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Protocols

HGDP-CEPH specifications

Information


Unique identifier OMICS_17669
Name HGDP-CEPH
Alternative name Human Genome Diversity Cell Line Panel - Centre d’Etude du Polymorphisme Humain
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Version 3.0
Maintained Yes

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HGDP-CEPH citations

 (41)
library_books

Enrichment of low frequency functional variants revealed by whole genome sequencing of multiple isolated European populations

2017
Nat Commun
PMCID: 5490002
PMID: 28643794
DOI: 10.1038/ncomms15927

[…] Shared ancestry between the populations studied here was evaluated using ADMIXTURE v1.22 (ref. ). The relationships between the populations studied here, combined with worldwide populations from the HGDP-CEPH panel, were also examined using ancestry graph analyses implemented in TreeMix v.1.12 (ref. ). We also used formal test of f3-statistics to investigate population mixture in the history of t […]

call_split

Genetic polymorphism and evolutionary differentiation of Eastern Chinese Han: a comprehensive and comparative analysis on KIRs

2017
Sci Rep
PMCID: 5311978
PMID: 28205529
DOI: 10.1038/srep42486
call_split See protocol

[…] with complete KIR genotyping files of 16 KIR genes exclusive of KIR1D which are Jilin Han, Shaanxi Han, Shenzhen Han, Sichuan Han, Xinjiang Han, Yunnan Han and the complete list of 52 populations in HGDP-CEPH distributed around the world. The Heatmap is constructed using Hierarchical Clustering algorithm based on Euclidean distance. The Hierarchical Clustering model generally refers to the assump […]

call_split

Outlining the Ancestry Landscape of Colombian Admixed Populations

2016
PLoS One
PMCID: 5063461
PMID: 27736937
DOI: 10.1371/journal.pone.0164414
call_split See protocol

[…] ons in the studied populations, supervised analyses were then performed using prior information on the geographic origin of the reference samples. Ancestry analyses were initially conducted using the HGDP-CEPH populations as a reference []. We then investigated the possible impact of considering different Native groups (i.e., HGDP-CEPH, Emberá-Chami, Motilón-Barí and Guainía) as the American ances […]

library_books

Genetic variation in Tunisia in the context of human diversity worldwide

2016
PMCID: 5084816
PMID: 27192181
DOI: 10.1002/ajpa.23008

[…] ALFRED: http://alfred.med.yale.edu HGDP‐CEPH Database: http://www.cephb.fr/en/index.php HGDP selection browser: http://hgdp.uchicago.edu/cgi-bin/gbrowse/HGDP/CLUMPAK (Cluster Markov Packager Across K): http://clumpak.tau.ac.il/ […]

call_split

Refining the Y chromosome phylogeny with southern African sequences

2016
Hum Genet
PMCID: 4835522
PMID: 27043341
DOI: 10.1007/s00439-016-1651-0
call_split See protocol

[…] ing 500 bp of each target region covered by the reads, giving a total of 964,809 callable sites (data available in Online Resource 3). To improve SNP calling, the reads were merged with the available HGDP-CEPH data (Lippold et al. ). SNP calling and quality filtering were performed with GATK with the following settings: QD < 2.0, MQ < 40.0, FS > 60, Haplotypescore > 13.0, MQrankSum < −12.5, ReadPo […]

library_books

Distribution of two OCA2 polymorphisms associated with pigmentation in East Asian populations

2015
Hum Genome Var
PMCID: 4785538
PMID: 27081560
DOI: 10.1038/hgv.2015.58

[…] 330, with a primary focus on the allelic frequencies observed in East Asia. Briefly, the two polymorphisms were genotyped in the Human Genome Diversity Project–Centre d’Étude du Polymorphisme Humain (HGDP–CEPH) samples (http://www.cephb.fr/en/hgdp_panel.php) by LCG Genomics (Beverly, MA, USA) by using KASP genotyping technology. The HGDP–CEPH panel includes samples for more than 1,000 individuals […]


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