Correction: Exome sequencing of Pakistani consanguineous families identifies 30 novel candidate genes for recessive intellectual disability

This Article was originally published under a CC BY-NC-SA 4.0 license, but has now been made available under a CC BY 4.0 license. The PDF and HTML versions of the Article have been modified accordingly.

Mental health and behavioural problems in children with XXYY: a comparison with intellectual disabilities

BACKGROUND

The phenotype of children with XXYY has predominantly been defined by comparison to other sex chromosome aneuploidies trisomies affecting male children; however, the intellectual ability of children with XXYY is lower than children with other sex chromosome aneuploidies trisomies. It is not known to what extent the phenotype identified to date is specific to XXYY, rather than a reflection of lower IQ. This study evaluates the mental health and behaviour of children with XXYY, in comparison to children with intellectual disabilities of heterogeneous genetic origin.

METHODS

Fifteen children with XXYY and 30 controls matched for age (4-14 years), sex and intellectual ability were ascertained from the IMAGINE ID study. IMAGINE ID participants have intellectual disabilities due to genetic anomalies confirmed by National Health Service Regional Genetic Centre laboratories. The mental health and behaviour of participants was examined with the Development and Well-being Assessment and the Strengths and Difficulties Questionnaire.

RESULTS

Children with XXYY experienced significantly more frequent and intense temper outbursts than the control group.

CONCLUSION

Our results suggest that temper outbursts may be specifically associated with the XXYY phenotype. These problems have a significant impact on the daily lives of boys with XXYY and their families. It is crucial to ensure that families are well supported to manage these difficulties.

Functional Analyses of a Novel Splice Variant in the CHD7 Gene, Found by Next Generation Sequencing, Confirm Its Pathogenicity in a Spanish Patient and Diagnose Him with CHARGE Syndrome

Mutations in CHD7 have been shown to be a major cause of CHARGE syndrome, which presents many symptoms and features common to other syndromes making its diagnosis difficult. Next generation sequencing (NGS) of a panel of intellectual disability related genes was performed in an adult patient without molecular diagnosis. A splice donor variant in CHD7 (c.5665 + 1G > T) was identified. To study its potential pathogenicity, exons and flanking intronic sequences were amplified from patient DNA and cloned into the pSAD^® splicing vector. HeLa cells were transfected with this construct and a wild-type minigene and functional analysis were performed. The construct with the c.5665 + 1G > T variant produced an aberrant transcript with an insert of 63 nucleotides of intron 28 creating a premature termination codon (TAG) 25 nucleotides downstream. This would lead to the insertion of 8 new amino acids and therefore a truncated 1896 amino acid protein. As a result of this, the patient was diagnosed with CHARGE syndrome. Functional analyses underline their usefulness for studying the pathogenicity of variants found by NGS and therefore its application to accurately diagnose patients.

Genetic testing and screening of individuals at risk of NF2

Genetic testing and management of the at-risk individual for neurofibromatosis type 2 (NF2) is complicated by the well-documented risk of mosaicism that causes a milder later onset more asymmetrical disease course. Risks of NF2 were derived from genetic testing of over 1000 individuals through the Manchester NF2-testing service. Individuals are at risk of NF2 or have 'potential' NF2 if they have features of the disease that fall short of diagnostic criteria or are the first-degree relative of someone with NF2 or suspected NF2. The present protocol devised for the Nationally Commissioned Group (NCG) NF2 service in England addresses the risks, genetic testing and screening protocol for individuals at risk of NF2. Screening with cranial magnetic resonance imaging is advised until the risk of NF2 falls below a pragmatic threshold of 1%. Multiple case scenarios are shown to illustrate how to use the protocol.

Genetic research on rare familial disorders: consent and the blurred boundaries between clinical service and research

OBJECTIVES

To study the consent process experienced by participants who are enrolled in a molecular genetic research study that aims to find new genetic mutations responsible for an apparently inherited disorder.

DESIGN

Semi-structured interviews and analysis/description of main themes.

PARTICIPANTS

78 members of 52 families who had been recruited to a molecular genetic study.

RESULTS

People were well informed about the goals, risks and benefits of the genetic research study but could not remember the consent process. They had mostly been recruited to take part by trusted clinicians or their relatives but had little memory of, or concern about signing consent forms. Families appeared to regard the research as a continuation of their, or their relatives', clinical care.

CONCLUSIONS

Ethical review should be more flexible in its attitude to consent forms and written information sheets for some sorts of research. For rare genetic disease studies where research has been discussed fully within the clinical setting then the consent obtained at that time could suffice rather than needing extra consent at a later stage. However, clinician-researchers will need to ensure that their duty of care extends for the duration of the research and beyond.

Reduced penetrance alleles for Huntington's disease: a multi-centre direct observational study

OBJECTIVE

To obtain penetrance data for Huntington's disease when DNA results are in the range of 36-39 CAG repeats and assess the consistency of reporting the upper allele from two reference centres.

METHOD

Data were collected anonymously on age of onset or age last known to be unaffected from a cohort of individuals with results in this range. DNA samples were re-analysed in two reference centres. Kaplan-Meier analysis was used to construct an age of onset curve and penetrance figures.

RESULTS

Clinical data and concordant DNA results from both reference centres were available for 176 samples; penetrance figures (and 95% confidence intervals) for this cohort, at age 65 and 75 years, were 63.9% (55.5% to 73.2%) and 74.2% (64.2% to 84.2%), respectively. Inclusion of 28 additional subjects for whom repeat DNA results were unavailable, obtained from only one reference centre, or discrepant by one repeat within this range, gave penetrance data (including 95% confidence intervals) at ages 65 and 75 years of 62.4% (54.4% to 70.4%) and 72.7.% (63.3% to 82.1%), respectively. 238 duplicate results were available from the reference centres; 10 (4.2%) differed by one CAG repeat in the reporting of the upper allele and in two (0.84%) of these cases the discrepancy was between 39 and 40 repeats.

CONCLUSION

When DNA results are in this range, a conservative approach is to say that there is at least a 40% chance the person will be asymptomatic at age 65 years and at least a 30% chance the person will be asymptomatic at age 75 years.

Mutations in the RSK2(RPS6KA3) gene cause Coffin-Lowry syndrome and nonsyndromic X-linked mental retardation

We describe three families with X-linked mental retardation, two with a deletion of a single amino acid and one with a missense mutation in the proximal domain of the RSK2(RPS6KA3) (ribosomal protein S6 kinase, 90 kDa, polypeptide 3) protein similar to mutations found in Coffin-Lowry syndrome (CLS). In two families, the clinical diagnosis had been nonsyndromic X-linked mental retardation. In the third family, although CLS had been suspected, the clinical features were atypical and the degree of intellectual disability much less than expected. These families show that strict reliance on classical clinical criteria for mutation testing may result in a missed diagnosis. A less targeted screening approach to mutation testing is advocated.

Mutations in FRMD7, a newly identified member of the FERM family, cause X-linked idiopathic congenital nystagmus

Idiopathic congenital nystagmus is characterized by involuntary, periodic, predominantly horizontal oscillations of both eyes. We identified 22 mutations in FRMD7 in 26 families with X-linked idiopathic congenital nystagmus. Screening of 42 singleton cases of idiopathic congenital nystagmus (28 male, 14 females) yielded three mutations (7%). We found restricted expression of FRMD7 in human embryonic brain and developing neural retina, suggesting a specific role in the control of eye movement and gaze stability.

Partial NSD1 deletions cause 5% of Sotos syndrome and are readily identifiable by multiplex ligation dependent probe amplification

BACKGROUND

Most cases of Sotos syndrome are caused by intragenic NSD1 mutations or 5q35 microdeletions. It is uncertain whether allelic or genetic heterogeneity underlies the residual cases and it has been proposed that other mechanisms, such as 11p15 defects, might be responsible for Sotos cases without NSD1 mutations or 5q35 microdeletions.

OBJECTIVE

To develop a multiplex ligation dependent probe amplification (MLPA) assay to screen NSD1 for exonic deletions/duplications.

METHODS

Analysis was undertaken of 18 classic Sotos syndrome cases in which NSD1 mutations and 5q35 microdeletions were excluded. Long range polymerase chain reaction (PCR) was used to characterise the mechanism of generation of the partial NSD1 deletions.

RESULTS

Eight unique partial NSD1 deletions were identified: exons 1-2 (n = 4), exons 3-5, exons 9-13, exons 19-21, and exon 22. Using long range PCR six of the deletions were confirmed and the precise breakpoints in five cases characterised. This showed that three had arisen through Alu-Alu recombination and two from non-homologous end joining.

CONCLUSIONS

MLPA is a robust, inexpensive, simple technique that reliably detects both 5q35 microdeletions and partial NSD1 deletions that together account for approximately 15% of Sotos syndrome.

X linked mental retardation: a clinical guide

Mental retardation is more common in males than females in the population, assumed to be due to mutations on the X chromosome. The prevalence of the 24 genes identified to date is low and less common than expansions in FMR1, which cause Fragile X syndrome. Systematic screening of all other X linked genes in X linked families with mental retardation is currently not feasible in a clinical setting. The phenotypes of genes causing syndromic and non-syndromic mental retardation (NLGN3, NLGN4, RPS6KA3(RSK2), OPHN1, ATRX, SLC6A8, ARX, SYN1, AGTR2, MECP2, PQBP1, SMCX, and SLC16A2) are first discussed, as these may be the focus of more targeted mutation analysis. Secondly, the relative prevalence of genes causing only non-syndromic mental retardation (IL1RAPL1, TM4SF2, ZNF41, FTSJ1, DLG3, FACL4, PAK3, ARHGEF6, FMR2, and GDI) is summarised. Thirdly, the problem of recurrence risk where a molecular genetics diagnosis has not been made and what proportion of the male excess of mental retardation is due to monogenic disorders of the X chromosome are discussed.

Genetic services for people with intellectual disability and their families

This paper reviews the advances in molecular genetics over the recent years and discusses the impact it may have on those with intellectual disability and their families. The aim is not to present a comprehensive scientific treatise but rather to use illustrations from genetics to highlight our current thinking and draw attention to areas of uncertainty and misinformation. As our knowledge and understanding of the genetic basis of disease increases over the years, there may be significant benefits to some families, but the potential for discrimination against individuals on genetic grounds will also increase.

Identification of a 650 kb duplication at the X chromosome breakpoint in a patient with 46,X,t(X;8)(q28;q12) and non-syndromic mental retardation

A female patient with non-syndromic mental retardation was shown by high resolution GTL banding to have inherited an apparently balanced translocation, 46,X,t(X;8)(q28;q12)mat. Replication studies in the mother and daughter showed a skewed X inactivation pattern in lymphocytes, with the normal X chromosome preferentially inactivated. The mother also had significant intellectual disability. To investigate the possibility that a novel candidate gene for XLMR was disrupted at the X chromosome translocation breakpoint, we mapped the breakpoint using fluorescence in situ hybridisation (FISH). This showed that the four known genes involved in non-syndromic mental retardation in Xq28, FMR2, SLC6A8, MECP2, and GDI1, were not involved in the translocation. Intriguingly, we found that the X chromosome breakpoint in the daughter could not be defined by a single breakpoint spanning genomic clone and further analysis showed a 650 kb submicroscopic duplication between DXS7067 and DXS7060 on either side of the X chromosome translocation breakpoint. This duplicated region contains 11 characterised genes, of which nine are expressed in brain. Duplication of one or several of the genes within the 650 kb interval is likely to be responsible for the mental retardation phenotype seen in our patient. Xq28 appears to be an unstable region of the human genome and genomic rearrangements are recognised as major causes of two single gene defects, haemophilia A and incontinentia pigmenti, which map within Xq28. This patient therefore provides further evidence for the instability of this genomic region.

Hypophosphatasia associated with increased nuchal translucency: a report of two affected pregnancies

Perinatal hypophosphatasia is a lethal autosomal recessive skeletal abnormality with a birth prevalence of about 1 per 100 000. It is characterized by deficiency of the tissue-nonspecific isoenzyme of alkaline phosphatase causing abnormal bone mineralization. In the two affected fetuses from the same family ultrasound examination at 14 and 12 weeks, respectively, demonstrated increased nuchal translucency thickness, hypomineralization of the skull and spine, narrowing of the chest and shortening of the limbs.

A new approach to the elucidation of complex chromosome rearrangements illustrated by a case of Rieger syndrome

A patient with a complex chromosome rearrangement and unilateral Rieger syndrome is presented. This rearrangement involves four chromosomes and six breakpoints, one of which is at 4q25, the candidate region for Rieger syndrome. We discuss a novel approach to the elucidation of this case using a multiprobe fluorescence in situ hybridisation method to show rearrangements unpredictable from G banded analysis, and the clear and unambiguous presentation of the karyotype using computer generated colour ideograms.

Four cases of amelia of the upper limb associated with anal atresia--is this VACTERL with extreme limb involvement?

Amelia is an extremely rare abnormality with a highest reported incidence of 1 in 67,500 liveborn infants. We now report four cases in each of which amelia involving one upper limb occurred in association with anal atresia. The pattern of other abnormalities present in these cases suggests that this combination of amelia and anal atresia falls within the spectrum of the VACTERL association.

Spectrum of clinical features associated with interstitial chromosome 22q11 deletions: a European collaborative study

We present clinical data on 558 patients with deletions within the DiGeorge syndrome critical region of chromosome 22q11. Twenty-eight percent of the cases where parents had been tested had inherited deletions, with a marked excess of maternally inherited deletions (maternal 61, paternal 18). Eight percent of the patients had died, over half of these within a month of birth and the majority within 6 months. All but one of the deaths were the result of congenital heart disease. Clinically significant immunological problems were very uncommon. Nine percent of patients had cleft palate and 32% had velopharyngeal insufficiency, 60% of patients were hypocalcaemic, 75% of patients had cardiac problems, and 36% of patients who had abdominal ultrasound had a renal abnormality. Sixty-two percent of surviving patients were developmentally normal or had only mild learning problems. The majority of patients were constitutionally small, with 36% of patients below the 3rd centile for either height or weight parameters.

Prenatal diagnosis of 22q11 deletions: a series of five cases with congenital heart defects

We report a series of five patients with congenital heart defects in whom a prenatal diagnosis of 22q11 deletion has been made. The accurate cardiac and cytogenetic diagnoses were made between 20 and 23 weeks' gestation in all cases and the cardiac findings were all confirmed postnatally. The cardiac abnormalities included tetralogy of Fallot with absent pulmonary valve, pulmonary atresia with VSD, common arterial trunk, and left atrial isomerism with double outlet right ventricle. The problems of genetic counselling in these cases are discussed. A recommendation is made to test all fetuses with conotruncal heart abnormalities detected prenatally for a 22q11 deletion, whereas guidelines for other congenital heart disease types are less clear.

Isomerism of the atrial appendages associated with 22q11 deletion in a fetus

There is a strong association between prenatally diagnosed structural heart disease and fetal chromosomal abnormalities. Isomerism of the atrial appendages is an exception to this because the fetal karyotype is usually normal in this condition. A case of atrial isomerism diagnosed antenatally with a normal female karyotype but with a microdeletion of chromosome 22q11 is reported.

The antigenicity and evolution of influenza H1 haemagglutinin, from 1950-1957 and 1977-1983: two pathways from one gene

Nucleotide sequence analysis of the region of the haemagglutinin gene coding for the HA1 domain of the protein was performed on 19 human influenza A strains of H1 subtype representative of the two epidemic periods from 1977-1983 and from 1950-1957. The amino acid changes relative to A/USSR/90/77 are summarised and are consistent with the view that variation in these field strains involves changes largely at the Sb and Ca antigenic sites previously characterised in laboratory mutants of the haemagglutinin of influenza A/PR/8/34. The Sa and Cb sites are less variant and are probably masked by carbohydrate side chains. We discuss the significance of other amino acid changes which do not correspond to previously defined antigenic sites. We also define the "mainstream" amino acid changes characteristic of the divergent evolutionary pathways of the 1950-1957 and 1977-1983 periods and note that the rate of evolution is faster in the earlier period.

Antigenicity and evolution amongst recent influenza viruses of H1N1 subtype

The sequence of the HA1 subunit region of the haemagglutinin gene of influenza A/USSR/90/77, and A/Brazil/11/78, A/Lackland/3/78, A/England/333/80 and A/India/6263/80 was determined by dideoxy-sequencing methods using total virion RNA and specific oligonucleotide primers for reverse transcriptase. These 1977-1980 strains share a minimum of 85% amino acid sequence homology with influenza A/PR/8/34. Most of the surface amino acid substitutions which occurred during the evolution of A/PR/8/34 to A/USSR/90/77 and subsequently in the 1978-1980 strains are located in the 4 antigenic sites previously defined by an analysis of laboratory-selected mutants of A/PR/8/34. We deduce an evolutionary pathway for the 1977-80 strains and suggest their different epidemic properties may be a consequence of only a few amino acid changes.