SibJoin: A Fast Heuristic for Half-Sibling Reconstruction

Author(s):  
Daniel G. Brown ◽  
Daniel Dexter
Keyword(s):  
1991 ◽  
Vol 36 (5) ◽  
pp. 413-413
Author(s):  
Elizabeth A. Wehner ◽  
Wyndol Furman

2010 ◽  
Vol 08 (02) ◽  
pp. 337-356 ◽  
Author(s):  
SAAD I. SHEIKH ◽  
TANYA Y. BERGER-WOLF ◽  
ASHFAQ A. KHOKHAR ◽  
ISABEL C. CABALLERO ◽  
MARY V. ASHLEY ◽  
...  

While full-sibling group reconstruction from microsatellite data is a well-studied problem, reconstruction of half-sibling groups is much less studied, theoretically challenging, and computationally demanding. In this paper, we present a formulation of the half-sibling reconstruction problem and prove its APX-hardness. We also present exact solutions for this formulation and develop heuristics. Using biological and synthetic datasets we present experimental results and compare them with the leading alternative software COLONY. We show that our results are competitive and allow half-sibling group reconstruction in the presence of polygamy, which is prevalent in nature.


2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 80-81
Author(s):  
Cierrah J Kassetas ◽  
Joel Caton ◽  
James D Kirsch ◽  
Sheri T Dorsam ◽  
Kacie L McCarthy ◽  
...  

Abstract Thirty-six half-sibling yearling Angus bulls [256 ± 8 d; initial BW = 320 ± 2 kg] were assigned one of three diets: 1) 60% concentrate as corn (CON; n = 12); 2) 60% DDGS (60DDGS; n = 12); 3) CON diet + equivalent sulfur of 60DDGS as CaSO4 (SULF; n = 12) to evaluate effects of feeding 60% DDGS or sulfur as CaSO4 on trace mineral (TM) concentrations in serum and seminal plasma. Bulls were fed in Calan gates for 112 days and targeted to gain 1.6 kg/d. Data were analyzed as repeated measures using PROC MIXED in SAS. In serum, treatment × day interactions were observed (P ≤ 0.03) for Cu, Se, and Mo. For Cu, no differences (P > 0.15) were observed at d 0 or 56, but at d 112, 60DDGS was reduced (P < 0.01) compared with SULF and CON. At d 0, no differences (P > 0.09) were observed for Se; however, at d 56 and 112, 60DDGS was greater (P < 0.01) than CON and SULF. For Mo, at d 0, 60DDGS was greater (P = 0.03) than CON, whereas SULF was intermediate, but at d 56 and 112, CON was greater (P < 0.01) than SULF and 60DDGS. In seminal plasma, treatment × day interactions were observed (P ≤ 0.02) for Cu and Mo. For Cu, no differences (P ≥ 0.09) were observed at d 0 or 56, but at d 112, CON and 60DDGS were greater (P < 0.01) compared with SULF. For Mo, at d 0, 60DDGS was greater (P = 0.03) than SULF, whereas CON was intermediate, but on d 56 and 112, CON was greater (P < 0.01) than 60DDGS and SULF. Differences observed for TM may have influenced enzyme activity and semen kinematics which were previously reported.


2018 ◽  
Vol 36 (05) ◽  
pp. 498-504
Author(s):  
Maya Tabet ◽  
Louise Flick ◽  
Hong Xian ◽  
Jen Chang

Background There has been a call for customized rather than population-based birthweight standards that would classify smallness based on an infant's own growth potential. Thus, this study aimed to examine the association between the difference in sibling birthweight and the likelihood of neonatal death among second births in a U.S. population. Study Design This was a population-based cohort study including 179,300 women who delivered their first two nonanomalous singleton live births in Missouri (1989–2005). We performed binary logistic regression to evaluate the association between being relatively smaller than the elder full- or half-sibling (i.e., smaller by at least 500 g) and neonatal death (i.e., deaths in the first 28 days of life) among second births after controlling for sociodemographic and pregnancy-related variables in the second pregnancy. Results The adjusted odds of neonatal death were 2.54-times higher among second births who were relatively smaller than their elder sibling. Among relatively small second births, every 100-g increase in the difference in sibling birthweight was associated with a 13% increase in the odds of neonatal death. Conclusion The deviation from the elder sibling's birthweight predicts neonatal death. Taking into consideration the elder sibling's birthweight may be warranted in clinical and research settings.


Heredity ◽  
2019 ◽  
Vol 124 (2) ◽  
pp. 299-312 ◽  
Author(s):  
Tetsuya Akita

Abstract In this study, we developed a nearly unbiased estimator of contemporary effective mother size in a population, which is based on a known maternal half-sibling relationship found within the same cohort. Our method allows for variance of the average number of offspring per mother (i.e., parental variation, such as age-specific fecundity) and variance of the number of offspring among mothers with identical reproductive potential (i.e., nonparental variation, such as family-correlated survivorship). We also developed estimators of the variance and coefficient of variation of contemporary effective mother size and qualitatively evaluated the performance of the estimators by running an individual-based model. Our results provide guidance for (i) a sample size to ensure the required accuracy and precision when the order of effective mother size is available and (ii) a degree of uncertainty regarding the estimated effective mother size when information about the size is unavailable. To the best of our knowledge, this is the first report to demonstrate the derivation of a nearly unbiased estimator of effective population size; however, its current application is limited to effective mother size and situations, in which the sample size is not particularly small and maternal half-sibling relationships can be detected without error. The results of this study demonstrate the usefulness of a sibship assignment method for estimating effective population size; in addition, they have the potential to greatly widen the scope of genetic monitoring, especially in the situation of small sample size.


BMJ ◽  
2019 ◽  
pp. l803 ◽  
Author(s):  
Yu Tian ◽  
Elham Kharazmi ◽  
Kristina Sundquist ◽  
Jan Sundquist ◽  
Hermann Brenner ◽  
...  

AbstractObjectiveTo explore the risk of colorectal cancer in family members of patients with colorectal cancer, with an emphasis on subtypes of second degree relatives, especially half siblings, which were lacking in the literature.DesignAmbidirectional cohort study.SettingNationwide Swedish Family Cancer Data (record linkage).ParticipantsAll people residing in Sweden and born after 1931, with their biological parents, totalling >16 million individuals (follow-up: 1958-2015); of those with clear genealogy, 173 796 developed colorectal cancer.Main outcome measuresLifetime (0-79 years) cumulative risk and standardised incidence ratio of colorectal cancer among first degree relatives and second degree relatives.ResultsThe overall lifetime cumulative risk of colorectal cancer in siblings of patients was 7%, which represents a 1.7-fold (95% confidence interval 1.6 to 1.7; n=2089) increase over the risk in those without any family history of colorectal cancer. A similarly increased lifetime cumulative risk (6%) was found among half siblings (standardised incidence ratio 1.5, 95% confidence interval 1.3 to 1.8; n=140). The risk in people with colorectal cancer in both a parent and a half sibling (standardised incidence ratio 3.6, 2.4 to 5.0; n=32) was close to the risk in those with both an affected parent and an affected sibling (2.7, 2.4 to 3.0; n=396). Family history of colorectal cancer in only one second degree relative other than a half sibling (without any affected first degree relatives), such as a grandparent, uncle, or aunt, showed minor association with the risk of colorectal cancer.ConclusionFamily history of colorectal cancer in half siblings is similarly associated with colorectal cancer risk to that in siblings. The increase in risk of colorectal cancer among people with one affected second degree relative was negligible, except for half siblings, but the risk was substantially increased for a combination of family history in one affected second degree relative and an affected first degree relative (or even another second degree relative). These evidence based findings provide novel information to help to identify people at high risk with a family history of colorectal cancer that can potentially be used for risk adapted screening.


2017 ◽  
Vol 95 (4) ◽  
pp. 118-122 ◽  
Author(s):  
M McGowan ◽  
C Smith ◽  
A Ferguson ◽  
B Stone ◽  
D Vankan ◽  
...  

2020 ◽  
Vol 83 (11) ◽  
pp. 2014-2017
Author(s):  
JESSICA L. JONES ◽  
KERI A. LYDON ◽  
WILLIAM C. WALTON

ABSTRACT Vibrio parahaemolyticus and Vibrio vulnificus are naturally occurring human pathogenic bacteria commonly found in estuarine environments where oysters are cultured. The use of triploid oysters has increased due to their rapid growth rate and because they maintain a high quality throughout the year. Previous work suggested levels of Vibrio spp. may be lower in triploid oysters than diploid oysters. Therefore, this study aimed to determine whether there is a difference in the abundances of V. parahaemolyticus and V. vulnificus between half-sibling diploid and triploid American oysters (Crassostrea virginica). In four trials, 100 individual oysters (either iced or temperature abused) were analyzed for V. parahaemolyticus and V. vulnificus by using direct plating followed by colony hybridization. Mean levels of V. parahaemolyticus in iced and abused diploid oysters were 3.55 and 4.21 log CFU/g, respectively. Mean levels in iced and abused triploid oysters were 3.49 and 4.27 log CFU/g, respectively. Mean levels of V. vulnificus in iced and abused diploid oysters were 3.53 and 4.56 log CFU/g, respectively. Mean levels in iced and abused triploid oysters were 3.54 and 4.55 log CFU/g, respectively. The differences in Vibrio spp. abundances between diploid and triploid oysters was not significant (P > 0.05). However, the differences across treatments were significant (P < 0.05), with the exception of V. parahaemolyticus levels in trial 3 (P = 0.83). Variation between individual oysters was also observed, with 12 of 808 measurements being outside of the 95th percentile. This phenomenon of occasional statistical outliers (“hot” or “cold” oysters) has been previously described and supports the appropriateness of composite sampling to account for inherent animal variability. In summary, the data indicate that abundances of V. parahaemolyticus and V. vulnificus are not dependent on the ploidy of cultured oysters but vary with the type of handling. HIGHLIGHTS


Genome ◽  
2015 ◽  
Vol 58 (9) ◽  
pp. 393-403 ◽  
Author(s):  
Andrea L. Kocmarek ◽  
Moira M. Ferguson ◽  
Roy G. Danzmann

We tested whether genes differentially expressed between large and small rainbow trout co-localized with familial QTL regions for body size. Eleven chromosomes, known from previous work to house QTL for weight and length in rainbow trout, were examined for QTL in half-sibling families produced in September (1 XY male and 1 XX neomale) and December (1 XY male). In previous studies, we identified 108 candidate genes for growth expressed in the liver and white muscle in a subset of the fish used in this study. These gene sequences were BLASTN aligned against the rainbow trout and stickleback genomes to determine their location (rainbow trout) and inferred location based on synteny with the stickleback genome. Across the progeny of all three males used in the study, 63.9% of the genes with differential expression appear to co-localize with the QTL regions on 6 of the 11 chromosomes tested in these males. Genes that co-localized with QTL in the mixed-sex offspring of the two XY males primarily showed up-regulation in the muscle of large fish and were related to muscle growth, metabolism, and the stress response.


Death Studies ◽  
2014 ◽  
Vol 38 (9) ◽  
pp. 557-562 ◽  
Author(s):  
Pernilla Avelin ◽  
Göran Gyllenswärd ◽  
Kerstin Erlandsson ◽  
Ingela Rådestad
Keyword(s):  

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