Complex chromosomal 6q rearrangements revealed by combined long-molecule genomics technologies.

Technologies for detecting structural variation (SV) have advanced with the advent of long-read sequencing, which enables the validation of SV at a nucleotide level. Optical genome mapping (OGM), a technology based on physical mapping, can also provide comprehensive SVs analysis. We applied long-read whole genome sequencing (LRWGS) to accurately reconstruct breakpoint (BP) segments in a patient with complex chromosome 6q rearrangements that remained elusive by conventional karyotyping. Although all BPs were precisely identified by LRWGS, there were two possible ways to construct the BP segments in terms of their orders and orientations. Thus, we also used OGM analysis. Notably, OGM recognized entire inversions exceeding 500 kb in size, which LRWGS could not characterize. Consequently, here we successfully unveil the full genomic structure of this complex chromosomal 6q rearrangement and cryptic SVs through combined long-molecule genomic analyses, showcasing how LRWGS and OGM can complement each other in SV analysis.

De novo non-synonymous DPYSL2 (CRMP2) variants in two patients with intellectual disabilities and documentation of functional relevance through zebrafish rescue and cellular transfection experiments.

Collapsin response mediator protein 2 (Crmp2) is an evolutionarily well-conserved tubulin-binding cytosolic protein that plays critical roles in the formation of neural circuitry in model organisms including zebrafish and rodents. No clinical evidence that CRMP2 variants are responsible for monogenic neurogenic disorders in humans presently exists. Here, we describe two patients with de novo non-synonymous variants (S14R and R565C) of CRMP2 and intellectual disability associated with hypoplasia of the corpus callosum. We further performed various functional assays of CRMP2 variants using zebrafish and zebrafish Crmp2 (abbreviated as z-CRMP2 hereafter) and an antisense morpholino oligonucleotide [AMO]-based experimental system in which crmp2-morphant zebrafish exhibit the ectopic positioning of caudal primary (CaP) motor neurons. Whereas the co-injection of wild-type z-CRMP2 mRNA suppressed the ectopic positioning of CaP motor neurons in Crmp2-morphant zebrafish, the co-injection of R566C or S15R, z-CRMP2, which corresponds to R565C and S14R of human CRMP2, failed to rescue the ectopic positioning. Transfection experiments of zebrafish or rat Crmp2 using plasmid vectors in HeLa cells, with or without a proteasome inhibitor, demonstrated that the expression levels of mutant Crmp2 protein encoded by R565C and S14R CRMP2 variants were decreased, presumably because of increased degradation by proteasomes. When we compared CRMP2-tubulin interactions using co-immunoprecipitation and cellular localization studies, the R565C and S14R mutations weakened the interactions. These results collectively suggest that the CRMP2 variants detected in the present study consistently led to the loss-of-function of CRMP2 protein and support the notion that pathogenic variants in CRMP2 can cause intellectual disabilities in humans.

Development of individuals with thanatophoric dysplasia surviving beyond infancy.

BACKGROUND: This study aimed to analyze the physical and psychosocial development of long-term survivors (age >1 year) of thanatophoric dysplasia (TD). METHODS: The participants were 20 long-term survivors recruited from a cohort obtained through a nationwide survey for TD conducted across 147 pediatric departments in Japan between 2012 and 2016. Their guardians consented to participate in this study. Medical and psychosocial information was collected through questionnaires and interviews with primary physicians and guardians. RESULTS: The participants were 1.2-27.8 years old, and all showed marked growth deficiency. The mean length at birth was 36 cm (-3.4 SD to -7.9 SD). The adult height (age >16 years) was <-15.2 SD. All individuals showed severely delayed psychomotor development. The highest level of psychosocial development was equivalent to that at 2 years of age. Skin disorders (acanthosis nigricans and seborrheic keratoses) were common. Eleven subjects had been hospitalized or institutionalized consistently after birth, and nine had been moved to home care, and four were exclusively orally fed. All individuals required assisted ventilation. CONCLUSIONS: Long-term survival of TD individuals is common. Some individuals enjoy home-based lives; however, they are severely psychosocially and physically disabled and require meticulous respiratory and nutritional support.

Ferroportin Disease Caused by a Heterozygous Variant p.Cys326Phe in the SLC40A1 Gene and the Efficacy of Therapeutic Phlebotomy in Children.

Therapeutic phlebotomy is recommended for treating hereditary hemochromatosis. However, the procedure and its efficacy for children remain unclear. We describe a young female patient with ferroportin disease, which was confirmed from excess iron deposition within hepatocytes and by identifying a heterozygous variant p.Cys326Phe in SLC40A1. She had been followed without phlebotomy. Liver histology at age 13 years revealed iron deposition progression. Phlebotomy was initiated and her iron markers and imaging findings improved without severe adverse effects. Therapeutic phlebotomy for children is effective and well-tolerated and should be considered as early as possible after a hemochromatosis diagnosis.

National survey of prevalence and prognosis of thanatophoric dysplasia in Japan.

BACKGROUND: Thanatophoric dysplasia (TD) is a rare congenital disease of the skeletal system, with an incidence of 1.68-8.3 per 100 000 births, but statistical data on the estimated number of TD patients across Japan are not available. The aim of this study was therefore to investigate the prevalence and prognosis of TD in Japan. METHODS: A nationwide primary questionnaire survey was conducted. RESULTS: A total of 127 obstetric, 186 pediatric, and 115 orthopedic facilities provided responses. Excluding duplications, we identified 73 patients with TD. Of the 73 cases, 15 were abortions, four were stillbirths, 51 were live births, and three had unknown details. Of the 51 live newborns, 27 died ≤7 days after birth, with an early neonatal mortality rate of 56%. Of the 24 newborns who survived the early neonatal period, 16 survived for ≥1 year. All of the 24 newborns received respiratory management and survived during the early neonatal period. Of the 51 live newborns, 25 did not receive respiratory management and died ≤2 days after birth. CONCLUSIONS: The prevalence of TD in Japan is estimated to be at 1.1 (95%CI: 0.84-1.37) per 100 000 births, but the actual incidence is expected to be higher. To our knowledge, we have confirmed for the first time that newborns with TD may not always die during the early neonatal period but can survive the early neonatal period with appropriate respiratory management. Therefore, the term "thanatophoric dysplasia" does not accurately reflect the nature of the disease.

Self-perceptions from people with Down syndrome in Japan.

Self-perception of people with Down Syndrome (DS) was originally studied in the United States in 2011; this study indicated that 99% of people with DS are happy with their lives. In this study, we investigated self-perceptions of people with DS in Japan and compared the results to the previous study made in the United States. The participants (n = 300) were 12 years old or older and members of Japan Down Syndrome Society (JDS). The questionnaire was collected between 30 October 2015 and 26 November 2015. Of 96(32%) responses, 76 (97%) agreed they are happy with their lives. We found that most people with DS in Japan also feel positive about themselves and their lives. Along with the start of Non-Invasive Prenatal Testing in Japan, DS draws an attention from Japanese people because maternal age has been increasing. This has resulted in the growth of the number of prenatal tests marketed in Japan. Therefore, we expect our results to be relevant to genetic counseling for the couples considering prenatal tests or parents raising their children with DS so that they have a clearer image about life with DS and can better visualize their life plans.

Novel compound heterozygous DPH1 mutations in a patient with the unique clinical features of airway obstruction and external genital abnormalities.

The diphthamide biosynthesis 1 (DPH1) gene encodes one of the essential components of the enzyme catalyzing the first step of diphthamide formation on eukaryotic elongation factor 2 (EEF2). Diphthamide is the posttranslationally modified histidine residue on EEF2 that promotes protein chain elongation in the ribosome. DPH1 defects result in a failure of protein synthesis involving EEF2, leading to growth defects, embryonic lethality, and cell death. In humans, DPH1 mutations cause developmental delay with a short stature, dysmorphic features, and sparse hair, and are inherited in an autosomal recessive manner (MIM#616901). To date, only two homozygous missense mutations in DPH1 (c.17T>A, p.Met6Lys and c.701T>C, p.Leu234Pro) have been reported. We used WES to identify novel compound heterozygous mutations in DPH1 (c.289delG, p.Glu97Lysfs*8 and c.491T>C, p.Leu164Pro) in a patient from a nonconsanguineous family presenting with intellectual disability, a short stature, craniofacial abnormalities, and external genital abnormalities. The clinical phenotype of all patients with DPH1 mutations, including the current patient, revealed core features, although the external genital anomaly was newly recognized in our case.

Psychological distress in post-partum women after non-invasive prenatal testing (NIPT) in Japan.

AIM: The purpose of this study was to clarify the characteristics of psychological mental distress in post-partum women after non-invasive prenatal testing (NIPT) in Japan. METHODS: Psychological mental distress was assessed using the Kessler Psychological Distress Scale (K6). We compared patients with (i) low pre-NIPT K6 and low post-partum K6 scores (control group), and (ii) low pre-NIPT K6 and a high post-partum K6 scores (case group). RESULTS: Among the 697 women who underwent NIPT, 29 (4.2%) had low pre-NIPT K6 and high post-partum K6 scores (case group) and 668 (95.8%) had low pre-NIPT K6 and low post-partum K6 scores (control). Among women with negative NIPT findings, post-partum women with a high K6 score were compared to a control group of women with a low K6 score. Logistic regression analysis showed that primiparity (P = 0.007), low birthweight (P = 0.005) and use of intracytoplasmic sperm injection (P = 0.02) and assisted reproductive technology (P = 0.05) were significantly different between the groups. CONCLUSION: Even if women do not feel mental distress before NIPT, they may develop mental stress post-partum. In particular, primipara women who conceived through assisted reproductive technology (especially intracytoplasmic sperm injection) and gave birth to a low birthweight baby were more susceptible to developing post-partum distress. Thus, it is important to educate women that support is available, with consultation with other healthcare professionals during genetic counseling if necessary. Further studies are needed in order to determine the factors associated with post-partum mental distress.

The severe clinical phenotype for a heterozygous Fabry female patient correlates to the methylation of non-mutated allele associated with chromosome 10q26 deletion syndrome.

Heterozygous Fabry females usually have an attenuated form of Fabry disease, causing them to be symptomatic; however, in rare cases, they can present with a severe phenotype. In this study, we report on a 37-year-old woman with acroparesthesia, a dysmorphic face, left ventricular hypertrophy, and intellectual disability. Her father had Fabry disease and died due to chronic renal and congestive cardiac failure. Her paternal uncle had chronic renal failure and intellectual disability, and her paternal aunt was affected with congestive cardiac failure. The patient has two sisters with no significant medical illness. However, her nephew has acroparesthesia, anhidrosis, and school phobia, and her niece shows mild phenotypes. The patient's enzyme analysis showed very low α-galactosidase A (α-gal A) activity in dried blood spot (DBS), lymphocytes, and skin fibroblasts with massive excretion of Gb3 and Gb2 in urine and lyso-Gb3 in DBS and plasma. Electron microscopic examination showed a large accumulation of sphingolipids in vascular endothelial cells and keratinocytes. Chromosomal analysis and comparative genomic hybridization microarray showed 10q26 terminal deletion. Molecular data showed a novel heterozygous stop codon mutation in exon 1 of the GLA gene in her sisters and niece, and a hemizygous state in her nephew. When we checked the methylation status, we found her non-mutated allele in the GLA gene was methylated. However, the non-mutated alleles of her sisters were non-methylated, and those of her niece were partially methylated. The chromosomal and methylation study may speculate the severity of her clinical phenotypes.

Genetic Counseling for Couples Seeking Noninvasive Prenatal Testing in Japan: Experiences of Pregnant Women and their Partners.

The recent advent of noninvasive prenatal testing (NIPT) has had a significant impact in the field of prenatal testing. Although reports on pregnant women who used NIPT have accumulated, little is known about the experiences of their male partners. In this study, we assessed the experiences of couples who were expecting a child and undergoing NIPT, with a focus on both the pregnant women and their partners. Questionnaires were administered to 282 participants focusing on their specific experiences at three time points: after pre-test counseling (first visit), when undergoing NIPT (second visit), and when results were received (third visit). Responses were analyzed to assess the differences between pregnant women and their partners. We found that more partners selected "family" as their first information source about NIPT and "my partner" as the first person to request NIPT than did pregnant women (35.6 vs. 5.9 %; p < 0.001 and 19.3 vs.1.5 %; p < 0.001). However, pregnant women more often consulted others including family and friends until undergoing NIPT than their partners (89.1 vs. 54.6 %; p < 0.001). Our findings suggest that it is important to encourage male partners to be actively involved in the NIPT decision-making process. Differences between pregnant women and their partners should be seriously considered when providing genetic counseling.

SNP array screening of cryptic genomic imbalances in 450 Japanese subjects with intellectual disability and multiple congenital anomalies previously negative for large rearrangements.

Intellectual disability (ID) is a heterogeneous condition affecting 2-3% of the population, often associated with multiple congenital anomalies (MCA). The genetic cause remains largely unexplained for most cases. To investigate the causes of ID/MCA of unknown etiology in the Japanese population, 645 subjects have been recruited for the screening of pathogenic copy-number variants (CNVs). Two screenings using bacterial artificial chromosome (BAC) arrays were previously performed, which identified pathogenic CNVs in 133 cases (20.6%; Hayashi et al., J. Hum. Genet., 2011). Here, we present the findings of the third screening using a single-nucleotide polymorphism (SNP) array, performed in 450 negative cases from our previous report. Pathogenic CNVs were found in 22 subjects (4.9%), in which 19 CNVs were located in regions where clinical significance had been previously established. Among the 22 cases, we identified PPFIA2 as a novel candidate gene for ID. Analysis of copy-neutral loss of heterozygosity (CNLOH) detected one case in which the CNLOH regions seem to be significant. The SNP array detected a modest fraction of small causative CNVs, which is explained by the fact that the majority of causative CNVs have larger sizes, and those had been mostly identified in the two previous screenings.

Background of couples undergoing non-invasive prenatal testing in Japan.

AIM: Our purpose was to assess the background of couples who were undergoing non-invasive prenatal testing (NIPT) in Japan. METHODS: The characteristics of 2486 women who had visited Nagoya City University Hospital for NIPT were compared with Japanese Demographic Trends as controls. The questionnaire included items regarding the maternal and paternal age, maternal age at marriage, age at first live birth, and conception mode. RESULTS: Compared with the controls, the percentage of women who were 4 or more years older than their partners was larger in the NIPT group (11.8% vs 6.5%). The maternal age at marriage, age at first live birth, and the duration between marriage and first birth tended to be greater in the NIPT group (32.6 years vs 29.3 years, 36.9 years vs 30.4 years, and 3.6 years vs 2.4 years, respectively), and the percentage of women who underwent assisted reproductive technology tended to be higher in the NIPT group (35-39 years: 21.2% vs 7.5%, 40-45 years: 36.2% vs 12.6%), compared with the controls. CONCLUSION: Knowing the specific backgrounds of couples who have undergone NIPT may be important for improving the quality of genetic counseling for NIPT.

Additional patients with 4q deletion: Severe growth delay and polycystic kidney disease associated with 4q21q22 loss.

BACKGROUND: To the best of our knowledge, this is the third report concerning 4q21q22 deletions. In this report, we describe the cases of two girls with 4q deletion and polycystic kidney disease. G-banding confirmed the deletion in one patient but not in the other. METHODS: We describe the cases of two girls with 4q deletion and polycystic kidney disease. Chromosomal deletions were mapped to 4q21-22. One patient had a simple 4q contiguous gene deletion, whereas the other patient had a complicated chromosomal rearrangement. In patient 1, a smaller part of the 4q deletion was translocated to the 3p region. RESULTS: Fifty-four genes and 72 genes were deleted in patients 1 and 2, respectively. In both patients, 52 genes were consistently deleted. CONCLUSION: The present two patients had a similar phenotype, including severe growth and developmental retardation, and a characteristic facial appearance. The loss of RPKG2 and RASGEF1B causes severe growth defect. PKD2 loss causes kidney cysts.

Hypergonadotropic hypogonadism and hypersegmented neutrophils in a patient with ataxia-telangiectasia-like disorder: potential diagnostic clues?

Ataxia-telangiectasia-like disorder (ATLD) is a rare autosomal recessive disorder, and has symptoms similar to ataxia-telangiectasia (AT). ATLD is caused by mutations in the MRE11 gene, involved in DNA double-strand break repair (DSBR). In contrast to AT, ATLD patients lack key clinical features, such as telangiectasia or immunodeficiency, and are therefore difficult to be diagnosed. We report a female ATLD patient presenting with hypergonadotropic hypogonadism and hypersegmented neutrophils, previously undescribed features in this disorder, and potential diagnostic clues to differentiate ATLD from other conditions. The patient showed slowly progressive cerebellar ataxia from 2 years of age, and MRI revealed atrophy of the cerebellum, oculomotor apraxia, mild cognitive impairment, writing dystonia, hypergonadotropic hypogonadism with primary amenorrhea, and hypersegmented neutrophils. Western blot assay demonstrated total loss of MRE11 and reduction of ATM-dependent phosphorylation; thus, we diagnosed ATLD. Genetically, a novel missense mutation (c.140C>T) was detected in the MRE11 gene, but no other mutation was found in the patient. Our presenting patient suggests that impaired DSBR may be associated with hypergonadotropic hypogonadism and neutrophil hypersegmentation. In conclusion, when assessing patients with ataxia of unknown cause, ATLD should be considered, and the gonadal state and peripheral blood smear samples evaluated.

Compound heterozygous deletions in pseudoautosomal region 1 in an infant with mild manifestations of langer mesomelic dysplasia.

Haploinsufficiency of SHOX on the short arm pseudoautosomal region (PAR1) leads to Leri-Weill dyschondrosteosis (LWD), and nullizygosity of SHOX results in Langer mesomelic dysplasia (LMD). Molecular defects of LWD/LMD include various microdeletions in PAR1 that involve exons and/or the putative upstream or downstream enhancer regions of SHOX, as well as several intragenic mutations. Here, we report on a Japanese male infant with mild manifestations of LMD and hitherto unreported microdeletions in PAR1. Clinical analysis revealed mesomelic short stature with various radiological findings indicative of LMD. Molecular analyses identified compound heterozygous deletions, that is, a maternally inherited ∼46 kb deletion involving the upstream region and exons 1-5 of SHOX, and a paternally inherited ∼500 kb deletion started from a position ∼300 kb downstream from SHOX. In silico analysis revealed that the downstream deletion did not affect the known putative enhancer regions of SHOX, although it encompassed several non-coding elements which were well conserved among various species with SHOX orthologs. These results provide the possibility of the presence of a novel enhancer for SHOX in the genomic region ∼300 to ∼800 kb downstream of the start codon.

Clinical application of array-based comparative genomic hybridization by two-stage screening for 536 patients with mental retardation and multiple congenital anomalies.

Recent advances in the analysis of patients with congenital abnormalities using array-based comparative genome hybridization (aCGH) have uncovered two types of genomic copy-number variants (CNVs); pathogenic CNVs (pCNVs) relevant to congenital disorders and benign CNVs observed also in healthy populations, complicating the screening of disease-associated alterations by aCGH. To apply the aCGH technique to the diagnosis as well as investigation of multiple congenital anomalies and mental retardation (MCA/MR), we constructed a consortium with 23 medical institutes and hospitals in Japan, and recruited 536 patients with clinically uncharacterized MCA/MR, whose karyotypes were normal according to conventional cytogenetics, for two-stage screening using two types of bacterial artificial chromosome-based microarray. The first screening using a targeted array detected pCNV in 54 of 536 cases (10.1%), whereas the second screening of the 349 cases negative in the first screening using a genome-wide high-density array at intervals of approximately 0.7 Mb detected pCNVs in 48 cases (13.8%), including pCNVs relevant to recently established microdeletion or microduplication syndromes, CNVs containing pathogenic genes and recurrent CNVs containing the same region among different patients. The results show the efficient application of aCGH in the clinical setting.

HRAS mutants identified in Costello syndrome patients can induce cellular senescence: possible implications for the pathogenesis of Costello syndrome.

Costello syndrome (CS) is a congenital disease that is characterized by a distinctive facial appearance, failure to thrive, mental retardation and cardiomyopathy. In 2005, we discovered that heterozygous germline mutations in HRAS caused CS. Several studies have shown that CS-associated HRAS mutations are clustered in codons 12 and 13, and mutations in other codons have also been identified. However, a comprehensive comparison of the substitutions identified in patients with CS has not been conducted. In the current study, we identified four mutations (p.G12S, p.G12A, p.G12C and p.G12D) in 21 patients and analyzed the associated clinical manifestations of CS in these individuals. To examine functional differences among the identified mutations, we characterized a total of nine HRAS mutants, including seven distinct substitutions in codons 12 and 13, p.K117R and p.A146T. The p.A146T mutant demonstrated the weakest Raf-binding activity, and the p.K117R and p.A146T mutants had weaker effects on downstream c-Jun N-terminal kinase signaling than did codon 12 or 13 mutants. We demonstrated that these mutant HRAS proteins induced senescence when overexpressed in human fibroblasts. Oncogene-induced senescence is a cellular reaction that controls cell proliferation in response to oncogenic mutation and it has been considered one of the tumor suppression mechanisms in vivo. Our findings suggest that the HRAS mutations identified in CS are sufficient to cause oncogene-induced senescence and that cellular senescence might therefore contribute to the pathogenesis of CS.

A familial case of overgrowth syndrome caused by a 9q22.3 microdeletion in a mother and daughter.

Microdeletions in the 9q22.3 chromosomal region can cause macrosomia with characteristic features, including prenatal-onset overgrowth, metopic craniosynostosis, hydrocephalus, developmental delay, and intellectual disability, in addition to manifestations of nevoid basal cell carcinoma syndrome (NBCCS). Haploinsufficiency of PTCH1 may be responsible for accelerated overgrowth, but the mechanism of macrosomia remains to be elucidated. We report a familial case with a 9q22.3 microdeletion, manifesting with prenatal-onset overgrowth in a mother and post-natal overgrowth in her daughter. Although both were clinically diagnosed with NBCCS, they had characteristic features of 9q22.3 microdeletion, especially the daughter. Microarray comparative genomic hybridization analysis revealed a 4.0 Mb deletion of chromosome 9q22.3 in both individuals. Among the 11 reported patients of overgrowth and/or macrosomia, a 550 Kb region encompassing PTCH1, C9orf3, FANCC, and 5 miRNAs is the most commonly deleted region. The let-7 family miRNAs, which are involved in diverse cellular processes including growth and tumor processes, were identified in the deleted regions in 10 of 11 patients. Characteristic features of 9q22.3 microdeletion might be associated with decreased expression of let-7.

A family case of X-linked Alport syndrome patients with a novel variant in COL4A5.

We herein report 2 Japanese patients with X-linked Alport syndrome (XLAS), with a novel variant in COL4A5. Patient 1 was a 16-year-old Japanese girl with a history of microscopic hematuria, without proteinuria, renal dysfunction, deafness, or ocular abnormalities. At 13 years of age, renal biopsy was performed; however, a diagnosis of AS was not considered. When her mother (patient 2) was 40 years of age (3 years after patient 1 underwent a renal biopsy), patient 2 was found to have asymptomatic hematuria, proteinuria, and an increased serum creatinine level, without deafness and ocular abnormalities. Subsequently, immunofluorescence staining for alpha 5 chains of type IV collagen was performed in patient 1. Pathological findings were consistent with AS, and genetic analysis demonstrated that both patients had a heterozygous mutation in COL4A5 (NM_000495.4: exon41:c.C3769T: p.Q1257X). To date, more than 900 different COL4A5 mutations have been identified; however, this variant has not been previously described. Physicians have to consider AS when they perform a renal biopsy in all patients with hematuria despite absent/present of family history, hearing loss, and ocular abnormality. Especially, when findings of light microscopy and immunofluorescence microscope are unclear, it should be considered carefully. Electron microscopy findings are very important.