{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T11:15:27Z","timestamp":1775646927946,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"2","funder":[{"name":"Division of Intramural Research of the National Heart, Lung, and Blood Institute"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Estimating the individual inbreeding coefficient and pairwise kinship is an important problem in human genetics (e.g. in disease mapping) and in animal and plant genetics (e.g. inbreeding design). Existing methods, such as sample correlation-based genetic relationship matrix, KING, and UKin, are either biased, or not able to estimate inbreeding coefficients, or produce a large proportion of negative estimates that are difficult to interpret. This limitation of existing methods is partly due to failure to explicitly model inbreeding. Since all humans are inbred to various degrees by virtue of shared ancestries, it is prudent to account for inbreeding when inferring kinship between individuals.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present \u201cKindred,\u201d an approach that estimates inbreeding and kinship by modeling latent identity-by-descent states that accounts for all possible allele sharing\u2014including inbreeding\u2014between two individuals. Kindred used non-negative least squares method to fit the model, which not only increases computation efficiency compared to the maximum likelihood method, but also guarantees non-negativity of the kinship estimates. Through simulation, we demonstrate the high accuracy and non-negativity of kinship estimates by Kindred. By selecting a subset of SNPs that are similar in allele frequencies across different continental populations, Kindred can accurately estimate kinship between admixed samples. In addition, we demonstrate that the realized kinship matrix estimated by Kindred is effective in reducing genomic control values via linear mixed model in genome-wide association studies. Finally, we demonstrate that Kindred produces sensible heritability estimates on an Australian height dataset.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Kindred is implemented in C with multi-threading. It takes vcf file or stream as input and works seamlessly with bcftools. Kindred is freely available at https:\/\/github.com\/haplotype\/kindred.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae082","type":"journal-article","created":{"date-parts":[[2024,2,12]],"date-time":"2024-02-12T16:49:11Z","timestamp":1707756551000},"source":"Crossref","is-referenced-by-count":15,"title":["Estimation of inbreeding and kinship coefficients via latent identity-by-descent states"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8055-2192","authenticated-orcid":false,"given":"Yongtao","family":"Guan","sequence":"first","affiliation":[{"name":"Framingham Heart Study , Framingham, MA 01702, United States"},{"name":"Population Sciences Branch, National Heart, Lung, and Blood Institute , Bethesda, DC 20892, United States"}]},{"given":"Daniel","family":"Levy","sequence":"additional","affiliation":[{"name":"Framingham Heart Study , Framingham, MA 01702, United States"},{"name":"Population Sciences Branch, National Heart, Lung, and Blood Institute , Bethesda, DC 20892, United States"}]}],"member":"286","published-online":{"date-parts":[[2024,2,13]]},"reference":[{"key":"2024022909074546900_btae082-B1","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","author":"Auton","year":"2015","journal-title":"Nature"},{"key":"2024022909074546900_btae082-B2","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1002\/(SICI)1099-128X(199709\/10)11:5<393::AID-CEM483>3.0.CO;2-L","article-title":"A fast non-negativity-constrained least squares algorithm","volume":"11","author":"Bro","year":"1997","journal-title":"J Chemometrics"},{"key":"2024022909074546900_btae082-B3","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1016\/j.ajhg.2016.02.012","article-title":"Control for population structure and relatedness for binary traits in genetic association studies via logistic mixed models","volume":"98","author":"Chen","year":"2016","journal-title":"Am J Hum Genet"},{"key":"2024022909074546900_btae082-B4","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1111\/j.0006-341X.1999.00997.x","article-title":"Genomic control for association studies","volume":"55","author":"Devlin","year":"1999","journal-title":"Biometrics"},{"key":"2024022909074546900_btae082-B5","doi-asserted-by":"crossref","first-page":"4121","DOI":"10.1111\/mec.14833","article-title":"How to estimate kinship","volume":"27","author":"Goudet","year":"2018","journal-title":"Mol Ecol"},{"key":"2024022909074546900_btae082-B6","doi-asserted-by":"crossref","first-page":"e008108","DOI":"10.1161\/JAHA.117.008108","article-title":"Protein biomarkers of cardiovascular disease and mortality in the community","volume":"7","author":"Ho","year":"2018","journal-title":"J Am Heart Assoc"},{"key":"2024022909074546900_btae082-B7","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.2307\/2528643","article-title":"Genetic information given by a relative","volume":"28","author":"Jacquard","year":"1972","journal-title":"Biometrics"},{"key":"2024022909074546900_btae082-B8","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1186\/s12859-022-05082-2","article-title":"An unbiased kinship estimation method for genetic data analysis","volume":"23","author":"Jiang","year":"2022","journal-title":"BMC Bioinformatics"},{"key":"2024022909074546900_btae082-B9","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1038\/ng.548","article-title":"Variance component model to account for sample structure in genome-wide association studies","volume":"42","author":"Kang","year":"2010","journal-title":"Nat Genet"},{"key":"2024022909074546900_btae082-B10","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1093\/oxfordjournals.aje.a112813","article-title":"An investigation of coronary heart disease in families. 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