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Annals of Human Genetics

Tonghanyu Liu, Feng Jiang, Xin Liu, Hongye Zhang, Lefeng Wang, Wenzhi Liu, Xingyu Wang
ATP-binding cassette, superfamily G, member 2 (ABCG2 ) has been shown to play an important role in the development of ischemic stroke in European and African American populations. The aim of the present study is to test the hypothesis that there are associations between ABCG2 polymorphisms and ischemic stroke risk in a Chinese population. We conducted a case-control study including 967 participants with ischemic stroke and 939 stroke-free controls. The rs2231137C > T and rs2231142G > T were genotyped using a TaqMan real-time polymerase chain reaction assay...
June 13, 2018: Annals of Human Genetics
Zhengyang Zhou, Hung-Chih Ku, Guan Xing, Chao Xing
In case-control genetic association studies, a standard practice is to perform the Cochran-Armitage (CA) trend test under the assumption of the additive model because of its robustness. We could even identify situations in which it outperformed the analysis model consistent with the underlying inheritance mode. In this article, we analytically reveal the statistical basis that leads to the phenomenon. By elucidating the origin of the CA trend test as a linear regression model, we decompose Pearson's χ2 -test statistic into two components-one is the CA trend test statistic that measures the goodness of fit of the linear regression model, and the other measures the discrepancy between data and the linear regression model...
May 31, 2018: Annals of Human Genetics
Pratibha Bhai, Sunita Bijarnia-Mahay, Ratna D Puri, Renu Saxena, Deepti Gupta, Udhaya Kotecha, Anil Sachdev, Dhiren Gupta, Vyomesh Vyas, Divya Agarwal, Vivek Jain, Rajeev K Bansal, Tapisha G Kumar, Ishwar Chander Verma
Fructose-1, 6-bisphosphatase deficiency is an autosomal recessive disorder of gluconeogenesis caused by genetic defect in the FBP1 gene. It is characterized by episodic, often life-threatening metabolic acidosis, liver dysfunction, and hyperlactatemia. Without a high index of suspicion, it may remain undiagnosed with devastating consequences. Accurate diagnosis can be achieved either by enzyme assay or gene studies. Enzyme assay requires a liver biopsy and is tedious, invasive, expensive, and not easily available...
May 18, 2018: Annals of Human Genetics
Wen-Chi Hsueh, Peter H Bennett, Julian Esparza-Romero, Rene Urquidez-Romero, Mauro E Valencia, Eric Ravussin, Robert C Williams, William C Knowler, Leslie J Baier, Leslie O Schulz, Robert L Hanson
Prevalence of diabetes and obesity in Mexican Pima Indians is low, while prevalence in US Pima Indians is high. Although lifestyle likely accounts for much of the difference, the role of genetic factors is not well explored. To examine this, we genotyped 359 single nucleotide polymorphisms, including established type 2 diabetes and obesity variants from genome-wide association studies (GWAS) and 96 random markers, in 342 Mexican Pimas. A multimarker risk score of obesity variants was associated with body mass index (BMI; β = 0...
May 17, 2018: Annals of Human Genetics
Isabella Brasil Succi, Luís Cristóvão Pôrto, Dayse Silva, Adriana Nascimento, Ronald Costa Neto, João Carlos Fonseca
Porphyria cutanea tarda (PCT) is a multifactorial disease; clinical expression depends on both genetic and acquired factors. Few studies have examined the connection between PCT and the regulation of iron metabolism genes other than the HFE gene. We selected five polymorphisms in the CYBRD1, CP, SLC40A1, and HAMP genes to determine whether these polymorphisms can act as genetic modulators in patients with sporadic PCT. None of the 29 patients carried the C282Y mutation. Genomic DNA from 29 PCT patients was isolated...
May 17, 2018: Annals of Human Genetics
Daniela Zanetti, Michael E Weale
Genome-wide association studies (GWASs) have allowed researchers to identify thousands of single nucleotide polymorphisms (SNPs) and other variants associated with particular complex traits. Previous studies have reported differences in the strength and even the direction of GWAS signals across different populations. These differences could be due to a combination of (1) lack of power, (2) allele frequency differences, (3) linkage disequilibrium (LD) differences, and (4) true differences in causal variant effect sizes...
May 7, 2018: Annals of Human Genetics
Hao Li, Jianhua Zhang, Jiang Long, Jiarun Shi, Yuhui Luo
The calcium-sensing receptor (CaSR) gene plays an important role in regulating the Ca2+ balance and reducing the risk for calcium stones. In this study, we evaluated the association of CaSR polymorphisms with calcium nephrolithiasis in the population of Yi nationality in Southwestern China. Biochemical variables were evaluated in 624 calcium nephrolithiasis patients and 470 age-matched healthy controls without a history of nephrolithiasis. CaSR polymorphisms rs7652589, rs1501899, rs1801725 (Ala986Ser), rs1042636 (Arg990Gly) and rs1801726 (Gln1011Glu) were investigated between the calcium nephrolithiasis patients and healthy controls, using direct sequencing...
April 16, 2018: Annals of Human Genetics
Qin Zeng, Ke-Hao Wu, Kun Liu, Yuan Hu, Xiang-Ding Chen, Lei Zhang, Hui Shen, Qin Tian, Lan-Juan Zhao, Hong-Wen Deng, Li-Jun Tan
Recent studies suggested that long noncoding RNAs (lncRNAs) were widely transcribed in the genome, but their potential roles in the genetic complexity of human disorders required further exploration. The purpose of the present study was to explore genetic polymorphisms of lncRNAs associated with bone mineral density (BMD) and its potential value. Based on the lncRNASNP database, 55,906 lncSNPs were selected to conduct a genome-wide association study meta-analysis among 11,140 individuals of seven independent studies for BMDs at femoral neck (FN), lumbar spine, and total hip (HIP)...
April 16, 2018: Annals of Human Genetics
João Paulo Limongi França Guilherme, Rômulo Bertuzzi, Adriano Eduardo Lima-Silva, Alexandre da Costa Pereira, Antonio Herbert Lancha Junior
In recent years, there have been an increasing number of genetic variants associated with athletic phenotypes. Here, we selected a set of sports-relevant polymorphisms that have been previously suggested as genetic markers for human physical performance, and we examined their association with athletic status in a large cohort of Brazilians. We evaluated a sample of 1,622 individuals, in which 966 were nonathletes, and 656 were athletes: 328 endurance athletes and 328 power athletes. Only the AGT M268T minor allele was nominally associated with the endurance status...
March 30, 2018: Annals of Human Genetics
Manik Vohra, Anu Radha Sharma, Bobby Paul, Manoj K Bhat, Kapaettu Satyamoorthy, Padmalatha S Rai
Folate metabolism genes are pivotal to critical biological processes and are related to several conditions, including developmental, cognitive, and cardiovascular anomalies. A systematic catalog of genetic polymorphisms in protein coding regions, regulatory transcription factor binding sites, and miRNA binding sites associated with folate pathway genes may contribute to personalized medicine. We performed a comprehensive computational survey of single nucleotide polymorphisms (SNPs) of folate pathway genes to highlight functional polymorphisms in the coding region, transcription factor binding sites, and miRNAs binding sites...
March 25, 2018: Annals of Human Genetics
Asmat Ullah, Muhammad Umair, Dost Muhammad, Muhammad Bilal, Kwanghyuk Lee, Suzanne M Leal, Wasim Ahmad
Acromesomelic dysplasia is genetically heterogeneous group of skeletal disorders characterized by short stature and acromelia and mesomelia of limbs. Acromesomelic dysplasia segregates in an autosomal recessive pattern and is caused by biallelic sequence variants in three genes (NPR2, GDF5, and BMPR1B). A consanguineous family of Pakistani origin segregating a subtype of acromesomelic dysplasia called Hunter-Thompson was clinically and genetically evaluated. Genotyping of microsatellite markers and linkage analysis revealed a 7...
May 2018: Annals of Human Genetics
Lukana Ngiwsara, James R Ketudat-Cairns, Phannee Sawangareetrakul, Ratana Charoenwattanasatien, Voraratt Champattanachai, Chulaluck Kuptanon, Suthipong Pangkanon, Thipwimol Tim-Aroon, Duangrurdee Wattanasirichaigoon, Jisnuson Svasti
BACKGROUND: Mucopolysaccharidosis type I (MPS I) is a rare autosomal-recessive disorder caused by defects in alpha-L-iduronidase (IDUA), a lysosomal enzyme encoded by the IDUA gene. Herein, we characterized IDUA mutations underlying mucopolysaccharidosis type I intermediate form (Hurler-Scheie syndrome) and its molecular pathogenic mechanisms. METHODS: Clinical data, activity of the IDUA enzyme in leukocytes, and a mutation of the IDUA gene were analyzed. Pathogenesis associated with an IDUA mutation was further investigated by evaluating the mutant cDNA sequence, protein expression and activity in COS-7 cells...
May 2018: Annals of Human Genetics
Anwar Kamal Khan, Noor Muhammad, Sher Alam Khan, Waheed Ullah, Abdul Nasir, Sibtain Afzal, Khushnooda Ramzan, Sulman Basit, Saadullah Khan
Primary hypertrophic osteoarthropathy (PHO) is a congenital multisystemic entity characterized by three major clinical symptoms: pachydermia, periostosis, and digital clubbing. Recently it has been reported that pathogenic mutations in two genes are known to be associated with PHO: HPGD and SLCO2A1. In the present study, a five-generation consanguineous Pakistani family harboring primary hypertrophic osteoarthropathy in autosomal-recessive pattern was ascertained. Whole genome single nucleotide polymorphisms (SNPs) genotyping and sequence analysis revealed a novel homozygous missense mutation (c...
May 2018: Annals of Human Genetics
Xulong Cai, Mali Lin, Shan Cao, Yunguang Liu, Na Lin
Asthma is a common, heterogeneous chronic respiratory disease characterized by chronic inflammation of the airway, airway hyperreactivity, and airway remodeling. The RAR-related orphan receptor A (RORA) gene has been identified for the pathogenesis of asthma. The purpose of this research was to investigate the relationship between RORA gene polymorphisms and asthma susceptibility in the Chinese Zhuang population. This was a case-control study including 231 children with asthma and 343 healthy controls. The RORA gene polymorphisms were measured by the polymerase chain reaction-ligase detection reaction genotyping assays and confirmed by sequencing...
May 2018: Annals of Human Genetics
Ahmed Alfares, Ibtihal Alhufayti, Lamia Alsubaie, Mohammed Alowain, Rawan Almass, Majid Alfadhel, Namik Kaya, Wafaa Eyaid
INTRODUCTION: Primary microcephaly type 3 is a genetically heterogeneous condition caused by a homozygous or compound heterozygous mutation in CDK5 regulatory subunit associated protein 2 (CDK5RAP2) and characterized by reduced head circumference (<5th percentile) with additional phenotypes varying from pigmentary abnormalities to sensorineural hearing loss. Until now, congenital cataracts have not been reported in patients with primary microcephaly type 3. CLINICAL REPORT: We report multiple affected family members from a consanguineous Saudi family with microcephaly and congenital cataracts...
May 2018: Annals of Human Genetics
Luanna Munhoz Zabaglia, Mayara Luciana Sallas, Mônica Pezenatto Dos Santos, Wilson Aparecido Orcini, Rita Luiza Peruquetti, Dulce Helena Constantino, Elizabeth Chen, Marilia De Arruda Cardoso Smith, Spencer-Luiz Marques Payão, Lucas Trevizani Rasmussen
miRNAs appear to play an important role in controlling the expression of several genes, and they are a potential biomarker and prognostic tool in gastric diseases. We analyzed 53 controls, 86 patients with gastritis, and 19 patients with gastric cancer. Real-time-PCR was used to determine the expression levels of miRNA-146a, miRNA-155, IL-2, and TNF-α. The subsequent analysis of the target genes was performed using the bioinformatics approach. There was no difference in IL-2 expression between the groups. However, there was a significant increase in TNF-α expression in the gastritis group relative to the control and a significant decrease in the gastric cancer group relative to the control...
May 2018: Annals of Human Genetics
María Correa-Rodríguez, Jacqueline Schmidt Rio-Valle, Blanca Rueda-Medina
Ultrasound bone mass measurement has been postulated as a valuable bone-health assessment tool for primary care. The aim of this study was to analyse the possible relationship between the SPTBN1, RSPO3, CCDC170, DKK1, GPATCH1, and TMEM135 genes, with calcaneal quantitative ultrasound (QUS) in a population of young adults. These genes were first associated with broadband ultrasound attenuation (BUA) in the GEFOS/GENOMOS study. A cross-sectional study was conducted on 575 individuals (mean age 20.41 ± 2...
May 2018: Annals of Human Genetics
Chee Wei Yew, Mohd Zahirul Hoque, Jacqueline Pugh-Kitingan, Alexander Minsong, Christopher Lok Yung Voo, Julian Ransangan, Sophia Tiek Ying Lau, Xu Wang, Woei Yuh Saw, Rick Twee-Hee Ong, Yik-Ying Teo, Shuhua Xu, Boon-Peng Hoh, Maude E Phipps, S Vijay Kumar
The region of northern Borneo is home to the current state of Sabah, Malaysia. It is located closest to the southern Philippine islands and may have served as a viaduct for ancient human migration onto or off of Borneo Island. In this study, five indigenous ethnic groups from Sabah were subjected to genome-wide SNP genotyping. These individuals represent the "North Borneo"-speaking group of the great Austronesian family. They have traditionally resided in the inland region of Sabah. The dataset was merged with public datasets, and the genetic relatedness of these groups to neighboring populations from the islands of Southeast Asia, mainland Southeast Asia and southern China was inferred...
March 9, 2018: Annals of Human Genetics
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March 2018: Annals of Human Genetics
Arjun Sondhi, Kenneth Martin Rice
In large-scale genetic studies, a primary aim is to test for an association between genetic variants and a disease outcome. The variants of interest are often rare and appear with low frequency among subjects. In this situation, statistical tests based on standard asymptotic results do not adequately control the type I error rate, especially if the case : control ratio is unbalanced. In this article, we propose the use of permutation and approximate unconditional tests for testing association with rare variants...
March 2018: Annals of Human Genetics
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