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mapping snp panels  (Illumina Inc)


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    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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    Images

    1) Product Images from "Congruence as a measurement of extended haplotype structure across the genome"

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

    Journal: Journal of Translational Medicine

    doi: 10.1186/1479-5876-10-32

    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
    Figure Legend 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

    Techniques Used: 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
    Figure Legend 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

    Techniques Used: Sequencing

    Related Articles

    other:

    Article Title: Defining multiple common "completely" conserved major histocompatibility complex SNP haplotypes
    Article Snippet: Next, data from the Illumina mapping SNP panel, the exon-centric SNP panel, and HLA were combined.

    Article Title: Replication and Further Characterization of a Type 1 Diabetes-Associated Locus at the Telomeric End of the Major Histocompatibility Complex
    Article Snippet: Next, data from the Illumina mapping SNP panel, the exon-centric SNP panel, and HLA were combined using custom Java programs.

    Article Title: Replication and further characterization of a Type 1 diabetes-associated locus at the telomeric end of the major histocompatibility complex.
    Article Snippet: Next, data from the Illumina mapping SNP panel, the exon-centric SNP panel, and HLA were combined using custom Java programs.

    Software:

    Article Title: The HLA-B 3906 allele imparts a high risk of diabetes only on specific HLA-DR/DQ haplotypes.
    Article Snippet: .. Next, data from the Illumina mapping SNP panel, the exon-centric SNP panel, and HLA were combined using custom Java programs.Merlin software (www.sph.umich.edu/csg/abecasis/ Merlin) [15] was used to phase the SNP and HLA genotype data from families into chromosomes. ..



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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 <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
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    Image Search Results


    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