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Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing

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 an...

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Autores principales: Masset, Heleen, Ding, Jia, Dimitriadou, Eftychia, Ardeshirdavani, Amin, Debrock, Sophie, Tšuiko, Olga, Smits, Katrien, Peeraer, Karen, Moreau, Yves, Voet, Thierry, Zamani Esteki, Masoud, Vermeesch, Joris R
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9226495/
https://www.ncbi.nlm.nih.gov/pubmed/35212381
http://dx.doi.org/10.1093/nar/gkac134
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author Masset, Heleen
Ding, Jia
Dimitriadou, Eftychia
Ardeshirdavani, Amin
Debrock, Sophie
Tšuiko, Olga
Smits, Katrien
Peeraer, Karen
Moreau, Yves
Voet, Thierry
Zamani Esteki, Masoud
Vermeesch, Joris R
author_facet Masset, Heleen
Ding, Jia
Dimitriadou, Eftychia
Ardeshirdavani, Amin
Debrock, Sophie
Tšuiko, Olga
Smits, Katrien
Peeraer, Karen
Moreau, Yves
Voet, Thierry
Zamani Esteki, Masoud
Vermeesch, Joris R
author_sort Masset, Heleen
collection PubMed
description 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.
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spelling pubmed-92264952022-06-28 Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing Masset, Heleen Ding, Jia Dimitriadou, Eftychia Ardeshirdavani, Amin Debrock, Sophie Tšuiko, Olga Smits, Katrien Peeraer, Karen Moreau, Yves Voet, Thierry Zamani Esteki, Masoud Vermeesch, Joris R Nucleic Acids Res Methods Online 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. Oxford University Press 2022-02-25 /pmc/articles/PMC9226495/ /pubmed/35212381 http://dx.doi.org/10.1093/nar/gkac134 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Methods Online
Masset, Heleen
Ding, Jia
Dimitriadou, Eftychia
Ardeshirdavani, Amin
Debrock, Sophie
Tšuiko, Olga
Smits, Katrien
Peeraer, Karen
Moreau, Yves
Voet, Thierry
Zamani Esteki, Masoud
Vermeesch, Joris R
Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing
title Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing
title_full Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing
title_fullStr Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing
title_full_unstemmed Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing
title_short Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing
title_sort single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9226495/
https://www.ncbi.nlm.nih.gov/pubmed/35212381
http://dx.doi.org/10.1093/nar/gkac134
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