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Human Heredity

Xin Gao, Zhi Wei, Hakon Hakonarson
BACKGROUND: tRNAscan-SE is the leading tool for transfer RNA (tRNA) annotation, which has been widely used in the field. However, tRNAscan-SE can return a significant number of false positives when applied to large sequences. Recently, conventional machine learning methods have been proposed to address this issue, but their efficiency can be still limited due to their dependency on handcrafted features. With the growing availability of large-scale genomic data-sets, deep learning methods, especially convolutional neural networks, have demonstrated excellent power in characterizing sequence patterns in genomic sequences...
January 25, 2019: Human Heredity
Wendy J Huss, Qiang Hu, Sean T Glenn, Kalyan J Gangavarapu, Jianmin Wang, Jesse D Luce, Paul K Quinn, Elizabeth A Brese, Fenglin Zhan, Jeffrey M Conroy, Gyorgy Paragh, Barbara A Foster, Carl D Morrison, Song Liu, Lei Wei
BACKGROUND: Advances in single-cell sequencing provide unprecedented opportunities for clinical examination of circulating tumor cells, cancer stem cells, and other rare cells responsible for disease progression and drug resistance. On the genomic level, single-cell whole exome sequencing (scWES) started to gain popularity with its unique potentials in characterizing mutational landscapes at a single-cell level. Currently, there is little known about the performance of different exome capture kits in scWES...
January 22, 2019: Human Heredity
Jun Wang, Jiashun Zheng, Zengmiao Wang, Hao Li, Minghua Deng
OBJECTIVES: Genome-wide association studies (GWASs) have revealed many candidate SNPs, but the mechanisms by which these SNPs influence diseases are largely unknown. In order to decipher the underlying mechanisms, several methods have been developed to predict disease-associated genes based on the integration of GWAS and eQTL data (e.g., Sherlock and COLOC). A number of studies have also incorporated information from gene networks into GWAS analysis to reprioritize candidate genes. METHODS: Motivated by these two different approaches, we have developed a statistical framework to integrate information from GWAS, eQTL, and protein-protein interaction (PPI) data to predict disease-associated genes...
January 22, 2019: Human Heredity
Vladimir Kogan, Joshua Millstein, Stephanie J London, Carole Ober, Steven R White, Edward T Naureckas, W James Gauderman, Daniel J Jackson, Albino Barraza-Villarreal, Isabelle Romieu, Benjamin A Raby, Carrie V Breton
OBJECTIVES: There is evidence to suggest that asthma pathogenesis is affected by both genetic and epigenetic variation independently, and there is some evidence to suggest that genetic-epigenetic interactions affect risk of asthma. However, little research has been done to identify such interactions on a genome-wide scale. The aim of this studies was to identify genes with genetic-epigenetic interactions associated with asthma. METHODS: Using asthma case-control data, we applied a novel nonparametric gene-centric approach to test for interactions between multiple SNPs and CpG sites simultaneously in the vicinities of 18,178 genes across the genome...
January 22, 2019: Human Heredity
Shuo Shi, Na Yuan, Ming Yang, Zhenglin Du, Jinyue Wang, Xin Sheng, Jiayan Wu, Jingfa Xiao
Genotype imputation is a process of estimating missing ge-notypes from the haplotype or genotype reference panel. It can effectively boost the power of detecting single nucleotide polymorphisms (SNPs) in genome-wide association studies, integrate multi-studies for meta-analysis, and be applied in fine-mapping studies. The performance of genotype imputation is affected by many factors, including software, reference selection, sample size, and SNP density/sequencing coverage. A systematical evaluation of the imputation performance of current popular software will benefit future studies...
January 22, 2019: Human Heredity
Junwen Wang, Kai Wang, Xiaoming Liu, Pak Sham, Zhongming Zhao
No abstract text is available yet for this article.
January 9, 2019: Human Heredity
(no author information available yet)
No abstract text is available yet for this article.
June 1, 2018: Human Heredity
(no author information available yet)
No abstract text is available yet for this article.
April 18, 2018: Human Heredity
Lucy Blondell, August Blackburn, Mark Z Kos, John Blangero, Harald H H Göring
OBJECTIVES: An interesting consequence of consanguinity is that the inbred singleton becomes informative for genetic variance. We determine the contribution of an inbred singleton to variance component analysis of heritability and linkage. METHODS: Statistical theory for the power of variance component analysis of quantitative traits is used to determine the expected contribution of an inbred singleton to likelihood-ratio tests of heritability and linkage. RESULTS: In variance component models, an inbred singleton contributes relatively little to a test of heritability but can contribute substantively to a test of linkage...
2018: Human Heredity
Jeanette Prinz, Mohamad Koohi-Moghadam, Hongzhe Sun, Jean-Pierre A Kocher, Junwen Wang
AIMS: We propose a novel machine learning approach to expand the knowledge about drug-target interactions. Our method may help to develop effective, less harmful treatment strategies and to enable the detection of novel indications for existing drugs. METHODS: We developed a novel machine learning strategy to predict drug-target interactions based on drug side effects and traits from genome-wide association studies. We integrated data from the databases SIDER and GWASdb and utilized them in a unique way by a neural network approach...
2018: Human Heredity
Fatemeh Keyfi, Mojila Nasseri, Samira Nayerabadi, Amin Alaei, Armin Mokhtariye, Abdolreza Varasteh
OBJECTIVE: Inborn errors of metabolism (IEMs) are disorders with various manifestations that occur mainly in the pediatric population. In countries where consanguineous marriage is common, the association between consanguinity and IEMs is highly important. No studies have been conducted in Iran examining the impact of consanguinity on IEMs. METHODS: In this retrospective study, the incidences of metabolic disorders were evaluated for the years 2006 through 2016 in the North East Iran Regional Diagnostic Laboratory (Pardis Clinical and Genetic Laboratory)...
2018: Human Heredity
Timothy D O'Brien, Peilin Jia, Melinda C Aldrich, Zhongming Zhao
OBJECTIVE: Lung cancer is classified as a single entity comprised of multiple histological subtypes. But how similar are these subtypes on a genetic level? This paper aims to address this question through a concise overview of germline and somatic differences between small cell lung cancer, lung adenocarcinoma, and lung squamous cell carcinoma. METHODS: We reveal the weak overlap found between these 3 lung cancer subtypes using published data from one of the largest germline genetic studies on lung cancer to date and somatic mutation data from Catalogue of Somatic Mutations in Cancer (COSMIC)...
2018: Human Heredity
Ming He, Kun Lin, Youguang Huang, Licun Zhou, Qingcheng Yang, Shude Li, Weiying Jiang
OBJECTIVES: To estimate the prevalence and mutation types of G6PD deficiency and evaluate the relationship between G6PD genotypes and erythrocyte phenotypes in the Dai and Jingpo ethnic groups in the Dehong prefecture of the Yunnan province, China. METHODS: G6PD deficiency was screened in Dai (1,530 individuals) and Jingpo (372 individuals) populations using a modified G6PD/6PGD ratio assay. Red blood cell traits were analyzed using the Sysmex XE2100 fully automated blood analyzer...
2018: Human Heredity
Charith B Karunarathna, Jinko Graham
BACKGROUND AND AIMS: Many methods can detect trait association with causal variants in candidate genomic regions; however, a comparison of their ability to localize causal variants is lacking. We extend a previous study of the detection abilities of these methods to a comparison of their localization abilities. METHODS: Through coalescent simulation, we compare several popular association methods. Cases and controls are sampled from a diploid population to mimic human studies...
2018: Human Heredity
(no author information available yet)
No abstract text is available yet for this article.
April 4, 2017: Human Heredity
Markus Brugger, Susanne Rospleszcz, Konstantin Strauch
BACKGROUND/AIMS: Theoretically, the trait-model parameters (disease allele frequency and penetrance function) can be estimated without bias in a MOD score linkage analysis. We aimed to practically evaluate the MOD score approach regarding its ability to provide unbiased trait-model parameters for various pedigree-type and trait-model scenarios. We further investigated the ability of the MOD score approach to detect imprinting using affected sib pairs (ASPs) and affected half-sib pairs (AHSPs) when all parental genotypes are missing...
2016: Human Heredity
Janis Stavusis, Inna Inashkina, Baiba Lace, Dita Pelnena, Svetlana Limborska, Andrey Khrunin, Vaidutis Kucinskas, Astrida Krumina, Linda Piekuse, Branko Zorn, Violeta Fodina, Margus Punab, Juris Erenpreiss
OBJECTIVES: The PMCA gene family consists of 4 genes and at least 21 splice variants; among these, the Ca2+ ATPase 4 (PMCA4) gene encodes a plasma membrane protein abundantly expressed in several tissues, including the kidney, heart, and sperm. Knockout of PMCA4 causes infertility due to immotile sperm in mouse models. We therefore investigated variants in this gene for potential association with infertility in groups of Estonian (n = 191) and Latvian (n = 92) men with reduced sperm motility...
2016: Human Heredity
Jonathan T L Kang, Amy Goldberg, Michael D Edge, Doron M Behar, Noah A Rosenberg
OBJECTIVES: Recent studies have highlighted the potential of analyses of genomic sharing to produce insight into the demographic processes affecting human populations. We study runs of homozygosity (ROH) in 18 Jewish populations, examining these groups in relation to 123 non-Jewish populations sampled worldwide. METHODS: By sorting ROH into 3 length classes (short, intermediate, and long), we evaluate the impact of demographic processes on genomic patterns in Jewish populations...
2016: Human Heredity
Mary L Roop, David E C Cole, David C Hamilton
BACKGROUND: Linkage disequilibrium (LD) is the non-random association between alleles at different loci and remains important for disease mapping studies in humans. A common measure of LD is the sample correlation between indicator variables for alleles at the 2 loci. Knowledge of LD estimate precision may help inform biomedical decisions based on those estimates. OBJECTIVES AND METHODS: Variance formulae are obtained for correlation measures of LD in 4 scenarios...
2016: Human Heredity
Anthony M Musolf, Claire L Simpson, Mariza de Andrade, Diptasri Mandal, Colette Gaba, Ping Yang, Yafang Li, Ming You, Elena Y Kupert, Marshall W Anderson, Ann G Schwartz, Susan M Pinney, Christopher I Amos, Joan E Bailey-Wilson
OBJECTIVE: One of four American cancer patients dies of lung cancer. Environmental factors such as tobacco smoking are known to affect lung cancer risk. However, there is a genetic factor to lung cancer risk as well. Here, we perform parametric linkage analysis on family-based genotype data in an effort to find genetic loci linked to the disease. METHODS: 197 individuals from families with a high-risk history of lung cancer were recruited and genotyped using an Illumina array...
2016: Human Heredity
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