<img height="1" width="1" src="https://www.facebook.com/tr?id=1582471781774081&amp;ev=PageView &amp;noscript=1">
  • Menu
  • crown-logo-symbol-1-400x551

Find it Quickly

Get Started

Select the option that best describes what you are looking for

  • Services
  • Models
  • Scientific Information

Search Here For Services

Click Here to Start Over

Search Here For Models

Click Here to Start Over

Search Here For Scientific Information

Click Here to Start Over

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.

Learn More

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.

Learn More


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

Learn More

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.

Learn More

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.

Learn More


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

Learn More


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

Learn More

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.

Learn More

Patient Tissue

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

Learn More


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.

Learn More

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.

Learn More


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.

Learn More


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.

Learn More

In Vitro High Content Imaging

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

Learn More

Mass Spectrometry-based Proteomics

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

Learn More

Ex Vivo Patient Tissue

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

Learn More

Spatial Multi-Omics Analysis

Certified CRO services with NanoString GeoMx Digital Spatial Profiling.

Learn More

Biomarker Discovery

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

Learn More

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.

Learn More

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.

Learn More

Laboratory Services

Employ cutting-edge multi-omics methods to obtain accurate and comprehensive data for optimal data-based decisions.

Learn More

Pharmacology & Bioanalytical Services

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

Learn More


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

Learn More


Carry out safety pharmacology studies as standalone assessments or embedded within our overall toxicological profiling to assess cardiovascular, metabolic and renal/urinary systems.

Learn More

Our Company

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

Learn More

Our Purpose

Learn more about the impact we make through our scientific talent, high-quality standards, and innovation.

Learn More

Our Responsibility

We build a sustainable future by supporting employee growth, fostering leadership, and exceeding customer needs. Our values focus on innovation, social responsibility, and community well-being.

Learn More

Meet Our Leadership Team

We build a sustainable future by fostering leadership, employee growth, and exceeding customer needs with innovation and social responsibility.

Learn More

Scientific Advisory Board

Our Scientific Advisory Board of experts shapes our strategy and ensures top scientific standards in research and development.

Learn More

News & Events

Stay updated with Crown Bioscience's latest news, achievements, and announcements. Check our schedule for upcoming events and plan your visit.

Learn More

Career Opportunities

Join us for a fast-paced career addressing life science needs with innovative technologies. Thrive in a respectful, growth-focused environment.

Learn More

Scientific Publications

Access our latest scientific research and peer-reviewed articles. Discover cutting-edge findings and insights driving innovation and excellence in bioscience.

Learn More


Discover valuable insights and curated materials to support your R&D efforts. Explore the latest trends, innovations, and expertly curated content in bioscience.

Learn More


Explore our blogs for the latest insights, research breakthroughs, and industry trends. Stay educated with expert perspectives and in-depth articles driving innovation in bioscience.

Learn More

  • Platforms
  • Target Solutions
  • Technologies
  • Service Types

Factors to Consider When Selecting a Next Generation Sequencing (NGS) Technology

DNA strands on a genome sequenceExplore the main factors you need to consider before choosing and using next generation sequencing (NGS).

How to Choose the Right Next Generation Sequencing (NGS) Technology

Many factors need to be considered when selecting the best NGS technology to use for your study. Different technology features not only affect the cost and time it will take to complete your project, but can also affect the chances that your project will succeed.

The main considerations for selecting a NGS technology which are discussed in this post are:

  • Strategies for using NGS
  • Depth of sequencing coverage
  • Length of sequencing reads
  • Single-end versus paired-end sequencing

Strategies for Employing NGS

Traditional single gene sequencing approaches have largely been replaced by NGS. This is because NGS allows ultra-high throughput of DNA/RNA sequencing that is more rapid and less expensive, while allowing for very high coverage of sequences.

As we discussed in a previous post there are different NGS strategies that are employed for genomic sequencing projects, including:

  • Whole Exome Sequencing (WES): This approach is used to read all protein-coding regions of all genes known as the exome. WES allows for the detection of variants in candidate genes that might not be covered in a targeted sequencing approach. It can also detect novel mutations that have not previously been associated with the disease in question.

  • Targeted Sequencing (Panels or Regions of Interest): Typically used to read a limited number of genomic regions of interest which are usually well-described genes and mutations.

  • Whole Genome Sequencing (WGS): Entails the sequencing of the complete genome, including regulatory regions, introns, and even mitochondrial DNA. WGS is very powerful since it allows for the identification of complex structural variations at very high resolution and is often used to detect pathogenic mutations in novel genes or intronic regions.

  • RNA Sequencing (RNA-Seq): This strategy is used to directly sequence and quantify the number of mRNA molecules in the entire transcriptome.

Depth of Sequencing Coverage

The depth of sequencing coverage provides an indication as to the average number of sequencing reads that align to, or "cover", each base in a sequenced sample. This is an important parameter to keep in mind since sequencing is an inherently error prone process. Therefore, the higher the coverage, the higher the confidence you can have in the sequenced bases. Notably, the level of recommended coverage depends on several factors, including your research question and sequencing application. For instance, for WGS and WES applications, the recommended coverage is lower than other applications such as transcriptomic or DNA target-based sequencing.

Coverage (C) is commonly calculated using the Lander/Waterman equation which takes into consideration the read length (L), number of reads (N), and haploid genome length (G): C = LN / G

Length of Sequencing Reads

Read length refers to the number of base pairs sequenced from a DNA/RNA fragment. The regions of overlap between reads are used to later assemble and align the reads to a reference genome to reconstruct the full genomic sequence.

There are both short-read sequencing (SRS) and long-read sequencing (LRS) technologies available.

With high-throughput SRS technologies, millions of short DNA strands are read in parallel. SRS is the most used high-throughput sequencing system, and the approach is supported by a wide range of bioinformatics tools. SRS methods generally provide low cost and high-accuracy data that are used for a variety of applications including variant discovery.

In contrast, high-throughput LRS technologies are capable of generating reads that are hundreds of thousands of base pairs in length (averaging ~10-100kbp). While LRS can be more expensive and take longer than SRS approaches, it allows for greater resolution of the genome since it can span complex genomic features. Furthermore, since LRS does not use PCR, the DNA/RNA remains in its native state which enables LRS to also be used to detect base modifications such as methylation.

Since LRS provides read lengths that can span repetitive regions, it can be informative to resolve these regions (including those with high GC content) and for de novo genome assembly applications. Additional applications include identifying disease causing structural variants (i.e. large genomic alterations typically classified as deletions, duplications, insertions, inversions, and translocations describing different combinations of DNA gains, losses, or rearrangements), and determining specific isoforms of RNA transcripts, among other applications that are not possible with SRS. However, not all applications can use LRS, such as those with highly fragmented DNA.

Determining whether to use an SRS or LRS method is not always a straightforward decision and some problems may actually require a combination of these approaches. Selecting the sequencing read length is highly contextual and depends on the sample type, application, and desired coverage.

Single-End versus Paired-End Sequencing

Single-end sequencing involves the sequencing of DNA fragments from one end to the other and tends to be used for specific applications, such as RNA-seq. In general, this method is rapid and very cost-effective.

Paired-end sequencing is the most used NGS approach. This method involves the sequencing of DNA fragments from both ends to provide twice the number of sequencing reads. This method provides high confidence read alignments and can improve the ability to detect the relative position of sequencing reads and to identify gene insertions, deletions, repetitive sequences, and other rearrangements.

Overview of Several Commercially Available Sequencing Platforms

There are many different commercially available NGS platforms that vary on capability and the underlying technology, with some of the major players being Illumina, BGI Group, Thermo Fisher, Pacific Biosciences, Oxford Nanopore Technologies, and Roche (among others).

The SRS market is largely dominated by Illumina (e.g. NextSeq, NovaSeq), but other important players include BGI Group (e.g. MGISEQ) and Thermo Fisher (Ion Torrent). The LRS market is currently dominated by Pacific Biosciences’ (PacBio) single-molecule real-time (SMRT) sequencing and Oxford Nanopore Technologies’ (ONT) nanopore sequencing.

Other technologies are focused on structural variants and genome assembly such as Bionano Genomics’ Saphyr System. This technology uses a non-sequencing based optical mapping technology to analyze long strands of genomic DNA.

The following table provides a snapshot of four commercially available solutions to provide a sense of their capabilities and typical applications.

Name of Commercial Sequencer Description Typical Applications
Illumina NovaSeq 6000
Used patterned flow cells and uses Illumina’s 2-channel sequencing by synthesis chemistry WGS, WES, targeted sequencing, transcriptomics
Uses DNA nanoball nanoarrays with polymerase-based stepwise sequencing (DNBseq) for short reads WGS, WES, targeted sequencing, transcriptomics
PacBio® Sequel II
Pacific Biosciences
Real-Time (SMRT®) Sequencing technology produces highly accurate long reads Whole genome de novo assemblies, full-length transcriptomes
Bionano Saphyr System
Imaging of extremely long, high-molecular-weight DNA in its native state Structural variant analysis, genome mapping


Next generation sequencing is a powerful tool that has revolutionized many aspects of how basic, applied, and clinical research is conducted. Selecting the right NGS method and technology depends on a variety of factors, and consideration should be given to the various options so that the optimal choice is made for your specific research program. The opportunities of using NGS in preclinical research programs are broad and can help maximize the success of your preclinical development program so that your investigational agent is well-positioned for clinical success.

Related Posts