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Human Genomics

Hua Hu, Li Wang, Jiayan Wu, Peng Zhou, Jingli Fu, Jiuchen Sun, Weiyi Cai, Hailiang Liu, Ying Yang
BACKGROUND: Noninvasive prenatal testing (NIPT) for fetal aneuploidies by scanning cell-free fetal DNA in maternal plasma is rapidly becoming a first-tier aneuploidy screening test in clinical practices. With the development of whole-genome sequencing technology, small subchromosomal deletions and duplications that could not be detected by conventional karyotyping are now able to be detected with NIPT technology. METHODS: In the present study, we examined 8141 single pregnancies with NIPT to calculate the positive predictive values of each of the chromosome aneuploidies and the subchromosomal microdeletions and microduplications...
March 12, 2019: Human Genomics
Nur Afiqah Mohamad, Vasudevan Ramachandran, Hazlita Mohd Isa, Yoke Mun Chan, Nor Fariza Ngah, Siew Mooi Ching, Fan Kee Hoo, Wan Aliaa Wan Sulaiman, Liyana Najwa Inche Mat, Mohd Hazmi Mohamed
BACKGROUND: The association of HTRA1 rs11200638 and ARMS2 rs10490924 gene polymorphisms with response to intravitreal ranibizumab therapy among neovascular AMD (nAMD) subjects in Malaysia was determined in this study, followed by the expression of HTRA1 and ARMS2 genes. RESULTS: Both single nucleotide polymorphisms (SNPs) recorded a significant association between nAMD and controls with HTRA1 rs11200638 at P = 0.018 (OR = 1.52, 95% CI = 1.07-215) and ARMS2 rs10490924 at P < 0...
February 22, 2019: Human Genomics
Julyann Pérez-Mayoral, Marievelisse Soto-Salgado, Ebony Shah, Rick Kittles, Mariana C Stern, Myrta I Olivera, María Gonzalez-Pons, Segundo Rodriguez-Quilichinni, Marla Torres, Jose S Reyes, Luis Tous, Nicolas López, Victor Carlo Chevere, Marcia Cruz-Correa
BACKGROUND: Colorectal cancer (CRC) is the first cause of cancer deaths among Puerto Ricans. The incidence and mortality of CRC in Puerto Rico continue to be on the rise. The burden of CRC in Puerto Rico is higher than among US Hispanics and is second only to African Americans, thus supporting the importance of studying this CRC health disparity. The genetic background of the Puerto Rican population is a mix of European, African, and Amerindian races, which may account, in part, for the differences observed in the CRC mortality rates among Puerto Ricans...
February 20, 2019: Human Genomics
Georgia Charkoftaki, Yewei Wang, Monica McAndrews, Elspeth A Bruford, David C Thompson, Vasilis Vasiliou, Daniel W Nebert
Lipocalins (LCNs) are members of a family of evolutionarily conserved genes present in all kingdoms of life. There are 19 LCN-like genes in the human genome, and 45 Lcn-like genes in the mouse genome, which include 22 major urinary protein (Mup) genes. The Mup genes, plus 29 of 30 Mup-ps pseudogenes, are all located together on chromosome (Chr) 4; evidence points to an "evolutionary bloom" that resulted in this Mup cluster in mouse, syntenic to the human Chr 9q32 locus at which a single MUPP pseudogene is located...
February 19, 2019: Human Genomics
Phuong T Lam, Stephanie L Padula, Thanh V Hoang, Justin E Poth, Lin Liu, Chun Liang, Adam S LeFever, Lindsay M Wallace, Ruth Ashery-Padan, Penny K Riggs, Jordan E Shields, Ohad Shaham, Sheldon Rowan, Nadean L Brown, Tom Glaser, Michael L Robinson
BACKGROUND: Despite a number of different transgenes that can mediate DNA deletion in the developing lens, each has unique features that can make a given transgenic line more or less appropriate for particular studies. The purpose of this work encompasses both a review of transgenes that lead to the expression of Cre recombinase in the lens and a comparative analysis of currently available transgenic lines with a particular emphasis on the Le-Cre and P0-3.9GFPCre lines that can mediate DNA deletion in the lens placode...
February 15, 2019: Human Genomics
Man Tang, Mohammad Shabbir Hasan, Hongxiao Zhu, Liqing Zhang, Xiaowei Wu
BACKGROUND: Accurate and reliable identification of sequence variants, including single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (INDELs), plays a fundamental role in next-generation sequencing (NGS) applications. Existing methods for calling these variants often make simplified assumptions of positional independence and fail to leverage the dependence between genotypes at nearby loci that is caused by linkage disequilibrium (LD). RESULTS AND CONCLUSION: We propose vi-HMM, a hidden Markov model (HMM)-based method for calling SNPs and INDELs in mapped short-read data...
February 13, 2019: Human Genomics
Xin-Ying Tang, Jin-Huan Lin, Wen-Bin Zou, Emmanuelle Masson, Arnaud Boulling, Shun-Jiang Deng, David N Cooper, Zhuan Liao, Claude Férec, Zhao-Shen Li, Jian-Min Chen
BACKGROUND: The clinical significance of SPINK1 intronic variants in chronic pancreatitis has been previously assessed by various approaches including a cell culture-based full-length gene assay. A close correlation between the results of this assay and in silico splicing prediction was apparent. However, until now, a clinical diagnostic pipeline specifically designed to classify SPINK1 intronic variants accurately and efficiently has been lacking. Herein, we present just such a pipeline and explore its efficacy and potential utility in potentiating the classification of newly described SPINK1 intronic variants...
February 12, 2019: Human Genomics
Hadi Charati, Min-Sheng Peng, Wei Chen, Xing-Yan Yang, Roghayeh Jabbari Ori, Mohsen Aghajanpour-Mir, Ali Esmailizadeh, Ya-Ping Zhang
BACKGROUND: The ability to digest dietary lactose is associated with lactase persistence (LP) in the intestinal lumen in human. The genetic basis of LP has been investigated in many populations in the world. Iran has a long history of pastoralism and the daily consumption of dairy products; thus, we aim to assess how LP has evolved in the Iranian population. We recruited 400 adult individuals from seven Iranian ethnic groups, from whom we investigated their lactose tolerance and screened the genetic variants in their lactase gene locus...
February 11, 2019: Human Genomics
Anna L Guyatt, Rebecca R Brennan, Kimberley Burrows, Philip A I Guthrie, Raimondo Ascione, Susan M Ring, Tom R Gaunt, Angela Pyle, Heather J Cordell, Debbie A Lawlor, Patrick F Chinnery, Gavin Hudson, Santiago Rodriguez
BACKGROUND: Mitochondrial DNA copy number (mtDNA CN) exhibits interindividual and intercellular variation, but few genome-wide association studies (GWAS) of directly assayed mtDNA CN exist. We undertook a GWAS of qPCR-assayed mtDNA CN in the Avon Longitudinal Study of Parents and Children (ALSPAC) and the UK Blood Service (UKBS) cohort. After validating and harmonising data, 5461 ALSPAC mothers (16-43 years at mtDNA CN assay) and 1338 UKBS females (17-69 years) were included in a meta-analysis...
January 31, 2019: Human Genomics
Yilan Li, Shipeng Wang, Dandan Zhang, Xueming Xu, Bo Yu, Yao Zhang
BACKGROUND: The association of platelet endothelial cell adhesion molecule 1 (PECAM1), hypoxia-inducible factor 1 subunit alpha (HIF1A), and KIAA1462 in myocardial infarction (MI) was investigated. The study included 401 Han Chinese MI patients and 409 controls. Three tag single-nucleotide polymorphisms (SNPs)-PECAM1 rs1867624, HIF1A rs2057482, and KIAA1462 rs3739998-were selected. SNP genotyping was performed by an improved multiplex ligation detection reaction assay. A systematic review and meta-analysis of studies including 3314 cases and 2687 controls on the association of 5 HIF1A SNPs and the overall risk of MI or coronary artery disease (CAD) was performed...
January 24, 2019: Human Genomics
J C Fernández-Lopez, S Romero-Córdoba, R Rebollar-Vega, L A Alfaro-Ruiz, S Jiménez-Morales, F Beltrán-Anaya, R Arellano-Llamas, A Cedro-Tanda, M Rios-Romero, M Ramirez-Florencio, V Bautista-Piña, C Dominguez-Reyes, F Villegas-Carlos, A Tenorio-Torres, A Hidalgo-Miranda
Interpretation of variants of unknown significance (VUS) in genetic tests is complicated in ethnically diverse populations, given the lack of information regarding the common spectrum of genetic variation in clinically relevant genes. Public availability of data obtained from high-throughput genotyping and/or exome massive parallel sequencing (MPS)-based projects from several thousands of outbred samples might become useful tools to evaluate the pathogenicity of a VUS, based on its frequency in different populations...
January 10, 2019: Human Genomics
Dandan Yi, Lei Xu, Jiaqi Luo, Xiaobin You, Tao Huang, Yi Zi, Xiaoting Li, Ru Wang, Zaixuan Zhong, Xiaoqiao Tang, Ang Li, Yujian Shi, Jianmei Rao, Yifen Zhang, Jianfeng Sang
BACKGROUND: Germline BRCA1/2 prevalence is relatively low in sporadic triple-negative breast cancer (TNBC). We hypothesized that non-BRCA genes may also have significant germline contribution to Chinese sporadic TNBC, and the somatic mutational landscape of TNBC may vary between ethnic groups. We therefore conducted this study to investigate germline and somatic mutations in 43 cancer susceptibility genes in Chinese sporadic TNBC. PATIENTS AND METHODS: Sixty-six Chinese sporadic TNBC patients were enrolled in this study...
January 10, 2019: Human Genomics
Haiko Schurz, Muneeb Salie, Gerard Tromp, Eileen G Hoal, Craig J Kinnear, Marlo Möller
The X chromosome and X-linked variants have largely been ignored in genome-wide and candidate association studies of infectious diseases due to the complexity of statistical analysis of the X chromosome. This exclusion is significant, since the X chromosome contains a high density of immune-related genes and regulatory elements that are extensively involved in both the innate and adaptive immune responses. Many diseases present with a clear sex bias, and apart from the influence of sex hormones and socioeconomic and behavioural factors, the X chromosome, X-linked genes and X chromosome inactivation mechanisms contribute to this difference...
January 8, 2019: Human Genomics
Li-Ya Wang, Xing-Qiang Rao, Yu-Qin Luo, Bei Liu, Chun-Fang Peng, Dan Chen, Kai Yan, Ye-Qing Qian, Yan-Mei Yang, Ying-Zhi Huang, Min Chen, Yi-Xi Sun, Hong-Ge Li, Ying-Hui Ye, Fan Jin, Hai-Liang Liu, Min-Yue Dong
BACKGROUND: Recent advances in semiconductor sequencing platform (SSP) have provided new methods for preimplantation genetic diagnosis/screening (PGD/S). The present study aimed to evaluate the applicability and efficiency of SSP in PGD/S. METHODS: The artificial positive single-cell-like DNAs and normal single-cell samples were chosen to test our semiconductor sequencing platform for preimplantation genetic diagnosis/screening (SSP-PGD/S) method with two widely used whole-genome amplification (WGA) kits...
January 3, 2019: Human Genomics
Jiantao Sun, Jiemei Yang, Jing Chi, Xue Ding, Nan Lv
BACKGROUND: Cardiac hypertrophy and acute myocardial infarction (AMI) are two common heart diseases worldwide. However, research is needed into the exact pathogenesis and effective treatment strategies for these diseases. Recently, microRNAs (miRNAs) have been suggested to regulate the pathological pathways of heart disease, indicating a potential role in novel treatments. RESULTS: In our study, we constructed a miRNA-gene-drug network and analyzed its topological features...
December 4, 2018: Human Genomics
Jonas Langerud, Elisabeth Jarhelle, Marijke Van Ghelue, Sarah Louise Ariansen, Nina Iversen
BACKGROUND: Deleterious variants in the tumour suppressor BRCA1 are known to cause hereditary breast and ovarian cancer syndrome (HBOC). Missense variants in BRCA1 pose a challenge in clinical care, as their effect on protein functionality often remains unknown. Many of the pathogenic missense variants found in BRCA1 are located in the BRCA1 C-terminal (BRCT) domains, domains that are known to be vital for key functions such as homologous recombination repair, protein-protein interactions and trans-activation (TA)...
November 20, 2018: Human Genomics
Lejla Mahmutovic, Betul Akcesme, Camil Durakovic, Faruk Berat Akcesme, Aida Maric, Muhamed Adilovic, Nour Hamad, Matthias Wjst, Oliver Feeney, Sabina Semiz
BACKGROUND: Increasing evidence is demonstrating that a patient's unique genetic profile can be used to detect the disease's onset, prevent its progression, and optimize its treatment. This led to the increased global efforts to implement personalized medicine (PM) and pharmacogenomics (PG) in clinical practice. Here we investigated the perceptions of students from different universities in Bosnia and Herzegovina (BH) towards PG/PM as well as related ethical, legal, and social implications (ELSI)...
November 14, 2018: Human Genomics
Weiwei Duan, Ruyang Zhang, Yang Zhao, Sipeng Shen, Yongyue Wei, Feng Chen, David C Christiani
BACKGROUND: Modeling thousands of markers simultaneously has been of great interest in testing association between genetic biomarkers and disease or disease-related quantitative traits. Recently, an expectation-maximization (EM) approach to Bayesian variable selection (EMVS) facilitating the Bayesian computation was developed for continuous or binary outcome using a fast EM algorithm. However, it is not suitable to the analyses of time-to-event outcome in many public databases such as The Cancer Genome Atlas (TCGA)...
November 6, 2018: Human Genomics
Sanghoon Moon, Young Lee, Sungho Won, Juyoung Lee
BACKGROUND: Metabolic syndrome is a risk factor for type 2 diabetes and cardiovascular disease. We identified common genetic variants that alter the risk for metabolic syndrome in the Korean population. To isolate these variants, we conducted a multiple-genotype and multiple-phenotype genome-wide association analysis using the family-based quasi-likelihood score (MFQLS) test. For this analysis, we used 7211 and 2838 genotyped study subjects for discovery and replication, respectively...
November 1, 2018: Human Genomics
Masoud Arabfard, Kaveh Kavousi, Ahmad Delbari, Mina Ohadi
BACKGROUND: Despite their vast biological implication, the relevance of short tandem repeats (STRs)/microsatellites to the protein-coding gene translation initiation sites (TISs) remains largely unknown. METHODS: We performed an Ensembl-based comparative genomics study of all annotated orthologous TIS-flanking sequences in human and 46 other species across vertebrates, on the genomic DNA and cDNA platforms (755,956 TISs), aimed at identifying human-specific STRs in this interval...
October 29, 2018: Human Genomics
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