Marybeth Hummel

A copy number variation morbidity map of developmental delay

To understand the genetic heterogeneity underlying developmental delay, we compared copy number variants (CNVs) in 15,767 children with intellectual disability and various congenital defects (cases) to CNVs in 8,329 unaffected adult controls. We estimate that ∼14.2% of disease in these children is caused by CNVs >400 kb. We observed a greater enrichment of CNVs in individuals with craniofacial anomalies and cardiovascular defects compared to those with epilepsy or autism. We identified 59 pathogenic CNVs, including 14 new or previously weakly supported candidates, refined the critical interval for several genomic disorders, such as the 17q21.31 microdeletion syndrome, and identified 940 candidate dosage-sensitive genes. We also developed methods to opportunistically discover small, disruptive CNVs within the large and growing diagnostic array datasets. This evolving CNV morbidity map, combined with exome and genome sequencing, will be critical for deciphering the genetic basis of developmental delay, intellectual disability and autism spectrum disorders.

22q11.2 Distal Deletion: A Recurrent Genomic Disorder Distinct from DiGeorge Syndrome and Velocardiofacial Syndrome

Microdeletions within chromosome 22q11.2 cause a variable phenotype, including DiGeorge syndrome (DGS) and velocardiofacial syndrome (VCFS). About 97% of patients with DGS/VCFS have either a common recurrent approximately 3 Mb deletion or a smaller, less common, approximately 1.5 Mb nested deletion. Both deletions apparently occur as a result of homologous recombination between nonallelic flanking low-copy repeat (LCR) sequences located in 22q11.2. Interestingly, although eight different LCRs are located in proximal 22q, only a few cases of atypical deletions utilizing alternative LCRs have been described. Using array-based comparative genomic hybridization (CGH) analysis, we have detected six unrelated cases of deletions that are within 22q11.2 and are located distal to the approximately 3 Mb common deletion region. Further analyses revealed that the rearrangements had clustered breakpoints and either a approximately 1.4 Mb or approximately 2.1 Mb recurrent deletion flanked proximally by LCR22-4 and distally by either LCR22-5 or LCR22-6, respectively. Parental fluorescence in situ hybridization (FISH) analyses revealed that none of the available parents (11 out of 12 were available) had the deletion, indicating de novo events. All patients presented with characteristic facial dysmorphic features. A history of prematurity, prenatal and postnatal growth delay, developmental delay, and mild skeletal abnormalities was prevalent among the patients. Two patients were found to have a cardiovascular malformation, one had truncus arteriosus, and another had a bicuspid aortic valve. A single patient had a cleft palate. We conclude that distal deletions of chromosome 22q11.2 between LCR22-4 and LCR22-6, although they share some characteristic features with DGS/VCFS, represent a novel genomic disorder distinct genomically and clinically from the well-known DGS/VCF deletion syndromes.

Molecular and phenotypic characterization of ring chromosome 22.

We performed a phenotype study of 35 individuals (19 males, 16 females) with ring chromosome 22 or r(22) with a mean age of 10 years. In common with other studies, a phenotype of moderate‐to‐profound learning difficulties and delay or absence of speech affected all individuals with the exception of the case with the smallest deletion. Autistic traits were significantly associated with r(22), as shown by an autism screening questionnaire. Mild and variable dysmorphic features, predominantly craniofacial and distal limb, were observed. Internal organ involvement was uncommon. Even though ring chromosomes are reportedly associated with growth abnormalities, only 2 out of 24 individuals showed evidence of growth failure, while 2 showed accelerated growth. Chromosome 22 long arm deletions, as determined by hemizygosity for informative microsatellite markers, varied from <67 kb to 10.2 Mb in size (or <0.15 to 21% of total chromosome length), with no significant differences in the parental origin of the ring chromosome. Few phenotypic features correlated with deletion size suggesting a critical gene, or genes, of major effect lies close to the telomere. Loss of the SHANK3/PROSAP2 gene has been proposed to be responsible for the main neurological developmental deficits observed in 22q13 monosomies. This study supports this candidate gene by identifying a phenotypically normal r(22) individual whose ring chromosome does not disrupt SHANK3. All other r(22) individuals were hemizygous for SHANK3, and we propose it to be a candidate gene for autism or abnormal brain development.

Left-sided CHILD syndrome caused by a nonsense mutation in the NSDHL gene

Congenital hemidysplasia with ichthyosiform nevus and limb defects (CHILD) syndrome is a rare X‐linked dominant malformation syndrome characterized by unilaterally distributed ichthyosiform nevi, often sharply delimited at the midline, and ipsilateral limb defects. At least two‐thirds of cases demonstrate involvement of the right side. Mutations in an essential enzyme of cholesterol biosynthesis, NAD(P)H steroid dehydrogenase‐like [NSDHL], have been reported in five unrelated patients with right‐sided CHILD syndrome and in a sixth patient with bilaterally, symmetric nevi and mild skeletal anomalies, but not with CHILD syndrome as originally defined. Although all of the molecularly diagnosed cases with the CHILD phenotype to date have had right‐sided disease, we report here a novel nonsense mutation (E151X) of NSDHL in an infant with left‐sided CHILD syndrome. This result demonstrates that both right‐ and left‐sided CHILD syndrome can be caused by mutations in the same gene.

Molecular characterization of an 11q interstitial deletion in a patient with the clinical features of jacobsen syndrome

The 11q terminal deletion disorder or Jacobsen syndrome is a contiguous gene disorder. It is characterized by psychomotor retardation, cardiac defects, blood dyscrasias (Paris‐Trousseau syndrome) and craniofacial anomalies. We report on a female patient with an approximately 10 Mb interstitial deletion with many of the features of Jacobsen syndrome: A congenital heart defect, dysmorphic features, developmental delay, and Paris‐Trousseau syndrome. The karyotype of the patient is 46,XX,del(11)(q24.1q24.3). The interstitial deletion was confirmed using FISH probes for distal 11q, and the breakpoints were characterized by microarray analysis. This is the first molecularly characterized interstitial deletion in a patient with the clinical features of Jacobsen syndrome. The deletion includes FLI‐1, but not JAM‐3, which will help to determine the critical genes involved in this syndrome.

Familial recurrence of SOX2 anophthalmia syndrome: Phenotypically normal mother with two affected daughters†

The SOX2 anophthalmia syndrome is emerging as a clinically recognizable disorder that has been identified in 10–15% of individuals with bilateral anophthalmia. Extra‐ocular anomalies are common. The majority of SOX2 mutations identified appear to arise de novo in probands ascertained through the presence of anophthalmia or microphthalmia. In this report, we describe two sisters with bilateral anophthalmia/microphthalmia, brain anomalies and a novel heterozygous SOX2 gene single‐base pair nucleotide deletion, c.551delC, which predicts p.Pro184ArgfsX19. The hypothetical protein product is predicted to lead to haploinsufficient SOX2 function. Mosaicism for this mutation in the SOX2 gene was also identified in their clinically unaffected mother in peripheral blood DNA. Thus it cannot be assumed that all SOX2 mutations in individuals with anophthalmia/microphthalmia are de novo. Testing of parents is indicated when a SOX2 mutation is identified in a proband.

Mosaic ring 12p and total anomalous pulmonary venous return

An infant born with total anomalous pulmonary venous return (TAPVR) was found to have an extra chromosome present as a small ring. Spectral karyotyping and FISH analysis identified the material as a duplication involving the short arm of chromosome 12. Previous cases describing a variety of cytogenetic abnormalities that have been associated with TAPVR are reviewed along with prior cases of duplication 12p with their associated findings. We believe ours is the first case to report the occurrence of mosaic ring 12p and its association with TAPVR.

Prenatal diagnosis of tetrasomy 9p

Dhandha et al. [2002] report three cases of tetrasomy 9p andprovide a useful and interesting case review from the literature. Tetrasomy 9p is a rare clinical syndrome with only 32 cases reported to date, with reports of both mosaic and non-mosaic cases. The phenotypic differences of tetrasomy 9p seem to be the result of the degree of mosaicism. We recently identified a patient with tetrasomy 9p diagnosed prenatally and report our findings here. The mother was a 22-year-old gravida 1 para 0 white woman.During the pregnancy,multiple fetal anomalies were identified by repeated ultrasounds, as early as 22 weeks of gestation. These fetal anomalies included a strawberry shaped skull, mildly enlarged fetal ventricles, bilateral cleft lip and palate, a small-sized stomach, a possible horseshoe kidney, and rockerbottom deformityof the footand/or clubfeet.Alsonotedwaspersistent abnormal posturing of the fetal fists with overlapping of the fetal digits. Amniocentesis was performed at 24weeks of gestation,which showed47,XX,þi(9)(p10) in 20 cells. The isochromosome was confirmed as chromosome 9 by FISH. The patient was born by induced labor at 3557-week gestation due to premature rupture of membranes. The infant was a female weighing 1,730 g, 41 cm long, with occipital frontal circumference (OFC) of 28.5 cmat birth. Apgar scores were 1 and 6 at 1 and 5 min, respectively. Physical examination at birth revealed strawberryshaped head, downslanting palpebral fissures, large anterior fontanel, hypertelorism, bilateral small low-set ears, micrognathia, beaked nose, bilateral cleft lip and cleft palate, brachydactyly with hypoplastic thumb, and bilateral foot deformities with eversion. The patient was also found to have patent foramen ovale, bicuspid aortic valve, and patent ductus arteriosus. At 33 days of age, the patient died of aspiration pneumonitis with respiratory distress. Ultrasound and MRI of the head were performed postnatally, and diagnoses of hydrocephalus, ventriculomegaly with left ventricle being larger in size than the right one, agenesis of the corpus callosum, and Dandy– Walker variantweremade. The above physical findings, along with ventriculomegaly, Dandy–Walker variant, and horseshoe kidney detected by ultrasound, are consistent with the emerging phenotype for tetrasomy 9p, summarized by Dhandha et al. [2002]. Karyotyping from amniocentesis confirmed our case as tetrasomy 9p. Chromosomal analysis was also performed on peripheral blood lymphocytes and cord fibroblasts of the infant at birth.All but one of the 20 cells from lymphocytes, and all but three of the 20 cells from fibroblasts, showed identicalkaryotypeasheramniocytes, 47,XX,þi(9)(p10). The one cell from lymphocytes and three cells from fibroblasts analyzed showed anormal female karyotype, suggesting low level of mosaicism. In our patient, we were able to analyze three different tissues, and found low level of mosaicism in two of the three cell types. No early deaths are reported for mosaic cases of tetrasomy 9p. The level of mosaicism seen in our case at birth was very low. Considering that all of her amniocytes analyzed had an abnormal karyotype, this could represent a non-mosaic case of tetrasomy 9p in the fetus, and thus account for the early death in our patient.

Trisomy 8 mosaicism: Selective growth advantage of normal cells vs. growth disadvantage of trisomy 8 cells

A fetus with trisomy 8 mosaicism was identified prenatally due to an abnormal maternal serum triple screen. Tissue samples were taken at birth to determine the level of trisomy 8 mosaicism found within embryonic and extra‐embryonic tissues, rates of cell division for the two cell lines, and the effect of mosaicism on the phenotype. The level of trisomy 8 cells in blood and fibroblasts was higher than in placental tissue. Cell cycle kinetics, by incorporation of bromodeoxyuridine for 48 hr, was not significantly different between the trisomy 8 and normal cells for blood or amnion. Fluorescent in situ hybridization (FISH) using centromeric probe for chromosome 8 showed significantly more trisomy 8 in interphase vs. metaphase in lymphoblasts, umbilical cord fibroblasts, and chorion. The loss of trisomy 8 cells is not due to anaphase lag, as determined by micronuclei analysis. The similarity of cell cycle kinetics between trisomy 8 cells and normal diploid cells suggests some trisomy 8 cells are exiting the cell cycle prematurely. This growth disadvantage of trisomy 8 cells results in the appearance of growth advantage for diploid cells.

Newborn infant with inherited ring and de novo interstitial deletion on homologous chromosome 22s

A 2-day-old infant was evaluated and suspected of having 22q11.2 deletion based on microcephaly, short and narrow palpebral fissures, a prominent nose with hypoplastic alae nasi, thin fingers, and a right aortic arch. He also had an imperforate anus, which is not in the del 22q11.2 syndrome. Karyotype analysis identified a ring 22, while fluorescence in situ hybridization (FISH) for the DiGeorge syndrome critical region identified a 22q deletion on the other homologue. The karyotype designation was 46,XY,r(22)(p13q13.3).ish del(22)(q11.2q11.2) (D22S75-). Both parents function in the mildly mentally retarded range. The fathers karyotype was normal whereas the mother had the ring 22 that was inherited by her son. This is the first case reported for abnormalities on both 22 homologues.