[3] Illumina Universal Bead Arrays

Fan, Jian‐Bing; Gunderson, Kevin L.; Bibikova, Marina; Yeakley, Joanne M.; Chen, Jing; Garcia, Eliza Wickham; Lebruska, Lori L.; Laurent, Marc; Shen, Richard; Barker, David

doi:10.1016/s0076-6879(06)10003-8

Cited by 278 publications

(193 citation statements)

References 34 publications

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“…Leaf samples were harvested from 15 plants of each line and bulked for extraction of total genomic DNA. All lines were genotyped using two 1,536-SNP chips via a GoldenGate assay (38). One chip was designed based on random candidate genes (RA chip), which were chosen with no prior knowledge or consideration of the function of the proteins (or RNAs) that they encode.…”

Section: Methodsmentioning

confidence: 99%

Joint linkage–linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maize

Zhang

Shah

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

198

129

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This paper describes two joint linkage-linkage disequilibrium (LD) mapping approaches: parallel mapping (independent linkage and LD analysis) and integrated mapping (datasets analyzed in combination). These approaches were achieved using 2,052 single nucleotide polymorphism (SNP) markers, including 659 SNPs developed from drought-response candidate genes, screened across three recombinant inbred line (RIL) populations and 305 diverse inbred lines, with anthesis-silking interval (ASI), an important trait for maize drought tolerance, as the target trait. Mapping efficiency was improved significantly due to increased population size and allele diversity and balanced allele frequencies. Integrated mapping identified 18 additional quantitative trait loci (QTL) not detected by parallel mapping. The use of haplotypes improved mapping efficiency, with the sum of phenotypic variation explained (PVE) increasing from 5.4% to 23.3% for single SNPbased analysis. Integrated mapping with haplotype further improved the mapping efficiency, and the most significant QTL had a PVE of up to 34.7%. Normal allele frequencies for 113 of 277 (40.8%) SNPs with minor allele frequency (<5%) in 305 lines were recovered in three RIL populations, three of which were significantly associated with ASI. The candidate genes identified by two significant haplotype loci included one for a SET domain protein involved in the control of flowering time and the other encoding aldo/keto reductase associated with detoxification pathways that contribute to cellular damage due to environmental stress. Joint linkage-LD mapping is a powerful approach for detecting QTL underlying complex traits, including drought tolerance.anthesis-silking interval | drought resistance | haplotype loci | integrated quantitative trait locus mapping

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Section: Methodsmentioning

confidence: 99%

Joint linkage–linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maize

Zhang

Shah

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

198

129

View full text Add to dashboard Cite

show abstract

“…The EZ DNA methylation kit (Zymo Research, Orange, CA, USA) was used for bisulfite conversion of 500 ng of DNA, and the remaining assay steps were performed as previously published using Illumina-supplied reagents and conditions. 20,21 The Illumina Infinium II Bead Array uses allele-specific annealing to either methylation-specific probes or non-methylation probes to detect the methylation grade of 27 578 individual CpG sites spread across the promoter regions of 14 495 genes.…”

Section: Illumina Humanmethylation27 Beadchip Arraymentioning

confidence: 99%

Gene-specific and global methylation patterns predict outcome in patients with acute myeloid leukemia

et al. 2010

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This study was designed to analyze the effect of global and gene-specific DNA methylation patterns on the outcome of patients with acute myeloid leukemia (AML). Methylation of CDKN2B (p15), E-cadherin (CDH) and hypermethylated in cancer 1 (HIC1) promoters and global DNA methylation by luminometric methylation assay (LUMA) was analyzed in 107 AML patients and cytogenetic and molecular mutational analysis was performed. In addition, genome-wide promoterassociated methylation was assessed using the Illumina HumanMethylation27 array in a proportion of the patients. Promoter methylation was discovered in 66, 66 and 51% of the patients for p15, CDH and HIC1, respectively. In multivariate analysis, low global DNA methylation was associated with higher complete remission rate (hazard ratio (HR) 5.9, P ¼ 0.005) and p15 methylation was associated with better overall (HR 0.4, P ¼ 0.001) and disease-free survival (HR 0.4, P ¼ 0.016). CDH and HIC1 methylation were not associated with clinical outcome. Mutational status and karyotype were not significantly associated with gene-specific methylation or global methylation. Increased genome-wide promoter-associated methylation was associated with better overall and disease-free survival as well as with LUMA hypomethylation. We conclude that global and gene-specific methylation patterns are independently associated with the clinical outcome in AML patients.

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“…Unfortunately, FFPE samples provide in most cases RNA unfit for standard analysis by microarray-based methods, 16 due to extensive RNA degradation by formalin treatment and during storage. 17,18 We tested here the recently developed cDNA-mediated annealing, selection, extension and ligation (DASL) methodology for gene expression profiling of highly degraded human RNA samples, 19,20 applying it to in vitro degraded RNA from human MTs and FFPE MT biopsies. In the DASL assay, total RNA is converted into cDNA in a reverse transcription reaction using biotinylated primers, followed by hybridization to query oligonucleotides (in general up to three distinct for each mRNA), primer extension and ligation, fluorescence labeling by polymerase chain reaction (PCR) and annealing (capture) into the array substrate (beads).…”

mentioning

confidence: 99%

Quantitative expression profiling of highly degraded RNA from formalin-fixed, paraffin-embedded breast tumor biopsies by oligonucleotide microarrays

Ravo

Mutarelli

Ferraro

et al. 2008

Laboratory Investigation

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Microarray-based gene expression profiling is well suited for parallel quantitative analysis of large numbers of RNAs, but its application to cancer biopsies, particularly formalin-fixed, paraffin-embedded (FFPE) archived tissues, is limited by the poor quality of the RNA recovered. This represents a serious drawback, as FFPE tumor tissue banks are available with clinical and prognostic annotations, which could be exploited for molecular profiling studies, provided that reliable analytical technologies are found. We applied and evaluated here a microarray-based cDNA-mediated annealing, selection, extension and ligation (DASL) assay for analysis of 502 mRNAs in highly degraded total RNA extracted from cultured cells or FFPE breast cancer (MT) biopsies. The study included quantitative and qualitative comparison of data obtained by analysis of the same RNAs with genome-wide oligonucleotide microarrays vs DASL arrays and, by DASL, before and after extensive in vitro RNA fragmentation. The DASL-based expression profiling assay applied to RNA extracted from MCF-7 cells, before or after 24 h stimulation with a mitogenic dose of 17b-estradiol, consistently allowed to detect hormone-induced gene expression changes following extensive RNA degradation in vitro. Comparable results where obtained with tumor RNA extracted from FFPE MT biopsies (6 to 19 years old). The method proved itself sensitive, reproducible and accurate, when compared to results obtained by microarray analysis of RNA extracted from snap-frozen tissue of the same tumor.

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[3] Illumina Universal Bead Arrays

Cited by 278 publications

References 34 publications

Joint linkage–linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maize

Joint linkage–linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maize

Gene-specific and global methylation patterns predict outcome in patients with acute myeloid leukemia

Quantitative expression profiling of highly degraded RNA from formalin-fixed, paraffin-embedded breast tumor biopsies by oligonucleotide microarrays

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