Clinical and molecular characterization of three genomic rearrangements at chromosome 22q13.3 associated with autism spectrum disorder.

OBJECTIVES: Chromosome 22q13 is a hot region of genomic rearrangements that may result in deletion, duplication, and translocation, and that may lead to neurodevelopmental disorders in affected patients. MATERIALS AND METHODS: We carried out an array-based comparative genomic hybridization analysis to detect copy number variations (CNVs) of genomic DNA in patients with autism spectrum disorders (ASD) who were consecutively recruited into our molecular genetic study of ASD. Karyotyping, fluorescent in-situ hybridization analysis, and real time-quantitative PCR were used for validation tests. RESULTS: We completed a genome-wide CNV analysis of 335 patients with ASD from Taiwan. Three unrelated male patients were found to carry three different CNVs at 22q13.3, respectively, including a de novo terminal deletion of ∼106 kb at 22q13.33, a de novo interstitial duplication of ∼1.8 Mb at 22q13.32-q13.33, and a microdeletion of ∼147 kb at 22q13.33. These three CNVs all involved the dosage change of the SHANK3 gene. The last patient also carried a genomic duplication of ∼3.86 Mb at 19q13.42-q13.4 in addition to a microdeletion of ∼147 kb at 22q13.33. His younger sister also carried these two CNVs, but she had developmental delay and other neurological deficits without ASD. These two CNVs were transmitted from their unaffected father, who carried a balanced translocation between chromosome 22q and 19q. CONCLUSION: Our data support that recurrent genomic rearrangements at 22q13.3 are part of the genetic landscape of ASD in our patients and changes in SHANK3 dosage are associated with neurodevelopmental disorders. However, the clinical symptoms of patients with 22q13.3 rearrangements can vary depending on other genetic and nongenetic factors, not limited to genes involved in CNVs in this region.

Complex genomic variants contribute toward the genetic architecture of autism spectrum disorder.

Genetic factor plays a critical role in the etiology of autism spectrum disorder (ASD). Both common variants with a small effect and rare mutations with a large effect contribute toward the genetic basis of ASD, showing the high genetic heterogeneity of ASD. Genomic rearrangements account for around 10-15% of its genetic landscape. However, they are highly individualized and each of them has a very rare frequency.

Prenatal diagnosis of the maternal derivative chromosome der(15)t(Y;15)(q12;p13) in a dizygotic twin pregnancy.

Sex chromosome translocations are unique and must be considered separately from translocations between autosomes. Here, we describe the first prenatal case of one twin fetus with an unbalanced translocation between chromosome Y and chromosome 15, presenting a 46,XY,der(15)t(Y;15) karyotype. The other twin had a normal 46,XY karyotype. Cytogenetic analysis of the parental chromosomes revealed that the father had a normal 46,XY karyotype, whereas the mother exhibited a 46,XX,der(15) t(Y;15) karyotype. Thus, the proband inherited this translocation from the mother. Fluorescence in situ hybridization analyses demonstrated that the breakpoint on chromosome Y involved a heterochromatin region (Yq12), while that on chromosome 15 involved a p-arm region (15p13). At 37 gestational weeks, healthy twins were delivered vaginally. We conclude that accurate identification of der(15) chromosomal content can facilitate not only prenatal diagnosis of a chromosomal aberration in one twin, but also prediction of the fetal phenotype.

Chromosomal abnormalities in patients with autism spectrum disorders from Taiwan.

Autism spectrum disorders (ASD) are childhood-onset neurodevelopmental disorders characterized by verbal communication impairments, social reciprocity deficits, and the presence of restricted interests and stereotyped behaviors. Genetic factors contribute to the incidence of ASD evidently. However, the genetic spectrum of ASD is highly heterogeneous. Chromosomal abnormalities contribute significantly to the genetic deficits of syndromic and non-syndromic ASD. In this study, we conducted karyotyping analysis in a sample of 500 patients (447 males, 53 females) with ASD from Taiwan, the largest cohort in Asia, to the best of our knowledge. We found three patients having sex chromosome aneuploidy, including two cases of 47, XXY and one case of 47, XYY. In addition, we detected a novel reciprocal chromosomal translocation between long arms of chromosomes 4 and 14, designated t(4;14)(q31.3;q24.1), in a patient with Asperger's disorder. This translocation was inherited from his unaffected father, suggesting it might not be pathogenic or it needs further hits to become pathogenic. In line with other studies, our study revealed that subjects with sex chromosomal aneuploidy are liable to neurodevelopmental disorders, including ASD, and conventional karyotyping analysis is still a useful tool in detecting chromosomal translocation in patients with ASD, given that array-based comparative genomic hybridization technology can provide better resolution in detecting copy number variations of genomic DNA.

Identification and characterization of three inherited genomic copy number variations associated with familial schizophrenia.

Schizophrenia is a complex mental disorder with high degree of genetic influence in its etiology. Several recent studies revealed that copy number variations (CNVs) of genomic DNA contributed significantly to the genetic architecture of sporadic schizophrenia. This study aimed to investigate whether CNVs also contribute to the familial forms of schizophrenia. Using array-based comparative genomic hybridization technology, we searched for pathogenic CNV associated with schizophrenia in a sample of 60 index cases from multiplex schizophrenia families. We detected three inherited CNVs that were associated with schizophrenia in three families, including a microdeletion of ~4.4Mb at chromosome 6q12-q13, a microduplication of ~1Mb at chromosome 18q12.3, and an interstitial duplication of ~5Mb at chromosome 15q11.2-q13.1. Our data indicate that CNVs contribute to the genetic underpinnings of the familial forms of schizophrenia as well as of the sporadic form. As 15q11-13 duplication is a well-known recurrent CNV associated with autism in the literature, the detection of the 15q11.2-q13.1 duplication in our schizophrenia patients provides additional support to other studies reporting that schizophrenia is part of the clinical spectrum of 15q11-q13 duplication syndrome.

Clinical and molecular characterization of a transmitted reciprocal translocation t(1;12)(p32.1;q21.3) in a family co-segregating with mental retardation, language delay, and microcephaly.

BACKGROUND: Chromosome translocation associated with neurodevelopmental disorders provides an opportunity to identify new disease-associated genes and gain new insight into their function. During chromosome analysis, we identified a reciprocal translocation between chromosomes 1p and 12q, t(1; 12)(p32.1; q21.3), co-segregating with microcephaly, language delay, and severe psychomotor retardation in a mother and her two affected boys. METHODS: Fluorescence in situ hybridization (FISH), long-range PCR, and direct sequencing were used to map the breakpoints on chromosomes 1p and 12q. A reporter gene assay was conducted in human neuroblastoma (SKNSH) and Chinese hamster ovary (CHO) cell lines to assess the functional implication of the fusion sequences between chromosomes 12 and 1. RESULTS: We determined both breakpoints at the nucleotide level. Neither breakpoint disrupted any known gene directly. The breakpoint on chromosome 1p was located amid a gene-poor region of ~ 1.1 Mb, while the breakpoint on chromosome 12q was located ~ 3.4 kb downstream of the ALX1 gene, a homeobox gene. In the reporter gene assay, we discovered that the fusion sequences construct between chromosomes 12 and 1 had a ~ 1.5 to 2-fold increased reporter gene activity compared with the corresponding normal chromosome 12 sequences construct. CONCLUSION: Our findings imply that the translocation may enhance the expression of the ALX1 gene via the position effect and result in the clinical symptoms of this family. Our findings may also expand the clinical phenotype spectrum of ALX1-related human diseases as loss of the ALX1 function was recently reported to result in abnormal craniofacial development.

Molecular cytogenetic analysis and clinical manifestations of a case with de novo mosaic ring chromosome 7.

AIM: Clinical and molecular cytogenetic investigations of a newborn girl exhibiting facial dysmorphism with developmental delay. METHODS: Phenotypic evaluation was first applied to examine the proband's developmental status. Computed tomography and colour transcranial Doppler were used then to investigate her brain structure and function. Subsequently, chromosomal abnormalities were examined by karyotyping and fluorescent in situ hybridization was performed to investigate size of fragments lost at the two distal ends of the ring chromosome 7. In addition, multicolour banding was applied to rule out structural rearrangement occurs in between the ring chromosome 7. RESULTS: The proband was born with mosaic supernumerary ring chromosome 7, without a normal karyotype detected in the peripheral blood lymphocytes. The distal arm of chromosome 7p (at least 255 kb from the telomere) was part of an extra ring chromosome 7. In addition, the distal arm of 7q, at least 8 kb from the telomere, was missing. There was no other chromosomal rearrangement detected by multicolour banding. INTERPRETATION: This is the 19th reported case of complete ring chromosome 7 mosaicism and the first survived case with mosaic supernumerary ring 7 without a normal karyotype detected in the peripheral lymphocytes.

Identification of a microdeletion at Xp22.13 in a Taiwanese family presenting with Nance-Horan syndrome.

Nance-Horan syndrome (NHS) is a rare X-linked disorder characterized by congenital cataracts, dental anomalies and mental retardation. The disease has been linked to a novel gene termed NHS located at Xp22.13. The majority of pathogenic mutations of the disease include nonsense mutations and small deletions and insertions that lead to truncation of the NHS protein. In this study, we identified a microdeletion of ∼ 0.92 Mb at Xp22.13 detected by array-based comparative genomic hybridization in two brothers presenting congenital cataract, dental anomalies, facial dysmorphisms and mental retardation. The deleted region encompasses the REPS2, NHS, SCML1 and RAI2 genes, and was transmitted from their carrier mother who presented only mild cataract. Our findings are in line with several recent case reports to indicate that genomic rearrangement involving the NHS gene is an important genetic etiology underlying NHS.

No association of a dodecamer duplication in the human opposite paired (HOPA) gene with mental retardation and schizophrenia in Chinese patients from Taiwan.

The human opposite paired-containing (HOPA) gene is believed to be a co-activator of the thyroid hormone receptor and involved in thyroid hormone signal transduction. The gene consists of 45 exons and includes a dodecamer duplication in exon 43, which has been reported to be associated with mental retardation, autism, psychiatric disorders and hypothyroidism. We were interested to know if the 12-bp duplication variant of the HOPA gene is a risk factor for mental retardation and schizophrenia in the Chinese population. We investigated the prevalence of the 12-bp variant in a sample of Chinese mental retardation and schizophrenic patients from Taiwan by PCR-based genotyping. None of the mentally retarded and schizophrenic patients were found to have this dodecamer duplication variant. Our results indicate that the HOPA polymorphism might be very rare in our population and is unlikely to be a major risk factor for mental retardation and schizophrenia in the Chinese population.

Prenatal diagnosis of occipital encephalocele, mega-cisterna magna, mesomelic shortening, and clubfeet associated with pure tetrasomy 20p.

We present the first case of a fetus with pure tetrasomy 20p proven by cord-blood sampling at 24 weeks of gestation. This case was diagnosed in utero with multiple congenital anomalies including occipital encephalocele, mega-cisterna magna, mesomelic shortening, and clubfeet. An analysis of GTG-banded chromosomes of 20 metaphase cells was performed. Female karyotype [47,XX, +i(20)(p10)] was revealed in all cells. Pure tetrasomy 20p was confirmed using fluorescent in situ hybridization (FISH) with a telomere probe for chromosome 20p in all seven metaphase cells. The pregnancy was terminated because of associated multiple anomalies and severe oligohydramnios. The postmortem examination confirmed the prenatal diagnosis.

Evaluation of the frequencies of chromosomal aberrations in a population exposed to prolonged low dose-rate 60Co gamma-irradiation.

PURPOSE: Chromosomal aberration analysis in peripheral blood lymphocytes was performed to evaluate late cytogenetic effects of long-term low dose-rate gamma-irradiation exposure among students and residents exposed in radiocontaminated buildings. MATERIALS AND METHODS: Blood samples were taken from 1913 subjects (age 17.8+/-13.6, mean+/-SD) 5-8 years after their relocation from radioactive environments as well as from 176 non-exposed subjects (age 29.6+/-11.9) from the local community. Their lymphocytes were cultured for 48 h and metaphase spreads were prepared. A total of 208 900 metaphases were analysed for different types of chromosomal aberrations. RESULTS: Relatively higher frequencies of translocations (2.1 x 10(-3)), rings (0.6 x 10(-3)) and dicentrics (0.6 x 10(-3)) were noted in the exposed population as compared with the nonexposed reference populations. Moreover, 356 (78.6%) of the 453 inversions were found on 14q11.2q32 in the exposed population. Among 392 well-demonstrated translocations, 167 (42.6%) and 175 (44.6%) occurred in chromosomes 7 and 14, respectively, while 139 (35.5%) occurred as t(7;14). In particular, the aberrations t(7;14)(p13;q11.2), t(7;14)(p15;q11.2) and t(7;14)(q36;q11.2) were the most prevalent, occurring with frequencies of 19 (13.7%), 20 (14.4%) and 27 (19.4%), respectively. In these, 3205 breakpoints were documented, with chromosomes 7, 9 and 14 shown to carry significantly higher frequencies of breakpoints than expected (chi(2)-test, p<0.0001). A further six hotspots were identified on 7p15 (57, 1.8%), 7q36 (42, 1.3%), 9q12 (244, 7.6%), 9q13 (86, 2.7%), 14q11.2 (509, 15.9%) and 14q32 (387, 12.1%) in the exposed population. CONCLUSION: In comparison with the unexposed population, we observed increased frequencies of various chromosomal aberrations in this human population with previous exposure to prolonged low dose-rate gamma-radiation. Moreover, several hotspot breakpoints and inversions and translocations were observed on chromosomes 7 and 14.