Interstitial deletion of chromosome 15: two cases

Prenatal diagnosis of a 15q24.1 microdeletion in a fetus with cerebral and urogenital abnormalities

15q24.1 microdeletion syndrome is a recently described condition often resulting from non-allelic homologous recombination (NAHR). Typical clinical features include pre and post-natal growth retardation, facial dysmorphism, developmental delay and intellectual disability. Nonspecific urogenital, skeletal, and digit abnormalities may be present, although other congenital malformations are less frequent. Consequently, only one case was reported prenatally, complicating the genotype-phenotype correlation and the genetic counseling. We identified prenatally a second case, presenting with cerebral abnormalities including hydrocephaly, macrocephaly, cerebellum hypoplasia, vermis hypoplasia, rhombencephalosynapsis, right kidney agenesis with left kidney duplication and micropenis. Genome-wide aCGH assay allowed a diagnosis at 26 weeks of amenorrhea revealing a 1.6 Mb interstitial deletion on the long arm of chromosome 15 at 15q24.1-q24.2 (arr[GRCh37] 15q24.1q24.2(74,399,112_76,019,966)x1). A deep review of the literature was undertaken to further delineate the prenatal clinical features and the candidate genes involved in the phenotype. Cerebral malformations are typically nonspecific, but microcephaly appears to be the most frequent in postnatal cases. Our case is the first reported with a frank cerebellar involvement.

CHD2-Related CNS Pathologies

Epileptic encephalopathies (EE) are severe epilepsy syndromes characterized by multiple seizure types, developmental delay and even regression. This class of disorders are increasingly being identified as resulting from de novo genetic mutations including many identified mutations in the family of chromodomain helicase DNA binding (CHD) proteins. In particular, several de novo pathogenic mutations have been identified in the gene encoding chromodomain helicase DNA binding protein 2 (CHD2), a member of the sucrose nonfermenting (SNF-2) protein family of epigenetic regulators. These mutations in the CHD2 gene are causative of early onset epileptic encephalopathy, abnormal brain function, and intellectual disability. Our understanding of the mechanisms by which modification or loss of CHD2 cause this condition remains poorly understood. Here, we review what is known and still to be elucidated as regards the structure and function of CHD2 and how its dysregulation leads to a highly variable range of phenotypic presentations.

Witteveen-Kolk syndrome: The first patient from Turkey

Witteveen-Kolk syndrome is a rare genetic disorder characterized by intellectual disability, developmental delay and dysmorphic facial features including a long face with prominent forehead, depressed nasal bridge, long-smooth philtrum and malformed ears. Skeletal abnormalities, microcephaly and malformation of the brain are other findings. This syndrome is caused by mutations in the SIN3A gene or microdeletions encompassing this gene. The protein encoded by SIN3A gene plays a regulatory role in the control of various developmental processes, especially cortical expansion and maturation. To date, 17 patients have been reported in the medical literature. In this article, we reported a patient with Witteveen-Kolk syndrome who had a retrognathia as an unusually finding. To the best of our knowledge, this is the first patient of Witteveen-Kolk syndrome reported from Turkey.

Coexistence of urogenital malformations in a female fetus with de novo 15q24 microdeletion and a literature review

Background

15q24 microdeletion is a relatively new syndrome caused by nonallelic homologous recombination (NAHR) between low‐copy repeats (LCRs) in the 15q24 chromosome region. This syndrome is characterized by a spectrum of clinical symptoms including global developmental delay, intellectual disability, facial dysmorphisms, and congenital malformations of the extremities, eye, gastrointestinal tract, genitourinary system, and genitalia.

Method

Molecular cytogenetic analysis was performed using whole genome single‐nucleotide polymorphism (SNP) microarray analysis. Autopsy examination including gross and microscopic examination were performed. In addition, a thorough review of the literature on 15q24 microdeletion was completed and summarized in table format.

Result

Molecular cytogenetic analysis revealed a 3.88 MB interstitial deletion within 15q24.1 to 15q24.3 (74,353,735–78,228,485 bp) in our case. Autopsy examination showed congenital malformations within the genitourinary system and genitalia, including left kidney agenesis and uterus didelphys. After thorough literature review, we found a series of midline defects associated with 15q24 microdeletion syndrome.

Conclusion

We report the first case of coexistence of urogenital abnormalities, including left kidney agenesis and uterus didelphys, with 15q24 microdeletion syndrome, which is also associated with midline defects secondary to abnormal development. Since 15q24 microdeletion syndrome is a relatively new entity, fully characterizing its variation and severity requires additional examination of the genetics, molecular profile and structural and functional abnormalities in affected patients. Due to the limited data in the literature, statistical analysis of abnormalities in each organ system is not possible. However, we can predict that novel genetic pathways involving cell migration, adhesion, apoptosis, and embryo development might be discovered with the advanced study of 15q24 microdeletion syndrome.

Clinical and molecular characterization of a patient with 15q21.2q22.2 deletion syndrome

We report on a 16-year-old girl with a complex phenotype, including intellectual disability, facial dysmorphisms, and obesity. During her infancy, she presented with weak sucking, global developmental delay, and later with excessive eating with central obesity. The girl was clinically diagnosed with probable Prader-Willi syndrome. Chromosomal analysis showed a de novo deletion 46,XX,del(15)(q21q22). However, the use of the Affymetrix CytoScan HD Array defined the exact breakpoints of the deleted 15q21q22 region. The imbalance, about 10.5 Mb in size, is to date the second largest deletion ever described in this chromosomal region. In addition, our patient carries a microdeletion in the 1q44 region and a gain in 9p24. The array result was arr[hg19] 9p24.1(6,619,823-6,749,335)×3, 1q44(248,688,586-248,795,277)×1, 15q21.2 q22.2(50,848,301-61,298,006)×1. Although our patient presents additional chromosomal alterations, we provide a correlation between the clinical findings and the phenotype of the 15q21 deletion syndrome.

De novointerstitial deletion of 15q22q23 with global developmental delay and hypotonia: the first Korean case

Interstitial deletions involving the chromosome band 15q22q24 are very rare and only nine cases have been previously reported. Here, we report on a 12-day-old patient with a de novo 15q22q23 interstitial deletion. He was born by elective cesarean section with a birth weight of 3,120 g at 41.3-week gestation. He presented with hypotonia, sensory and neural hearing loss, dysmorphism with frontal bossing, flat nasal bridge, microretrognathia with normal palate and uvula, thin upper lip in an inverted V-shape, a midline sacral dimple, severe calcanovalgus at admission, and severe global developmental delay at 18 months of age. Fluorescence in situ hybridization findings confirmed that the deleted regions contained at least 15q22. The chromosome analysis revealed a karyotype of 46,XY,del(15) (q22q23). Parental chromosome analysis was performed and results were normal. After reviewing the limited literature on interstitial 15q deletions, we believe that the presented case is the first description of mapping of an interstitial deletion involving the chromosome 15q22q23 segment in Korea. This report adds to the knowledge of the clinical phenotype associated with the 15q22q23 deletion.

Phenotype-genotype correlation of a patient with a "balanced" translocation 9;15 and cryptic 9q34 duplication and 15q21q25 deletion

We report on a 2-year-old boy with intellectual disabilities, distinctive facies, hypotonia, cardiac, and renal malformations. During his infancy he had recurrent episodes of apnea, cyanosis, and bradycardia. Chromosomal analysis showed a de novo apparently balanced translocation 46,XY,t(9;15)(q31;q26)dn. The use of array-comparative genomic hybridization (CGH) however, revealed the presence of additional cryptic complex chromosomal rearrangements involving a approximately 5-5.8 Mb distal duplication on chromosome 9 (9q34.1 --> 9q34.3), and deletions on three separate regions of chromosome 15 adding to approximately 8.1-12.2 Mb (15q21.2 --> 15q21.3, 15q22.31 --> 15q23, 15q25.1 --> 15q25.2). During confirmation with fluorescence in situ hybridization (FISH) an inversion was unexpectedly revealed on chromosome 15 (15q21.1 --> 15q21.2). To our knowledge this is the first patient reported whose phenotype is due to partial trisomy 9q, and complex interstitial deletions of 15q, not involving the Prader-Willi/Angelman region and encompassing the critical region 15q21q25. We provide correlation between the clinical findings of our patient and the phenotype of the 9q34 duplication syndrome, the 15q21, and the 15q25 deletion syndromes.

Genotype-phenotype correlation in four 15q24 deleted patients identified by array-CGH

Microdeletion 15q24 is an emerging syndrome recently described, mainly due to increased use of array-CGH. Clinical features associate mild to moderate developmental delay, typical facial characteristics (high forehead and frontal hairline, broad eyebrows, downslanting palpebral features, long philtrum), hands (particularly proximal implanted thumbs) and genital anomalies (micropenis, hypospadias). We report here on four de novo cases having 2.5-6.1 Mb deletions involving 15q24: one 15q23q24.2 (Patient 1) and three 15q24.1q24.2 deletions (Patients 2-4). We correlate phenotype to genotype according to molecular boundaries of these deletions. Since bilateral iris coloboma and severe ano-rectal malformation were only present in Patient 1, we could link these anomalies to haploinsufficiency of 15q23 genes. Neither hypospadias nor micropenis were present in Patient 3 bearing the smallest deletion, therefore we could define 500 kb 15q24.1 region linked to these anomalies.

Redefined genomic architecture in 15q24 directed by patient deletion/duplication breakpoint mapping

We report four new patients with a submicroscopic deletion in 15q24 manifesting developmental delay, short stature, hypotonia, digital abnormalities, joint laxity, genital abnormalities, and characteristic facial features. These clinical features are shared with six recently reported patients with a 15q24 microdeletion, supporting the notion that this is a recognizable syndrome. We describe a case of an ~2.6 Mb microduplication involving a portion of the minimal deletion critical region in a 15-year-old male with short stature, mild mental retardation, attention deficit hyperactivity disorder, Asperger syndrome, decreased joint mobility, digital abnormalities, and characteristic facial features. Some of these features are shared with a recently reported case with a 15q24 microduplication involving the minimal deletion critical region. We also report two siblings and their mother with duplication adjacent and distal to this region exhibiting mild developmental delay, hypotonia, tapering fingers, characteristic facial features, and prominent ears. The deletion and duplication breakpoints were mapped by array comparative genomic hybridization and the genomic structure in 15q24 was analyzed further. Surprisingly, in addition to the previously recognized three low-copy repeat clusters (BP1, BP2, and BP3), we identified two other paralogous low-copy repeat clusters that likely mediated the formation of alternative sized 15q24 genomic rearrangements via non-allelic homologous recombination.

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 7.18Mb 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 further case of the recurrent 15q24 microdeletion syndrome, detected by array CGH

We report on a 10-year-old patient with developmental delay, craniofacial dysmorphism, digital and genital abnormalities. In addition, muscular hypotonia, strabism, and splenomegaly were observed; inguinal and umbilical hernias were surgically corrected. Mucopolysaccharidoses and CDG syndromes could not be found. Chromosome analysis revealed a normal male karyotype (46,XY). A more detailed investigation of the patient's genomic DNA by microarray-based comparative genomic hybridization (array CGH) detected an interstitial 3.7 Mb deletion ranging from 15q24.1 to 15q24.3 which was shown to be de novo. Interstitial deletions involving 15q24 are rare. Sharp et al. (Hum Mol Genet 16:567-572, 2007) recently characterized a recurrent 15q24 microdeletion syndrome with breakpoints in regions of segmental duplications. The de novo microdeletion described here colocalizes with the minimal deletion region of the 15q24 microdeletion syndrome. The distinct clinical phenotype associated with this novel microdeletion syndrome is similar to the phenotype of our patient with respect to specific facial features, developmental delay, microcephaly, digital abnormalities, and genital abnormalities in males. We present a genotype-phenotype correlation and comparison with patients from the literature.

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.

Disruption of chromodomain helicase DNA binding protein 2 (CHD2) causes scoliosis

Herein we characterize an apparently balanced de novo translocation, t(X;15)(p22.2;q26.1)dn, in a female patient with scoliosis, hirsutism, learning problems, and developmental delay (DGAP025). Other clinical findings include a high-arched palate, 2-3 syndactyly of the toes, and mildly elevated serum testosterone. No known or predicted genes are disrupted by the Xp22.2 breakpoint. The 15q26.1 breakpoint disrupts chromodomain helicase DNA binding protein 2 (CHD2). Another member of the chromatin-remodeling gene family, CHD7, has been associated with a defined constellation of congenital anomalies known as coloboma, heart anomaly, choanal atresia, mental retardation, genital and ear anomalies syndrome (CHARGE) and idiopathic scoliosis. Monosomy of 15q26 also has been associated with a spectrum of congenital abnormalities and growth retardation that overlaps with those of DGAP025. To provide a biological correlate, we characterized a mutant mouse model with Chd2 disruption that is associated with embryonic and perinatal lethality. Expression analysis indicated that Chd2 is expressed in the heart, forebrain, extremities, facial and dorsal regions during specific times of embryonic development. Chd2(+/m) mice showed pronounced lordokyphosis, reduced body fat, postnatal runting, and growth retardation. These data suggest that haploinsufficiency for CHD2 could result in a complex of abnormal human phenotypes that includes scoliosis and possibly features similar to CHARGE syndrome.

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.

Case presentation

We report a child with coarctation of the aorta, partial agenesis of corpus callosum and mild to moderate developmental delay, with a de novo deletion of 15q21.1q22.2, detected by the array Comparative Genomic Hybridization (CGH). We utilized chromosome 15-specific microarray-based CGH to define the chromosomal breakpoints in this patient.

Conclusion

This is the first description of mapping of an interstitial deletion involving the chromosome 15q21q22 segment using the chromosome 15-specific array-CGH. The report also expands the spectrum of clinical phenotype associated with 15q21q22 deletion.

A report of three patients with an interstitial deletion of chromosome 15q24

Partial monosomy of the q2 region of chromosome 15 has been infrequently reported. Moreover, interstitial deletions involving 15q22-q24 have been described in only nine patients to date. The phenotype of these reported individuals is subject to the extent of the deletion but typically includes altered muscle tone and significant developmental delays. In addition, eye abnormalities, such as strabismus, microphthalmia, or colobomas, ear abnormalities including cleft earlobe and preauricular tags, and urogenital defects are common features. Congenital heart defects, diaphragmatic hernia, abnormalities of the central nervous system, and skeletal anomalies have been reported but appear to be less frequent clinical manifestations. In this report, we describe three new patients with interstitial deletions involving 15q24, two with cryptic deletions identified by fluorescence in situ hybridization (FISH) with a probe for the PML gene and one with a cytogenetically visible deletion of 15q22.3-q24. The clinical presentation of these individuals is similar to those previously described and includes global developmental delays, hypotonia, and genital abnormalities in the males. The identification of these three cases demonstrates that the above clinical features are associated with a new cytogenetic deletion syndrome. Furthermore, we suggest that FISH analysis with a probe for the PML gene be performed in patients with these physical findings.

Craniosynostosis and congenital heart anomalies associated with a maternal deletion of 15q15-22.1

We report an infant with multiple congenital anomalies, including craniosynostosis, tetralogy of Fallot variant, and limb anomalies associated with a maternal deletion of 15q15-22.1. Only two other patients have been reported with a similar deletion, but the deletion was paternal in both cases. We review our patient's findings and compare them to previously reported individuals with similar 15q abnormalities. Our patient allows an expansion of phenotype associated with mid-15q deletions to include severe craniosynostosis, congenital heart disease, and limb anomalies. This will assist in prenatal counseling and predicting postnatal outcome for other affected individuals. The specific breakpoints in our patient and the other patients with similar deletions may also assist in determining a critical region for suture formation.

Postnatal overgrowth by 15q-trisomy and intrauterine growth retardation by 15q-monosomy due to familial translocation t(13;15): dosage effect of IGF1R?

We report a 4-year-old boy, a 6-month-old girl, and a 17-week-old fetus all with a chromosomal imbalance derived from a balanced translocation t(13;15)(q34;q26.1) of their father. The boy had a partial trisomy for 15q26.1-qter (46,XY,der(13)t(13;15)(q34;q26.1)) and postnatal overgrowth, as well as craniosynostosis, facial anomalies, and finger joint contractures, while the girl with the same chromosomal aberration did not show overgrowth, although she had similar craniofacial and skeletal abnormalities. The fetus had a partial monosomy for 15q26.1-qter and intrauterine growth retardation (IUGR). Fluorescence in situ hybridization (FISH) analysis with a BAC clone covering the insulin-like growth factor 1 receptor gene (IGF1R) that is located to 15q25-q26 revealed three copies in the boy, one copy in the fetus, and two copies in their phenotypically normal father. Since deletion of IGF1Rhas repeatedly been reported to be associated with IUGR, it is tempting to speculate that the dosage of IGF1R may have determined growth in these children.

Deletion 15q24-26 in prenatally detected diaphragmatic hernia: increasing evidence of a candidate region for diaphragmatic development

Survival of children with congenital diaphragmatic hernia (CDH) is mainly dependent on the extent of lung hypoplasia and the presence of additional congenital anomalies or chromosomal aberrations. A chromosomal deletion 15q25-q26.2 in a fetus with prenatally diagnosed CDH and growth retardation is reported. Despite optimal pre- and neonatal management the baby died shortly after birth. There is increasing evidence that the long arm of chromosome 15, and especially the region 15q24 to 15q26, plays a crucial role in the development of the diaphragm. The finding of a deletion within 15q24-26 in a fetus with CDH has to be considered a predictor of poor prognosis. It is of utmost interest for proper parental counselling to search in fetuses with CDH for subtle chromosomal lesions paying special attention to chromosome 15q.

Partial trisomy 8q and partial monosomy 15q associated with congenital hydrocephalus, diaphragmatic hernia, urinary tract anomalies, congenital heart defect and kyphoscoliosis

We describe perinatal findings in a female fetus with partial trisomy 8q(8q24.1-->8qter) and partial monosomy 15q(15q26.1-->15qter) resulting from a paternal t(8;15) reciprocal translocation. Prenatal sonographic examination showed intra-uterine growth retardation, bilateral ventriculomegaly, cardiomegaly with arrhythmia, anhydramnios, and absent kidney and urinary bladder images. The pregnancy was terminated at 28 weeks of gestation. At birth, the infant manifested typical dysmorphic features of partial trisomy 8q. Necropsy further revealed hydrocephalus, congenital diaphragmatic hernia, ventricular septal defect, a horseshoe kidney with renal hypoplasia, and kyphoscoliosis. Our case shows that the coexistence of partial trisomy 8q24.1-->8qter and partial monosomy 15q26.1-->15qter are more detrimental than either defect alone and can result in a complex of major malformations. Prenatal ultrasound examination and cytogenetic assessment should be offered in subsequent pregnancies.

Brachydactyly in a child with duplication-deficiency subsequent to t(15;20)(q25.2;p12.2)mat. Candidate regions on one or both chromosomes?

We report a child with a duplication-deficiency subsequent to t(15;20)(q25.2;p12.2), transmitted in at least 5 generations, who showed features of 15q- syndrome. We speculate that brachydactyly--most likely because of brachymesophalangism--is a feature of the phenotype of this chromosomal aberration and points to candidate gene(s) in this region. A similar brachydactyly was, however, reported with dup(20p1-pter).

A de novo interstitial deletion of chromosome 15 band q25 as revealed by FISH-technique

We report a new chromosomal finding in a 20 month-old girl. The minor clinical features included: moderate mental retardation, microcephaly, mild hypotonia and hypertelorism. Initially, what appeared to be a terminal deletion of the long arm of one chromosome 15 [15q26-->qter] was determined to be an interstitial deletion involving band 15q25 as revealed by FISH-technique, showing the presence of intact telomeric hybridization signals. The cytogenetic diagnosis was thus modified to 46,XX, del (15) (pter-->q24::q26--> qter). Nevertheless, the function of the enzyme telomerase should not be ignored, as healing could occur following such terminal deletions. Consequently, it will remain a difficult task to distinguish terminal deletions from those that are interstitial.

Cytogenetic and molecular cytogenetic studies of a case of interstitial deletion of proximal 15q

A 4-month-old child with multiple anomalies was determined to have an interstitial deletion of chromosome 15, i.e., del(15) (q12q14). The deletion appears not to be a typical deletion of 15q12 such as seen in Angelman and Prader-Willi syndromes, but appears to be more distal, involving either loss of all of 15q12 and part of 15q14, or part of 15q12 and most of 15q14. In either case, 15q13 is missing. Fluorescent in situ hybridization with probes for 15 centromere (D15Z), pericentromeric satellite sequences (D15Z1), and chromosome 15 painting probes shows the deleted chromosome to involve only 15 and no other acrocentric chromosome. Hybridization with probes for the AS and PWS loci (D15S11 and GABAB3, Oncor) show both sites to be intact in the deleted 15. The case is compared with two other reports with overlapping interstitial deletions of proximal 15q, neither of which shows typical features of Angelman or Prader-Willi syndromes.

An infant with deletion of the distal long arm of chromosome 15 (q26.1----qter) and loss of insulin-like growth factor 1 receptor gene

We report on an infant with a previously undescribed chromosome 15 deletion (q26.1----qter) and compare the clinical findings with those of 7 reported patients with deletions of distal 15q, as well as ring chromosome 15 syndrome patients. Most of the patients with deletions of distal 15q, including our patient, have intrauterine growth retardation (IUGR), microcephaly, abnormal face and ears, micrognathia, highly arched palate, renal abnormalities, lung hypoplasia, failure to thrive, and developmental delay/mental retardation. Several genes have been assigned to the 15q25----qter region, including insulin-like growth factor 1 receptor (IGF1R). DNA analysis from our patient documented the loss of one IGF1R gene copy. Our study further localizes the IGF1R gene distal to the 15q26.1 band. It is interesting to speculate that the severe IUGR and postnatal growth deficiency of our patient and other patients with similar chromosome 15 deletions are related to the loss of an IGF1R gene copy which may lead to an abnormal number and/or structure of the receptors.

A de novo interstitial deletion of 15(q21.2q22.1) in a moderately retarded adult male

An adult male is described with a de novo deletion 15q21.2-q22.1. He shares some minor dysmorphic features with similar cases but the degree of mental retardation is markedly less severe.

Craniosynostosis in an infant with an interstitial deletion of 15q [46,XY,del(15)(q15q22.1)]

An interstitial deletion of 15q [46,XY,del(15)(q15q22.1)] was found in a malformed infant with craniosynostosis. Although the parents had normal chromosomes, the study of heteromorphic markers of chromosome 15 showed that the deleted chromosome 15 was of paternal origin. The 2 previously reported cases with an interstitial deletion of the middle portion of 15q were not complicated with craniosynostosis, and their deleted region did not include 15q15 band. The deletion of chromosome band 15q15 might be responsible for craniosynostosis.