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https://www.readbyqxmd.com/read/28534081/power-of-pedigree-likelihood-analysis-in-extended-pedigrees-to-classify-rare-variants-of-uncertain-significance-in-cancer-risk-genes
#1
Elisabeth A Rosenthal, John Michael O Ranola, Brian H Shirts
Rare and private variants of uncertain significance (VUS) are routinely identified in clinical panel, exome, and genome sequencing. We investigated the power of single family co-segregation analysis to aid classification of VUS. We simulated thousands of pedigrees using demographics in China and the United States, segregating benign and pathogenic variants. Genotypes and phenotypes were simulated using penetrance models for Lynch syndrome and breast/ovarian cancer. We calculated LOD scores adjusted for proband ascertainment (LODadj), to determine power to yield quantitative evidence for, or against, pathogenicity of the VUS...
May 22, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28534046/genetic-analysis-of-age-at-onset-variation-in-spinocerebellar-ataxia-type-2
#2
K P Figueroa, Hilary Coon, Nieves Santos, Luis Velazquez, Luis Almaguer Mederos, Stefan-M Pulst
OBJECTIVE: To examine heritability of the residual variability of spinocerebellar ataxia type 2 (SCA2) age at onset (AO) after controlling for CAG repeat length. METHODS: From 1955 to 2001, dates of birth, CAG repeat lengths, AO, sex, familial inheritances, and clinical manifestations were collected for a large Cuban SCA2 cohort of 382 affected individuals, including 129 parent-child pairs and 69 sibships. Analyses were performed with log-transformed AO in the GENMOD procedure to predict AO using repeat length, taking into account family structure...
June 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28532469/a-pipeline-combining-multiple-strategies-for-prioritizing-heterozygous-variants-for-the-identification-of-candidate-genes-in-exome-datasets
#3
Teresa Requena, Alvaro Gallego-Martinez, Jose A Lopez-Escamez
BACKGROUND: The identification of disease-causing variants in autosomal dominant diseases using exome-sequencing data remains a difficult task in small pedigrees. We combined several strategies to improve filtering and prioritizing of heterozygous variants using exome-sequencing datasets in familial Meniere disease: an in-house Pathogenic Variant (PAVAR) score, the Variant Annotation Analysis and Search Tool (VAAST-Phevor), Exomiser-v2, CADD, and FATHMM. We also validated the method by a benchmarking procedure including causal mutations in synthetic exome datasets...
May 22, 2017: Human Genomics
https://www.readbyqxmd.com/read/28527809/accuracy-of-genomic-predictions-in-gyr-bos-indicus-dairy-cattle
#4
S A Boison, A T H Utsunomiya, D J A Santos, H H R Neves, R Carvalheiro, G Mészáros, Y T Utsunomiya, A S do Carmo, R S Verneque, M A Machado, J C C Panetto, J F Garcia, J Sölkner, M V G B da Silva
Genomic selection may accelerate genetic progress in breeding programs of indicine breeds when compared with traditional selection methods. We present results of genomic predictions in Gyr (Bos indicus) dairy cattle of Brazil for milk yield (MY), fat yield (FY), protein yield (PY), and age at first calving using information from bulls and cows. Four different single nucleotide polymorphism (SNP) chips were studied. Additionally, the effect of the use of imputed data on genomic prediction accuracy was studied...
May 17, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28526729/phased-genotyping-by-sequencing-enhances-analysis-of-genetic-diversity-and-reveals-divergent-copy-number-variants-in-maize
#5
Heather Manching, Subhajit Sengupta, Keith R Hopper, Shawn W Polson, Yuan Ji, Randall J Wisser
High-throughput sequencing of reduced representation genomic libraries has ushered in an era of genotyping-by-sequencing (GBS), where genome-wide genotype data can be obtained for nearly any species. However, there remains a need for imputation-free GBS methods for genotyping large samples taken from heterogeneous populations of heterozygous individuals. This requires a number of issues encountered with GBS be considered, including the sequencing of non-overlapping sets of loci across multiple GBS libraries, a common missing data problem that results in low call rates for markers per individual, and a tendency for applicability only in inbred line samples with sufficient linkage disequilibrium for accurate imputation...
May 19, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28525987/genetic-correlation-of-the-plasma-lipidome-with-type-2-diabetes-prediabetes-and-insulin-resistance-in-mexican-american-families
#6
Hemant Kulkarni, Manju Mamtani, Gerard Wong, Jacquelyn M Weir, Christopher K Barlow, Thomas D Dyer, Laura Almasy, Michael C Mahaney, Anthony G Comuzzie, Ravindranath Duggirala, Peter J Meikle, John Blangero, Joanne E Curran
BACKGROUND: Differential plasma concentrations of circulating lipid species are associated with pathogenesis of type 2 diabetes (T2D). Whether the wide inter-individual variability in the plasma lipidome contributes to the genetic basis of T2D is unknown. Here, we investigated the potential overlap in the genetic basis of the plasma lipidome and T2D-related traits. RESULTS: We used plasma lipidomic data (1202 pedigreed individuals, 319 lipid species representing 23 lipid classes) from San Antonio Family Heart Study in Mexican Americans...
May 19, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28521728/a-method-for-the-allocation-of-sequencing-resources-in-genotyped-livestock-populations
#7
Serap Gonen, Roger Ros-Freixedes, Mara Battagin, Gregor Gorjanc, John M Hickey
BACKGROUND: This paper describes a method, called AlphaSeqOpt, for the allocation of sequencing resources in livestock populations with existing phased genomic data to maximise the ability to phase and impute sequenced haplotypes into the whole population. METHODS: We present two algorithms. The first selects focal individuals that collectively represent the maximum possible portion of the haplotype diversity in the population. The second allocates a fixed sequencing budget among the families of focal individuals to enable phasing of their haplotypes at the sequence level...
May 18, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28521058/enhanced-expression-of-proteins-involved-in-energy-production-and-transfer-in-breast-muscle-of-pedigree-male-broilers-exhibiting-high-feed-efficiency
#8
W G Bottje, K Lassiter, S Dridi, N Hudson, B-W Kong
In cells with fluctuating energy demand (e.g., skeletal muscle), a transfer system of proteins across the inner and outer mitochondrial membranes links mitochondrial oxidative phosphorylation to cytosolic phosphorylated creatine (PCr) that serves as a phosphate reservoir for rapid repletion of cytosolic adenosine triphosphate (ATP). Crucial proteins of this energy transfer system include several creatine kinase (CK) isoforms found in the cytosol and mitochondria. In a recent proteomic study (Kong et al., 2016), several components of this system were up-regulated in high feed efficiency (FE) compared to low FE breast muscle; notably adenine nucleotide translocase (ANT), voltage dependent activated channel (VDAC), the brain isoform of creatine kinase (CK-B), and several proteins of the electron transport chain...
May 17, 2017: Poultry Science
https://www.readbyqxmd.com/read/28520805/identification-of-key-contributors-in-complex-population-structures
#9
Markus Neuditschko, Herman W Raadsma, Mehar S Khatkar, Elisabeth Jonas, Eike J Steinig, Christine Flury, Heidi Signer-Hasler, Mirjam Frischknecht, Ruedi von Niederhäusern, Tosso Leeb, Stefan Rieder
Evaluating the genetic contribution of individuals to population structure is essential to select informative individuals for genome sequencing, genotype imputation and to ascertain complex population structures. Existing methods for the selection of informative individuals for genomic imputation solely focus on the identification of key ancestors, which can lead to a loss of phasing accuracy of the reference population. Currently many methods are independently applied to investigate complex population structures...
2017: PloS One
https://www.readbyqxmd.com/read/28513615/exome-sequencing-of-two-italian-pedigrees-with-non-isolated-chiari-malformation-type-i-reveals-candidate-genes-for-cranio-facial-development
#10
Elisa Merello, Lorenzo Tattini, Alberto Magi, Andrea Accogli, Gianluca Piatelli, Marco Pavanello, Domenico Tortora, Armando Cama, Zoha Kibar, Valeria Capra, Patrizia De Marco
Chiari malformation type I (CMI) is a congenital abnormality of the cranio-cerebral junction with an estimated incidence of 1 in 1280. CMI is characterized by underdevelopment of the occipital bone and posterior fossa (PF) and consequent cerebellar tonsil herniation. The presence for a genetic basis to CMI is supported by many lines of evidence. The cellular and molecular mechanisms leading to CM1 are poorly understood. The occipital bone formation is dependent on complex interactions between genes and molecules with pathologies resulting from disruption of this delicate process...
May 17, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28513614/recurrent-somatic-jak-stat-pathway-variants-within-a-runx1-mutated-pedigree
#11
Kiran Tawana, Jun Wang, Péter A Király, Krisztián Kállay, Gábor Benyó, Marianna Zombori, Judit Csomor, Ahad Al Seraihi, Ana Rio-Machin, András Matolcsy, Claude Chelala, Jamie Cavenagh, Jude Fitzgibbon, Csaba Bödör
Germline variants within the transcription factor RUNX1 are associated with familial platelet disorder and acute leukemia in over 40% of carriers. At present, the somatic events triggering leukemic transformation appear heterogeneous and profiles of leukemia initiation across family members are poorly defined. We report a new RUNX1 family where three sisters harboring a germline nonsense RUNX1 variant, c.601C>T (p.(Arg201*)), developed acute myelomonocytic leukemia (AML) at 5 years of age. Whole-exome sequencing of tumor samples revealed all three siblings independently acquired variants within the JAK-STAT pathway, specifically targeting JAK2 and SH2B3 (a negative regulator of JAK2), while also sharing the 46/1 haplotype linked with sporadic JAK2-positive myeloproliferative neoplasms...
May 17, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28508489/prediction-of-whole-genome-risk-for-selection-and-management-of-hyperketonemia-in-holstein-dairy-cattle
#12
K A Weigel, R S Pralle, H Adams, K Cho, C Do, H M White
Hyperketonemia (HYK), a common early postpartum health disorder characterized by elevated blood concentrations of β-hydroxybutyrate (BHB), affects millions of dairy cows worldwide and leads to significant economic losses and animal welfare concerns. In this study, blood concentrations of BHB were assessed for 1,453 Holstein cows using electronic handheld meters at four time points between 5 and 18 days postpartum. Incidence rates of subclinical (1.2 ≤ maximum BHB ≤ 2.9 mmol/L) and clinical ketosis (maximum BHB ≥ 3...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508486/pedigree-based-estimation-of-covariance-between-dominance-deviations-and-additive-genetic-effects-in-closed-rabbit-lines-considering-inbreeding-and-using-a-computationally-simpler-equivalent-model
#13
E N Fernández, A Legarra, R Martínez, J P Sánchez, M Baselga
Inbreeding generates covariances between additive and dominance effects (breeding values and dominance deviations). In this work, we developed and applied models for estimation of dominance and additive genetic variances and their covariance, a model that we call "full dominance," from pedigree and phenotypic data. Estimates with this model such as presented here are very scarce both in livestock and in wild genetics. First, we estimated pedigree-based condensed probabilities of identity using recursion. Second, we developed an equivalent linear model in which variance components can be estimated using closed-form algorithms such as REML or Gibbs sampling and existing software...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508482/solving-efficiently-large-single-step-genomic-best-linear-unbiased-prediction-models
#14
I Strandén, K Matilainen, G P Aamand, E A Mäntysaari
Single-step genomic BLUP (ssGBLUP) requires a dense matrix of the size equal to the number of genotyped animals in the coefficient matrix of mixed model equations (MME). When the number of genotyped animals is high, solving time of MME will be dominated by this matrix. The matrix is the difference of two inverse relationship matrices: genomic (G) and pedigree (A22 ). Different approaches were used to ease computations, reduce computing time and improve numerical stability. Inverse of A22 can be computed as A22-1=A22-A21A11-1A12 where A(ij) , i, j = 1,2, are sparse sub-matrices of A(-1) , and numbers 1 and 2 refer to non-genotyped and genotyped animals, respectively...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508481/a-comparison-of-identity-by-descent-and-identity-by-state-matrices-that-are-used-for-genetic-evaluation-and-estimation-of-variance-components
#15
R L Fernando, H Cheng, X Sun, D J Garrick
The genetic covariance matrix conditional on pedigree is proportional to the pedigree-based additive relationship matrix (PARM), which is twice the matrix of identity-by-descent (IBD) probabilities. In genomic prediction, IBD probabilities in the PARM, which are expected genetic similarities between relatives that are derived from the pedigree, are substituted by realized similarities that are derived from genotypes to obtain a genomic additive relationship matrix (GARM). Different definitions of similarity lead to different GARMs, and two commonly used GARMS are the matrix G, which is based on an allele substitution effect model, and the matrix T, which is based on an allele effect model...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508480/beyond-genomic-selection-the-animal-model-strikes-back-one-generation
#16
R J C Cantet, C A García-Baccino, A Rogberg-Muñoz, N S Forneris, S Munilla
Genome inheritance is by segments of DNA rather than by independent loci. We introduce the ancestral regression (AR) as a recursive system of simultaneous equations, with grandparental path coefficients as novel parameters. The information given by the pedigree in the AR is complementary with that provided by a dense set of genomic markers, such that the resulting linear function of grandparental BV is uncorrelated to the average of parental BV in the absence of inbreeding. AR is then connected to segmental inheritance by a causal multivariate Gaussian density for BV...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508084/clinicopathologic-and-molecular-spectrum-of-rnaseh1-related-mitochondrial-disease
#17
Enrico Bugiardini, Olivia V Poole, Andreea Manole, Alan M Pittman, Alejandro Horga, Iain Hargreaves, Cathy E Woodward, Mary G Sweeney, Janice L Holton, Jan-Willem Taanman, Gordon T Plant, Joanna Poulton, Massimo Zeviani, Daniele Ghezzi, John Taylor, Conrad Smith, Carl Fratter, Meena A Kanikannan, Arumugam Paramasivam, Kumarasamy Thangaraj, Antonella Spinazzola, Ian J Holt, Henry Houlden, Michael G Hanna, Robert D S Pitceathly
OBJECTIVE: Pathologic ribonuclease H1 (RNase H1) causes aberrant mitochondrial DNA (mtDNA) segregation and is associated with multiple mtDNA deletions. We aimed to determine the prevalence of RNase H1 gene (RNASEH1) mutations among patients with mitochondrial disease and establish clinically meaningful genotype-phenotype correlations. METHODS: RNASEH1 was analyzed in patients with (1) multiple deletions/depletion of muscle mtDNA and (2) mendelian progressive external ophthalmoplegia (PEO) with neuropathologic evidence of mitochondrial dysfunction, but no detectable multiple deletions/depletion of muscle mtDNA...
June 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28507388/congenital-nuclear-cataracts-in-a-holstein-dairy-herd
#18
Stephanie Osinchuk, Lyall Petrie, Marina Leis, Fritz Schumann, Bianca Bauer, Lynne Sandmeyer, Kayla Madder, Fiona Buchanan, Bruce Grahn
This report describes congenital nuclear cataracts and posterior lenticonus in a closed purebred Holstein dairy herd in Canada. Ophthalmic examinations were completed on 30 male and 249 female cattle aged newborn to 10 years old. Nutritional, infectious, and toxic etiologies were investigated. Necropsies of 3 affected calves were performed and eyes of 2 additional affected calves were examined with light microscopy. Bilateral nuclear cataracts were identified in 53/279 (19%) animals. Additional congenital anomalies observed included posterior lenticonus, iris to lens persistent pupillary membranes (n = 7), and lenticular colobomata (n = 1)...
May 2017: Canadian Veterinary Journal. la Revue Vétérinaire Canadienne
https://www.readbyqxmd.com/read/28507329/breeding-histories-and-selection-criteria-for-oilseed-rape-in-europe-and-china-identified-by-genome-wide-pedigree-dissection
#19
Xiaohua Wang, Yan Long, Nian Wang, Jun Zou, Guangda Ding, Martin R Broadley, Philip J White, Pan Yuan, Qianwen Zhang, Ziliang Luo, Peifa Liu, Hua Zhao, Ying Zhang, Hongmei Cai, Graham J King, Fangsen Xu, Jinling Meng, Lei Shi
Selection breeding has played a key role in the improvement of seed yield and quality in oilseed rape (Brassica napus L.). We genotyped Tapidor (European), Ningyou7 (Chinese) and their progenitors with the Brassica 60 K Illumina Infinium SNP array and mapped a total of 29,347 SNP markers onto the reference genome of Darmor-bzh. Identity by descent (IBD) refers to a haplotype segment of a chromosome inherited from a shared common ancestor. IBDs identified on the C subgenome were larger than those on the A subgenome within both the Tapidor and Ningyou7 pedigrees...
May 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28506960/familial-analysis-of-epistatic-and-sex-dependent-association-of-genes-of-the-renin-angiotensin-aldosterone-system-and-blood-pressure
#20
Katrina J Scurrah, Angela Lamantia, Justine A Ellis, Stephen B Harrap
BACKGROUND: Renin-angiotensin-aldosterone system genes have been inconsistently associated with blood pressure, possibly because of unrecognized influences of sex-dependent genetic effects or gene-gene interactions (epistasis). METHODS AND RESULTS: We tested association of systolic blood pressure with single-nucleotide polymorphisms (SNPs) at renin (REN), angiotensinogen (AGT), angiotensin-converting enzyme (ACE), angiotensin II type 1 receptor (AGTR1), and aldosterone synthase (CYP11B2), including sex-SNP or SNP-SNP interactions...
June 2017: Circulation. Cardiovascular Genetics
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