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Publication Review

Single-Cell Research Review

Most of the impetus for single-cell tissue sequencing has come from cancer research, where cell lineage and the detection of residual disease are of paramount concern. The same approaches are being used to improve our understanding of massively complex biological systems, such as neural development and immunology.
This document highlights recent publications that demonstrate the use of Illumina technology for single-cell sequencing and very low input applications and techniques. Access PDF »
 
Publication Review

Genomic solutions for cell biology and complex disease research

Complex diseases are the result of multiple genetic and environmental factors. They are distinguished from Mendelian traits (or simple traits) as they do not follow a specific model of inheritance and are usually more frequent in the population. Although some of these diseases are highly heritable, currently known genetic variants can explain only some of the estimated heritability. This review gives a general overview on how genomic technologies and NGS can help in the study of complex diseases. Access PDF »
 
 
Single-Cell Research Review
 
 
Genomic solutions for cell biology and complex disease research
 
 
Microbes and Metagenomics in Human Health
 
 
Sequencing Methods Review
 
 

These research reviews highlight some of the key ways Illumina technology is furthering scientific research.

Single-Cell Research Review

Most of the impetus for single-cell tissue sequencing has come from cancer research, where cell lineage and the detection of residual disease are of paramount concern. The same approaches are being used to improve our understanding of massively complex biological systems, such as neural development and immunology.

This document highlights recent publications that demonstrate the use of Illumina technology for single-cell sequencing and very low input applications and techniques.

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Learn more about ultra-low-input and single-cell RNA-Seq »

Genomic solutions for cell biology and complex disease research

Complex diseases are the result of multiple genetic and environmental factors. They are distinguished from Mendelian traits (or simple traits) as they do not follow a specific model of inheritance and are usually more frequent in the population. Although some of these diseases are highly heritable, currently known genetic variants can explain only some of the estimated heritability. This review gives a general overview on how genomic technologies and NGS can help in the study of complex diseases.

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Neurobiology Research Review

This review provides a summary of recent publications that use the power of next-generation sequencing technology to understand neurological disorders. It covers common neurological disease types, along with their genetic mechanisms and diagnostic tools. It also provides an overview of model systems being developed to study the underlying biology of these diseases.

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Genomic Selection in Agriculture

Genomic selection (GS) and technologies in general are revolutionizing the agricultural world, and will be crucial tools in addressing challenges, such as environmental changes, population expansion, and the increasing demand for nutrition. This review covers the applications of GS, and gives an overview of the recent achievements that have been made since the introduction of NGS in the field of agriculture.

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Cardiology Research Review

The increased information obtained from next-generation sequencing (NGS) is providing remarkable insight into the genomic and environmental components that underlie cardiac diseases. This information has the potential to substantially improve the detection, risk assessment, and treatment of cardiac diseases.

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Sequencing Methods Review

llumina has compiled a collection of NGS library preparation methods from the scientific literature. Read our methods review to find library prep method descriptions, pros and cons, publication summaries, and references. For detailed experimental protocols, refer to the original publications referenced in the review.

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See our extensive collection of library preparation methods available in poster format.

Cancer and Immune System Research Review

Advances in high-throughput sequencing have dramatically improved our knowledge of the cancer genome and the intracellular mechanisms involved in tumor progression and response to treatment. While the primary focus to date has been on the cancer cell, this technology can also be used to understand the interaction of the tumor cells and the cells in the surrounding tumor microenvironment.

Expression analysis of the RNA levels can be used to determine the activation of pathways in the tumor microenvironment. Since common signaling pathways are involved in manifestation of several hallmarks of cancer, including cancer cell proliferation, survival, invasion, metastasis, and immunosuppression, targeting these shared signaling pathways in combination with immunotherapy may be a promising strategy for cancer treatment.1

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Use RNA sequencing (RNA-Seq) to study cancer gene expression and transcriptome changes »

Immunology Research Review

Repertoire sequencing has enabled researchers to identify unique receptor variants found in individuals with susceptibility to hematological malignancies, autoimmune diseases, and allergen response.2

Illumina next-generation sequencing provides the quality, throughput, and read lengths required by the research community to map the human immune response at high resolution. The emergence of new approaches such as phase-defined sequencing and single-cell sequencing can be expected to accelerate this knowledge base.

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Microbes and Metagenomics in Human Health

Metagenomics refers to the study of genomic DNA obtained from microorganisms that cannot be cultured in the laboratory. Recent technical improvements allow nearly complete genome assembly from individual microbes directly from environmental samples or clinical specimens, without the need to develop cultivation methods3. This accumulation of sequence information has greatly expanded the appreciation of the dynamic nature of microbial populations and their impact on the environment and human health.

With this extraordinary and powerful set of sequencing tools now available, it is no surprise that metagenomics has become one of the fastest growing scientific disciplines. This document highlights recent publications that demonstrate the use of Illumina sequencing technologies in metagenomics.

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Learn more about methods such as shotgun metagenomic sequencing »

Viral Detection and Research

Next-generation sequencing has developed into a powerful tool that can be used to detect, identify and quantify novel viruses in one step4. It is proving to be a sensitive method for detecting putative infectious agents associated with human tissues and viral transcripts can be detected at frequencies lower than 1 in 1,000,0005.

One of the fortunate consequences of deep sequencing is the coincidental sequencing of viral DNA or RNA, which has led to the discovery of an increasing number of new viruses6. This comes at a time when the globalization of travel and trade, as well as climate change and its effects on vector distribution, are facilitating the emergence and reemergence of zoonoses7.

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Gain genetic insight into viruses with microbial sequencing »

Genetic Disease Research Review

NGS is creating significant interest as a tool that can objectively examine each patient’s genome individually to find potentially causative mutations. This is ideal for the discovery of new mutations or investigation of high penetrance rare diseases, but it may also provide long-awaited breakthroughs to understanding complex diseases. In addition, it provides the benefit of a common, standardizable approach that can be used to address confusing clinical presentations.8

The ethical issues around genetic testing have been discussed extensively9 and are out of the scope of this review. In short, a family history of disease reveals much about a patient’s risk of disease, but the detailed nature of sequencing tests and the uncertainty of the interpretation raise concerns. As our understanding of genetic diseases improves and genetic testing becomes routine, it may well be possible to address those concerns so that patients can benefit from this remarkable technology.

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Learn more about Illumina genetic disease research technologies »

Cancer Review

In cancer research each cancer sample presents the researcher with an altered genome that contains a unique and unpredictable number of point mutations, indels, translocations, fusions, and other aberrations. Since many of these alterations might never have been observed before and might not necessarily reside in coding regions of the genome, whole-genome sequencing is increasingly seen as the only rigorous approach that can find all the variants in a cancer genome.

The key characteristic of next-generation sequencing technologies is that billions of independent sequence reads are generated in parallel, with each read derived from a single molecule of DNA. The resultant data approximate a random sample of DNA molecules which, in turn, represents the genomes of individual cells contained in the tumor sample.11 This provides us with a powerful toolbox to untangle the causes and mechanisms of cancer.

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Learn more about cancer genomics technologies »

Infectious Disease Review

Whole-genome next generation sequencing can both detect and identify infections agents in one assay without any prior knowledge of the clinical presentation. The same assay will also provide information about the antibiotic resistance, virulence and origin of the infectious agent.

A more accurate diagnosis and treatment will lead to reduced hospital stays and the more considered use of antibiotics, but the ultimate beneficiary will be the patient who will benefit from the improved level of care. This document is intended to highlight recent publications that demonstrate the application and potential of next-generation sequencing technologies to detect and control of infectious agents.

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Learn more about NGS methods for infectious disease surveillance »

Microbial Genomics Research Review

Next-generation sequencing12 lends itself particularly well to the microbial laboratory, where the genomes are small. The appealing difference between sequencing and all other laboratory measurements is that the results can be directly related to a genomic locus and a potential explanation of the biological impact.

Historically the spread of global epidemics was followed over a period of years. With the single base resolution of next-generation sequencing applied to bacterial genomes, it is possible to rapidly track epidemics within a local population, hospital, or even within a family over a period of weeks.

This review highlights recent examples where Illumina sequencing technology is used to track rapid genetic adaptation in nature, the laboratory, and the clinic.

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Learn more about NGS methods for microbial genomics »

1 Kawakami Y., Yaguchi T., Sumimoto H., Kudo-Saito C., Iwata-Kajihara T., et al. (2013) Improvement of cancer immunotherapy by combining molecular targeted therapy. Front Oncol 3: 136 2 Robins H. (2013) Immunosequencing: applications of immune repertoire deep sequencing. Curr Opin Immunol 25:646-652 3 Lasken R. S. (2013) Single-cell sequencing in its prime. Nat Biotechnol 31: 211-212 4 Dunowska M., Biggs P. J., Zheng T. and Perrott M. R. (2012) Identification of a novel nidovirus associated with a neurological disease of the Australian brushtail possum (Trichosurus vulpecula). Vet Microbiol 156: 418-424 5 Moore R. A., Warren R. L., Freeman J. D., Gustavsen J. A., Chenard C., et al. (2011) The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue. PLoS ONE 6: e19838 6 Li S. C., Chan W. C., Lai C. H., Tsai K. W., Hsu C. N., et al. (2011) UMARS: Un-MAppable Reads Solution. BMC Bioinformatics 12 Suppl 1: S9 7 Lipkin W. I. and Firth C. (2013) Viral surveillance and discovery. Curr Opin Virol 3: 199-204 8 Need, A. C., Shashi, V., Hitomi, Y., Schoch, K., Shianna, K. V., et al. (2012) Clinical application of exome sequencing in undiagnosed genetic conditions. J Med Genet 49: 353-361 9 Chadwick, R. (2011) Personal genomes: no bad news? Bioethics 25: 62-65 10 Lipson D., Capelletti M., Yelensky R., Otto G., Parker A., et al. (2012) Identification of new ALK and RET gene fusions from colorectal and lung cancer biopsies. Nat Med 18: 382-384
11 Yates L. R. and Campbell P. J. (2012) Evolution of the cancer genome. Nat Rev Genet 13: 795-806 12 Next-generation sequencing (NGS) and massively parallel sequencing (MPS) are often used interchangeably to refer to high throughput sequencing technologies. Sequencing by synthesis (SBS) refers specifically to Illumina sequencing technology.