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Kinship testing

Manish Roorkiwal, Abhishek Rathore, Roma R Das, Muneendra K Singh, Ankit Jain, Samineni Srinivasan, Pooran M Gaur, Bharadwaj Chellapilla, Shailesh Tripathi, Yongle Li, John M Hickey, Aaron Lorenz, Tim Sutton, Jose Crossa, Jean-Luc Jannink, Rajeev K Varshney
Genomic selection (GS) unlike marker-assisted backcrossing (MABC) predicts breeding values of lines using genome-wide marker profiling and allows selection of lines prior to field-phenotyping, thereby shortening the breeding cycle. A collection of 320 elite breeding lines was selected and phenotyped extensively for yield and yield related traits at two different locations (Delhi and Patancheru, India) during the crop seasons 2011-12 and 2012-13 under rainfed and irrigated conditions. In parallel, these lines were also genotyped using DArTseq platform to generate genotyping data for 3000 polymorphic markers...
2016: Frontiers in Plant Science
Rafael Del-Pino-Casado, María Del Mar Pastor-Bravo, Pedro A Palomino-Moral, Antonio Frías-Osuna
A cross-sectional study was developed in Spain to analyse gender differences in intensity of care, care recipient needs and subjective burden, as well as the moderating effects of kinship on the relationship between gender and subjective burden. A probabilistic sample of 200 primary caregivers (100 male and 100 female) of older relatives was interviewed by expert nurses. Socio-demographic data and several scales regarding objective and subjective burden were used to collect data. Descriptive statistics, Student's t-test, ANOVA and multiple linear regression were used to analyse the data...
November 21, 2016: Archives of Gerontology and Geriatrics
Weian Du, Ling Chen, Hong Liu, Pingming Qiu, Fayuan Li, Jing Gao, Yu Zhou, Bangchao Wang, Chao Liu
The HomyGene19+14Y System (HG19+14Y) is a PCR-based amplification kit that enables typing of 18 autosomal short tandem repeat (STR) loci (i.e., CSF1PO, D2S1338, D3S1358, D5S818, D6S1043, D7S820, D8S1179, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, FGA, Penta E, TPOX, TH01, vWA), 14 widely used Y chromosome STR (Y-STR) loci (Y_GATA_H4, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS438, DYS439, DYS456, DYS458, DYS635), and amelogenin. This multiplex system was designed for the simultaneous analysis of amelogenin-Y allele mutation, single-source searches, kinship (including familial searching), mixture profiles, international data sharing, and other forensic applications...
December 1, 2016: International Journal of Legal Medicine
Tania Hossain, Mahamud Hasan, Ashish K Mazumder, Pilu Momtaz, Abu Sufian, Jabedul Alam Khandaker, Sharif Akhteruzzaman
Genetic polymorphism of 22 autosomal STR loci included in PowerPlex® Fusion System (D3S1358, D1S1656, D2S441, D10S1248, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433, FGA and D22S1045) was studied in 188 unrelated Bangladeshi Bengali individuals. Allele frequencies and forensic efficiency parameters such as, the power of discrimination (PD), observed and expected heterozygosity (Ho & He), polymorphism information content (PIC), probability of match (PM), power of exclusion (PE) and typical paternity index was calculated for the loci...
November 2016: Legal Medicine
Gustavo Martínez, Alicia Borosky, Daniel Corach, Cintia Llull, Laura Locarno, Mercedes Lojo, Miguel Marino, María Cecilia Miozzo, Nidia Modesti, Carla Pacharoni, Juan Pablo Pilili, María Isabel Ramella, Andrea Sala, Cecilia Schaller, Carlos Vullo, Ulises Toscanini
Currently, autosomal Short Tandem Repeat (STR) markers represent the method of election in forensic human identification. Commercial kits of most common use nowadays -e.g. PowerPlex(®)Fusion, Promega Corp.; AmpFlSTR GlobalFiler, Thermofisher scientific; Investigator 24Plex QS,Qiagen-, allow the co-amplification of 23 highly polymorphic STR loci providing a high discrimination power in human identity testing. However, in complex kinship analysis and familial database searches involving distant relationships, additional DNA typing is often required in order to achieve well-founded conclusions...
October 18, 2016: Forensic Science International. Genetics
S Stucki, P Orozco-terWengel, B R Forester, S Duruz, L Colli, C Masembe, R Negrini, E Landguth, M R Jones, M W Bruford, P Taberlet, S Joost
With the increasing availability of both molecular and topo-climatic data, the main challenges facing landscape genomics-i.e. the combination of landscape ecology with population genomics - include processing large numbers of models and distinguishing between selection and demographic processes (e.g. population structure). Several methods address the latter, either by estimating a null model of population history or by simultaneously inferring environmental and demographic effects. Here we present Samβada, an approach designed to study signatures of local adaptation, with special emphasis on high performance computing of large-scale genetic and environmental datasets...
November 1, 2016: Molecular Ecology Resources
Kalin Vidinov, Dragomira Nikolova
In recent years, there are numerous reports indicating the presence of familial papillary carcinoma. Unfortunately, no genetic defect can be linked directly to the disease. In this study, we set the goal to make a retrospective analysis of the cases with papillary carcinoma in the Department of Endocrine Surgery for the past 10 years, to compare the characteristics of sporadic and familial forms of the disease and to find families with hereditary papillary carcinoma. The study included 810 patients treated for thyroid cancer in the Department of Endocrine Surgery, USBALE "Acad...
October 22, 2016: Endocrine Pathology
Siobhán M Mattison, Bret Beheim, Bridget Chak, Peter Buston
Son preference predominates in China, yet there are patterned exceptions to this rule. In this paper, we test whether lineality (patrilineal versus matrilineal inheritance and descent) is associated with son versus daughter preference among the ethnic Mosuo (Na) of Southwest China. Our results show (i) an increased probability of continued fertility among matrilineal women after having a son compared with a daughter and (ii) an increased probability of continued fertility among patrilineal women after having a daughter compared with a son...
September 2016: Royal Society Open Science
Qiu-Ling Liu, Li Xue, Wei-Wei Wu, Xin He, Kai-Yan Liu, Hu Zhao, De-Jian Lu
In this study, a panel of 13 STR loci locate on chromosome 3, 4, and 17 (D3S2402, D3S2452, D3S1766, D3S4554, D3S2388, D3S3051, D3S3053, D4S2404, D4S2364, AC001348A, AC001348B, D17S975, and D17S1294) were assessed for pairwise kinship analysis. Map distances between these STR loci ranged from 0.07 cM to 97.03 cM. The population genetic study of Chinese Han population showed that linkage disequilibrium exists in two clusters of closely linked markers (D4S2404-D4S2364 and D17S975-D17S1294), in which the recombination fractions were 0...
October 4, 2016: Electrophoresis
Jesse D Raffa, Elizabeth A Thompson
Correlation between study units in quantitative genetics studies often makes it difficult to compare important inferential aspects of studies. Describing the relatedness between study units is critical to capture features of pedigree studies involving heritability, including power and precision of heritability estimates. Blangero et al (2012) showed that in pedigree studies the power to detect heritability is a function of the true heritability and the eigenvalues of the kinship matrix. We extend this to a more general setting which allows statements about expected precision of heritability estimates...
October 2016: Statistics in Biosciences
Frank R Wendt, David H Warshauer, Xiangpei Zeng, Jennifer D Churchill, Nicole M M Novroski, Bing Song, Jonathan L King, Bobby L LaRue, Bruce Budowle
Short tandem repeat (STR) loci are the traditional markers used for kinship, missing persons, and direct comparison human identity testing. These markers hold considerable value due to their highly polymorphic nature, amplicon size, and ability to be multiplexed. However, many STRs are still too large for use in analysis of highly degraded DNA. Small bi-allelic polymorphisms, such as insertions/deletions (INDELs), may be better suited for analyzing compromised samples, and their allele size differences are amenable to analysis by capillary electrophoresis...
September 20, 2016: Forensic Science International. Genetics
Roksana Ewa Zofia Malak, Agnieszka Krawczyk-Wasielewska, Katarzyna Głodowska, Bartosz Grobelny, Paweł Kleka, Ewa Mojs, Przemysław Keczmer, Włodzimierz Samborski
INTRODUCTION: Caregivers of demented relatives devote their time and attention in order to help the beloved members of the family. Those who are informal caregivers require support in order to avoid being overburdened. Many such caregivers may suffer from chronic health problems, for instance, depression. OBJECTIVE: The aim was to assess the factors of depression in caregivers, and to discover the determinants of depression among informal family caregivers of demented individuals...
September 2016: Annals of Agricultural and Environmental Medicine: AAEM
Maud I Tenaillon, Domenica Manicacci, Stéphane D Nicolas, Francois Tardieu, Claude Welcker
Little is known about the factors driving within species Genome Size (GS) variation. GS may be shaped indirectly by natural selection on development and adaptative traits. Because GS variation is particularly pronounced in maize, we have sampled 83 maize inbred lines from three well described genetic groups adapted to contrasted climate conditions: inbreds of tropical origin, Flint inbreds grown in temperate climates, and Dent inbreds distributed in the Corn Belt. As a proxy for growth rate, we measured the Leaf Elongation Rate maximum during nighttime (LERmax) as well as GS in all inbred lines...
2016: PeerJ
Xuli Zhu, Huan Li, Meixia Ye, Libo Jiang, Mengmeng Sang, Rongling Wu
Allopolyploids are a group of polyploids with more than two sets of chromosomes derived from different species. Previous linkage analysis of allopolyploids is based on the assumption that different chromosomes pair randomly during meiosis. A more sophisticated model to relax this assumption has been developed for allotetraploids by incorporating the preferential pairing behavior of homologous over homoeologous chromosomes. Here, we show that the basic principle of this model can be extended to perform linkage analysis of higher-ploidy allohexaploids, where multiple preferential pairing factors are used to characterize chromosomal-pairing meiotic features between different constituent species...
September 19, 2016: Briefings in Bioinformatics
M D Coble, J Buckleton, J M Butler, T Egeland, R Fimmers, P Gill, L Gusmão, B Guttman, M Krawczak, N Morling, W Parson, N Pinto, P M Schneider, S T Sherry, S Willuweit, M Prinz
The use of biostatistical software programs to assist in data interpretation and calculate likelihood ratios is essential to forensic geneticists and part of the daily case work flow for both kinship and DNA identification laboratories. Previous recommendations issued by the DNA Commission of the International Society for Forensic Genetics (ISFG) covered the application of bio-statistical evaluations for STR typing results in identification and kinship cases, and this is now being expanded to provide best practices regarding validation and verification of the software required for these calculations...
September 4, 2016: Forensic Science International. Genetics
Coline M Arnaud, Takafumi Suzumura, Eiji Inoue, Mark J Adams, Alexander Weiss, Miho Inoue-Murayama
Using long-term maternal pedigree data, microsatellite analysis, and behavioral tests, we examined whether personality differences in wild Japanese macaques (Macaca fuscata) are associated with additive genetic effects, maternal influences, or belonging to a particular social group. Behaviors elicited by novel-object tests were defined by a component related to caution around novel-objects (Ob-PC1) and behaviors elicited by novel food-tests were defined by correlated components related to consummatory responses (Fo-PC1) and caution around novel foods (Fo-PC2)...
September 12, 2016: Primates; Journal of Primatology
A E Sanders, T Sofer, Q Wong, K F Kerr, C Agler, J R Shaffer, J D Beck, S Offenbacher, C R Salazar, K E North, M L Marazita, C C Laurie, R H Singer, J Cai, T L Finlayson, K Divaris
Chronic periodontitis (CP) has a genetic component, particularly its severe forms. Evidence from genome-wide association studies (GWASs) has highlighted several potential novel loci. Here, the authors report the first GWAS of CP among a large community-based sample of Hispanics/Latinos. The authors interrogated a quantitative trait of CP (mean interproximal clinical attachment level determined by full-mouth periodontal examinations) among 10,935 adult participants (mean age: 45 y, range: 18 to 76 y) from the Hispanic Community Health Study / Study of Latinos...
September 6, 2016: Journal of Dental Research
Marco Scutari, Ian Mackay, David Balding
The prediction of phenotypic traits using high-density genomic data has many applications such as the selection of plants and animals of commercial interest; and it is expected to play an increasing role in medical diagnostics. Statistical models used for this task are usually tested using cross-validation, which implicitly assumes that new individuals (whose phenotypes we would like to predict) originate from the same population the genomic prediction model is trained on. In this paper we propose an approach based on clustering and resampling to investigate the effect of increasing genetic distance between training and target populations when predicting quantitative traits...
September 2016: PLoS Genetics
Dana Pfefferle, Kurt Hammerschmidt, Roger Mundry, Angelina V Ruiz-Lambides, Julia Fischer, Anja Widdig
In social animals, kin relations strongly shape the social structure of a group. In female-bonded species, maternal relatedness is likely to be mediated via familiarity, but evidence is accumulating that non-human primates are able to recognize kin that they are not familiar with and adjust their behavior accordingly. In playback experiments, female rhesus macaques showed increased interest in 'coo' calls produced by unfamiliar paternal half-sisters compared to 'coo' calls produced by unfamiliar unrelated females, suggesting that these calls should have some common structural characteristics that facilitate the discrimination of kin from non-kin...
2016: PloS One
Marijana Vujkovic, Richard Aplenc, Todd A Alonzo, Alan S Gamis, Yimei Li
Regression analysis is commonly used in genome-wide association studies (GWAS) to test genotype-phenotype associations but restricts the phenotype to a single observation for each individual. There is an increasing need for analytic methods for longitudinally collected phenotype data. Several methods have been proposed to perform longitudinal GWAS for family-based studies but few methods are described for unrelated populations. We compared the performance of three statistical approaches for longitudinal GWAS in unrelated subjectes: (1) principal component-based generalized estimating equations (PC-GEE); (2) principal component-based linear mixed effects model (PC-LMEM); (3) kinship coefficient matrix-based linear mixed effects model (KIN-LMEM), in a study of single-nucleotide polymorphisms (SNPs) on the duration of 4 courses of chemotherapy in 624 unrelated children with de novo acute myeloid leukemia (AML) genotyped on the Illumina 2...
2016: Frontiers in Genetics
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