DNA-encoded chemical libraries are large collections of small organic molecules, individually coupled to DNA fragments that serve as amplifiable identification bar codes. Illumina sequencing was used to analyze DNA-encoded chemical libraries, yielding over 10 million DNA sequence tags per lane of each flow cell. The technology can be multiplexed, enabling the study of very large DNA encoded chemical libraries and reducing decoding costs.
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Buller F, Steiner M, Scheuermann J, Manococci L, Nissen I, et al.
High-throughput sequencing for the identification of binding molecules from DNA encoded chemical libraries. Bioorg Med Chem Lett
Transcriptome analysis of the mosquito that transmits dengue virus was performed using Illumina sequencing. Mosquitoes exposed to insecticides or manmade pollutants showed considerable transcriptome modifications. Genes and molecular mechanisms potentially involved in xenobiotic response and insecticide tolerance were identified, suggesting that transcriptome variations can provide useful information for the detection of novel transcripts.
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David JP, Coissac E, Melodelima C, Poupardin R, Riaz MA, et al.
Transcriptome response to pollutants and insecticides in the dengue vector Aedes aegypti using next-generation sequencing technology. BMC Genomics
Illumina sequencing was used to detect and type viruses from human swab samples collected during recent influenza virus infections. Over 5.9 million reads per run were generated within 48 h, allowing identification of bacteria, fungi, protozoa and viruses from each sample. Novel (H1N1) and seasonal (H3N2) influenza virus-derived sequences were detected without prior genetic information, suggesting that this approach could be a valuable tool for diagnosing emerging infectious diseases.
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Yongfeng H, Fan Y, Jie D, Jian Y, Ting Z, et al.
Direct pathogen detection from swab samples using a new high-throughput sequencing technology. Clin Microbiol Infect
Inherited loss-of-function mutations in known genes predispose individuals to breast and/or ovarian cancer. Using Illumina sequencing, a genomic assay was developed to detect all mutations in 21 target genes. No false-positive calls of nonsense mutations, frameshift mutations, or genomic rearrangements were detected in any of the test samples, suggesting that next-generation sequencing can be successfully used for genetic testing and personalized risk assessment for breast and ovarian cancer.
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Walsh T, Lee MK, Casadei S, Thornton AM, Stray SM, et al.
Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Proc Natl Acad Sci U S A
Metachondromatosis (MC) is an autosomal dominant skeletal disease resulting in bony tumors. Using Illumina technology, a single MC patient genome was sequenced and an 11 bp deletion in exon four of PTPN11 was identified that alters frame, results in premature translation termination, and co-segregates with the phenotype. These results were confirmed in a second MC family. Next-generation sequencing and classical genetic approaches provide a powerful strategy to discover the genes responsible for unexplained Mendelian disorders.
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Sobreira NL, Cirulli ET, Avramopoulos D, Wohler E, Oswald GL, et al.
Whole-genome sequencing of a single proband together with linkage analysis identifies a Mendelian disease gene. PLoS Genet
RNA-Seq revealed extensive transcriptional complexity underlying berry development in the Corvina grape varietal. More than 59 million sequence reads were generated from three developmental stages. Over 17,000 genes were expressed during berry development, 6,695 of which were expressed in a stage-specific manner, suggesting differences in numerous functional categories of gene expression. RNA-Seq is a powerful approach for describing changes in plant transcriptomes during development.
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Zenoni S, Ferrarini A, Giacomelli E, Xumerle L, Fasoli M, et al.
Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq. Plant Physiol
The Illumina GAIIx platform was used to sequence a diverse array of 25 environmental samples and three known microbial 'mock communities'. The results showed excellent consistency in taxonomic recovery and recapturing diversity patterns. Using only 2,000 Illumina single-end reads, the same sample relationships were observed compared with those from the full dataset, suggesting that large-scale studies to survey microbial communities can now be performed at unprecedented spatial and temporal resolution.
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Caporaso JG, Lauber CL, Walters WA, Ber-Lyons D, Lozupone CA, et al.
Microbes and Health Sackler Colloquium: Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A
Twelve new risk loci for type 2 diabetes were identified through a large-scale genome-wide association and replication study in individuals of European ancestry. The risk loci include an X-chromosomal association, and an overlap between loci implicated in monogenic and multifactorial forms of diabetes. The remaining identified loci affect both beta-cell function and insulin action, and are enriched for genes involved in cell cycle regulation.
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Voight BF , Scott LJ , Steinthorsdottir V, Morris AP, Dina C, et al.
Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet
Using Illumina genotyping data, the proportion of human height variance was estimated by 294,831 SNPs genotyped on 3,925 unrelated individuals using linear model analysis. 45% of variance can be explained by considering all SNPs simultaneously, suggesting that “missing heritability” results from individual effects that are too small to pass stringent significance tests. The remaining heritability is due to incomplete linkage disequilibrium between causal variants and genotyped SNPs, exacerbated by causal variants having lower minor allele frequency.
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Yang J, Benyamin B, McEvoy BP , Gordon S, Henders AK, et al.
Common SNPs explain a large proportion of the heritability for human height. Nat Genet
Deletions at 16p13.11 are associated with schizophrenia, mental retardation, and epilepsy. Using several Illumina BeadChips and sequencing, genome-wide screens were performed on a group of patients with a diverse spectrum of epilepsy syndromes. 16p13.11 and possibly other large deletions were identified as risk factors for a wide range of epilepsy disorders, pointing toward haploinsufficiency as a contributor to the pathogenicity of these deletions.
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Heinzen EL, Radtke RA, Urban TJ, Cavalleri GL, Depondt C, et al.
Rare deletions at 16p13.11 predispose to a diverse spectrum of sporadic epilepsy syndromes. Am J Hum Genet
