Martin Bobrow

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.

Prepublication data sharing.

Rapid release of prepublication data has served the field of genomics well. Attendees at a workshop in Toronto recommend extending the practice to other biological data sets.

Mutations in UPF3B , a member of the nonsense-mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation

Nonsense-mediated mRNA decay (NMD) is of universal biological significance. It has emerged as an important global RNA, DNA and translation regulatory pathway. By systematically sequencing 737 genes (annotated in the Vertebrate Genome Annotation database) on the human X chromosome in 250 families with X-linked mental retardation, we identified mutations in the UPF3 regulator of nonsense transcripts homolog B (yeast) (UPF3B) leading to protein truncations in three families: two with the Lujan-Fryns phenotype and one with the FG phenotype. We also identified a missense mutation in another family with nonsyndromic mental retardation. Three mutations lead to the introduction of a premature termination codon and subsequent NMD of mutant UPF3B mRNA. Protein blot analysis using lymphoblastoid cell lines from affected individuals showed an absence of the UPF3B protein in two families. The UPF3B protein is an important component of the NMD surveillance machinery. Our results directly implicate abnormalities of NMD in human disease and suggest at least partial redundancy of NMD pathways.

Psychological impact of genetic testing for familial hypercholesterolemia within a previously aware population: A randomized controlled trial

This trial tests the hypothesis that confirming a clinical diagnosis of familial hypercholesterolemia (FH) by finding a genetic mutation reduces patients perceptions of control over the disease and adherence to risk‐reducing behaviors. Three hundred forty‐one families, comprising 341 hypercholesterolemia probands and 128 adult relatives, were randomized to one of two groups: (a) routine clinical diagnosis; (b) routine clinical diagnosis plus genetic testing (mutation searching in probands and direct gene testing in relatives). The main outcome measures were perceptions of control over hypercholesterolemia, adherence to cholesterol‐lowering medication, diet, physical activity, and smoking. There was no support for the main hypothesis: finding a mutation had no impact on perceived control or adherence to risk‐reducing behavior (all P‐valuesu2009>u20090.10). While all groups believed that lowering cholesterol was an effective way of reducing the risk of a heart attack, participants in whom a mutation was found believed less strongly in the efficacy of diet in reducing their cholesterol level (Pu2009=u20090.02 at 6 months) and showed a trend in believing more strongly in the efficacy of cholesterol‐lowering medication (Pu2009=u20090.06 at 6 months). In conclusion, finding a mutation to confirm a clinical diagnosis of FH in a previously aware population does not reduce perceptions of control or adherence to risk‐reducing behaviors. The pattern of findings leads to the new hypothesis that genetic testing does not affect the extent to which people feel they have control over a condition, but does affect their perceptions of how control is most effectively achieved. Further work is needed to determine whether similar results will be obtained in populations with little previous awareness of their risks.

Mutations in CUL4B, Which Encodes a Ubiquitin E3 Ligase Subunit, Cause an X-linked Mental Retardation Syndrome Associated with Aggressive Outbursts, Seizures, Relative Macrocephaly, Central Obesity, Hypogonadism, Pes Cavus, and Tremor

We have identified three truncating, two splice-site, and three missense variants at conserved amino acids in the CUL4B gene on Xq24 in 8 of 250 families with X-linked mental retardation (XLMR). During affected subjects adolescence, a syndrome emerged with delayed puberty, hypogonadism, relative macrocephaly, moderate short stature, central obesity, unprovoked aggressive outbursts, fine intention tremor, pes cavus, and abnormalities of the toes. This syndrome was first described by Cazebas et al., in a family that was included in our study and that carried a CUL4B missense variant. CUL4B is a ubiquitin E3 ligase subunit implicated in the regulation of several biological processes, and CUL4B is the first XLMR gene that encodes an E3 ubiquitin ligase. The relatively high frequency of CUL4B mutations in this series indicates that it is one of the most commonly mutated genes underlying XLMR and suggests that its introduction into clinical diagnostics should be a high priority.

Mutations in the DLG3 Gene Cause Nonsyndromic X-Linked Mental Retardation

We have identified truncating mutations in the human DLG3 (neuroendocrine dlg) gene in 4 of 329 families with moderate to severe X-linked mental retardation. DLG3 encodes synapse-associated protein 102 (SAP102), a member of the membrane-associated guanylate kinase protein family. Neuronal SAP102 is expressed during early brain development and is localized to the postsynaptic density of excitatory synapses. It is composed of three amino-terminal PDZ domains, an src homology domain, and a carboxyl-terminal guanylate kinase domain. The PDZ domains interact directly with the NR2 subunits of the NMDA glutamate receptor and with other proteins responsible for NMDA receptor localization, immobilization, and signaling. The mutations identified in this study all introduce premature stop codons within or before the third PDZ domain, and it is likely that this impairs the ability of SAP102 to interact with the NMDA receptor and/or other proteins involved in downstream NMDA receptor signaling pathways. NMDA receptors have been implicated in the induction of certain forms of synaptic plasticity, such as long-term potentiation and long-term depression, and these changes in synaptic efficacy have been proposed as neural mechanisms underlying memory and learning. The disruption of NMDA receptor targeting or signaling, as a result of the loss of SAP102, may lead to altered synaptic plasticity and may explain the intellectual impairment observed in individuals with DLG3 mutations.

Mutations in ZDHHC9, which encodes a palmitoyltransferase of NRAS and HRAS, cause X-linked mental retardation associated with a marfanoid habitus

We have identified one frameshift mutation, one splice-site mutation, and two missense mutations in highly conserved residues in ZDHHC9 at Xq26.1 in 4 of 250 families with X-linked mental retardation (XLMR). In three of the families, the mental retardation phenotype is associated with a Marfanoid habitus, although none of the affected individuals meets the Ghent criteria for Marfan syndrome. ZDHHC9 is a palmitoyltransferase that catalyzes the posttranslational modification of NRAS and HRAS. The degree of palmitoylation determines the temporal and spatial location of these proteins in the plasma membrane and Golgi complex. The finding of mutations in ZDHHC9 suggests that alterations in the concentrations and cellular distribution of target proteins are sufficient to cause disease. This is the first XLMR gene to be reported that encodes a posttranslational modification enzyme, palmitoyltransferase. Furthermore, now that the first palmitoyltransferase that causes mental retardation has been identified, defects in other palmitoylation transferases become good candidates for causing other mental retardation syndromes.

Data Sharing in the Post-Genomic World: The Experience of the International Cancer Genome Consortium (ICGC) Data Access Compliance Office (DACO)

The scientific community, research funders, and governments have repeatedly recognized the importance of open access to genomic data for scientific research and medical progress [1]–[4]. Open access is becoming a well-established practice for large-scale, publicly funded, data-intensive community science projects, particularly in the field of genomics. Given this consensus, restrictions to open access should be regarded as exceptional and treated with caution. Yet, several developments [5] have led scientists and policymakers to investigate and implement open access restrictions [5]–[9]. Notably, there are privacy concerns within the genomics community and critiques from some researchers that open access, if left completely unregulated, could raise significant scientific, ethical, and legal issues (e.g., quality of the data, appropriate credit to data generators, relevance of the system for small and medium projects, etc.) [1]–[10]. A recent paper by Greenbaum and colleagues in this journal [11] identified protecting the privacy of study participants as the main challenge to open genomic data sharing. n nOne possible way to reconcile open data sharing with privacy concerns is to use a tiered access system to separate access into “open” and “controlled.” Open access remains the norm for data that cannot be linked with other data to generate a dataset that would uniquely identify an individual. A controlled access mechanism, on the other hand, regulates access to certain, more sensitive data (e.g., detailed phenotype and outcome data, genome sequences files, raw genotype calls) by requiring third parties to apply to a body (e.g., custodian, original data collectors, independent body, or data access committee) and complete an access application that contains privacy safeguards. This mechanism, while primarily designed to protect study participants, can also be used to protect investigators, database hosting institutions, and funders from perceptions or acts of favoritism or impropriety. The experience of controlled access bodies to date has been only minimally documented in the literature [9], [12]. To address this lacuna, we present the experience of the Data Access Compliance Office (DACO) of the International Cancer Genome Consortium (ICGC). The goal is to provide information on this increasingly important type of database governance body.

Information recall in genetic counselling: A pilot study of its assessment

One of the main aims of genetic counselling is to provide information to patients that they can understand and recall. Measuring information recall is problematic and most studies do not make the comparison between recalled information and the information that is given in consultations. The aim of this study was to determine the validity of using genetic counsellors reports of information given in genetic consultations as the basis for a measure of patient recall. Counsellors in 35 routine genetic counselling consultations were asked to indicate important information given during consultations by highlighting items in their summary letters sent to patients. This was checked by a researcher against tape-recordings of the consultations. One month later, patients were telephoned by the researcher and asked to recall as much information as they could from the consultation and to rate its importance. Over 95% of the information that counsellors identified as important had been given during the consultation. Patients rated this information as important. Although there was an association between the overall number of items that counsellors and patients judged to be important, patients more frequently judged information about family implications to be important than did counsellors. On the other hand, counsellors more frequently judged information about test, diagnosis and prognosis to be important than did patients. These results suggest that counsellors summary letters are a valid baseline against which to measure patient recall. This measure will not, however, capture all the information that patients consider important.

Mutations in the BRWD3 Gene Cause X-Linked Mental Retardation Associated with Macrocephaly

In the course of systematic screening of the X-chromosome coding sequences in 250 families with nonsyndromic X-linked mental retardation (XLMR), two families were identified with truncating mutations in BRWD3, a gene encoding a bromodomain and WD-repeat domain-containing protein. In both families, the mutation segregates with the phenotype in affected males. Affected males have macrocephaly with a prominent forehead, large cupped ears, and mild-to-moderate intellectual disability. No truncating variants were found in 520 control X chromosomes. BRWD3 is therefore a new gene implicated in the etiology of XLMR associated with macrocephaly and may cause disease by altering intracellular signaling pathways affecting cellular proliferation.