Data Access Committee for Deciphering Developmental Disorders (DDD) Project

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Data Sharing Sanger
datasharing@sanger.ac.uk

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This DAC controls 26 datasets

Dataset ID	Description	Technology	Samples
EGAD00001001114	DDD DATAFREEZE 2013-12-18: 1133 trios - exome sequence BAM files (Ref: DDD Nature 2015)		-
EGAD00001001355	DDD DATAFREEZE 2013-12-18: 1133 trios - VCF files (Ref: DDD Nature 2015)		-
EGAD00001001413	DDD DATAFREEZE 2013-12-18: 1133 trios - README, family trios, phenotypes, validated DNMs (Ref: DDD Nature 2015)		-
EGAD00001001848	DDD DATAFREEZE 2014-11-04: 4293 trios - VCF files		-
EGAD00001001977	DDD DATAFREEZE 2014-11-04: 4293 trios - phenotypic and family descriptions		-
EGAD00001002748	DDD DATAFREEZE 2014-11-04: 4293 trios - exome sequence CRAM files		-
EGAD00001003340	DDD DATAFREEZE 2016-10-03: 7831 trios - VCF files		-
EGAD00001003350	DDD DATAFREEZE 2016-10-03: 7831 trios - phenotypic and family descriptions		-
EGAD00001003406	DDD DATAFREEZE 2016-10-03: 7831 trios - exome sequence CRAM files		-
EGAD00001004388	DDD DATAFREEZE 2017-12-15: 13,462 trios and probands only - phenotypic and family descriptions		-
EGAD00001004389	DDD DATAFREEZE 2017-12-15: 13,462 trios and probands only - exome sequence VCF files		-
EGAD00001004390	DDD DATAFREEZE 2017-12-15: 13,462 trios and probands only - exome sequence CRAM files		-
EGAD00001004586	Variants and WGS data for Gardner et al. 2018 (biorxiv 471375). One VCF each for Alu, L1, and SVA. Flat text file and WGS for processed pseudogenes.	HiSeq X Ten	-
EGAD00001005728	aCGH CNV detection by CNsolidate for 6,827 DDD probands		-
EGAD00001008497	CRAM files and VCF for DDD_1 and their parents. Also de novo mutations file for hypermutated DDD_1 child as described in the manuscript ‘Genetic and chemotherapeutic influences of germline hypermutation’ by Kaplanis et al. which will be published in Nature shortly.	HiSeq X Ten	3
EGAD00001010136	DDD resource files (e.g. link between sample and individual ids)		-
EGAD00001010137	Candidate diagnostic variants reported into DECIPHER by 4 April 2022, annotated with clinical and automated pathogenicity assertions (see DOI: 10.1056/NEJMoa2209046). Genomic Diagnosis of Rare Pediatric Disease in the United Kingdom and Ireland, Wright et al, NEJM 2023.		-
EGAD00010000702	SNP-chip genotyping data for one proband in the DDD study (Ref : Carvalho AJHG 2015)		1
EGAD00010001598	Batch 1 of unfiltered genotype data for DDD Study patients (N=2,997), some of which were used in the neurodevelopmental disorder discovery GWAS (Niemi et al., Nature 2018). Samples were genotyped on the Illumina HumanCoreExome BeadChip. QC'd data is available in release EGAD00010001604	Illumina HumanCoreExome-24v1-0	3000
EGAD00010001600	Batch 2 of unfiltered genotype for DDD Study patients (N=8,286), some of which were used in the neurodevelopmental disorder discovery GWAS (Niemi et al., Nature 2018). Samples were genotyped on the Illumina InfiniumCoreExome Beadchip. QC'd data is available in release EGAD00010001604	Illumina HumanCoreExome-24v1-1	8207
EGAD00010001602	Unfiltered genotype data for DDD Study trios (patient and parents) (N=2,166 samples), some of which were used for replication of neurodevelopmental disorder polygenic risk (Niemi et al., Nature 2018). Samples were genotyped on the Illumina HumanOmniExpress BeadChip	Illumina SangerDDD_OmniExPlusv1_15019773	3822
EGAD00010001604	Post-QC (pre-imputation) genotype data for N=6,983 DDD probands included in the neurodevelopmental disorder discovery GWAS (Niemi et al., Nature 2018). Consists of filtered set of samples and variants from EGAD00010001598 and EGAD00010001600. Includes patient HPO phenotype terms and GWAS summary statistics (including imputed variants). Samples were genotyped on the Illumina HumanCoreExome BeadChip and Illumina InfiniumCoreExome Beadchip	Illumina HumanCoreExome-24v1	6987
EGAD00010001606	Post-QC (pre-imputation) genotype data for N=2,166, a subset of trios described in EGAD00010001602. These data form N=722 complete trios in which the proband has a neurodevelopmental phenotype (Niemi et al. Nature 2018). Includes HPO phenotype terms for patients. Samples were genotyped on the Illumina HumanOmniExpress BeadChip	Illumina SangerDDD_OmniExPlusv1_15019773 MiSeq	2225
EGAD00010002567	Unfiltered genotype data for a pilot study (Batch 1) of 1,140 DDD Study participants (and 12 "Empty" samples). Samples include 380 mothers, 382 fathers and 378 probands, and form 376 trios. Most of the probands have been previously genoyped on the llumina HumanCoreExome BeadChip (EGAD00010001598) or the Illumina InfiniumCoreExome Beadchip (EGAD00010001600). All samples were genotyped on the Illumina Global Screening Array.	Illumina Global Screening Array	1140
EGAD00010002568	QC-ed data of 9,534 DDD Study participants, including 8,879 individuals with inferred GBR ancestry. Details of genotype QC can be found in https://www.medrxiv.org/content/10.1101/2023.04.20.23288860v1.full.pdf. Genome builds are indicated in the file name. Related individuals have not been removed. Of the 9,534 samples there are 3,148 mothers, 3,138 fathers and 3,248 probands, which form 3,099 trios. Of the 8,879 GBR samples, there are 2,931 mothers, 2,937 father and 3,011 probands, which form 2,788 trios. Most of the probands have been previously genoyped on the llumina HumanCoreExome BeadChip (EGAD00010001598) or the Illumina InfiniumCoreExome Beadchip (EGAD00010001600). All samples were genotyped on the Illumina Global Screening Array.	Illumina Global Screening Array	9534
EGAD00010002569	Unfiltered genotype data for a larger batch (Batch 2) of 8,697 DDD Study participants (and 1 "Blank" sample). Samples include 2,858 mothers, 2,857 fathers and 2,982 probands, and form 2,918 trios. Most of the probands have been previously genoyped on the llumina HumanCoreExome BeadChip (EGAD00010001598) or the Illumina InfiniumCoreExome Beadchip (EGAD00010001600). All samples were genotyped on the Illumina Global Screening Array.	Illumina Global Screening Array	9846