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Annals of Human Genetics

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https://www.readbyqxmd.com/read/28067407/analysis-of-whole-exome-sequencing-with-cardiometabolic-traits-using-family-based-linkage-and-association-in-the-iras-family-study
#1
Keri L Tabb, Jacklyn N Hellwege, Nicholette D Palmer, Latchezar Dimitrov, Satria Sajuthi, Kent D Taylor, Maggie C Y Ng, Gregory A Hawkins, Yii-der Ida Chen, W Mark Brown, David McWilliams, Adrienne Williams, Carlos Lorenzo, Jill M Norris, Jirong Long, Jerome I Rotter, Joanne E Curran, John Blangero, Lynne E Wagenknecht, Carl D Langefeld, Donald W Bowden
Family-based methods are a potentially powerful tool to identify trait-defining genetic variants in extended families, particularly when used to complement conventional association analysis. We utilized two-point linkage analysis and single variant association analysis to evaluate whole exome sequencing (WES) data from 1205 Hispanic Americans (78 families) from the Insulin Resistance Atherosclerosis Family Study. WES identified 211,612 variants above the minor allele frequency threshold of ≥0.005. These variants were tested for linkage and/or association with 50 cardiometabolic traits after quality control checks...
January 9, 2017: Annals of Human Genetics
https://www.readbyqxmd.com/read/28054334/comprehensive-candidate-gene-analysis-for-symptomatic-or-asymptomatic-outcomes-of-leishmania-infantum-infection-in-brazil
#2
Jason L Weirather, Priya Duggal, Eliana L Nascimento, Gloria R Monteiro, Daniella R Martins, Henio G Lacerda, Michaela Fakiola, Jenefer M Blackwell, Selma M B Jeronimo, Mary E Wilson
Genetic risk factors contribute to asymptomatic versus symptomatic visceral leishmaniasis (VL) outcomes following infection with Leishmania infantum. We therefore carried out a family-based (n = 918 post-quality control fully genotyped and phenotyped individuals) candidate gene study for symptomatic VL or asymptomatic delayed-type hypersensitivity (DTH) skin test phenotypes in highly endemic neighborhoods of northeast Brazil. A total of 248 SNPs were genotyped in 42 genes selected as candidates on the basis of prior genetic, immunological, and transcriptional profiling studies...
January 4, 2017: Annals of Human Genetics
https://www.readbyqxmd.com/read/28025823/hla-alleles-are-genetic-markers-for-susceptibility-and-resistance-towards-leprosy-in-a-mexican-mestizo-population
#3
Maribel Aguilar-Medina, Monica Escamilla-Tilch, Luis Octavio Frías-Castro, Geovanni Romero-Quintana, Iris Estrada-García, Sergio Estrada-Parra, Julio Granados, Eliakym Arambula Meraz, Guzman Sánchez-Schmitz, Shabaana Abdul Khader, Javier Rangel-Moreno, Rosalío Ramos-Payán
Despite the use of multidrug therapy, leprosy remains endemic in some countries. The association of several human leucocyte antigen (HLA) alleles and gene polymorphisms with leprosy has been demonstrated in many populations, but the major immune contributors associated to the spectrum of leprosy have not been defined yet. In this study, genotyping of HLA-A, -B, -DR, and -DQ alleles was performed in leprosy patients (n = 113) and control subjects (n = 117) from the region with the highest incidence for the disease in México...
December 27, 2016: Annals of Human Genetics
https://www.readbyqxmd.com/read/28009044/disease-concordant-twins-empower-genetic-association-studies
#4
Qihua Tan, Weilong Li, Fabio Vandin
Genome-wide association studies with moderate sample sizes are underpowered, especially when testing SNP alleles with low allele counts, a situation that may lead to high frequency of false-positive results and lack of replication in independent studies. Related individuals, such as twin pairs concordant for a disease, should confer increased power in genetic association analysis because of their genetic relatedness. We conducted a computer simulation study to explore the power advantage of the disease-concordant twin design, which uses singletons from disease-concordant twin pairs as cases and ordinary healthy samples as controls...
December 23, 2016: Annals of Human Genetics
https://www.readbyqxmd.com/read/27943244/genetic-variations-in-bilirubin-metabolism-genes-and-their-association-with-unconjugated-hyperbilirubinemia-in-adults
#5
Ashish S Chiddarwar, Selma Z D'Silva, Roshan B Colah, Kanjaksha Ghosh, Malay B Mukherjee
OBJECTIVE: The present study was undertaken to investigate the genotype and allele frequencies of the variants in the four bilirubin metabolism genes (UGT1A1, OATP2, HMOX1, and BLVRA) and their association with hyperbilirubinemia. MATERIAL AND METHODS: Genotyping of 17 genetic variants was performed in 115 adults with hyperbilirubinemia and 150 controls by PCR-RFLP, GeneScan analysis, and direct DNA sequencing. RESULTS: Genetic polymorphisms of the UGT1A1 promoter, specifically the T-3279G phenobarbital-responsive enhancer module and (TA)7 dinucleotide repeat, as well as the intron and coding region variants of the OATP2, HMOX1, and BLVRA genes, were significantly higher among the cases than the controls...
December 12, 2016: Annals of Human Genetics
https://www.readbyqxmd.com/read/27935012/mutational-analysis-of-agxt-in-tunisian-population-with-primary-hyperoxaluria-type-1
#6
Saoussen M'dimegh, Asma Omezzine, Ibtihel M'barek, Amira Moussa, Sameh Mabrouk, Hayet Kaarout, Geneviéve Souche, Jalel Chemli, Sabra Aloui, Cécile Aquaviva-Bourdain, Abdellatif Achour, Saoussen Abroug, Ali Bouslama
BACKGROUND: Primary hyperoxaluria type 1 (PH1) is an autosomal recessive metabolic disorder caused by inherited mutations in the AGXT gene encoding liver peroxisomal alanine:glyoxylate aminotransferase (AGT). PH1 is a clinically and genetically heterogeneous disorder. The aim of our study was to analyze and characterize the mutational spectrum of PH1 in Tunisian patients. MATERIALS AND METHODS: Molecular studies of 146 Tunisian patients suspected with PH were performed by PCR/Restriction fragment length polymorphism (RFLP) to detect seven mutations described as the most common...
December 9, 2016: Annals of Human Genetics
https://www.readbyqxmd.com/read/28084001/no-evidence-for-association-of-%C3%AE-defensin-genomic-copy-number-with-hiv-susceptibility-hiv-load-during-clinical-latency-or-progression-to-aids
#7
Razan Abujaber, Patrick R Shea, Paul J McLaren, Shabir Lakhi, Jill Gilmour, Susan Allen, Jacques Fellay, Edward J Hollox
Common single-nucleotide variation in the host accounts for 25% of the variability in the plasma levels of HIV during the clinical latency stage (viral load set point). However, the role of rare variants and copy number variants remains relatively unexplored. Previous work has suggested copy number variation of a cluster of β-defensin genes affects HIV load in treatment-naïve sub-Saharan Africans and rate of response to antiretroviral treatment. Here we analyse a total of 1827 individuals from two cohorts of HIV-infected individuals from Europe and sub-Saharan Africa to investigate the role of β-defensin copy number variation on HIV load at set point...
January 2017: Annals of Human Genetics
https://www.readbyqxmd.com/read/27870115/mica-gene-deletion-in-3411-dna-samples-from-five-distinct-populations-in-mainland-china-and-lack-of-association-with-nasopharyngeal-carcinoma-npc-in-a-southern-chinese-han-population
#8
WenYi Wang, Wei Tian, FaMing Zhu, LiXin Li, JinHong Cai, Fan Wang, KangLong Liu, HeKun Jin, JunLong Wang
Deletion of major histocompatibility complex class I chain-related genes A (MICA*Del) was investigated in 3,411 DNA samples from two southern Chinese Han populations (Hunan Han, HNH; Guangdong Han, GDH), two northern Chinese populations (Inner Mongolia Han, IMH; Inner Mongolia Mongol, IMM) and one southeastern Chinese Han population (Fujian Han, FJH) using an in-house polymerase chain reaction-sequence specific priming (PCR-SSP) assay, which enables direct discrimination between heterozygote and homozygote for MICA*Del...
November 2016: Annals of Human Genetics
https://www.readbyqxmd.com/read/27870114/the-molecular-genetics-of-autosomal-recessive-nonsyndromic-intellectual-disability-a-mutational-continuum-and-future-recommendations
#9
REVIEW
Muzammil Ahmad Khan, Saadullah Khan, Christian Windpassinger, Muhammad Badar, Zafar Nawaz, Ramzi M Mohammad
Intellectual disability (ID) is a clinical manifestation of the central nervous system without any major dysmorphologies of the brain. Biologically it affects learning capabilities, memory, and cognitive functioning. The basic defining features of ID are characterized by IQ<70, age of onset before 18 years, and impairment of at least two of the adaptive skills. Clinically it is classified in a syndromic (with additional abnormalities) and a nonsyndromic form (with only cognitive impairment). The study of nonsyndromic intellectual disability (NSID) can best explain the pathophysiology of cognition, intelligence and memory...
November 2016: Annals of Human Genetics
https://www.readbyqxmd.com/read/27870113/targeted-resequencing-of-deafness-genes-reveals-a-founder-myo15a-variant-in-northeastern-brazil
#10
Gabrielle N Manzoli, Guney Bademci, Angelina X Acosta, Têmis M Félix, F Basak Cengiz, Joseph Foster, Danniel S Dias Da Silva, Ibis Menendez, Isalis Sanchez-Pena, Demet Tekin, Susan H Blanton, Kiyoko Abe-Sandes, Xue Zhong Liu, Mustafa Tekin
Identifying the genetic etiology in a person with hearing loss (HL) is challenging due to the extreme genetic heterogeneity in HL and the population-specific variability. In this study, after excluding GJB2 variants, targeted resequencing of 180 deafness-related genes revealed the causative variants in 11 of 19 (58%) Brazilian probands with autosomal recessive HL. Identified pathogenic variants were in MYO15A (10 families) and CLDN14 (one family). Remarkably, the MYO15A p.(Val1400Met) variant was identified in eight families from the city of Monte Santo in the northeast region of Brazil...
November 2016: Annals of Human Genetics
https://www.readbyqxmd.com/read/27714771/in-vitro-functional-analyses-of-infrequent-nucleotide-variants-in-the-lactase-enhancer-reveal-different-molecular-routes-to-increased-lactase-promoter-activity-and-lactase-persistence
#11
Anke Liebert, Bryony L Jones, Erik Thomas Danielsen, Anders Krüger Olsen, Dallas M Swallow, Jesper T Troelsen
The genetic trait that allows intestinal lactase to persist into adulthood in some 35% of humans worldwide operates at the level of transcription, the effect being caused by cis-acting nucleotide changes upstream of the lactase gene (LCT). A single nucleotide substitution, -13910 C>T, the first causal variant to be identified, accounts for lactase persistence over most of Europe. Located in a region shown to have enhancer function in vitro, it causes increased activity of the LCT promoter in Caco-2 cells, and altered transcription factor binding...
November 2016: Annals of Human Genetics
https://www.readbyqxmd.com/read/27699784/association-of-rs11643718-slc12a3-and-rs741301-elmo1-variants-with-diabetic-nephropathy-in-south-indian-population
#12
Dhanasekaran Bodhini, Manickam Chidambaram, Samuel Liju, Balakannan Revathi, Dhandapani Laasya, Natarajan Sathish, Sekar Kanthimathi, Saurabh Ghosh, Ranjit Mohan Anjana, Viswanathan Mohan, Venkatesan Radha
This study reports on the association of genetic variants selected from previous genome-wide association studies for type 2 diabetic nephropathy in south Indians. Eight variants were genotyped in 601 type 2 diabetic subjects without nephropathy (DM) and 583 type 2 diabetic subjects with nephropathy (DN) by MassARRAY. The minor allele frequencies of rs11643718 SLC12A3 variant and rs741301 ELMO1 variant were significantly different between DM and DN groups (P = 0.029 and 0.016, respectively). A combined analysis showed that the subjects carrying the risk genotypes of both these variants (GG of rs11643718 + AG/AA of rs741301) had a significant association with DN with an odds ratio [adjusted for age, sex, Body Mass Index (BMI), HbA1c, and systolic Blood Pressure (BP)] of 1...
November 2016: Annals of Human Genetics
https://www.readbyqxmd.com/read/27699767/glucuronic-acid-epimerase-glce-variant-rs3865014-a-g-is-associated-with-bmi-blood-hemoglobin-hypertension-and-cerebrovascular-events-the-tamrisk-study
#13
Tarja Kunnas, Tiina Solakivi, Kirsi Määttä, Seppo T Nikkari
Heparan sulfate proteoglycans modulate many physiological systems, and genes responsible for proteoglycan assembly and disassembly may affect their interaction. We sought to determine whether polymorphisms of the glucuronic acid epimerase (GLCE) rs3865014 and sulfatase-2 (SULF2) rs2281279, genes coding for enzymes participating in heparan sulfate side chain activity, associate with hypertension, selected cardiometabolic risk factors and cardiovascular events in the Tampere adult population cardiovascular risk study...
November 2016: Annals of Human Genetics
https://www.readbyqxmd.com/read/27530450/evidence-for-association-between-sh2b1-gene-variants-and-glycated-hemoglobin-in-nondiabetic-european-american-young-adults-the-add-health-study
#14
Leslie A Lange, Mariaelisa Graff, Ethan M Lange, Kristin L Young, Andrea S Richardson, Karen L Mohlke, Kari E North, Kathleen M Harris, Penny Gordon-Larsen
Glycated hemoglobin (HbA1c) is used to classify glycaemia and type 2 diabetes (T2D). Body mass index (BMI) is a predictor of HbA1c levels and T2D. We tested 43 established BMI and obesity loci for association with HbA1c in a nationally representative multiethnic sample of young adults from the National Longitudinal Study of Adolescent to Adult Health [Add Health: age 24-34 years; n = 5641 European Americans (EA); 1740 African Americans (AA); 1444 Hispanic Americans (HA)] without T2D, using two levels of covariate adjustment (Model 1: age, sex, smoking, and geographic region; Model 2: Model 1 covariates plus BMI)...
September 2016: Annals of Human Genetics
https://www.readbyqxmd.com/read/27530449/interaction-between-peroxisome-proliferator-activated-receptor-%C3%AE-and-epithelial-membrane-protein-2-polymorphisms-influences-hdl-c-levels-in-the-chinese-population
#15
Tingjing Ke, Rajkumar Dorajoo, Yi Han, Chiea-Chuen Khor, Rob M van Dam, Jian-Min Yuan, Woon-Puay Koh, Jianjun Liu, Yik Ying Teo, Daniel Y T Goh, E Shyong Tai, Tien Yin Wong, Ching-Yu Cheng, Yechiel Friedlander, Chew-Kiat Heng
Peroxisome proliferator activated receptors (PPARs) are transcription factors involved in the regulation of key metabolic pathways. Numerous in vivo and in vitro studies have established their important roles in lipid metabolism. A few SNPs in PPAR genes have been reported to be associated with lipid levels. In this study, we aimed to investigate the interactive effects between single nucleotide polymorphisms (SNPs) in three PPAR isoforms α/δ/γ and other genetic variants across the genome on plasma high-density lipoprotein-cholesterol (HDL-C) levels...
September 2016: Annals of Human Genetics
https://www.readbyqxmd.com/read/27530448/genetic-epidemiology-of-mitochondrial-pathogenic-variants-causing-nonsyndromic-hearing-loss-in-a-large-cohort-of-south-indian-hearing-impaired-individuals
#16
Mahalingam Subathra, Arabandi Ramesh, Mathiyalagan Selvakumari, N P Karthikeyen, C R Srikumari Srisailapathy
Mitochondria play a critical role in the generation of metabolic energy in the form of ATP. Tissues and organs that are highly dependent on aerobic metabolism are involved in mitochondrial disorders including nonsyndromic hearing loss (NSHL). Seven pathogenic variants leading to NSHL have so far been reported on two mitochondrial genes: MT-RNR1 encoding 12SrRNA and MT-TS1 encoding tRNA for Ser((UCN)) . We screened 729 prelingual NSHL subjects to determine the prevalence of MT-RNR1 variants at position m.961, m...
September 2016: Annals of Human Genetics
https://www.readbyqxmd.com/read/27461153/variants-in-9p21-predicts-severity-of-coronary-artery-disease-in-a-chinese-han-population
#17
Jinjin Jing, Li Su, Ying Zeng, Xiaojun Tang, Jie Wei, Long Wang, Li Zhou
Recent genome-wide association studies identified the common genetic variants in 9p21 were associated with the coronary artery disease (CAD). However, whether this locus could predict the severity of CAD in Chinese Han population is unclear. 499 CAD patients who underwent coronary angiography (CAG) have been enrolled for this study. The single-nucleotide polymorphisms rs2383207 and rs2383206 in 9p21 were genotyped in 499 CAG cases and 1519 controls in Chinese Han population. The gene dosage of 9p21 was stratified by the degree of vascular lesions and tested for association with the severity of CAD...
September 2016: Annals of Human Genetics
https://www.readbyqxmd.com/read/27402348/circulating-micrornas-and-life-expectancy-among-identical-twins
#18
Shenghui Wu, Taek-Kyun Kim, Xiaogang Wu, Kelsey Scherler, David Baxter, Kai Wang, Ruth E Krasnow, Terry Reed, Jun Dai
Human life expectancy is influenced not only by longevity assurance mechanisms and disease susceptibility loci but also by the environment, gene-environment interactions, and chance. MicroRNAs (miRNAs) are a class of small noncoding RNAs closely related to genes. Circulating miRNAs have been shown as promising noninvasive biomarkers in the development of many pathophysiological conditions. However, the concentration of miRNA in the circulation may also be affected by environmental factors. We used a next-generation sequencing platform to assess the association of circulating miRNA with life expectancy, for which deaths are due to all causes independent of genes...
September 2016: Annals of Human Genetics
https://www.readbyqxmd.com/read/27346736/hexokinase-domain-containing-1-hkdc1-gene-variants-and-their-association-with-gestational-diabetes-mellitus-in-a-south-indian-population
#19
Sekar Kanthimathi, Samuel Liju, Dhandapani Laasya, Ranjit Mohan Anjana, Viswanathan Mohan, Venkatesan Radha
Hexokinase domain containing 1 (HKDC1), a novel human hexokinase gene, is known to affect glucose metabolism and was shown to have a strong association with 2-h plasma glucose in pregnant women in a recent genome wide association study. This study aimed to evaluate the association of these regulatory variants of HKDC1 (rs1076224, rs4746822, rs2394529 and rs9645501) with gestational diabetes mellitus (GDM) in a South Indian population. The regulatory variants of HKDC1 were genotyped in unrelated 500 women with GDM and 510 non-GDM individuals by using the MassARRAY system and by direct DNA sequencing...
July 2016: Annals of Human Genetics
https://www.readbyqxmd.com/read/27346735/de-novo-truncating-mutation-of-trim8-causes-early-onset-epileptic-encephalopathy
#20
Yasunari Sakai, Ryoko Fukai, Yuki Matsushita, Noriko Miyake, Hirotomo Saitsu, Satoshi Akamine, Michiko Torio, Momoko Sasazuki, Yoshito Ishizaki, Masafumi Sanefuji, Hiroyuki Torisu, Chad A Shaw, Naomichi Matsumoto, Toshiro Hara
BACKGROUND: Early-onset epileptic encephalopathy (EOEE) is a heterogeneous group of neurodevelopmental disorders characterised by infantile-onset intractable epilepsy and unfavourable developmental outcomes. Hundreds of mutations have been reported to cause EOEE; however, little is known about the clinical features of individuals with rare variants. CASE REPORT AND METHODS: We present a 10-year-old boy with severe developmental delay. He started experiencing recurrent focal seizures at 2 months old...
July 2016: Annals of Human Genetics
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