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Intensity SNP-array data have been used to infer mLOY status and to determine its prominent role in male disease. However, discrepancies of reported findings can be due to the uncertainty and variability of the methods used for mLOY detection and to the differences in the tissue-matrix used.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      We created a publicly available software tool called\n                      <jats:italic>MADloy<\/jats:italic>\n                      (Mosaic Alteration Detection for LOY) that incorporates existing methods and includes a new robust approach, allowing efficient calling in large studies and comparisons between methods.\n                      <jats:italic>MADloy<\/jats:italic>\n                      optimizes mLOY calling by correctly modeling the underlying reference population with no-mLOY status and incorporating B-deviation information. We observed improvements in the calling accuracy to previous methods, using experimentally validated samples, and an increment in the statistical power to detect associations with disease and mortality, using simulation studies and real dataset analyses. To understand discrepancies in mLOY detection across different tissues, we applied\n                      <jats:italic>MADloy<\/jats:italic>\n                      to detect the increment of mLOY cellularity in blood on 18 individuals after 3\u00a0years and to confirm that its detection in saliva was sub-optimal (41%). We additionally applied MADloy to detect the down-regulation genes in the chromosome Y in kidney and bladder tumors with mLOY, and to perform pathway analyses for the detection of mLOY in blood.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      <jats:italic>MADloy<\/jats:italic>\n                      is a new software tool implemented in R for the easy and robust calling of mLOY status across different tissues aimed to facilitate its study in large epidemiological studies.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-020-03768-z","type":"journal-article","created":{"date-parts":[[2020,11,23]],"date-time":"2020-11-23T05:03:55Z","timestamp":1606107835000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["MADloy: robust detection of mosaic loss of chromosome Y from genotype-array-intensity data"],"prefix":"10.1186","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3267-2146","authenticated-orcid":false,"given":"Juan R.","family":"Gonz\u00e1lez","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcos","family":"L\u00f3pez-S\u00e1nchez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alejandro","family":"C\u00e1ceres","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pere","family":"Puig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tonu","family":"Esko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luis A.","family":"P\u00e9rez-Jurado","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,11,23]]},"reference":[{"key":"3768_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-018-30759-1","volume":"8","author":"E Loftfield","year":"2018","unstructured":"Loftfield E, Zhou W, Graubard BI, Yeager M, Chanock SJ, Freedman ND, Machiela MJ. 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The project is conducted in accordance with the Estonian Gene Research Act (\n                      \n                      ) and all subjects have been recruited randomly, on a voluntary basis by general practitioners and physicians in hospitals. All subjects provided written informed consent prior to participation and the approval for the study was granted by the Ethics Review Committee on Human Research at the University of Tartu. All other data used in the study is freely available and their consent to participate is available in their web page projects.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"533"}}