Clinical and genetic analysis of long QT syndrome in two Malay children.

Long QT syndrome (LQTS) is predominantly a genetic cardiac arrhythmia disorder. We report here our study on long QT syndrome from two children from Kelantan, Malaysia. Clinical and genetic findings of these two unrelated Malay children with LQTS is discussed. We found a Long QT, type 1 causal mutation, p.Ile567Thr in the KCNQ1 gene in the first child. A pathogenic mutation could not be detected in the second child, explaining the heterogeneity of this disease.

Allele-specific PCR for a cost-effective & time-efficient diagnostic screening of spinal muscular atrophy.

BACKGROUND & OBJECTIVES: Genetic diagnosis of spinal muscular atrophy (SMA) is complicated by the presence of SMN2 gene as majority of SMA patients show absence or deletion of SMN1 gene. PCR may amplify both the genes non selectively in presence of high amount of DNA. We evaluated whether allele-specific PCR for diagnostic screening of SMA is reliable in the presence of high amount of genomic DNA, which is commonly used when performing diagnostic screening using restriction enzymes. METHODS: A total of 126 blood DNA samples were tested in amounts ranging 80-200 ng, referred for the genetic diagnosis of SMA using both conventional PCR-RFLP and allele-specific PCR. RESULTS: The results from both methods showed agreement. Further, allele-specific PCR was found to be a time-efficient and cost-effective method. INTERPRETATION & CONCLUSIONS: Our study demonstrated the accuracy of our allele-specific PCR and the results were comparable compatible with that of PCR-RFLP, indicating its practical application in SMA diagnostic screening.

Prevalence and molecular study of G6PD deficiency in Malaysian Orang Asli.

This study aims to define the prevalence and the molecular basis of G6PD deficiency in the Negrito tribe of the Malaysian Orang Asli. Four hundred and eighty seven consenting Negrito volunteers were screened for G6PD deficiency through the use of a fluorescent spot test. DNA from deficient individuals underwent PCR-RFLP analysis using thirteen recognized G6PD mutations. In the instances when the mutation could not be identified by PCR-RFLP, the entire coding region of the G6PD gene was subjected to DNA sequencing. In total, 9% (44/486) of the sample were found to be G6PD-deficient. However, only 25 samples were subjected to PCR-RFLP and DNA sequencing. Of these, three were found to carry Viangchan, one Coimbra and 16, a combination of C1311T in exon 11 and IVS11 T93C. Mutation(s) for the five remaining samples are unknown. The mean G6PD enzyme activity ranged 5.7 IU/gHb in deficient individuals. Our results demonstrate that the frequency of G6PD deficiency is higher among the Negrito Orang Asli than other Malaysian races. The dual presence of C1311T and IVS11 T93C in 64% of the deficient individuals (16/44) could well be a result of genetic drift within this isolated group.

De novo interstitial deletion of 1q32.2-q32.3 including the entire IRF6 gene in a patient with oral cleft and other dysmorphic features.

BACKGROUND: Microdeletion of the Van der Woude syndrome (VWS) critical region is a relatively rare event, and only a few cases have been reported in the medical literature. The extent of the deletion and the genotype-phenotype correlation are 2 crucial issues. METHODS AND RESULTS: During analysis of the VWS critical region in 95 families with an isolated cleft of the lip with or without cleft palate, we found a de novo interstitial deletion of 1q32.2-q32.3 in a patient with cleft lip and other dysmorphic features. The present case showed new proximal and distal end breakpoints compared to those previously reported. The results of a short tandem repeat analysis was confirmed using high resolution array-based comparative genomic hybridization and showed an interstitial deletion of approximately 2.98 Mb which involved 25 genes, including the entire IRF6 gene. Direct sequencing of the non-deleted allele of the IRF6 gene did not show any mutation, which supports a haploinsufficiency mechanism of the IRF6 gene in the development of the oral cleft. CONCLUSION: The present report adds to the collective knowledge that oral cleft is a major clinical feature of the 1q32.2-q32.3 deletion.

Contribution of 6p24 to non-syndromic cleft lip and palate in a Malay population: association of variants in OFC1.

Non-syndromic cleft lip, with or without cleft palate, is a heterogeneous, complex disease with a high incidence in the Asian population. Several association studies have been done on cleft candidate genes, but no reports have been published thus far on the Orofacial Cleft 1 (OFC1) genomic region in an Asian population. This study investigated the association between the OFC1 genomic region and non-syndromic cleft lip with or without cleft palate in 90 Malay father-mother-offspring trios. Results showed a preferential over-transmission of a 101-bp allele of marker D6S470 in the allele- and haplotype-based transmission disequilibrium test (TDT), as well as an excess of maternal transmission. However, no significant p-value was found for a maternal genotype effect in a log-linear model, although single and double doses of the 101-bp allele showed a slightly increased cleft risk (RR = 1.37, 95% CI, 0.527-3.4, p-value = 0.516). Carrying two copies of the 101-bp allele was significantly associated with an increased cleft risk (RR = 2.53, 95% CI, 1.06-6.12, p-value = 0.035). In conclusion, we report evidence of the contribution of the OFC1 genomic region to the etiology of clefts in a Malay population.

Chromosomal alterations in Malaysian patients with nasopharyngeal carcinoma analyzed by comparative genomic hybridization.

Nasopharyngeal carcinoma (NPC) is one of the most common cancers in Malaysia, mainly occurring among the Chinese population. To detect common genetic alterations in NPC, we screened seven cases of NPC using the comparative genomic hybridization (CGH) technique. Before proceeding to the CGH technique, the tumors were first confirmed to consist of 75% tumor cells or more. In brief, the technique consists of binding tumor DNA with normal DNA and human Cot-1 DNA, which is then hybridized to normal metaphase spreads. The slides were then counterstained with 4,6 diamino-2-phenylindole (DAPI II) for detection. Analyses were performed using CGH software (Cytovision). We found genetic alterations in all seven NPC samples. The common chromosomal gains (57%, four cases) were found on chromosome arms 1q, 4p, 5, 7q, 11, 14p, 15q, 18p, and 21p, and common chromosomal losses (43%, three cases) were found on chromosome arm 16p. Our results showed chromosomal alterations in all seven NPC cases in the Malaysian population. This result provides the platform for further investigations to locate tumor suppressor genes and oncogenes at specific chromosomal regions in Malaysian NPC patients.

Chromosomal abnormalities and reproductive outcome in Malaysian couples with miscarriages.

INTRODUCTION: This study was done to determine the prevalence of chromosomal abnormalities and the subsequent reproductive outcome in couples who had two or more miscarriages. METHODS: 56 couples with a history of at least two previous miscarriages were evaluated for prevalence and types of chromosomal abnormalities from their karyotype records. The study was a retrospective one, and subsequent reproductive outcome after a period of 12-24 months from the time of karyotyping was obtained by telephone interviews and scrutiny of the case records. The comparison of reproductive outcome was done by chi-square statistics. RESULTS: Five couples (8.9 percent) had a chromosomal abnormality in one partner. Three cases of reciprocal translocations t(5;11), t(9;14), dup(9q); one Robertsonian D/D translocation 13/14; and one mosaic Down syndrome male karyotype were found. Among the 32 couples available for follow-up, there was a lower incidence of subsequent live healthy births among chromosomally-normal couples (35.7 percent) compared to chromosomally-abnormal ones (25 percent). However, the difference was not statistically significant (p-value is 1.0). There was a lower incidence of subsequent abortions in chromosomally-normal couples (42.8 percent) compared to chromosomally-abnormal ones (50 percent), but the difference was also not statistically significant (p-value is 1.0). CONCLUSION: Chromosomal abnormalities were seen in 8.9 percent of the couples, and translocations were the commonest abnormality found. The frequencies of subsequent live healthy births and subsequent abortions showed no significant difference between couples having normal karyotypes and those having chromosomal abnormality in one partner.

Clinical manifestations in trisomy 9.

Complete trisomy 9 is a lethal diagnosis and most fetuses diagnosed thus die prenatally or during the early postnatal period and majority of such cases have been known to end in spontaneous abortion in the first trimester itself. One such rare survival of fetus ending in normal delivery and surviving until 20 days is reported here detailing the clinical manifestations of the child during the period of survival. The salient clinical features observed were small face, wide fontanel, prominent occiput, micrognathia, low set ears, upslanting palpebral fissures, high arched palate, short sternum, overlapping fingers, limited hip abduction, rocker bottom feet, heart murmurs and also webbed neck, characteristic of this trisomy 9 syndrome.

Screening of dystrophin gene deletions in Malaysian patients with Duchenne muscular dystrophy.

Duchenne Muscular Dystrophy (DMD) is an X-linked recessive genetic disorder characterized by rapidly progressive muscle weakness. The disease is caused by deletion, duplication or point mutation of the dystrophin gene, located on the X chromosome (Xp21). Deletion accounts for 60% of the mutations within the 79 exons of the dystrophin gene. Seven exons (43, 44, 45, 46, 49, 50, and 51) were found to be most commonly deleted among the Asian patients. To detect the frequency of deletion of these 7 exons in Malaysian DMD patients, we carried out a molecular genetic analysis in 20 Malaysian DMD patients. The mean age of initial presentation was 60 months (SD 32 months, range 5-120 months). Fourteen patients were found to have deletion of at least one of the seven exons. The remaining six patients did not show any deletion on the tested exons. Deletions of exons 49, 50 and 51 were the most frequent (71.43%) and appear to be the hot spots in our cohort of patients.

Turner syndrome diagnosed in northeastern Malaysia.

INTRODUCTION: Turner syndrome affects about one in 2,000 live-born females, and the wide range of somatic features indicates that a number of different X-located genes are responsible for the complete phenotype. This retrospective study highlights the Turner syndrome cases confirmed through cytogenetic analysis at the Human Genome Centre of Universiti Sains Malaysia, from 2001 to 2006. METHODS: Lymphocyte cultures were set up using peripheral blood samples, chromosomes were prepared, G-banded, karyotyped and analysed in accordance to guidelines from the International System for Human Cytogenetic Nomenclature. RESULTS: The various karyotype patterns observed were 45,X; 46,X,i, (Xq); 45,X/45,X,+mar; 45,X/46,X,i,(Xq) and 45,X/46,XY. The mean age of our patients with Turner syndrome was 21 years, and the most common clinical features encountered in all these patients were short stature (100 percent), primary amenorrhoea (85.7 percent), absence of secondary sexual characteristics (57.1 percent), scanty pubic and axillary hair (50 percent), webbed neck (42.9 percent), wide carrying angle (42.9 percent), rudimentary uterus with bilateral streak ovaries (42.9 percent), underdeveloped breasts (35.7 percent) and wide-spaced nipples (21.4 percent). CONCLUSION: Even though there is no causal therapy for Turner syndrome, management and treatment are possible for malformations and conditions associated with it. In addition, counselling of the parents and of the patients themselves are necessary. Hence, establishing an early diagnosis, educating and increasing awareness among doctors, and if possible, a prenatal diagnosis, will help in early intervention, genetic counselling and in improving the quality of life in these patients.

Two cases of deletion 5p syndrome: one with paternal involvement and another with atypical presentation.

We report two cases of deletion 5p or cri du chat syndrome (CdCS) with different presentations and risks of transmission: one case with paternal chromosome 5 involvement and another, a de novo case with atypical clinical presentation. Cytogenetic analysis was performed on the two cases and their parents. GTG-banded karyotype analysis of Cases 1 and 2 revealed abnormal 46,XY,del(5)(p13-15) male karyotypes. For Case 1, the mother showed normal female karyotype while the father showed an abnormal karyotype involving a balanced translocation 46,XY,t(5;10)(p13;p15). For Case 2, however, both parents showed a normal karyotype pattern. In Case 1, the clinical features, particularly the distinct facial phenotype in combination with a characteristic cat-like cry and hypotonia, aided in the diagnosis at birth and the karyotype analysis was resolutive. The boy in Case 2 presented with atypical clinical features. Even though this patient had multiple syndromic features, the typical high pitched cat-like cry was not prominent. Instead, the patient manifested persistent stridor (from day three of life), which might have prevented the clinician from suspecting CdCS at birth. However, when this patient was presented at seven months of age for cytogenetic analysis, a confirmatory diagnosis of CdCS was established. For children with congenital abnormalities, an early clinical diagnosis confirmed through cytogenetic and molecular investigations, is important for providing personalised diagnostic and prognostic evaluation, and also for genetic counselling on the reproductive risk, particularly for patients with parental chromosome translocation involvement.

Screening for gap junction protein beta-2 gene mutations in Malays with autosomal recessive, non-syndromic hearing loss, using denaturing high performance liquid chromatography.

OBJECTIVE: To determine the frequency and type of gap junction protein beta-2 gene mutations in Malay patients with autosomal recessive, non-syndromic hearing loss. METHODS: A total of 33 Malay patients with autosomal recessive, non-syndromic hearing loss were screened for mutations in the Cx26 coding region. Deoxyribonucleic acid was extracted from buccal swab samples and subjected to polymerase chain reaction. Slow-reannealing was performed, followed by screening using denaturing high performance liquid chromatography. RESULTS: Eight of the samples (24.2 per cent) showed heterozygous peaks, and further sequencing of these samples revealed four patients (50.0 per cent) with the W24X mutation, two (25.0 per cent) with the V37I mutation and another two (25.0 per cent) with the G4D mutation. CONCLUSIONS: Analysis of buccal swab samples by denaturing high performance liquid chromatography is noninvasive and suitable for rapid and reliable screening of gap junction protein beta-2 gene mutations in patients with autosomal recessive, non-syndromic hearing loss. Malay patients with autosomal recessive, non-syndromic hearing loss have different kinds of gap junction protein beta-2 gene mutations which are rarely found in other populations.

Detection of beta-globin gene mutations among Kelantan Malay thalassaemia patients by polymerase chain reaction restriction fragment length polymorphism.

INTRODUCTION: Beta-thalassaemia major is an autosomal recessive disorder that results in severe microcytic, hypochromic, haemolytic anaemia among affected patients. Beta-thalassaemia has emerged as one of the most common public health problems in Malaysia, particularly among Malaysian Chinese and Malays. This study aimed to observe the spectrum of mutations found in Kelantan Malay beta-thalassaemia major patients who attended the Paediatrics Daycare Unit, Hospital Universiti Sains Malaysia, Kelantan, Malaysia, the data of which was being used in establishing the prenatal diagnosis in this Human Genome Centre. METHODS: This was a cross-sectional study conducted with 35 Kelantan Malay beta-thalassaemia major patients. DNA was extracted from the blood collected from the patients and subjected to polymerase chain reaction (PCR) amplification. Six restriction enzymes were used to digest the PCR products for the detection of mutations. RESULTS: Five out of the six beta-globin gene defects were detected, namely, IVS-1 nt5 (G>C), IVS-1 nt1 (G>T), codon 26 (G>A), codon 41-42 (4 bp del) and codon 19 (A>G). The mutation which was not observed in this study was in codon 15 (G>A). The two most common mutations observed were codon 26 (G>A) and IVS-1 nt5 (G>C), which was detected in 26 and 17 patients, respectively. Two patients did not show any of the six mutations. CONCLUSION: Our results added to the existing data on the common beta-globin gene defects in Kelantan Malay beta-thalassaemia patients.

Cytogenetic and clinical profile of Down syndrome in Northeast Malaysia.

INTRODUCTION: This study was designed to evaluate the karyotype pattern, clinical features and other systemic anomalies of patients with Down syndrome in Malaysia. METHODS: Retrospective analysis was performed on the case records of 149 patients confirmed as Down syndrome by cytogenetic analysis at Human Genome Centre and Genetic Clinic at the Universiti Sains Malaysia. RESULTS: Among the 149 cases of Down syndrome presenting over a period of 4.2 years, free trisomy (non-disjunction) was present in 141 cases (94.6 percent). One case (0.7 percent) had translocation, and seven cases (4.7 percent) were mosaics. Average age at presentation was 10.6 months. Average maternal age at birth of the affected child was 32.3 years. The prominent craniofacial features noted were upslanting palpebral fissures (89.3 percent), flat facial profile (64.9 percent), low set ears (56.1 percent), epicanthic folds (17.5 percent) and protruding tongue (19.2 percent). A total of 52.6 percent of the cases had documented hypotonia. Characteristic limb and dermatoglyphic anomalies included short stubby fingers (24.5 percent), sandal gap (33.3 percent), unilateral or bilateral simian crease (36.8 percent) and clinodactyly (19.2 percent). Ophthalmological abnormalities, such as hypertelorism, were presented in 33.3 percent of the cases. Congenital heart disease was diagnosed in 35 out of 71 cases (49.3 percent) and gastrointestinal anomalies were noted in 18 out of 79 cases (22.7 percent) analysed. CONCLUSION: Efforts to establish early diagnosis and a proper screening for high association with systemic anomalies should be undertaken among the Down syndrome patients in this population.

Two cases of isochromosome 18q syndrome.

Patients with isochromosome 18q, a rare cytogenetic abnormality, also reported as Edwards syndrome, is the second most common autosomal trisomy. However, the phenotypic features and survival of these patients are not uniform and depend upon the portion of chromosomes getting duplicated or deleted. The survival of these children may be longer, hence a good cytogenetic diagnosis is a must. Morphological characteristics of isochromosome 18q are not yet fully delineated because of the rarity of the cases and as most cases are aborted medically or terminate spontaneously. We report two cases of isochromosome 18q, one male aged two years old and the other a male aged eight months old, and review the literature on this rare syndrome.

An improved rapid genotyping method for the study of beta-2 adrenergic receptor gene polymorphisms using single tube allele specific multiplex PCR.

BACKGROUND: Seventeen single nucleotide polymorphisms (SNPs) have been identified so far, within the beta-2 receptor (beta(2) AR) gene. The presence of so many SNPs within the beta(2) AR gene causes a problem, for those studying beta(2) AR pharmacogenetics, in relation to which SNPs to choose. Most of the work has focused on the three common SNPs within the coding block (alleles 16, 27 and 164) and the techniques developed have been for these three functionally important alleles. OBJECTIVE: We report an improved polymerase chain reaction (PCR)-based method for the simultaneous detection of five functionally important beta(2) AR alleles, namely beta 16A/G, beta utr-20C/T, beta 27C/G, beta utr-47C/T and beta 164C/T. METHODS: Genomic DNA was used as a template for duplex and triplex PCR to detect the polymorphic sites of the five alleles. RESULT: DNA sequencing analysis confirmed the specificity of this PCR method. CONCLUSION: This simplified single-tube multiplexed PCR assay provides an easier, faster and more cost-effective method than those available for studying the specified polymorphisms of the beta(2)AR gene.

A Malay boy with the Cornelia de Lange syndrome: clinical and molecular findings.

The Cornelia de Lange syndrome is a multiple congenital anomaly syndrome characterised by dysmorphic facial features, hirsutism, severe growth and developmental delays, and malformed upper limbs. The prevalence is estimated to be one per 10,000. Recently, several independent groups proved that Cornelia de Lange syndrome is caused by mutations in the NIPBL gene, the human homologue of the Drosophila Nipped-B gene. Here, we present the first clinical case report of a Malay child, a 9-year-old boy with the Cornelia de Lange syndrome. We also report the molecular investigation of the NIPBL gene in this patient.

Ocular findings in Malaysian children with Down syndrome.

INTRODUCTION: Down syndrome was first described as Mongoloid children with European parentage. Although their facial features resemble Orientals or Asians, ocular findings have not been well-documented in Asians, especially Malaysians. Our aim was to identify the ocular findings of Malaysian children with Down syndrome. METHODS: A total of 60 children with Down syndrome, aged between one month and 17 years, were examined for ocular findings from January 1995 to January 2004. Ocular examination, which includes visual acuity assessment, slit lamp biomicroscopy, ocular motility, cycloplegic refraction and ophthalmoscopy were performed whenever possible. RESULTS: The ocular findings include epicanthic fold in 96.7 percent (58), nystagmus in 33.3 percent (20), and strabismus in 26.7 percent (16) of children with Down syndrome, all of whom were esotropic. Other findings were bilateral congenital cataract in 13.3 percent (8), blepharoconjunctivitis in 10.0 percent (6), eyelid abnormalities in 6.7 percent (4), glaucoma in 6.7 percent (4), nasolacrimal duct obstruction in 3.3 percent (2), bilateral retinoblastoma in 1.7 percent (1), bilateral retinal detachment in 1.7 percent (1), and chronic uveitis in 1.7 percent (1) of children. Visual assessment showed that 47.3 percent of patients achieved good vision (6/12 to 6/6). Cycloplegic refraction was done in 24 patients (41.7 percent). Out of the 24 patients, 29.2 percent (7) were myopic, 25.0 percent (6) were hyperopic, and astigmatism was observed in 8.3 percent (2). CONCLUSION: Malaysian children with Down syndrome demonstrated high incidences of epicanthic fold, nystagmus, and strabismus, and absence of Brushfield spots or keratoconus, which are in contrast to the ocular findings in Caucasian patients with Down syndrome. Rare ocular findings, such as bilateral retinoblastoma and retinal detachment, were also observed but their association with Down syndrome is not well-established.

Detection of F508del mutation in cystic fibrosis transmembrane conductance regulator gene mutation among Malays.

INTRODUCTION: Cystic fibrosis (CF) is one of the common genetic disorders in the western world. It has been reported to be very rare in Asian populations. According to the Cystic Fibrosis Genetic Analysis Consortium, more than 1,000 mutations of the CF gene have been identified. The CF gene, named the cystic fibrosis transmembrane conductance regulator (CFTR), is located on chromosome 7 and composed of 27 exons. This study aims to detect possible CFTR gene mutations in Malays. METHODS: We analysed 50 blood samples from healthy Malays with no symptoms of CF. DNA was extracted from blood using commercially available extraction kits (Eppendorf, Germany). Identification of CFTR gene mutation was performed using the CF OLA (Oligonucleotide Ligation Assay) kit (Applied Biosystems, USA). The PCR-ligation products were electrophoresed on eight percent sequagel using an ABI PRISM 377 genetic analyser (Applied Biosystems, USA). Electrophoresis data was analysed using the Genotyper software and a report of the CF genotype for all loci tested was created using the CF Genotyper Template software. Out of 50, one sample (two percent) was detected to have the F508del mutation (3bp deletion at exon 10), which is one of the most common CFTR gene mutations in Caucasians. RESULTS: The F508del mutation allele was detected in one subject. This indicates that she was a CF carrier. CONCLUSION: We report the finding of a carrier of the F508del mutation of the CFTR gene in the Malay population. Our finding revealed that CF could also affect the Malay population. Larger studies are necessary to determine the exact gene frequency of this population.

Genetic polymorphism of CYP2D6 in patients with cardiovascular disease -- a cohort study.

BACKGROUND: Cardiovascular diseases are complex diseases that are influenced by both environmental and genetic factors. CYP2D6 found in the brain and the heart is involved in the metabolism of many environmental and some endogenous substances and neurotransmitters responsible for maintaining homeostasis. This raises an interesting hypothesis that it may have a role in the development of or protection against cardiovascular diseases. OBJECTIVE: To study the distribution of genotypes of CYP2D6 among patients with cardiovascular diseases in Malaysia. METHOD: We obtained DNA from 128 patients who were followed up for cardiovascular diseases. Polymerase chain reaction-based methods were used to determine common CYP2D6 alleles. RESULTS: One hundred and twenty-eight patients were enrolled. Most of the patients also had concurrent illnesses. Eleven genotypes were identified in the patients and 41% carried CYP2D6*1/*10. The second most common genotype was homozygous for the wild type gene, followed by homozygous CYP2D6*10/*10 at 14.48 %. A small percentage of the patients were heterozygous CYP2D6*1/*4. One patient was genotyped homozygous CYP2D6*4/*4 predicting a poor metabolizer prevalence of 0.78% (95% CI +/- 1.52%). Analysis using Hardy-Weinberg equilibrium showed that all of the gnotypes were consistent with equilibrium except for CYP2D6*1/*10 (chi(2); P < 0.05). CONCLUSION: Our study suggests a possible involvement of CYP2D6 genotypes in cardiovascular system diseases, which need to be validated by further studies.