Genomics Specialised Solutions
About
ESR provides tailored genomics solutions to meet your needs, covering everything from study initiation to the extraction of unique and challenging samples, as well as bioinformatics analysis and interpretation.
About
The Institute of Environmental Science and Research (ESR) is a leader in genomic analysis in New Zealand, leveraging advanced tools and extensive experience. We specialise in DNA extraction from a wide variety of organisms, including animals, plants, and microbes, consistently delivering high-quality results.
We provide a comprehensive suite of sequencing services for health and environmental samples, ranging from basic sequencing to all-inclusive packages that cover study design, analysis, and in-depth interpretation.
With our modular approach, you can select any combination of our services to address your specific research or genomics needs.
Contact us
To discuss your project, send an enquiry to GenomESR@esr.cri.nz and one of our scientists will get in touch. Please note that during outbreaks or other high-demand periods, our capacity may be limited.
NOTE: This is a commercial and research-based service. For diagnostic subtyping of human derived or clinical samples, please contact ngsrequests@esr.cri.nz
Our expertise
Available expertise modules
Study design
Our genomics team can work with you to create a tailored study design that meets your research or project goals. Whether you're conducting a small-scale project or a large, complex study, we can provide expert guidance to ensure your experiment is set up for success, including sample collection strategies, controls, and methodologies suited to your needs.
Sample extraction
We offer expert sample extraction services for a wide variety of biological materials, including animals, plants and microbes. We have the expertise to extract for unique, challenging samples.
Previous sample types we have worked with include (but not limited to) -
- Species: Animal (guinea pig, lobster, birds, coral, marine sponge), human, plant (Radiata pine), bacteria, avian, fish
- Sample types:
- Tissue: e.g. Mammalian adipose, liver, muscle, stomach, jejunum, brain, heart, formalin fixed samples
- Body fluids: e.g. saliva, blood (whole, serum, plasma), CSF
Read more about our tools and platforms below
Sequencing
Our state-of-the-art sequencing capabilities cover everything from basic DNA or RNA sequencing to more advanced applications like whole-genome sequencing, targeted sequence enrichment (adaptive sampling), epigenetic modifications and metagenomics/transcriptomics. We provide high-quality data using the latest technologies (ONT and Illumina), ensuring that your sequencing needs are met efficiently and with precision.
Read more about our tools and platforms below.
Analysis
Once your samples are sequenced, our team of bioinformatics specialists can help process and analyse the data. We offer in-depth genomic data interpretation, ranging from variant calling to genome assembly and more. This ensures that you have meaningful, actionable insights from your results.
Interpretation and detailed study reports
Our team will deliver comprehensive reports relevant to your needs. For instance: appropriate data interpretation, bioinformatics insights, and expert commentary. We ensure that the results are explained in the context of your study, providing clear, detailed information to support your research objectives, whether for publication, clinical application, or further study.
Platforms and tools
Current tools available at ESR include:
- Oxford Nanopore technology GridION and P2solo
- Illumina Next Seq and MiSeq
- Agilent Tape station
- Amplicon sequencing - we have developed an in-house amplicon sequencing pipeline (AmpSeq) that is a high throughput method for sequencing amplicon reactions. Consensus sequences can be generated for amplicon species within a sample generating greater resolution and insight than Sanger sequencing. AmpSeq is currently accredited under ISO.
Other unique offerings and methods include:
- ONT long read or ultra long read sequencing
- Targeted enrichment of regions of interest using ONT's adaptive sampling
- Base modifications (e.g. DNA Methylation, RNA modifications)
- Short-read Illumina sequencing
- Metagenomics
- Metatranscriptomics
- Development of diagnostic assays using isothermal amplification techniques such as loop-mediated isothermal amplifications or padlock rolling circle amplification.
- Sample enrichment/depletion prior to sequencing
- Standard molecular biology techniques available in any fully equipped PC1/PC2 laboratory.
- Bioinformatic analysis raging from genome assembly and species identification to source tracking and variant calling.
Please contact us on GenomESR@esr.cri.nz if any of the above services would suit your needs.
NOTE: This is a commercial or research-based service. For diagnostic subtyping of human derived or clinical samples, please contact ngsrequests@esr.cri.nz
Case study
Case Studies
What could ESR's genomic solutions look like for your organisation? Explore our case study to see how we turn genomic data into actionable insights for better outcomes.
News and highlights
Read more about our genomics expertise
News
Creating a 'hybrid' whole genome sequence: a local solution to testing bacteria used in the food industry
10 March 2025
Case Study
The power and potential of whole genome sequencing
01 October 2021
Insight
Tiny tech, big impact: how nanopore sequencing is saving vulnerable lives
17 September 2024
News
ESR scientists contribute to new publication exploring Aotearoa’s ground-breaking genomics toolbox for tackling COVID-19
19 June 2023
News
Nanopore sequencing supports probiotic development
03 March 2022
Publications
Draft genome sequences of Escherichia spp. isolates from New Zealand environmental sources
Escherichia coli is often used as a fecal indicator bacterium for water quality monitoring. We report the draft genome sequences of 500 Escherichia isolates including newly described Escherichia species, namely Escherichia marmotae, Escherichia ruysiae, and Escherichia whittamii, obtained from diverse environmental sources to assist with improved public health risk assessments.
Pangenome graphs in infectious disease: a comprehensive genetic variation analysis of Neisseria meningitidis leveraging Oxford Nanopore long reads
Whole genome sequencing has revolutionized infectious disease surveillance for tracking and monitoring the spread and evolution of pathogens. However, using a linear reference genome for genomic analyses may introduce biases, especially when studies are conducted on highly variable bacterial genomes of the same species. Pangenome graphs provide an efficient model for representing and analyzing multiple genomes and their variants as a graph structure that includes all types of variations. In this study, we present a practical bioinformatics pipeline that employs the PanGenome Graph Builder and the Variation Graph toolkit to build pangenomes from assembled genomes, align whole genome sequencing data and call variants against a graph reference. The pangenome graph enables the identification of structural variants, rearrangements, and small variants (e.g., single nucleotide polymorphisms and insertions/deletions) simultaneously. We demonstrate that using a pangenome graph, instead of a single linear reference genome, improves mapping rates and variant calling for both simulated and real datasets of the pathogen Neisseria meningitidis. Overall, pangenome graphs offer a promising approach for comparative genomics and comprehensive genetic variation analysis in infectious disease. Moreover, this innovative pipeline, leveraging pangenome graphs, can bridge variant analysis, genome assembly, population genetics, and evolutionary biology, expanding the reach of genomic understanding and applications.
Genomic diversity of Listeria monocytogenes isolates from seafood, horticulture and factory environments in New Zealand
Listeria monocytogenes is a foodborne human pathogen that causes systemic infection, fetal-placental infection in pregnant women causing abortion and stillbirth and meningoencephalitis in elderly and immunocompromised individuals. This study aimed to analyse L. monocytogenes from different sources from New Zealand (NZ) and to compare them with international strains. We used pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and whole-genome single nucleotide polymorphisms (SNP) to study the population structure of the NZ L. monocytogenes isolates and their relationship with the international strains. The NZ isolates formed unique clusters in PFGE, MLST and whole-genome SNP comparisons compared to the international isolates for which data were available. PFGE identified 31 AscI and 29 ApaI PFGE patterns with indistinguishable pulsotypes being present in seafood, horticultural products and environmental samples. Apart from the Asc0002:Apa0002 pulsotype which was distributed across different sources, other pulsotypes were site or factory associated. Whole-genome analysis of 200 randomly selected L. monocytogenes isolates revealed that lineage II dominated the NZ L. monocytogenes populations. MLST comparison of international and NZ isolates with lineage II accounted for 89% (177 of 200) of the total L. monocytogenes population, while the international representation was 45.3% (1674 of 3473). Rarefaction analysis showed that sequence type richness was greater in NZ isolates compared to international trend, however, it should be noted that NZ isolates predominantly came from seafood, horticulture and their respective processing environments or factories, unlike international isolates where there was a good mixture of clinical, food and environmental isolates.
DNA methylation in blood—Potential to provide new insights into cell biology.
Epigenetics plays a fundamental role in cellular development and differentiation; epigenetic mechanisms, such as DNA methylation, are involved in gene regulation and the exquisite nuance of expression changes seen in the journey from pluripotency to final differentiation. Thus, DNA methylation as a marker of cell identify has the potential to reveal new insights into cell biology. We mined publicly available DNA methylation data with a machine-learning approach to identify differentially methylated loci between different white blood cell types. We then interrogated the DNA methylation and mRNA expression of candidate loci in CD4+, CD8+, CD14+, CD19+ and CD56+ fractions from 12 additional, independent healthy individuals (6 male, 6 female). ‘Classic’ immune cell markers such as CD8 and CD19 showed expected methylation/expression associations fitting with established dogma that hypermethylation is associated with the repression of gene expression. We also observed large differential methylation at loci which are not established immune cell markers; some of these loci showed inverse correlations between methylation and mRNA expression (such as PARK2, DCP2). Furthermore, we validated these observations further in publicly available DNA methylation and RNA sequencing datasets. Our results highlight the value of mining publicly available data, the utility of DNA methylation as a discriminatory marker and the potential value of DNA methylation to provide additional insights into cell biology and developmental processes.
miRNA Signatures of Insulin Resistance in Obesity
Objective: Extracellular microRNAs (miRNAs) represent functional biomarkers for obesity and related disorders; this study investigated plasma miRNAs in insulin resistance phenotypes in obesity. Methods: One hundred seventy-five miRNAs were analyzed in females with obesity (insulin sensitivity, n = 11; insulin resistance, n = 19; type 2 diabetes, n = 15) and without obesity (n = 12). Correlations between miRNA level and clinical parameters and levels of 15 miRNAs in a murine obesity model were investigated.