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

Li YR, van Setten J, Verma SS, Lu Y, Holmes MV, Gao H, Lek M, Nair N, Chandrupatla H, Chang B, Karczewski KJ, Wong C, Mohebnasab M, Mukhtar E, Phillips R, Tragante V, Hou C, Steel L, Lee T, Garifallou J, Guettouche T, Cao H, Guan W, Himes A, van Houten J, Pasquier A, Yu R, Carrigan E, Miller MB, Schladt D, Akdere A, Gonzalez A, Llyod KM, McGinn D, Gangasani A, Michaud Z, Colasacco A, Snyder J, Thomas K, Wang T, Wu B, Alzahrani AJ, Al-Ali AK, Al-Muhanna FA, Al-Rubaish AM, Al-Mueilo S, Monos DS, Murphy B, Olthoff KM, Wijmenga C, Webster T, Kamoun M, Balasubramanian S, Lanktree MB, Oetting WS, Garcia-Pavia P, MacArthur DG, de Bakker PI, Hakonarson H, Birdwell KA, Jacobson PA, Ritchie MD, Asselbergs FW, Israni AK, Shaked A, Keating BJ - Genome Med (2015)

Bottom Line: We demonstrate much higher capture of the natural killer cell immunoglobulin-like receptor (KIR) region versus comparable platforms.Overall, we show that the genotyping quality and coverage of the TxArray is very high when compared to reference samples and to other genome-wide genotyping platforms.We have designed a comprehensive genome-wide genotyping tool which enables accurate association testing and imputation of ungenotyped SNPs, facilitating powerful and cost-effective large-scale genotyping of transplant-related studies.

View Article: PubMed Central - PubMed

Affiliation: Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

ABSTRACT

Background: In addition to HLA genetic incompatibility, non-HLA difference between donor and recipients of transplantation leading to allograft rejection are now becoming evident. We aimed to create a unique genome-wide platform to facilitate genomic research studies in transplant-related studies. We designed a genome-wide genotyping tool based on the most recent human genomic reference datasets, and included customization for known and potentially relevant metabolic and pharmacological loci relevant to transplantation.

Methods: We describe here the design and implementation of a customized genome-wide genotyping array, the 'TxArray', comprising approximately 782,000 markers with tailored content for deeper capture of variants across HLA, KIR, pharmacogenomic, and metabolic loci important in transplantation. To test concordance and genotyping quality, we genotyped 85 HapMap samples on the array, including eight trios.

Results: We show low Mendelian error rates and high concordance rates for HapMap samples (average parent-parent-child heritability of 0.997, and concordance of 0.996). We performed genotype imputation across autosomal regions, masking directly genotyped SNPs to assess imputation accuracy and report an accuracy of >0.962 for directly genotyped SNPs. We demonstrate much higher capture of the natural killer cell immunoglobulin-like receptor (KIR) region versus comparable platforms. Overall, we show that the genotyping quality and coverage of the TxArray is very high when compared to reference samples and to other genome-wide genotyping platforms.

Conclusions: We have designed a comprehensive genome-wide genotyping tool which enables accurate association testing and imputation of ungenotyped SNPs, facilitating powerful and cost-effective large-scale genotyping of transplant-related studies.

No MeSH data available.


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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Fig4: 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)

Mentions: The TxArray also provided efficient coverage of markers across the exonic, KIR, and MHC regions when compared to the commonly-used Illumina 1M platform (Fig. 4a, b, and c, respectively). While mean expected coverage is comparable for the exonic and MHC regions, the TxArray provides a significantly improved coverage of markers across the KIR locus, which has been a region that has arguably received insufficient attention in most transplant association studies.Fig. 4


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

Li YR, van Setten J, Verma SS, Lu Y, Holmes MV, Gao H, Lek M, Nair N, Chandrupatla H, Chang B, Karczewski KJ, Wong C, Mohebnasab M, Mukhtar E, Phillips R, Tragante V, Hou C, Steel L, Lee T, Garifallou J, Guettouche T, Cao H, Guan W, Himes A, van Houten J, Pasquier A, Yu R, Carrigan E, Miller MB, Schladt D, Akdere A, Gonzalez A, Llyod KM, McGinn D, Gangasani A, Michaud Z, Colasacco A, Snyder J, Thomas K, Wang T, Wu B, Alzahrani AJ, Al-Ali AK, Al-Muhanna FA, Al-Rubaish AM, Al-Mueilo S, Monos DS, Murphy B, Olthoff KM, Wijmenga C, Webster T, Kamoun M, Balasubramanian S, Lanktree MB, Oetting WS, Garcia-Pavia P, MacArthur DG, de Bakker PI, Hakonarson H, Birdwell KA, Jacobson PA, Ritchie MD, Asselbergs FW, Israni AK, Shaked A, Keating BJ - Genome Med (2015)

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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Fig4: 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)
Mentions: The TxArray also provided efficient coverage of markers across the exonic, KIR, and MHC regions when compared to the commonly-used Illumina 1M platform (Fig. 4a, b, and c, respectively). While mean expected coverage is comparable for the exonic and MHC regions, the TxArray provides a significantly improved coverage of markers across the KIR locus, which has been a region that has arguably received insufficient attention in most transplant association studies.Fig. 4

Bottom Line: We demonstrate much higher capture of the natural killer cell immunoglobulin-like receptor (KIR) region versus comparable platforms.Overall, we show that the genotyping quality and coverage of the TxArray is very high when compared to reference samples and to other genome-wide genotyping platforms.We have designed a comprehensive genome-wide genotyping tool which enables accurate association testing and imputation of ungenotyped SNPs, facilitating powerful and cost-effective large-scale genotyping of transplant-related studies.

View Article: PubMed Central - PubMed

Affiliation: Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

ABSTRACT

Background: In addition to HLA genetic incompatibility, non-HLA difference between donor and recipients of transplantation leading to allograft rejection are now becoming evident. We aimed to create a unique genome-wide platform to facilitate genomic research studies in transplant-related studies. We designed a genome-wide genotyping tool based on the most recent human genomic reference datasets, and included customization for known and potentially relevant metabolic and pharmacological loci relevant to transplantation.

Methods: We describe here the design and implementation of a customized genome-wide genotyping array, the 'TxArray', comprising approximately 782,000 markers with tailored content for deeper capture of variants across HLA, KIR, pharmacogenomic, and metabolic loci important in transplantation. To test concordance and genotyping quality, we genotyped 85 HapMap samples on the array, including eight trios.

Results: We show low Mendelian error rates and high concordance rates for HapMap samples (average parent-parent-child heritability of 0.997, and concordance of 0.996). We performed genotype imputation across autosomal regions, masking directly genotyped SNPs to assess imputation accuracy and report an accuracy of >0.962 for directly genotyped SNPs. We demonstrate much higher capture of the natural killer cell immunoglobulin-like receptor (KIR) region versus comparable platforms. Overall, we show that the genotyping quality and coverage of the TxArray is very high when compared to reference samples and to other genome-wide genotyping platforms.

Conclusions: We have designed a comprehensive genome-wide genotyping tool which enables accurate association testing and imputation of ungenotyped SNPs, facilitating powerful and cost-effective large-scale genotyping of transplant-related studies.

No MeSH data available.