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In Vitro

Boost oncology drug discovery with XenoBase®, featuring the largest cell line selection and exclusive 3D organoid models. Benefit from OrganoidXplore™ and OmniScreen™ for rapid, in-depth analysis.

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In Vivo

Enhance drug development with our validated in vivo models, in vitro/ex vivo assays, and in silico modeling. Tailored solutions to optimize your candidates.

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Tissue

Experience ISO-certified biobanking quality. Access top biospecimens from a global clinical network, annotated by experts for precise research.

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Biomarkers and Bioanalysis

Leverage our global labs and 150+ scientists for fast, tailored project execution. Benefit from our expertise, cutting-edge tech, and validated workflows for reliable data outcomes.

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Data Science and Bioinformatics

Harness your data and discover biomarkers with our top bioinformatics expertise. Maximize data value and gain critical insights to accelerate drug discovery and elevate projects.

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KRAS

Accelerate innovative cancer treatments with our advanced models and precise drug screening for KRAS mutations, efficiently turning insights into clinical breakthroughs.

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EGFR

Advance translational pharmacology with our diverse pre-clinical models, robust assays, and data science-driven biomarker analysis, multi-omics, and spatial biology.

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Drug Resistance

Our suite integrates preclinical solutions, bioanalytical read-outs, and multi-omics to uncover drug resistance markers and expedite discovery with our unique four-step strategy.

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Patient Tissue

Enhance treatments with our human tumor and mouse models, including xenografts and organoids, for accurate cancer biology representation.

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Bioinformatics

Apply the most appropriate in silico framework to your pharmacology data or historical datasets to elevate your study design and analysis, and to improve your chances of clinical success.

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Biomarker Analysis

Integrate advanced statistics into your drug development projects to gain significant biological insight into your therapeutic candidate, with our expert team of bioinformaticians.

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CRISPR/Cas9

Accelerate your discoveries with our reliable CRISPR solutions. Our global CRISPR licenses cover an integrated drug discovery platform for in vitro and in vivo efficacy studies.

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Genomics

Rely on our experienced genomics services to deliver high quality, interpretable results using highly sensitive PCR-based, real-time PCR, and NGS technologies and advanced data analytics.

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In Vitro High Content Imaging

Gain more insights into tumor growth and disease progression by leveraging our 2D and 3D fluorescence optical imaging.

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Mass Spectrometry-based Proteomics

Next-generation ion mobility mass spectrometry (MS)-based proteomics services available globally to help meet your study needs.

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Ex Vivo Patient Tissue

Gain better insight into the phenotypic response of your therapeutic candidate in organoids and ex vivo patient tissue.

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Spatial Multi-Omics Analysis

Certified CRO services with NanoString GeoMx Digital Spatial Profiling.

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De-risk your drug development with early identification of candidate biomarkers and utilize our biomarker discovery services to optimize clinical trial design.

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DMPK Services

Rapidly evaluate your molecule’s pharmaceutical and safety properties with our in vivo drug metabolism and pharmacokinetic (DMPK) services to select the most robust drug formulations.

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Efficacy Testing

Explore how the novel HuGEMM™ and HuCELL™ platforms can assess the efficacy of your molecule and accelerate your immuno-oncology drug discovery programs.

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Leverage our suite of structural biology services including, recombinant protein expression and protein crystallography, and target validation services including RNAi.

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Screens

Find the most appropriate screen to accelerate your drug development: discover in vivo screens with MuScreen™ and in vitro cell line screening with OmniScreen™.

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Global CRO in California, USA offering preclinical and translational oncology platforms with high-quality in vivo, in vitro, and ex vivo models.

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Next Generation Sequencing 101

next generation sequencing (NGS) 101A look at the range of next-generation sequencing technologies available today including whole genome, RNA, and whole exome sequencing.

Use of Next-Generation Sequencing (NGS) in Understanding Disease

Decoding the information in an individual’s genome has led to a greater understanding of the interpersonal variability in disease progression and treatment response. This expanded knowledge has led to the proliferation of personalized medicine strategies to prevent, diagnose, and treat diseases based on each individual’s unique genetic (and molecular) profile. Therefore, being able to sequence an individual’s genomes (wholly or in parts) is the first step in personalized medicine.

The first commercialized method of DNA sequencing was the Sanger method. Sanger sequencing involves three mains steps:

  1. A chain-termination PCR reaction
  2. An electrophoresis step to separate the amplified fragments
  3. Analysis to determine the sequences

Sequencing the human genome using Sanger sequencing took 13 years and cost ~2.7 billion US dollars.

To speed up the sequencing process, new technologies were developed allowing for parallel sequencing of multiple DNA fragments utilizing chemical reactions and various optical detection techniques. These technologies are called next-generation sequencing (NGS) or second-generation sequencing, and resulted in a dramatic shortening of the time to sequence whole genomes with a concomitant drop in cost. The cost of sequencing a whole genome today has fallen to below $1000 and takes a matter of hours.

Next-Generation Sequencing

NGS is an umbrella term for various modern sequencing technologies that allow for high throughput DNA and RNA sequencing, which is faster and cheaper than Sanger sequencing. The advent of NGS has allowed for greater advancements in the field of molecular biology, genomics, and even oncology and other disease areas.

There are several NGS platforms available commercially. The current market leader is Illumina. Illumina has multiple platforms available, dependent on need, including MiSeq which can produce same-day sequencing results for very small panels. Thermo Fisher Scientific’s platform is the Ion Torrent or Ion Proton which utilizes detection of pH differences for sequencing. Pacific Biosciences’ platform offers single molecule, real-time technology utilizing a chip with single DNA molecules attached. Zero-mode waveguide technology enables isolation of a single nucleotide for the DNA polymerase to add fluorescent labels for detection of each base. This technology offers average read lengths of more than 10,000 base pairs.

Whole Genome Sequencing (WGS)

WGS, as the name implies, refers to sequencing the entire genome. This includes chromosomal as well as mitochondrial DNA (or chloroplasts in the case of plants). Microorganisms can also have their genomes sequenced using WGS methodologies. The advantages of WGS are:

  • Providing the highest resolution of all the NGS protocols
  • Detection of both large and small variants that might be missed with targeted sequencing approaches
  • Identification of variants not in coding regions that may be implicated in disease
  • Sequencing and assembling novel genomes

Of the current NGS technologies, WGS is still the costliest, albeit still relatively affordable. It also takes the longest time to read since the entire genome has to be covered.

RNA sequencing (RNAseq)

RNAseq assays the quantity and sequences of a transcriptome (total transcribed RNA including mRNA, rRNA and tRNA) within a sample. Understanding the transcriptome gives us information on gene expression levels and the knowledge of what and when genes are turned on/off in a sample. RNAseq also captures information about alternative splicing events which would not be identified by DNA sequencing methods. This technique can also identify certain post-transcriptional modifications such as polyadenylation and 5’ capping. Applications that utilize RNAseq include SNP identification and analyses, transcriptional profiling, and RNA editing and differential gene expression analysis.

The typical RNAseq protocol involves four steps:

  1. RNA extraction and purification
  2. cDNA library construction. Converting the extracted RNA into a cDNA library allows for the addition of the adapters required for NGS techniques for sequencing.
  3. Sequencing of the cDNA library. There are various options and platforms that can be used for sequencing. Single-read sequencing sequences the cDNA from just one end, whilst paired-end sequencing sequence from both ends. This makes single-read sequencing the cheaper and faster option of the two. In addition, there are strand-specific and non-strand-specific protocols. Strand-specific methods determines which DNA strand the RNA was transcribed from.
  4. Data analysis. At the end of sequencing, there will be millions of reads. Software is then used to align these reads with a reference genome and an RNA sequence map is produced. There are various software and methods used to analyze and output the results.

Whole Exome Sequencing (WES)

Exome sequencing or whole exome sequencing (WES) involves only sequencing the protein-coding regions of the genome known as the exome. The human exome is only about 3% of the entire human genome, however, it is thought that around 85% of disease-related mutations occur in the exome.

The advantages of WES compared to WGS, are

  1. WES focuses on the coding regions of the genome instead of the entire genome
  2. WES provides a cost-effective alternative to WGS, provided you are researching changes in coding sequences (SNVs, Indels, etc.)
  3. The data size from WES is smaller (4-5 Gb) vs WGS (approximately 90 Gb) and therefore more manageable with faster analysis
  4. Faster sequencing times, entire exomes can be sequenced to the required coverages in a matter of minutes

Third Generation Sequencing (TGS)

Third generation sequencing platforms seek to move away from the amplification process used in current next generation sequencing platforms. TGS platforms have the promise of being able to perform single-cell sequencing by utilizing the physical properties of DNA. Oxford Nanopore is one of the industry leading companies that commercialized the technology. The MiniION by Oxford Nanopore Technologies, allows sequencing on a desktop computer via a USB device. The DNA is passed through a protein nanopore membrane and sequencing detection is determined by the creation of an ionic current that changes based on the nucleotide.


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