Rehan Sadiq Shaikh

Loss-of-function mutations of ILDR1 cause autosomal-recessive hearing impairment DFNB42.

By using homozygosity mapping in a consanguineous Pakistani family, we detected linkage of nonsyndromic hearing loss to a 7.6 Mb region on chromosome 3q13.31-q21.1 within the previously reported DFNB42 locus. Subsequent candidate gene sequencing identified a homozygous nonsense mutation (c.1135G>T [p.Glu379X]) in ILDR1 as the cause of hearing impairment. By analyzing additional consanguineous families with homozygosity at this locus, we detected ILDR1 mutations in the affected individuals of 10 more families from Pakistan and Iran. The identified ILDR1 variants include missense, nonsense, frameshift, and splice-site mutations as well as a start codon mutation in the family that originally defined the DFNB42 locus. ILDR1 encodes the evolutionarily conserved immunoglobulin-like domain containing receptor 1, a putative transmembrane receptor of unknown function. In situ hybridization detected expression of Ildr1, the murine ortholog, early in development in the vestibule and in hair cells and supporting cells of the cochlea. Expression in hair cell- and supporting cell-containing neurosensory organs is conserved in the zebrafish, in which the ildr1 ortholog is prominently expressed in the developing ear and neuromasts of the lateral line. These data identify loss-of-function mutations of ILDR1, a gene with a conserved expression pattern pointing to a conserved function in hearing in vertebrates, as underlying nonsyndromic prelingual sensorineural hearing impairment.

Mutation Spectrum of MYO7A and Evaluation of a Novel Nonsyndromic Deafness DFNB2 Allele with Residual Function

Recessive mutations of MYO7A, encoding unconventional myosin VIIA, can cause either a deaf‐blindness syndrome (type 1 Usher syndrome; USH1B) or nonsyndromic deafness (DFNB2). In our study, deafness segregating as a recessive trait in 24 consanguineous families showed linkage to markers for the DFNB2/USH1B locus on chromosome 11q13.5. A total of 23 of these families segregate USH1 due to 17 homozygous mutant MYO7A alleles, of which 14 are novel. One family segregated nonsyndromic hearing loss DFNB2 due to a novel three‐nucleotide deletion in an exon of MYO7A (p.E1716del) encoding a region of the tail domain. We hypothesized that DFNB2 alleles of MYO7A have residual myosin VIIA. To address this question we investigated the effects of several mutant alleles by making green fluorescent protein (GFP) tagged cDNA expression constructs containing engineered mutations of mouse Myo7a at codons equivalent to pathogenic USH1B and DFNB2 alleles of human MYO7A. We show that in transfected mouse hair cells an USH1B mutant GFP‐myosin VIIa does not localize properly to inner ear hair cell stereocilia. However, a GFP‐myosin VIIa protein engineered to have an equivalent DFNB2 mutation to p.E1716del localizes correctly in transfected mouse hair cells. This finding is consistent with the hypothesis that p.E1716del causes a less severe phenotype (DFNB2) than the USH1B‐associated alleles because the resulting protein retains some degree of normal function. Hum Mutat 29(4), 502–511, 2008. Published 2008 Wiley‐Liss, Inc.

OCA5, a novel locus for non-syndromic oculocutaneous albinism, maps to chromosome 4q24.

To the Editor : Oculocutaneous albinism (OCA) is a genetically heterogeneous disorder manifested as a loss of pigmentation in the eyes, skin and hair (1). On the basis of its clinical presentation, OCA can manifest in either isolated or syndromic fashion under a variety of inheritance models (1). To date, four loci have been mapped for recessively inherited isolated OCA, and genes for all of these loci have been identified (2). However, mutations in these four genes do not account for all cases of non-syndromic OCA. In published studies, the detection rate of mutations varies, and up to 30% of OCA

Association of XRCC1, XRCC3, and XPD genetic polymorphism with an increased risk of hepatocellular carcinoma because of the hepatitis B and C virus.

Objective The south-east Asian and sub-Saharan African populations are the most susceptible to hepatocellular carcinoma (HCC). We aimed to establish whether XRCC1, XRCC3, and XPD are associated with liver cancer in Pakistan and to examine the interaction of hepatitis B virus (HBV) or hepatitis C virus (HCV) with repaired genes in the occurrence of liver cancer. Materials and methods We enrolled 74 healthy individuals, 75 had either HBV or HCV, and 50 were HCC patients. The characteristic information of all the study participants were collected through a standard interviewer-administered questionnaire. The PCR-RFLP was used to identify the genotype of the patients. Results The results of our study indicated that the patients infected with HBV or HCV had a four or three-fold greater risk of developing liver cancer. Patients older than 55 years of age had a significantly higher risk of developing cancer compared with younger patients. The homozygous wild types Arg/Arg for 280 and Thr/Thr for 241 were more frequent in the controls than in the cases. The allelic frequency of mutant 280His and 399Gln was more pronounced among HCC cases than the controls or the HBV-infected patients. Conclusion The frequency of the XPD gene in the controls was in Hardy–Weinberg equilibrium, indicating that the gene played a protective role in the Pakistani population. XRCC1 or XRCC3 was associated with liver cancer in the Pakistani population; however, the XPD gene played a vital role in the repair of DNA damage.

A study on the determination of risk factors associated with babesiosis and prevalence of Babesia sp., by PCR amplification, in small ruminants from Southern Punjab (Pakistan)

Babesiosis is a parasitic infection due to the multiplication of tick borne parasite, Babesia sp., in erythrocytes of host, which includes a wide variety of vertebrates including small ruminants causing decreased livestock output and hence economic losses. The objective of the present study was to establish a PCR based method for the detection of Babesia sp. in small ruminant population in Southern Punjab and to determine the risk factors involve in the spread of babesiosis. A total of 107 blood samples were collected from 40 sheep and 67 goats in seven districts of Southern Punjab from randomly selected herds. Data on the characteristics of the animals and the herd were collected through questionnaires. 36 blood samples (34% of total) produced the DNA fragment specific for 18S rRNA gene of Babesia sp., by PCR amplification, of which 20 were sheep and 16 were goats. Samples from all seven district contained Babesia positive samples and prevalence varied between 18 to 68%. It was observed that male animals (P = 0.009) and young animals under one year of age (P = 0.01) were more prone to the parasite. It was observed that herds consist of more than 15 animals (P = 0.007), composed of mixed species of small ruminants (P = 0.022), associated with dogs (P = 0.003) and dogs having ticks on their bodies (P = 0.011) were among the major risk factors for the spread of babesiosis in small ruminants.

A report on the high prevalence of Anaplasma sp. in buffaloes from two provinces in Pakistan

The present study was designed to use a PCR-RFLP protocol for the molecular detection of Anaplasma sp. and to compare its prevalence in blood samples from buffaloes (Bubalus bubalis) from 2 provinces of Pakistan and to determine the risk factors associated with the spread of Anaplasma infection. A total of 281 blood samples were collected from adults and calves of buffaloes from 4 sampling sites in Southern Punjab (Bahawalnagar, Burewala, Layyah, and Multan districts) and 2 in Khyber Pukhtoon Khwa (Peshawer and Kohat districts) from randomly selected herds. Data on the characteristics of the animals (gender, age, tick presence or absence, prior treatment for Anaplasma infection) and the herd (location, size, dogs associated with the herds, tick burden of dogs associated with the herds) were collected through questionnaires. One hundred and sixteen blood samples (41% of total) produced the 577-base pairs DNA fragment specific for the 16S rRNA gene of Anaplasma sp. by PCR amplification. Twenty of the 116 Anaplasma sp.-positive PCR products were confirmed to be Anaplasma marginale upon restriction with BssNa1, specific to cut A. marginale sequences. ANOVA results revealed a highly significant association between sampling sites and prevalence of Anaplasma sp. (P<0.001) indicating that Anaplasma sp. prevalence was variable among all 6 sampling sites. Risk factor analysis indicated that the association of dogs with the herd was the only significant (P=0.029) risk factor associated with the spread of Anaplasma sp. in buffaloes while sex, age, presence of ticks on animals or herd size showed no association with Anaplasma infection.

Combined effect of menopause age and genotype on occurrence of breast cancer risk in Pakistani population.

UNLABELLED Cancer incidences and mortality rates are rapidly increasing and breast cancer is among the most frequent malignancy experienced in women worldwide. The occurrence of breast cancer could be associated with various social, cultural, environmental, life-style, hormonal and genetic factors. OBJECTIVE To establish if PvuII and XbaI polymorphisms of estrogen receptor alpha would make Pakistani women more susceptible to breast cancer. Furthermore, association between breast cancer and various factors was also explored to establish the contributing factors in breast cancer in Pakistani population. SUBJECTS AND METHODS Two hundred samples, aged 15-65 years, consisting of 100 breast cancer patients and 100 control samples were ascertained for this case-control study in order to evaluate the factors related to disease incidence. 5-7 ml of blood sample of each participating women in the study was collected and analyzed for polymorphisms of PvuII and XbaI using PCR-RFLP method. RESULTS The menopause had strong influence on incidences of cancer with ca 18-fold increase in risk of breast cancer in women with menopause compared with non-menopaused. Furthermore significant impact of menopause age (P<0.0001) was observed on the incidence of cancer, as high rate of cancer incidence was observed in patients with age between 36 and 45 years (P<0.0001). Similarly, the genotype XbaI had significant influence on the incidence of the disease with heterozygous genotype of XbaI was 45% higher than wild type in cancerous cases. The menopausal women having heterozygous and homozygous mutants of PvuII or XbaI genotypes were strongly correlated with breast cancer (P<0.01). CONCLUSION The polymorphism of genes involving estrogen-metabolizing pathway and estrogen receptor pathway may play an important role in the etiology of breast cancer in Pakistani women.

Effects of glutathione-S-transferase polymorphisms on the risk of breast cancer: A population-based case-control study in Pakistan

Cancer is widely accepted as one of the major health issues. Diet composition and exposure to environmental genotoxic and carcinogenic agents such as polycyclic aromatic hydrocarbons (PAHs) are among the causative factors for various types of cancers, including breast cancer. Low penetrance genes including glutathione S transferases (GST) in association with environmental factors can contribute greatly in the development of breast cancer. We were interested to investigate the association of the polymorphisms of GSTM1, GSTT1, GSTP1 and GSTO2 with the risk of breast cancer in the Pakistani population. One hundred women visiting the Department of Radiology and Oncology, Nishter Hospital, Multan with pathologically confirmed breast cancer, and 100 healthy volunteers from central Pakistan were enrolled in the present study. The strength of the association of various factors with breast cancer was measured by calculating odd ratios (ORs) which were determined by logistic regression. All P values cited are two-sided; differences resulting in a P value of less or equal to 0.05 were declared statistically significant. The Hardy Weinberg equilibrium was tested for the genotype proportions in the control group, as a measure of quality control. Those aged 36-45, in menopause or with a history of cancer in the family had a significantly higher prevalence of breast cancer compared with controls. The frequency of GSTM1 and GSTT1 was similar in both control and patients suggesting no association with the risk of cancer development, however GSTM1 and GSTT1 were significantly linked with the risk of breast cancer in smokers and in women with a history of breast cancer in the family respectively. Similarly women homozygous for GSTP1 or GSTO2 and with a history of breast cancer, or in menopause, were at greater risk of breast cancer than wild type or heterozygotes. Our data suggest that genetic differences in some GST genes may be linked with an increased susceptibility to breast cancer. Furthermore it also gives an insight into the interaction between the GST polymorphisms and pre-menopausal diagnosis of breast cancer.

Molecular genetic studies and delineation of the oculocutaneous albinism phenotype in the Pakistani population

BackgroundOculocutaneous albinism (OCA) is caused by a group of genetically heterogeneous inherited defects that result in the loss of pigmentation in the eyes, skin and hair. Mutations in the TYR, OCA2, TYRP1 and SLC45A2 genes have been shown to cause isolated OCA. No comprehensive analysis has been conducted to study the spectrum of OCA alleles prevailing in Pakistani albino populations.MethodsWe enrolled 40 large Pakistani families and screened them for OCA genes and a candidate gene, SLC24A5. Protein function effects were evaluated using in silico prediction algorithms and ex vivo studies in human melanocytes. The effects of splice-site mutations were determined using an exon-trapping assay.ResultsScreening of the TYR gene revealed four known (p.Arg299His, p.Pro406Leu, p.Gly419Arg, p.Arg278*) and three novel mutations (p.Pro21Leu, p.Cys35Arg, p.Tyr411His) in ten families. Ex vivo studies revealed the retention of an EGFP-tagged mutant (p.Pro21Leu, p.Cys35Arg or p.Tyr411His) tyrosinase in the endoplasmic reticulum (ER) at 37°C, but a significant fraction of p.Cys35Arg and p.Tyr411His left the ER in cells grown at a permissive temperature (31°C). Three novel (p.Asp486Tyr, p.Leu527Arg, c.1045-15 T > G) and two known mutations (p.Pro743Leu, p.Ala787Thr) of OCA2 were found in fourteen families. Exon-trapping assays with a construct containing a novel c.1045-15 T > G mutation revealed an error in splicing. No mutation in TYRP1, SLC45A2, and SLC24A5 was found in the remaining 16 families. Clinical evaluation of the families segregating either TYR or OCA2 mutations showed nystagmus, photophobia, and loss of pigmentation in the skin or hair follicles. Most of the affected individuals had grayish-blue colored eyes.ConclusionsOur results show that ten and fourteen families harbored mutations in the TYR and OCA2 genes, respectively. Our findings, along with the results of previous studies, indicate that the p.Cys35Arg, p.Arg278* and p.Gly419Arg alleles of TYR and the p.Asp486Tyr and c.1045-15 T > G alleles of OCA2 are the most common causes of OCA in Pakistani families. To the best of our knowledge, this study represents the first documentation of OCA2 alleles in the Pakistani population. A significant proportion of our cohort did not have mutations in known OCA genes. Overall, our study contributes to the development of genetic testing protocols and genetic counseling for OCA in Pakistani families.

A new locus for nonsyndromic deafness DFNB51 maps to chromosome 11p13-p12.

viewed to construct the pedigrees and to confirm the relationships in these consanguineous families. Inheritance of deafness in both of the families is consistent with an autosomal recessive trait. All the participating members of families PKDF240 and PKDF407 underwent a physical examination. Clinical histories were obtained from all of the individuals to rule out environmental causes of hearing loss such as mumps, rubella, meningitis, ototoxic drugs, or chronic otitis media. Pure tone audiometry tests for air conduction were performed at frequencies ranging from 250 to 8,000 Hz. Funduscopic examination was conducted to determine gross ocular status and to rule out a retinopathy, while vestibular function was evaluated by using the tandem gait and Romberg tests. All affected individuals of these two families exhibited prelingual bilateral profound sensorineural hearing loss, with no obvious vestibular or ocular abnormalities. No other medical problem was found to co-segregate with the deafness.