Rare DNA copy number variants in cardiovascular malformations with extracardiac abnormalities

1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA [2] Children's Nutrition Research Center, Houston, TX, USA.
European journal of human genetics: EJHG (Impact Factor: 4.35). 08/2012; 21(2). DOI: 10.1038/ejhg.2012.155
Source: PubMed


Clinically significant cardiovascular malformations (CVMs) occur in 5-8 per 1000 live births. Recurrent copy number variations (CNVs) are among the known causes of syndromic CVMs, accounting for an important fraction of cases. We hypothesized that many additional rare CNVs also cause CVMs and can be detected in patients with CVMs plus extracardiac anomalies (ECAs). Through a genome-wide survey of 203 subjects with CVMs and ECAs, we identified 55 CNVs >50 kb in length that were not present in children without known cardiovascular defects (n=872). Sixteen unique CNVs overlapping these variants were found in an independent CVM plus ECA cohort (n=511), which were not observed in 2011 controls. The study identified 12/16 (75%) novel loci including non-recurrent de novo 16q24.3 loss (4/714) and de novo 2q31.3q32.1 loss encompassing PPP1R1C and PDE1A (2/714). The study also narrowed critical intervals in three well-recognized genomic disorders of CVM, such as the cat-eye syndrome region on 22q11.1, 8p23.1 loss encompassing GATA4 and SOX7 and 17p13.3-p13.2 loss. An analysis of protein-interaction databases shows that the rare inherited and de novo CNVs detected in the combined cohort are enriched for genes encoding proteins that are direct or indirect partners of proteins known to be required for normal cardiac development. Our findings implicate rare variants such as 16q24.3 loss and 2q31.3-q32.1 loss, and delineate regions within previously reported structural variants known to cause CVMs.European Journal of Human Genetics advance online publication, 29 August 2012; doi:10.1038/ejhg.2012.155.

Download full-text


Available from: Sau Wai Cheung, Nov 08, 2015
  • Source
    • "As mentioned in this review, patients with INAD or an autosomal-recessive syndrome with severe hypotonia, speech impairment, and cognitive delay have seizures (Al-Sayed et al., 2013; Koroglu et al., 2013). Seizures were also reported for patients with chromosome 13q deletions in regions that contain the NALCN gene (Kirchhoff et al., 2009; Lalani et al., 2013). Recently, a whole genome linkage analysis in three-generations of a south Indian family who had multiple members affected with juvenile myoclonic epilepsy (JME) found a critical genetic interval of 24 Mb between markers D2S116 and D2S2390 (Ratnapriya et al., 2010). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Ion channels are crucial components of cellular excitability and are involved in many neurological diseases. This review focuses on the sodium leak, G protein-coupled receptors (GPCRs)-activated NALCN channel that is predominantly expressed in neurons where it regulates the resting membrane potential and neuronal excitability. NALCN is part of a complex that includes not only GPCRs, but also UNC-79, UNC-80, NLF-1 and src family of Tyrosine kinases (SFKs). There is growing evidence that the NALCN channelosome critically regulates its ion conduction. Both in mammals and invertebrates, animal models revealed an involvement in many processes such as locomotor behaviors, sensitivity to volatile anesthetics, and respiratory rhythms. There is also evidence that alteration in this NALCN channelosome can cause a wide variety of diseases. Indeed, mutations in the NALCN gene were identified in Infantile Neuroaxonal Dystrophy (INAD) patients, as well as in patients with an Autosomal Recessive Syndrome with severe hypotonia, speech impairment, and cognitive delay. Deletions in NALCN gene were also reported in diseases such as 13q syndrome. In addition, genes encoding NALCN, NLF- 1, UNC-79, and UNC-80 proteins may be susceptibility loci for several diseases including bipolar disorder, schizophrenia, Alzheimer's disease, autism, epilepsy, alcoholism, cardiac diseases and cancer. Although the physiological role of the NALCN channelosome is poorly understood, its involvement in human diseases should foster interest for drug development in the near future. Toward this goal, we review here the current knowledge on the NALCN channelosome in physiology and diseases.
    Frontiers in Cellular Neuroscience 05/2014; 8:132. DOI:10.3389/fncel.2014.00132 · 4.29 Impact Factor
  • Source
    • "deletion disorder. The 17p13.2 deletion is rarely reported in the literature, and thus far, only two 17p13 deletions [38], [39] and one 17p13 duplication [40] have been reported in patients with intellectual disability. A re-evaluation of this individual with the 17p13.2 "
    [Show abstract] [Hide abstract]
    ABSTRACT: Ongoing studies using genomic microarrays and next-generation sequencing have demonstrated that the genetic contributions to cardiovascular diseases have been significantly ignored in the past. The aim of this study was to identify rare copy number variants in individuals with congenital pulmonary atresia (PA). Based on the hypothesis that rare structural variants encompassing key genes play an important role in heart development in PA patients, we performed high-resolution genome-wide microarrays for copy number variations (CNVs) in 82 PA patient-parent trios and 189 controls with an Illumina SNP array platform. CNVs were identified in 17/82 patients (20.7%), and eight of these CNVs (9.8%) are considered potentially pathogenic. Five de novo CNVs occurred at two known congenital heart disease (CHD) loci (16p13.1 and 22q11.2). Two de novo CNVs that may affect folate and vitamin B12 metabolism were identified for the first time. A de novo 1-Mb deletion at 17p13.2 may represent a rare genomic disorder that involves mild intellectual disability and associated facial features. Rare CNVs contribute to the pathogenesis of PA (9.8%), suggesting that the causes of PA are heterogeneous and pleiotropic. Together with previous data from animal models, our results might help identify a link between CHD and folate-mediated one-carbon metabolism (FOCM). With the accumulation of high-resolution SNP array data, these previously undescribed rare CNVs may help reveal critical gene(s) in CHD and may provide novel insights about CHD pathogenesis.
    PLoS ONE 05/2014; 9(5):e96471. DOI:10.1371/journal.pone.0096471 · 3.23 Impact Factor
  • Source
    • "Recent studies have also shown that rare de novo and inherited copy number variants (CNVs) occur in 5–10 % of probands with CHD, classified in a variety of ways (Breckpot et al. 2010, 2011; Erdogan et al. 2008; Greenway et al. 2009; Hitz et al. 2012; Lalani et al. 2013; Silversides et al. 2012; Soemedi et al. 2012b). This evidence points to great heterogeneity among the genetic factors implicated in CHD. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Congenital heart disease (CHD) is the most common congenital malformation, with evidence of a strong genetic component. We analyzed data from 223 consecutively ascertained families, each consisting of at least one child affected by a conotruncal defect (CNT) or hypoplastic left heart disease (HLHS) and both parents. The NimbleGen HD2-2.1 comparative genomic hybridization platform was used to identify de novo and rare inherited copy number variants (CNVs). Excluding 10 cases with 22q11.2 DiGeorge deletions, we validated de novo CNVs in 8 % of 148 probands with CNTs, 12.7 % of 71 probands with HLHS and none in 4 probands with both. Only 2 % of control families showed a de novo CNV. We also identified a group of ultra-rare inherited CNVs that occurred de novo in our sample, contained a candidate gene for CHD, recurred in our sample or were present in an affected sibling. We confirmed the contribution to CHD of copy number changes in genes such as GATA4 and NODAL and identified several genes in novel recurrent CNVs that may point to novel CHD candidate loci. We also found CNVs previously associated with highly variable phenotypes and reduced penetrance, such as dup 1q21.1, dup 16p13.11, dup 15q11.2-13, dup 22q11.2, and del 2q23.1. We found that the presence of extra-cardiac anomalies was not related to the frequency of CNVs, and that there was no significant difference in CNV frequency or specificity between the probands with CNT and HLHS. In agreement with other series, we identified likely causal CNVs in 5.6 % of our total sample, half of which were de novo.
    Human Genetics 08/2013; 133(1). DOI:10.1007/s00439-013-1353-9 · 4.82 Impact Factor
Show more