Kenji Naritomi

Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome.

By exome sequencing, we found de novo SMARCB1 mutations in two of five individuals with typical Coffin-Siris syndrome (CSS), a rare autosomal dominant anomaly syndrome. As SMARCB1 encodes a subunit of the SWItch/Sucrose NonFermenting (SWI/SNF) complex, we screened 15 other genes encoding subunits of this complex in 23 individuals with CSS. Twenty affected individuals (87%) each had a germline mutation in one of six SWI/SNF subunit genes, including SMARCB1, SMARCA4, SMARCA2, SMARCE1, ARID1A and ARID1B.

Spectrum of MLL2 (ALR) mutations in 110 cases of Kabuki syndrome.

Kabuki syndrome is a rare, multiple malformation disorder characterized by a distinctive facial appearance, cardiac anomalies, skeletal abnormalities, and mild to moderate intellectual disability. Simplex cases make up the vast majority of the reported cases with Kabuki syndrome, but parent‐to‐child transmission in more than a half‐dozen instances indicates that it is an autosomal dominant disorder. We recently reported that Kabuki syndrome is caused by mutations in MLL2, a gene that encodes a Trithorax‐group histone methyltransferase, a protein important in the epigenetic control of active chromatin states. Here, we report on the screening of 110 families with Kabuki syndrome. MLL2 mutations were found in 81/110 (74%) of families. In simplex cases for which DNA was available from both parents, 25 mutations were confirmed to be de novo, while a transmitted MLL2 mutation was found in two of three familial cases. The majority of variants found to cause Kabuki syndrome were novel nonsense or frameshift mutations that are predicted to result in haploinsufficiency. The clinical characteristics of MLL2 mutation‐positive cases did not differ significantly from MLL2 mutation‐negative cases with the exception that renal anomalies were more common in MLL2 mutation‐positive cases. These results are important for understanding the phenotypic consequences of MLL2 mutations for individuals and their families as well as for providing a basis for the identification of additional genes for Kabuki syndrome.

Clinical correlations of mutations affecting six components of the SWI/SNF complex: Detailed description of 21 patients and a review of the literature

Mutations in the components of the SWItch/sucrose nonfermentable (SWI/SNF)‐like chromatin remodeling complex have recently been reported to cause Coffin–Siris syndrome (CSS), Nicolaides–Baraitser syndrome (NCBRS), and ARID1B‐related intellectual disability (ID) syndrome. We detail here the genotype‐phenotype correlations for 85 previously published and one additional patient with mutations in the SWI/SNF complex: four with SMARCB1 mutations, seven with SMARCA4 mutations, 37 with SMARCA2 mutations, one with an SMARCE1 mutation, three with ARID1A mutations, and 33 with ARID1B mutations. The mutations were associated with syndromic ID and speech impairment (severe/profound in SMARCB1, SMARCE1, and ARID1A mutations; variable in SMARCA4, SMARCA2, and ARID1B mutations), which was frequently accompanied by agenesis or hypoplasia of the corpus callosum. SMARCB1 mutations caused “classical” CSS with typical facial “coarseness” and significant digital/nail hypoplasia. SMARCA4 mutations caused CSS without typical facial coarseness and with significant digital/nail hypoplasia. SMARCA2 mutations caused NCBRS, typically with short stature, sparse hair, a thin vermillion of the upper lip, an everted lower lip and prominent finger joints. A SMARCE1 mutation caused CSS without typical facial coarseness and with significant digital/nail hypoplasia. ARID1A mutations caused the most severe CSS with severe physical complications. ARID1B mutations caused CSS without typical facial coarseness and with mild digital/nail hypoplasia, or caused syndromic ID. Because of the common underlying mechanism and overlapping clinical features, we propose that these conditions be referred to collectively as “SWI/SNF‐related ID syndromes”.

The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations

The Japanese Archipelago stretches over 4000u2009km from north to south, and is the homeland of the three human populations; the Ainu, the Mainland Japanese and the Ryukyuan. The archeological evidence of human residence on this Archipelago goes back to >30u2009000 years, and various migration routes and root populations have been proposed. Here, we determined close to one million single-nucleotide polymorphisms (SNPs) for the Ainu and the Ryukyuan, and compared these with existing data sets. This is the first report of these genome-wide SNP data. Major findings are: (1) Recent admixture with the Mainland Japanese was observed for more than one third of the Ainu individuals from principal component analysis and frappe analyses; (2) The Ainu population seems to have experienced admixture with another population, and a combination of two types of admixtures is the unique characteristics of this population; (3) The Ainu and the Ryukyuan are tightly clustered with 100% bootstrap probability followed by the Mainland Japanese in the phylogenetic trees of East Eurasian populations. These results clearly support the dual structure model on the Japanese Archipelago populations, though the origins of the Jomon and the Yayoi people still remain to be solved.

Missense mutations in the DNA-binding/dimerization domain of NFIX cause Sotos-like features

Sotos syndrome is characterized by prenatal and postnatal overgrowth, characteristic craniofacial features and mental retardation. Haploinsufficiency of NSD1 causes Sotos syndrome. Recently, two microdeletions encompassing Nuclear Factor I-X (NFIX) and a nonsense mutation in NFIX have been found in three individuals with Sotos-like overgrowth features, suggesting possible involvements of NFIX abnormalities in Sotos-like features. Interestingly, seven frameshift and two splice site mutations in NFIX have also been found in nine individuals with Marshall–Smith syndrome. In this study, 48 individuals who were suspected as Sotos syndrome but showing no NSD1 abnormalities were examined for NFIX mutations by high-resolution melt analysis. We identified two heterozygous missense mutations in the DNA-binding/dimerization domain of the NFIX protein. Both mutations occurred at evolutionally conserved amino acids. The c.179T>C (p.Leu60Pro) mutation occurred de novo and the c.362G>C (p.Arg121Pro) mutation was inherited from possibly affected mother. Both mutations were absent in 250 healthy Japanese controls. Our study revealed that missense mutations in NFIX were able to cause Sotos-like features. Mutations in DNA-binding/dimerization domain of NFIX protein also suggest that the transcriptional regulation is abnormally fluctuated because of NFIX abnormalities. In individuals with Sotos-like features unrelated to NSD1 changes, genetic testing of NFIX should be considered.

Identification of Four Novel Synonymous Substitutions in the X-Linked Genes Neuroligin 3 and Neuroligin 4X in Japanese Patients with Autistic Spectrum Disorder

Mutations in the X-linked genes neuroligin 3 (NLGN3) and neuroligin 4X (NLGN4X) were first implicated in the pathogenesis of X-linked autism in Swedish families. However, reports of mutations in these genes in autism spectrum disorder (ASD) patients from various ethnic backgrounds present conflicting results regarding the etiology of ASD, possibly because of genetic heterogeneity and/or differences in their ethnic background. Additional mutation screening study on another ethnic background could help to clarify the relevance of the genes to ASD. We scanned the entire coding regions of NLGN3 and NLGN4X in 62 Japanese patients with ASD by polymerase chain reaction-high-resolution melting curve and direct sequencing analyses. Four synonymous substitutions, one in NLGN3 and three in NLGN4X, were identified in four of the 62 patients. These substitutions were not present in 278 control X-chromosomes from unrelated Japanese individuals and were not registered in the database of Single Nucleotide Polymorphisms build 132 or in the Japanese Single Nucleotide Polymorphisms database, indicating that they were novel and specific to ASD. Though further analysis is necessary to determine the physiological and clinical importance of such substitutions, the possibility of the relevance of both synonymous and nonsynonymous substitutions with the etiology of ASD should be considered.

A commentary on the promise of whole-exome sequencing in medical genetics.

The dawn of next-generation sequencers (NGSs) and innovative sequencing technologies have brought a paradigm shift in medical research and clinical practice. Furthermore, the cost reduction of NGSs enables personalized medicine to come to fruition. However, whole-genome sequencing (WGS) remains expensive when applied to personal genome analysis. WGS generates a large amount of data that requires highperformance computer processing. Targeted whole-exon capture and sequencing [wholeexome sequencing (WES)] is more costeffective when compared with WGS because exons represent only B1–2% of the genome and also higher sequence coverage can be achieved by NGSs. In addition, most Mendelian disorders are caused by exonic mutations or splice-junction mutations, and protein-coding genes harbor B85% of the mutations that have large effects on diseaserelated traits.1 Thus, WES will provide many advantages and lower costs than WGS when analyzing personal genomes. WES was first successfully used in 2010 to discover the gene responsible for Miller syndrome, a Mendelian disorder.2 Since then, WES has been increasingly used as a fast and accurate genomic discovery approach to investigate both rare genetic disorders and common diseases. WES is widely applied across different areas of medicine, because it has the added advantage of reduced cost and requires analysis of a much smaller but essential dataset when compared with WGS. In addition, recent clinical molecular diagnostics have used WES to detect heterogeneous Mendelian diseases.3,4 A recent review of WES approaches in medical genetics describes the usefulness of WES in medicine and medical research and the impact of WES on clinical diagnoses.5 WES approaches have greatly facilitated the discovery of candidate genes or gene variants in Mendelian disorders and rare variants in common diseases and genomic characterization in cancer. Currently, WES is increasingly being applied to disease gene discovery, cancer typing and molecular diagnosis.5 Presently, WES is an essential tool in medical genetics, especially in the research of Mendelian disorders. WES or multigene tests using NGSs are widely applied to heterogeneous disorders including deafness or ciliopathy.5,6 WES is also being increasingly applied to genetic testing for undiagnosed patients.4,5 Yang et al.4 performed WES in undiagnosed patients whose phenotypes were suggestive of potential genetic disorders and achieved a molecular diagnosis for 62 of 250 (25%) patients. Because WES detects individual genetic variation, it can be used to construct a variation database of anthropic and ethnic populations. At the same time, because WES can detect groups of genetic variations that are unrelated to the indication for the first diagnostic purpose but are of medical value for individual patient care, such ‘incidental findings’ pose potential ethical problems that should be strongly considered and discussed in clinical practice.5,7 WES is a widely applied technique in medical genetics that is capable of detecting variations in whole exons. However, in practical use, understanding WES methodology and limitations are important. Current WES techniques are not capable of detecting all of the variations surrounding exons. Detecting variation by WES is limited by the experimental methods, probe coverage and/or platforms used.8–10 Hence, WES may not always detect pathogenic or causative variations in a genetic disease. In addition, because WES is a method to detect genomic sequence variations, when a candidate of causative variation in the disease is detected, it requires verification or support by secondary analyses. In particular, further functional analyses are important to confirm whether the variant is pathogenic or benign. Nevertheless, WES enables the unprecedented low cost and highly efficient analysis of whole exons. WES can be easily used to comprehensively detect individual variations in exons. It is without doubt that WES is a powerful tool in genome analysis, and it greatly progresses medical genetics. Although WESs’ limitations need to be overcome, we anticipate that WES will be used not only in medical research but also in clinical practice for example, molecular diagnosis (whole-gene test) and personal genomics before WGS becomes a common place in medical genetics. Thus, a paradigm shift in medicine by advancement in both WES and WGS is expected to continue.

Prenatal diagnosis of X‐linked recessive Lenz microphthalmia syndrome

Lenz microphthalmia syndrome comprises microphthalmia–anophthalmia with mental retardation, malformed ears and skeletal anomalies, and is inherited in an X‐linked recessive pattern. In 2004, it was reported that the missense mutation (BCL‐6 co‐repressor gene [BCOR] c.254C>T, p.P85L) in a single family with Lenz microphthalmia syndrome co‐segregated with the disease phenotype. We report a case of prenatal diagnosis for X‐linked recessive Lenz microphthalmia syndrome with the mutation. A 32‐year‐old gravida 5, para 2 Japanese woman was referred to Nagoya City University Hospital at 15 weeks of gestation. After genetic counseling and informed consent, amniocentesis was performed for fetal karyotyping, which was 46,XY. Using the extracted DNA from cultured amniotic cells, fetal search for BCOR c.254C>T mutation was undertaken. The couple requested medical termination of pregnancy, and the postabortion examination confirmed the diagnosis. This is the third report of a BCOR mutation, associated with X‐linked syndromic microphthalmia, and most importantly, it is always the same mutation. The prenatal genetic diagnosis of the Lenz microphthalmia syndrome allowed time for parental counseling and delivery planning.

A commentary on The diagnostic utility of exome sequencing in Joubert syndrome and related disorders

A commentary on The diagnostic utility of exome sequencing in Joubert syndrome and related disorders

Pathogenic substitution of IVS15 + 5G > A in SLC26A4 in patients of Okinawa Islands with enlarged vestibular aqueduct syndrome or Pendred syndrome

BackgroundPendred syndrome (PS) and nonsyndromic hearing loss associated with enlarged vestibular aqueduct (EVA) are caused by SLC26A4 mutations. The Okinawa Islands are the southwestern-most islands of the Japanese archipelago. And ancestral differences have been reported between people from Okinawa Island and those from the main islands of Japan. To confirm the ethnic variation of the spectrum of SLC26A4 mutations, we investigated the frequencies of SLC26A4 mutations and clinical manifestations of patients with EVA or PS living in the Okinawa Islands.MethodsWe examined 22 patients with EVA or PS from 21 unrelated families in Okinawa Islands. The patient’s clinical history, findings of physical and otoscopic examinations, hearing test, and computed tomography (CT) scan of the temporal bones were recorded. To detect mutations, all 21 exons and the exon–intron junctions of SLC26A4 were sequenced for all subjects. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) for SLC26A4 and calculations using the comparative CT (2−ΔΔCT) method were used to determine the pathogenicity associated with gene substitutions.ResultsSLC26A4 mutations were identified in 21 of the 22 patients. We found a compound heterozygous mutation for IVS15u2009+u20095G > A/H723R in nine patients (41%), a homozygous substitution of IVS15u2009+u20095G > A in six patients (27%), and homozygous mutation for H723R in five patients (23%). The most prevalent types of SLC26A4 alleles were IVS15u2009+u20095G > A and H723R, which both accounted for 15/22 (68%) of the patients. There were no significant correlations between the types of SLC26A4 mutation and clinical manifestations. Based on qRT-PCR results, expression of SLC26A4 was not identified in patients with the homozygous substitution of IVS15u2009+u20095G > A.ConclusionsThe substitution of IVS15u2009+u20095G > A in SLC26A4 was the most common mutation in uniquely found in patients with PS and EVA in Okinawa Islands. This suggested that the spectrum of SLC26A4 mutation differed from main islands of Japan and other East Asian countries. The substitution of IVS15u2009+u20095G > A leads to a loss of SLC26A expression and results in a phenotype of PS and EVA.