Platinum-Pedigree-Datasets

Platinum Pedigree Consortium includes whole genome sequencing using five technologies on a 4-generation family. This is the CEPH-Utah (CEU) family 1463 and includes 4 grandparents from 1st generation, 2 parents from 2nd generation, 5 children from 3rd generation, 9 individuals from the 4th generation representing 2 branches of the 3rd generation, and their 2 additional parents. Family was not selected for disease, rather large size to study genetic transmission and human variation.

Accessing the Amazon Open Data

To access the S3 bucket use the amazon awscli:

List all datasets:

aws s3 ls --no-sign-request s3://platinum-pedigree-data/

List all mapped sequencing data:

aws s3 ls --no-sign-request s3://platinum-pedigree-data/data/

List all assemblies:

aws s3 ls --no-sign-request s3://platinum-pedigree-data/assemblies/

List all variant calls:

aws s3 ls --no-sign-request s3://platinum-pedigree-data/variants/

Accessing controlled samples

Not all samples described in Porubsky et al. 2024 are consented for an open access. Five samples in the third generation (NA12883 (2298), NA12884 (2215), and NA12887 (2187)) as well as two samples from the fourth generation (200103 and 200105) are available via controlled access at dbGaP (accession id: phs003793.v1.p1):

https://www.ncbi.nlm.nih.gov/gap/

datasets

Mapped Element data:
data/element/

Mapped HiFi data:
data/hifi/

Mapped Illumina data:
data/illumina

Mapped ONT data:
data/ont

Mapped and raw Strand-seq data:
data/strandseq

variants

Pedigree consistent merged structural variant calls:
variants/merged_sv_truthset/GRCh38/merged_hg38.svs.sort.oa.vcf.gz

Pedigree consistent merged structural variant calls removing overlapping TRs:
variants/merged_sv_truthset/GRCh38/merged_hg38.svs.TRexclusion.sort.oa.vcf.gz

Pedigree consistent tandem repeats:
variants/tr_truthset/GRCh38/ceph_1463_tandem_repeats.oa.vcf.gz

Pedigree consistent merged small variant calls (truthset):
  variants/small_variant_truthset/GRCh38/CEPH1463.GRCh38.family-truthset.ov.vcf.gz
  variants/small_variant_truthset/GRCh38/hq_regions_final.bed.gz

DeepVariant (HiFi) calls:
variants/small_variants/(GRCh38|CHM13)/CEPH1463.GRCh38.deepvariant.glnexus.oa.vcf.gz

Dragen (Illumina) calls:
variants/small_variants/(GRCh38|CHM13)/CEPH1463.GRCh38.illumina-dragen.oa.vcf.gz

Clair3 (ONT) calls:
variants/small_variants/(GRCh38|CHM13)/CEPH1463.GRCh38.ont-clair3.glnexus.oa.vcf.gz

Assembly-based variant calls with respect to both GRCh38 and T2T-CHM13 (CHM13) human references reported by dipcall variant caller:
variants/assembly-based/dipcall

Reported by PAV variant caller:
variants/assembly-based/pav
 

sample meta data

ped	id	father	mother	sex	sec.id	primary.id	Generation
1463	2281	0	0	1	GM12889	NA12889	G1
1463	2280	0	0	2	GM12890	NA12890	G1
1463	2214	0	0	1	GM12891	NA12891	G1
1463	2213	0	0	2	GM12892	NA12892	G1
1463	2209	2281	2280	1	GM12877	NA12877	G2
1463	2188	2214	2213	2	GM12878	NA12878	G2
1463	2216	2209	2188	2	GM12879	NA12879	G3
1463	2211	2209	2188	2	GM12881	NA12881	G3
1463	2212	2209	2188	1	GM12882	NA12882	G3
1463	2298	2209	2188	1	GM12883	NA12883	G3
1463	2215	2209	2188	1	GM12884	NA12884	G3
1463	2217	2209	2188	2	GM12885	NA12885	G3
1463	2189	2209	2188	1	GM12886	NA12886	G3
1463	2187	2209	2188	2	GM12887	NA12887	G3
1463	200080			1	NA	200080	Spouse
1463	200081			2	NA	200081	G4
1463	200082			2	NA	200082	G4
1463	200084			1	NA	200084	G4
1463	200085			1	NA	200085	G4
1463	200086			2	NA	200086	G4
1463	200087			1	NA	200087	G4
1463	200100			2	NA	200100	Spouse
1463	200101			1	NA	200101	G4
1463	200102			1	NA	200102	G4
1463	200103			2	NA	200103	G4
1463	200104			2	NA	200104	G4
1463	200105			1	NA	200105	G4
1463	200106			2	NA	200106	G4

Ethics declarations

Human subjects: Informed consent was obtained from the CEPH/Utah individuals, and the University of Utah Institutional Review Board approved the study (University of Utah IRB reference IRB_00065564).

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Thanks to Amazon Open Data for sponsorship