Microarray, RNA-Seq or Exome? Choosing a Genomic Method by Research Question Under JRP 1.0
Under JRP 1.0 of the Prima Nexus Joint Research Program, three genomic services can be supported with in-kind funding. Which one fits depends on the research question, and every approved project starts with a Lead Genomic Scientist consultation on that choice.
· Research funding
JRP 1.0 applications are open until 30 December 2026. See the services and in-kind funding.
KUALA LUMPUR, 2 November 2026: Prima Nexus has set out a short guide for researchers deciding which genomic method to propose under JRP 1.0, the first phase of the Prima Nexus Joint Research Program. Three services can be supported with in-kind funding: the human genotyping microarray, mRNA sequencing and human whole exome sequencing. The right one depends on what the study needs to learn.
Start with the question
The Genomics page puts the choice in one rule of thumb: known variants in many people, choose the microarray; new or rare variants, choose sequencing; gene expression across the board, choose RNA-seq; a few genes, choose real-time PCR. JRP 1.0 supports the first three kinds of study through its funded services.
Human genotyping microarray: known variants across many people
The Illumina Infinium Global Screening Array reads about 654,000 known variants across the genome in one run, at a cost per sample that suits cohort studies. It fits pharmacogenomics, ancestry and population questions, and imputation can extend it to millions of variants. It takes human samples only, and it reads a fixed panel of known variants, not the whole sequence.
Samples can be saliva, whole blood, fresh or frozen tissue, a cell pellet or a buccal swab, with the DNA extracted for you, or genomic DNA of at least 200 ng.
Human whole exome sequencing: rare and new variants in genes
Whole exome sequencing reads every base of the protein-coding genes, where most known disease variants sit, at about 100x average coverage. It suits rare disease, inherited conditions and the search for new variants in genes, for example in a family. It takes purified human genomic DNA of at least 100 ng, and precious or low-input samples down to about 10 ng.
It reads the protein-coding genes only, about 1 to 2% of the genome. When variation outside the genes matters, whole genome sequencing is the method, offered as a service on the Genomics page.
mRNA sequencing: which genes switch on or off
mRNA sequencing measures every gene being expressed and how strongly, in any species, to show the pathways behind a condition, a treatment or an environmental change. The standard service is stranded mRNA sequencing at 6 Gb per sample, from purified RNA of at least 0.2 µg with a RIN of 7 or above.
Comparing groups needs at least three biological replicates per group, so the design has to be settled before samples are collected. Under JRP 1.0, non-human studies qualify when they link back to human health or population genomics: a gut microbiome study of human health is eligible, while a study of microbes that break down plastic is not.
Not sure? The consultation decides it with you
Every approved JRP 1.0 project is aligned with the Lead Genomic Scientist before data generation starts, and Prima Nexus prepares a full proposal for every project it handles, setting out the method, the samples and the analysis before any work begins. Advanced bioinformatics support can take the analysis further. Each of the three services takes about 6 to 8 weeks from samples that pass quality checks.
A clear research question is enough to apply. A fully developed study, ready samples or ethics approval are not needed at this stage; where ethics approval is needed, it must be in place before samples are processed. Applications take about ten minutes and close on 30 December 2026.
About Prima Nexus
Founded in 2014, Prima Nexus Sdn Bhd is a Malaysian research, scientific consulting and integrated research support company advancing scientific discovery and healthcare innovation. We provide end-to-end research solutions, from early-stage discovery and experimental design to cell-based studies, preclinical animal testing, clinical trials and commercialization. Our multidisciplinary expertise spans genomics, genetic applications, proteomics, molecular biology, stem cell research, bioinformatics and clinical research. Through strategic collaborations with universities, research institutions, industry and global technology partners, we connect scientific expertise and advanced technologies to accelerate research into real-world applications. Our collaborations have supported more than 150 papers in peer-reviewed journals and research teams at more than 40 institutions across Malaysia. More about Prima Nexus.
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