@article {662, title = {Identification and association of recurrent ALOXE3 mutation with non-bullous congenital ichthyosiform erythroderma in two ethnically distinct Pakistani families.}, journal = {Congenit Anom (Kyoto)}, volume = {59}, year = {2019}, month = {2019 May}, pages = {93-98}, abstract = {

Non-bullous congenital ichthyosiform erythroderma (NCIE) is characterized by skin scaling with erythema. In this study, two Pakistani families with NCIE are genetically characterized through Whole Exome and Sanger sequencing to identify molecular basis of the disease. We identified a nonsense homozygous c.2026C>T mutation of ALOXE3, causing premature termination of the eLOX3 protein (p.Q676X). In silico studies predicted impaired enzymatic activity of the premature truncated eLOX3, leading to abnormal synthesis of specific hepoxilin derivatives, essential for epidermal barrier formation. It is the first ever study reporting homozygotes of p.Q676X mutation in ethnically distinct two Pakistani families; otherwise, heterozygotes of the said mutation have been reported in South Asian population only. Hence, mutation seems to be region-specific and may be useful for molecular diagnosis of NCIE. Moreover, our findings should help in genetic counseling and career screening.

}, keywords = {8,11,14-Eicosatrienoic Acid, Adolescent, Adult, Base Sequence, Case-Control Studies, Child, Child, Preschool, Codon, Nonsense, Ethnic Groups, Female, Flavanones, Gene Expression, Homozygote, Humans, Ichthyosis, Lamellar, Lipoxygenase, Male, Middle Aged, Molecular Docking Simulation, Pakistan, Pedigree, Protein Binding, Protein Structure, Secondary, Skin, Whole Exome Sequencing}, issn = {1741-4520}, doi = {10.1111/cga.12303}, author = {Rahman, Simeen Ber and Mir, Asif and Ahmad, Nafees and Haider, Syed Husnain and Malik, Salman Akbar and Nasir, Muhammad} } @article {415, title = {Increasing Generality and Power of Rare-Variant Tests by Utilizing Extended Pedigrees.}, journal = {Am J Hum Genet}, volume = {99}, year = {2016}, month = {2016 Oct 06}, pages = {846-859}, abstract = {

Recently, multiple studies have performed whole-exome or whole-genome sequencing to identify groups of rare variants associated with complex traits and diseases. They have primarily utilized case-control study designs that often require thousands of individuals to reach acceptable statistical power. Family-based studies can be more powerful because a rare variant can be enriched in an extended pedigree and segregate with the phenotype. Although many methods have been proposed for using family data to discover rare variants involved in a disease, a majority of them focus on a specific pedigree structure and are designed to analyze either binary or continuously measured outcomes. In this article, we propose RareIBD, a general and powerful approach to identifying rare variants involved in disease susceptibility. Our method can be applied to large extended families of arbitrary structure, including pedigrees with only affected individuals. The method accommodates both binary and quantitative traits. A series of simulation experiments suggest that RareIBD is a powerful test that outperforms existing approaches. In addition, our method accounts for individuals in top generations, which are not usually genotyped in extended families. In contrast to available statistical tests, RareIBD generates accurate p values even when genetic data from these individuals are missing. We applied RareIBD, as well as other methods, to two extended family datasets generated by different genotyping technologies and representing different ethnicities. The analysis of real data confirmed that RareIBD is the only method that properly controls type I error.

}, keywords = {Datasets as Topic, Ethnic Groups, Family, Female, Genetic Predisposition to Disease, Genetic Variation, Genotype, Humans, Male, Models, Genetic, Pedigree, Phenotype, Research Design}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2016.08.015}, author = {Sul, Jae Hoon and Cade, Brian E and Cho, Michael H and Qiao, Dandi and Silverman, Edwin K and Redline, Susan and Sunyaev, Shamil} } @article {219, title = {RNF213 rare variants in an ethnically diverse population with Moyamoya disease.}, journal = {Stroke}, volume = {45}, year = {2014}, month = {2014 Nov}, pages = {3200-7}, abstract = {

BACKGROUND AND PURPOSE: Moyamoya disease (MMD) is a rare, genetically heterogeneous cerebrovascular disease resulting from occlusion of the distal internal carotid arteries. A variant in the Ring Finger 213 gene (RNF213), altering arginine at position 4810 (p.R4810K), is associated with MMD in Asian populations. However, there are a lack of data on the role of RNF213 in patients with MMD of additional ethnicities and diasporic Asian populations. We investigate the contribution of RNF213 alterations to MMD in an ethnically diverse population based in the United States.

METHODS: We initially sequenced RNF213 exons 43, 44, and 45 (encoding the eponymous RING finger domain) and exon 60 (encoding p.R4810K) in 86 ethnically diverse patients with MMD. Comprehensive exome sequencing data from 24 additional patients with MMD was then analyzed to identify RNF213 variants globally. Segregation of variants with MMD and other vascular diseases was assessed in families.

RESULTS: RNF213 p.R4810K was identified in 56\% (9/16) of patients with MMD of Asian descent and not in 94 patients of non-Asian descent. 3.6\% (4/110) of patients had variants in the exons encoding the RING finger domain. Seven additional variants were identified in 29\% (7/24) of patients with MMD who underwent exome sequencing. Segregation analysis supported an association with MMD for 2 variants and a lack of association with disease for 1 variant.

CONCLUSIONS: These results confirm that alterations in RNF213 predispose patients of diverse ethnicities to MMD, and that the p.R4810K variant predisposes individuals of Asian descent in the United States to MMD.

}, keywords = {Adenosine Triphosphatases, Adolescent, Adult, Child, Cohort Studies, Ethnic Groups, Female, Genetic Variation, Humans, Male, Moyamoya Disease, Population Surveillance, Ubiquitin-Protein Ligases, Young Adult}, issn = {1524-4628}, doi = {10.1161/STROKEAHA.114.006244}, author = {Cecchi, Alana C and Guo, Dongchuan and Ren, Zhao and Flynn, Kelly and Santos-Cortez, Regie Lyn P and Leal, Suzanne M and Wang, Gao T and Regalado, Ellen S and Steinberg, Gary K and Shendure, Jay and Bamshad, Michael J and Grotta, James C and Nickerson, Deborah A and Pannu, Hariyadarshi and Milewicz, Dianna M} }