Sample types in genomics and oncology research: capability advancements in automation

Understanding the importance of quality in processing of specific sample types within oncology research is crucial for driving discovery in downstream molecular applications. Less-invasive sample types like saliva and urine are emerging as key contributors to future diagnostic research and screening of particular cancer life-cycles. Genomics applications involving bone marrow and whole blood have a need for high-quality processing. In all cases, streamlining workflows through automation capabilities is a necessity in the field to increase productivity in our labs. This allows for a focus on innovation and research advancements enabling us to develop future diagnostic capabilities in scientific fields such as biobanking, multiomics, and liquid biopsy for cancer research. The evolving advancements of automated sample purification protocols on Thermo Scientific KingFisher particle processing instruments utilizing Applied Biosystems MagMAX kits are playing such roles in supporting automation capabilities across various application platforms.

Saliva

As an easily and less-invasive source of genetic material, saliva samples can provide valuable information of various cancers or even some head, neck, or lung injuries. This allows for the furthering of retrospective studies for genetic biomarker discovery. In relation to liquid biopsy, saliva samples can be a fundamental source for early detection and monitoring of oral and gastric cancers (1). Extracting fragmented cell-free DNA (cfDNA) within saliva samples is a process that can be considered difficult, as it is necessary to avoid excess protein, mucin, and larger DNA molecules which can inhibit the targeted cfNA in the elution.

Bone Marrow

Bone marrow samples are key to understanding hematological malignancies.(2) In the realm of biobanking, bone marrow samples are precious resources for storing and studying hematopoietic stem cells and malignant cells. They open doors to investigating disease progression, identifying genetic mutations, and developing targeted therapies. Studying DNA from bone marrow has the power to drive discovery in minimal residual disease research and monitor treatment response research for future treatment of relevant cancer types.

Large Volume Urine

Isolated cfDNA from urine is making itself known as a potential diagnostic research tool for early detection of cancers such as bladder, prostate, and kidney. Urine can be readily available in larger quantities which makes it ideal for disease monitoring research, biobanking, and genomics testing. Urine samples provide us with the opportunity to store them for retrospective analysis, biomarker discovery, and validation (3). Genomic, proteomic, and metabolomic alterations associated with urinary tract cancers can be found within urine samples (4). Larger volumes of urine can be processed with automation to procure the relevant nucleic acids giving researchers the power to support future diagnostic treatment, disease research, and genomics testing with reliability.

Large Volume Whole Blood

Enabling scalable genomic DNA isolation from whole blood provides an avenue for insight into personalized medicine approaches (5). As the gold-standard, peripheral blood provides high-quality genomic information that fuels disease research, lineage testing, multi-omic research, and more. Genetic, transcriptomic, proteomic, and metabolomic alterations associated with various cancers can all be found in peripheral blood samples. Scalable high-quality automated DNA isolation of peripheral blood is needed for larger volumes which provide linear increase in DNA elutions.

Automated Sample Purification Protocols and MagMAX Kits with KingFisher Instruments

Automated sample purification is our secret weapon for processing large volumes and diverse types of samples with ease and reproducibility. Robust and reliabe, MagMAX isolation kits are qualified and validated for various applications using a range of sample types and sample volumes. Streamlined processing for either genomic DNA or cfNA can be obtained with just a single KingFIsher instrument utilizing MagMAX chemistries. With the latest workflow validations using our MagMAX Cell-Free DNA and Multi-Sample Ultra 2.0 isolation kits on KingFisher instruments, we can streamline the sample purification process, help save time and enhance efficiency in genomic research, drive cancer research forward with less invasive liquid biopsy samples, and advance biobanking capabilities.

Conclusion

To all researchers – emerging sample types like saliva, bone marrow, large volume urine, and large volume whole blood are becoming a driving force behind oncology and genomics research breakthroughs. Whether you’re diving into biobanking, multiomics, or liquid biopsy, these samples hold the key to unlocking valuable insights into cancer biology, discovering biomarkers, and developing future personalized diagnostic and therapeutic approaches. By leveraging the power of automated sample purification protocols, with the MagMAX kits and KingFisher instruments leading the charge, our research journey can become smoother and more efficient. Together, we can make significant strides in helping drive future cancer research and genomic discoveries.

More related cancer research resources

• End to end workflow solutions for your cancer research
• Application note: Genomic DNA extraction from bone marrow aspirates and peripheral blood mononuclear cells

References

1. Swarup, N., Cheng, J., Choi, I. et al.Multi-faceted attributes of salivary cell-free DNA as liquid biopsy biomarkers for gastric cancer detection. Biomark Res 11, 90 (2023). https://doi.org/10.1186/s40364-023-00524-2
2. Méndez-Ferrer S, Bonnet D, Steensma DP, Hasserjian RP, Ghobrial IM, Gribben JG, Andreeff M, Krause DS. Bone marrow niches in haematological malignancies. Nat Rev Cancer. 2020 May;20(5):285-298. doi: 10.1038/s41568-020-0245-2. Epub 2020 Feb 28. PMID: 32112045; PMCID: PMC9912977.
3. Lommen K, Odeh S, Theije CC, Smits KM. Biobanking in Molecular Biomarker Research for the Early Detection of Cancer. Cancers (Basel). 2020 Mar 25;12(4):776. doi: 10.3390/cancers12040776. PMID: 32218259; PMCID: PMC7226426.
4. Augustus E, Van Casteren K, Sorber L, van Dam P, Roeyen G, Peeters M, Vorsters A, Wouters A, Raskin J, Rolfo C, Zwaenepoel K, Pauwels P. The art of obtaining a high yield of cell-free DNA from urine. PLoS One. 2020 Apr 6;15(4):e0231058. doi: 10.1371/journal.pone.0231058. PMID: 32251424; PMCID: PMC7135229.
5. Wei H, Pares R, Liu L, Blair M. Automated Genomic DNA Extraction from Large Volume Whole Blood. J Biomol Tech. 2019 Dec;30(Suppl):S5–6. PMCID: PMC6936181.

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