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https://www.readbyqxmd.com/read/27922091/an-increased-duplication-of-zrs-region-that-caused-more-than-one-supernumerary-digits-preaxial-polydactyly-in-a-large-chinese-family
#1
Bin Wang, Yutao Diao, Qiji Liu, Hongqiang An, Ruiping Ma, Guosheng Jiang, Nannan Lai, Ziwei Li, Xiaoxiao Zhu, Lin Zhao, Qiang Guo, Zhen Zhang, Rong Sun, Xia Li
Preaxial polydactyly (PPD) is inherited in an autosomal dominant fashion and characterized by the presence of one or more supernumerary digits on the thumb side. It had been identified that point mutation or genomic duplications of the long-range limb-specific cis-regulator - zone of polarizing activity regulatory sequence (ZRS) cause PPD or other limb deformities such as syndactyly type IV (SD4) and Triphalangeal thumb-polysyndactyly syndrome (TPTPS). Most previously reported cases involved with no more than one extra finger; however, the role of the point mutation or genomic duplications of ZRS in the case of more than one redundant finger polydactyly remains unclear...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27920797/genome-wide-association-study-for-identifying-loci-that-affect-fillet-yield-carcass-and-body-weight-traits-in-rainbow-trout-oncorhynchus-mykiss
#2
Dianelys Gonzalez-Pena, Guangtu Gao, Matthew Baranski, Thomas Moen, Beth M Cleveland, P Brett Kenney, Roger L Vallejo, Yniv Palti, Timothy D Leeds
Fillet yield (FY, %) is an economically-important trait in rainbow trout aquaculture that affects production efficiency. Despite that, FY has received little attention in breeding programs because it is difficult to measure on a large number of fish and cannot be directly measured on breeding candidates. The recent development of a high-density SNP array for rainbow trout has provided the needed tool for studying the underlying genetic architecture of this trait. A genome-wide association study (GWAS) was conducted for FY, body weight at 10 (BW10) and 13 (BW13) months post-hatching, head-off carcass weight (CAR), and fillet weight (FW) in a pedigreed rainbow trout population selectively bred for improved growth performance...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27919305/a-new-model-for-parent-of-origin-effect-analyses-applied-to-brown-swiss-cattle-slaughterhouse-data
#3
I Blunk, M Mayer, H Hamann, N Reinsch
Genomic imprinting is a phenomenon that arises when the expression of genes depends on the parental origin of alleles. Epigenetic mechanisms may induce the full or partial suppression of maternal or paternal alleles, thereby leading to different types of imprinting. However, imprinting effects have received little consideration in animal breeding programmes, although their relevance to some agricultural important traits has been demonstrated. A recently proposed model (imprinting model) with two path-of-transmission (male and female)-specific breeding values for each animal accounts for all types of imprinting simultaneously (paternal, maternal, full and partial)...
December 6, 2016: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/27918542/the-role-of-break-induced-replication-in-large-scale-expansions-of-cag-n-ctg-n-repeats
#4
Jane C Kim, Samantha T Harris, Teresa Dinter, Kartik A Shah, Sergei M Mirkin
Expansions of (CAG)n/(CTG)n trinucleotide repeats are responsible for over a dozen neuromuscular and neurodegenerative disorders. Large-scale expansions are commonly observed in human pedigrees and may be explained by iterative small-scale events such as strand slippage during replication or repair DNA synthesis. Alternatively, a distinct mechanism may lead to a large-scale repeat expansion as a single step. To distinguish between these possibilities, we developed a novel experimental system specifically tuned to analyze large-scale expansions of (CAG)n/(CTG)n repeats in Saccharomyces cerevisiae...
December 5, 2016: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/27917542/genomic-evaluation-of-regional-dairy-cattle-breeds-in-single-breed-and-multibreed-contexts
#5
D Jónás, V Ducrocq, S Fritz, A Baur, M-P Sanchez, P Croiseau
An important prerequisite for high prediction accuracy in genomic prediction is the availability of a large training population, which allows accurate marker effect estimation. This requirement is not fulfilled in case of regional breeds with a limited number of breeding animals. We assessed the efficiency of the current French routine genomic evaluation procedure in four regional breeds (Abondance, Tarentaise, French Simmental and Vosgienne) as well as the potential benefits when the training populations consisting of males and females of these breeds are merged to form a multibreed training population...
December 4, 2016: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/27913617/evaluating-sequence-based-genomic-prediction-with-an-efficient-new-simulator
#6
Miguel Pérez-Enciso, Natalia Forneris, Gustavo de Los Campos, Andrés Legarra
The vast amount of sequence data to analyze complex traits is posing new challenges in terms of analysis and interpretation of the results. Although simulation is a fundamental tool to investigate the reliability of genomic analyses and to optimize experimental design, existing software cannot simulate complete genomes realistically. To remedy this, we have developed a new strategy (Sequence Based Virtual Breeding, SBVB) that consists of using real sequence data and simulating new offspring genomes and phenotypes in a very efficient and flexible manner...
December 2, 2016: Genetics
https://www.readbyqxmd.com/read/27910110/runs-of-homozygosity-current-knowledge-and-applications-in-livestock
#7
REVIEW
E Peripolli, D P Munari, M V G B Silva, A L F Lima, R Irgang, F Baldi
This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping to minimize the inbreeding rate and also helping to expose deleterious variants in the genome...
December 1, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27908293/autosomal-genetic-control-of-human-gene-expression-does-not-differ-across-the-sexes
#8
Irfahan Kassam, Luke Lloyd-Jones, Alexander Holloway, Kerrin S Small, Biao Zeng, Andrew Bakshi, Andres Metspalu, Greg Gibson, Tim D Spector, Tonu Esko, Grant W Montgomery, Joseph E Powell, Jian Yang, Peter M Visscher, Allan F McRae
BACKGROUND: Despite their nearly identical genomes, males and females differ in risk, incidence, prevalence, severity and age-at-onset of many diseases. Sexual dimorphism is also seen in human autosomal gene expression, and has largely been explored by examining the contribution of genotype-by-sex interactions to variation in gene expression. RESULTS: In this study, we use data from a mixture of pedigree and unrelated individuals with verified European ancestry to investigate the sex-specific genetic architecture of gene expression measured in whole blood across n=1048 males and n=1005 females by treating gene expression intensities in the sexes as two distinct traits and estimating the genetic correlation (r G) between them...
December 1, 2016: Genome Biology
https://www.readbyqxmd.com/read/27905875/a-nonsense-mutation-in-the-col7a1-gene-causes-epidermolysis-bullosa-in-vorderwald-cattle
#9
Hubert Pausch, Simon Ammermüller, Christine Wurmser, Henning Hamann, Jens Tetens, Cord Drögemüller, Ruedi Fries
BACKGROUND: The widespread use of individual sires for artificial insemination promotes the propagation of recessive conditions. Inadvertent matings between unnoticed carriers of deleterious alleles may result in the manifestation of fatal phenotypes in their progeny. Breeding consultants and farmers reported on Vorderwald calves with a congenital skin disease. The clinical findings in affected calves were compatible with epidermolysis bullosa. RESULTS: Pedigree analysis indicated autosomal recessive inheritance of epidermolysis bullosa in Vorderwald cattle...
December 1, 2016: BMC Genetics
https://www.readbyqxmd.com/read/27905268/mapt-mutation-associated-with-frontotemporal-dementia-and-parkinsonism-ftdp-17
#10
Robert Haussmann, Marek Wysocki, Moritz D Brandt, Andreas Hermann, Markus Donix
We present a 56-year-old patient suffering from frontotemporal dementia with parkinsonism linked to chromosome 17 (FTDP-17). The history included a three-generation pedigree and the patient was found to be a mutation carrier. The diagnosis was hindered by late appearance of the hypokinetic movement disorder. For clinicians, it is important to consider rare neurodegenerative disease variants in early-onset familial dementia syndromes with behavioral, cognitive, and motor symptoms.
December 1, 2016: International Psychogeriatrics
https://www.readbyqxmd.com/read/27903644/a-reference-data-set-of-5-4-million-phased-human-variants-validated-by-genetic-inheritance-from-sequencing-a-three-generation-17-member-pedigree
#11
Michael A Eberle, Epameinondas Fritzilas, Peter Krusche, Morten Källberg, Benjamin L Moore, Mitchell A Bekritsky, Zamin Iqbal, Han-Yu Chuang, Sean J Humphray, Aaron L Halpern, Semyon Kruglyak, Elliott H Margulies, Gil McVean, David R Bentley
Improvement of variant calling in next-generation sequence data requires a comprehensive, genome-wide catalog of high-confidence variants called in a set of genomes for use as a benchmark. We generated deep, whole-genome sequence data of 17 individuals in a three-generation pedigree and called variants in each genome using a range of currently available algorithms. We used haplotype transmission information to create a phased "Platinum" variant catalog of 4.7 million single-nucleotide variants (SNVs) plus 0...
November 30, 2016: Genome Research
https://www.readbyqxmd.com/read/27903632/genomic-prediction-with-pedigree-and-genotype-%C3%A3-environment-interaction-in-spring-wheat-grown-in-south-and-west-asia-north-africa-and-mexico
#12
Sivakumar Sukumaran, Jose Crossa, Diego Jarquin, Marta Lopes, Mathew P Reynolds
Developing genomic selection (GS) models is an important step in applying GS to accelerate the rate of genetic gain in grain yield in plant breeding. In this study, seven genomic prediction models under two cross-validation scenarios were tested on 287 advanced elite spring wheat lines phenotyped for grain yield (GY), thousand-grain weight (GW), grain number (GN), and thermal time for flowering (TTF) in 18 international environments (year-location combinations) in major wheat producing countries in 2010 and 2011...
November 30, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27902807/improving-genetic-gain-with-genomic-selection-in-autotetraploid-potato
#13
Anthony T Slater, Noel O I Cogan, John W Forster, Benjamin J Hayes, Hans D Daetwyler
Potato ( L.) breeders consider a large number of traits during cultivar development and progress in conventional breeding can be slow. There is accumulating evidence that some of these traits, such as yield, are affected by a large number of genes with small individual effects. Recently, significant efforts have been applied to the development of genomic resources to improve potato breeding, culminating in a draft genome sequence and the identification of a large number of single nucleotide polymorphisms (SNPs)...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27902803/alphasim-software-for-breeding-program-simulation
#14
Anne-Michelle Faux, Gregor Gorjanc, R Chris Gaynor, Mara Battagin, Stefan M Edwards, David L Wilson, Sarah J Hearne, Serap Gonen, John M Hickey
This paper describes AlphaSim, a software package for simulating plant and animal breeding programs. AlphaSim enables the simulation of multiple aspects of breeding programs with a high degree of flexibility. AlphaSim simulates breeding programs in a series of steps: (i) simulate haplotype sequences and pedigree; (ii) drop haplotypes into the base generation of the pedigree and select single-nucleotide polymorphism (SNP) and quantitative trait nucleotide (QTN); (iii) assign QTN effects, calculate genetic values, and simulate phenotypes; (iv) drop haplotypes into the burn-in generations; and (v) perform selection and simulate new generations...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27902800/aghmatrix-r-package-to-construct-relationship-matrices-for-autotetraploid-and-diploid-species-a-blueberry-example
#15
Rodrigo R Amadeu, Catherine Cellon, James W Olmstead, Antonio A F Garcia, Marcio F R Resende, Patricio R Muñoz
Progress in the rate of improvement in autopolyploid species has been limited compared with diploids, mainly because software and methods to apply advanced prediction and selection methodologies in autopolyploids are lacking. The objectives of this research were to (i) develop an R package for autopolyploids to construct the relationship matrix derived from pedigree information that accounts for autopolyploidy and double reduction and (ii) use the package to estimate the level and effect of double reduction in an autotetraploid blueberry breeding population with extensive pedigree information...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27902382/the-genetic-diversity-and-phenotypic-associations-of-feline-caliciviruses-from-cats-in-switzerland
#16
Andrea M Spiri, Julien Thézé, Marina L Meli, Valentino Cattori, Alice Berger, Adolf Steinrigl, Oliver G Pybus, Regina Hofmann-Lehmann, Barbara Willi
Feline calicivirus (FCV) is a common viral pathogen in domestic cats worldwide. The variable regions of the capsid (VP1) gene of FCV have one of the highest recorded rates of molecular evolution. Understanding the genetic diversity and phylogeny of FCV is a prerequisite to exploring the epidemiology and pathogenesis of this virus and to the development of efficacious vaccine strategies. In this study, we undertook a nationwide molecular characterization of FCV using for the first time nearly complete capsid (VP1) gene sequences...
October 7, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27899191/genetic-predisposition-to-endocrine-tumors-diagnosis-surveillance-and-challenges-in-care
#17
REVIEW
Elisabeth Joye Petr, Tobias Else
Endocrine tumor syndromes, eg, multiple endocrine neoplasia types 1 and 2, were among the first recognized hereditary predisposition syndromes to tumor development. Over time, the number of endocrine tumor syndromes has significantly expanded, eg, with the recent inclusion of hereditary paraganglioma syndromes. Associations of non-endocrine tumors with hereditary endocrine tumor syndromes and endocrine tumors with non-classical endocrine tumor syndromes have emerged. These findings have certainly expanded the scope of care, necessitating a multidisciplinary approach by a team of medical professionals and researchers, integrating shared patient decision-making at every step of surveillance, diagnosis, and treatment...
October 2016: Seminars in Oncology
https://www.readbyqxmd.com/read/27898949/modeling-response-to-heat-stress-in-pigs-from-nucleus-and-commercial-farms-in-different-locations-in-the-united-states
#18
B O Fragomeni, D A L Lourenco, S Tsuruta, S Andonov, K Gray, Y Huang, I Misztal
The purpose of this study was to analyze the impact of seasonal losses due to heat stress in different environments and genetic group combinations. Data were available for 2 different swine populations: purebred Duroc animals raised in nucleus farms in Texas and North Carolina and crosses of Duroc and F females (Landrace × Large White) raised in commercial farms in Missouri and North Carolina; pedigrees provided links between animals from different states. Traits included BW at harvest age for purebred animals and HCW for crossbred animals...
November 2016: Journal of Animal Science
https://www.readbyqxmd.com/read/27898866/genomic-analyses-of-tropical-beef-cattle-fertility-based-on-genotyping-pools-of-brahman-cows-with-unknown-pedigree
#19
A Reverter, L R Porto-Neto, M R S Fortes, R McCulloch, R E Lyons, S Moore, D Nicol, J Henshall, S A Lehnert
We introduce an innovative approach to lowering the overall cost of obtaining genomic EBV (GEBV) and encourage their use in commercial extensive herds of Brahman beef cattle. In our approach, the DNA genotyping of cow herds from 2 independent properties was performed using a high-density bovine SNP chip on DNA from pooled blood samples, grouped according to the result of a pregnancy test following their first and second joining opportunities. For the DNA pooling strategy, 15 to 28 blood samples from the same phenotype and contemporary group were allocated to pools...
October 2016: Journal of Animal Science
https://www.readbyqxmd.com/read/27898850/genetic-evaluations-for-growth-heat-tolerance-in-angus-cattle
#20
H L Bradford, B O Fragomeni, J K Bertrand, D A L Lourenco, I Misztal
The objectives were to assess the impact of heat stress and to develop a model for genetic evaluation of growth heat tolerance in Angus cattle. The American Angus Association provided weaning weight (WW) and yearling weight (YW) data, and records from the Upper South region were used because of the hot climatic conditions. Heat stress was characterized by a weaning (yearling) heat load function defined as the mean temperature-humidity index (THI) units greater than 75 (70) for 30 (150) d prior to the weigh date...
October 2016: Journal of Animal Science
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