Multiplex amplification of large sets of human exons

Porreca, Gregory J.; Zhang, Kun; Li, Jin Billy; Xie, Bin; Austin, Derek; Vassallo, Sara L; LeProust, Emily; Peck, Bill; Emig, Christopher J.; Dahl, Fredrik A.; Gao, Yuan; Church, George M.; Shendure, Jay

doi:10.1038/nmeth1110

Cited by 383 publications

(324 citation statements)

References 24 publications

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“…Unwanted DNA is then washed off, and the captured material eluted and prepared for sequencing. The capture capacity ranges from a few Mb up to the entire exome (Hodges et al 2007;Porreca et al 2007) using two general methodologies: conventional solid state arrays (on-array capture) and paramagnetic beads (in-solution capture) (Albert et al 2007;Chou et al 2010;Gnirke et al 2009). A number of custom hybridisation platforms are available including Agilent, Roche Nimblegen and Illumina.…”

Section: Targeting Methodsmentioning

confidence: 99%

Review of massively parallel DNA sequencing technologies

Moorthie

Mattocks

Wright

2011

HUGO J

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Since the development of technologies that can determine the base-pair sequence of DNA, the ability to sequence genes has contributed much to science and medicine. However, it has remained a relatively costly and laborious process, hindering its use as a routine biomedical tool. Recent times are seeing rapid developments in this field, both in the availability of novel sequencing platforms, as well as supporting technologies involved in processes such as targeting and data analysis. This is leading to significant reductions in the cost of sequencing a human genome and the potential for its use as a routine biomedical tool. This review is a snapshot of this rapidly moving field examining the current state of the art, forthcoming developments and some of the issues still to be resolved prior to the use of new sequencing technologies in routine clinical diagnosis.

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Section: Targeting Methodsmentioning

confidence: 99%

Review of massively parallel DNA sequencing technologies

Moorthie

Mattocks

Wright

2011

HUGO J

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“…This equates to the sequencing of 10,000 loci in 10,000 individuals to a depth of about 1000× at a cost of less than US$1 per sample. Multiplexed primer-based assay technologies have the potential to deconvolve the sequencing read data to count and map haplotype assemblies in several lines 86 . Complementary approaches such as linked-read 43 sequencing and long-read sequencing 35 also show promise for the large-scale genetic analyses of populations in genomics-led breeding strategies.…”

Section: Crop Breeding As a Dna-assembly Problemmentioning

confidence: 99%

Genomic innovation for crop improvement

Bevan

Uauy

Wulff

et al. 2017

Nature

313

219

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Crop production needs to increase to secure future food supplies, while reducing its impact on ecosystems. Detailed characterization of plant genome structure and genetic diversity is crucial for meeting these challenges. Advances in genome sequencing and assembly are being used to access to the large and complex genomes of crops and their wild relatives. Sequencing of wild crop relatives is identifying a wide spectrum of genetic variation, permitting the association of genetic diversity with diverse agronomic phenotypes. In combination with improved and automated phenotyping assays and functional genomic studies, genomics is providing new foundations for crop-breeding systems. In the twentieth century, famines caused by political crises, mismanagement of food production or genocide killed an estimated 70 million people and were second only to war as the greatest manmade cause of death 1 . The father of the Green Revolution, Norman Borlaug, summarized the importance of crops: "Without food, people perish, social and political organizations disintegrate, and civilizations collapse. " For thousands of years, people have dedicated considerable resources to securing food supplies; for example, grain supplies to ancient Rome were secured through an extensive network of long-distance transport, and the distribution of grain was coordinated and subsidized by the cura annonae ('care for the grain supply'), an important figure who contributed to the maintenance of political unity and power.During the past 10,000 years, a period known as the Holocene, Earth's environment has been unusually stable. This probably facilitated the domestication of crops from wild species, resulting in steadily improved yields and adaptation to new agricultural areas. The production of food is now carried out on a vast scale, with 38% of Earth's surface dedicated to agriculture 2 . This increased production is having a pervasive influence on ecosystems worldwide: nitrogen production for agriculture accounts for 1.2% of global energy consumption 3 ; photosynthesis can no longer maintain stable levels of atmospheric carbon dioxide; and food production consumes around 70% of freshwater supplies. The modelling of crop responses to increases in temperature predicts that there will be a considerable reduction in the yield of rice, an important crop around the world 4 . Climate change could also alter the dynamics of crop pathogenic agents by altering the range of vectors and by compromising the immune response of crops 5 .Crop production must therefore adapt to more variable environments and the substantial impact it has on the environment needs to be reduced. Productivity must also increase at a much greater rate than in the past to meet the needs of Earth's growing population 6 . Genetic improvements in crop performance continue to be crucial for increasing crop productivity, but current rates of improvement are unable to meet the demands of sustainability and food security 7 . Plant genomics has a central role in the improvement of crops, includi...

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“…Cyclic array sequencing techniques facilitate the detection of rare mutations. Recent affinity-enrichment techniques allow subsets of the genome to be enriched before sequencing (for example, all known exons), thereby decreasing the cost of targeted sequencing 83 .…”

Section: Dna-sequence Abnormalitiesmentioning

confidence: 99%

Translating insights from the cancer genome into clinical practice

Chin

Gray

2008

Nature

262

205

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Cancer cells have diverse biological capabilities that are conferred by numerous genetic aberrations and epigenetic modifications. Today's powerful technologies are enabling these changes to the genome to be catalogued in detail. Tomorrow is likely to bring a complete atlas of the reversible and irreversible alterations that occur in individual cancers. The challenge now is to work out which molecular abnormalities contribute to cancer and which are simply 'noise' at the genomic and epigenomic levels. Distinguishing between these will aid in understanding how the aberrations in a cancer cell collaborate to drive pathophysiology. Past successes in converting information from genomic discoveries into clinical tools provide valuable lessons to guide the translation of emerging insights from the genome into clinical end points that can affect the practice of cancer medicine.A human 'cancer genome', or oncogenome, harbours numerous alterations at the level of the chromosomes, the chromatin (the fibres that constitute the chromosomes) and the nucleotides. These alterations include irreversible aberrations in the DNA sequence or structure and in the number of particular sequences, genes or chromosomes (that is, the copy number of the DNA). They also include potentially reversible changes, known as epigenetic modifications to the DNA and/or to the histone proteins, which are closely associated with the DNA in chromatin (Fig. 1). These reversible and irreversible changes can affect hundreds to thousands of genes and/or regulatory transcripts. Collectively, they result in the activation or inhibition of various biological events, thereby causing aspects of cancer pathophysiology, including angiogenesis, immune evasion, metastasis, and altered cell growth, death and metabolism 1 .Mining the cancer genome and epigenome for aberrations that control these processes has become a major activity in cancer research, because it is widely understood that these aberrations provide clues to the mechanisms of disease pathogenesis. These studies can inform efforts to identify molecular events that can be targeted for therapy and to discover molecular biomarkers (biological indicators) that aid in early detection, diagnosis, prognosis (that is, prediction of clinical outcome) and the prediction of responses to therapies.

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Multiplex amplification of large sets of human exons

Cited by 383 publications

References 24 publications

Review of massively parallel DNA sequencing technologies

Review of massively parallel DNA sequencing technologies

Genomic innovation for crop improvement

Translating insights from the cancer genome into clinical practice

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