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Human Heredity

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https://www.readbyqxmd.com/read/28910803/consanguinity-rates-predict-long-runs-of-homozygosity-in-jewish-populations
#1
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...
September 15, 2017: Human Heredity
https://www.readbyqxmd.com/read/28376496/45th-european-mathematical-genetics-meeting-emgm-2017-tartu-estonia-april-4-7-2017-abstracts
#2
(no author information available yet)
No abstract text is available yet for this article.
April 4, 2017: Human Heredity
https://www.readbyqxmd.com/read/28881353/variance-formulae-for-correlation-measures-of-linkage-disequilibrium
#3
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
https://www.readbyqxmd.com/read/28817824/parametric-linkage-analysis-identifies-five-novel-genome-wide-significant-loci-for-familial-lung-cancer
#4
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
https://www.readbyqxmd.com/read/28810240/efficient-statistical-method-for-association-analysis-of-x-linked-variants
#5
Heejin Jin, Taesung Park, Sungho Won
BACKGROUND/AIMS: Unlike the gene-poor Y chromosome, the X chromosome contains over 1,000 genes that are essential for viability of cells. Females have 2 X chromosomes, and thus female X-linked gene expression would be expected to be twice that of males. To adjust this imbalance, one of the 2 X-linked genes is often inactivated, and this is known as X-chromosome inactivation (XCI). However, recent studies described that a gene can be nonrandomly selected for inactivation from 2 X-linked genes and that XCI is not observed in some X-linked genes...
2016: Human Heredity
https://www.readbyqxmd.com/read/28768256/estimation-of-fst-and-the-impact-of-de-novo-mutation
#6
Daniel Shriner, Guanjie Chen, Adebowale Adeyemo, Charles N Rotimi
OBJECTIVES: Wright defined FST as a measure of genetic differentiation. Cockerham developed an estimator of FST based on binary indicators in an ANOVA framework. Here, we address 2 issues regarding the estimation of FST. First, we derive a new estimator of FST based on the ANOVA framework using the doubly truncated normal distribution as an approximation of the binomial distribution to estimate variances. Second, we consider the impact of de novo mutation on FST estimation. METHODS: We compare our estimator to Weir and Cockerham's estimator via computer simulation...
2016: Human Heredity
https://www.readbyqxmd.com/read/28743105/statistical-interactions-from-a-growth-curve-perspective
#7
Sean M Devlin, Jaya M Satagopan
Logistic regression is widely used to evaluate the association between risk factors and a binary outcome. The logistic curve is symmetric around its point of inflection. Alternative families of curves, such as the additive Gompertz or Guerrero-Johnson models, have been proposed in various scenarios due to their asymmetry: disease risk may initially increase rapidly and be followed by a longer period where the rate of growth slowly decreases. When modeling binary outcomes in relation to risk factors, an additive logistic model may not provide a good fit to the data...
2016: Human Heredity
https://www.readbyqxmd.com/read/28728153/genetic-variants-of-cytochrome-cyp2d6-in-two-mixed-chilean-populations
#8
Mónica Acuña, Eric Pinto, Paulina Olivares, Carolina Ríos
OBJECTIVES: It is known that the interindividual and interethnic variability of the genetic polymorphisms of CYP2D6 plays an important role in the presentation of adverse drug reactions and concerning lack of therapeutic effects in humans. However, there are few data available from mixed populations of Latin America, including the Chilean. The aim of this study was therefore to estimate the frequencies of CYP2D6 variants in two samples of hospitals from the northern (Hospital San José, HSJ) and eastern (Clínica Las Condes, CLC) parts of Santiago, Chile, with different degrees of Amerindian admixture (HSJ: 34...
2016: Human Heredity
https://www.readbyqxmd.com/read/28728147/efficient-maximum-likelihood-estimation-for-pedigree-data-with-the-sum-product-algorithm
#9
Alexander Engelhardt, Anna Rieger, Achim Tresch, Ulrich Mansmann
OBJECTIVE: We analyze data sets consisting of pedigrees with age at onset of colorectal cancer (CRC) as phenotype. The occurrence of familial clusters of CRC suggests the existence of a latent, inheritable risk factor. We aimed to compute the probability of a family possessing this risk factor as well as the hazard rate increase for these risk factor carriers. Due to the inheritability of this risk factor, the estimation necessitates a costly marginalization of the likelihood. METHODS: We propose an improved EM algorithm by applying factor graphs and the sum-product algorithm in the E-step...
2016: Human Heredity
https://www.readbyqxmd.com/read/28315880/an-analytic-solution-to-the-computation-of-power-and-sample-size-for-genetic-association-studies-under-a-pleiotropic-mode-of-inheritance
#10
Derek Gordon, Douglas Londono, Payal Patel, Wonkuk Kim, Stephen J Finch, Gary A Heiman
Our motivation here is to calculate the power of 3 statistical tests used when there are genetic traits that operate under a pleiotropic mode of inheritance and when qualitative phenotypes are defined by use of thresholds for the multiple quantitative phenotypes. Specifically, we formulate a multivariate function that provides the probability that an individual has a vector of specific quantitative trait values conditional on having a risk locus genotype, and we apply thresholds to define qualitative phenotypes (affected, unaffected) and compute penetrances and conditional genotype frequencies based on the multivariate function...
2016: Human Heredity
https://www.readbyqxmd.com/read/28214848/human-birth-weight-and-reproductive-immunology-testing-for-interactions-between-maternal-and-offspring-kir-and-hla-c-genes
#11
Michelle M Clark, Olympe Chazara, Eric M Sobel, Håkon K Gjessing, Per Magnus, Ashley Moffett, Janet S Sinsheimer
BACKGROUND/AIMS: Maternal and offspring cell contact at the site of placentation presents a plausible setting for maternal-fetal genotype (MFG) interactions affecting fetal growth. We test hypotheses regarding killer cell immunoglobulin-like receptor (KIR) and HLA-C MFG effects on human birth weight by extending the quantitative MFG (QMFG) test. METHODS: Until recently, association testing for MFG interactions had limited applications. To improve the ability to test for these interactions, we developed the extended QMFG test, a linear mixed-effect model that can use multi-locus genotype data from families...
2016: Human Heredity
https://www.readbyqxmd.com/read/28171865/how-can-we-explain-very-low-odds-ratios-in-gwas-i-polygenic-models
#12
Susan E Hodge, David A Greenberg
Genome-wide association studies of common diseases often identify a number of disease-related SNPs that reach highly significant p values but at the same time show very low disease odds ratios (ORs), most <1.5 and many <1.2. Despite their statistical significance, associations involving very low ORs explain little about the genetic contribution to the disease and nothing about disease inheritance. A commonly accepted explanation for very low ORs involves a model of polygenic inheritance, i.e., where the disease being studied is caused by a large number of interacting genes, each gene contributing only a small increment to disease risk...
2016: Human Heredity
https://www.readbyqxmd.com/read/28076869/computational-prediction-of-the-global-functional-genomic-landscape-applications-methods-and-challenges
#13
REVIEW
Weiqiang Zhou, Ben Sherwood, Hongkai Ji
Technological advances have led to an explosive growth of high-throughput functional genomic data. Exploiting the correlation among different data types, it is possible to predict one functional genomic data type from other data types. Prediction tools are valuable in understanding the relationship among different functional genomic signals. They also provide a cost-efficient solution to inferring the unknown functional genomic profiles when experimental data are unavailable due to resource or technological constraints...
2016: Human Heredity
https://www.readbyqxmd.com/read/28076868/sages-2015-symposium-of-advances-in-genomics-epidemiology-and-statistics-2015-abstracts
#14
(no author information available yet)
No abstract text is available yet for this article.
2016: Human Heredity
https://www.readbyqxmd.com/read/28076867/identifying-host-genetic-variants-associated-with-microbiome-composition-by-testing-multiple-beta-diversity-matrices
#15
Xing Hua, James J Goedert, Maria Teresa Landi, Jianxin Shi
OBJECTIVES: Host genetics have been recently reported to affect human microbiome composition. We previously developed a statistical framework, microbiomeGWAS, to identify host genetic variants associated with microbiome composition by testing a distance matrix. However, statistical power depends on the choice of a microbiome distance matrix. To achieve more robust statistical power, we aim to extend microbiomeGWAS to test the association with many distance matrices, which are defined based on multilevel taxa abundances and phylogenetic information...
2016: Human Heredity
https://www.readbyqxmd.com/read/28076866/biophysically-motivated-regulatory-network-inference-progress-and-prospects
#16
REVIEW
Tarmo Äijö, Richard Bonneau
Thanks to the confluence of genomic technology and computational developments, the possibility of network inference methods that automatically learn large comprehensive models of cellular regulation is closer than ever. This perspective focuses on enumerating the elements of computational strategies that, when coupled to appropriate experimental designs, can lead to accurate large-scale models of chromatin state and transcriptional regulatory structure and dynamics. We highlight 4 research questions that require further investigation in order to make progress in network inference: (1) using overall constraints on network structure such as sparsity, (2) use of informative priors and data integration to constrain individual model parameters, (3) estimation of latent regulatory factor activity under varying cell conditions, and (4) new methods for learning and modeling regulatory factor interactions...
2016: Human Heredity
https://www.readbyqxmd.com/read/28076865/gene-mapping-in-admixed-families-a-cautionary-note-on-the-interpretation-of-the-transmission-disequilibrium-test-and-a-possible-solution
#17
Xuexia Wang, Rui Xiao, Xiaofeng Zhu, Mingyao Li
A family-based study design is commonly used in gene mapping studies of complex human diseases. Most family-based studies use the transmission of alleles to assess evidence of association. It is generally believed that the transmission disequilibrium test (TDT) is robust against spurious association due to population stratification or admixture. While this is true when population stratification is due to discrete population structure, one should use the TDT-type methods with caution when they are applied to admixed populations in which population structure exists in local genomic regions...
2016: Human Heredity
https://www.readbyqxmd.com/read/28076859/title-page-table-of-contents
#18
(no author information available yet)
No abstract text is available yet for this article.
2016: Human Heredity
https://www.readbyqxmd.com/read/28076858/non-coding-loss-of-function-variation-in-human-genomes
#19
REVIEW
Zachary Zappala, Stephen B Montgomery
Whole-genome and exome sequencing in human populations has revealed the tolerance of each gene for loss-of-function variation. By understanding this tolerance, it has become increasingly possible to identify genes that would make safe therapeutic targets and to identify rare genetic risk factors and phenotypes at the scale of individual genomes. To date, the vast majority of surveyed loss-of-function variants are in protein-coding regions of the genome mainly due to the focus on these regions by exome-based sequencing projects and their relative ease of interpretability...
2016: Human Heredity
https://www.readbyqxmd.com/read/28002825/from-common-to-rare-variants-the-genetic-component-of-alzheimer-disease
#20
REVIEW
Gaël Nicolas, Camille Charbonnier, Dominique Campion
Alzheimer disease (AD) is a remarkable example of genetic heterogeneity. Extremely rare variants in the APP, PSEN1, or PSEN2 genes, or duplications of the APP gene cause autosomal dominant forms, generally with complete penetrance by the age of 65 years. Nonautosomal dominant forms are considered as a complex disorder with a high genetic component, whatever the age of onset. Although genetically heterogeneous, AD is defined by the same neuropathological criteria in all configurations. According to the amyloid cascade hypothesis, the Aβ peptide, which aggregates in AD brains, is a key player...
2016: Human Heredity
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