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Featured Publication

Actionable diagnosis of neuroleptospirosis by next-generation sequencing

Many cases of encephalitis remain undiagnosed despite extensive clinical testing. Investigators sequenced DNA isolated from the cerebrospinal fluid of a patient with severe encephalitis. Sequencing identified the presence of a Leptospira strain that was later confirmed as the cause of the illness.
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Featured Publication

Development and validation of a next-generation sequencing-based protocol for 24-chromosome aneuploidy screening of embryos

An abnormal number of chromosomes, or chromosomal aneuploidy, is a major cause of in vitro fertilization (IVF) failure. Preimplantation genetic screening (PGS) of embryos increases the likelihood of successful implantation and pregnancy. Using HiSeq and MiSeq Systems, researchers demonstrated that next-generation sequencing–based PGS delivers results that are consistent with conventional array-based methods, while offering potential advantages.
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Featured Publication

XBP1 promotes triple-negative breast cancer by controlling the HIF1α pathway

Triple-negative breast cancer (TNBC) is an aggressive form of breast cancer in which tumor cells do not express estrogen receptor, progesterone receptor, and HER2 genes. Using ChIP-Seq, investigators discovered that activation of the XBP1 protein regulates the HIF1α pathway, driving tumorigenesis and TNBC progression. The finding may inform treatment strategies for this cancer subtype.
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Featured Publication Review

Metagenomics 2nd Edition

Metagenomics is the study of genomic DNA obtained from microorganisms that cannot be cultured in the laboratory. This document highlights recent publications that demonstrate the use of Illumina sequencing technologies in metagenomics.
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Actionable diagnosis of neuroleptospirosis by next-generation sequencing
NGS-based protocol for 24-chromosome aneuploidy screening of embryos
XBP1 promotes triple-negative breast cancer by controlling the HIF1α pathway
Featured Publication Review: Metagenomics 2nd Edition
PubMed Articles
Research Reviews

Actionable diagnosis of neuroleptospirosis by next-generation sequencing

Many cases of encephalitis remain undiagnosed despite extensive clinical testing. Investigators sequenced DNA isolated from the cerebrospinal fluid of a patient with severe encephalitis. Sequencing identified the presence of a Leptospira strain that was later confirmed as the cause of the illness.

Read more at PubMed »

Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing  New England Journal of Medicine

Integrated exome and transcriptome sequencing reveals ZAK isoform usage in gastric cancer

Researchers used exome and transcriptome sequencing as well as microarrays to characterize 51 gastric tumors and 32 cell lines. Meta-analysis identified gene and splice site mutations in addition to mutation-independent protein isoforms. Results revealed that over-expression of the ZAK kinase TV1 isoform activates multiple cancer-related pathways and is associated with tumorigenesis.

Read more at PubMed »

Liu J, McCleland M, Stawiski EW, Gnad F, Mayba O, et al. Integrated exome and transcriptome sequencing reveals ZAK isoform usage in gastric cancer  Nature Communications

Development and validation of a next-generation sequencing-based protocol for 24-chromosome aneuploidy screening of embryos

An abnormal number of chromosomes, or chromosomal aneuploidy, is a major cause of in vitro fertilization (IVF) failure. Preimplantation genetic screening (PGS) of embryos increases the likelihood of successful implantation and pregnancy. Using HiSeq and MiSeq Systems, researchers demonstrated that next-generation sequencing–based PGS delivers results that are consistent with conventional array-based methods, while offering potential advantages.

Read more at PubMed »

Fiorentino F, Biricik A, Bono S, Spizzichino L, Cotroneo E, et al. Development and validation of a next-generation sequencing-based protocol for 24-chromosome aneuploidy screening of embryos  Fertility and Sterility

Integrated next-generation sequencing and avatar mouse models for personalized cancer treatment

To investigate the potential of using genomic data to personalize cancer treatment, researchers generated patient-derived xenografts in mice to test proposed treatment strategies in vivo. Whole-exome sequencing of patients with advanced solid tumors identified putative tumor-specific alterations. Treatments targeting these mutations were tested in the mouse models, reflecting clinical response and informing patient therapy.

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Garralda E, Paz K, López-Casas PP, Jones S, Katz A, et al. Integrated next-generation sequencing and avatar mouse models for personalized cancer treatment  Clinical Cancer Research

XBP1 promotes triple-negative breast cancer by controlling the HIF1α pathway

Triple-negative breast cancer (TNBC) is an aggressive form of breast cancer in which tumor cells do not express estrogen receptor, progesterone receptor, and HER2 genes. Using ChIP-Seq, investigators discovered that activation of the XBP1 protein regulates the HIF1α pathway, driving tumorigenesis and TNBC progression. The finding may inform treatment strategies for this cancer subtype.

Read more at PubMed »

Chen X, Iliopoulos D, Zhang Q, Tang Q, Greenblatt MB, et al. XBP1 promotes triple-negative breast cancer by controlling the HIF1α pathway  Nature

Identification of genomic alterations in oesophageal squamous cell cancer

Current methods for early diagnosis and treatment of esophageal squamous cell carcinoma (ESCC) are limited. To understand the genomic events that contribute to ESCC pathogenesis, investigators performed whole-genome and whole-exome sequencing of tumor and matched normal samples. Results uncovered gene mutations, novel biomarkers, and tumorigenic pathways that may influence therapeutic strategies.

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Song Y, Li L, Ou Y, Gao Z, Li E, et al. Identification of genomic alterations in oesophageal squamous cell cancer  Nature

Germline and somatic SMARCA4 mutations characterize small cell carcinoma of the ovary, hypercalcemic type

Researchers used HiSeq Systems to sequence the exomes of families affected by small cell carcinoma of the ovary, hypercalcemic type (SCCOHT). Sequencing identified at least one deleterious germline or somatic SMARCA4 mutation in a majority of the cases. Results indicated that SMARCA4 alterations contribute significantly to SCCOHT.

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Witkowski L, Carrot-Zhang J, Albrecht S, Fahiminiya S, Hamel N, et al. Germline and somatic SMARCA4 mutations characterize small cell carcinoma of the ovary, hypercalcemic type  Nature Genetics

Recurrent PTPRB and PLCG1 mutations in angiosarcoma

Researchers used whole-genome, whole-exome, and targeted sequencing with HiSeq Systems to study the genetic changes that contribute to angiosarcoma. Sequencing identified recurrent mutations in the PTPRB and PLCG1 signaling genes that regulate angiogenesis. These findings support the development of targeted therapies for angiosarcoma.

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Behjati S, Tarpey PS, Sheldon H, Martincorena I, Van Loo P, et al. Recurrent PTPRB and PLCG1 mutations in angiosarcoma  Nature Genetics

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

Featured Publication: Metagenomics 2nd Edition

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 methods1. 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 step2. 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 1,000,0003.

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 viruses4. 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 zoonoses5.

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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.6

The ethical issues around genetic testing have been discussed extensively7 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 technologies »

Oncology Review

The ideal cancer treatment is a protocol designed to target the specific molecular mechanism of the tumor and is well tolerated by the patient. The challenge has been that the same clinical presentation can represent several different molecular mechanisms and patients can vary widely in their tolerance to cancer therapies. Recent publications offer a glimpse at how the advances in cancer genetics, technology, and therapeutics development can move clinical decisions from heuristic to evidence based decisions.8

Next-generation sequencing is a highly sensitive tool to determine mutations and it is now accessible, affordable, and robust. Future studies will have much larger cohorts to provide statistically robust associations and build increasingly complete mutation databases. The ultimate goal is that this accumulated knowledge will help clinicians to provide the right drug to the right patient at the right time.

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Learn more about the Illumina oncology portfolio »

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.9 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 sequencing10 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 Lasken R. S. (2013) Single-cell sequencing in its prime. Nat Biotechnol 31: 211-212
2 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
3 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
4 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
5 Lipkin W. I. and Firth C. (2013) Viral surveillance and discovery. Curr Opin Virol 3: 199-204
6 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
7 Chadwick, R. (2011) Personal genomes: no bad news? Bioethics 25: 62-65
8 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
9 Yates L. R. and Campbell P. J. (2012) Evolution of the cancer genome. Nat Rev Genet 13: 795-806
10 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.