Mother and son with deletion of 3p25-pter

Monosomy 3pter-p25.3 and trisomy 1q42.13-qter in a boy with profound growth and developmental restriction, multiple congenital anomalies, and early death

Albeit rare, 3pter-p25 monosomy or 1q42-qter trisomy syndromes have been documented in the literature. Here, we report a unique case with a combination of 3pter-p25 monosomy and 1q42-qter trisomy, delineated by array comparative genomic hybridization analysis. The proband was a newborn male with multiple congenital anomalies that included brain malformation, ocular anomalies, trachea-laryngomalacia, cardiac defects, intestinal malrotation, and cutaneous findings in conjunction with biochemical anomalies, profound growth and developmental restriction, and early death. To our knowledge, this is the first case report of this unique chromosomal imbalance.

Distal 3p deletion syndrome: detailed molecular cytogenetic and clinical characterization of three small distal deletions and review

The distal 3p deletion syndrome is characterized by developmental delay, low birth weight and growth retardation, micro- and brachycephaly, ptosis, long philtrum, micrognathia, and low set ears. We have used FISH and BACs in order to map three 3p deletions in detail at the molecular level. The deletions were 10.2-11 Mb in size and encompassed 47-51 known genes, including the VHL gene. One of the deletions was interstitial, with an intact 3p telomere. In nine previously published patients with 3p deletions, the size of the deletion was estimated using molecular or molecular cytogenetic techniques. The genotype, including genes of interest, and the phenotype of these cases are compared and discussed. The localization of the proximal breakpoint in one of our patients suggests that the previously identified critical region for heart defects may be narrowed down, now containing three candidate genes. We can also conclude that deletion of the gene ATP2B2 alone is not enough to cause hearing impairment, which is frequently found in patients with 3p deletion. This is the third reported case with an interstitial deletion of distal 3p.

Directly transmitted unbalanced chromosome abnormalities and euchromatic variants

In total, 200 families were reviewed with directly transmitted, cytogenetically visible unbalanced chromosome abnormalities (UBCAs) or euchromatic variants (EVs). Both the 130 UBCA and 70 EV families were divided into three groups depending on the presence or absence of an abnormal phenotype in parents and offspring. No detectable phenotypic effect was evident in 23/130 (18%) UBCA families ascertained mostly through prenatal diagnosis (group 1). In 30/130 (23%) families, the affected proband had the same UBCA as other phenotypically normal family members (group 2). In the remaining 77/130 (59%) families, UBCAs had consistently mild consequences (group 3). In the 70 families with established EVs of 8p23.1, 9p12, 9q12, 15q11.2, and 16p11.2, no phenotypic effect was apparent in 38/70 (54%). The same EV was found in affected probands and phenotypically normal family members in 30/70 families (43%) (group 2), and an EV co-segregated with mild phenotypic anomalies in only 2/70 (3%) families (group 3). Recent evidence indicates that EVs involve copy number variation of common paralogous gene and pseudogene sequences that are polymorphic in the normal population and only become visible at the cytogenetic level when copy number is high. The average size of the deletions and duplications in all three groups of UBCAs was close to 10 Mb, and these UBCAs and EVs form the "Chromosome Anomaly Collection" at http://www.ngrl.org.uk/Wessex/collection. The continuum of severity associated with UBCAs and the variability of the genome at the sub-cytogenetic level make further close collaboration between medical and laboratory staff essential to distinguish clinically silent variation from pathogenic rearrangement.

Disruption of contactin 4 (CNTN4) results in developmental delay and other features of 3p deletion syndrome

3p deletion syndrome is a rare contiguous-gene disorder involving the loss of the telomeric portion of the short arm of chromosome 3 and characterized by developmental delay, growth retardation, and dysmorphic features. All reported cases have involved, at a minimum, the deletion of chromosome 3 telomeric to the band 3p25.3. Despite the presence of several genes in this region that are involved in neural development, a causative relationship between a particular transcript and the observed clinical manifestations has remained elusive. We have identified a child with characteristic physical features of 3p deletion syndrome and both verbal and nonverbal developmental delay who carries a de novo balanced translocation involving chromosomes 3 and 10. Fine mapping of this rearrangement demonstrates that the translocation breakpoint on chromosome 3 falls within the recently identified minimal candidate region for 3p deletion syndrome and disrupts the Contactin 4 (CNTN4) mRNA transcript at 3p26.2-3p26.3. This transcript (also known as BIG-2) is a member of the immunoglobulin super family of neuronal cell adhesion molecules involved in axon growth, guidance, and fasciculation in the central nervous system (CNS). Our results demonstrate the association of CNTN4 disruption with the 3p deletion syndrome phenotype and strongly suggest a causal relationship. These findings point to an important role for CNTN4 in normal and abnormal CNS development.

Telomeres: a diagnosis at the end of the chromosomes

In recent years, subtelomeric rearrangements have been identified as a major cause of mental retardation and/or malformation syndromes. So far, over 2500 subjects with mental retardation have been tested and reported of whom approximately 5% appeared to have a subtelomeric rearrangement. In this review, the clinical aspects of each known (submicroscopic) subtelomeric deletion will be presented and the various methods available for detecting subtelomeric abnormalities will be discussed. Not only will the patients and their families benefit from a good collection and report of the various telomeric abnormalities and their clinical phenotype, but it will also give more insight into the aetiology of mental retardation and malformation syndromes.

Molecular cytogenetic characterization of a subtle interstitial del(3)(p25.3p26.2) in a patient with deletion 3p syndrome

Deletion 3p syndrome is associated with characteristic facial features, growth failure, and mental retardation. Typically, individuals with deletion 3p syndrome have terminal deletions that result in loss of material from 3p25 to 3pter. We present a child with a clinical phenotype consistent with deletion 3p syndrome (ptosis, microcephaly, growth retardation, and developmental delay) and a subtle interstitial deletion in the distal portion of the short arm of chromosome 3, del(3)(p25.3p26.2). Fluorescence in situ hybridization (FISH) studies using 3p subtelomeric probes confirmed the terminal region of chromosome 3 was present. Sequence tagged sites (STS)-linked BAC clones mapping to chromosomal region 3p25-p26 were used to characterize the interstitial deletion by FISH. The results indicate the deletion is within a region of approximately 4.5 Mb between STS markers D3S3630 and D3S1304. This interstitial deletion lies within all previously reported terminal deletions in deletion 3p syndrome individuals, and represents the smallest reported deletion associated with deletion 3p syndrome. Characterization of the deletion may help identify genes important to growth and development that contribute to the deletion 3p syndrome phenotype when present in a hemizygous state.

A terminal deletion of the short arm of chromosome 3: karyotype 46, XY, del (3) (p25-pter); a case report and literature review

We describe a boy with a deletion of the short arm of chromosome 3; (46, XY, del (3) (p25-pter) who presented several minor craniofacial anomalies at birth. Only 34 cases of small distal 3p deletion have been described in the literature, seven of them showed hearing loss and four of the 34 cases had brain anomalies. But in none of the 34 cases the middle and internal ear were radiographically examined. Despite the severe hearing loss detected by auditory brainstem evoked responses (ABR), computerized tomographic scanning (CT-scan) of the ear showed a normal anatomy in this patient. The head CT-scan and magnetic resonance imaging (MRI) disclosed a hypoplastic corpus callosum and an enlargement of the lateral ventricles.

Precise localisation of 3p25 breakpoints in four patients with the 3p-syndrome

In patients with the 3p-syndrome, hemizygous deletion of 3p25-pter is associated with profound growth failure, characteristic facial features, and mental retardation. We performed a molecular genetic analysis of 3p25 breakpoints in four patients with the 3p- syndrome, and a fifth patient with a more complex abnormality, 46,XY,der(3)t(3;?)(p25.3;?). EBV transformed lymphoblasts from each of the patients were initially characterised using fluorescent in situ hybridisation (FISH) and polymorphic microsatellite analyses. The 3p-chromosome from each patient was isolated from the normal chromosome 3 in somatic cell hybrid lines and subsequently analysed with polymorphic and monomorphic PCR amplifiable markers from 3p25. The analysis clearly shows that all five breakpoints are distinct. Furthermore, we have identified yeast artificial chromosomes that cross the 3p25 breakpoints of all four 3p-patients. Two of the patients were deleted for the von Hippel-Lindau (VHL) tumour suppressor gene, although neither has yet developed evidence of VHL disease. The patient with the most centromeric breakpoint, between D3S1585 and D3S1263, had the most severe clinical phenotype including an endocardial cushion defect that was not observed in any of the four patients who had more telomeric breakpoints. This study should provide useful insights into critical regions within 3p25 that are involved in normal human growth and development.

Prenatal diagnosis of partial monosomy 3p and partial trisomy 2p in a fetus associated with shortening of the long bones and a single umbilical artery

The prenatal and postnatal findings of a fetus with partial deletion of 3p25 -> pter and duplication of 2p25.3 -> pter are described. The proband postnatally displayed mental and growth retardation, psychomotor delay, microcephaly, ptosis, micrognathia, a narrow palate, and cryptorchidism. All of these anomalies were consistent with those described in 3p- and partial trisomy 2p syndromes, and also frequently seen in patients with other chromosomal disorders. However, the prenatal sonograms revealed unusual shortening of the long bones, a single umbilical artery, and normal development of the skull. Our case suggests that skeletal growth retardation of the long bones may occur earlier than that of the skull in fetuses associated with chromosomal aberrations such as del(3p)/dup(2p). Shortening of the long bones and a single umbilical artery together with other abnormalities detected by prenatal ultrasound thus warrant a fetal cytogenetic study.

Unbalanced translocation in a mother and her son in one of two 5;10 translocation families

We present two families with different distal long arm 5;10 translocations. In one family the propositus and his mother inherited the same derived chromosome 10 from the maternal grandfather who has a balanced t(5;10)(q35.3;q26.13). The phenotype of both the affected patients is milder and only partially overlaps with that of previous cases of distal 10q deletion. Other previously reported cases of transmitted imbalance are also remarkable for mild phenotype, occurrence of deletions rather than duplications and a strong bias toward maternal as opposed to paternal transmission. In the second family, the propositus inherited a derived chromosome 10 from his mother who carries a balanced (t(5;10)(q35.1;q26.3) translocation; his clinical manifestations are consistent with an emerging phenotype for distal 5q duplications.

Direct transmission of a tandem duplication in the short arm of chromosome 8

A family is described in which a mother and her two children carry a tandem duplication of the short arm of chromosome 8. Their phenotypes are similar and characterised by distinct facial dysmorphism, small stature and mild mental retardation. This is one of the first cases of direct familial transmission of a partial duplication of an autosomal chromosome segment.

Physical mapping of chromosome 3p25-p26 by fluorescence in situ hybridisation (FISH)

As part of our effort to isolate and characterise the von Hippel-Lindau (VHL) disease gene, we constructed a physical map of chromosome 3p25-26 by fluorescence in situ hybridisation (FISH) studies on a panel of cytogenetic rearrangements involving this region. Biotinylated cosmid and lambda probes were hybridised to metaphase chromosome spreads and positioned with respect to each cytogenetic breakpoint. These studies unequivocally established the order of five loci linked to the VHL disease gene: cen-(RAF1,312)-D3S732-D3S1250-D3S601-D3S18 -pter and determined the position of three other probes within this map. These results ordered RAF1 and D3S732 for the first time, confirmed the localisation of D3S1250 between RAF1 and D3S601 and determined the position of D3S651 with respect to other chromosome 3p25-p26 loci. The establishment of an ordered set of cytogenetic aberrations will enable the rapid assignment of polymorphic and nonpolymorphic cloned sequences within the chromosome region 3p25-p26.

Clinical and molecular analyses of deletion 3p25-pter syndrome

Hemizygous deletion of 3p25-pter is associated with a phenotype of profound growth failure, microcephaly, characteristic facial changes, and mental retardation. Since the severity may be quite variable, we have studied 3 cases of del 3p25-pter to define the clinical manifestations and the critical chromosome region for phenotypic expression. The patient we now report died at age 6 months and provided an opportunity for a detailed necropsy analysis for only the second time in a del(3p) patient. He had marked hypoplasia of all organs, hypomyelination of white matter, and multiple renal cortical microcysts. Ordered genomic markers from the distal regions of chromosome 3p aided in determining the parent of origin of each deletion and in defining the boundaries of the deleted chromosomal segments. The deleted markers distal to the RAF1 oncogene in 2 of the 3 patients were consistently hemizygous. One patient had an interstitial deletion based on evidence of diploid inheritance of one of the most distal loci (D3S17). Available genetic linkage maps suggest that the deletion spans at least 19 centimorgans (cM).