{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T19:37:08Z","timestamp":1782848228628,"version":"3.54.5"},"reference-count":62,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2022,2,25]],"date-time":"2022-02-25T00:00:00Z","timestamp":1645747200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003130","name":"Fonds Wetenschappelijk Onderzoek","doi-asserted-by":"publisher","award":["11A7119N"],"award-info":[{"award-number":["11A7119N"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004040","name":"KU Leuven","doi-asserted-by":"publisher","award":["C14\/18\/092"],"award-info":[{"award-number":["C14\/18\/092"]}],"id":[{"id":"10.13039\/501100004040","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,6,24]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Single-cell whole-genome haplotyping allows simultaneous detection of haplotypes associated with monogenic diseases, chromosome copy-numbering and subsequently, has revealed mosaicism in embryos and embryonic stem cells. Methods, such as karyomapping and haplarithmisis, were deployed as a generic and genome-wide approach for preimplantation genetic testing (PGT) and are replacing traditional PGT methods. While current methods primarily rely on single-nucleotide polymorphism (SNP) array, we envision sequencing-based methods to become more accessible and cost-efficient. Here, we developed a novel sequencing-based methodology to haplotype and copy-number profile single cells. Following DNA amplification, genomic size and complexity is reduced through restriction enzyme digestion and DNA is genotyped through sequencing. This single-cell genotyping-by-sequencing (scGBS) is the input for haplarithmisis, an algorithm we previously developed for SNP array-based single-cell haplotyping. We established technical parameters and developed an analysis pipeline enabling accurate concurrent haplotyping and copy-number profiling of single cells. We demonstrate its value in human blastomere and trophectoderm samples as application for PGT for monogenic disorders. Furthermore, we demonstrate the method to work in other species through analyzing blastomeres of bovine embryos. Our scGBS method opens up the path for single-cell haplotyping of any species with diploid genomes and could make its way into the clinic as a PGT application.<\/jats:p>","DOI":"10.1093\/nar\/gkac134","type":"journal-article","created":{"date-parts":[[2022,2,11]],"date-time":"2022-02-11T20:10:18Z","timestamp":1644610218000},"page":"e63-e63","source":"Crossref","is-referenced-by-count":40,"title":["Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0215-8990","authenticated-orcid":false,"given":"Heleen","family":"Masset","sequence":"first","affiliation":[{"name":"Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven , Leuven , 3000 , Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia","family":"Ding","sequence":"additional","affiliation":[{"name":"Center of Human Genetics, University Hospitals of Leuven , Leuven , 3000 , Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eftychia","family":"Dimitriadou","sequence":"additional","affiliation":[{"name":"Center of Human Genetics, University Hospitals of Leuven , Leuven , 3000 , Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amin","family":"Ardeshirdavani","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics , KU Leuven, Leuven, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sophie","family":"Debrock","sequence":"additional","affiliation":[{"name":"Leuven University Fertility Center, University Hospitals Leuven , Leuven , 3000 , Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olga","family":"T\u0161uiko","sequence":"additional","affiliation":[{"name":"Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven , Leuven , 3000 , Belgium"},{"name":"Center of Human Genetics, University Hospitals of Leuven , Leuven , 3000 , Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katrien","family":"Smits","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Reproduction and Population Medicine, Ghent University , Merelbeke, 9820, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen","family":"Peeraer","sequence":"additional","affiliation":[{"name":"Leuven University Fertility Center, University Hospitals Leuven , Leuven , 3000 , Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yves","family":"Moreau","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics , KU Leuven, Leuven, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thierry","family":"Voet","sequence":"additional","affiliation":[{"name":"Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven , Leuven , 3000 , Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3909-0050","authenticated-orcid":false,"given":"Masoud","family":"Zamani\u00a0Esteki","sequence":"additional","affiliation":[{"name":"Department of Clinical Genetics, Maastricht University Medical Center , Maastricht , 6202 AZ, The Netherlands"},{"name":"Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University , Maastricht, 6229 ER, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joris\u00a0R","family":"Vermeesch","sequence":"additional","affiliation":[{"name":"Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven , Leuven , 3000 , Belgium"},{"name":"Center of Human Genetics, University Hospitals of Leuven , Leuven , 3000 , Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,2,25]]},"reference":[{"key":"2022081810473483900_B1","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1038\/nature09807","article-title":"Tumour evolution inferred by single-cell sequencing","volume":"472","author":"Navin","year":"2011","journal-title":"Nature"},{"key":"2022081810473483900_B2","doi-asserted-by":"crossref","first-page":"6119","DOI":"10.1093\/nar\/gkt345","article-title":"Single-cell paired-end genome sequencing reveals structural variation per cell cycle","volume":"41","author":"Voet","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2022081810473483900_B3","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1038\/nbt.3721","article-title":"Single-cell analysis at the threshold","volume":"34","author":"Chen","year":"2016","journal-title":"Nat. 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