The involvement of U-type dicentric chromosomes in the formation of terminal deletions with or without adjacent inverted duplications.

An inverted duplication with a terminal deletion (inv-dup-del) is one of the complex constitutional structural rearrangements that can occur in a chromosome. Although breakages of dicentric chromosome have been suggested, the precise mechanism of this is yet to be fully understood. In our present study, we investigated the genomic structure of 10 inv-dup-del cases to elucidate this mechanism. Two recurrent 8p inv-dup-del cases harbored a large copy-number-neutral region between the duplication and deletion in common. Although the other non-recurrent cases did not appear to have this copy-number-neutral region, refined sequencing analysis identified that they contained a small intervening region at the junction between the inverted and non-inverted segment. The size of this small intervening region ranged from 1741 to 3728 bp. Combined with a presence of microhomology at the junction, a resolution of the replication fork stalling through template switching within the same replication fork is suggested. We further observed two cases with mosaicism of the dicentric chromosome and various structural rearrangements related to the dicentric chromosome. Refined analysis allowed us to identify different breakpoints on the same chromosome in the same case, implicating multiple rounds of U-type formation and its breakage. From these results, we propose that a replication-based mechanism generates unstable dicentric chromosomes and that their breakage leads to the formation of inv-dup-dels and other related derivative chromosomes.

Neonatal Death Caused by Interrupted Aortic Arch Associated With 22q11.2 Deletion Syndrome: An Autopsy Case Report.

A case of clinically unsuspected fatal interrupted aortic arch (IAA) is described. A 17-day-old Japanese girl unexpectedly entered respiratory arrest at home. On autopsy, the heart was hypertrophic, with no apparent connection between the ascending and descending aortas. The ascending aorta branched into common carotid and right subclavian arteries, whereas the left subclavian artery arose from the descending aorta, which was supplied by the ductus arteriosus, indicating type B IAA. In addition, ventricular septal defect, bicuspid aortic valve, patent foramen ovale, and thymic aplasia were identified. The immediate cause of death was assumed to be "ductal shock." Because of the known strong association between type B and 22q11.2 deletion, her parents received genetic counseling and requested chromosomal analysis of the child. Fluorescence in situ hybridization worked well on a frozen blood sample, identifying the suspected deletion. This case was thus diagnosed as 22q11.2 deletion syndrome exhibiting IAA and thymic defect.

Classification of Uniparental Isodisomy Patterns That Cause Autosomal Recessive Disorders: Proposed Mechanisms of Different Proportions and Parental Origin in Each Pattern.

Patients with autosomal recessive (AR) disorders are usually born to parents both of whom are heterozygous carriers of the disease. However, in some instances only one of the parents is a carrier and a mutation is segregated to the patient through uniparental isodisomy (UPiD). Recently, an increasing number of such case reports has been published, and it has become clear that there are several different UPiD patterns that cause AR disorders. In this article, we report 3 remarkable patients with different patterns of UPiD. We then review 85 cases collected in the literature. We realized that they can be classified into 3 patterns: UPiD of the whole chromosome, segmental UPiD with uniparental heterodisomy (UPhD), and segmental UPiD caused by post-zygotic mitotic recombination (MiRe). Whole chromosomal UPiD accounted for the majority of cases, with paternal origin accounting for approximately twice as many cases as maternal origin. Most cases of segmental UPiD with UPhD were of maternal origin, with a dominancy of nondisjunction in meiosis I, while segmental UPiD through MiRe is the smallest pattern with equal parental origin. These differences in proportion and parental origin in each pattern can be explained by considering nondisjunction during oogenesis as the starting point and UPiD as subsequent events.

Prenatal diagnosis of premature chromatid separation/mosaic variegated aneuploidy (PCS/MVA) syndrome.

Premature chromatid separation/mosaic variegated aneuploidy (PCS/MVA) syndrome is a rare genetic disorder. In this case report, we describe the prenatal diagnosis of PCS/MVA syndrome in a 24-year-old, gravida 1, para 1, woman who was referred to us in her second trimester due to fetal growth restriction and extreme microcephaly (-5.0 standard deviations). Amniocentesis and chromosomal analysis confirmed PCS in 80% of cultured fetal cells. PCS findings were positive in 9% of paternal cells and 11% of maternal cells, indicative that both were PCS carriers. Genetic analysis confirmed that the fetus carried a combined heterozygote of maternal G > A point mutation of the promoter area of the BUB1B gene and a paternal Alu sequence insertion between intron 8 and exon 9 of the BUB1B gene. As PCS/MVA syndrome is associated with the development of various malignancies in early life, prenatal diagnosis is important for effective planning of post-natal care.

Human Malformation Syndromes of Defective GLI: Opposite Phenotypes of 2q14.2 (GLI2) and 7p14.2 (GLI3) Microdeletions and a GLIA/R Balance Model.

GLI family zinc finger proteins are transcriptional effectors of the sonic hedgehog signaling pathway. GLI regulates gene expression and repression at various phases of embryonic morphogenesis. In humans, 4 GLI genes are known, and GLI2 (2q14.2) and GLI3 (7p14.1) mutations cause different syndromes. Here, we present 2 distinctive cases with a chromosomal microdeletion in one of these genes. Patient 1 is a 14-year-old girl with Culler-Jones syndrome. She manifested short stature, cleft palate, and mild intellectual/social disability caused by a 6.6-Mb deletion of 2q14.1q14.3. Patient 2 is a 2-year-old girl with Greig cephalopolysyndactyly contiguous gene deletion syndrome. She manifested macrocephaly, preaxial polysyndactyly, psychomotor developmental delay, cerebral cavernous malformations, and glucose intolerance due to a 6.2-Mb deletion of 7p14.1p12.3 which included GLI3, GCK, and CCM2. Each patient manifests a different phenotype which is associated with different functions of each GLI gene and different effects of the chromosomal contiguous gene deletion. We summarize the phenotypic extent of GLI2/3 syndromes in the literature and determine that these 2 syndromes manifest opposite features to a certain extent, such as midface hypoplasia or macrocephaly, and anterior or posterior side of polydactyly. We propose a GLIA/R balance model that may explain these findings.

Angelman Syndrome Caused by Chromosomal Rearrangements: A Case Report of 46,XX,+der(13)t(13;15)(q14.1;q12)mat,-15 with an Atypical Phenotype and Review of the Literature.

Less than 1% of the cases with Angelman syndrome (AS) are caused by chromosomal rearrangements. This category of AS is not well defined and may manifest atypical phenotypes. Here, we report a girl with AS due to der(13)t(13;15)(q14.1;q12)mat. SNP array detected the precise deletion/duplication points and the parental origin of the 15q deletion. Multicolor FISH confirmed a balanced translocation t(13;15)(q14.1;q12) in her mother. Her facial appearance showed some features of dup(13)(pter→q14). Also, she lacked the most characteristic and unique behavioral symptoms of AS, i.e., frequent laughter, happy demeanor, and easy excitability. A review of the literature indicated that AS cases caused by chromosomal rearrangements can be classified into 2 major categories and 4 groups. The first category is paternal uniparental disomy 15, which is subdivided into isodisomy by de novo rob(15;15) and heterodisomy caused by paternal translocation. The second category is the deletion of the AS locus due to maternal reciprocal translocation, which is subdivided into 2 groups associated with partial monosomy by 3:1 segregation and partial trisomy by adjacent-2 segregation. Classification into these categories facilitates the understanding of the mechanisms of chromosomal rearrangements and helps in accurate diagnosis and genetic counseling of these rare forms of AS.

Signature of backward replication slippage at the copy number variation junction.

Copy number abnormalities such as deletions and duplications give rise to a variety of medical problems and also manifest innocuous genomic variations. Aberrant DNA replication is suggested as the mechanism underlying de novo copy number abnormalities, but the precise details have remained unknown. In our present study, we analyzed the del(2)(q13q14.2) chromosomal junction site observed in a woman with a recurrent pregnancy loss. Microarray analyses allowed us to precisely demarcate a 2.8 Mb deletion in this case, which does not appear in the database of human genomic variations. This deletion includes only one brain-specific gene that could not be related to the reproduction failure of the patient. At the junction of the deletion, we found that 11-13-nucleotide sequence, originally located at the proximal breakpoint region, was repeated four times with a single-nucleotide microhomology at the joint between each repeat. The proximal region and the distal region was finally joined with six-nucleotide microhomology. The structure of the junction is consistent with backward replication slippage proposed previously. Our data lend support to the notion that a common DNA replication-mediated pathway generates copy number variation in the human genome.

Establishment of human induced pluripotent stem cell lines, KMUGMCi006, from a patient with Tuberous sclerosis complex (TSC) bearing mosaic nonsense mutations in the Tuberous sclerosis complex 2 (TSC2) gene.

Tuberous sclerosis complex (TSC) is an autosomal dominant disorder characterized by neuropsychiatric symptoms and multiple dysplastic organ lesions, caused by loss of function mutations in either TSC1 or TSC2. The peripheral blood mononuclear cells (PBMCs) from a patient carrying mosaic nonsense mutation of TSC2 gene were reprogrammed using the CytoTune-iPS2.0 Sendai Reprogramming Kit. The human induced pluripotent cell (hiPSC) lines with the mutation and without the mutation were established. The heterozygous nonsense mutation in TSC2 will cause the truncated protein, which is known to associated with TSC. The established hiPSC lines will enable proper in vitro disease modelling of TSC.

Establishment of a human induced pluripotent stem cell line, KMUGMCi007-A, from a patient with prolidase deficiency (PD) bearing homozygous in-frame mutation in the PEPD gene.

Prolidase deficiency (PD) is a rare autosomal recessive disorder characterized mainly by skin lesions of the legs and feet, respiratory infections and mental retardation, and impaired immune system. To date, no effective PD treatment has been developed. The PD case are caused by homozygous mutation in PEPD gene. The peripheral blood mononuclear cells from a patient carrying homozygous in-frame mutation of the PEPD gene were reprogrammed using the CytoTune-iPS2.0 Sendai Reprogramming Kit. The homozygous in-frame mutation in PEPD will cause the abnormal protein variant. The established human induced pluripotent cell line will enable proper in vitro disease modelling of PD.

Paternal uniparental isodisomy of chromosome 22 in a patient with metachromatic leukodystrophy.

Metachromatic leukodystrophy (MLD) is an autosomal recessive lysosomal storage disease caused by deficiency of the enzyme arylsulfatase A encoded by the ARSA gene located on 22q13.33. Typically, in autosomal recessive disease, a patient inherits two mutations from both parents who are heterozygous carriers. However, in some instances, it is possible to develop the disease by uniparental isodisomy (UPiD), in which two copies of the same mutated allele are inherited from only one carrier parent. Here, we report the first patient with MLD caused by UPiD of chromosome 22. The patient has a homozygous missense mutation, P136T, on ARSA. Family study of the ARSA gene and leukocyte enzyme activity revealed that his father and sister were heterozygous carriers, but his mother possessed only wild-type alleles and normal enzyme activity. Karyotypes of the patient and the parents were normal. Microsatellite analysis showed no discrepancy of parentage, and paternal UPiD of chromosome 22 was indicated. Finally, genome-wide single-nucleotide polymorphism array confirmed the region of UPiD was extended to the entire chromosome 22 of the patient.

Establishment of a human induced pluripotent stem cell line, KMUGMCi001-A, from a patient bearing a heterozygous c.772 + 3_772 + 4dup mutation in the ACVRL1 gene leading Telangiectasia, hereditary hemorrhagic, type 2 (HHT2).

Telangiectasia, hereditary hemorrhagic, type 2 (HHT2) is a rare autosomal dominant disease caused by a mutated ACVRL1 gene (Letteboer et al., 2005). The peripheral blood mononuclear cells (PBMCs) from a patient carrying a heterozygous 2 bp duplication in intron 6 of the ACVRL1 gene, NG_009549.1(NM_000020.2):c.772 + 3_772 + 4dup, were reprogrammed using episomal vectors. The inserted mutation in ACVRL1 will causes the abnormal splicing, which will be associated with HHT2. The cell line will enable proper in vitro disease modelling of HHT2(Roman and Hinck, 2017).

Establishment of a human induced pluripotent stem cell line, KMUGMCi002-A, from a patient bearing a heterozygous c.6362_6364del mutation in the NIPBL gene leading Cornelia de Lange syndrome (CdLS).

Cornelia de Lange syndrome (CdLS) is a multiple congenital anomalies syndrome caused by mutations in the cohesion complex. The mutations in NIPBL, one of cohesion regulatory proteins, are the most frequent cause of CdLS. The peripheral blood mononuclear cells (PBMCs) from a patient carrying a heterozygous 3 bp deletion in Exon 37 of the NIPBL gene were reprogrammed using the CytoTune-iPS2.0 Sendai Reprogramming Kit. The deleted mutation in NIPBL will cause the abnormal truncated protein, which is known to associated with CdLS. The established human induced pluripotent cell (hiPSC) line will enable proper in vitro disease modelling of CdLS. Resource Table.

Confined placental mosaicism of trisomy 6 detected through genome-wide NIPT was associated with placental abruption.

Confined placental mosaicism (CPM) leads to discordant noninvasive prenatal testing (NIPT) results. We describe a very rare case of CPM of trisomy 6 detected through genome-wide NIPT. This case was associated with placental abruption, which might suggest an association between certain types of CPM detected by NIPT and pregnancy complications.

Odontogenic myxofibroma with HMGA2 overexpression and HMGA2 rearrangement.

Odontogenic myxofibromas are variants of odontogenic myxomas that contain considerable amounts of collagen fibers in the myxoid stroma. Cytogenetic studies of odontogenic myxomas/myxofibromas have rarely been reported. This report describes the first case of an odontogenic myxofibroma presenting with HMGA2 protein overexpression and HMGA2 rearrangement in a 40-year-old woman. A 2.7-cm tumor in the premolar region of the right mandible was curettaged. There was no evidence of recurrence or metastasis at 12 months after the surgery. Histological examination revealed that the tumor comprised spindle or stellate cells with mild nuclear pleomorphism, abundant myxoid matrix and partly dense collagen fibers. Mitotic figures were rarely observed. Immunohistochemically, the tumor cells were diffusely positive for vimentin and HMGA2. Less than 1% of the tumor cells were positive for Ki-67. We detected split signals by interphase fluorescence in situ hybridization (FISH) in paraffin sections using HMGA2 break-apart probes. The breaks were certainly located within or near the HMGA2 gene. No rearrangement of the FUS gene was detected by FISH, implying discrimination from low-grade fibromyxoid sarcoma. It is suggested that HMGA2 rearrangement and HMGA2 protein overexpression may be associated with the tumorigenesis of odontogenic myxomas/myxofibromas, similar to the case for many other benign mesenchymal tumors.

Low-grade malignant soft-tissue perineurioma: interphase fluorescence in situ hybridization.

Perineuriomas are usually benign soft-tissue tumors that arise from perineurial cells of the peripheral nerve sheath. Low-grade malignant perineurioma is a rare type of perineurioma, presenting with infiltrative growth, low mitotic activity, and a lack of necrosis. This report describes a case of low-grade malignant perineurioma in a 60-year-old man who presented with a growing tumor on the dorsal side of his left wrist. The tumor was surgically excised and showed no adhesion to the surrounding muscle and no continuity with nerves. There was no evidence of recurrence or metastases 12 months after surgery. Histology indicated that the tumor contained hypercellular and hypocellular areas with spindle-shaped cells proliferating in storiform patterns or perivascular whorling. There was moderate infiltrative growth into the surrounding tissue. There was an evident central infarction but no coagulative necrosis. Mitotic figures were observed at 5/10 high-power fields. On immunohistochemistry tumor cells were found to be positive for epithelial membrane antigen, glucose transporter protein 1, and claudin-1. Approximately 18.4% of tumor nuclei were labelled for Ki-67. Interphase fluorescence in situ hybridization on paraffin sections indicated a loss of chromosome 13. This suggests that chromosome 13 abnormalities could also be involved in perineurioma with low-grade malignant potential.

Variation in GABA-A subunit gene copy number in an autistic patient with mosaic 4 p duplication (p12p16).

Autism has been associated with chromosomal aberrations, including duplications at chromosome 4, and the identification of genetic factors contributing to the etiology of this disease is the focus of much research. Here we report a Japanese girl with mosaic of chromosome 4p duplication, mos 46,XX,dup(4)(p12p16)[54]/46,XX[6], who was diagnosed with autism at 3 years of age. Fluorescence in situ hybridization (FISH) with probes covering the region spanning a cluster of the gamma aminobutyric acid A (GABA-A) receptor subunit genes in the proximal short arm of chromosome 4 demonstrated total three signals for the GABRG1, GABRA4, and GABRA2 genes, but only two signals for GABRB1. This suggests that aberrant copy number of the GABA-A receptor subunit genes may contribute to the etiology of autism in this patient.

Extrauterine endometrial stromal sarcoma with JAZF1/JJAZ1 fusion confirmed by RT-PCR and interphase FISH presenting as an inguinal tumor.

Endometrial stromal sarcomas are rare malignant mesenchymal tumors that usually develop in the uterine corpus and occasionally arise at various extrauterine sites. This report describes the first case of primary extrauterine endometrial stromal sarcoma arising in the extraperitoneal portion of the round ligament presenting as a solitary inguinal mass in a 46-year-old woman. The patient presented gradually growing tumor in the right inguinal region. Local tumor resection was performed and no recurrence or metastasis was found at 15 months after the operation. Histological examination revealed that the tumor comprised uniform, spindle-shaped cells with blunt nuclear figure and scattered small arteries, and infiltrated into adjacent tissue. No endometriosis was morphologically identified in the lesion. Immunohistochemically, the tumor cells were positive for CD10, estrogen receptor, progesterone receptor, alpha-smooth muscle actin, and calponin. We confirmed JAZF1/JJAZ1 fusion by reverse transcription-polymerase chain reaction and the corresponding chromosomal translocation by interphase fluorescence in situ hybridization on paraffin sections. It is essential that the inguinal region should be recognized as a possible primary site of endometrial stromal sarcoma, and the detection of a JAZF1/JJAZ1 fusion can be useful when the diagnosis is not confirmed by microscopic observation or immunohistochemistry for the tumor arising in extrauterine sites.

PCS/MVA syndrome caused by an Alu insertion in the BUB1B gene.

We report a case of premature chromatid separation/mosaic variegated aneuploidy syndrome identified by microcephaly on fetal ultrasound and confirmed by cytogenetic analysis of amniotic fluid. Initial mutational analysis of the entire coding region of the BUB1B gene failed to identify any causative mutations. However, further analysis revealed a known compound heterozygous mutation in the upstream region of this gene and a novel Alu insertion mutation in the intron.

A girl with infantile neuronal ceroid lipofuscinosis caused by novel PPT1 mutation and paternal uniparental isodisomy of chromosome 1.

BACKGROUND: Infantile neuronal ceroid lipofuscinosis (INCL) is an autosomal recessive disorder starting in infancy as early as 12-month-old, caused by PPT1 (palmitoyl-protein thioesterase 1) mutations, and characterized by progressive psychomotor deterioration, brain atrophy, myoclonic jerk and visual impairment. INCL can be diagnosed by brain magnetic resonance image (MRI) prior to rapid deterioration stage. To date, there is no INCL patient whose manifestation was caused by uniparental isodisomy (UPiD). PATIENT: We reported a girl diagnosed with INCL. Genetic analysis revealed a novel PPT1 mutation c.20_47del28:p.Leu7Hisfs*21. Only the father of the patient was found as a carrier of this mutation. SNP array showed the mutation became homozygous by paternal UPiD of chromosome 1. DISCUSSION: Although ICNL is a rare disease except in Finland, it is not difficult to diagnose it since the clinical symptoms and MRI findings are characteristic. Genetic testing is useful for definitive diagnosis, and distinction of UPiD is essential for genetic counseling.

Incidence of diffuse large B-cell lymphoma of germinal center B-cell origin in whole diffuse large B-cell lymphoma: tissue fluorescence in situ hybridization using t(14;18) compared with immunohistochemistry.

Diffuse large B-cell lymphoma (DLBCL) can be divided into prognostically important categories such as germinal center B (GCB)-like and non-GCB-like groups. The t(14;18)(q32;q21) translocation defines a unique subset of DLBCL cases with a GCB gene expression profile. Two-color fluorescence in situ hybridization (FISH) analysis was applied to detect t(14;18) (q32;q21) in the nuclei of paraffin-embedded tissue sections from 61 patients with de novo DLBCL. Nine (15%) of 61 cases had a positive pattern. Fifty-seven cases were subclassified in an immunohistochemical study with anti-CD10, anti-bcl-6, and anti-MUM1 antibodies. In this classification, 21 cases (37%) were placed in the GCB group, and 36 (63%) were placed in the non-GCB group. There was a discrepancy between t(14;18) occurrence and bcl-2 protein expression. Bcl-2 protein expression was positive in 40 (67%) of 60 cases. The expression of bcl-2 protein in the GCB and non-GCB groups was not significantly different: 15 (71%) of 21 cases in the GCB group and 24 (67%) of 36 cases in the non-GCB group tested positive. We found no difference between the FISH-positive and FISH-negative groups in overall survival time (P = .6019, log-rank test). The overall survival rates of GCB and non-GCB groups did not differ significantly by immunohistochemical classification (P = .5399, log-rank test). Overall survival was significantly longer in the group with a low International Prognostic Index (IPI) score than in the group with a high IPI score (P = .0002, log-rank test). Our results suggest that immunohistochemical study and cytogenetic study with t(14;18) FISH cannot predict the clinical outcomes of DLBCL patients. A study with a larger number of patients may show a difference in clinical outcomes between FISH-positive and FISH-negative groups and between GCB and non-GCB groups.