Sinitdhorn Rujirabanjerd

A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation

Large-scale systematic resequencing has been proposed as the key future strategy for the discovery of rare, disease-causing sequence variants across the spectrum of human complex disease. We have sequenced the coding exons of the X chromosome in 208 families with X-linked mental retardation (XLMR), the largest direct screen for constitutional disease-causing mutations thus far reported. The screen has discovered nine genes implicated in XLMR, including SYP, ZNF711 and CASK reported here, confirming the power of this strategy. The study has, however, also highlighted issues confronting whole-genome sequencing screens, including the observation that loss of function of 1% or more of X-chromosome genes is compatible with apparently normal existence.

Mutations in the guanine nucleotide exchange factor gene IQSEC2 cause nonsyndromic intellectual disability

The first family identified as having a nonsyndromic intellectual disability was mapped in 1988. Here we show that a mutation of IQSEC2, encoding a guanine nucleotide exchange factor for the ADP-ribosylation factor family of small GTPases, caused this disorder. In addition to MRX1, IQSEC2 mutations were identified in three other families with X-linked intellectual disability. This discovery was made possible by systematic and unbiased X chromosome exome resequencing.

Identification and characterization of two novel JARID1C mutations: suggestion of an emerging genotype–phenotype correlation

Mental retardation (MR) is characterized by cognitive impairment with an IQ <70. Many of the major causes are genetically determined and the ∼30% male excess suggests that mutations in genes carried on the X chromosome are disproportionably represented. One such gene, jumonji AT-rich interactive domain 1C (JARID1C) on Xp11.2, has been identified in families with X-linked MR (XLMR), with 18 different mutations reported to date. As part of a systematic resequencing of 720 genes in 208 XLMR families of the International Genetic of Learning Disability (IGOLD) consortium, two novel nucleotide changes in the JARID1C coding region were identified, with the nucleotide changes segregating with the disease phenotype in the two families. The first mutation is a single-nucleotide insertion in exon 21 (c.3258_3259insC p.K1087fs*43) causing a frameshift and resulting in a premature termination codon (PTC). Such PTC-containing mRNAs are generally degraded by nonsense-mediated mRNA decay (NMD) surveillance, but our results show that this is not the case with this mutation. The other change is a single-nucleotide substitution in exon 12 (c.1160C>A) in a published family with nonsyndromic MR, MRX13. This change occurs in a highly conserved amino acid, with proline (P) being substituted by threonine (T) (p.P544T). Functional analysis shows that this amino-acid substitution compromises both tri- and didemethylase activity of the JARID1C protein. We conclude that the two novel changes impair JARID1C protein function and are disease-causing mutations in these families.

A distinctive gene expression fingerprint in mentally retarded male patients reflects disease-causing defects in the histone demethylase KDM5C

BackgroundMental retardation is a genetically heterogeneous disorder, as more than 90 genes for this disorder has been found on the X chromosome alone. In addition the majority of patients are non-syndromic in that they do not present with clinically recognisable features. This makes it difficult to determine the molecular cause of this disorder on the basis of the phenotype alone. Mutations in KDM5C (previously named SMCX or JARID1C), a gene that encodes a transcriptional regulator with histone demethylase activity specific for dimethylated and trimethylated H3K4, are a comparatively frequent cause of non-syndromic X-linked mental retardation (NS-XLMR). Specific transcriptional targets of KDM5C, however, are still unknown and the effects of KDM5C deficiency on gene expression have not yet been investigated.ResultsBy whole-mount in situ hybridisation we showed that the mouse homologue of KDM5C is expressed in multiple tissues during mouse development.We present the results of gene expression profiling performed on lymphoblastoid cell lines as well as blood from patients with mutations in KDM5C. Using whole genome expression arrays and quantitative reverse transcriptase polymerase chain reaction (QRT-PCR) experiments, we identified several genes, including CMKOR1, KDM5B and KIAA0469 that were consistently deregulated in both tissues.ConclusionsOur findings shed light on the pathological mechanisms underlying mental retardation and have implications for future diagnostics of this heterogeneous disorder.

De novo subtelomeric deletion of 15q associated with satellite translocation in a child with developmental delay and severe growth retardation.

We report on a case of satellited 15q with subtelomeric deletion in a girl with delayed development and severe growth retardation. The patient also has a triangular face, downturned angles of the mouth, micrognathia, and minor limb malformations including mild talipes equinovarus, genu recurvatum, and increased dorsiflexion of both limbs. Cytogenetic analysis using standard GTG banding showed a female karyotype with a satellited‐like structure at the distal long arm of one chromosome 15. Silver staining of the nucleolar organizing region (AgNOR) confirmed the presence of a satellite DNA translocation at the lesion. Analysis using fluorescent in situ hybridization (FISH) detected a subtelomeric deletion of the terminal 15q. Additional molecular analysis using microsatellite markers along the long arm of chromosome 15 defined a maximally deleted region at approximately 4.7 Mb. Haploinsufficiency of the IGF1R gene expression is thought to be the cause of growth delay in all 15q terminal deletion including our patient.

Prenatal diagnosis of complete trisomy 9 with a novel sonographic finding of heart calcification.

Complete trisomy 9 is a rare chromosomal disorder. The prenatal sonographic features of fetuses with complete trisomy 9 are nonspecific. There are also some reports showing rare features such as abnormal calcification in the liver and hypochondral region.1–4 Complete trisomy 9 was first described in 1973 from cultured lymphocytes in an infant with congenital heart defects, skeletal abnormalities, and severe dysmorphism.5 Most cases of complete trisomy 9 result in spontaneous first-trimester abortion. Fetuses who survive to term generally have a mosaic state.6,7 Since the prognosis of fetuses with complete trisomy 9 is poor, and the survival rate is very low, prenatal diagnosis of this condition is beneficial to provide useful information for genetic counseling and prenatal care. Sonography is a noninvasive and helpful tool in detecting this condition, especially when fetal karyotyping is unavailable. Although there are overlapping prenatal sonographic findings between trisomy 9 and trisomy 18, the main characteristic findings of complete trisomy 9 are cardiovascular defects, intrauterine growth restriction, genitourinary abnormalities, and limb anomalies. Craniofacial dysmorphism and a single umbilical artery can also be detected in some cases.8,9 Most reported cases were confirmed by fetal karyotyping, either from amniotic fluid or lymphocyte cultures. Here we report a new sonographic finding in a complete trisomy 9 case, which was confirmed postnatally by autopsy along with fetal karyotyping. This finding provides useful information, which will help in prenatal diagnosis of this lethal condition. A 37-year-old woman, gravida 4, para 2012, was referred to our institution at a gestational age of 16 weeks 5 days for amniocentesis due to advanced maternal age and a history of a child with trisomy 21. The first fetal sonographic examination showed a singleton fetus with a strawberry head shape, a moderately hyperechoic bowel, overlapping fingers, and a single umbilical artery. A fetal echocardiogram revealed situs solitus and abnormal left-axis deviation. Interestingly, abnormal cardiac calcification was also detected in both ventricular walls and the interventricular septum (Figure 1). The estimated fetal weight was appropriate for gestational age. Amniocentesis was subsequently performed, and fetal karyotyping showed 47,XX,+9 by the standard G-banding technique. The second sonographic examination was performed at 19 weeks’ gestation. Intrauterine growth restriction was not observed, and no additional physical anomalies were detected. Genetic counseling was provided to the family. Cordocentesis was performed, which confirmed the complete trisomy 9 female karyotype. Termination of pregnancy was performed at 21 weeks 5 days, after which an autopsy report indicated a female abortus weighing 270 g with multiple dysmorphic features, including a broad-based nose, hypertelorism, micrognathia, low-set ears, clenched hands, a 2-vessel cord, and an imperforate anus. The heart with calcification in both ventricular walls and interventic-

Erratum: Identification and characterization of two novel JARID1C mutations: Suggestion of an emerging genotype-phenotype correlation (European Journal of Human Genetics (2010) 18 (330-335) DOI: 10.1038/ejhg.2009.175)

Post publication, the authors noticed that there was a miscalculation in table 6, which also had implications within the text of their article. The corrected table and text are published here. The authors would like to apologise for their errors. Page 5: PGD uptake The sentence ‘Over a period of 10 years, the uptake of PGD for HD in Belgium was 8.5%, in the Netherlands the uptake was 5.8% and in France 3.7%.’ should be replaced by ‘Over a period of 10 years, the uptake of PGD for HD in Belgium was 1.7%; in the Netherlands, it was 1.2%; and in France, it was 0.7%.’ Page 7: Uptake The sentence ‘The 10-year uptake of PGD for HD in Belgium in the at-risk population in the reproductive age was 8.5%, in the Netherlands it was 5.8% and in France 3.7%’. should be replaced by ‘The 10-year uptake of PGD for HD in Belgium, in the at-risk population in the reproductive age, was 1.7%; in the Netherlands, it was 1.2%; and in France, it was 0.7%.’ Additional text correction: Page 4, upper line, right column: The word ‘either’ should be erased.