Duplication of the distal long arm of chromosome 15: Report of three new patients and review of the literature

The Application of Optical Genome Mapping (OGM) in Severe Short Stature Caused by Duplication of 15q14q21.3

(1) Background: Optical genome mapping (OGM) is a novel approach to identifying genomic structural variations with high accuracy and resolution. We report a proband with severe short stature caused by 46, XY, der (16) ins (16;15) (q23; q21.3q14) that was detected by OGM combined with other tests and review the clinical features of patients with duplication within 15q14q21.3; (2) Methods: OGM, whole exon sequencing (WES), copy number variation sequencing (CNV-seq), and karyotyping were used; (3) Results: The proband was a 10.7-year-old boy with a complaint of severe short stature (-3.41SDS) and abnormal gait. He had growth hormone deficiency, lumbar lordosis, and epiphyseal dysplasia of both femurs. WES and CNV-seq showed a 17.27 Mb duplication of chromosome 15, and there was an insertion in chromosome 16 found by karyotyping. Furthermore, OGM revealed that duplication of 15q14q21.3 was inversely inserted into 16q23.1, resulting in two fusion genes. A total of fourteen patients carried the duplication of 15q14q21.3, with thirteen previously reported and one from our center, 42.9% of which were de novo. In addition, neurologic symptoms (71.4%,10/14) were the most common phenotypes; (4) Conclusions: OGM combined with other genetic methods can reveal the genetic etiology of patients with the clinical syndrome, presenting great potential for use in properly diagnosing in the genetic cause of the clinical syndrome.

Monochorionic twins with 15q26.3 duplication presenting with selective intrauterine growth restriction and discordant cardiac anomalies: A case report

BACKGROUND

Duplication of the distal end of chromosome 15q has been previously implicated in a characteristic overgrowth syndrome. Additionally, many patients have other congenital malformations, including cardiac, renal, genital, and musculoskeletal anomalies. However, some patients may present with intrauterine growth restriction and short stature. Different breakpoints within 15q, as well as different environmental factors, may underlie these varied presentations.

CASE PRESENTATION

We discuss monochorionic-diamniotic twins with a ~345 kb maternally inherited duplication in 15q26.3. The twins presented with discordant pathology-one twin with a single umbilical artery, selective intrauterine growth restriction, and multiple cardiac defects including aortic coarctation, aortic valve stenosis, and ventricular septal defect, whereas the other twin was unaffected. To our knowledge, this case represents the smallest reported duplication of distal 15q.

CONCLUSION

The discordant phenotype seen in the twins is likely due to a complex interplay between genetic and environmental causes. The affected infant presented prenatally with growth restriction and a single umbilical artery rather than overgrowth, potentially due to a unique breakpoint within 15q. This, in turn, may have produced hemodynamic perturbations between the twins, leading to discordant cardiac disease. Our report thus highlights the importance of genetic and nongenetic mechanisms underlying discordant anomalies in monochorionic twins.

A Tiered Genetic Screening Strategy for the Molecular Diagnosis of Intellectual Disability in Chinese Patients

Objective: Intellectual disability (ID) is one of the most common developmental disabilities. To identify the genetic etiology of IDs in Chongqing, we conducted a multistage study in Chinese Han patients. Methods: We collected the clinical and etiological data of 1665 ID patients, including 1,604 from the disabled children evaluation center and 61 from the pediatric rehabilitation unit. Routine genetic screening results were obtained, including karyotype and candidate gene analysis. Then 105 idiopathic cases with syndromic and severe ID/developmental delay (DD) were selected and tested by chromosomal microarray (CMA) and whole exome sequencing (WES) sequentially. The pathogenicity of the CNVs and SNVs were evaluated according to ACMG guidelines. Results: Molecular diagnosis was made by routine genetic screening in 216 patients, including 196 chromosomal syndromes. Among the 105 idiopathic patients, 49 patients with pathogenic/likely pathogenic CNVs and 21 patients with VUS were identified by CMA. Twenty-six pathogenic CNVs underlying well-known syndromic cases, such as Williams-Beuren syndrome, were confirmed by multiplex ligation-dependent probe amplification (MLPA). Nine novel mutations were identified by WES in thirty-fix CNV-negative ID cases. Conclusions: The study illustrated the genetic aberrations distribution of a large ID cohort in Chongqing. Compared with conventional or single methods, a tiered high-throughput diagnostic strategy was developed to greatly improve the diagnostic yields and extend the variation spectrum for idiopathic syndromic ID cases.

Clinical, cytogenetic and molecular analyses of a rare case with ring chromosome 15 and review of the literature

OBJECTIVE

Ring chromosome 15 [r (15)], accompanied by a series of clinical symptoms, is a rare genetic disease. The genotype and phenotypic diversity of patients with r (15) still needed further enrichment. In this study we present a rare case of mosaic ring chromosome 15 with facial anomalies and extremities slenderness.

CASE REPORT

This case involves a 30-year-old woman, unpregnancy within 6 years. Clinical examination of the patient only revealed facial anomalies and extremities slenderness. The result of routine G-band karyotyping was 46,XX,r(15)(p12q26.3)[53]/46,XX,r(15;15)(p11.2q26.3;p11.2q11.2)[28]/45,XX, -15[10]/46,XX,r(15;15)(p11q26.3;p11q26.3)[4]. SNP array was employed to investigate the genome copy number variations (CNVs). The result revealed that there was a micro-duplication of 2.0 Mb at 15q26.3(arr[ph19]15q26.3 (100,400,214- 102,429,112)×3). The duplicated chromosomal section encompassed genes including CHSY1, ALDHIA3, LRRK1, and INS1. We further compared to the cytogenetic characteristics and clinical symptoms of the patient with those already reported by reviewing the literature.

CONCLUSION

This report is especially helpful to supplement the phenotypic diversity of patients with r (15).

Prenatal diagnosis of a pure 15q distal trisomy derived from a maternal pericentric inversion: A case report

Distal trisomy or duplication of 15q is a very rare chromosomal disorder; most of the previously reported cases were derived from unbalanced translocations involving chromosome 15 and another chromosome, whereas other mechanisms (e.g. duplication) have rarely been reported. We herein report a very rare prenatal case of a partial 15q trisomy, a 42.64-Mb duplication of 15q22.2-q26.3, arising from a maternal pericentric inversion of chromosome 15 (p11q22) that was not the result of an unbalanced translocation or duplication, and was not associated with concomitant partial monosomy. Fetal ultrasound revealed isolated thickened nuchal translucency at 12 weeks and multiple abnormalities in the second trimester, including early growth restriction, unilateral ventriculomegaly, narrow cavum septi pellucidi with hypoplasia of the corpus callosum, unilateral postaxial polydactyly, clenched hands and clubfoot with clawing of the toes, and a particular general dysplastic and hypotrophic aspect of the heart. The distinctive aspects of the present case may help to refine the phenotype associated with distal duplication 15q. To the best of our knowledge, this is the first report of a prenatal diagnosis with a 15q22.2-q26.3 duplication that did not result from an unbalanced translocation and did not have a concomitant monosomic component.

Refining critical regions in 15q24 microdeletion syndrome pertaining to autism

Chromosome 15q24 microdeletion syndrome is characterized by developmental delay, facial dysmorphism, hearing loss, hypotonia, recurrent infection, and other congenital malformations including microcephaly, scoliosis, joint laxity, digital anomalies, as well as sometimes having autism spectrum disorder (ASD) and attention deficit hyperactivity disorder. Here, we report a boy with a 2.58-Mb de novo deletion at chromosome 15q24. He is diagnosed with ASD and having multiple phenotypes similar to those reported in cases having 15q24 microdeletion syndrome. To delineate the critical genes and region that might be responsible for these phenotypes, we reviewed all previously published cases. We observe a potential minimum critical region of 650 kb (LCR15q24A-B) affecting NEO1 among other genes that might pertinent to individuals with ASD carrying this deletion. In contrast, a previously defined minimum critical region downstream of the 650-kb interval (LCR15q24B-D) is more likely associated with the developmental delay, facial dysmorphism, recurrent infection, and other congenital malformations. As a result, the ASD phenotype in this individual is potentially attributed by genes particularly NEO1 within the newly proposed critical region.

Prenatal diagnosis of a de novo tetrasomy 15q24.3-25.3: Case report and literature review

BACKGROUND

Terminal duplication on chromosome 15q is a rare chromosomal variation. Affected individuals show similar features such as growth dysplasia or the development of frontal bossing, body deformities, facial abnormalities, and genitourinary or cardiovascular disorders. However, it is not yet clear whether such 15q repeats lead to identifiable patterns of clinical abnormalities. Therefore, the purpose of this study was to analyze the prenatal diagnostic results and clinical manifestations of a fetus with 15q duplication and to summarize the literature.

METHODS

The case was a fetus at 28 weeks of gestation. The risk of Down syndrome from second-trimester screening was 1/140. Prenatal ultrasound and amniocentesis were performed, and chromosomal microarray analysis (CMA) was used for genetic analysis.

RESULTS

The fetus had abnormal clinical features, including intracardiac echogenic focus in the left ventricle, an aberrant right subclavian artery, and growth delay. The fetal chromosomal karyotype was 46,XX,15q?,12q?,21pstk+, and CMA revealed a 10.163 Mb duplication at 15q24.3-q25.3. The couple chose to terminate the pregnancy after careful consideration.

CONCLUSIONS

The combination and rational application of cytogenetics technology and molecular genetics technology such as CMA will open up the field of clinical application and provide useful genetic counseling for parents of fetuses carrying such chromosomal duplications.

Pseudoacromegaly

Individuals with acromegaloid physical appearance or tall stature may be referred to endocrinologists to exclude growth hormone (GH) excess. While some of these subjects could be healthy individuals with normal variants of growth or physical traits, others will have acromegaly or pituitary gigantism, which are, in general, straightforward diagnoses upon assessment of the GH/IGF-1 axis. However, some patients with physical features resembling acromegaly - usually affecting the face and extremities -, or gigantism - accelerated growth/tall stature - will have no abnormalities in the GH axis. This scenario is termed pseudoacromegaly, and its correct diagnosis can be challenging due to the rarity and variability of these conditions, as well as due to significant overlap in their characteristics. In this review we aim to provide a comprehensive overview of pseudoacromegaly conditions, highlighting their similarities and differences with acromegaly and pituitary gigantism, to aid physicians with the diagnosis of patients with pseudoacromegaly.

Prenatal diagnosis and molecular cytogenetic characterization of a de novo duplication of 15q24.3-q26.1

Reported cases of distal 15q interstitial duplications are uncommon and do not result in a recognizable pattern of abnormalities. Some studies report prenatal overgrowth, while others describe growth retardation. We present molecular cytogenetic characterization of a 14 Mb interstitial duplication, encompassing 81 Online Mendelian Inheritance in Man (OMIM) genes, in a fetus with single umbilical artery and short limbs. We propose that growth restriction, previously described and present in our patient, may be due to duplication of a gene or genes contained in the 15q24 region.

Molecular cytogenetic characterization of a duplication of 15q24.2-q26.2 associated with anencephaly and neural tube defect

OBJECTIVE

We present molecular cytogenetic characterization of a duplication of 15q24.2-q26.2 associated with anencephaly and neural tube defect (NTD).

CASE REPORT

A 35-year-old pregnant woman was found to have a fetus with anencephaly by prenatal ultrasound at 12 weeks of gestation. The pregnancy was subsequently terminated, and a malformed fetus was delivered with anencephaly. Cytogenetic analysis of the cultured placental tissues revealed a karyotype of 46,XX,dup(15) (q24.2q26.2). Parental karyotypes were normal. Array comparative genomic hybridization analysis of the placental tissues revealed a 20.36-Mb duplication of 15q24.2-q26.2 encompassing 100 Online Mendelian Inheritance of in Man (OMIM) genes including LINGO1, MTHFS, KIF7 and CHD2. Metaphase fluorescence in situ hybridization analysis using 15q25.1-specidic probe confirmed a duplication of 15q25.1. Polymorphic DNA marker analysis showed a maternal origin of the duplication.

CONCLUSION

A duplication of chromosome 15q24.2-q26.2 can be associated with NTD.

Chromosome 15 structural abnormalities: effect on IGF1R gene expression and function

Insulin-like growth factor 1 receptor (IGF1R), mapping on the 15q26.3 chromosome, is required for normal embryonic and postnatal growth. The aim of the present study was to evaluate the IGF1R gene expression and function in three unrelated patients with chromosome 15 structural abnormalities. We report two male patients with the smallest 15q26.3 chromosome duplication described so far, and a female patient with ring chromosome 15 syndrome. Patient one, with a 568 kb pure duplication, had overgrowth, developmental delay, mental and psychomotor retardation, obesity, cryptorchidism, borderline low testis volume, severe oligoasthenoteratozoospermia and gynecomastia. We found a 1.8-fold increase in the IGF1R mRNA and a 1.3-fold increase in the IGF1R protein expression (P < 0.05). Patient two, with a 650 kb impure duplication, showed overgrowth, developmental delay, mild mental retardation, precocious puberty, low testicular volume and severe oligoasthenoteratozoospermia. The IGF1R mRNA and protein expression was similar to that of the control. Patient three, with a 46,XX r(15) (p10q26.2) karyotype, displayed intrauterine growth retardation, developmental delay, mental and psychomotor retardation. We found a <0.5-fold decrease in the IGF1R mRNA expression and an undetectable IGF1R activity. After reviewing the previously 96 published cases of chromosome 15q duplication, we found that neurological disorders, congenital cardiac defects, typical facial traits and gonadal abnormalities are the prominent features in patients with chromosome 15q duplication. Interestingly, patients with 15q deletion syndrome display similar features. We speculate that both the increased and decreased IGF1R gene expression may play a role in the etiology of neurological and gonadal disorders.

Two familial microduplications of 15q26.3 causing overgrowth and variable intellectual disability with normal copy number of IGF1R

Terminal duplications of 15q26.3 are associated with an overgrowth phenotype, distinct facial features and intellectual disability, with the smallest reported microduplication to date being 3.16 Mb in size. We report two familial 15q26.3 microduplication cases that are less than half this size, re-defining the minimal critical region for this duplication syndrome. In both families the duplication (albeit a complex copy number gain in one family) is associated with tall stature, early speech delay and variable cognitive problems. Neither familial copy number gains encompass the gene encoding for the insulin-like growth factor 1 receptor (IGF1R), the most-cited candidate for the overgrowth phenotype. In one family, whole genome sequence data and break point mapping excludes disruption of known IGF1R regulatory elements due to potential insertion within these elements. These cases highlight the possibility that the distal region of 15q contains another gene regulating human growth, with LRRK1 being a potential candidate.

Chromosomal imbalance letter: Phenotypic consequences of combined deletion 8pter and duplication 15qter

Exact breakpoint determination by oligonucleotide array-CGH has improved the analysis of genotype-phenotype correlations in cases with chromosome aberrations allowing a more accurate definition of relevant genes, particularly their isolated or combined impact on the phenotype in an unbalanced state. Chromosomal imbalances have been identified as one of the major causes of mental retardation and/or malformation syndromes and they are observed in ~2-5% of the cases. Here we report a female child born to non-consanguineous parents and having multiple congenital anomalies such as atrial septal defect and multiple ventricular septal defects, convergent strabismus, micropthalmia, seizures and mental retardation, with her head circumference and stature normal for her age. Cytogenetic study suggested 46,XX,add(8)(p23). Further analysis by array-CGH using 44K oligonucleotide probe confirmed deletion on 8p23.3p23.1 of 7.1 Mb and duplication involving 15q23q26.3 of 30 Mb size leading to 46,XX,der(8)t(8;15)(p23.3;q23)pat.arr 8p23.3p23.1(191,530-7,303,237)x1,15q23q26.3(72,338,961-102,35,195)x3. The unique phenotypic presentation in our case may have resulted from either loss or gain of a series of contiguous genes which may have resulted in a direct phenotypic effect and/or caused a genetic regulatory disturbance. Double segmental aberrations may have conferred phenotypic variability, as in our case, making it difficult to predict the characteristics that evolved as a result of the global gene imbalance, caused by the concomitant deletion and duplication.

Insertional translocation of 15q25-q26 into 11p13 and duplication at 8p23.1 characterized by high resolution arrays in a boy with congenital malformations and aniridia

We report on a boy presenting submucous cleft palate, hydronephrosis, ventriculoseptal defect, aniridia, and developmental delay. Additional material on 11p13 was cytogenetically visible and array analyses identified a duplicated segment on 15q25-26 chromosome region; further, array analyses revealed a small deletion (49 kb) at 11p13 region involving the ELP4 gene and a duplication at 8p23.1. Results were confirmed with both molecular and molecular cytogenetics techniques. Possibilities for etiological basis of clinical phenotype are discussed.

Pure duplication of the distal long arm of chromosome 15 with ebstein anomaly and clavicular anomaly

This report is of a patient with pure trisomy of 15q24-qter who presents with the rare Ebstein anomaly and a previously unreported skeletal anomaly. Chromosome microarray analysis allowed high-resolution identification of the extent of the trisomy and provided a means of achieving higher-resolution breakpoint data. The phenotypic expression of unbalanced chromosomal regions is a complex phenomenon, and fine mapping of the involved region, as described here, is only a first step on the path to its full understanding. Overexpression of the LINGO-1 and CSPG4 genes has been implicated in developmental delay seen in other patients with trisomy of 15q24-qter, but our patient is currently too young to ascertain developmental progress. The genetic underpinning of Ebstein anomaly and the skeletal anomaly reported here is unclear based on our high-resolution dosage mapping.

A girl with 15q overgrowth syndrome and dup(15)(q24q26.3) that included telomeric sequences

Distal 15q trisomy or tetrasomy is associated with a characteristic phenotype that includes mild to moderate intellectual disability, abnormal behavior, speech impairment, overgrowth, hyperlaxity, long face, prominent nose, puffy cheeks, pointed chin, small ears, and hand anomalies (mainly arachno- and camptodactyly). We present the case of a 13-yr-old girl with the main clinical features of 15q overgrowth syndrome and a 46,XX,dup(15)(q24q26.3)[117]/46,XX[3].ish dup(15)(q24q26.3) (SNPRN+,PML+,subtel++,tel++) de novo karyotype. The findings in this case are consistent with those in the previous distal 15q trisomy cases that presented with overgrowth and mental retardation. Further, the rearranged chromosome had a double set of directly oriented telomeric and subtelomeric sequences.

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.

Tall stature and duplication of the insulin-like growth factor I receptor gene

Trisomy of 15q26-qter is frequently associated with tall stature and mental retardation. Here we describe a patient with such trisomy, without a partial monosomy of another chromosome. The tall stature in this patient is most probably caused by duplication of the IGF1R gene. A duplication of the IGF1R gene is not a frequent finding in patients with tall stature. In 38 patients with features of Sotos syndrome without NSD1 alterations, a duplication was found only once. This patient was already known to have an unbalanced 2;15 translocation. Looking for a duplication of the 15qter region is still worth consideration in patients with tall stature and features of Sotos syndrome without an NSD1 alteration, especially when there is craniosynostosis or marked speech delay.

Trisomy 15q25.2-qter in an autistic child: genotype-phenotype correlations

We report on the case of a male child with autistic disorder, postnatal overgrowth, and a minor brain malformation. Karyotyping and fluorescent in situ hybridization (FISH) analysis showed the presence of an extra copy of the distal portion of chromosome 15q (15q25.2-qter) transposed to chromosome 15p leading to 15q25.2-qter pure trisomy. This karyotype-phenotype study further supports the evidence for a specific phenotype related to trisomy 15q25 or 26-qter and suggests that distal chromosome 15q may be implicated in specific behavioral phenotypes.

Ebstein anomaly and duplication of the distal arm of chromosome 15: Report of two patients

Ebstein anomaly of the tricuspid valve is an uncommon congenital heart defect. We report two unrelated patients with Ebstein anomaly and duplication of the distal long arm of chromosome 15 (15q22 --> qter and 15q24 --> qter). Duplication of 15q is a well-described phenotype that includes congenital heart defects, and these are the first cases with Ebstein anomaly. Duplication of 15q likely affects the early morphogenesis of cardiac structures, including the normal formation of the tricuspid valve.