Screening of the LAMB2, WT1, NPHS1, and NPHS2 Genes in Pediatric Nephrotic Syndrome

Mutations in the NPHS1, NPHS2, LAMB2, and the WT1 genes are responsible for causing nephrotic syndrome (NS) in two third of the early onset cases. This study was carried out to assess the frequencies of mutations in these genes in a cohort of pediatric NS patients. A total of 64 pediatric familial or sporadic SRNS cases were recruited. Among these, 74% had a disease onset of up to 3 years of age. We found one homozygous frameshift mutation in the NPHS1 gene in one CNS case and two homozygous mutations in the NPHS2 gene. Six mutations in four cases in the LAMB2 gene were also identified. No mutation was detected in the WT1 gene in isolated SRNS cases. LAMB2 gene missense mutations were segregating in NS cases with no extra-renal abnormalities. Analysis of the population genomic data (1000 genome and gnomAD databases) for the prevalence estimation revealed that NS is more prevalent than previously determined from clinical cohorts especially in Asian population compared with overall world populations (prevalence worldwide was 1in 189036 and in South-Asian was 1in 56689). Our results reiterated a low prevalence of mutations in the NPHS1, NPHS2, LAMB2, and WT1 genes in the studied population from Pakistan as compared to some European population that showed a high prevalence of mutations in these genes. This is a comprehensive screening of the genes causing early onset NS in sporadic and familial NS cases suggesting a more systematic and robust approach for mutation identification in all the 45 disease-causing genes in NS in our population is required

"Like sugar in milk": reconstructing the genetic history of the Parsi population.

BACKGROUND: The Parsis are one of the smallest religious communities in the world. To understand the population structure and demographic history of this group in detail, we analyzed Indian and Pakistani Parsi populations using high-resolution genetic variation data on autosomal and uniparental loci (Y-chromosomal and mitochondrial DNA). Additionally, we also assayed mitochondrial DNA polymorphisms among ancient Parsi DNA samples excavated from Sanjan, in present day Gujarat, the place of their original settlement in India. RESULTS: Among present-day populations, the Parsis are genetically closest to Iranian and the Caucasus populations rather than their South Asian neighbors. They also share the highest number of haplotypes with present-day Iranians and we estimate that the admixture of the Parsis with Indian populations occurred ~1,200 years ago. Enriched homozygosity in the Parsi reflects their recent isolation and inbreeding. We also observed 48% South-Asian-specific mitochondrial lineages among the ancient samples, which might have resulted from the assimilation of local females during the initial settlement. Finally, we show that Parsis are genetically closer to Neolithic Iranians than to modern Iranians, who have witnessed a more recent wave of admixture from the Near East. CONCLUSIONS: Our results are consistent with the historically-recorded migration of the Parsi populations to South Asia in the 7th century and in agreement with their assimilation into the Indian sub-continent's population and cultural milieu "like sugar in milk". Moreover, in a wider context our results support a major demographic transition in West Asia due to the Islamic conquest

Host Genetic and Epigenetic Factors in Determining Clinical Outcome of Coronavirus Disease-2019

The infection caused by Severe Acute Respiratory Syndrome-Corona Virus 2 (SARS-CoV-2) has rapidly emerged as a serious pandemic, causing substantial morbidity and sometimes mortality with a significant healthcare burden. Unfortunately, Pakistan is among top twenty countries of the world affected by COVID19. The clinical spectrum in COVID-19 is diverse, ranging from mild disease having flu-like symptoms to potentially fatal ARDS, cytokine storm, multiple organ failure and death. Common risk factors associated with severe outcome in COVID-19 infection include male gender, older age and presence of comorbidities such as hypertension, diabetes and cardiovascular disease. Here we reviewed the available literature and report that the underlying mechanisms that account for a broad range of symptoms during respiratory viral infections, that have been well studied in the case of influenza viruses, adenoviruses, SARS-CoV and MERS-CoV, suggest that host genetic and epigenetic factors may also play a significant role in determining susceptibility and clinical outcome in COVID-19 infection. In this review we discuss the potential roles of host genetic factors including cellular receptors for COVID-19, HLA and inflammatory cytokine genes. Based on the SARS-CoV-2 genome and protein-protein interactions map between host and viral proteins we also describe the potential roles of several viral proteins in epigenetic modulation of host inflammatory innate immune response by targeting different cellular pathways particularly NF-&kappa;B activation, which may lead to the inflammatory cytokine storm and a severe COVID-19 disease. Investigations of these genetic and epigenetic mechanisms during COVID-19, especially in local settings, will be helpful in management of patients with higher risks and in the development of novel antiviral therapeutics.</p

Investigation of TNF-&amp;alpha; and DC-SIGN Promoter Polymorphisms in Patients with Dengue Fever in Lahore City of Pakistan

Background and Objective: Dengue fever (DF) has been a major health concern globally. Pakistan is also combating this infection for the last decade. Cytokine genes play an important role in DF pathogenesis. This study aimed to analyze dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN) and tumor necrosis factor &alpha; (TNF-&alpha;) genes promoter polymorphisms in DF patients. Methods: A total of 140 (n = 140) dDF patients were recruited for study at the Department of Human Genetics and Molecular Biology of University of Health Sciences, Lahore, Pakistan over a period of 3 years. Simple DF was noted in 105 patients (75%) while 35 (25%) showed bleeding complications. All patients were found positive for dengue non-structural protein or dengue IgM. All patients were tested for two polymorphisms in TNF-&alpha; (-238G/A, and -308G/A) and one polymorphism in DC-SIGN (-336G/A) using restriction fragment length polymorphism technique. A single nucleotide polymorphism stats program was used for statistical analysis. Results: Susceptibility to develop dengue infection in the presence of -336G allele odds ratio (OR = 27.95, p = &lt;0.0001) and GG genotype (OR = 183.77, p = &lt;0.0001) was found to be significantly associated in this study. Presence of a combination of alleles -336G/-238A/-308A was noted in 59.4% of DF cases and 7.6% healthy controls, a difference with statistical significance (OR = 31.46, p = &lt;0.0001). Moreover, prevalence of DF symptoms showed a trend higher in G-carriers versus non-G-carriers of DC-SIGN -336 polymorphism. Conclusion: This work suggests a potential association of DC-SIGN -336 polymorphism with susceptibility to develop symptomatic dengue illness. However, no potential association was found between TNF-&alpha; promoter polymorphisms and dengue infection in this study.</p

Molecular Characterization of Haemoglobin E

Objectives: To detect mutation in cases having haemoglobin A2 level 7percent on high performance liquid chromatography. Method: The cross-sectional, descriptive study was conducted from July 2017 to December 2018 at the Department of Haematology and Human Genetics and Molecular Biology, University of Health Sciences, Lahore, Pakistan, and comprised patients of either gender with haemoglobin A2 7percent. The samples were collected from different cities of Punjab in collaboration with the Punjab Thalassemia Prevention Programme, Lahore. The samples were subjected to complete blood count and high performance liquid chromatography using automated haematology analysers and a beta thalassemia short programme, respectively. To analyse haemoglobin E mutations at the molecular level, polymerase chain reaction-restriction fragment length polymorphism (PCR_RFLP) was performed using a type IIS restriction endonuclease known as Mnl1 (derived from Moraxella nonliquefaciens) to cleave DNA at specific sites and the results were further confirmed on randomly selected samples using Sanger sequencing. Data was analysed using SPSS 25. Results: Of the 39 patients, 15(38.5percent) were males and 24(61.5percent) were females. The overall median age was 14 (23) years. There were 29 (74.4percent) patients a thalassemia family history, and 22(56.4percent) had a positive family history of transfusion related to thalassemia, while no patient had a family history of iron therapy. The media haemoglobin A, haemoglobin A2 and haemoglobin F levels were 72.2 (65.2-79.1) percent, 26.6 (19.1-34.0) percent and 0.9 (-0.8-2.6) percent, respectively. After molecular investigation, HbAE mutation was found in 23(59percent) patients, while wild type HbAA genotype was found in 16(41percent). The heterozygous HbE mutation was present in 23(59percent) patients. Conclusions: Frequently missed/undiagnosed cases of haemoglobin E that co-elute with haemoglobin A2 in the same high performance liquid chromatography window were detected among those with haemoglobin A2 7percent. Key Words: Haemoglobin E, Beta-thalassemia, High performance liquid chromatography, Restriction fragment length polymorphism

Genetic Analysis of Inhibin Alpha (INH&amp;alpha;) Mutation (769G&amp;gt;A) in Patients with Premature Ovarian Failure in a Local Population

Background and Objective:&nbsp;&nbsp;Premature ovarian failure is a worldwide concern effecting 1% of females of reproductive age. The objective of the present study was to analyze the role of inhibin alpha (INH&alpha;) gene mutation (769G&gt;A) in patients with premature ovarian failure (POF) in the local population. Methods:&nbsp;&nbsp;This case-control association studywas conducted in Department of Gynecology, Jinnah Hospital and The Children&rsquo;s Hospital and Institute of Child Health&nbsp; from July 2015-July 2016. A total of n = 100&nbsp; were recruited for this study and divided into two gropus females with equal number (n = 50)of patients andnormal controls of reproductive age (14 &ndash; 40 years). The screening of theINH&alpha; for 769G&gt;A variation in exon 2 was done through DNA sequencing. Results:&nbsp;&nbsp;A higher frequency of the major allele G was seen in both the patients (99%) and the controls (87%) while comparing to minor allele A (1% in patients and 13% in controls). None of the patients was found to be homozygous (AA = 0%) for allele A, whereas, four of the controls were homozygous (AA = 8%). The frequency of the minor A allele in controls was found to be statistically significant (P-value = 0.002). Conclusion:&nbsp;&nbsp;An association of decreased risk of POFwith A allele of the 769G&gt;A variant rather than increasing the risk of development of ovarian failure.</p

Refinement of the locus for autosomal recessive cone-rod dystrophy (CORD8) linked to chromosome 1q23-q24 in a Pakistani family and exclusion of candidate genes

Cone-rod retinal dystrophy (CORD) characteristically leads to early impairment of vision due to the simultaneous involvement of both cone and rod photoreceptor cells. Several loci/genes have been identified for CORD, including the cone-rod dystrophy (CORD8) locus [OMIM#605549] identified for a Pakistani family. All members of this family underwent detailed clinical re-examination to determine the nature of the dystrophy. All affected individuals suffered from bilateral CORD8 with an autosomal recessive mode of inheritance. The CORD8 locus, mapped on chromosome 1q12-q24, consisted of a very large critical disease region of 21 cM. Analysis with more recently available micro-satellite markers within the reported region showed heterozygosity with some of the new markers, and the crossovers lead to a refinement of the disease region from 21 to 11.53 cM. Mutation screening has excluded some of the candidate genes in the region. The disease phenotype of this family could be due to a mutation in a novel gene located within the refined CORD8 locus

The Kalash Genetic Isolate? The Evidence for Recent Admixture Response

none8noneAyub, Q; Mezzavilla, M; PAGANI, Luca; Haber, M; Mohyuddin, A; Khaliq, S; Mehdi, SQ; Tyler-Smith, CAyub, Q; Mezzavilla, M; Pagani, Luca; Haber, M; Mohyuddin, A; Khaliq, S; Mehdi, Sq; Tyler Smith, C

Locus for autosomal recessive nonsyndromic persistent hyperplastic primary vitreous

PURPOSE. To map the disease locus in a six-generation, consanguineous Pakistani family affected by nonsyndromic autosomal recessive persistent hyperplastic primary vitreous (arPHPV). All affected individuals had peripheral anterior synechiae and corneal opacities with variable degrees of cataract and a retrolenticular white mass behind the lens. METHODS. Genomic DNA from family members was typed for alleles at more than 400 known polymorphic genetic markers, by polymerase chain reaction. Alleles were assigned to individuals, which allowed calculation of lod scores. RESULTS. A maximum two-point lod score of 4.07 was obtained with marker D10S1225 with no recombination. Two recombinations with marker D10S208 and D10S537 localized the disease within a region of approximately 30 centimorgans (cM). However, homozygosity across the region refined the arPHPV locus to 13 cM. CONCLUSIONS. Linkage analysis shows localization of nonsyndromic arPHPV to chromosome10q11-q21