Enrichment of ultraconserved elements among genomic imbalances causing mental delay and congenital anomalies

Background

In translational cancer research, gene expression data is collected together with clinical data and genomic data arising from other chip based high throughput technologies. Software tools for the joint analysis of such high dimensional data sets together with clinical data are required.

Results

We have developed an open source software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data together with associated clinical data, array CGH data and SNP array data. The different data types are organized by a comprehensive data manager. Interactive tools are provided for all graphics: heatmaps, dendrograms, barcharts, histograms, eventcharts and a chromosome browser, which displays genetic variations along the genome. All graphics are dynamic and fully linked so that any object selected in a graphic will be highlighted in all other graphics. For exploratory data analysis the software provides unsupervised data analytics like clustering, seriation algorithms and biclustering algorithms.

Conclusions

The SEURAT software meets the growing needs of researchers to perform joint analysis of gene expression, genomical and clinical data.     

Interstitial deletion of chromosome 13 and associated congenital anomalies

Summary An interstitial deletion of chromosome 13 with breakpoints at 13q22 and 13q32 is presented. The clinical findings associated with this deletion are discussed in relation to the correlations of specific chromosomal bands with constellations of congenital defects as described by Niebuhr and Ottosen (1973), Niebuhr (1977), Lewandowski and Yunis (1975), and Noel et al. (1976).     

De novo 3q22.1 q24 deletion associated with multiple congenital anomalies,growth retardation and intellectual disability

We describe a boy with a de novo deletion of 15.67 Mb spanning 3q22.1q24. He has bilateral micropthalmia, ptosis, cleft palate, global developmental delay and brain, skeletal and cardiac abnormalities. In addition, he has bilateral inguinal hernia and his right kidney is absent. We compare his phenotype with seven other patients with overlapping and molecularly defined interstitial 3q deletions. This patient has some phenotypic features that are not shared by the other patients. More cases with smaller deletions defined by high resolution aCGH will enable better genotype–phenotype correlations and prioritizing of candidate genes for the identification of pathways and disease mechanisms.     

Patterns and trends of multiple congenital anomalies in birth defects surveillance systems

Infants with multiple congenital anomalies (MCA) can provide important clues in the detection of teratogenic agents. Definition, classification, and ascertainment of MCA vary, however. We present comparative epidemiologic data on MCA from two U.S. surveillance systems: the Metropolitan Atlanta Congenital Defects Program, which ascertains major birth defects during the first year of life, and the Birth Defects Monitoring Program, a nationwide system that relies on newborn hospital-discharge diagnoses. This system has two components: the Commission on Public Hospitals Activities (CPHA) and the McDonnell Douglas Health Information System (MDHIS). Our analyses were based on over 600,000 births occurring in Atlanta, and over 5 million births occurring nationwide. Infants were classified as having MCA if they had two or more major defects from different categories (central nervous system, eye, orofacial, gastrointestinal, cardiovascular, genitourinary, and musculoskeletal). Additional analyses were also done on infants with three or more defects. Compared with the nationwide system, Atlanta showed 1) a much higher rate of MCA (16.2 per 10,000 births vs. 4.9 and 3.8 per 10,000 births in CPHA and MDHIS, respectively) and 2) a higher rate of MCA with chromosomal syndromes (2.0 per 10,000 births vs. 0.6 and 0.3 per 10,000 births in CPHA and MDHIS, respectively). Moreover, in Atlanta, the proportion of MCA with recorded chromosomal syndromes increased substantially during 20 years. These data point to differences in the ascertainment of MCAs in birth defects surveillance systems. More effort is needed to improve the ascertainment and comparability of MCA in surveillance systems, an important step toward better detection of human teratogens.     

Congenital anomalies and developmental delay in a boy with double chromosome 6 derived supernumerary marker

The frequency of small supernumerary marker chromosomes has been estimated to approximately 0.45 per 1000 newborns. They are usually seen as single marker chromosomes in a mosaic state. Two cytogenetically identical markers have been observed only occasionally. We report on a boy, with congenital heart defect, neonatal hypotonia, hypogenitalism, delayed psychomotor development and mild dysmorphic facial features. The GTG karyotype performed on peripheral blood lymphocytes revealed a mosaic male karyotype with three cell lines. One cell line had a normal karyotype. In the other two either single or double chromosome 6 derived supernumerary markers were present, leading to partial trisomy or partial tetrasomy of chromosome 6, respectively.     

Trisomy 1q43 syndrome: a consistent phenotype with macrocephaly, characteristic face, developmental delay and cardiac anomalies

Trisomy 1q43 syndrome: a consistent phenotype with macrocephaly, characteristic face, developmental delay and cardiac anomalies: Patients with trisomy (1)(q42-qter) present with psychomotor retardation, macrocephaly, occasional presence of facial capillary naevi, cardio-vascular anomalies and small size for gestational age. We report on a girl with the same pattern of malformations, who has pure trisomy 1 q43: duplication of the region (1) (q43) and the translocation of the terminal region of the other chromosome 1 to the derivative 1, narrowing down the critical region for the characteristic traits of severe developmental delay, macrocephaly and congenital cardiac malformations.     

DNA polymorphism unique for a complotype with deletion of HLA-linked C4B and 21-hydroxylase B genes causing congenital adrenal hyperplasia

Summary Defects in the enzyme steroid 21-hydroxylase (21-OH) result in congenital adrenal hyperplasia (CAH), a frequent disorder of steroid biosynthesis. The gene encoding the enzyme, 21-OHB, has been mapped adjacent to the complement component C4B gene in the human HLA gene complex. DNA-level analyses of patients with CAH have shown that the 21-OHB gene has often been deleted, but the detection of 21-OHB delections in heterozygotes is often problematic because it is based on relative band intensities. We here report a DNA polymorphism in the C4A91 gene unique to one particular type of 21-OHB deletion occurring solely with a complement phenotype BfF C4A91 B null, shown earlier to be frequent in CAH patients. This marker makes direct detection of the 21-OHB deletion in heterozygotes possible.     

Molecular cytogenetic characterization of a constitutional complex intrachromosomal 4q rearrangement in a patient with multiple congenital anomalies

Constitutional Complex Chromosomal Rearrangements (CCRs) are very rare. While the vast majority of CCRs involve more than one chromosome, only seven cases describe CCRs with four or more breakpoints within a single chromosome. Here, we present a patient with multiple congenital anomalies and mental retardation. Array Comparative Genomic Hybridisation (array CGH), FISH and Multicolour Banding FISH revealed a de novo complex rearrangement with two deletions, a duplication and an inversion of 4q. This CCR involving at least seven breakpoints is one of the most complex rearrangements of a single chromosome reported thus far. Potential mechanisms generating such complex rearrangements are discussed.     

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.     

On the symmetry of limb deficiencies among children with multiple congenital anomalies

In humans, unpaired organs are placed in a highly ordered pattern along the left-right axis. As indicated by animal studies, a cascade of signaling molecules establish left-right asymmetry in the developing embryo. Some of the same genes are involved also in limb patterning. To provide a better insight into the connection between these processes in humans, we analysed the symmetry of limb deficiencies among infants with multiple congenital anomalies. The study was based on data collected by the International Clearinghouse for Birth Defects Monitoring Systems (ICBDMS). Registries of the ICBDMS provided information on infants who, in addition to a limb deficiency, also had at least one major congenital anomaly in other organ systems. We reviewed 815 such cases of which 149 cases (18.3 %) were syndromic and 666 (81.7 %) were nonsyndromic. The comparisons were made within the associated limb deficiencies, considering the information on symmetry, using a comparison group with malformations associated not involved in the index association. Among the non-syndromic cases, the left-right distribution of limb deficiencies did not differ appreciably between limb deficiency subtypes (e.g., preaxial, transverse, longitudinal). The left-right distribution of limb anomalies did not differ among most types of non-limb anomalies, though a predominance of left-sided limb deficiencies was observed in the presence of severe genital defects - odds ratio [OR], 2.6; 95 % CI, 1.1-6.4). Limb deficiencies (LDs) were more often unilateral than bilateral when accompanied by gastroschisis (OR, 0.1) or axial skeletal defects (OR, 0.5). On the contrary, LDs were more often bilateral than unilateral when associated with cleft lip with or without cleft palate (OR, 3.9) or micrognathia (OR, 2.6). Specifically, we found an association between bilateral preaxial deficiencies and cleft lip, bilateral amelia with gastroschisis and urinary tract anomalies, and bilateral transverse deficiencies and gastroschisis and axial skeleton defects. Of 149 syndromic cases, 62 (41.6 %) were diagnosed as trisomy 18. Out of the 30 cases of trisomy 18 with known laterality, 20 cases were bilateral. In the remainder the right and left sides were equally affected. Also, in most cases (74.4 %) only the upper limbs were involved. In conclusion the left-right distribution of limb deficiencies among some non-limb anomalies may suggest a relationship between the development of the limb and the left-right axis of the embryo.     

Exome sequencing reveled a compound heterozygous mutations in RTTN gene causing developmental delay and primary microcephaly

RTTN (Rotatin) (OMIM 614833) is a large centrosomal protein coding gene. RTTN mutations are responsible for syndromic forms of malformation of brain development, leading to polymicrogyria, microcephaly, primordial dwarfism, seizure along with many other malformations. In this study we have identified a compound heterozygous mutation in RTTN gene having NM_173630 c.5225A > G p.His1742Arg in exon 39 and NM_173630 c.6038G > T p.Cys2013Phe in exon 45 of a consanguineous Saudi family leading to brain malformation, seizure, developmental delay, dysmorphic feature and microcephaly. Whole exome sequencing (WES) techniques was used to identify the causative mutation in the affected members of the family. WES data analysis was done and obtained data were further confirmed by using Sanger sequencing analysis. Moreover, the mutation was ruled out in 100 healthy control from normal population. To the best of our knowledge the novel compound heterozygous mutation observed in this study is the first report from Saudi Arabia. The identified compound heterozygous mutation will further explain the role of RTTN gene in development of microcephaly and neurodevelopmental disorders.