supplementaryTable4.pdf (518.48 kB)
Supplementary Table 4. Comparison of Ancestry methods
dataset
posted on 2017-12-22, 13:27 authored by Anuradha Jagadeesan, Ellen D. Gunnarsdóttir, S. Sunna Ebenesersdóttir, Valdis B. Guðmundsdóttir, Elisabet Linda Thordardottir, Margrét S. Einarsdóttir, Hákon Jónsson, Jean-Michel Dugoujon, Cesar Fortes-Lima, Florence Migot-Nabias, Achille Massougbodji, Gil Bellis, Luisa Pereira, Gísli Másson, Augustine Kong, Kári Stefánsson, Agnar HelgasonWe ran HAPMIX and LAMP-LD with 1000G phase 3 haplotypes. The European source panel consisted of 503 samples from British From England and Scotland [GBR], Toscani in Italia [TSI], Iberian Populations in Spain [IBS], Finnish in Finland [FIN] , and CEPH (U.S. Utah residents with ancestry from northern and western Europe) [CEU]. The African source panel consisted of 504 samples from Esan in Nigeria [ESN], Gambian in Western Division – Mandinka [GWD], Luhya in Webuye, Kenya [LWK], Mende in Sierra Leone [MSL] and Yoruba in Ibadan, Nigeria [YRI]. We retrieved phased alleles for 1,343,587 markers. We also ran LAMP-LD with only CEU and YRI populations. We applied the same filtering criteria to all the three analysis as described in the paper and the compared them.
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Human GeneticsHuman ancestrygenetic variation datasetGeneaologyAfrican microarray SNP datasetsingle nucleotide polymorphismgenetic variantsIcelandic populationAfrican ancestrydense genetic dataadmixed populationsancestry fragmentSNPwhole genome sequenceWGSgenome reconstructionIcelandic ancestrychromosome fragmentsphased source population genotype data
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