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Annals of Human Genetics

Sonal Saxena, Poornima Kkani, Chellamuthu Ramasubramanian, Srinivasan Ganesh Kumar, Raghav Monisha, Gundugurti Prasad Rao, Kommu Naga Mohan
Copy number variants (CNVs) of 15q11.2 yielded conflicting reports on their association with schizophrenia (SZ), indicating the need for replication studies. Because there are no 15q11.2 CNV studies on Indian patients, we began by testing 307 SZ patients and 359 age- and sex-matched controls from South India. Using an improved multiplex ligation probe amplification, six deletions were found in patients and three in controls (p = 0.31), whereas one duplication was found in patients and three in controls (p = 0...
February 19, 2019: Annals of Human Genetics
Molly Went, Amit Sud, Ni Li, David C Johnson, Jonathan S Mitchell, Martin Kaiser, Richard S Houlston
Genomic regions of homozygosity (ROH), detectable in outbred populations, have been implicated as determinants of inherited risk. To examine whether ROH is associated with risk of multiple myeloma (MM), we performed whole-genome homozygosity analysis using single-nucleotide polymorphism genotype data from 2,282 MM cases and 5,197 controls, with replication in an additional 878 MM cases and 7,083 controls. Globally, the distribution of ROH between cases and controls was not significantly different. However, one ROH at chromosome 9q21, harboring the B-cell transcription factor gene KLF9, showed evidence of a consistent association and may therefore warrant further investigation as a candidate risk factor for MM...
February 15, 2019: Annals of Human Genetics
Aram Yang, Jinsup Kim, Ja-Hyun Jang, Chung Lee, Ji-Eun Lee, Sung Yoon Cho, Dong-Kyu Jin
Multiple osteochondromas (MOs) or hereditary multiple exostoses is a rare autosomal-dominant disease characterized by growths of MOs, which are benign cartilage-capped bone tumors that grow away from the growth plates. Almost 90% of MOs have a molecular explanation and 10% are unexplained. MOs are genetically heterogeneous with two causal genes on 8q24.11 (EXT1) and 11p12 (EXT2), with a higher frequency in EXT1. MO is a very rare genetic disorder, and the genotype-phenotype of MO with EXT2 mutation has not been well investigated in Korea...
February 7, 2019: Annals of Human Genetics
Nazli Ecem Dal, Pamir Cerci, Umit Olmez, Goksal Keskin
BACKGROUND: Behçet's disease (BD) is an inflammatory disorder characterized by oral aphthous lesions, uveitis, and genital ulcerations. The vitamin D receptor (VDR) has a crucial role in the pathogenesis of this disease because it mediates the functions of vitamin D in the immune system. Alterations of VDR expression related to polymorphic alleles of the VDR gene may play a pathogenic role in BD and BD's clinical presentations. METHODS: 150 BD patients and 150 healthy controls were included and genotyping was carried out by polymerase chain reaction/restriction fragment length polymorphism...
February 7, 2019: Annals of Human Genetics
Erica C Heinrich, Lu Wu, Elijah S Lawrence, Amy M Cole, Cecilia Anza-Ramirez, Francisco C Villafuerte, Tatum S Simonson
EGLN1 encodes the hypoxia-inducible factor (HIF) pathway prolyl hydroxylase 2 (PHD2) that serves as an oxygen-sensitive regulator of HIF activity. The EGLN1 locus exhibits a signature of positive selection in Tibetan and Andean populations and is associated with hemoglobin concentration in Tibetans. Recent reports provide evidence for functional roles of protein-coding variants within the first exon of EGLN1 (rs186996510, rs12097901) that are linked to an adaptive signal in Tibetans, yet whether these same variants are present and contribute to adaptation in Andean highlanders is unknown...
February 4, 2019: Annals of Human Genetics
Dalila L Zanette, Rayra P Santiago, Ivana Paula Ribeiro Leite, Sanzio S Santana, Caroline da Guarda, Vitor V Maffili, Junia Raquel Dutra Ferreira, Corynne Stephanie Ahouefa Adanho, Setondji Cocou Modeste Alexandre Yahouedehou, Isa Lyra Menezes, Marilda Souza Goncalves
Sickle cell anemia is one of the most prevalent genetic diseases worldwide, showing great clinical heterogeneity. This study compared the gene expression patterns between sickle cell anemia pediatric patients in steady state and in crisis state, as compared to age-paired, healthy individuals. RNA sequencing was performed from these groups of patients/controls using Illumina HiSeq 2500 equipment. The resulting differentially expressed genes were loaded into QIAGEN's ingenuity pathway analysis. The results showed that EIF2 pathway and NRF2-mediated oxidative stress-response pathways were more highly activated both in steady state and in crisis patients, as compared to healthy individuals...
January 30, 2019: Annals of Human Genetics
Mohamed A Mahfouz, Juan A Nepomuceno
BACKGROUND AND OBJECTIVE: The major difficulty of the analysis of the input gene expression data in a microarray-based approach for an automated diagnosis of cancer is the large number of genes (high dimensionality) with many irrelevant genes (noise) compared to the very small number of samples. This research study tackles the dimensionality reduction challenge in this area. METHODS: This research study introduces a dimension-reduction technique termed graph coloring approach (GCA) for microarray data-based cancer classification based on analyzing the absolute correlation between gene-gene pairs and partitioning genes into several hubs using graph coloring...
January 15, 2019: Annals of Human Genetics
Tai-Ping Wang
OBJECTIVE: To investigate the correlation of tumor necrosis factor α (TNF-α) polymorphisms with upper gastrointestinal bleeding (UGIB) induced by enteric-coated aspirin in coronary heart disease (CHD) patients. METHODS: In total, 154 CHD patients taking enteric-coated aspirin were enrolled in this study. Patients were divided into the UGIB group (n = 57) and non-UGIB group (n = 97) based on the presence or absence of signs of UGIB, respectively. TNF-α polymorphism (-857C > T, -863C > A, and -1031T > C) genotyping was performed using polymerase chain reaction (PCR) amplification with sequence-specific primers (PCR-SSP)...
December 2, 2018: Annals of Human Genetics
Jin-Feng Xuan, Atif Adnan, Rehan Ali Khan, Jia-Xin Xing, Jun Yao, Bao-Jie Wang
BACKGROUND: China harbors 56 ethnic groups, including Korean, with a population size of approximately 1.92 million at the 2010 census. Most of the Koreans live in Northeastern parts of China, including Jilin (59.64%), Heilongjiang (20.21%), and Liaoning (12.55%) provinces, and the rest are spread to other parts of China. Koreans across China share a common culture, which is similar to Korea. METHODS: We have explored the genetic characteristics of 20 Y-chromosomal short tandem repeat (Y-STR) loci in 252 unrelated Chinese Korean male individuals from Jilin Province, using a Goldeneye 20Y amplification kit...
December 2, 2018: Annals of Human Genetics
Lei Pi, Yufen Xu, Lanyan Fu, Li Zhang, Yunfeng Liu, Huazhong Zhou, Di Che, Xiaoqiong Gu
Kawasaki disease (KD) is an acute systemic vasculitis that is most seriously complicated by coronary artery aneurysm (CAA). The polymorphisms of platelet endothelial aggregation receptor 1 (PEAR1), notably rs12041331 and rs12566888, were found to be closely related to cardiac disease. However, little is known regarding the connection between PEAR1 and KD. In this study, we genotyped PEAR1 rs12566888 and rs12041331 in 637 healthy infants and 694 KD patients (74 with CAA). Subsequently, odds ratio (OR) and 95% confidence interval (CI) were calculated to assess the strength of their relationships...
January 2019: Annals of Human Genetics
B Ozsait-Selcuk, E Komurcu-Bayrak, M Jylhä, T Luukkaala, M Perola, K Kristiansson, N Mononen, M Hurme, M Kähönen, S Goebeler, R Laaksonen, A Hervonen, N Erginel-Unaltuna, P J Karhunen, T Lehtimäki
Upstream transcription factor 1 (USF1) regulates the transcription of many genes related to cell and organism survival processes such as stress and immune response, regulation of cellular senesce, and carcinogenesis. In this study, our aim was to investigate the effect of USF1 single nucleotide variations (SNVs) on longevity in the Vitality 90+ study, a population-based study of nonagenarians (90 ±1 years of age) living in the area of Tampere municipality, Finland. Altogether 509 voluntary nonagenarians (115 males, 394 females) were genotyped using the 5'-nuclease assay for rs2774279G > A, rs2516839T > C, and rs2073658C > T SNVs...
January 2019: Annals of Human Genetics
Ansar El Andari, Lama Mourad, Issam Mansour
Population representative short tandem repeat (STR) allele frequencies are crucial for proper probabilistic interpretation of DNA forensic evidence. STR allele frequencies also provide information about the genetic diversity of a given population. The Lebanese population is characterized by the presence of more than 18 religious communities that have high recorded rates of endogamous and consanguineous marriages, where the choice of marriages is mainly influenced by their respective geographical distributions and religious affiliation...
November 22, 2018: Annals of Human Genetics
Luz María Medrano, Virginia Pascual, Andrés Bodas, Natalia López-Palacios, Isabel Salazar, Laura Espino-Paisán, Beatriz González-Pérez, Elena Urcelay, Juan Luis Mendoza, Concepción Núñez
Autoimmune diseases like celiac disease (CeD) and ulcerative colitis (UC) show a common genetic background defined by the existence of shared susceptibility loci. We aimed to go deeper into this common genetic background through performing a cross-disease study based on gene expression. We measured the expression of 21 genes located in 13 CeD-UC susceptibility regions, and 10 genes in five CeD risk regions. Determinations were carried out in colon/rectum samples from 13 UC patients (inflamed and uninflamed tissue) and four colon samples from controls...
November 6, 2018: Annals of Human Genetics
Ji Yoon Han, Woori Jang, Joonhong Park, Myungshin Kim, Yonggoo Kim, In Goo Lee
The child with global developmental delay (GDD)/intellectual disability (ID) is deserving of the appropriate evaluation available for improving the health and well-being of patients and their families. To better elucidate the diagnostic approach of genetic tests for patients with GDD and/or ID, we evaluated the results in a cohort of 75 patients with clinical features of GDD and/or ID who were referred for diagnostic workup. A total of 75 children were investigated for GDD or ID in the pediatric neurology department...
November 6, 2018: Annals of Human Genetics
Ying Weng, Xiaoping Luo, Ling Hou
Single-nucleotide polymorphism (SNP) arrays have been widely used to identify novel genomic imbalances. Many of these genomic imbalances have been confirmed to interact with developmental delays, intellectual disabilities (IDs), and congenital defects. Here, we identify a Chinese girl with a 3.18-Mb deletion at 12q12 (human genome build 19: 43,418,911-46,601,627) who showed postnatal growth delay, low-set ears, small hands and feet, widely spaced nipples, and blue sclerae. Deletions at 12q12 are extremely rare chromosomal imbalances; only four cases involving a deletion of this type have previously been reported...
November 2018: Annals of Human Genetics
Fan Wang, Isabel Z Wang, Stephen Ellis, Stephen Archacki, John Barnard, Carlos Hubbard, Eric J Topol, Qiuyun Chen, Qing K Wang
Apolipoprotein A5 (APOA5) regulates the metabolisms of triglyceride and HDL. APOA5 variants have been linked to coronary artery disease (CAD), but their causal roles are not well studied yet. This study aims to identify the causal effects of APOA5 variants on premature CAD. Sequencing analysis of APOA5 in 128 premature, familiar CAD patients from GeneQuest identified 11 genomic variants, including p.S19W (rs3135506). SKAT analysis showed that all sequenced variants, in aggregate, significantly increased the risk of premature CAD (P-skat = 0...
November 2018: Annals of Human Genetics
Rajesh Talluri, Sanjay Shete
Obesity and type 2 diabetes are major public health issues with known interdependence. Genetic variants have been associated with obesity, type 2 diabetes, or both; thus, we hypothesize that some single nucleotide polymorphisms (SNPs) associated with both conditions may be mediated through obesity to affect type 2 diabetes or vice versa. We propose a framework for bidirectional mediation analyses. Simulations show that this approach accurately estimates the parameters, whether the mediation is unidirectional or bidirectional...
November 2018: Annals of Human Genetics
Xiaoyu Liang, Qiuying Sha, Shuanglin Zhang
In the study of complex diseases, several correlated phenotypes are usually measured. There is also increasing evidence showing that testing the association between a single-nucleotide polymorphism (SNP) and multiple-dependent phenotypes jointly is often more powerful than analyzing only one phenotype at a time. Therefore, developing statistical methods to test for genetic association with multiple phenotypes has become increasingly important. In this paper, we develop an Allele-based Clustering Approach (ACA) for the joint analysis of multiple non-normal phenotypes in association studies...
November 2018: Annals of Human Genetics
Julimary Suematsu Aquino, Eliane Papa Ambrosio-Albuquerque, Hugo Vicentin Alves, Luciana Conci Macedo, Lorena Visentainer, Ana Maria Sell, Jeane Eliete Laguila Visentainer
We evaluated the influence of the IL8 T-738A (nonidentified rs), IL8 T-353A (rs4073), IL17A G197A (rs2275913), and IL17F T7488C (rs763780) single-nucleotide polymorphisms on leprosy. The AA genotype of IL8 T-353A was observed as a risk factor for multibacillary leprosy, regardless of gender and age-of-onset of disease, considering the recessive model (OR, 3.8; 95% CI, 1.1-13.5; P, 0.023). Furthermore, the AA genotype of IL17A G197A was associated with leprosy type 1 reaction (OR, 2.4; 95% CI, 1.1-5.1; P, 0...
October 10, 2018: Annals of Human Genetics
V Alesi, M L Dentici, S Loddo, S Genovese, V Orlando, C Calacci, D Pompili, B Dallapiccola, M C Digilio, A Novelli
Cornelia de Lange syndrome (CdLS) is a genetically and clinical heterogeneous condition characterized by congenital malformation, intellectual disability, and peculiar dysmorphic features. Recently, BRD4 (19p13.12) was proposed as a new critical gene associated with a mild CdLS because of a similar presentation of the patients carrying point mutations and of its involvement in the NIPBL pathway. Patients harboring a 19p interstitial deletion shared some physical features with BRD4 mutation carriers, which results in a more complex phenotype because of the involvement of several neighboring genes...
October 10, 2018: Annals of Human Genetics
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