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Data Access Committee (DAC) of KU Leuven

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Joris Vermeesch
joris.vermeesch@kuleuven.be

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This DAC controls 5 datasets

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
EGAD00010002220	Single blastomeres from blastocyst and familial samples for haplotyping and copy-number profiling via SNP array	Illumina HumanCytoSNP-12 v2.1	21
EGAD50000000787	This dataset contains long-read whole-genome sequencing (lrWGS) data from 12 samples. Three lrWGS data are from single-cell (sc), multi-cell (mc, 10 cells), and bulk samples of HG002. The remaining nine lrWGS data are from two preimplantation genetic testing (PGT) families, including four from blood bulk DNA of the parental pairs and five from trophectoderm biopsies of two embryos from one family and three embryos from another family. The data are provided in raw FASTQ format and were generated using the PromethION device from Oxford Nanopore Technologies.	PromethION	12