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Fig. 4 | Genome Medicine

Fig. 4

From: Concept and design of a genome-wide association genotyping array tailored for transplantation-specific studies

Fig. 4

Comparison of coverage between TxArray and ILMN_1M genotyping platforms across exonic regions, the extended MHC and the KIR-encoding locus. a Coverage (ordinate) for all exonic markers and UTR region markers in the 1000 genomes reference panel was assessed using max r2 (abscissa), at an MAF cutoff of 0.05 (a) and 0.01 (b), in (1) European ancestry ((CEU) and Tuscany in Italia (TSI)); (2) African ancestry (AAM) (Yoruba in Ibadan, Nigeria (YRI)) and Americans of African Ancestry in SouthWest, USA (ASW); (3) Admixed American (AMR) (Colombians from Medellin, Colombia (CLM), Mexican Ancestry from Los Angeles, USA (MXL), and Puerto Ricans from Puerto Rico (PUR)); and (4) Asian (ASN) (Han Chinese in Beijing (CHB), Southern Han Chinese (CHS), Japanese in Tokyo, Japan (JPT)) HapMap and 1KGP individuals. The compared platforms include the TxArray using 767,203 SNPs that passed manufacturing and standard genotyping QC. ILMN_1M refer to Illumina’s Infinium one million SNP GWAS array. b Comparison of coverage across variants within KIR-encoding regions using the TxArray (TX) or the Illumina 1M (ILMN_1M) genotyping platforms across the four major HapMap populations (European (CTU): CEU+TSI; AAM: ASW+YRI; AMR: CLM+MXL+PUR; ASN: CHB+CHS+JPT). Coverage is based on mean r2 of variants included in the 1000 genomes phase I reference panel with a MAF of >0.01 (top) or >0.05 (bottom). KIR genes included: (KIR2DP1, KIR2DL1, KIR2DL2, KIR2DL3, KIR2DL4, KIR2DL5A, KIR2DL5B, KIR2DS1, KIR2DS2, KIR2DS3, KIR2DS4, KIR2DS5, KIR3DL1, KIR3DL2, KIR3DL3, KIR3DP1, KIR3DS1, KIR3DX1). Coverage was compared for either all KIR region markers (left) or only those in exonic regions (right). c Comparison of coverage across the extended MHC (25,500,000–34,000,000) using either the TxArray (TX) or the Illumina 1M (ILMN_1M) genotyping platforms across the four major HAPMAP populations (CTU: CEU/TSI; AAM: ASW/YRI; AMR: CLM/MXL/PUR; ASN: CHB/CHS/JPT). Coverage rate is calculated based on the mean achieved r2 for variants included in the 1000 Genomes Project (1KGP) Phase I reference panel with a MAF of >0.01 (left) or >0.05 (right)

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