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mapping snp panels  (Illumina Inc)
90
Illumina Inc mapping snp panels
Congruence is widespread across the MHC and is not limited to the DR3-B8A1 haplotype . A : Percent congruence of 132 extended DQ-DR-B-A haplotype groups <t>from</t> <t>HLA-DRB1</t> to HLA-A . Plotted is the percent of chromosomes (both cases and controls) within each HLA haplotype group that meet the rules for congruence from HLA-DRB1 to HLA-A . The number of chromosomes in each group ranged from 8 to 747 (mean = 34, median = 17), and specific details for each haplotype group are given in Additional file : Table S1. Arrows identify haplotype groups that will be discussed further in the paper (number = DR.B.A: 7 = 3.8.1, 12 = 7.44.23, 129 = 3.7.2). B : Examples of congruence within two haplotype groups. In these two images, each column represents one founder chromosome (represented by 1,818 SNPs across 2.64 Mb ranging from HLA-DRB1 to HLA-A on chromosome 6) with the specified HLA alleles (e.g., DR7, B44 and A23). Each row illustrates data for one <t>SNP.</t> Yellow represents alleles that match the consensus sequence, whereas blue represents alleles that do not match the consensus. White denotes missing or unphased alleles. Congruent chromosomes are indicated by a tick mark at the bottom of the image. The DR7-B44-A23 haplotype group exhibits extreme congruence from HLA-DRB1 to HLA-A , seen by the high frequency of chromosomes that are congruent for the entire region (yellow from HLA-DRB1 to HLA-A ). In contrast, DR3-B7-A2 shows an example of a haplotype group in which only one of the chromosomes is congruent across the region. Because the consensus chromosome is derived from a set of chromosomes, it is not necessarily an exact match to any particular chromosome. Thus the one congruent chromosome in this haplotype group does not have 100% allele identity
Mapping Snp Panels, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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snp mapping panel  (Illumina Inc)
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Illumina Inc snp mapping panel
Congruence is widespread across the MHC and is not limited to the DR3-B8A1 haplotype . A : Percent congruence of 132 extended DQ-DR-B-A haplotype groups <t>from</t> <t>HLA-DRB1</t> to HLA-A . Plotted is the percent of chromosomes (both cases and controls) within each HLA haplotype group that meet the rules for congruence from HLA-DRB1 to HLA-A . The number of chromosomes in each group ranged from 8 to 747 (mean = 34, median = 17), and specific details for each haplotype group are given in Additional file : Table S1. Arrows identify haplotype groups that will be discussed further in the paper (number = DR.B.A: 7 = 3.8.1, 12 = 7.44.23, 129 = 3.7.2). B : Examples of congruence within two haplotype groups. In these two images, each column represents one founder chromosome (represented by 1,818 SNPs across 2.64 Mb ranging from HLA-DRB1 to HLA-A on chromosome 6) with the specified HLA alleles (e.g., DR7, B44 and A23). Each row illustrates data for one <t>SNP.</t> Yellow represents alleles that match the consensus sequence, whereas blue represents alleles that do not match the consensus. White denotes missing or unphased alleles. Congruent chromosomes are indicated by a tick mark at the bottom of the image. The DR7-B44-A23 haplotype group exhibits extreme congruence from HLA-DRB1 to HLA-A , seen by the high frequency of chromosomes that are congruent for the entire region (yellow from HLA-DRB1 to HLA-A ). In contrast, DR3-B7-A2 shows an example of a haplotype group in which only one of the chromosomes is congruent across the region. Because the consensus chromosome is derived from a set of chromosomes, it is not necessarily an exact match to any particular chromosome. Thus the one congruent chromosome in this haplotype group does not have 100% allele identity
Snp Mapping Panel, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/mapping+snp+panel/mapping+snp+panel/pm31951021-127-8-7
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medium density snp mapping panel  (Illumina Inc)
90
Illumina Inc medium density snp mapping panel
Congruence is widespread across the MHC and is not limited to the DR3-B8A1 haplotype . A : Percent congruence of 132 extended DQ-DR-B-A haplotype groups <t>from</t> <t>HLA-DRB1</t> to HLA-A . Plotted is the percent of chromosomes (both cases and controls) within each HLA haplotype group that meet the rules for congruence from HLA-DRB1 to HLA-A . The number of chromosomes in each group ranged from 8 to 747 (mean = 34, median = 17), and specific details for each haplotype group are given in Additional file : Table S1. Arrows identify haplotype groups that will be discussed further in the paper (number = DR.B.A: 7 = 3.8.1, 12 = 7.44.23, 129 = 3.7.2). B : Examples of congruence within two haplotype groups. In these two images, each column represents one founder chromosome (represented by 1,818 SNPs across 2.64 Mb ranging from HLA-DRB1 to HLA-A on chromosome 6) with the specified HLA alleles (e.g., DR7, B44 and A23). Each row illustrates data for one <t>SNP.</t> Yellow represents alleles that match the consensus sequence, whereas blue represents alleles that do not match the consensus. White denotes missing or unphased alleles. Congruent chromosomes are indicated by a tick mark at the bottom of the image. The DR7-B44-A23 haplotype group exhibits extreme congruence from HLA-DRB1 to HLA-A , seen by the high frequency of chromosomes that are congruent for the entire region (yellow from HLA-DRB1 to HLA-A ). In contrast, DR3-B7-A2 shows an example of a haplotype group in which only one of the chromosomes is congruent across the region. Because the consensus chromosome is derived from a set of chromosomes, it is not necessarily an exact match to any particular chromosome. Thus the one congruent chromosome in this haplotype group does not have 100% allele identity
Medium Density Snp Mapping Panel, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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snp fine-mapping panels  (Biotechnology Information)
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Biotechnology Information snp fine-mapping panels
Congruence is widespread across the MHC and is not limited to the DR3-B8A1 haplotype . A : Percent congruence of 132 extended DQ-DR-B-A haplotype groups <t>from</t> <t>HLA-DRB1</t> to HLA-A . Plotted is the percent of chromosomes (both cases and controls) within each HLA haplotype group that meet the rules for congruence from HLA-DRB1 to HLA-A . The number of chromosomes in each group ranged from 8 to 747 (mean = 34, median = 17), and specific details for each haplotype group are given in Additional file : Table S1. Arrows identify haplotype groups that will be discussed further in the paper (number = DR.B.A: 7 = 3.8.1, 12 = 7.44.23, 129 = 3.7.2). B : Examples of congruence within two haplotype groups. In these two images, each column represents one founder chromosome (represented by 1,818 SNPs across 2.64 Mb ranging from HLA-DRB1 to HLA-A on chromosome 6) with the specified HLA alleles (e.g., DR7, B44 and A23). Each row illustrates data for one <t>SNP.</t> Yellow represents alleles that match the consensus sequence, whereas blue represents alleles that do not match the consensus. White denotes missing or unphased alleles. Congruent chromosomes are indicated by a tick mark at the bottom of the image. The DR7-B44-A23 haplotype group exhibits extreme congruence from HLA-DRB1 to HLA-A , seen by the high frequency of chromosomes that are congruent for the entire region (yellow from HLA-DRB1 to HLA-A ). In contrast, DR3-B7-A2 shows an example of a haplotype group in which only one of the chromosomes is congruent across the region. Because the consensus chromosome is derived from a set of chromosomes, it is not necessarily an exact match to any particular chromosome. Thus the one congruent chromosome in this haplotype group does not have 100% allele identity
Snp Fine Mapping Panels, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/mapping+snp+panel/snp+fine+mapping+panels/pmc04480874-84-0-10
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500k nsp genechip snp mapping panel  (Thermo Fisher)
90
Thermo Fisher 500k nsp genechip snp mapping panel
Congruence is widespread across the MHC and is not limited to the DR3-B8A1 haplotype . A : Percent congruence of 132 extended DQ-DR-B-A haplotype groups <t>from</t> <t>HLA-DRB1</t> to HLA-A . Plotted is the percent of chromosomes (both cases and controls) within each HLA haplotype group that meet the rules for congruence from HLA-DRB1 to HLA-A . The number of chromosomes in each group ranged from 8 to 747 (mean = 34, median = 17), and specific details for each haplotype group are given in Additional file : Table S1. Arrows identify haplotype groups that will be discussed further in the paper (number = DR.B.A: 7 = 3.8.1, 12 = 7.44.23, 129 = 3.7.2). B : Examples of congruence within two haplotype groups. In these two images, each column represents one founder chromosome (represented by 1,818 SNPs across 2.64 Mb ranging from HLA-DRB1 to HLA-A on chromosome 6) with the specified HLA alleles (e.g., DR7, B44 and A23). Each row illustrates data for one <t>SNP.</t> Yellow represents alleles that match the consensus sequence, whereas blue represents alleles that do not match the consensus. White denotes missing or unphased alleles. Congruent chromosomes are indicated by a tick mark at the bottom of the image. The DR7-B44-A23 haplotype group exhibits extreme congruence from HLA-DRB1 to HLA-A , seen by the high frequency of chromosomes that are congruent for the entire region (yellow from HLA-DRB1 to HLA-A ). In contrast, DR3-B7-A2 shows an example of a haplotype group in which only one of the chromosomes is congruent across the region. Because the consensus chromosome is derived from a set of chromosomes, it is not necessarily an exact match to any particular chromosome. Thus the one congruent chromosome in this haplotype group does not have 100% allele identity
500k Nsp Genechip Snp Mapping Panel, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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5k snp array illumina linkage ivb mapping panel  (Illumina Inc)
90
Illumina Inc 5k snp array illumina linkage ivb mapping panel
Congruence is widespread across the MHC and is not limited to the DR3-B8A1 haplotype . A : Percent congruence of 132 extended DQ-DR-B-A haplotype groups <t>from</t> <t>HLA-DRB1</t> to HLA-A . Plotted is the percent of chromosomes (both cases and controls) within each HLA haplotype group that meet the rules for congruence from HLA-DRB1 to HLA-A . The number of chromosomes in each group ranged from 8 to 747 (mean = 34, median = 17), and specific details for each haplotype group are given in Additional file : Table S1. Arrows identify haplotype groups that will be discussed further in the paper (number = DR.B.A: 7 = 3.8.1, 12 = 7.44.23, 129 = 3.7.2). B : Examples of congruence within two haplotype groups. In these two images, each column represents one founder chromosome (represented by 1,818 SNPs across 2.64 Mb ranging from HLA-DRB1 to HLA-A on chromosome 6) with the specified HLA alleles (e.g., DR7, B44 and A23). Each row illustrates data for one <t>SNP.</t> Yellow represents alleles that match the consensus sequence, whereas blue represents alleles that do not match the consensus. White denotes missing or unphased alleles. Congruent chromosomes are indicated by a tick mark at the bottom of the image. The DR7-B44-A23 haplotype group exhibits extreme congruence from HLA-DRB1 to HLA-A , seen by the high frequency of chromosomes that are congruent for the entire region (yellow from HLA-DRB1 to HLA-A ). In contrast, DR3-B7-A2 shows an example of a haplotype group in which only one of the chromosomes is congruent across the region. Because the consensus chromosome is derived from a set of chromosomes, it is not necessarily an exact match to any particular chromosome. Thus the one congruent chromosome in this haplotype group does not have 100% allele identity
5k Snp Array Illumina Linkage Ivb Mapping Panel, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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snp linkage-mapping panel  (Illumina Inc)
90
Illumina Inc snp linkage-mapping panel
Congruence is widespread across the MHC and is not limited to the DR3-B8A1 haplotype . A : Percent congruence of 132 extended DQ-DR-B-A haplotype groups <t>from</t> <t>HLA-DRB1</t> to HLA-A . Plotted is the percent of chromosomes (both cases and controls) within each HLA haplotype group that meet the rules for congruence from HLA-DRB1 to HLA-A . The number of chromosomes in each group ranged from 8 to 747 (mean = 34, median = 17), and specific details for each haplotype group are given in Additional file : Table S1. Arrows identify haplotype groups that will be discussed further in the paper (number = DR.B.A: 7 = 3.8.1, 12 = 7.44.23, 129 = 3.7.2). B : Examples of congruence within two haplotype groups. In these two images, each column represents one founder chromosome (represented by 1,818 SNPs across 2.64 Mb ranging from HLA-DRB1 to HLA-A on chromosome 6) with the specified HLA alleles (e.g., DR7, B44 and A23). Each row illustrates data for one <t>SNP.</t> Yellow represents alleles that match the consensus sequence, whereas blue represents alleles that do not match the consensus. White denotes missing or unphased alleles. Congruent chromosomes are indicated by a tick mark at the bottom of the image. The DR7-B44-A23 haplotype group exhibits extreme congruence from HLA-DRB1 to HLA-A , seen by the high frequency of chromosomes that are congruent for the entire region (yellow from HLA-DRB1 to HLA-A ). In contrast, DR3-B7-A2 shows an example of a haplotype group in which only one of the chromosomes is congruent across the region. Because the consensus chromosome is derived from a set of chromosomes, it is not necessarily an exact match to any particular chromosome. Thus the one congruent chromosome in this haplotype group does not have 100% allele identity
Snp Linkage Mapping Panel, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/mapping+snp+panel/snp+linkage+panel/pm23489303-148-6-2
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mapping snp panel  (Illumina Inc)
90
Illumina Inc mapping snp panel
Congruence is widespread across the MHC and is not limited to the DR3-B8A1 haplotype . A : Percent congruence of 132 extended DQ-DR-B-A haplotype groups <t>from</t> <t>HLA-DRB1</t> to HLA-A . Plotted is the percent of chromosomes (both cases and controls) within each HLA haplotype group that meet the rules for congruence from HLA-DRB1 to HLA-A . The number of chromosomes in each group ranged from 8 to 747 (mean = 34, median = 17), and specific details for each haplotype group are given in Additional file : Table S1. Arrows identify haplotype groups that will be discussed further in the paper (number = DR.B.A: 7 = 3.8.1, 12 = 7.44.23, 129 = 3.7.2). B : Examples of congruence within two haplotype groups. In these two images, each column represents one founder chromosome (represented by 1,818 SNPs across 2.64 Mb ranging from HLA-DRB1 to HLA-A on chromosome 6) with the specified HLA alleles (e.g., DR7, B44 and A23). Each row illustrates data for one <t>SNP.</t> Yellow represents alleles that match the consensus sequence, whereas blue represents alleles that do not match the consensus. White denotes missing or unphased alleles. Congruent chromosomes are indicated by a tick mark at the bottom of the image. The DR7-B44-A23 haplotype group exhibits extreme congruence from HLA-DRB1 to HLA-A , seen by the high frequency of chromosomes that are congruent for the entire region (yellow from HLA-DRB1 to HLA-A ). In contrast, DR3-B7-A2 shows an example of a haplotype group in which only one of the chromosomes is congruent across the region. Because the consensus chromosome is derived from a set of chromosomes, it is not necessarily an exact match to any particular chromosome. Thus the one congruent chromosome in this haplotype group does not have 100% allele identity
Mapping Snp Panel, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/mapping+snp+panel/mapping+snp+panel/pmc03610173-104-5-4
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Congruence is widespread across the MHC and is not limited to the DR3-B8A1 haplotype . A : Percent congruence of 132 extended DQ-DR-B-A haplotype groups from HLA-DRB1 to HLA-A . Plotted is the percent of chromosomes (both cases and controls) within each HLA haplotype group that meet the rules for congruence from HLA-DRB1 to HLA-A . The number of chromosomes in each group ranged from 8 to 747 (mean = 34, median = 17), and specific details for each haplotype group are given in Additional file : Table S1. Arrows identify haplotype groups that will be discussed further in the paper (number = DR.B.A: 7 = 3.8.1, 12 = 7.44.23, 129 = 3.7.2). B : Examples of congruence within two haplotype groups. In these two images, each column represents one founder chromosome (represented by 1,818 SNPs across 2.64 Mb ranging from HLA-DRB1 to HLA-A on chromosome 6) with the specified HLA alleles (e.g., DR7, B44 and A23). Each row illustrates data for one SNP. Yellow represents alleles that match the consensus sequence, whereas blue represents alleles that do not match the consensus. White denotes missing or unphased alleles. Congruent chromosomes are indicated by a tick mark at the bottom of the image. The DR7-B44-A23 haplotype group exhibits extreme congruence from HLA-DRB1 to HLA-A , seen by the high frequency of chromosomes that are congruent for the entire region (yellow from HLA-DRB1 to HLA-A ). In contrast, DR3-B7-A2 shows an example of a haplotype group in which only one of the chromosomes is congruent across the region. Because the consensus chromosome is derived from a set of chromosomes, it is not necessarily an exact match to any particular chromosome. Thus the one congruent chromosome in this haplotype group does not have 100% allele identity

Journal: Journal of Translational Medicine

Article Title: Congruence as a measurement of extended haplotype structure across the genome

doi: 10.1186/1479-5876-10-32

Figure Lengend Snippet: Congruence is widespread across the MHC and is not limited to the DR3-B8A1 haplotype . A : Percent congruence of 132 extended DQ-DR-B-A haplotype groups from HLA-DRB1 to HLA-A . Plotted is the percent of chromosomes (both cases and controls) within each HLA haplotype group that meet the rules for congruence from HLA-DRB1 to HLA-A . The number of chromosomes in each group ranged from 8 to 747 (mean = 34, median = 17), and specific details for each haplotype group are given in Additional file : Table S1. Arrows identify haplotype groups that will be discussed further in the paper (number = DR.B.A: 7 = 3.8.1, 12 = 7.44.23, 129 = 3.7.2). B : Examples of congruence within two haplotype groups. In these two images, each column represents one founder chromosome (represented by 1,818 SNPs across 2.64 Mb ranging from HLA-DRB1 to HLA-A on chromosome 6) with the specified HLA alleles (e.g., DR7, B44 and A23). Each row illustrates data for one SNP. Yellow represents alleles that match the consensus sequence, whereas blue represents alleles that do not match the consensus. White denotes missing or unphased alleles. Congruent chromosomes are indicated by a tick mark at the bottom of the image. The DR7-B44-A23 haplotype group exhibits extreme congruence from HLA-DRB1 to HLA-A , seen by the high frequency of chromosomes that are congruent for the entire region (yellow from HLA-DRB1 to HLA-A ). In contrast, DR3-B7-A2 shows an example of a haplotype group in which only one of the chromosomes is congruent across the region. Because the consensus chromosome is derived from a set of chromosomes, it is not necessarily an exact match to any particular chromosome. Thus the one congruent chromosome in this haplotype group does not have 100% allele identity

Article Snippet: Next, data from the each of the two Illumina mapping SNP panels and the HLA panel were combined using custom Java programs.

Techniques: Sequencing, Derivative Assay

Comparison of two haplotype groups from the T1DGC . A : Congruence was calculated separately for two haplotype groups, DRB1 *03- B *08 and DRB1 *0401- B *08 ( DQB1 *0302). There is a significant difference in the congruence between the two groups centromeric of HLA-B , while the congruence within the two groups is not significantly different telomeric of HLA-B . B : In these two images, each column illustrates one founder chromosome (represented by 1,818 SNPs across 2.64 Mb ranging from HLA-DRB1 to HLA-A on chromosome 6) with the specified HLA alleles (e.g., DRB1 *03 and B *08). Each row illustrates data for one SNP. Yellow represents alleles that match the consensus sequence, whereas blue represents alleles that do not match the consensus. White denotes missing or unphased alleles. Congruent chromosomes are indicated by a tick mark at the bottom of the image. The DRB1 *03- B *08 chromosomes are highly congruent across the entire region from HLA-DRB1 to HLA-B , and in many cases from HLA-DRB1 to HLA-A . On the other hand, the DRB1 *04- B *08 ( DQB1 *0302) chromosomes are congruent around HLA-B but are not congruent near HLA-DRB1 or HLA-A

Journal: Journal of Translational Medicine

Article Title: Congruence as a measurement of extended haplotype structure across the genome

doi: 10.1186/1479-5876-10-32

Figure Lengend Snippet: Comparison of two haplotype groups from the T1DGC . A : Congruence was calculated separately for two haplotype groups, DRB1 *03- B *08 and DRB1 *0401- B *08 ( DQB1 *0302). There is a significant difference in the congruence between the two groups centromeric of HLA-B , while the congruence within the two groups is not significantly different telomeric of HLA-B . B : In these two images, each column illustrates one founder chromosome (represented by 1,818 SNPs across 2.64 Mb ranging from HLA-DRB1 to HLA-A on chromosome 6) with the specified HLA alleles (e.g., DRB1 *03 and B *08). Each row illustrates data for one SNP. Yellow represents alleles that match the consensus sequence, whereas blue represents alleles that do not match the consensus. White denotes missing or unphased alleles. Congruent chromosomes are indicated by a tick mark at the bottom of the image. The DRB1 *03- B *08 chromosomes are highly congruent across the entire region from HLA-DRB1 to HLA-B , and in many cases from HLA-DRB1 to HLA-A . On the other hand, the DRB1 *04- B *08 ( DQB1 *0302) chromosomes are congruent around HLA-B but are not congruent near HLA-DRB1 or HLA-A

Article Snippet: Next, data from the each of the two Illumina mapping SNP panels and the HLA panel were combined using custom Java programs.

Techniques: Sequencing