exons Search Results


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  • 99
    Thermo Fisher genechip human exon 1 0 st array
    Analysis of DCK expression. (A) Distribution of DCK mRNA expression measured on the Affymetrix <t>GeneChip</t> Human Exon 1.0 ST array in the CEU and YRI cell lines ( P = .02). (B) Association between level of DCK protein expression and log 2 AUC in a subset of
    Genechip Human Exon 1 0 St Array, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1535 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Agilent technologies sureselect human all exon kit
    The workflow for designing the <t>SureSelect</t> library specific for bisulfite-converted DNA.
    Sureselect Human All Exon Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 1301 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Agilent technologies exons
    Enrichment efficiency of the three updated exome enrichment platforms (Agilent, NimbleGen and Illumina) performed by four vendors <t>(V1,</t> V2, V3 and V4). ( A ) Mean number of aligned reads (as million reads), mean read depth and percentage of coverage at 20× for each designed target region as well as mean percentage of on-target reads (i.e. within designed target regions) and mean percentage of off-target reads (i.e. within regions more than ±500 bp outside the designed target regions). Note that values for aligned reads indicate the total number of mapped reads without duplicates for V1 and V2 and only uniquely mapped reads without duplicates for V3 and V4 (Supplementary Table S3). ( B ) Mean read depth and percentage of coverage at 20× for all and only coding <t>exons</t> of the RefSeq database as well as uniformity of the coverage of RefSeq coding exons calculated as the fraction of exons reaching an average read depth within ±70% of mean read depth over all coding exons (uniformity coding). ( C ) Mean read depth and percentage of coverage at 15 and 20× for RefSeq coding exons as well as for −50-bp and +20-bp flanking intronic regions. Given are means of all six DNA samples ( n = 6); error bars indicate 95% confidence intervals. Values were calculated using the SeqMonk program ( http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ ) and are presented in Supplementary Tables S4-S8 and S12–S13. For complete coverage of RefSeq coding exons see Figure 3 .
    Exons, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 93/100, based on 1071 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Illumina Inc exons
    Agarose gel electrophoresis for the confirmation of small deletions. (A) 17 bp deletion in the Promoter region was observed in blood samples of patient <t>RB1</t> and his father. (B) 29 bp deletion in <t>Exon</t> 1 was observed in blood samples of patient RB11, her mother and siblings. The size of actual and deleted product is indicated by straight and dotted arrows respectively in both gels.
    Exons, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 1410 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Thermo Fisher human exon 1 0
    Application to archived data. MaLTE, trained using the GTEx data, was applied to predict gene expression from published microarray data based on brain samples for which RNA-Seq data was also available. Despite the fact that the two studies used different array platforms (Affymetrix Human Exon 1.0 ST arrays and Affymetrix Human Gene 1.1 ST arrays for the brain and GTEx studies, respectively), MaLTE predictions exceeded the within-sample correlations obtained using median-polish and PLIER. MaLTE predictions were based on probes shared between the two array platforms. Box plots of ( a ) Pearson and ( b ) Spearman within correlations are shown. ( c ) Pearson and ( d ) Spearman cross sample correlations with OOB filtering. The black line represents the number of genes/transcripts at each level
    Human Exon 1 0, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 1377 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher human exon 1 0 st array
    Identification of a short alternative transcript of TSP2 that is highly expressed in bladder cancer-associated blood vessels.  a  Blood vascular endothelial cells (BECs) were isolated from frozen sections of invasive bladder cancers (tBEC) and adjacent normal (nBEC) bladder tissue ( n  = 6). RNA was isolated and hybridized to Human Exon 1.0 ST arrays.  a  Detection of alternative splicing and transcription was performed using three different bioinformatics analysis tools, namely MIDAS, ANOSVA, and FIRMA. The numbers indicate the number of genes with alternative splicing or alternative transcription identified by each method and their overlap.  b  Exon array expression levels of the full-length and the short transcript of TSP2 and exon structure as shown in the GenBank database.  c  qRT-PCR analysis of the expression of the full-length and the short TSP2 transcripts in tumor-associated vessels and in vessels of healthy bladder tissue. For five out of six patients, matched samples of tumor-associated and healthy vessels could be analyzed as highlighted by the connecting dotted lines. The positions of the primers used are indicated by arrows in  b . Horizontal lines represent median values. Dots represent patient samples. Relative expression was normalized to expression of vessels from healthy tissues in both groups. * p
    Human Exon 1 0 St Array, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 1038 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Agilent technologies sureselect human all exon v5 kit
    Identification of a short alternative transcript of TSP2 that is highly expressed in bladder cancer-associated blood vessels.  a  Blood vascular endothelial cells (BECs) were isolated from frozen sections of invasive bladder cancers (tBEC) and adjacent normal (nBEC) bladder tissue ( n  = 6). RNA was isolated and hybridized to Human Exon 1.0 ST arrays.  a  Detection of alternative splicing and transcription was performed using three different bioinformatics analysis tools, namely MIDAS, ANOSVA, and FIRMA. The numbers indicate the number of genes with alternative splicing or alternative transcription identified by each method and their overlap.  b  Exon array expression levels of the full-length and the short transcript of TSP2 and exon structure as shown in the GenBank database.  c  qRT-PCR analysis of the expression of the full-length and the short TSP2 transcripts in tumor-associated vessels and in vessels of healthy bladder tissue. For five out of six patients, matched samples of tumor-associated and healthy vessels could be analyzed as highlighted by the connecting dotted lines. The positions of the primers used are indicated by arrows in  b . Horizontal lines represent median values. Dots represent patient samples. Relative expression was normalized to expression of vessels from healthy tissues in both groups. * p
    Sureselect Human All Exon V5 Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 334 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Agilent technologies sureselect human all exon v5
    Coverage efficiency in the medically interpretable genome (MIG). Shown is the cumulative distribution of on-target sequence coverage obtained from sequencing NA12878 across multiple platforms: Personalis Accuracy and Content Enhanced (ACE) Clinical Exome, Agilent <t>SureSelect</t> Clinical Research Exome (SSCR), Agilent SureSelect Human All <t>Exon</t> v5 plus untranslated regions (UTR) (SS), lllumina’s Nextera Exome Enrichment (NX), NimbleGen SeqCap EZ Human Exome Library v3.0 (NG), and 31× whole-genome sequencing (WGS) using an Illumina PCR-free protocol. For clinical applications, we indicate ≥20× as the minimum coverage threshold required (gray line) among all coding (left) and non-coding (right) regions. For reference, insets show an expanded distribution of sequence coverage. ACE and conventional WES data are normalized to 100× mean target coverage
    Sureselect Human All Exon V5, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 90/100, based on 297 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Agilent technologies sureselect human all exon v4
    Venn diagrams showing commonality of targeting between capture kits (A,B) and properties of encompassed SNPs (C). Overlap between exome capture kits is presented in Mbp (A) and number of SNPs with an AF ≥0.3 (B) . Agilent - <t>SureSelect</t> Human All Exon V4; Illumina - TruSeq Exome Enrichment; Nimblegen - SeqCap EZ Human Exome Library V3.0. For a subset of SNPs present in both the intersection of the three kits shown, and the Illumina TruSight Exome kit, a breakdown of fulfilment of the four classes of candidate filtering criteria is shown (C) (see the main text for details of filtering criteria); 117 SNPs exhibited all desired characteristic; 74 SNPs exhibited none of the desired characteristics.
    Sureselect Human All Exon V4, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 90/100, based on 338 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher affymetrix exon 1 0
    Extent of alternative splicing in the MHC. Absolute values of exon level intensities normalized against gene intensities [NI = log 2 (exon/gene)] were computed from the median signal of the three PGF sample replicates hybridized to the <t>Affymetrix</t> Exon 1.0 ST array. Thus, absolute NI > 1 indicates that the exon is expressed at least twice more or less than the overall gene level. Mean percentage of exons ( A ) and of genes with at least one exon ( B ) with NI value(s) exceeding the indicated thresholds for MHC (gray bars) and non-MHC genes (white bars). Error bars depict standard errors of the means of the three replicates ( C–E ) Comparisons of the median NIs (dashed vertical line) in the 131 MHC genes ( C , E ) or in 733 non-MHC immune genes ( D ) having at least four annotated exons in Vega with the density distribution of median NIs obtained in 10,000 random sets of similar numbers of non-MHC ( C ), non-MHC non-immune ( D ), and non-MHC immune ( E ) genes.
    Affymetrix Exon 1 0, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 484 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Agilent technologies sureselect human all exon v6 kit
    Title: IGV visualization of the control Alu insertion using BAMfile generated with the Agilent kit Legend: Screenshots of IGV outputs restricted to the genomic region where the Alu element insertion occurred (c.1739_1740insAlu in BRCA1 ) in the positive control sample. The BAMfile used for IGV visualization was generated from WES data obtained with the <t>SureSelect</t> Human All Exon V6 kit (exome capture kit) from Agilent. Group alignment is by chromosome of mate. Note that this exome capture kit generates much less discordantly mapped read pairs than the kit from Roche (2 versus 22, compare with Figure 2 ). Accordingly, the required number (five) of discordantly mapped read pairs containing a long polyA track will not be reached and the insertion will not be revealed with our detection strategy. Note that all other characteristics observed for a retrotransposon insertion when using the exome capture kit from Roche (see Figure 2 ) are also observed when using the kit from Agilent.
    Sureselect Human All Exon V6 Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 91/100, based on 232 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Agilent technologies exonic sequences
    Title: IGV visualization of the control Alu insertion using BAMfile generated with the Agilent kit Legend: Screenshots of IGV outputs restricted to the genomic region where the Alu element insertion occurred (c.1739_1740insAlu in BRCA1 ) in the positive control sample. The BAMfile used for IGV visualization was generated from WES data obtained with the <t>SureSelect</t> Human All Exon V6 kit (exome capture kit) from Agilent. Group alignment is by chromosome of mate. Note that this exome capture kit generates much less discordantly mapped read pairs than the kit from Roche (2 versus 22, compare with Figure 2 ). Accordingly, the required number (five) of discordantly mapped read pairs containing a long polyA track will not be reached and the insertion will not be revealed with our detection strategy. Note that all other characteristics observed for a retrotransposon insertion when using the exome capture kit from Roche (see Figure 2 ) are also observed when using the kit from Agilent.
    Exonic Sequences, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 91/100, based on 437 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Biotechnology Information exons
    The HvDWARF gene structure with <t>exons</t> depicted as blue rectangles with consecutive numbers and <t>introns</t> as black line. Positions of the mutations identified in the brd1-a , brd1-b , brd1-c and brd1-d alleles are shown.
    Exons, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 93/100, based on 430 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Thermo Fisher mouse exon 1 0
    Schematic showing the experimental design of the study to identify the  Mta1  regulated genes with/without the effect of  P53 . RNA was extracted from all the samples Wild Type (WT),  Mta1  knock out ( Mta1- KO),  Mta1  Re-expression in the  Mta1  knock out MEFS ( Mta1 -KO/ Mta1 ), P53 knock out ( P53 -KO),  Mta1  over expression (OE) in the  P53  knock out MEFs (  P53 -KO/ Mta1 ). cDNA was prepared, processed and hybridized onto the Affymetrix Mouse Exon 1.0 ST arrays followed by the data analysis. Samples were compared to identify the differentially regulated genes and in turn the genes regulated by  Mta1  in  p53  dependent/independent manner and irrespective of  P53  status. Candidate genes were selected; these genes were validated using RT-qPCR assays in MEFs followed by RT-qPCR assays in MCF-7 human breast cancer cell line with the human homologs of the candidate mouse genes.
    Mouse Exon 1 0, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 89/100, based on 391 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Thermo Fisher genechip mouse exon 1 0 st array
    Mouse-adaptive NS1 mutations regulate mouse gene expression by two different mechanisms. Mouse M1 cells were infected in triplicate at an MOI of 2 with rHK NS mutants or HK-wt virus, and total RNA isolated at 8 hpi was analyzed by microarray using <t>GeneChip</t> Mouse Exon 1.0 ST Array (Affymetrix, Santa Clara, CA, USA). Microarray gene expression data were normalized and analyzed by Flexarray 1.6.1. Genes were considered as up or down regulated relative to mock infected cells if they were ≤1 or ≥1 log2 fold different (≤ or ≥2 fold differences) expression level (p≤0.05; ANOVA). (A) The number of differentially regulated host genes that were significantly up or down regulated ≤2 or ≥2 fold at the p≤0.05 by ANOVA is plotted for each mutant. The mutants formed two groups with either “low gene regulation” (LGR) or “high t gene regulation” (HGR) phenotypes. (B) Heat map of differentially regulated genes in mouse cells infected with HK-wt or rHK NS1 mutant viruses relative to mock infected M1 cells. Genes (total = 5274) were included for hierarchical clustering analysis among mutants if they were differentially regulated (≤2 −1 or ≥2 1 fold differences) and significantly different from mock infected cells for one or more of the mutants, and gene regulation signatures were also analyzed for hierarchical clustering among viruses. The scale depicts up (red) and down (blue) regulated genes according to the log2 scale shown; equal expression is indicated in white (log 2 0 = 1).
    Genechip Mouse Exon 1 0 St Array, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 96/100, based on 561 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Agilent technologies sureselect human all exon v6
    Mouse-adaptive NS1 mutations regulate mouse gene expression by two different mechanisms. Mouse M1 cells were infected in triplicate at an MOI of 2 with rHK NS mutants or HK-wt virus, and total RNA isolated at 8 hpi was analyzed by microarray using <t>GeneChip</t> Mouse Exon 1.0 ST Array (Affymetrix, Santa Clara, CA, USA). Microarray gene expression data were normalized and analyzed by Flexarray 1.6.1. Genes were considered as up or down regulated relative to mock infected cells if they were ≤1 or ≥1 log2 fold different (≤ or ≥2 fold differences) expression level (p≤0.05; ANOVA). (A) The number of differentially regulated host genes that were significantly up or down regulated ≤2 or ≥2 fold at the p≤0.05 by ANOVA is plotted for each mutant. The mutants formed two groups with either “low gene regulation” (LGR) or “high t gene regulation” (HGR) phenotypes. (B) Heat map of differentially regulated genes in mouse cells infected with HK-wt or rHK NS1 mutant viruses relative to mock infected M1 cells. Genes (total = 5274) were included for hierarchical clustering analysis among mutants if they were differentially regulated (≤2 −1 or ≥2 1 fold differences) and significantly different from mock infected cells for one or more of the mutants, and gene regulation signatures were also analyzed for hierarchical clustering among viruses. The scale depicts up (red) and down (blue) regulated genes according to the log2 scale shown; equal expression is indicated in white (log 2 0 = 1).
    Sureselect Human All Exon V6, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 91/100, based on 122 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    MRC-Holland exons
    Detection of GALC <t>exon</t> 1–14 deletions/duplications by <t>MLPA</t> in GLD patients and a normal control, and a detailed analysis of the GALC gene deletion region in patient 1.
    Exons, supplied by MRC-Holland, used in various techniques. Bioz Stars score: 93/100, based on 568 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Agilent technologies sureselect human all exon v4 kit
    Detection of GALC <t>exon</t> 1–14 deletions/duplications by <t>MLPA</t> in GLD patients and a normal control, and a detailed analysis of the GALC gene deletion region in patient 1.
    Sureselect Human All Exon V4 Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 91/100, based on 289 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Agilent technologies sureselectxt human all exon v5
    Detection of GALC <t>exon</t> 1–14 deletions/duplications by <t>MLPA</t> in GLD patients and a normal control, and a detailed analysis of the GALC gene deletion region in patient 1.
    Sureselectxt Human All Exon V5, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 89/100, based on 115 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Analysis of DCK expression. (A) Distribution of DCK mRNA expression measured on the Affymetrix GeneChip Human Exon 1.0 ST array in the CEU and YRI cell lines ( P = .02). (B) Association between level of DCK protein expression and log 2 AUC in a subset of

    Journal: Blood

    Article Title: Population-specific genetic variants important in susceptibility to cytarabine arabinoside cytotoxicity

    doi: 10.1182/blood-2008-05-154302

    Figure Lengend Snippet: Analysis of DCK expression. (A) Distribution of DCK mRNA expression measured on the Affymetrix GeneChip Human Exon 1.0 ST array in the CEU and YRI cell lines ( P = .02). (B) Association between level of DCK protein expression and log 2 AUC in a subset of

    Article Snippet: Assessment of gene expression in the LCLs was performed using the Affymetrix GeneChip Human Exon 1.0 ST array (Affymetrix, Santa Clara, CA), as previously described.

    Techniques: Expressing

    Expression profiling indicates similar numbers of mRNAs are upregulated and downreglated in alveolar macrophages of cigarette smokers and nonsmokers. Smoker-to-nonsmoker mRNA expression ratios were determined using RNA from alveolar macrophages as template in GeneChip Human Exon 1.0 ST cDNA microarrays (Affymetrix). The RNA was collected from alveolar macrophages directly isolated from four nonsmokers and four smokers (cohort 1). A) Smoker-to-nonsmoker expression ratios are represented by black circles in order from lowest to highest for the 17,860 detected cDNAs. The arrow indicates the point where specific mRNA expression ratios in smokers and nonsmokers = 1. B) The expression ratios are shown for several commonly used endogenous controls. (ACTB = actin, beta; B2M = beta-2-microglobulin; GAPDHS = glyceraldehyde-3-phosphate dehydrogenase, spermatogenic; PGK1 = phosphoglycerate kinase 1; peptidylprolyl isomerase A; RPLP0 = ribosomal protein, large, P0; TBP = TATA box-binding protein).

    Journal: PLoS ONE

    Article Title: Cigarette Smoking Decreases Global MicroRNA Expression in Human Alveolar Macrophages

    doi: 10.1371/journal.pone.0044066

    Figure Lengend Snippet: Expression profiling indicates similar numbers of mRNAs are upregulated and downreglated in alveolar macrophages of cigarette smokers and nonsmokers. Smoker-to-nonsmoker mRNA expression ratios were determined using RNA from alveolar macrophages as template in GeneChip Human Exon 1.0 ST cDNA microarrays (Affymetrix). The RNA was collected from alveolar macrophages directly isolated from four nonsmokers and four smokers (cohort 1). A) Smoker-to-nonsmoker expression ratios are represented by black circles in order from lowest to highest for the 17,860 detected cDNAs. The arrow indicates the point where specific mRNA expression ratios in smokers and nonsmokers = 1. B) The expression ratios are shown for several commonly used endogenous controls. (ACTB = actin, beta; B2M = beta-2-microglobulin; GAPDHS = glyceraldehyde-3-phosphate dehydrogenase, spermatogenic; PGK1 = phosphoglycerate kinase 1; peptidylprolyl isomerase A; RPLP0 = ribosomal protein, large, P0; TBP = TATA box-binding protein).

    Article Snippet: mRNA Expression Analysis Measurements of genome-wide macrophage mRNA expression were conducted using the GeneChip Human Exon 1.0 ST Arrays (Affymetrix).

    Techniques: Expressing, Isolation, Binding Assay

    The workflow for designing the SureSelect library specific for bisulfite-converted DNA.

    Journal: Nucleic Acids Research

    Article Title: In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes

    doi: 10.1093/nar/gks1467

    Figure Lengend Snippet: The workflow for designing the SureSelect library specific for bisulfite-converted DNA.

    Article Snippet: Using the Agilent SureSelect Human All Exon Kit where native DNA is also captured and then bisulfite treated, Wang et al. ( ) demonstrated that with the optimization of the experimental conditions, 2 µg of input gDNA can be successfully used to enrich 38 Mb of genomic sequence ( ).

    Techniques:

    Coverage distribution across 90 PCR-capture amplicons between FF and FFPE samples. Coverage distribution across the 90 ‘AmpliSeq Colon and Lung Cancer Panel’ regions displays a similar trend between the FF (blue) and FFPE (red) libraries in both Agilent SureSelect ( a ) and Roche NimbleGen ( b ) libraries respectively, with a slightly better coverage in FFPE samples. Each amplicon is identified by a number as reported in Additional file 3 : TableS7

    Journal: BMC Cancer

    Article Title: Performance comparison of two commercial human whole-exome capture systems on formalin-fixed paraffin-embedded lung adenocarcinoma samples

    doi: 10.1186/s12885-016-2720-4

    Figure Lengend Snippet: Coverage distribution across 90 PCR-capture amplicons between FF and FFPE samples. Coverage distribution across the 90 ‘AmpliSeq Colon and Lung Cancer Panel’ regions displays a similar trend between the FF (blue) and FFPE (red) libraries in both Agilent SureSelect ( a ) and Roche NimbleGen ( b ) libraries respectively, with a slightly better coverage in FFPE samples. Each amplicon is identified by a number as reported in Additional file 3 : TableS7

    Article Snippet: WES standard metrics comparison WES was performed on all samples (5 FF and matching FFPE), comparing two commercially available exome capture systems: Roche NimbleGen SeqCap EZ Human Exome Library v. 3.0 (64 Mb) and Agilent SureSelect Human All Exon v. 5 (50 Mb).

    Techniques: Polymerase Chain Reaction, Formalin-fixed Paraffin-Embedded, Amplification

    Coverage distribution across all the coding exons of 623 cancer-related genes in both WES platforms. Distribution summary of 623 cancer-related genes according to their coverage performance achieved in the two tested WES systems ( a ). Specifically, 36 % of the genes (red) were completely well covered by both Agilent and Roche kits; 29 % (blue) had at least one ‘critical’ region in both kits; 18 % were completely well covered by Roche NimbleGen kit, but had one or more ‘critical’ region in Agilent SureSelect kit; finally, 17 % of the genes were completely well covered by Agilent SureSelect kit, but had one or more problematic region in Roche NimbleGen kit. Distribution summary of cancer-related genes having one (73 %), two (12 %) or more (15 %) critical regions in NimbleGen Roche kit, but completely well-covered in Agilent SureSelect kit ( b ). Distribution summary of cancer-related genes having one (66 %), two (25 %) or more (9 %) critical regions in Agilent SureSelect kit, but completely well-covered in Roche NimbleGen kit ( c )

    Journal: BMC Cancer

    Article Title: Performance comparison of two commercial human whole-exome capture systems on formalin-fixed paraffin-embedded lung adenocarcinoma samples

    doi: 10.1186/s12885-016-2720-4

    Figure Lengend Snippet: Coverage distribution across all the coding exons of 623 cancer-related genes in both WES platforms. Distribution summary of 623 cancer-related genes according to their coverage performance achieved in the two tested WES systems ( a ). Specifically, 36 % of the genes (red) were completely well covered by both Agilent and Roche kits; 29 % (blue) had at least one ‘critical’ region in both kits; 18 % were completely well covered by Roche NimbleGen kit, but had one or more ‘critical’ region in Agilent SureSelect kit; finally, 17 % of the genes were completely well covered by Agilent SureSelect kit, but had one or more problematic region in Roche NimbleGen kit. Distribution summary of cancer-related genes having one (73 %), two (12 %) or more (15 %) critical regions in NimbleGen Roche kit, but completely well-covered in Agilent SureSelect kit ( b ). Distribution summary of cancer-related genes having one (66 %), two (25 %) or more (9 %) critical regions in Agilent SureSelect kit, but completely well-covered in Roche NimbleGen kit ( c )

    Article Snippet: WES standard metrics comparison WES was performed on all samples (5 FF and matching FFPE), comparing two commercially available exome capture systems: Roche NimbleGen SeqCap EZ Human Exome Library v. 3.0 (64 Mb) and Agilent SureSelect Human All Exon v. 5 (50 Mb).

    Techniques:

    Variant calling comparison between Ion PGM data and both WES systems. Variant calling comparison between Ion PGM data (blue) and both Agilent SureSelect (green) and Roche NimbleGen (red) data in exon regions shows 88 % of concordance (44/50) in both WES capture systems ( a ). Both systems failed to call 4 genetic variants (*) detected by Ion PGM platform at low frequencies (4-16 %). Further 4 variants were missed as follows: 2 by Agilent (COSM6225, rs80338963) and 2 by Roche NimbleGen (COSM40942, rs35775721). Horizontal axis reports the genetic variants (Additional file 3 : Table S8a) ordered from lowest to highest frequency (vertical axis) as assessed by Ion PGM platform. Variant coverage displays a quite similar trend between Agilent (green) and Roche NimbleGen (red) libraries, and is far lower than Ion PGM platform (blue) ( b ). Two Roche libraries report a low coverage in the uncalled variants (COSM40942, rs35775721). Vertical axis displays the variant coverage in logarithmic scale. Variant calling comparison between Ion PGM data (blue) and both Agilent (green) and Roche NimbleGen (red) data in non-exon regions shows a poor performance of both WES technologies ( c ). Both WES systems failed to call the rs839541 (*) SNP in ERBB4 gene, whereas rs1558544 SNP in EGFR was missed by all 10 Agilent libraries. Vertical axis reports the frequency of the genetic variants. Variant coverage comparison between Ion PGM data (blue) and both Agilent (green) and Roche NimbleGen (red) data in non-exon (intron/downstream/upstream) regions reports a low coverage in both exome capture kits ( d ); rs839541 SNP was completely uncovered in Agilent libraries. Vertical axis displays coverage values in logarithmic scale

    Journal: BMC Cancer

    Article Title: Performance comparison of two commercial human whole-exome capture systems on formalin-fixed paraffin-embedded lung adenocarcinoma samples

    doi: 10.1186/s12885-016-2720-4

    Figure Lengend Snippet: Variant calling comparison between Ion PGM data and both WES systems. Variant calling comparison between Ion PGM data (blue) and both Agilent SureSelect (green) and Roche NimbleGen (red) data in exon regions shows 88 % of concordance (44/50) in both WES capture systems ( a ). Both systems failed to call 4 genetic variants (*) detected by Ion PGM platform at low frequencies (4-16 %). Further 4 variants were missed as follows: 2 by Agilent (COSM6225, rs80338963) and 2 by Roche NimbleGen (COSM40942, rs35775721). Horizontal axis reports the genetic variants (Additional file 3 : Table S8a) ordered from lowest to highest frequency (vertical axis) as assessed by Ion PGM platform. Variant coverage displays a quite similar trend between Agilent (green) and Roche NimbleGen (red) libraries, and is far lower than Ion PGM platform (blue) ( b ). Two Roche libraries report a low coverage in the uncalled variants (COSM40942, rs35775721). Vertical axis displays the variant coverage in logarithmic scale. Variant calling comparison between Ion PGM data (blue) and both Agilent (green) and Roche NimbleGen (red) data in non-exon regions shows a poor performance of both WES technologies ( c ). Both WES systems failed to call the rs839541 (*) SNP in ERBB4 gene, whereas rs1558544 SNP in EGFR was missed by all 10 Agilent libraries. Vertical axis reports the frequency of the genetic variants. Variant coverage comparison between Ion PGM data (blue) and both Agilent (green) and Roche NimbleGen (red) data in non-exon (intron/downstream/upstream) regions reports a low coverage in both exome capture kits ( d ); rs839541 SNP was completely uncovered in Agilent libraries. Vertical axis displays coverage values in logarithmic scale

    Article Snippet: WES standard metrics comparison WES was performed on all samples (5 FF and matching FFPE), comparing two commercially available exome capture systems: Roche NimbleGen SeqCap EZ Human Exome Library v. 3.0 (64 Mb) and Agilent SureSelect Human All Exon v. 5 (50 Mb).

    Techniques: Variant Assay

    Variant calling comparison between Agilent SureSelect and Roche NimbleGen kit. Mean percentage ± SD of SNVs and InDels common to both library prep kits (blue), and private to either Roche (red) or Agilent (green) kit in both FF and FFPE samples. The average percentage of common SNVs ( a ) and InDels ( b ) was approximately 48 % (FF: 47.8 %; FFPE: 48.5 %) and 24 % (FF: 24 %; FFPE: 23.5 %) across the whole target region specific for each kit. The average percentage of common SNVs ( c ) and InDels ( d ) was approximately 92 % (FF: 91.9 %; FFPE: 93 %) and 69 % (FF: 69.7 %; FFPE: 69.1 %) across the 42 Mb target region shared between the two kits

    Journal: BMC Cancer

    Article Title: Performance comparison of two commercial human whole-exome capture systems on formalin-fixed paraffin-embedded lung adenocarcinoma samples

    doi: 10.1186/s12885-016-2720-4

    Figure Lengend Snippet: Variant calling comparison between Agilent SureSelect and Roche NimbleGen kit. Mean percentage ± SD of SNVs and InDels common to both library prep kits (blue), and private to either Roche (red) or Agilent (green) kit in both FF and FFPE samples. The average percentage of common SNVs ( a ) and InDels ( b ) was approximately 48 % (FF: 47.8 %; FFPE: 48.5 %) and 24 % (FF: 24 %; FFPE: 23.5 %) across the whole target region specific for each kit. The average percentage of common SNVs ( c ) and InDels ( d ) was approximately 92 % (FF: 91.9 %; FFPE: 93 %) and 69 % (FF: 69.7 %; FFPE: 69.1 %) across the 42 Mb target region shared between the two kits

    Article Snippet: WES standard metrics comparison WES was performed on all samples (5 FF and matching FFPE), comparing two commercially available exome capture systems: Roche NimbleGen SeqCap EZ Human Exome Library v. 3.0 (64 Mb) and Agilent SureSelect Human All Exon v. 5 (50 Mb).

    Techniques: Variant Assay, Formalin-fixed Paraffin-Embedded

    Enrichment efficiency of the three updated exome enrichment platforms (Agilent, NimbleGen and Illumina) performed by four vendors (V1, V2, V3 and V4). ( A ) Mean number of aligned reads (as million reads), mean read depth and percentage of coverage at 20× for each designed target region as well as mean percentage of on-target reads (i.e. within designed target regions) and mean percentage of off-target reads (i.e. within regions more than ±500 bp outside the designed target regions). Note that values for aligned reads indicate the total number of mapped reads without duplicates for V1 and V2 and only uniquely mapped reads without duplicates for V3 and V4 (Supplementary Table S3). ( B ) Mean read depth and percentage of coverage at 20× for all and only coding exons of the RefSeq database as well as uniformity of the coverage of RefSeq coding exons calculated as the fraction of exons reaching an average read depth within ±70% of mean read depth over all coding exons (uniformity coding). ( C ) Mean read depth and percentage of coverage at 15 and 20× for RefSeq coding exons as well as for −50-bp and +20-bp flanking intronic regions. Given are means of all six DNA samples ( n = 6); error bars indicate 95% confidence intervals. Values were calculated using the SeqMonk program ( http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ ) and are presented in Supplementary Tables S4-S8 and S12–S13. For complete coverage of RefSeq coding exons see Figure 3 .

    Journal: Nucleic Acids Research

    Article Title: New insights into the performance of human whole-exome capture platforms

    doi: 10.1093/nar/gkv216

    Figure Lengend Snippet: Enrichment efficiency of the three updated exome enrichment platforms (Agilent, NimbleGen and Illumina) performed by four vendors (V1, V2, V3 and V4). ( A ) Mean number of aligned reads (as million reads), mean read depth and percentage of coverage at 20× for each designed target region as well as mean percentage of on-target reads (i.e. within designed target regions) and mean percentage of off-target reads (i.e. within regions more than ±500 bp outside the designed target regions). Note that values for aligned reads indicate the total number of mapped reads without duplicates for V1 and V2 and only uniquely mapped reads without duplicates for V3 and V4 (Supplementary Table S3). ( B ) Mean read depth and percentage of coverage at 20× for all and only coding exons of the RefSeq database as well as uniformity of the coverage of RefSeq coding exons calculated as the fraction of exons reaching an average read depth within ±70% of mean read depth over all coding exons (uniformity coding). ( C ) Mean read depth and percentage of coverage at 15 and 20× for RefSeq coding exons as well as for −50-bp and +20-bp flanking intronic regions. Given are means of all six DNA samples ( n = 6); error bars indicate 95% confidence intervals. Values were calculated using the SeqMonk program ( http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ ) and are presented in Supplementary Tables S4-S8 and S12–S13. For complete coverage of RefSeq coding exons see Figure 3 .

    Article Snippet: Indeed, the combination of the two best (Agilent and NimbleGen) and all three platforms left only 2.3 ± 0.5% and 1.7 ± 0.3% of the RefSeq coding exons uncovered at ≥20×, respectively, whereas the combined performance of both vendors using Agilent (V1 and V2) could only reduce the proportion of not completely covered exons from 7.2 ± 1.1% (Agilent alone by V2) to 6.8 ± 0.9% (Figure and Supplementary Table S10).

    Techniques:

    Complete (i.e. 100%) coverage of RefSeq coding exons. ( A ) Proportion of RefSeq coding exons 100% covered by each designed target region (design) and by ≥20 reads effectively produced by each vendor (vendors V1–V4). ( B ) Proportions of RefSeq coding exons not 100% covered at 20× (missed exons). If not otherwise indicated, data of all corresponding vendors are included. Given are means of all six DNA samples ( n = 6); error bars indicate 95% confidence intervals. Values were calculated using the SeqMonk program ( http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ ) and are presented in Supplementary Tables S2, S8 and S10.

    Journal: Nucleic Acids Research

    Article Title: New insights into the performance of human whole-exome capture platforms

    doi: 10.1093/nar/gkv216

    Figure Lengend Snippet: Complete (i.e. 100%) coverage of RefSeq coding exons. ( A ) Proportion of RefSeq coding exons 100% covered by each designed target region (design) and by ≥20 reads effectively produced by each vendor (vendors V1–V4). ( B ) Proportions of RefSeq coding exons not 100% covered at 20× (missed exons). If not otherwise indicated, data of all corresponding vendors are included. Given are means of all six DNA samples ( n = 6); error bars indicate 95% confidence intervals. Values were calculated using the SeqMonk program ( http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ ) and are presented in Supplementary Tables S2, S8 and S10.

    Article Snippet: Indeed, the combination of the two best (Agilent and NimbleGen) and all three platforms left only 2.3 ± 0.5% and 1.7 ± 0.3% of the RefSeq coding exons uncovered at ≥20×, respectively, whereas the combined performance of both vendors using Agilent (V1 and V2) could only reduce the proportion of not completely covered exons from 7.2 ± 1.1% (Agilent alone by V2) to 6.8 ± 0.9% (Figure and Supplementary Table S10).

    Techniques: Produced

    Differences among DNA samples. ( A ) Mean coverage of RefSeq exons ( n = 233 644) at 20× (expressed in percentage of the entire exon length) for all six platform-vendor combinations and DNA samples (44, 280, 326, 2905, 7344 and 7739) derived from blood, fibroblasts or saliva. Values were obtained by using the SeqMonk program ( www.bioinformatics.babraham.ac.uk/projects/seqmonk ) and are presented in Supplementary Tables S6 and S12. Error bars indicate 95% confidence intervals for the arithmetic means of all corresponding exons. ( B and C ) Mean coverage at ≥20 reads (B) and mean read depth (C) of RefSeq exons per GC content for each DNA sample exemplified by the WES data of V2 using Agilent, demonstrating its high performance stability across samples.

    Journal: Nucleic Acids Research

    Article Title: New insights into the performance of human whole-exome capture platforms

    doi: 10.1093/nar/gkv216

    Figure Lengend Snippet: Differences among DNA samples. ( A ) Mean coverage of RefSeq exons ( n = 233 644) at 20× (expressed in percentage of the entire exon length) for all six platform-vendor combinations and DNA samples (44, 280, 326, 2905, 7344 and 7739) derived from blood, fibroblasts or saliva. Values were obtained by using the SeqMonk program ( www.bioinformatics.babraham.ac.uk/projects/seqmonk ) and are presented in Supplementary Tables S6 and S12. Error bars indicate 95% confidence intervals for the arithmetic means of all corresponding exons. ( B and C ) Mean coverage at ≥20 reads (B) and mean read depth (C) of RefSeq exons per GC content for each DNA sample exemplified by the WES data of V2 using Agilent, demonstrating its high performance stability across samples.

    Article Snippet: Indeed, the combination of the two best (Agilent and NimbleGen) and all three platforms left only 2.3 ± 0.5% and 1.7 ± 0.3% of the RefSeq coding exons uncovered at ≥20×, respectively, whereas the combined performance of both vendors using Agilent (V1 and V2) could only reduce the proportion of not completely covered exons from 7.2 ± 1.1% (Agilent alone by V2) to 6.8 ± 0.9% (Figure and Supplementary Table S10).

    Techniques: Derivative Assay

    Agarose gel electrophoresis for the confirmation of small deletions. (A) 17 bp deletion in the Promoter region was observed in blood samples of patient RB1 and his father. (B) 29 bp deletion in Exon 1 was observed in blood samples of patient RB11, her mother and siblings. The size of actual and deleted product is indicated by straight and dotted arrows respectively in both gels.

    Journal: BMC Cancer

    Article Title: Targeted next generation sequencing of RB1 gene for the molecular diagnosis of Retinoblastoma

    doi: 10.1186/s12885-015-1340-8

    Figure Lengend Snippet: Agarose gel electrophoresis for the confirmation of small deletions. (A) 17 bp deletion in the Promoter region was observed in blood samples of patient RB1 and his father. (B) 29 bp deletion in Exon 1 was observed in blood samples of patient RB11, her mother and siblings. The size of actual and deleted product is indicated by straight and dotted arrows respectively in both gels.

    Article Snippet: A Primer library was custom-designed to amplify 27 exons, exon/intron boundaries and promoter region of RB1 gene using the Illumina Truseq custom Amplicon and Agilent SureSelect in-solution hybridization capture kits by the service provider (Scigenom, Kochi, India).

    Techniques: Agarose Gel Electrophoresis

    Application to archived data. MaLTE, trained using the GTEx data, was applied to predict gene expression from published microarray data based on brain samples for which RNA-Seq data was also available. Despite the fact that the two studies used different array platforms (Affymetrix Human Exon 1.0 ST arrays and Affymetrix Human Gene 1.1 ST arrays for the brain and GTEx studies, respectively), MaLTE predictions exceeded the within-sample correlations obtained using median-polish and PLIER. MaLTE predictions were based on probes shared between the two array platforms. Box plots of ( a ) Pearson and ( b ) Spearman within correlations are shown. ( c ) Pearson and ( d ) Spearman cross sample correlations with OOB filtering. The black line represents the number of genes/transcripts at each level

    Journal: BMC Bioinformatics

    Article Title: Seq-ing improved gene expression estimates from microarrays using machine learning

    doi: 10.1186/s12859-015-0712-z

    Figure Lengend Snippet: Application to archived data. MaLTE, trained using the GTEx data, was applied to predict gene expression from published microarray data based on brain samples for which RNA-Seq data was also available. Despite the fact that the two studies used different array platforms (Affymetrix Human Exon 1.0 ST arrays and Affymetrix Human Gene 1.1 ST arrays for the brain and GTEx studies, respectively), MaLTE predictions exceeded the within-sample correlations obtained using median-polish and PLIER. MaLTE predictions were based on probes shared between the two array platforms. Box plots of ( a ) Pearson and ( b ) Spearman within correlations are shown. ( c ) Pearson and ( d ) Spearman cross sample correlations with OOB filtering. The black line represents the number of genes/transcripts at each level

    Article Snippet: Application of MaLTE trained on GTEx data to independent microarray datasets To determine whether MaLTE regression models, trained on a diverse panel of GTEx tissues, can be applied to estimate expression from microarrays generated independently we downloaded a dataset, consisting of Affymetrix Human Exon 1.0 ST microarrays and RNA-Seq data from a set of brain samples from a recent study [ ].

    Techniques: Expressing, Microarray, RNA Sequencing Assay

    Identification of a short alternative transcript of TSP2 that is highly expressed in bladder cancer-associated blood vessels.  a  Blood vascular endothelial cells (BECs) were isolated from frozen sections of invasive bladder cancers (tBEC) and adjacent normal (nBEC) bladder tissue ( n  = 6). RNA was isolated and hybridized to Human Exon 1.0 ST arrays.  a  Detection of alternative splicing and transcription was performed using three different bioinformatics analysis tools, namely MIDAS, ANOSVA, and FIRMA. The numbers indicate the number of genes with alternative splicing or alternative transcription identified by each method and their overlap.  b  Exon array expression levels of the full-length and the short transcript of TSP2 and exon structure as shown in the GenBank database.  c  qRT-PCR analysis of the expression of the full-length and the short TSP2 transcripts in tumor-associated vessels and in vessels of healthy bladder tissue. For five out of six patients, matched samples of tumor-associated and healthy vessels could be analyzed as highlighted by the connecting dotted lines. The positions of the primers used are indicated by arrows in  b . Horizontal lines represent median values. Dots represent patient samples. Relative expression was normalized to expression of vessels from healthy tissues in both groups. * p

    Journal: Oncogene

    Article Title: Alternative transcription of a shorter, non-anti-angiogenic thrombospondin-2 variant in cancer-associated blood vessels

    doi: 10.1038/s41388-018-0129-z

    Figure Lengend Snippet: Identification of a short alternative transcript of TSP2 that is highly expressed in bladder cancer-associated blood vessels. a Blood vascular endothelial cells (BECs) were isolated from frozen sections of invasive bladder cancers (tBEC) and adjacent normal (nBEC) bladder tissue ( n  = 6). RNA was isolated and hybridized to Human Exon 1.0 ST arrays. a Detection of alternative splicing and transcription was performed using three different bioinformatics analysis tools, namely MIDAS, ANOSVA, and FIRMA. The numbers indicate the number of genes with alternative splicing or alternative transcription identified by each method and their overlap. b Exon array expression levels of the full-length and the short transcript of TSP2 and exon structure as shown in the GenBank database. c qRT-PCR analysis of the expression of the full-length and the short TSP2 transcripts in tumor-associated vessels and in vessels of healthy bladder tissue. For five out of six patients, matched samples of tumor-associated and healthy vessels could be analyzed as highlighted by the connecting dotted lines. The positions of the primers used are indicated by arrows in b . Horizontal lines represent median values. Dots represent patient samples. Relative expression was normalized to expression of vessels from healthy tissues in both groups. * p

    Article Snippet: Analysis of human exon 1.0 ST array In the human exon 1.0 ST array (Affymetrix), each exon is represented by a probeset comprising at least four oligonucleotides.

    Techniques: Isolation, Expressing, Quantitative RT-PCR

    Coverage efficiency in the medically interpretable genome (MIG). Shown is the cumulative distribution of on-target sequence coverage obtained from sequencing NA12878 across multiple platforms: Personalis Accuracy and Content Enhanced (ACE) Clinical Exome, Agilent SureSelect Clinical Research Exome (SSCR), Agilent SureSelect Human All Exon v5 plus untranslated regions (UTR) (SS), lllumina’s Nextera Exome Enrichment (NX), NimbleGen SeqCap EZ Human Exome Library v3.0 (NG), and 31× whole-genome sequencing (WGS) using an Illumina PCR-free protocol. For clinical applications, we indicate ≥20× as the minimum coverage threshold required (gray line) among all coding (left) and non-coding (right) regions. For reference, insets show an expanded distribution of sequence coverage. ACE and conventional WES data are normalized to 100× mean target coverage

    Journal: Genome Medicine

    Article Title: Achieving high-sensitivity for clinical applications using augmented exome sequencing

    doi: 10.1186/s13073-015-0197-4

    Figure Lengend Snippet: Coverage efficiency in the medically interpretable genome (MIG). Shown is the cumulative distribution of on-target sequence coverage obtained from sequencing NA12878 across multiple platforms: Personalis Accuracy and Content Enhanced (ACE) Clinical Exome, Agilent SureSelect Clinical Research Exome (SSCR), Agilent SureSelect Human All Exon v5 plus untranslated regions (UTR) (SS), lllumina’s Nextera Exome Enrichment (NX), NimbleGen SeqCap EZ Human Exome Library v3.0 (NG), and 31× whole-genome sequencing (WGS) using an Illumina PCR-free protocol. For clinical applications, we indicate ≥20× as the minimum coverage threshold required (gray line) among all coding (left) and non-coding (right) regions. For reference, insets show an expanded distribution of sequence coverage. ACE and conventional WES data are normalized to 100× mean target coverage

    Article Snippet: Agilent SureSelect Human All Exon v5 plus untranslated regions (UTR)

    Techniques: Sequencing, Polymerase Chain Reaction

    Venn diagrams showing commonality of targeting between capture kits (A,B) and properties of encompassed SNPs (C). Overlap between exome capture kits is presented in Mbp (A) and number of SNPs with an AF ≥0.3 (B) . Agilent - SureSelect Human All Exon V4; Illumina - TruSeq Exome Enrichment; Nimblegen - SeqCap EZ Human Exome Library V3.0. For a subset of SNPs present in both the intersection of the three kits shown, and the Illumina TruSight Exome kit, a breakdown of fulfilment of the four classes of candidate filtering criteria is shown (C) (see the main text for details of filtering criteria); 117 SNPs exhibited all desired characteristic; 74 SNPs exhibited none of the desired characteristics.

    Journal: Genome Medicine

    Article Title: A SNP profiling panel for sample tracking in whole-exome sequencing studies

    doi: 10.1186/gm492

    Figure Lengend Snippet: Venn diagrams showing commonality of targeting between capture kits (A,B) and properties of encompassed SNPs (C). Overlap between exome capture kits is presented in Mbp (A) and number of SNPs with an AF ≥0.3 (B) . Agilent - SureSelect Human All Exon V4; Illumina - TruSeq Exome Enrichment; Nimblegen - SeqCap EZ Human Exome Library V3.0. For a subset of SNPs present in both the intersection of the three kits shown, and the Illumina TruSight Exome kit, a breakdown of fulfilment of the four classes of candidate filtering criteria is shown (C) (see the main text for details of filtering criteria); 117 SNPs exhibited all desired characteristic; 74 SNPs exhibited none of the desired characteristics.

    Article Snippet: Candidate identification and panel selection Regions of overlap between three current commonly used whole-exome enrichment kits, (namely Agilent SureSelect Human All Exon V4, Illumina TruSeq Exome Enrichment and Nimblegen SeqCap EZ Human Exome Library V3.0 kits), and common SNPs (dbSNP 137, [ ]) were established using BEDTools [ ].

    Techniques:

    Extent of alternative splicing in the MHC. Absolute values of exon level intensities normalized against gene intensities [NI = log 2 (exon/gene)] were computed from the median signal of the three PGF sample replicates hybridized to the Affymetrix Exon 1.0 ST array. Thus, absolute NI > 1 indicates that the exon is expressed at least twice more or less than the overall gene level. Mean percentage of exons ( A ) and of genes with at least one exon ( B ) with NI value(s) exceeding the indicated thresholds for MHC (gray bars) and non-MHC genes (white bars). Error bars depict standard errors of the means of the three replicates ( C–E ) Comparisons of the median NIs (dashed vertical line) in the 131 MHC genes ( C , E ) or in 733 non-MHC immune genes ( D ) having at least four annotated exons in Vega with the density distribution of median NIs obtained in 10,000 random sets of similar numbers of non-MHC ( C ), non-MHC non-immune ( D ), and non-MHC immune ( E ) genes.

    Journal: Genome Research

    Article Title: Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex

    doi: 10.1101/gr.116681.110

    Figure Lengend Snippet: Extent of alternative splicing in the MHC. Absolute values of exon level intensities normalized against gene intensities [NI = log 2 (exon/gene)] were computed from the median signal of the three PGF sample replicates hybridized to the Affymetrix Exon 1.0 ST array. Thus, absolute NI > 1 indicates that the exon is expressed at least twice more or less than the overall gene level. Mean percentage of exons ( A ) and of genes with at least one exon ( B ) with NI value(s) exceeding the indicated thresholds for MHC (gray bars) and non-MHC genes (white bars). Error bars depict standard errors of the means of the three replicates ( C–E ) Comparisons of the median NIs (dashed vertical line) in the 131 MHC genes ( C , E ) or in 733 non-MHC immune genes ( D ) having at least four annotated exons in Vega with the density distribution of median NIs obtained in 10,000 random sets of similar numbers of non-MHC ( C ), non-MHC non-immune ( D ), and non-MHC immune ( E ) genes.

    Article Snippet: We hybridized samples from the unstimulated and stimulated triplicate cultures of COX, PGF, and QBL LCLs to custom MHC arrays, while only unstimulated samples were hybridized to commercial Affymetrix Exon 1.0 ST arrays.

    Techniques:

    Title: IGV visualization of the control Alu insertion using BAMfile generated with the Agilent kit Legend: Screenshots of IGV outputs restricted to the genomic region where the Alu element insertion occurred (c.1739_1740insAlu in BRCA1 ) in the positive control sample. The BAMfile used for IGV visualization was generated from WES data obtained with the SureSelect Human All Exon V6 kit (exome capture kit) from Agilent. Group alignment is by chromosome of mate. Note that this exome capture kit generates much less discordantly mapped read pairs than the kit from Roche (2 versus 22, compare with Figure 2 ). Accordingly, the required number (five) of discordantly mapped read pairs containing a long polyA track will not be reached and the insertion will not be revealed with our detection strategy. Note that all other characteristics observed for a retrotransposon insertion when using the exome capture kit from Roche (see Figure 2 ) are also observed when using the kit from Agilent.

    Journal: bioRxiv

    Article Title: A systematic screen of breast cancer patients’ exomes for retrotransposon insertions reveals disease associated genes

    doi: 10.1101/2020.06.04.123240

    Figure Lengend Snippet: Title: IGV visualization of the control Alu insertion using BAMfile generated with the Agilent kit Legend: Screenshots of IGV outputs restricted to the genomic region where the Alu element insertion occurred (c.1739_1740insAlu in BRCA1 ) in the positive control sample. The BAMfile used for IGV visualization was generated from WES data obtained with the SureSelect Human All Exon V6 kit (exome capture kit) from Agilent. Group alignment is by chromosome of mate. Note that this exome capture kit generates much less discordantly mapped read pairs than the kit from Roche (2 versus 22, compare with Figure 2 ). Accordingly, the required number (five) of discordantly mapped read pairs containing a long polyA track will not be reached and the insertion will not be revealed with our detection strategy. Note that all other characteristics observed for a retrotransposon insertion when using the exome capture kit from Roche (see Figure 2 ) are also observed when using the kit from Agilent.

    Article Snippet: The genomic DNA from the positive control was resubmitted for WES analysis using the SureSelect Human All Exon V6 kit from Agilent (performed by BGI Genomics Co, China) to compare both WES approaches.

    Techniques: Generated, Positive Control

    The HvDWARF gene structure with exons depicted as blue rectangles with consecutive numbers and introns as black line. Positions of the mutations identified in the brd1-a , brd1-b , brd1-c and brd1-d alleles are shown.

    Journal: International Journal of Molecular Sciences

    Article Title: A Reverse-Genetics Mutational Analysis of the Barley HvDWARF Gene Results in Identification of a Series of Alleles and Mutants with Short Stature of Various Degree and Disturbance in BR Biosynthesis Allowing a New Insight into the Process

    doi: 10.3390/ijms17040600

    Figure Lengend Snippet: The HvDWARF gene structure with exons depicted as blue rectangles with consecutive numbers and introns as black line. Positions of the mutations identified in the brd1-a , brd1-b , brd1-c and brd1-d alleles are shown.

    Article Snippet: Computational Analyses, Molecular Procedures and Physiological Tests Position and length of exons, introns and UTR sequences within the identified HvDWARF genomic sequence were verified using the Spidey software [ ] (National Center for Biotechnology Information: Bethesda, MD, USA).

    Techniques:

    Schematic showing the experimental design of the study to identify the  Mta1  regulated genes with/without the effect of  P53 . RNA was extracted from all the samples Wild Type (WT),  Mta1  knock out ( Mta1- KO),  Mta1  Re-expression in the  Mta1  knock out MEFS ( Mta1 -KO/ Mta1 ), P53 knock out ( P53 -KO),  Mta1  over expression (OE) in the  P53  knock out MEFs (  P53 -KO/ Mta1 ). cDNA was prepared, processed and hybridized onto the Affymetrix Mouse Exon 1.0 ST arrays followed by the data analysis. Samples were compared to identify the differentially regulated genes and in turn the genes regulated by  Mta1  in  p53  dependent/independent manner and irrespective of  P53  status. Candidate genes were selected; these genes were validated using RT-qPCR assays in MEFs followed by RT-qPCR assays in MCF-7 human breast cancer cell line with the human homologs of the candidate mouse genes.

    Journal: PLoS ONE

    Article Title: Gene Profiling of Mta1 Identifies Novel Gene Targets and Functions

    doi: 10.1371/journal.pone.0017135

    Figure Lengend Snippet: Schematic showing the experimental design of the study to identify the Mta1 regulated genes with/without the effect of P53 . RNA was extracted from all the samples Wild Type (WT), Mta1 knock out ( Mta1- KO), Mta1 Re-expression in the Mta1 knock out MEFS ( Mta1 -KO/ Mta1 ), P53 knock out ( P53 -KO), Mta1 over expression (OE) in the P53 knock out MEFs ( P53 -KO/ Mta1 ). cDNA was prepared, processed and hybridized onto the Affymetrix Mouse Exon 1.0 ST arrays followed by the data analysis. Samples were compared to identify the differentially regulated genes and in turn the genes regulated by Mta1 in p53 dependent/independent manner and irrespective of P53 status. Candidate genes were selected; these genes were validated using RT-qPCR assays in MEFs followed by RT-qPCR assays in MCF-7 human breast cancer cell line with the human homologs of the candidate mouse genes.

    Article Snippet: Finally, Affymetrix Mouse Exon 1.0 ST arrays were used for the hybridization, arrays were scanned and the expression data was obtained in the form of .CEL files.

    Techniques: Knock-Out, Expressing, Over Expression, Quantitative RT-PCR

    Mouse-adaptive NS1 mutations regulate mouse gene expression by two different mechanisms. Mouse M1 cells were infected in triplicate at an MOI of 2 with rHK NS mutants or HK-wt virus, and total RNA isolated at 8 hpi was analyzed by microarray using GeneChip Mouse Exon 1.0 ST Array (Affymetrix, Santa Clara, CA, USA). Microarray gene expression data were normalized and analyzed by Flexarray 1.6.1. Genes were considered as up or down regulated relative to mock infected cells if they were ≤1 or ≥1 log2 fold different (≤ or ≥2 fold differences) expression level (p≤0.05; ANOVA). (A) The number of differentially regulated host genes that were significantly up or down regulated ≤2 or ≥2 fold at the p≤0.05 by ANOVA is plotted for each mutant. The mutants formed two groups with either “low gene regulation” (LGR) or “high t gene regulation” (HGR) phenotypes. (B) Heat map of differentially regulated genes in mouse cells infected with HK-wt or rHK NS1 mutant viruses relative to mock infected M1 cells. Genes (total = 5274) were included for hierarchical clustering analysis among mutants if they were differentially regulated (≤2 −1 or ≥2 1 fold differences) and significantly different from mock infected cells for one or more of the mutants, and gene regulation signatures were also analyzed for hierarchical clustering among viruses. The scale depicts up (red) and down (blue) regulated genes according to the log2 scale shown; equal expression is indicated in white (log 2 0 = 1).

    Journal: PLoS ONE

    Article Title: Identification of Adaptive Mutations in the Influenza A Virus Non-Structural 1 Gene That Increase Cytoplasmic Localization and Differentially Regulate Host Gene Expression

    doi: 10.1371/journal.pone.0084673

    Figure Lengend Snippet: Mouse-adaptive NS1 mutations regulate mouse gene expression by two different mechanisms. Mouse M1 cells were infected in triplicate at an MOI of 2 with rHK NS mutants or HK-wt virus, and total RNA isolated at 8 hpi was analyzed by microarray using GeneChip Mouse Exon 1.0 ST Array (Affymetrix, Santa Clara, CA, USA). Microarray gene expression data were normalized and analyzed by Flexarray 1.6.1. Genes were considered as up or down regulated relative to mock infected cells if they were ≤1 or ≥1 log2 fold different (≤ or ≥2 fold differences) expression level (p≤0.05; ANOVA). (A) The number of differentially regulated host genes that were significantly up or down regulated ≤2 or ≥2 fold at the p≤0.05 by ANOVA is plotted for each mutant. The mutants formed two groups with either “low gene regulation” (LGR) or “high t gene regulation” (HGR) phenotypes. (B) Heat map of differentially regulated genes in mouse cells infected with HK-wt or rHK NS1 mutant viruses relative to mock infected M1 cells. Genes (total = 5274) were included for hierarchical clustering analysis among mutants if they were differentially regulated (≤2 −1 or ≥2 1 fold differences) and significantly different from mock infected cells for one or more of the mutants, and gene regulation signatures were also analyzed for hierarchical clustering among viruses. The scale depicts up (red) and down (blue) regulated genes according to the log2 scale shown; equal expression is indicated in white (log 2 0 = 1).

    Article Snippet: The microarray analysis was performed by StemCore Laboratories (Ottawa, Ontario, Canada) using Genechip Mouse Exon 1.0 ST Array (Affymetrix, Santa Clara, CA, USA).

    Techniques: Expressing, Infection, Isolation, Microarray, Mutagenesis

    Detection of GALC exon 1–14 deletions/duplications by MLPA in GLD patients and a normal control, and a detailed analysis of the GALC gene deletion region in patient 1.

    Journal: Human Genome Variation

    Article Title: Exonic deletions in GALC are frequent in Japanese globoid-cell leukodystrophy patients

    doi: 10.1038/s41439-018-0027-5

    Figure Lengend Snippet: Detection of GALC exon 1–14 deletions/duplications by MLPA in GLD patients and a normal control, and a detailed analysis of the GALC gene deletion region in patient 1.

    Article Snippet: All exons were analysed by the MLPA method using the SALSA MLPA kit P446 for GALC (MRC-Holland, Amsterdam, the Netherlands) according to the manufacturer’s protocol.

    Techniques: Multiplex Ligation-dependent Probe Amplification