{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T07:30:32Z","timestamp":1778830232516,"version":"3.51.4"},"reference-count":23,"publisher":"Springer Science and Business Media LLC","issue":"5","license":[{"start":{"date-parts":[[2024,5,14]],"date-time":"2024-05-14T00:00:00Z","timestamp":1715644800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,5,14]],"date-time":"2024-05-14T00:00:00Z","timestamp":1715644800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Comput Sci"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>For many genome-wide association studies, imputing genotypes from a haplotype reference panel is a necessary step. Over the past 15\u2009years, reference panels have become larger and more diverse, leading to improvements in imputation accuracy. However, the latest generation of reference panels is subject to restrictions on data sharing due to concerns about privacy, limiting their usefulness for genotype imputation. In this context, here we propose RESHAPE, a method that employs a recombination Poisson process on a reference panel to simulate the genomes of hypothetical descendants after multiple generations. This data transformation helps to protect against re-identification threats and preserves data attributes, such as linkage disequilibrium patterns and, to some degree, identity-by-descent sharing, allowing for genotype imputation. Our experiments on gold-standard datasets show that simulated descendants up to eight generations can serve as reference panels without substantially reducing genotype imputation accuracy.<\/jats:p>","DOI":"10.1038\/s43588-024-00630-7","type":"journal-article","created":{"date-parts":[[2024,5,14]],"date-time":"2024-05-14T06:03:06Z","timestamp":1715666586000},"page":"360-366","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["A resampling-based approach to share reference panels"],"prefix":"10.1038","volume":"4","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-9916-5525","authenticated-orcid":false,"given":"Th\u00e9o","family":"Cavinato","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simone","family":"Rubinacci","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna-Sapfo","family":"Malaspinas","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3906-8446","authenticated-orcid":false,"given":"Olivier","family":"Delaneau","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,5,14]]},"reference":[{"key":"630_CR1","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1038\/nrg2796","volume":"11","author":"J Marchini","year":"2010","unstructured":"Marchini, J. & Howie, B. Genotype imputation for genome-wide association studies. Nat. Rev. Genet. 11, 499\u2013511 (2010).","journal-title":"Nat. Rev. Genet."},{"key":"630_CR2","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1016\/j.ajhg.2018.07.015","volume":"103","author":"BL Browning","year":"2018","unstructured":"Browning, B. L., Zhou, Y. & Browning, S. R. A one-penny imputed genome from next-generation reference panels. Am. J. Hum. Genet. 103, 338\u2013348 (2018).","journal-title":"Am. J. Hum. Genet."},{"key":"630_CR3","doi-asserted-by":"publisher","first-page":"e1009049","DOI":"10.1371\/journal.pgen.1009049","volume":"16","author":"S Rubinacci","year":"2020","unstructured":"Rubinacci, S., Delaneau, O. & Marchini, J. Genotype imputation using the positional Burrows Wheeler transform. PLoS Genet. 16, e1009049 (2020).","journal-title":"PLoS Genet."},{"key":"630_CR4","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1038\/s41588-020-00756-0","volume":"53","author":"S Rubinacci","year":"2021","unstructured":"Rubinacci, S., Ribeiro, D. M., Hofmeister, R. J. & Delaneau, O. Efficient phasing and imputation of low-coverage sequencing data using large reference panels. Nat. Genet. 53, 120\u2013126 (2021).","journal-title":"Nat. Genet."},{"key":"630_CR5","doi-asserted-by":"publisher","first-page":"2213","DOI":"10.1093\/genetics\/165.4.2213","volume":"165","author":"N Li","year":"2003","unstructured":"Li, N. & Stephens, M. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165, 2213\u20132233 (2003).","journal-title":"Genetics"},{"key":"630_CR6","doi-asserted-by":"publisher","first-page":"2225","DOI":"10.1126\/science.1069424","volume":"296","author":"SB Gabriel","year":"2002","unstructured":"Gabriel, S. B. et al. The structure of haplotype blocks in the human genome. Science 296, 2225\u20132229 (2002).","journal-title":"Science"},{"key":"630_CR7","unstructured":"The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526, 68\u201374 (2015)."},{"key":"630_CR8","doi-asserted-by":"publisher","first-page":"1279","DOI":"10.1038\/ng.3643","volume":"48","author":"S McCarthy","year":"2016","unstructured":"McCarthy, S. et al. A reference panel of 64,976 haplotypes for genotype imputation. Nat. Genet. 48, 1279\u20131283 (2016).","journal-title":"Nat. Genet."},{"key":"630_CR9","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1038\/s41586-021-03205-y","volume":"590","author":"D Taliun","year":"2021","unstructured":"Taliun, D. et al. Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Nature 590, 290\u2013299 (2021).","journal-title":"Nature"},{"key":"630_CR10","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1038\/s41586-018-0579-z","volume":"562","author":"C Bycroft","year":"2018","unstructured":"Bycroft, C. et al. The UK Biobank resource with deep phenotyping and genomic data. Nature 562, 203\u2013209 (2018).","journal-title":"Nature"},{"key":"630_CR11","doi-asserted-by":"publisher","first-page":"732","DOI":"10.1038\/s41586-022-04965-x","volume":"607","author":"BV Halldorsson","year":"2022","unstructured":"Halldorsson, B. V. et al. The sequences of 150,119 genomes in the UK Biobank. Nature 607, 732\u2013740 (2022).","journal-title":"Nature"},{"key":"630_CR12","doi-asserted-by":"publisher","first-page":"1243","DOI":"10.1038\/s41588-023-01415-w","volume":"55","author":"RJ Hofmeister","year":"2023","unstructured":"Hofmeister, R. J. et al. Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank. Nat. Genet. 55, 1243\u20131249 (2023).","journal-title":"Nat. Genet."},{"key":"630_CR13","doi-asserted-by":"publisher","first-page":"e1000477","DOI":"10.1371\/journal.pgen.1000477","volume":"5","author":"CCA Spencer","year":"2009","unstructured":"Spencer, C. C. A., Su, Z., Donnelly, P. & Marchini, J. Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip. PLoS Genet. 5, e1000477 (2009).","journal-title":"PLoS Genet."},{"key":"630_CR14","doi-asserted-by":"publisher","first-page":"2304","DOI":"10.1093\/bioinformatics\/btr341","volume":"27","author":"Z Su","year":"2011","unstructured":"Su, Z., Marchini, J. & Donnelly, P. HAPGEN2: simulation of multiple disease SNPs. Bioinformatics 27, 2304\u20132305 (2011).","journal-title":"Bioinformatics"},{"key":"630_CR15","doi-asserted-by":"publisher","first-page":"btad535","DOI":"10.1093\/bioinformatics\/btad535","volume":"39","author":"S Wharrie","year":"2023","unstructured":"Wharrie, S. et al. HAPNEST: efficient, large-scale generation and evaluation of synthetic datasets for genotypes and phenotypes. Bioinformatics 39, btad535 (2023).","journal-title":"Bioinformatics"},{"key":"630_CR16","doi-asserted-by":"publisher","unstructured":"Naveed, M. et al. Privacy in the genomic era. 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Cell Syst. 12, 1108\u20131120.e4 (2021).","DOI":"10.1016\/j.cels.2021.07.010"},{"key":"630_CR20","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008","volume":"10","author":"P Danecek","year":"2021","unstructured":"Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience. 10, giab008 (2021).","journal-title":"GigaScience."},{"key":"630_CR21","doi-asserted-by":"publisher","first-page":"1299","DOI":"10.1038\/nature04226","volume":"437","author":"International HapMap Consortium.","year":"2005","unstructured":"International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299\u20131320 (2005).","journal-title":"Nature"},{"key":"630_CR22","doi-asserted-by":"crossref","unstructured":"Byrska-Bishop, M. et al. High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios. Cell 185, 3426\u20133440.e19 (2022).","DOI":"10.1016\/j.cell.2022.08.004"},{"key":"630_CR23","doi-asserted-by":"publisher","unstructured":"Cavinato, T., Rubinacci, S. & Delaneau, O. RESHAPE v1.0.0. Zenodo https:\/\/doi.org\/10.5281\/zenodo.10970473 (2023).","DOI":"10.5281\/zenodo.10970473"}],"container-title":["Nature Computational Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s43588-024-00630-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s43588-024-00630-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s43588-024-00630-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,29]],"date-time":"2024-05-29T12:11:50Z","timestamp":1716984710000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s43588-024-00630-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,5,14]]},"references-count":23,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2024,5]]}},"alternative-id":["630"],"URL":"https:\/\/doi.org\/10.1038\/s43588-024-00630-7","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.04.07.535812","asserted-by":"object"}]},"ISSN":["2662-8457"],"issn-type":[{"value":"2662-8457","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,5,14]]},"assertion":[{"value":"2 May 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 April 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 May 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"O.D. is a current employee of Regeneron Genetics Center which is a subsidiary of Regeneron Pharmaceuticals.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}