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

3 Datasets 1 Publication

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001007794	scGBS is a single-cell sequencing-based methodology to haplotype and copy-number profile single cells. Genomic size and complexity is reduced through restriction enzyme digestion and DNA is genotyped through sequencing of the restriction fragments. scGBS data serves as the input for haplarithmisis, an algorithm we previously developed for SNP array-based single-cell haplotyping (Zamani Esteki et al., 2015). We established technical parameters and developed an analysis pipeline enabling accurate concurrent haplotyping and copy-number profiling of single cells with the use of a HapMap cell line pedigree (7 single cells). A clinical validation of the methodology with a total of 14 single blastomeres and 3 trophectoderm samples biopsies from human preimplantation embryos for 6 PGT-M families were processed with scGBS and were previously haploptyped via SNP array.	Illumina HiSeq 2500 NextSeq 500	49
EGAD00010002168	HapMap samples for haplotyping and copy-number profiling via SNP array	Illumina HumanCytoSNP-12 v2.1	11
EGAD00010002169	PGT samples for haplotyping and copy-number profiling via SNP array	Illumina HumanCytoSNP-12 v2.1	39

Publications	Citations
Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing. Masset H, Ding J, Dimitriadou E, Debrock S, Tšuiko O, Smits K, Peeraer K, Voet T, Zamani Esteki M, Vermeesch JR. Nucleic Acids Res 50: 2022 e63	2