Targeted genomic capture and massively parallel sequencing to identify genes for hereditary hearing loss in Middle Eastern families

Background

Identification of genes responsible for medically important traits is a major challenge in human genetics. Due to the genetic heterogeneity of hearing loss, targeted DNA capture and massively parallel sequencing are ideal tools to address this challenge. Our subjects for genome analysis are Israeli Jewish and Palestinian Arab families with hearing loss that varies in mode of inheritance and severity.

Results

A custom 1.46 MB design of cRNA oligonucleotides was constructed containing 246 genes responsible for either human or mouse deafness. Paired-end libraries were prepared from 11 probands and bar-coded multiplexed samples were sequenced to high depth of coverage. Rare single base pair and indel variants were identified by filtering sequence reads against polymorphisms in dbSNP132 and the 1000 Genomes Project. We identified deleterious mutations in CDH23, MYO15A, TECTA, TMC1, and WFS1. Critical mutations of the probands co-segregated with hearing loss. Screening of additional families in a relevant population was performed. TMC1 p.S647P proved to be a founder allele, contributing to 34% of genetic hearing loss in the Moroccan Jewish population.

Conclusions

Critical mutations were identified in 6 of the 11 original probands and their families, leading to the identification of causative alleles in 20 additional probands and their families. The integration of genomic analysis into early clinical diagnosis of hearing loss will enable prediction of related phenotypes and enhance rehabilitation. Characterization of the proteins encoded by these genes will enable an understanding of the biological mechanisms involved in hearing loss.

X inactivation testing for identifying a non-syndromic X-linked mental retardation gene

The purpose of this study was to identify a gene causing non-syndromic X-linked mental retardation in an extended family, taking advantage of the X chromosome inactivation status of the females in order to determine their carrier state. X inactivation in the females was determined with the androgen receptor methylation assay; thereafter, the X chromosome was screened with evenly spaced polymorphic markers. Once initial linkage was identified, the region of interest was saturated with additional markers and the males were added to the analysis. Candidate genes were sequenced. Ten females showed skewed inactivation, while six revealed a normal inactivation pattern. A maximal lod score of 5.54 at θ = 0.00 was obtained with the marker DXS10151. Recombination events mapped the disease gene to a 17.4-Mb interval between the markers DXS10153 and DXS10157. Three candidate genes in the region were sequenced and a previously described missense mutation (P375L) was identified in the ACSL4/FACL4 gene. On the basis of the female X inactivation status, we have mapped and identified the causative mutation in a gene causing non-syndromic X-linked mental retardation.

Multiple congenital anomalies-hypotonia-seizures syndrome is caused by a mutation in PIGN

BACKGROUND

This study reports on a hitherto undescribed autosomal recessive syndrome characterised by dysmorphic features and multiple congenital anomalies together with severe neurological impairment, chorea and seizures leading to early death, and the identification of a gene involved in the pathogenesis of the disease.

METHODS

Homozygosity mapping was performed using Affymetrix Human Mapping 250k NspI arrays. Sequencing of all coding exons of the candidate genes was performed with primer sets designed using the Primer3 program. Fluorescence activated cell sorting was performed using conjugated antibody to CD59. Staining, acquisition and analysis were performed on a FACSCalibur flow cytometer.

RESULTS

Using homozygosity mapping, the study mapped the disease locus to 18q21.32-18q22.1 and identified the disease-causing mutation, c.2126G→A (p.Arg709Gln), in PIGN, which encodes glycosylphosphatidylinositol (GPI) ethanolamine phosphate transferase 1, a protein involved in GPI-anchor biosynthesis. Arginine at the position 709 is a highly evolutionarily conserved residue located in the PigN domain. The expression of GPI linked protein CD59 on fibroblasts from patients as compared to that in a control individual showed a 10-fold reduction in expression, confirming the pathogenic consequences of the mutation on GPI dependent protein expression.

CONCLUSIONS

The abundant expression of PIGN in various tissues is compatible with the diverse phenotypic features observed in the patients and with the involvement of multiple body systems. The presence of developmental delay, hypotonia, and epilepsy combined with multiple congenital anomalies, especially anorectal anomalies, should lead a clinician to suspect a GPI deficiency related disorder.

Expanding the panel of MEFV mutations for routine testing of patients with a clinical diagnosis of familial Mediterranean fever

BACKGROUND

Since the identification of the MEFV gene 198 mutations have been identified, not all of which are pathologic. The screening methods used in Israel to test patients suspected of having FMF include a kit that tests for the five main mutations (M694V, V726A, M680Ic/g, M694I, E148Q), and the sequencing of MEFV exon 10 in combination with restriction analysis for detecting additional mutations

OBJECTIVES

To determine the contribution of testing Ifor five additional mutations - A744S, K695R, M680Ic/t, R761H and P369S - to the molecular diagnosis of patients clinically suspected of having FMF.

METHODS

A total of 1637 patients were tested for FMF mutations by sequencing exon 10 and performing restriction analysis for mutations E148Q and P369S.

RESULTS

Nearly half the patients (812, 49.6%) did not have any detectable mutations, 581 (35.5%) had one mutation, 241 (14.7%) had two mutations, of whom 122 were homozygous and 119 compound heterozygous, and 3 had three mutations. Testing for the additional five mutations enabled us to identify 46 patients who would have been missedby the molecular diagnosis kit and 22 patients in whom only one mutation would have been found. Altogether, 4.3%of the patients would not have been diagnosed correctly had only the kit that tests for the five main mutations been used.

CONCLUSIONS

This study suggests that testing for the additional five mutations as well as the five main mutations in patients with a clinical presentation of FMF adds significantly to the molecular diagnosis of FMF in the Israeli population.

Diagnostic utility of array-based comparative genomic hybridization (aCGH) in a prenatal setting

OBJECTIVE

Array-based comparative genomic hybridization (aCGH) is a new technique for detecting submicroscopic deletions and duplications. There is limited information regarding its use in the prenatal setting. Here, we present our experience of 269 prenatal aCGHs between 2006 and 2009.

METHOD

The indications for testing were fetal anomalies on ultrasound (U/S), advanced maternal age (AMA), family history of a disorder of unknown etiology, parental concern, abnormal routine karyotype and abnormal serum biochemical screening for common fetal aneuploidies.

RESULTS

Of 15 cases with a known abnormal karyotype, 11 had a normal aCGH. This enabled us to reassure the families and the pregnancies were continued. The remaining four showed an abnormal aCGH, confirming the chromosomes were unbalanced, and were terminated. Of 254 cases with a normal karyotype, 3 had an abnormal aCGH and were terminated. Overall, new clinically relevant results were detected by aCGH in 18 cases, providing additional information for prenatal genetic counseling and risk assessment.

CONCLUSION

Our results suggest that prenatal aCGH should be offered particularly in cases with abnormal U/S. We found the rate of detecting an abnormality by aCGH in low-risk pregnancies was 1:84, but larger studies will be needed to expand our knowledge and validate our conclusions.

SOBP is mutated in syndromic and nonsyndromic intellectual disability and is highly expressed in the brain limbic system

Intellectual disability (ID) affects 1%-3% of the general population. We recently reported on a family with autosomal-recessive mental retardation with anterior maxillary protrusion and strabismus (MRAMS) syndrome. One of the reported patients with ID did not have dysmorphic features but did have temporal lobe epilepsy and psychosis. We report on the identification of a truncating mutation in the SOBP that is responsible for causing both syndromic and nonsyndromic ID in the same family. The protein encoded by the SOBP, sine oculis binding protein ortholog, is a nuclear zinc finger protein. In mice, Sobp (also known as Jxc1) is critical for patterning of the organ of Corti; one of our patients has a subclinical cochlear hearing loss but no gross cochlear abnormalities. In situ RNA expression studies in postnatal mouse brain showed strong expression in the limbic system at the time interval of active synaptogenesis. The limbic system regulates learning, memory, and affective behavior, but limbic circuitry expression of other genes mutated in ID is unusual. By comparing the protein content of the +/jc to jc/jc mice brains with the use of proteomics, we detected 24 proteins with greater than 1.5-fold differences in expression, including two interacting proteins, dynamin and pacsin1. This study shows mutated SOBP involvement in syndromic and nonsyndromic ID with psychosis in humans.

The novel Y371D myocilin mutation causes an aggressive form of juvenile open-angle glaucoma in a Caucasian family from the Middle-East

PURPOSE

To search for the genetic cause of juvenile open-angle glaucoma (JOAG) in a Caucasian family and to perform genotype/phenotype correlation studies in the kindred.

METHODS

Six members of a three-generation family originating from Uzbekistan and now living in the Middle East were recruited from one large clinic in Israel. Ophthalmologic investigations comprised of visual field assessments, intraocular pressure measurements, optic disc evaluation, and gonioscopy. Medical charts were obtained to date the onset of glaucoma and to evaluate aggressivity of the trait. We screened the myocilin gene (MYOC, OMIM 601652) by direct genomic sequencing of its three exons in all family members.

RESULTS

JOAG segregated as an autosomal dominant trait in four members of the family. The proband, a 14-year-old girl, had been diagnosed with juvenile open-angle glaucoma at 12 years old. Her mother, maternal aunt, and maternal grandfather all had JOAG that started at an early age. The disorder progressed rapidly even under optimal medical treatment, and all four patients had to undergo trabeculectomy. One missense mutation, Y371D (1111t-->g, Tyr [Y] 371 Asp [D]), was identified. This mutation cosegregated with the disorder in all affected members and was absent in 200 Caucasian controls. The Y371D MYOC mutation has not been reported before. One cousin of the proband was a silent heterozygotic carrier of the mutation and was still asymptomatic at nine years of age.

CONCLUSIONS

We identified a novel mutation (Y371D) in MYOC from a Caucasian family who presented with an aggressive form of JOAG that required early trabeculectomy. Genetic screening of the MYOC mutation was beneficial in predicting one asymptomatic heterozygotic carrier.

Impact of homocysteine-lowering vitamin therapy on long-term outcome of patients with coronary artery disease

Elevated homocysteine levels are associated with increased risk for mortality in patients with coronary artery disease (CAD). However, the benefit of homocysteine-lowering therapy remains controversial. The aim of this study was to examine the impact of homocysteine-lowering therapy on the long-term outcomes of patients with CAD and its interaction with the methylenetetrahydrofolate reductase genotype. The study sample included 492 patients with early-onset CAD who were genotyped for the C677T mutation in the methylenetetrahydrofolate reductase gene or screened for elevated homocysteine from January 1997 to December 2002. Folic acid > or =400 microg/day with or without additional B vitamins was administered at the attending physicians' discretion. There was no difference between treated (n = 140) and untreated patients in age, gender, or prevalence of coronary risk factors. Forty-six patients (9%) died during a median follow-up period of 115 months. Treatment was associated with significantly lower all-cause mortality in patients with homocysteine levels >15 micromol/L (4% vs 32%, p <0.001) but not in patients with lower levels (5% vs 7%, p >0.05). On Cox regression analysis, the following factors were independently associated with all-cause mortality: vitamin therapy (hazard ratio 0.33, 95% confidence interval 0.11 to 0.98, p = 0.046), elevated homocysteine level (hazard ratio 3.5, 95% confidence interval 1.31 to 9.43, p = 0.013), and older age (hazard ratio 1.1, 95% confidence interval 1.04 to 1.14, p <0.0001 for an increment of 5 years). The methylenetetrahydrofolate reductase genotype was not associated with outcomes. In conclusion, long-term folate-based vitamin therapy was independently associated with lower all-cause mortality in patients with CAD and elevated homocysteine levels. This association was not observed in patients with lower homocysteine levels.

RIN2 deficiency results in macrocephaly, alopecia, cutis laxa, and scoliosis: MACS syndrome

Inherited disorders of elastic tissue represent a complex and heterogeneous group of diseases, characterized often by sagging skin and occasionally by life-threatening visceral complications. In the present study, we report on an autosomal-recessive disorder that we have termed MACS syndrome (macrocephaly, alopecia, cutis laxa, and scoliosis). The disorder was mapped to chromosome 20p11.21-p11.23, and a homozygous frameshift mutation in RIN2 was found to segregate with the disease phenotype in a large consanguineous kindred. The mutation identified results in decreased expression of RIN2, a ubiquitously expressed protein that interacts with Rab5 and is involved in the regulation of endocytic trafficking. RIN2 deficiency was found to be associated with paucity of dermal microfibrils and deficiency of fibulin-5, which may underlie the abnormal skin phenotype displayed by the patients.

Mutations in NDUFAF3 (C3ORF60), encoding an NDUFAF4 (C6ORF66)-interacting complex I assembly protein, cause fatal neonatal mitochondrial disease

Mitochondrial complex I deficiency is the most prevalent and least understood disorder of the oxidative phosphorylation system. The genetic cause of many cases of isolated complex I deficiency is unknown because of insufficient understanding of the complex I assembly process and the factors involved. We performed homozygosity mapping and gene sequencing to identify the genetic defect in five complex I-deficient patients from three different families. All patients harbored mutations in the NDUFAF3 (C3ORF60) gene, of which the pathogenic nature was assessed by NDUFAF3-GFP baculovirus complementation in fibroblasts. We found that NDUFAF3 is a genuine mitochondrial complex I assembly protein that interacts with complex I subunits. Furthermore, we show that NDUFAF3 tightly interacts with NDUFAF4 (C6ORF66), a protein previously implicated in complex I deficiency. Additional gene conservation analysis links NDUFAF3 to bacterial-membrane-insertion gene cluster SecF/SecD/YajC and to C8ORF38, also implicated in complex I deficiency. These data not only show that NDUFAF3 mutations cause complex I deficiency but also relate different complex I disease genes by the close cooperation of their encoded proteins during the assembly process.

Microdeletion syndromes disclose replication timing alterations of genes unrelated to the missing DNA

Background

The temporal order of allelic replication is interrelated to the epigenomic profile. A significant epigenetic marker is the asynchronous replication of monoallelically-expressed genes versus the synchronous replication of biallelically-expressed genes. The present study sought to determine whether a microdeletion in the genome affects epigenetic profiles of genes unrelated to the missing segment. In order to test this hypothesis, we checked the replication patterns of two genes – SNRPN, a normally monoallelically expressed gene (assigned to 15q11.13), and the RB1, an archetypic biallelically expressed gene (assigned to 13.q14) in the genomes of patients carrying the 22q11.2 deletion (DiGeorge/Velocardiofacial syndrome) and those carrying the 7q11.23 deletion (Williams syndrome).

Results

The allelic replication timing was determined by fluorescence in situ hybridization (FISH) technology performed on peripheral blood cells. As expected, in the cells of normal subjects the frequency of cells showing asynchronous replication for SNRPN was significantly (P < 10^-12) higher than the corresponding value for RB1. In contrast, cells of the deletion-carrying patients exhibited a reversal in this replication pattern: there was a significantly lower frequency of cells engaging in asynchronous replication for SNRPN than for RB1 (P < 10^-4 and P < 10^-3 for DiGeorge/Velocardiofacial and Williams syndromes, respectively). Accordingly, the significantly lower frequency of cells showing asynchronous replication for SNRPN than for RB1 is a new epigenetic marker distinguishing these deletion syndrome genotypes from normal ones.

Conclusion

In cell samples of each deletion-carrying individual, an aberrant, reversed pattern of replication is delineated, namely, where a monoallelic gene replicates more synchronously than a biallelic gene. This inverted pattern, which appears to be non-deletion-specific, clearly distinguishes cells of deletion-carriers from normal ones. As such, it offers a potential epigenetic marker for suspecting a hidden microdeletion that is too small to be detected by conventional karyotyping methods.

Identification of the gene causing long QT syndrome in an Israeli family

BACKGROUND

Long QT syndrome is an inherited cardiac disease, associated with malignant arrhythmias and sudden cardiac death.

OBJECTIVES

To map and identify the gene responsible for LQTS in an Israeli family.

METHODS

A large family was screened for LQTS after one of them was successfully resuscitated from ventricular fibrillation. The DNA was examined for suspicious loci by whole genome screening and the coding region of the LQT2 gene was sequenced.

RESULTS

Nine family members, 6 males and 3 females, age (median and interquartile range) 26 years (13, 46), who were characterized by a unique T wave pattern were diagnosed as carrying the mutant gene. The LQTS-causing gene was mapped to chromosome 7 with the A614V mutation. All of the affected members in the family were correctly identified by electrocardiogram. Corrected QT duration was inversely associated with age in the affected family members and decreased with age.

CONCLUSIONS

Careful inspection of the ECG can correctly identify LQTS in some families. Genetic analysis is needed to confirm the diagnosis and enable the correct therapy in this disease.

Four USH2A founder mutations underlie the majority of Usher syndrome type 2 cases among non-Ashkenazi Jews

Type 2 Usher syndrome (USH2) is a recessively inherited disorder, characterized by the combination of early onset, moderate-to-severe, sensorineural hearing loss, and vision impairment due to retinitis pigmentosa. From 74% to 90% of USH2 cases are caused by mutations of the USH2A gene. USH2A is composed of 72 exons, encoding for usherin, an extracellular matrix protein, which plays an important role in the development and maintenance of neurosensory cells in both retina and cochlea. To date, over 70 pathogenic mutations of USH2A have been reported in individuals of various ethnicities. Many of these mutations are rare private mutations segregating in single families. The aim of the current work was to investigate the genetic basis for USH2 among Jews of various origins. We found that four USH2A mutations (c.239-240insGTAC, c.1000C>T, c.2209C>T, and c.12067-2A>G) account for 64% of mutant alleles underlying USH2 in Jewish families of non-Ashkenazi descent. Considering the very large size of the USH2A gene and the high number of mutations detected in USH2 patients worldwide, our findings have significant implications for genetic counseling and carrier screening in various Jewish populations.

[CV-METER--a computerized objective assessment for academic promotion]

We describe a new web-based program developed at the Sackler Faculty of Medicine at Tel Aviv University that serves as a tool to assist the academic promotion committee. The program incorporates the sum of the candidate's publications together with the impact factor of the journals and the contribution of the candidate according to his/her place in the list of authors. The program also "weighs" other academic achievements of the candidate, such as grades in teaching, contribution to the faculty and to the academy/ profession in general, and other parameters. The program then grades the candidate according to the percentile compared to other candidates who have applied for the same promotion and who are in a similar field of research with comparable opportunities for publication. The program allows for transparency and maximal objectivity in the assessment of the candidates for promotion, taking into consideration multiple parameters, which is difficult without computerization, as well as objective comparisons between different departments and different faculties/universities.

Impact of ethnicity and MTHFR genotype on age at onset of coronary artery disease in women in Israel

BACKGROUND

The C677T mutation in the methylenetetrahydrofolate reductase (MTHFR) gene is associated with early onset of coronary artery disease in some populations with certain ethnic backgrounds. However, data on its effect on CAD development in women are limited and conflicting.

OBJECTIVES

To investigate the effects of the MTHFR C677T mutation and ethnicity on the development and age at onset of CAD in women in Israel.

METHODS

The sample included 135 Jewish women with well-documented CAD (62 Ashkenazi, 44 Oriental and 29 of other origins) in whom CAD symptoms first developed at age < or = 65 years. DNA samples from 235 women served as the control.

RESULTS

CAD symptoms developed later in Ashkenazi than in Oriental women or women of other origins (51.0 +/- 7.0 years vs. 48.3 +/- 7.5 and 46.3 +/- 7.7 years, respectively, P= 0.024). Among Ashkenazi women, the T/T genotype was less common in patients in whom CAD symptoms appeared after age 50 (6.4%) than in patients with earlier CAD symptoms (25.8%, P= 0.037) and Ashkenazi control subjects (23.3%, P= 0.045). Among women from other origins, these differences were not significant. On logistic regression analysis, the T/T genotype was associated with a nearly fourfold increase in the risk of early onset (age < 45 years) of CAD (odds ratio 3.87, 95% confidence interval 1.12-13.45, adjusted for risk factors and origin) and a trend towards an influence of ethnicity (P= 0.08). Compared to Ashkenazi women, the risk of early development of CAD associated with the T/T genotype among Oriental ones was 0.46 (95%CI 0.189-1.114) and in women of other origins, 5.84 (95%CI 1.76-19.34). Each additional risk factor increased the risk of earlier onset of CAD by 42% (OR 1.42, 95%CI 1.06-1.89).

CONCLUSIONS

The age at onset of CAD in Israeli women is influenced by the MTHFR genotype, ethnic origin and coronary risk factors.

Thrombophilic polymorphisms in Israel

Three thrombophilic polymorphisms, FV G1691A, FII G20210A and MTHFR C677T were investigated in Israeli populations by FRET, (fluorescence resonance energy transfer) real-time PCR. We observe extensive variability in the frequencies of each of the polymorphisms, as has been observed in the study of other polymorphisms in these populations. Very high allele frequencies for FV G1691A (the highest 0.087 in Turkish and Greek Jews) and FII G20210A (the highest 0.061 in Georgian Jews) in some of the Israeli populations justify a clinical investigation to assess their risk for venous thrombosis. Principal Coordinates Analysis demonstrates that the Jewish populations are interspersed among the non-Jewish populations. The resemblance of some Jewish populations to certain non-Jewish populations coincides with findings based on classical markers.

Genetic carrier screening for spinal muscular atrophy and spinal muscular atrophy with respiratory distress 1 in an isolated population in Israel

Spinal muscular atrophy (SMA) is an autosomal recessive disease characterized by progressive muscle weakness. It is caused by a mutation in the survival motor neuron gene 1 (SMN1) gene. SMA with respiratory distress 1 (SMARD1), an uncommon variant of infantile SMA also inherited in an autosomal recessive manner, is caused by mutations in the immunoglobulin mu-binding protein 2 (IGHMBP2) gene. We carried out genetic carrier screening among the residents of an isolated Israeli Arab village with a high frequency of SMA in order to identify carriers of SMA type I and SMARD1. During 2006, 168 women were tested for SMA, of whom 13.1% were found to be carriers. Of 111 women tested for SMARD1, 9.9% were found to be carriers. Prenatal diagnosis was performed in one couple where both spouses were carriers of SMARD1; the fetus was found to be affected, and the pregnancy was terminated. To the best of our knowledge, this is the first example of the establishment of a large-scale carrier-screening program for SMA and SMARD1 in an isolated population. SMA has a carrier frequency of 1:33-1:60 in most populations and should be considered for inclusion in a population-based genetic-screening program.