic medulla were various in size and also in structure and number. The special structures of the thymic medullary region in children with ventricular septal defects and defects of outflow of the heart were big cystic Hassall’s corpuscles. In comparison with a size of Hassall’s corpuscles in normal thymuses the size of Hassall’s corpuscles in studied thymuses suprisingly ranged between 100–250 μm.     

The copy number of chloroplast gene minicircles changes dramatically with growth phase in the dinoflagellate Amphidinium operculatum

The chloroplast genome of algae and plants typically comprises a circular DNA molecule of 100-200kb, which harbours approximately 120 genes, and is present in 50-100 copies per chloroplast. However, in peridinin dinoflagellates, an ecologically important group of unicellular algae, the chloroplast genome is fragmented into plasmid-like 'minicircles', each of 2-3kb. Furthermore, the chloroplast gene content of dinoflagellates is dramatically reduced. Only 14 genes have been found on dinoflagellate minicircles, and recent evidence from EST studies suggests that most of the genes typically located in the chloroplast in other algae and plants are located in the nucleus. In this study, Southern blot analysis was used to estimate the copy number per cell of a variety of minicircles during different growth stages in the dinoflagellate Amphidinium operculatum. It was found that minicircle copy number is low during the exponential growth stage but increases during the later growth phase to resemble the situation seen in other plants and algae. The control of minicircle replication is discussed in the light of these findings.     

The prevalence of cytogenetic anomalies in children with congenital developmental defects (CDD)

The analysis of the cytogenetic anomalies frequencies in children with inborn defects of development was carried out, and the comparative evaluation of involving in cytogenetic anomalies of the individual chromosomes was determined. Chromosomes 9, 13 and 18 were most frequently involved in chromosomal anomalies. There no direct relations were revealed between peculiarities of inborn defects of development and definite cytogenetic anomalies.     

Regulation of Mu element copy number in maize lines with an active or inactive Mutator transposable element system

Summary In the progeny of an active Mutator plant, the number of Mu elements increases on self-pollination and maintains the average parental Mu content on outcrossing to a non-Mutator line; both patterns of transmission require an increase in the absolute number of Mu elements from one generation to the next. The same average copy number of Mu elements is transmitted through the male and female, but there is wide variation in the absolute copy number among the progeny. In inactive Mutator plants —defined both by the loss of somatic instability at a reporter gene (bronze2-mu1) and by modification of the HinfI sites in the terminal inverted repeat sequences of Mu elements —the absolute copy number of Mu elements is fixed in the parent. Thus, in outcrosses Mu element number is halved, and on self-pollination Mu copy number is constant. Reactivation of somatic mutability at cryptic bz2-mu1 alleles in inactive individuals by crossing to an active line seems not to involve an increase in Mu element copy number transmitted by the inactive individual. These and other results suggest that increases in Mu copy number occur late in plant development or in the gametophyte rather than after fertilization.     

The anti-infection resistance system and the pathogenesis of bacterial endocarditis in patients with congenital heart defects

The clinico-immuno-microbiological study of 24 patients with congenital heart diseases was made. Clinically, the patients were subdivided into two groups: 8 patients with diagnosed bacterial endocarditis (BE) prior to the operation and 16 patients without BE. The analysis of the results of investigation carried out prior to the operation showed that age, the form of the disease and its duration did not affect the level of anti-infectious resistance factors (AIRF): in both groups a decrease in the level of AIRF characteristics (cell-mediated and humoral) was noted and no characteristic differences were determined. The results of the study of microflora from the nasal and laryngeal mucosa showed no difference in both groups of the patients. At the same time the detailed analysis of the results made it possible to suggest that BE caused by Streptococcus epidermidis and Streptococcus aureus inhabiting the mucous membrane of the anterior sections of the nasal cavity, alpha-hemolytic streptococci and S. epidermidis inhibiting the laryngeal mucosa. The results of the analysis made 3-6 months after the operation were also indicative of the absence of essential differences between AIRF characteristics observed in patients with confirmed and clinically unconfirmed BE. The clinical manifestation of this fact was an increase in the percentage of diagnosed BE cases up to 70% as compared with that before the operation (33%). This clinico-immuno-microbiological study made it possible to come to the conclusion that any form of congenital heart disease develops in combination with BE and/or is its prodrome.     

Route of administration (enteral or parenteral) affects the contribution of L-glutamine to de novo L-arginine synthesis in mice: a stable-isotope study

A pathway from enteral L-glutamine as substrate for L-arginine synthesis is suggested by previous studies. L-Glutamine and L-glutamine dipeptides exhibit numerous beneficial effects in experimental and clinical studies. In trauma patients, enteral L-glutamine supply increased plasma L-arginine. The present study was designed to quantify the contribution of L-glutamine to the de novo L-citrulline and L-arginine synthesis in mice when L-glutamine is administered in a high dose of labeled L-glutamine or L-alanyl-L-glutamine by the enteral or parenteral route. For this purpose, male Swiss mice (n = 43) underwent a laparotomy, and catheters were inserted for sampling and infusion. A primed, constant, and continuous infusion of L-alanyl-L-[2-(15)N]glutamine (dipeptide groups) or L-[2-(15)N]glutamine (free L-glutamine groups), simultaneously with L-[ureido-(13)C,(2)H(2)]citrulline and L-[guanidino-(15)N(2),(2)H(2)]arginine, was given (steady-state model). Mice received the L-glutamine tracers intravenously (jugular vein) or enterally (duodenum). Enrichments of metabolites were measured by LC-MS. Arterial L-glutamine concentrations were the highest in the intravenous dipeptide group. L-Glutamine was converted to L-citrulline and L-arginine when L-[2-(15)N]glutamine and L-alanyl-L-[2-(15)N]glutamine were given by enteral or parenteral route. The contribution of L-glutamine to the de novo synthesis of L-citrulline and L-arginine was higher in the enteral groups when compared with the intravenous groups (P < 0.005). Therefore, the route of administration (enteral or parenteral) affects the contribution of L-glutamine, provided as free molecule or dipeptide, to the de novo synthesis of L-arginine in mice.     

Altered lymphatics in an ovine model of congenital heart disease with increased pulmonary blood flow

Abnormalities of the lymphatic circulation are well recognized in patients with congenital heart defects. However, it is not known how the associated abnormal blood flow patterns, such as increased pulmonary blood flow (PBF), might affect pulmonary lymphatic function and structure. Using well-established ovine models of acute and chronic increases in PBF, we cannulated the efferent lymphatic duct of the caudal mediastinal node and collected and analyzed lymph effluent from the lungs of lambs with acutely increased PBF (n = 6), chronically increased PBF (n = 6), and age-matched normal lambs (n = 8). When normalized to PBF, we found that lymph flow was unchanged following acute increases in PBF but decreased following chronic increases in PBF. The lymph:plasma protein ratio decreased with both acute and chronic increases in PBF. Lymph bioavailable nitric oxide increased following acute increases in PBF but decreased following chronic increases in PBF. In addition, we found perturbations in the transit kinetics of contrast material through the pleural lymphatics of lambs with chronic increases in PBF. Finally, there were structural changes in the pulmonary lymphatic system in lambs with chronic increases in PBF: lymphatics from these lambs were larger and more dilated, and there were alterations in the expression of vascular endothelial growth factor-C, lymphatic vessel endothelial hyaluronan receptor-1, and Angiopoietin-2, proteins known to be important for lymphatic growth, development, and remodeling. Taken together these data suggest that chronic increases in PBF lead to both functional and structural aberrations of lung lymphatics. These findings have important therapeutic implications that warrant further study.     

Unusual genotypes in the COL6A1 gene in parents of children with trisomy 21 and major congenital heart defects

Collagen type VI is a candidate for a role in the pathogenesis of congenital heart defects (CHD) in Down's syndrome. Three restriction fragment length polymorphisms of the COL6A1 gene were used to determine COL6A1 genotypes in 50 families of affected children with trisomy 21 (29 with congenital heart defects and 21 without) and 37 unrelated volunteers. We found seven unusual genotypes in the parents of affected children with Down's syndrome, five being unique to the parents of children with trisomy 21 and CHD. There were no unusual genotypes associated with other chromosome 21 loci. No single COL6A1 genotype was associated with CHD. Thus, the unusual genotypes unique to parents of affected children suggest that genetic variation in the COL6A1 gene region contributes to the pathogenesis of CHD in Down's syndrome.     

Serum IGF-1, IGFBP-3 and growth hormone levels in children with congenital heart disease: relationship with nutritional status, cyanosis and left ventricular functions

In this study we aimed to evaluate serum insulin-like growth factor-1 (IGF-1), insulin-like growth factor binding protein-3 (IGFBP-3) and growth hormone (GH) levels in children with congenital heart disease (CHD) and to determine if these parameters have any relationship to the cyanosis, nutritional status and the left ventricular systolic function. This study is prospective-randomized study which conducted in 94 CHD patients (36 girls and 58 boys, aged between one 1-192 months, 19 cyanotic CHD and 75 acyanotic CHD) and age-sex matched 54 children (26 girls and 28 boys) with no CHD. In the study group, 37 out of the 94 CHD patients (39.4%) and 16 out of the 54 controls (29.6%) had malnutrition. The difference between the cyanotic and acyanotic patients in respect to malnutrition was significant (57.9% and 34.6%, p<0.05). Serum IGF-1 levels were lower (41.8+/-3.9 microg/L, 106.9+/-17.9 microg/L respectively, p<0.001) and GH levels were higher (6.43+/-0.9 ng/ml, 3.87+/-0.5 respectively, p<0.05) in CHD patient group than the controls. Serum IGF-1 levels were significantly lower in cyanotic CHD patients than the acyanotic patients (17.2+/-3.2 microg/L, 48.7.0+/-4.6 microg/L respectively, p<0.001) and serum IGF-1 levels were both lower in acyanotic and cyanotic CHD patients than the controls (p<0.001 for both). Serum IGF-1 and GH levels were similar between the well-nourished CHD patients and CHD patients with malnutrition (p>0.05). In total study group, the most effective factors on serum IGF-1 levels was presence of CHD (p<0.001), in CHD patients, the presence of cyanosis is the most effective factor on serum IGF-1 level, the presence of malnutrition is the most effective factor on serum IGFBP-3 levels (p<0.01). In the acyanotic, cyanotic, and the entire CHD patient groups, we find no correlations between the serum IGF-1, IGFBP-3 levels and left ventricular systolic function measurements. But serum GH levels were negatively correlated with diastolic left ventricular interseptum diameter, diastolic left ventricular mass and left ventricular end-diastolic volume measurements in CHD patients. In conclusion, we determined that the most important factor on serum IGF-1 levels is cyanosis. Reduced IGF1 levels and decreased left ventricular mass with an elevated GH levels in CHD patients and these findings are prominent in the cases with cyanosis and malnutrition. For this reason we believe that chronic hypoxia plays a significant role in the pathogenesis of malnutrition and also we believe that IGF-1 deficiency seen in CHD patients may be responsible in the etiology of the decrease in left ventricular mass independently from GH.