Robust relationship inference in genome-wide association studies

By A. Manichaikul, J. Mychaleckyj, S. Rich, Kathy Daly, M. Sale, Wei-Min Chen. 2010

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In Genetics

Citations in the corpus

Genomic diagnosis for children with intellectual disability and/or developmental delay (2016, methodology): “KING, a robust relationship inference algorithm, was used to confirm familial relationships [10].”
Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance (2017, positive): “4 (Manichaikul et al., 2010) with options ‘‘–kinship–ibs’’ were used to estimate kinship coefficients and to identify related individuals among theMaryland mice.”
Genome-wide genetic data on ~500,000 UK Biobank participants (2017, methodology): “As noted by the authors of KING [42], we found that recent admixture (e.g “Mixed” ancestral backgrounds) tended to inflate the estimate of the kinship coefficient, as the estimator assumes HWE among markers with the same underlying allele frequencies within an individual.”
Maximum Likelihood Estimation of Biological Relatedness from Low Coverage Sequencing Data (2015, background): “Method of moment estimators (e.g. PLINK [33], KING [25], REAP [39]) tend to be the most frequently used due to their ability to deal with large datasets at reasonable speeds (tens to hundreds of thousands of loci), though a maximum likelihood (ML) estimator was recently described for dealing with po”
Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism (2019, methodology): “VQSR,estimated chimericreads, and estimated contamination were calculated by the Genome Analysis Toolkit (GATK); relatedness values were calculated by KING (Manichaikul et al., 2010); most data handling occurred in Hail 0.1 (http://hail.is; https://github.com/hail-is/hail).”
Large-scale whole-genome sequencing of three diverse Asian populations in Singapore (2018, neutral): “We classified as k-degree related pairs if 2< φ< 2.(61) Zero degree means monozygotic twins (MZ) or duplicates.”