scholarly journals Distinguishing pedigree relationships using multi-way identical by descent sharing and sex-specific genetic maps

2019 ◽  
Author(s):  
Ying Qiao ◽  
Jens Sannerud ◽  
Sayantani Basu-Roy ◽  
Caroline Hayward ◽  
Amy L. Williams
Keyword(s):  
Simulated Data ◽  
Genetic Maps ◽  
Fast Method ◽  
Identical By Descent ◽  
Generation Scotland ◽  
Paternal Relationship ◽  
Close Relatives ◽  
Inference Methods ◽  
Relationship Of ◽  
The Relationship

AbstractThe proportion of samples with one or more close relatives in a genetic dataset increases rapidly with sample size, necessitating relatedness modeling and enabling pedigree-based analyses. Despite this, relatives are generally unreported and current inference methods typically detect only the degree of relatedness of sample pairs and not pedigree relationships. We developed CREST, an accurate and fast method that identifies the pedigree relationships of close relatives. CREST utilizes identical by descent (IBD) segments shared between a pair of samples and their mutual relatives, leveraging the fact that sharing rates among these individuals differ across pedigree configurations. Furthermore, CREST exploits the profound differences in sex-specific genetic maps to classify pairs as maternally or paternally related—e.g., paternal half-siblings—using the locations of autosomal IBD segments shared between the pair. In simulated data, CREST correctly classifies 91.5-99.5% of grandparent-grandchild (GP) pairs, 70.5-97.0% of avuncular (AV) pairs, and 79.0-98.0% of half-siblings (HS) pairs compared to PADRE’s rates of 38.5-76.0% of GP, 60.5-92.0% of AV, 73.0-95.0% of HS pairs. Turning to the real 20,032 sample Generation Scotland (GS) dataset, CREST correctly determines the relationship of 99.0% of GP, 85.7% of AV, and 95.0% of HS pairs that have sufficient mutual relative data, completing this analysis in 10.1 CPU hours including IBD detection. CREST’s maternal and paternal relationship inference is also accurate, as it flagged five pairs as incorrectly labeled in the GS pedigrees— three of which we confirmed as mistakes, and two with an uncertain relationship—yielding 99.7% of HS and 93.5% of GP pairs correctly classified.

scholarly journals Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives

PLoS Genetics ◽  
2019 ◽  
Vol 15 (12) ◽  
pp. e1007979 ◽  
Author(s):  
Madison Caballero ◽  
Daniel N. Seidman ◽  
Ying Qiao ◽  
Jens Sannerud ◽  
Thomas D. Dyer ◽  
...  
Keyword(s):  
Genetic Maps ◽  
Crossover Interference ◽  
Identical By Descent ◽  
Close Relatives

scholarly journals Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives

2019 ◽  
Author(s):  
Madison Caballero ◽  
Daniel N. Seidman ◽  
Jens Sannerud ◽  
Thomas D. Dyer ◽  
Donna M. Lehman ◽  
...  
Keyword(s):  
Standard Deviation ◽  
Real Data ◽  
Genetic Maps ◽  
Pedigree Data ◽  
Crossover Interference ◽  
Interference Modeling ◽  
Identical By Descent ◽  
Close Relatives ◽  
The Impact ◽  
Number Of Segments

AbstractSimulations of close relatives and identical by descent (IBD) segments are common in genetic studies, yet most past efforts have utilized sex averaged genetic maps and ignored crossover interference, thus omitting features known to affect the breakpoints of IBD segments. We developed Ped-sim, a method for simulating relatives that can utilize either sex-specific or sex averaged genetic maps and also either a model of crossover interference or the traditional Poisson model for inter-crossover distances. To characterize the impact of previously ignored mechanisms, we simulated data for all four combinations of these factors. We found that modeling crossover interference decreases the standard deviation of the IBD proportion by 10.4% on average in full siblings through second cousins. By contrast, sex-specific maps increase this standard deviation by 4.2% on average, and also impact the number of segments relatives share. Most notably, using sex-specific maps, the number of segments half-siblings share is bimodal; and when combined with interference modeling, the probability that sixth cousins have non-zero IBD ranges from 9.0 to 13.1%, depending on the sexes of the individuals through which they are related. We present new analytical results for the distributions of IBD segments under these models and show they match results from simulations. Finally, we compared IBD sharing rates between simulated and real relatives and find that the combination of sex-specific maps and interference modeling most accurately captures IBD rates in real data. Ped-sim is open source and available fromhttps://github.com/williamslab/ped-sim.Author summarySimulations are ubiquitous throughout statistical genetics in order to generate data with known properties, enabling tests of inference methods and analyses of real world processes in settings where experimental data are challenging to collect. Simulating genetic data for relatives in a pedigree requires the synthesis of chromosomes parents transmit to their children. These chromosomes form as a mosaic of a given parent’s two chromosomes, with the location of switches between the two parental chromosomes known as crossovers. Detailed information about crossover generation based on real data from humans now exists, including the fact that men and women have overall different rates (women produce ~1.6 times more crossovers) and that real crossovers are subject tointerference—whereby crossovers are further apart from one another than expected under a model that selects their locations randomly. Our new method, Ped-sim, can simulate pedigree data using these less commonly modeled crossover features, and we used it to evaluate the importance of sex-specific rates and interference in real data. These comparisons show that both factors shape the amount of DNA two relatives share identically, and that their inclusion in models of crossover better fit data from real relatives.

scholarly journals Differential Covariance: A New Class of Methods to Estimate Sparse Connectivity from Neural Recordings

2017 ◽  
Vol 29 (10) ◽  
pp. 2581-2632 ◽  
Author(s):  
Tiger W. Lin ◽  
Anup Das ◽  
Giri P. Krishnan ◽  
Maxim Bazhenov ◽  
Terrence J. Sejnowski
Keyword(s):  
Functional Connectivity ◽  
Field Potential ◽  
Simulated Data ◽  
Neural Signals ◽  
Neural Recordings ◽  
New Class ◽  
Making Sense ◽  
Relationship Of ◽  
Sparse Connectivity ◽  
The Relationship

With our ability to record more neurons simultaneously, making sense of these data is a challenge. Functional connectivity is one popular way to study the relationship of multiple neural signals. Correlation-based methods are a set of currently well-used techniques for functional connectivity estimation. However, due to explaining away and unobserved common inputs (Stevenson, Rebesco, Miller, & Körding, 2008 ), they produce spurious connections. The general linear model (GLM), which models spike trains as Poisson processes (Okatan, Wilson, & Brown, 2005 ; Truccolo, Eden, Fellows, Donoghue, & Brown, 2005 ; Pillow et al., 2008 ), avoids these confounds. We develop here a new class of methods by using differential signals based on simulated intracellular voltage recordings. It is equivalent to a regularized AR(2) model. We also expand the method to simulated local field potential recordings and calcium imaging. In all of our simulated data, the differential covariance-based methods achieved performance better than or similar to the GLM method and required fewer data samples. This new class of methods provides alternative ways to analyze neural signals.

scholarly journals Studi Reliablilitas Hadis berdasarkan Teori Explosive Isnad dan Isnad Family

2018 ◽  
Vol 7 (2) ◽  
pp. 43
Author(s):  
Masadah Masadah
Keyword(s):  
Comparative Method ◽  
Family Relationship ◽  
Comparison Method ◽  
Study Data ◽  
Literature Study ◽  
Constant Comparative Method ◽  
Reliable Source ◽  
Close Relatives ◽  
Relationship Of ◽  
The Relationship

The purpose of this study is: The purpose of this study describes reliablilitas Hadith based on Explosive Theory Isnad and Isnad Family. This research method is literature study. Data analysis method used is constant comparison method (constant comparative method). The results of this study states that what is perceived by Nabia about Hadith and its development tend to follow the mindset of most scholars of hadith. Nabia's thinking is much different from that of other orientalists such as Ignaz Goldziher, Joseph Schacht, and G.H.A. Juynboll is more skeptical in understanding the Hadith. Nabia is not. At least he believes that the existence of the Hadith is a reliable source derived from the Prophet Muhammad. Therefore, the explosive isnad theory proposed by Nabia Abbott does not seem to be much different from the isnad system proposed by the scholars of Hadith. Both Nabia and the scholars of the Hadith concluded that the sanad was the beginning of its appearance at the time of the Prophet who then spread and more branches in later times. Nabia acknowledged the transmission of Hadith in the time of the Prophet, even according to him, the existence of Hadith was written when the Prophet was alive, although the writing movement is still non-massive. At that time the Hadith more quickly developed through the oral system (submission of Hadith from oral to oral), but it does not deny that there are some friends who have documented it through writing. This narrative activity continued even until Prophet Muhammad's death. In its development and dissemination, isnad has a concept which Nabia calls the isnad family and non-family. The word "family" in this case is related to the relationship of blood or close relatives (mawali). In other words, there is a family relationship between narrators. This isnad family, developed through several prominent friends and continued for three generations, with the formula "so-and-so" (which comes from his father and his grandfather), but at a certain moment the isnad family can also evolve only through a generation, if an older narrator finds his or her grandson, wants to follow in his footsteps or otherwise narrate a Hadith to an opposing path in the family chain, for example to a nephew, like a relationship normally encountered in an isnad.

Genetic maps of the sheep blowfly Lucilia cuprina: linkage-group correlations with other dipteran genera

Genome ◽  
1993 ◽  
Vol 36 (3) ◽  
pp. 495-506 ◽  
Author(s):  
G. L. Weller ◽  
G. G. Foster
Keyword(s):  
Drosophila Melanogaster ◽  
Ceratitis Capitata ◽  
Genetic Maps ◽  
Lucilia Cuprina ◽  
Linkage Data ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Relationship Of ◽  
The Relationship ◽  
Linkage Relationships

Linkage data and revised genetic maps for 72 autosomal loci in Lucilia cuprina are presented. Comparison of the linkage relationships of biochemically and morphologically similar mutations in Ceratitis capitata, Drosophila melanogaster, and Musca domestica supports the hypothesis that the major linkage elements have survived relatively intact during evolution of the higher Diptera. The relationship of the linkage groups of the mosquito Aedes aegypti to these species is less clear.Key words: Lucilia, Drosophila, Musca, Ceratitis, linkage maps.

scholarly journals Saline distribution during multicomponent salting in pre-cooked quail eggs

2012 ◽  
Vol 32 (2) ◽  
pp. 281-288 ◽  
Author(s):  
Dionísio Borsato ◽  
Mariete Barbosa Moreira ◽  
Ivanira Moreira ◽  
Marcos Vinicios Roberto Pina ◽  
Rui Sergio dos Santos Ferreira da Silva ◽  
...  
Keyword(s):  
Food Production ◽  
Water System ◽  
Simulated Data ◽  
Comsol Multiphysics ◽  
Predictive Capacity ◽  
Experimental Values ◽  
Relationship Of ◽  
The Mathematical Model ◽  
The Relationship ◽  
Good Agreement

The relationship of NaCl with problems of arterial hypertension has led to a reduction in the levels of this salt in food production. KCl has been used as a partial substitute for NaCl since it cannot be completely substituted without affecting the acceptability of the end product. In this study, the diffusion that occurs during quail egg salting in static and stirred brine was simulated. The mathematical model used was based on a generalization of the Fick's 2nd law, and the COMSOL Multiphysics software was used to simulate the diffusion in the NaCl-KCl-water system. The deviations in the simulated data and experimental data were 2.50% for NaCl and 6.98% for KCl in static brine, while in the stirred brine they were 3.48% for NaCl and 4.72% for KCl. The simulation results presented good agreement with the experimental values and validated the predictive capacity of the model.

scholarly journals THE PROGNOSTIC MODEL OF ANTITUMOR EFFECT OF TARGETED DRUGS IN IMMUNOTHERAPY

2016 ◽  
Vol 11 (4) ◽  
pp. 69-74 ◽  
Author(s):  
V. V. Burlyaev ◽  
А. А. Davydenko ◽  
O. M. Nikolaeva ◽  
L. I. Russu ◽  
I. A. Suetina ◽  
...  
Keyword(s):  
Information System ◽  
Statistical Analysis ◽  
Proliferative Activity ◽  
Prognostic Model ◽  
Antitumor Effect ◽  
Inductive Inference ◽  
Targeted Drugs ◽  
Inference Methods ◽  
Relationship Of ◽  
The Relationship

A prognostic model for constructing hypotheses about the relationship of combinations of cytokines with the proliferative activity of cancer cells is proposed. The model is based on the use of inductive inference methods. The methodology takes into account the synergistic interaction of cytokines and uses sequential construction of logical formulas for selecting groups of cytokines, a statistical analysis of contingency tables and logical integration of the obtained estimates. Implementation of the proposed method in the information system of forecasting the effect of targeted anticancer drugs in immunotherapy will greatly accelerate research in this area.

scholarly journals Inferring identical by descent sharing of sample ancestors promotes high resolution relative detection

2018 ◽  
Author(s):  
Monica D. Ramstetter ◽  
Sushila A. Shenoy ◽  
Thomas D. Dyer ◽  
Donna M. Lehman ◽  
Joanne E. Curran ◽  
...  
Keyword(s):  
Simulated Data ◽  
Identity By Descent ◽  
Identical By Descent ◽  
Novel Approach ◽  
Related Individuals ◽  
Using Data ◽  
Close Relatives ◽  
Multiple Samples ◽  
Combining Information ◽  
Relative Detection

AbstractAs genetic datasets increase in size, the fraction of samples with one or more close relatives grows rapidly, resulting in sets of mutually related individuals. We present DRUID—Deep Relatedness Utilizing Identity by Descent—a method that works by inferring the identical by descent (IBD) sharing profile of an ungenotyped ancestor of a set of close relatives. Using this IBD profile, DRUID infers relatedness between unobserved ancestors and more distant relatives, thereby combining information from multiple samples to remove one or more generations between the deep relationships to be identified. DRUID constructs sets of close relatives by detecting full siblings and also uses a novel approach to identify the aunts/uncles of two or more siblings, recovering 92.2% of real aunts/uncles with zero false positives. In real and simulated data, DRUID correctly infers up to 10.5% more relatives than PADRE when using data from two sets of distantly related siblings, and 10.7–31.3% more relatives given two sets of siblings and their aunts/uncles. DRUID frequently infers relationships either correctly or within one degree of the truth, with PADRE classifying 43.3–58.3% of tenth degree relatives in this way compared to 79.6–96.7% using DRUID.

New Cortinarius species from conifer-dominated forests of North America and Europe

Botany ◽  
2012 ◽  
Vol 90 (8) ◽  
pp. 743-754 ◽  
Author(s):  
Tuula Niskanen ◽  
Kare Liimatainen ◽  
Ilkka Kytövuori ◽  
Joseph F. Ammirati
Keyword(s):  
North America ◽  
Molecular Data ◽  
Wide Distribution ◽  
Similar Species ◽  
The Novel ◽  
Eastern Canada ◽  
Morphological And Molecular Data ◽  
Close Relatives ◽  
Relationship Of ◽  
The Relationship

Five new Cortinarius species with medium to large basidiomata are described based on morphological and molecular data. Three of them, Cortinarius aavae , Cortinarius brunneocalcarius , and Cortinarius grosmorneënsis , belong to subgenus Telamonia and one, Cortinarius subfloccopus , to clade /Fulvescentes. The relationship of the fifth species, Cortinarius brunneotinctus , was not solved but it resembles species of clade /Anomali. Cortinarius brunneocalcarius and C. aavae do not have close relatives within the subgenus Telamonia; whereas, C. grosmorneënsis belongs to section Brunnei. Cortinarius grosmorneënsis is only known from eastern Canada, but the other four species have a wide distribution: C. brunneocalcarius and C. subfloccopus occur in North America and Europe, and C. brunneotinctus and C. aavae in western and eastern North America. The descriptions of the novel species are presented and comparison to similar species provided.

scholarly journals Studi Reliablilitas Hadis berdasarkan Teori Explosive Isnad dan Isnad Family

2018 ◽  
Vol 7 (2) ◽  
pp. 43
Author(s):  
Masadah Masadah
Keyword(s):  
Comparative Method ◽  
Family Relationship ◽  
Comparison Method ◽  
Study Data ◽  
Literature Study ◽  
Constant Comparative Method ◽  
Reliable Source ◽  
Close Relatives ◽  
Relationship Of ◽  
The Relationship

The purpose of this study is: The purpose of this study describes reliablilitas Hadith based on Explosive Theory Isnad and Isnad Family. This research method is literature study. Data analysis method used is constant comparison method (constant comparative method). The results of this study states that what is perceived by Nabia about Hadith and its development tend to follow the mindset of most scholars of hadith. Nabia's thinking is much different from that of other orientalists such as Ignaz Goldziher, Joseph Schacht, and G.H.A. Juynboll is more skeptical in understanding the Hadith. Nabia is not. At least he believes that the existence of the Hadith is a reliable source derived from the Prophet Muhammad. Therefore, the explosive isnad theory proposed by Nabia Abbott does not seem to be much different from the isnad system proposed by the scholars of Hadith. Both Nabia and the scholars of the Hadith concluded that the sanad was the beginning of its appearance at the time of the Prophet who then spread and more branches in later times. Nabia acknowledged the transmission of Hadith in the time of the Prophet, even according to him, the existence of Hadith was written when the Prophet was alive, although the writing movement is still non-massive. At that time the Hadith more quickly developed through the oral system (submission of Hadith from oral to oral), but it does not deny that there are some friends who have documented it through writing. This narrative activity continued even until Prophet Muhammad's death. In its development and dissemination, isnad has a concept which Nabia calls the isnad family and non-family. The word "family" in this case is related to the relationship of blood or close relatives (mawali). In other words, there is a family relationship between narrators. This isnad family, developed through several prominent friends and continued for three generations, with the formula "so-and-so" (which comes from his father and his grandfather), but at a certain moment the isnad family can also evolve only through a generation, if an older narrator finds his or her grandson, wants to follow in his footsteps or otherwise narrate a Hadith to an opposing path in the family chain, for example to a nephew, like a relationship normally encountered in an isnad.

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