De novo 3q/7q translocation and associated interstitial 7q35 deletion

In the present report we describe a severely mentally retarded and dysmorphic female child with a de novo 3q/7q reciprocal translocation and loss of band 7q35. This finding supports the hyothesis that the occurrence of mental retardation and/or congenital malformations in de novo autosomal reciprocal translocation may be due to the loss of a small amount of chromatin material during this chromosomal rearrangement.     

De novo reciprocal 1p;2q translocation in a child with multiple congenital anomalies/mental retardation syndrome

A newborn male infant was found to have an unusual pattern of congenital anomalies associated with an apparently balanced de novo reciprocal translocation: 46,XY,t(1;2)(p22;q22). The infant had a previously apparently undescribed multiple congenital anomalies and mental retardation syndrome.     

A de novo 2.1-Mb deletion of 13q12.11 in a child with developmental delay and minor dysmorphic features

We report on a patient with an interstitial deletion at 13q12.11. He had mild developmental delay, craniofacial dysmorphism, a pectus excavatum, narrow shoulders, malformed toes, and café-au-lait spots. Array CGH analysis disclosed a de novo deletion spanning 2.1 Mb,within cytogenetic band 13q12.11.The deletion produces hemizygozity for 16 known genes, among which GJA3, GJB2, GJB6, IFT88, LATS2, and FGF9 have potential clinical significance. The observed phenotype may be due to mutation in one of the 16 genes, or to a combination of deletion and/or mutation in a number of them.     

Mild mental retardation in a child with a de novo interstitial deletion of 15q21.2q22.1: a comparison with previously described cases

We report on a child with mild mental retardation, hypotelorism, blepharophimosis, face slight asymmetry and partial hypoplasia of corpus callosum, with an interstitial deletion of a chromosome 15. The deletion was molecularly characterized by array-CGH and FISH techniques. This rearrangement has a 7.18 Mb extension and maps to 15q21.2q22.1. To date, there have been only six individuals reported with a deletion of 15q21; in three cases, the rearrangement was characterized by molecular cytogenetic techniques. After a comparison with these three cases, it appeared that the deletion we found is one of the smallest and it overlaps the distal portion of the ones taken into account. Finally, we tried to delineate the genotype–phenotype correlation in patients with a deletion of 15q21.     

A boy with developmental delay and a maternally inherited deletion in 15q11q13.

A boy was referred at 8 weeks of age for failure to thrive. Cytogenetic and molecular studies showed that he had a large proximal deletion of the maternally derived chromosome 15q. He did not have Angelman syndrome, but at 2 years of age was severely globally delayed. He died at 2 1/2 years of age.     

A patient with a de novo 15q24q26.1 interstitial deletion, developmental delay, mild dysmorphism, and very blue irises

We report on a patient with a de novo 15q24q26.1 interstitial deletion. She presented with developmental delay, behavioral characteristics, and mild dysmorphism with very blue irises. We review the limited literature of interstitial 15q deletions. There was no distinct phenotypic overlap between these two cases in literature and the present patient. Additional reports are necessary in order to establish a possible recognizable deletion 15q24q26.1 phenotype.     

De novo deletion 12q: Report of a patient with 12q24.31q24.33 deletion

We report on a patient with de novo interstitial deletion of the long arm of chromosome 12: 46,XY,del(12)(q24.31q24.33). To our knowledge this is the first patient with this chromosomal abnormality reported. He was born with minor anomalies, ambiguous genitalia, tracheomalacia, and he was developmentally delayed at age 9 months. The phenotype associated with this deletion may be characteristic. However, because of the absence of reported cases of other patients with loss of this chromosomal region, we cannot delineate the specific phenotype further. Ambiguous genitalia or hypogonadism has been reported in other patients with chromosomal rearrangements involving 12q24. Am. J. Med. Genet. 84:116–119, 1999. © 1999 Wiley-Liss, Inc.     

Paternally derived de novo interstitial duplication of proximal 15q in a patient with developmental delay

Interstitial duplications of proximal 15q containing the Prader-Willi syndrome/Angelman syndrome (PWS/AS) region have been found in patients with autism or atypical autism. In these cases with an abnormal phenotype, the duplications were maternally derived. Paternal origin of the duplication has been associated with a normal phenotype. We report on a patient who presented with nonspecific developmental delay and partial agenesis of the rostral corpus callosum. Fluorescence in situ hybridization (FISH) studies using probes specific for the PWS/AS region demonstrated a double signal on one chromosome 15, indicating the presence of an interstitial duplication of proximal 15q involving the PWS/ AS region in the patient. Parental chromosomes were normal with FISH studies. Methylation analysis at exon alpha of the SNRPN locus showed a maternal band at 4.2 kb and a paternal band of apparent double intensity at 0.9 kb, suggestive of one copy of the maternal allele and two copies of the paternal allele in the patient. Microsatellite analysis was informative at the GABRB3 locus in the family, which showed the inheritance of two different paternal alleles and a maternal allele in the patient consistent with the origin of this duplication from an unequal crossing over between the two chromosome 15 homologs in the father. This is the first report of an abnormal phenotype associated with a paternally derived duplication of proximal 15q shown to contain the PWS/AS region by molecular techniques.     

De novo 911 Kb interstitial deletion on chromosome 1q43 in a boy with mental retardation and short stature

Patients with distal deletions of chromosome 1q have a recognizable syndrome that includes microcephaly, hypoplasia or agenesis of the corpus callosum, and psychomotor retardation. Although these symptoms have been attributed to deletions of 1q42-1q44, the minimal chromosomal region involved has not yet defined. In this report, we describe a 7 years old male with mental retardation, cryptorchid testes, short stature and alopecia carrying only an interstitial de novo deletion of 911 Kb in the 1q43 region (239,597,095-240,508,817) encompassing three genes CHRM3, RPS7P5 and FMN2.     

Submicroscopic subtelomeric aberrations in Chinese patients with unexplained developmental delay/mental retardation

Background

Conserved non-coding regions (CNR) have been shown to harbor gene expression regulatory elements. Genetic variations in these regions may potentially contribute to complex disease susceptibility.

Methods

We targeted CNRs of cardiovascular disease (CVD) candidate gene, Na(+)-Ca(2+) exchanger (NCX1) with polymorphism screening among CVD patients (n = 46) using DHPLC technology. The flanking region (348 bp) of the 14 bp indel in intron 2 was further genotyped by DGGE assay in two Eastern-European CVD samples: essential hypertension (HYPEST; 470 cases, 652 controls) and coronary artery disease, CAD (CADCZ; 257 cases, controls 413). Genotype-phenotype associations were tested by regression analysis implemented in PLINK. Alignments of primate sequences were performed by ClustalW2.

Results

Nine of the identified NCX1 variants were either singletons or targeted by commercial platforms. The 14 bp intronic indel (rs11274804) was represented with substantial frequency in HYPEST (6.82%) and CADCZ (14.58%). Genotyping in Eastern-Europeans (n = 1792) revealed hypervariable nature of this locus, represented by seven alternative alleles. The alignments of human-chimpanzee-macaque sequences showed that the major human variant (allele frequency 90.45%) was actually a human-specific deletion compared to other primates. In humans, this deletion was surrounded by other short (5-43 bp) deletion variants and a duplication (40 bp) polymorphism possessing overlapping breakpoints. This indicates a potential indel hotspot, triggered by the initial deletion in human lineage. An association was detected between the carrier status of 14 bp indel ancestral allele and CAD (P = 0.0016, OR = 2.02; Bonferroni significance level alpha = 0.0045), but not with hypertension. The risk for the CAD development was even higher among the patients additionally diagnosed with metabolic syndrome (P = 0.0014, OR = 2.34). Consistent with the effect on metabolic processes, suggestive evidence for the association with heart rate, serum triglyceride and LDL levels was detected (P = 0.04).

Conclusions

Compared to SNPs targeted by large number of locus-specific and genome-wide assays, considerably less attention has been paid to short indel variants in the human genome. The data of genome dynamics, mutation rate and population genetics of short indels, as well as their impact on gene expressional profile and human disease susceptibility is limited. The characterization of NCX1 intronic hypervariable non-coding region enriched in human-specific indel variants contributes to this gap of knowledge.     

Craniosynostosis in a patient with a de novo 15q15-q22 deletion

Interstitial deletions involving the chromosomal band 15q15 are very rare. A total of five cases were previously reported. Here another case of a 15q15.2-q22.2 deletion is reported, presenting with severe craniosynostosis of coronary, metopic, and sagittal sutures. The chromosome 15 with the 17.7-Mb deletion was of the paternal origin. A critical region for craniosynostosis may be located at the 734-kb segment at 15q15.2. Interestingly, the entire FBN1 gene was deleted in this patient.     

De novo deletion of chromosome 18q in a baby with harlequin ichthyosis

Harlequin ichthyosis, (MIM 242500), is a rare, autosomal recessive skin disorder due to an inborn error of epidermal keratinization. The gene for this condition has not been localized. We present a case of HI in which there was a de novo deletion of chromosome 18q: the karyotype was 46, XY, del(18)(q21.3). We postulate that the gene for HI may lie at, or distal to 18q21.3 and that the deletion observed in this case may have unmasked this autosomal recessive disorder.     

Clinical features in a de novo interstitial deletion 15q13 to q15

A boy with several dysmorphic features and suffering from mental and motor retardation was found to have a de novo interstitial deletion of chromosome 15, involving bands q13 to q15. His clinical picture is described and compared with the clinical features reported in other deletions of this chromosome, located or extending distally from the region associated with Prader-Willi syndrome.     

Multiple congenital anomalies and developmental delay in a boy associated with a de novo 16p13.3 deletion

We describe a patient with multiple congenital anomalies including tracheobronchomalacia, CT-proven metopic craniosynostosis, glandular hypospadias and severe ventral chordee, torticollis, esotropia, strabismus, fifth finger clinodactyly, hallux valgus, and global developmental delay. Using high resolution chromosomal microarray analysis, we identified a de novo deletion of 555 kb on chromosome 16p13.3, 444 kb telomeric to the CREBBP gene and 623 kb centromeric of PKD1. Review of the literature revealed numerous reports of individuals with deletions involving adjacent regions including CREBBP, but only one overlapping with this isolated region of 16p13.3. Haploinsufficiency for one or more of the 25 candidate genes in the deleted genomic region may be responsible for these clinical features. No copy number variants (CNVs) span the entire region, but several small CNVs within the 555 kb genomic region reduce the likelihood for effects due to haploinsufficiency to 18 genes.     

De novo 21q interstitial deletion in a retarded boy with ulno-fibular dysostosis

A 9-year-old boy was referred for evaluation of multiple anomalies and mental retardation. Skeletal abnormalities had been noted at birth: joint contractures, right acetabular "dysplasia," ulno-fibular dysostosis, and bilateral talipes equinovarus with calcaneocuboid fusion. Additional findings at 9 years included short stature, unusual facial appearance, camptodactyly of several digits, undescended testes, and syndactyly of toes 4 and 5. On psychological testing he was found to be moderately retarded. Cytogenetic analysis of chromosome bands using Q, GTG, R, and C banding showed an interstitial deletion of 21q; karyotype designation: 46,XY, del (21)(pter----q11.2::q22.1----qter). Parental chromosomes were normal. Manifestations in this boy, including the joint contractures, are similar to those described in the monosomy 21 syndrome. Ulno-fibular dysostosis has not been reported previously with abnormalities of chromosome 21. To our knowledge, this is the second patient reported with an interstitial deletion of chromosome 21, and the patients are phenotypically dissimilar.     

Coarctation of the aorta and mild to moderate developmental delay in a child with a de novo deletion of chromosome 15(q21.1q22.2)

Background  

Deletion of 15q21q22 is a rare chromosomal anomaly. To date, there have been nine reports describing ten individuals with different segmental losses involving 15q21 and 15q22. Many of these individuals have common features of growth retardation, hypotonia and moderate to severe mental retardation. Congenital heart disease has been described in three individuals with interstitial deletion involving this region of chromosome 15.