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92 results for “pedigree”
Dataset of Pedigree, genotypes, clinical and biochemical characteristics of families of Northeastern Mexico
<p>This dataset combines pedigree, genotypes, clinical and biochemical data of 37 families of Northeastern Mexico. Primary reference is the article:</p> <p>Gallardo‑Blanco, H.L., Villarreal‑Perez, J.Z., Cerda‑Flores, R.M., Figueroa, A., Sanchez‑Dominguez, C.N., Gutierrez‑Valverde, J.M. ... Martinez‑Garza, L.E. (2017). Genetic variants in KCNJ11, TCF7L2 and HNF4A are associated with type 2 diabetes, BMI and dyslipidemia in families of Northeastern Mexico: A pilot study. Experimental and Therapeutic Medicine, 13, 523-529. https://doi.org/10.3892/etm.2016.3990</p> <p><strong>If you use these data please cite the corresponding manuscript, which can be downloaded here:</strong></p> <p>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5348709/</p> <p>https://www.spandidos-publications.com/10.3892/etm.2016.3990</p> <p>This dataset contains genotypes for the following SNPs:</p> <p>rs2986742</p> <p>rs4846051</p> <p>rs1801131</p> <p>rs1801133</p> <p>rs6541030</p> <p>rs12130799</p> <p>rs11208654</p> <p>rs1137100</p> <p>rs12405556</p> <p>rs3118378</p> <p>rs3737576</p> <p>rs10923931</p> <p>rs7554936</p> <p>rs3737787</p> <p>rs2516839</p> <p>rs1040404</p> <p>rs4670767</p> <p>rs7578597</p> <p>rs13400937</p> <p>rs10496971</p> <p>rs2627037</p> <p>rs1801262</p> <p>rs1569175</p> <p>rs2975760</p> <p>rs3792267</p> <p>rs10510228</p> <p>rs1801282</p> <p>rs3856806</p> <p>rs4955316</p> <p>rs9809104</p> <p>rs4607103</p> <p>rs6548616</p> <p>rs734873</p> <p>rs5400</p> <p>rs2030763</p> <p>rs4402960</p> <p>rs1513181</p> <p>rs9291090</p> <p>rs10010131</p> <p>rs10007810</p> <p>rs385194</p> <p>rs1799883</p> <p>rs2504853</p> <p>rs7754840</p> <p>rs7745461</p> <p>rs1800750</p> <p>rs1800629</p> <p>rs361525</p> <p>rs12200998</p> <p>rs2397060</p> <p>rs192655</p> <p>rs1044498</p> <p>rs4463276</p> <p>rs731257</p> <p>rs864745</p> <p>rs32314</p> <p>rs2330442</p> <p>rs4717865</p> <p>rs3173798</p> <p>rs10954737</p> <p>rs854555</p> <p>rs3917542</p> <p>rs662</p> <p>rs705308</p> <p>rs3943253</p> <p>rs751141</p> <p>rs1471939</p> <p>rs12544346</p> <p>rs13266634</p> <p>rs7844723</p> <p>rs2242103</p> <p>rs1408801</p> <p>rs10811661</p> <p>rs10511828</p> <p>rs12779790</p> <p>rs3793791</p> <p>rs4746136</p> <p>rs1111875</p> <p>rs10885390</p> <p>rs11196175</p> <p>rs7903146</p> <p>rs10885406</p> <p>rs12255372</p> <p>rs290487</p> <p>rs4918842</p> <p>rs2237892</p> <p>rs10839880</p> <p>rs1837606</p> <p>rs5210</p> <p>rs5218</p> <p>rs5219</p> <p>rs2946788</p> <p>rs11227699</p> <p>rs7930460</p> <p>rs1800849</p> <p>rs1387153</p> <p>rs948028</p> <p>rs2270031</p> <p>rs2416791</p> <p>rs7961581</p> <p>rs2070586</p> <p>rs1503767</p> <p>rs2269793</p> <p>rs8050136</p> <p>rs818386</p> <p>rs2966849</p> <p>rs1879488</p> <p>rs757210</p> <p>rs2033111</p> <p>rs11652805</p> <p>rs10512572</p> <p>rs2125345</p> <p>rs12946618</p> <p>rs12946115</p> <p>rs12950541</p> <p>rs1885088</p> <p>rs3907047</p> <p>rs2071023</p> <p>rs2833479</p> <p>rs2833483</p> <p>rs2300386</p> <p>rs2835370</p> <p>rs1296819</p> <p>rs1892848</p> <p>rs4821004</p> <p> </p>
Forward selection in a maritime pine polycross progeny trial using pedigree reconstruction.
<p>These two excel files gather genotyping data used in the following publication:</p> <p>Vidal M, Plomion C, Raffin A, Harvengt L, Bouffier L (2017) Forward selection in a maritime pine polycross progeny trial using pedigree reconstruction. Annals of Forest Science, 74(1). DOI 10.1007/s13595-016-0596-8</p> <p>The dataset describes genotyping profiles (with 56 or 63 SNPs) for the G1 and G2 individuals sampled in this paper. For each individual, the following information is mentioned: identity, preselection option (only for G2 individuals), the generation to which the individual belongs, pedigree (only for G2 individuals), alleles for each SNP.</p>
Complex basis of hybrid female sterility and Haldane's rule in Heliconius butterflies: Z-linkage and epistasis - RADseq and RNAseq reads, sterility phenotypes and pedigree
<p>RADseq and RNAseq reads (.fastq files), and sterility phenotypes and pedigree (.xlsx) using for QTL mapping of Heliconius pardalinus sterility crosses in Rosser, N., Edelman, N.B., Queste, L.M., Nelson, M., Seixas, F., Dasmahapatra, K.K. and Mallet, J., 2021. Complex basis of hybrid female sterility and Haldane’s rule in Heliconius butterflies: Z-linkage and epistasis, accepted for publication in Molecular Ecology. Queries to Neil Rosser (neil.rosser@york.ac.uk). </p> <p> </p>
Dataset related to article "Molecular Studies and ex vivo Complement assay on Endothelium Highlight the Genetic Complexity of Atypical Hemolytic Uremic Syndrome: The Case of a Pedigree With a Null CD46 Variant".
<p><em>The files contain raw data related to the article "Molecular Studies and ex vivo Complement assay on Endothelium Highlight the Genetic Complexity of Atypical Hemolytic Uremic Syndrome: The Case of a Pedigree With a Null CD46 Variant", available from <a href="https://www.frontiersin.org/articles/10.3389/fmed.2020.579418/full">https://www.frontiersin.org/articles/10.3389/fmed.2020.579418/ful</a>l.</em></p> <p>File <strong>"Genetic and clinical data"</strong>:</p> <ul> <li>In the sheet "485 aHUS patients" are reported data obtained from the screening of 485 unrelated patients with aHUS including rare variants (RVs) in complement disease-associated genes (<em>CFH, CD46, CFI, C3, CFB </em>and <em>THBD</em>), the presence of <em>CFH-CFHR</em> genomic rearrangements and/or anti-FH antibodies.</li> <li>In the sheet "Pedigrees with c.286+2T>G" are listed all pedigrees carrying the c.286+2T>G variant, the diseases status of all subjects and the age of disease onset of patients. In bold are indicated pedigrees (n=7) used to study the penetrance of aHUS in c.286+2T>G carriers.</li> <li>In the sheet "Haplotypes" are reported genotypes used to evaluate the association between the presence of <em>CFH-H3</em> and <em>CD46<sub>GGAAC</sub></em> risk haplotypes and aHUS. Results of this analysis are reported in Table 3 of the published paper.</li> <li>In the sheet "Raw data Fig.2" are reported data of "platelet count" and "serum creatinine" of the proband used to elaborate Figure 2.</li> </ul> <p>In the file <strong>"C3 and C5b-9 deposition"</strong> is reported the quantification of serum-induced C3 and C5b-9 deposition on human microvascular endothelial cell line (HMEC-1). The fluorescent staining was evaluated with Image J and expressed as pixel<sup>2 </sup>per field analyzed. The fields with the lowest and highest values were excluded from calculation. These values were used to elaborate data included in Table 2 and in Figure 5.</p> <p>In the file <strong>"CD46 protein expression"</strong> are reported data of CD46 expression on peripheral blood mononuclear cells (PBMCs) isolated from the proband, his relatives and healthy volunteers. Data of specific expression of CD46 (evaluated for SCR1 or for SCR4 as reported in the materials and methods section) are indicated as median fluorescence intensity (MFI) percentage compared with the control.</p> <p>In the ppt file <strong>"cDNA amplification and sequencing results"</strong> is reported:</p> <ul> <li>the agarose gel image of the amplified cDNA from the control (ctr), the proband (IV-8) and his healthy father (III-7).</li> <li>Electropherograms obtained from the cDNA sequencing of the control (ctr), the proband (IV-8) and his healthy father (III-7).</li> </ul> <p>Additional data will be made available by the authors, without undue reservation, to any qualified researcher. </p>
Data from: Genetic, maternal, and environmental influences on sociality in a pedigreed primate population
<p>Various aspects of sociality in mammals (e.g., dyadic connectedness) are linked with measures of biological fitness (e.g., longevity). How within- and between-individual variation in relevant social traits arises in uncontrolled wild populations is challenging to determine but is crucial for understanding constraints on the evolution of sociality. We use an advanced statistical method, known as the 'animal model', which incorporates pedigree information, to look at social, genetic, and environmental influences on sociality in a long-lived wild primate. We leverage a longitudinal database spanning 20 years of observation on individually recognized white-faced capuchin monkeys (Cebus capucinus imitator), with a multi-generational pedigree. We analyze two measures of spatial association, using repeat sampling of 376 individuals (mean: 53.5 months per subject, range: 6-185 months per subject). Conditioned on the effects of age, sex, group size, seasonality , and El Niño–Southern Oscillation phases, we show low to moderate long-term repeatability (across years) of the proportion of time spent social (posterior mode [95% Highest Posterior Density interval]: 0.207 [0.169, 0.265]) and of average number of partners (0.144 [0.113, 0.181]) (latent scale). Most of this long-term repeatability could be explained by modest heritability (<em>h<sup>2</sup></em><sub>social</sub>: 0.152 [0.094, 0.207]; <em>h<sup>2</sup></em><sub>partners</sub>: 0.113 [0.076, 0.149]) with small long-term maternal effects (<em>m<sup>2</sup></em><sub>social</sub>: 0.000 [0.000, 0.045]; <em>m<sup>2</sup></em><sub>partners</sub>: 0.000 [0.000, 0.041]). Our models capture the majority of variance in our behavioral traits, with much of the variance explained by temporally changing factors, such as group of residence, highlighting potential limits to the evolvability of our trait due to social and environmental constraints.</p>
Comparison and Assessment of Family- and Population-based Genotype Imputation Methods in Large Pedigrees Dataset
<p>Here is the data corresponding to the paper "Comparison and Assessment of Family- and Population-based Genotype Imputation Methods in Large Pedigrees" submitted to Genome Research. The data includes the following:<br> <br> Simulated data for 1200 African and European subjects in pedigrees.<br> Lists of subjects selected by each of the 4 subject selection methods examined; Primus, GIGI-Pick, Exome-Picks, and Random selection. <br> <br> The positions of sparse markers for gl_auto for African and European data.<br> <br> The lists of GWAS SNPs for AFR and EUR. </p> <p>Please see the paper for further details of the data generation, this metadata will be updated following publication. </p>
Data from: Dispersal in a house sparrow metapopulation: an integrative case study of genetic assignment calibrated with ecological data and pedigree information
<p class="western">Dispersal has a crucial role determining eco-evolutionary dynamics through both gene flow and population size regulation. However, to study dispersal and its consequences, one must distinguish immigrants from residents. Dispersers can be identified using telemetry, capture-mark-recapture (CMR) methods, or genetic assignment methods. All of these methods have disadvantages, such as, high costs and substantial field efforts needed for telemetry and CMR surveys, and adequate genetic distance required in genetic assignment. In this study, we used genome-wide 200K Single Nucleotide Polymorphism data and two different genetic assignment approaches (GSI_SIM, Bayesian framework; BONE, network-based estimation) to identify the dispersers in a house sparrow (<i>Passer domesticus</i>) metapopulation sampled over 16 years. Our results showed higher assignment accuracy with BONE. Hence, we proceeded to diagnose potential sources of errors in the assignment results from the BONE method due to variation in levels of inter-population genetic differentiation, intra-population genetic variation and sample size. We show that assignment accuracy is high even at low levels of genetic differentiation and that it increases with the proportion of a population that has been sampled. Finally, we highlight that dispersal studies integrating both ecological and genetic data provide robust assessments of the dispersal patterns in natural populations.</p>
Variance components of sex determination in the copepod Tigriopus californicus estimated from a pedigree analysis
<p>Extensive theory exists regarding population sex ratio evolution that predicts equal sex ratio (when parental investment is equal). In most animals, sex chromosomes determine the sex of offspring, and this fixed genotype for sex has made theory difficult to test since genotypic variance for the trait (sex) is lacking. It has long been argued that the genotype has become fixed in most animals due to the strong selection for equal sex ratios. The marine copepod <em>Tigriopus californicus</em> has no sex chromosomes, multiple genes affecting female brood sex ratio and a brood sex ratio that responds to selection. The species thus provides an opportune system in which to test established sex ratio theory. In this paper, we further our exploration of polygenic sex determination in <em>T. californicus</em> using an incomplete diallel crossing design for analysis of the variance components of sex determination in the species. Our data confirm the presence of extra-binomial variance for sex, further confirming that sex is not determined through simple Mendelian trait inheritance. In addition, our crosses and backcrosses of isofemale lines selected for biased brood sex ratios show intermediate phenotypic means, as expected if sex is a threshold trait determined by an underlying "liability" trait controlled by many genes of small effects. Furthermore, crosses between families from the same selection line had similar increases in phenotypic variance as crosses between families from different selection lines, suggesting families from artificial selection lines responded to selection pressure through different underlying genetic bases. Finally, we estimate heritability of an individual to be male or female on the observed binary scale as 0.09 (95% CI: 0.034-0.14). This work furthers our accumulating evidence for polygenic sex determination in <em>T. californicus</em> laying the foundation for this as a model species in future studies of sex ratio evolution theory.</p>
Data from: Genetic, maternal, and environmental influences on sociality in a pedigreed primate population
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Variance components of sex determination in the copepod Tigriopus californicus estimated from a pedigree analysis
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Data from: Dispersal in a house sparrow metapopulation: an integrative case study of genetic assignment calibrated with ecological data and pedigree information
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RecView: An interactive R application for locating recombination positions using pedigree data
<p><span>We present <em>RecView</em>, an interactive R application and </span><span>its homonymous R package</span><span>, to facilitate locating recombination positions along chromosomes or scaffolds using whole-genome genotype data of a three-generation pedigree. </span><span>We demonstrate applicability of <em>RecView </em>using the genotype data from two offspring, as well as their grandparents and parents, of the great reed warbler (<em>Acrocephalus arundinaceus</em>).</span></p>
Comparing genome-based estimates of relatedness for use in pedigree-based conservation management
<p>Researchers have long debated which estimator of relatedness best captures the degree of relationship between two individuals. In the genomics era, this debate continues, with relatedness estimates being sensitive to the methods used to generate markers, marker quality, and levels of diversity in sampled individuals. Here, we compare six commonly used genome-based relatedness estimators (kinship genetic distance (KGD), Wang Maximum Likelihood (TrioML), Queller and Goodnight (Rxy), Kinship INference for Genome-wide association studies (KING-robust), and Pairwise Relatedness (RAB), allele-sharing co-ancestry (AS)) across five species bred in captivity–including three birds and two mammals–with varying degrees of reliable pedigree data, using reduced-representation and whole genome resequencing data. Genome-based relatedness estimates varied widely across estimators, sequencing methods, and species, yet the most consistent results for known first order relationships were found using Rxy, RAB, and AS. However, AS was found to be less consistently correlated with known pedigree relatedness than either Rxy or RAB. Our combined results indicate there is not a single genome-based estimator that is ideal across different species and data types. To determine the most appropriate genome-based relatedness estimator for each new dataset, we recommend assessing the relative: (1) correlation of candidate estimators with known relationships in the pedigree and (2) precision of candidate estimators with known first-order relationships. These recommendations are broadly applicable to conservation breeding programs, particularly where genome-based estimates of relatedness can complement and complete poorly pedigreed populations. Given a growing interest in the application of wild pedigrees, our results are also applicable to in-situ wildlife management.</p>
Pedigree
<p>Pedigree illustration for a total of 6 generations with autosomal dominant inherited <em>REN</em> associated disease (c.45_47delGCT, p.Leu16del). Circles represent female family members, squares male family members. The clinical phenotype is indicated by the different coloring: cyan indicates the presence of chronic kidney disease, grey indicates the presence of hyperuricemia and gout, blue indicates the presence of renal cysts. Symbols with a question mark denote individuals with an unknown clinical status. mt/wt depicts the presence of heterozygous <em>REN</em> variant c.45_57delGCT leading to deletion of leucin at amino acid position 16 at the signal peptide of renin. <em>REN</em> wt/wt describes the presence of wildtype renin. <em>Abbreviations</em>: mt, mutant; wt wildtype. </p>
Estimation of breeding population size using DNA-based pedigree reconstruction in brown bears
Robust estimates of demographic parameters are critical for effective wildlife conservation and management, but are difficult to obtain for elusive species. We estimated the breeding and adult population sizes, as well as the minimum population size, in a high-density brown bear population on the Shiretoko Peninsula, in Hokkaido, Japan, using DNA-based pedigree reconstruction. A total of 1,288 individuals, collected in and around the Shiretoko Peninsula between 1998 and 2020, were genotyped at 21 microsatellite loci. Among them, 499 individuals were identified by intensive genetic sampling conducted in two consecutive years (2019 and 2020) mainly by noninvasive methods (e.g., hair and fecal DNA). Among them, both parents were assigned for 330 bears, and either maternity or paternity was assigned to 47 and 76 individuals, respectively. The subsequent pedigree reconstruction indicated a range of breeding and adult (≥4 years old) population sizes: 128–173 for female breeders and 66–91 male breeders, and 155–200 for female adults and 84–109 male adults. The minimum population size was estimated to be 449 (252 females and 197 males) in 2019. Long-term continuous genetic sampling prior to a short-term intensive survey would enable parentage to be identified in a population with a high probability, thus enabling reliable estimates of breeding population size for elusive species. --
Data files for Rivollat et al "Extensive pedigrees reveal the social organisation of a Neolithic community"
<p>Supporting data for Rivollat et al "Extensive pedigrees reveal social organisation of Neolithic communities" <em>Nature</em> (2023). https://doi.org/10.1038/s41586-023-06350-8</p> <p>Binomial_distribution_plots.zip > 4371 files</p> <p>IBD_degrees.zip > 11 files</p> <p>Strontium_individual_files.zip > 56 files</p>
Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur
<p>Mutations are the raw material on which evolution acts, and knowledge of their frequency and genomic distribution is crucial for understanding how evolution operates at both long and short timescales. At present, the rate and spectrum of <i>de novo</i> mutations have been directly characterized in relatively few lineages. Our study provides the first direct mutation rate estimate for a strepsirrhine (i.e., the lemurs and lorises), which comprise nearly half of the primate clade. Using high-coverage linked-read sequencing for a focal quartet of gray mouse lemurs (<i>Microcebus</i> <i>murinus</i>), we estimated the mutation rate to be 1.52 × 10<sup>–8</sup> (95% credible interval: 1.28 × 10<sup>−8</sup> to 1.78 × 10<sup>−8</sup>) mutations/site/generation, a rate among the highest calculated for a mammal. Further, we found an unexpectedly low count of paternal mutations, and only a modest overrepresentation of mutations at CpG-sites. Despite the surprising nature of these results, we found both the rate and spectrum to be robust to the manipulation of a wide range of computational filtering criteria. We also sequenced a technical replicate to estimate a false negative and false positive rate for our data and show that any point estimate of a <i>de novo </i>mutation rate should be considered with a large degree of uncertainty. To validate these observations, we conducted an independent analysis of context-dependent substitution types for gray mouse lemur and five additional primate species for which <i>de novo</i> mutation rates have also been estimated. These comparisons revealed general consistency of the mutation spectrum between the pedigree-based and the substitution rate analyses for all species compared.</p>
Philosophy [IO Bijapur 1b] Glosses and spiritual pedigree
<ul> <li><strong>Philosophy.</strong></li> <li><strong>This manuscript is now IO Bijapur 1B </strong><strong>in the India Office collections.</strong></li> <li><strong>[metadata:</strong><a href="https://de.wikipedia.org/wiki/Otto_Loth"> <strong>Otto Loth, </strong></a><strong><em><a href="http://doi.org/10.5281/zenodo.3923636">A Catalogue of the Arabic Manuscripts in the Library of the India Office</a></em>, (volume 1), no. 591 here with further notations and hyperlinks]</strong>.</li> </ul> <p><a href="https://archive.org/details/catalogueofarabi01greauoft/page/162/mode/2up"><strong>591</strong></a>.</p> <p>B 1b. Size 9<sup>1/2</sup> in. by 6 in.; foll. 56. Seventeen lines in a page.</p> <p><strong>I. Foll. 1-51</strong>. A fragment of Glosses on logical treatise, imperfect at the beginning.</p> <p><strong>II. Foll. 53-56</strong>. A spiritual pedigree, inscribed طريقه مصافحه سعيديه , <em>Persian</em>. Dated 13th Jum. II., 959.</p> <p>[Bijapur Collection]</p> <p> </p>
Wild pedigrees inform mutation rates and historic abundance in baleen whales
<p>Phylogeny-based estimates suggesting a low germline mutation rate (<em>μ</em>) in baleen whales have influenced research ranging from assessments of whaling impacts to evolutionary cancer biology. We estimated <em>μ</em> directly from pedigrees in four baleen whale species for both the mitochondrial control region and nuclear genome. The results suggest values higher than those obtained through phylogeny-based estimates and similar to pedigree-based values for primates and toothed whales. Applying our estimate of <em>μ</em> reduces previous genetic–based estimates of pre-exploitation whale abundance by 86% and suggests that <em>μ</em> cannot explain low cancer rates in gigantic mammals. Our study shows that it is feasible to estimate <em>μ</em> directly from pedigrees in natural populations, with wide-ranging implications for ecological and evolutionary research.</p>
RecView: An interactive R application for locating recombination positions using pedigree data
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