Runs of long homozygous stretches (ROH) are considered to be the result of consanguinity and usually contain recessive deleterious disease causing mutations (Szpiech et al., 2013). Several algorithms have been developed to detect ROHs.... more
Runs of long homozygous stretches (ROH) are considered to be the result of consanguinity and usually contain recessive deleterious disease causing mutations (Szpiech et al., 2013). Several algorithms have been developed to detect ROHs. Here, we developed a simple, alternative strategy by examining X chromosome non-pseudoautosomal region to detect the ROHs from next generation sequencing data utilizing the genotype probabilities and the Hidden Markov Model algorithm as a tool, namely ROHMM. It is implemented purely in java and contains both command-line and a graphical user interface. We tested ROHMM on simulated data as well as real population data from 1000G Project and a clinical sample. Our results have shown that ROHMM can perform robustly producing highly accurate homozygosity estimations under all conditions thereby meeting and even exceeding the performance of its natural competitors.
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Research Interests:
Thesis (Ph. D.)--Howard University, 1993. Includes bibliographical references.
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Autism spectrum disorders (ASD) is a neurodevelopmental disorder characterized by impaired social, communicative skills and repetitive behaviors. Altered sensory experiences are also common and most of the individuals present sensory... more
Autism spectrum disorders (ASD) is a neurodevelopmental disorder characterized by impaired social, communicative skills and repetitive behaviors. Altered sensory experiences are also common and most of the individuals present sensory hyper-or hypo-sensitivity in several modalities. It is also suggested that there is a deficit in the integration of the information from different sensory systems (i.e. auditory and visual). However, there is limited consensus regarding the cause of these sensory deficits in ASD. Neural oscillatory processes are known to be abnormal in ASD and alpha circuits (8–12 Hz) that are necessary for basic and complex brain processes, are shown to be different than typically developing individuals. During sensory stimulation alpha is typically greater over task-irrelevant cortical areas, and it is thought that alpha activity acts to filter out irrelevant sensory input. Irregular functioning of alpha circuits may disturb sensory perception which in turn would caus...
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Fallot tetralogy (FT) is the most frequently observed conotruncal heart defect (CTHD) and accompanies 15% of the 22q11 deletion syndromes, DiGeorge/ velocardiofacial (DGS/VCFS) syndromes. TBX1 is a gene located in the 22q11 region and has... more
Fallot tetralogy (FT) is the most frequently observed conotruncal heart defect (CTHD) and accompanies 15% of the 22q11 deletion syndromes, DiGeorge/ velocardiofacial (DGS/VCFS) syndromes. TBX1 is a gene located in the 22q11 region and has a role in neural crest migration and conotruncal development. The mouse Tbx1 locus shows 98% homology with TBX1. DGS/VCFS-like aortic arch abnormalities in the mouse were attributed to deletions in this locus. The T-box region, common to both mice and humans, is part of TBX1 with proven effects on heart outflow track anomalies. The role of TBX1 in non-syndromic CTHDs is still unclear. In this study, we screened the TBX1 gene T-box region exons in 50 FT patients without 22q11 deletion and in 50 healthy volunteers. Our study did not show any disease causing mutations, but one polymorphic change. These results do not support a major role of the T-box region in the etiology of isolated FT. Furthermore, this study also confirms that mouse cardiac-develo...
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A method for the analysis of concentration-response curves is described. The parameters of these curves, namely, maximal response, apparent affinity, and slope factor, are calculated by means of a semiiterative approach using a... more
A method for the analysis of concentration-response curves is described. The parameters of these curves, namely, maximal response, apparent affinity, and slope factor, are calculated by means of a semiiterative approach using a microcomputer. Considerably less computer processing time is required than with other iterative nonlinear curve fitting methods. The method is particularly helpful in cases in which accurate observation of maximal response is limited.
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Research Interests:
Research Interests:
Research Interests: Asthma, Adolescent, Humans, Male, Differential Diagnosis, and 4 moreDyspnea, Cough, Respiratory Sounds, and Dilatation
Aim: PTPN22 gene plays a role in TCR signaling. PTPN22 C1858T gene polymorphism has been recently found to be related to several autoimmune diseases through inappropriate T-cell activation caused by PTPN22 gene polymorphism. It is... more
Aim: PTPN22 gene plays a role in TCR signaling. PTPN22 C1858T gene polymorphism has been recently found to be related to several autoimmune diseases through inappropriate T-cell activation caused by PTPN22 gene polymorphism. It is suggested that T-lymphocytes also contribute to the pathogenesis of familial Mediterranean fever (FMF). The aim of this study is to investigate whether the PTPN22 C1858T gene polymorphism is a susceptible gene for the pathogenesis of FMF or not. Methods: We conducted a case-control study with 177 FMF patients and 180 healthy controls. The PTPN22 C1858T polymorphism (rs2476601) was genotyped by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP). In patients with FMF, clinical features, disease severity score, the frequencies of amyloidosis, positive family history and Mediterranean fever (MEFV) gene mutations were determined. Results: The frequencies of heterozygote genotype (CT) were 4.5% in FMF patients and 2.8% in healthy contr...
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Research Interests: Molecular Genetics, Adolescent, Environmental Risk, Humans, Female, and 15 moreMale, Psychotic Disorder, Pedigree, Phenotype, Aged, Middle Aged, ALOPECIA, Family Health, Adult, Odds ratio, Rickets, Psychotic Disorders, Nervous System, Psychology and Cognitive Sciences, and Medical and Health Sciences
Research Interests: Molecular Genetics, Adolescent, Environmental Risk, Humans, Female, and 15 moreMale, Psychotic Disorder, Pedigree, Phenotype, Aged, Middle Aged, ALOPECIA, Family Health, Adult, Odds ratio, Rickets, Psychotic Disorders, Nervous System, Psychology and Cognitive Sciences, and Medical and Health Sciences
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Research Interests:
Research Interests:
Objective To evaluate the effects of MEFV genotypes and the major histocompatibility complex class I chain-related gene A (MICA) triplet repeat polymorphism on the severity and clinical features of familial Medi-terranean fever (FMF) and... more
Objective To evaluate the effects of MEFV genotypes and the major histocompatibility complex class I chain-related gene A (MICA) triplet repeat polymorphism on the severity and clinical features of familial Medi-terranean fever (FMF) and amyloidosis in a group of ...