Journal: BMC Genomics

Article Title: Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

doi: 10.1186/s12864-021-07565-7

Figure Lengend Snippet: Frequency of discordant SNP calls across 16 individuals genotyped twice on each array

Article Snippet: Concordance between the Infinium 8 K and 20 K apple SNP arrays has not been reported, but integration of SNP data across these arrays was seamless in Vanderzande et al. [ ].

Techniques:

Journal: BMC Genomics

Article Title: Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

doi: 10.1186/s12864-021-07565-7

Figure Lengend Snippet: Distributions of SNPs included in the genetic map study grouped by compatible and incompatible classifications

Article Snippet: Concordance between the Infinium 8 K and 20 K apple SNP arrays has not been reported, but integration of SNP data across these arrays was seamless in Vanderzande et al. [ ].

Techniques:

Journal: BMC Genomics

Article Title: Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

doi: 10.1186/s12864-021-07565-7

Figure Lengend Snippet: Cumulative distribution plot demonstrating probe sequences for included/compatible SNPs have lower BLAST E-values. Only SNPs from the Illumina Infinium 20 K Apple SNP array with at least one significant BLAST hit from the 50 nt Infinium probe sequences vs. the GDDH13v1.1 whole genome sequence on the expected chromosome were considered ( N = 17,250). SNPs with accurate or inaccurate Infinium data were classified as included or excluded, respectively. SNPs with accurate or inaccurate Axiom data were deemed compatible or incompatible (with Infinium data), respectively

Article Snippet: Concordance between the Infinium 8 K and 20 K apple SNP arrays has not been reported, but integration of SNP data across these arrays was seamless in Vanderzande et al. [ ].

Techniques: Sequencing

Journal: BMC Genomics

Article Title: Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

doi: 10.1186/s12864-021-07565-7

Figure Lengend Snippet: negative correlation between positive number of BLAST hits and SNP inclusion/compatibility. All 18,019 SNPs from the Illumina Infinium 20 K Apple Infinium array were considered. Three different stringency thresholds for a successful BLAST hit from the 50 nt Infinium probe sequences vs. the GDDH13v1.1 whole genome sequence were considered: 1E-12, 1E-14, and 1E-16. The numbers of SNPs within each group are listed in the included table. Higher numbers of BLAST hits were grouped together because of the diminishing number of SNPs that had higher numbers of BLAST hits. SNPs with accurate Infinium data were classified as included

Article Snippet: Concordance between the Infinium 8 K and 20 K apple SNP arrays has not been reported, but integration of SNP data across these arrays was seamless in Vanderzande et al. [ ].

Techniques: Sequencing

Journal: BMC Genomics

Article Title: Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

doi: 10.1186/s12864-021-07565-7

Figure Lengend Snippet: Additional BLAST hits result in lower average cluster space in Infinium SNP array data. Three different stringency thresholds for a successful BLAST hit from the 50 nt Infinium probe sequences vs. the GDDH13v1.1 genome were considered: E < 1E-12 (solid line), E < 1E-14 (dashed line), and E < 1E-16 (dotted line). Data points were excluded from the figure if they were comprised of fewer than 10 SNPs. Cluster space was calculated for each SNP by the difference between 5 and 95% quantiles of observed Theta values from Infinium cluster plot data. SNPs with accurate or inaccurate Infinium data were classified as included or excluded, respectively

Article Snippet: Concordance between the Infinium 8 K and 20 K apple SNP arrays has not been reported, but integration of SNP data across these arrays was seamless in Vanderzande et al. [ ].

Techniques:

Journal: BMC Genomics

Article Title: Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

doi: 10.1186/s12864-021-07565-7

Figure Lengend Snippet: Closer proximity between secondary polymorphisms and target SNPs result in decreased SNP inclusion and compatibility rates. Secondary polymorphisms and their positions were identified via sequence alignment of 53 cultivars to the GDDH13v1.1 genome. SNPs with accurate Infinium data were classified as included and SNPs with accurate Axiom data were deemed compatible (with Infinium data). The inclusion rate of Infinium data is represented by black. The compatibility of these included SNPs with Axiom data with and without class C SNPs (those with additional heterozygous cluster(s) in Axiom cluster plots requiring manual adjustment to make compatible) being classified as compatible are represented by pink and blue, respectively. The horizontal lines represent the inclusion and compatibility rates for SNPs with no identified secondary polymorphisms at their probe site for the three respective data sources that sized 6632 (black), 6011 (pink), and 6011 (blue) SNPs. SNPs included in this analysis had their alternate allele present in at least 10% of the sequenced individuals, had no more than 25% missing data across the sequenced individuals, and had probe sequence with a single BLAST hit on the GDDH13 WGS with an E-value <1E-12

Article Snippet: Concordance between the Infinium 8 K and 20 K apple SNP arrays has not been reported, but integration of SNP data across these arrays was seamless in Vanderzande et al. [ ].

Techniques: Sequencing

Journal: BMC Genomics

Article Title: Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

doi: 10.1186/s12864-021-07565-7

Figure Lengend Snippet: SNP inclusion/exclusion summary from the Illumina Infinium 20 K array

Article Snippet: Concordance between the Infinium 8 K and 20 K apple SNP arrays has not been reported, but integration of SNP data across these arrays was seamless in Vanderzande et al. [ ].

Techniques:

Journal: BMC Genomics

Article Title: Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

doi: 10.1186/s12864-021-07565-7

Figure Lengend Snippet: Frequency of discordant SNP calls across 16 individuals genotyped twice on each array

Article Snippet: This need has been faced in apple ( Malus × domestica ), where a large amount of SNP array data has been generated using the Infinium® IRSC 8 K [ ] and 20 K apple SNP arrays [ ] on thousands of accessions through over thirty published, as well as ongoing, studies on pedigree reconstruction, genetic linkage map construction, identification of polyploids and aneuploids, quantitative trait loci identification, genome-wide association, and genomic selection; this data has also been used in downstream research like de novo genome assemblies and methodology development for the calling of SNPs [ , – ].

Techniques:

Journal: BMC Genomics

Article Title: Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

doi: 10.1186/s12864-021-07565-7

Figure Lengend Snippet: Distributions of SNPs included in the genetic map study grouped by compatible and incompatible classifications

Article Snippet: This need has been faced in apple ( Malus × domestica ), where a large amount of SNP array data has been generated using the Infinium® IRSC 8 K [ ] and 20 K apple SNP arrays [ ] on thousands of accessions through over thirty published, as well as ongoing, studies on pedigree reconstruction, genetic linkage map construction, identification of polyploids and aneuploids, quantitative trait loci identification, genome-wide association, and genomic selection; this data has also been used in downstream research like de novo genome assemblies and methodology development for the calling of SNPs [ , – ].

Techniques:

Journal: BMC Genomics

Article Title: Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

doi: 10.1186/s12864-021-07565-7

Figure Lengend Snippet: Cumulative distribution plot demonstrating probe sequences for included/compatible SNPs have lower BLAST E-values. Only SNPs from the Illumina Infinium 20 K Apple SNP array with at least one significant BLAST hit from the 50 nt Infinium probe sequences vs. the GDDH13v1.1 whole genome sequence on the expected chromosome were considered ( N = 17,250). SNPs with accurate or inaccurate Infinium data were classified as included or excluded, respectively. SNPs with accurate or inaccurate Axiom data were deemed compatible or incompatible (with Infinium data), respectively

Article Snippet: This need has been faced in apple ( Malus × domestica ), where a large amount of SNP array data has been generated using the Infinium® IRSC 8 K [ ] and 20 K apple SNP arrays [ ] on thousands of accessions through over thirty published, as well as ongoing, studies on pedigree reconstruction, genetic linkage map construction, identification of polyploids and aneuploids, quantitative trait loci identification, genome-wide association, and genomic selection; this data has also been used in downstream research like de novo genome assemblies and methodology development for the calling of SNPs [ , – ].

Techniques: Sequencing

Journal: BMC Genomics

Article Title: Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

doi: 10.1186/s12864-021-07565-7

Figure Lengend Snippet: negative correlation between positive number of BLAST hits and SNP inclusion/compatibility. All 18,019 SNPs from the Illumina Infinium 20 K Apple Infinium array were considered. Three different stringency thresholds for a successful BLAST hit from the 50 nt Infinium probe sequences vs. the GDDH13v1.1 whole genome sequence were considered: 1E-12, 1E-14, and 1E-16. The numbers of SNPs within each group are listed in the included table. Higher numbers of BLAST hits were grouped together because of the diminishing number of SNPs that had higher numbers of BLAST hits. SNPs with accurate Infinium data were classified as included

Article Snippet: This need has been faced in apple ( Malus × domestica ), where a large amount of SNP array data has been generated using the Infinium® IRSC 8 K [ ] and 20 K apple SNP arrays [ ] on thousands of accessions through over thirty published, as well as ongoing, studies on pedigree reconstruction, genetic linkage map construction, identification of polyploids and aneuploids, quantitative trait loci identification, genome-wide association, and genomic selection; this data has also been used in downstream research like de novo genome assemblies and methodology development for the calling of SNPs [ , – ].

Techniques: Sequencing

Journal: BMC Genomics

Article Title: Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

doi: 10.1186/s12864-021-07565-7

Figure Lengend Snippet: Additional BLAST hits result in lower average cluster space in Infinium SNP array data. Three different stringency thresholds for a successful BLAST hit from the 50 nt Infinium probe sequences vs. the GDDH13v1.1 genome were considered: E < 1E-12 (solid line), E < 1E-14 (dashed line), and E < 1E-16 (dotted line). Data points were excluded from the figure if they were comprised of fewer than 10 SNPs. Cluster space was calculated for each SNP by the difference between 5 and 95% quantiles of observed Theta values from Infinium cluster plot data. SNPs with accurate or inaccurate Infinium data were classified as included or excluded, respectively

Article Snippet: This need has been faced in apple ( Malus × domestica ), where a large amount of SNP array data has been generated using the Infinium® IRSC 8 K [ ] and 20 K apple SNP arrays [ ] on thousands of accessions through over thirty published, as well as ongoing, studies on pedigree reconstruction, genetic linkage map construction, identification of polyploids and aneuploids, quantitative trait loci identification, genome-wide association, and genomic selection; this data has also been used in downstream research like de novo genome assemblies and methodology development for the calling of SNPs [ , – ].

Techniques:

Journal: BMC Genomics

Article Title: Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

doi: 10.1186/s12864-021-07565-7

Figure Lengend Snippet: Closer proximity between secondary polymorphisms and target SNPs result in decreased SNP inclusion and compatibility rates. Secondary polymorphisms and their positions were identified via sequence alignment of 53 cultivars to the GDDH13v1.1 genome. SNPs with accurate Infinium data were classified as included and SNPs with accurate Axiom data were deemed compatible (with Infinium data). The inclusion rate of Infinium data is represented by black. The compatibility of these included SNPs with Axiom data with and without class C SNPs (those with additional heterozygous cluster(s) in Axiom cluster plots requiring manual adjustment to make compatible) being classified as compatible are represented by pink and blue, respectively. The horizontal lines represent the inclusion and compatibility rates for SNPs with no identified secondary polymorphisms at their probe site for the three respective data sources that sized 6632 (black), 6011 (pink), and 6011 (blue) SNPs. SNPs included in this analysis had their alternate allele present in at least 10% of the sequenced individuals, had no more than 25% missing data across the sequenced individuals, and had probe sequence with a single BLAST hit on the GDDH13 WGS with an E-value <1E-12

Article Snippet: This need has been faced in apple ( Malus × domestica ), where a large amount of SNP array data has been generated using the Infinium® IRSC 8 K [ ] and 20 K apple SNP arrays [ ] on thousands of accessions through over thirty published, as well as ongoing, studies on pedigree reconstruction, genetic linkage map construction, identification of polyploids and aneuploids, quantitative trait loci identification, genome-wide association, and genomic selection; this data has also been used in downstream research like de novo genome assemblies and methodology development for the calling of SNPs [ , – ].

Techniques: Sequencing

Journal: BMC Genomics

Article Title: Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

doi: 10.1186/s12864-021-07565-7

Figure Lengend Snippet: SNP inclusion/exclusion summary from the Illumina Infinium 20 K array

Article Snippet: This need has been faced in apple ( Malus × domestica ), where a large amount of SNP array data has been generated using the Infinium® IRSC 8 K [ ] and 20 K apple SNP arrays [ ] on thousands of accessions through over thirty published, as well as ongoing, studies on pedigree reconstruction, genetic linkage map construction, identification of polyploids and aneuploids, quantitative trait loci identification, genome-wide association, and genomic selection; this data has also been used in downstream research like de novo genome assemblies and methodology development for the calling of SNPs [ , – ].

Techniques:

Journal:

Article Title: Systematic Evaluation of Genetic Variation at the Androgen Receptor Locus and Risk of Prostate Cancer in a Multiethnic Cohort Study

doi:

Figure Lengend Snippet: SNPs and LD across the AR locus. A, Physical relationship of SNPs to the AR locus (from University of California–Santa Cruz Genome Bioinformatics build hg16); 32 working polymorphic SNPs were genotyped across the AR locus, which spanned a total of 275 kb—the SNPs covered from 56 kb upstream to 37 kb downstream of the AR gene. Using previously defined criteria (see the “Materials and Methods” section), these 32 markers describe two strong blocks of LD (188 kb and 66 kb) with gaps between adjacent blocks (bounded by the markers selected) of 11.9 kb. B, LD plot for entire population across the AR locus. Each square in the plot represents the pairwise LD relationships among all 32 markers. The two blocks (see the “Materials and Methods” section) are highlighted and are bounded by markers 1–25 and 26–32. Red denotes strong LD (as measured by D′) with a high degree of statistical confidence, pale blue denotes a high D′ with relatively low statistical confidence, and white denotes low D′.

Article Snippet: SNP Genotyping SNPs were identified in both the public ( dbSNP ) and private ( Celera ) databases.

Techniques: