Mastering Sample Handling: Insights from Hendrik Van de Voorde, COO of OHMX.bio

Joannes: Hello Hendrik, how are you doing today?

Hendrik: Hello Joannes, all good here.

Joannes: Great to hear! We’re here to discuss the processes around samples—how to store them, how to send them, and the specific types of samples for different end goals. As the COO and lab operations expert at OHMX.bio, you’re the perfect person to guide us through this. Let’s dive in with the first question: What types of samples does OHMX.bio commonly receive, or which ones are sent to your facility?

Hendrik: We accept a wide range of samples, from liquid biopsies to tissues, and from DNA and RNA that has already been extracted by the customer to protein samples. Essentially, we handle the full spectrum. These can come in the form of cells, tissue, or liquid biopsies, which we then extract to obtain the necessary material, such as DNA, RNA, or proteins. Alternatively, the samples can already be extracted by the customer.

Joannes: Interesting. Do you also accept Petri plates, such as colonies of bacteria?

Hendrik: We do, but we need to be careful with colonies under certain circumstances. We generally advise customers to send us the isolates in tubes. However, we can certainly also scrape the samples ourselves.

Joannes: What’s the most unusual type of sample you’ve ever received?

Hendrik: That would probably be Arctic ground squirrel tissues. We’ve received some unusual samples, like material already extracted from the North Sea, but the Arctic ground squirrel stands out as the most peculiar.

Joannes: OHMX.bio is known for its comprehensive sequencing capabilities—genomic, transcriptomic, translatomic, and proteomic. If a customer wants to send purified DNA, what’s the best way to send it to your facility?

Hendrik: Purified DNA is actually quite stable at room temperature or at four degrees Celsius. We strongly advise against freezing DNA samples because each freeze-thaw cycle can degrade the DNA, leading to fragmentation, which is not ideal for certain applications. Therefore, we recommend sending DNA samples on cool packs.

Joannes: How about if a customer wants to send a liquid biopsy or tissue sample from which you need to extract DNA?

Hendrik: In that case, we prefer the samples to be sent frozen on dry ice. This is crucial if we need to perform the extractions ourselves from tissue, cell lines, or liquid biopsies. We also recommend using specific shipment providers who can control the sample’s temperature during transit.

Joannes: So, if the DNA is already extracted, don’t freeze it, but if it’s not yet extracted, send it frozen?

Hendrik: Exactly. And if the customer wants to send RNA samples, which are already extracted, those must be sent frozen as well.

Joannes: Since RNA samples aren’t as stable, how are they usually shipped?

Hendrik: Extracted RNA samples are shipped frozen, ideally in low-bind tubes to minimize material loss, especially with low concentration or quantity samples. These tubes ensure that as much RNA as possible can be extracted from the tube.

Joannes: Do you also accept FFPE (Formalin-Fixed, Paraffin-Embedded) samples? And can you extract both DNA and RNA from them?

Hendrik: Yes, we can extract both DNA and RNA from FFPE samples. However, it’s important to note that the material won’t be optimal. The DNA is typically fragmented, and the RNA will likely have a low RIN (RNA Integrity Number) value.

Joannes: And in this case, they can be shipped at room temperature, correct?

Hendrik: Yes, FFPE samples can be shipped at room temperature, either as slides or punches. Pathologists can prepare slides and mark areas of interest, such as tumor regions, or the samples can be sent as slightly larger FFPE punches. Both formats are feasible for extraction.

Joannes: OHMX.bio is also known for its ribosome profiling (RiboSeq) services, which provide a snapshot of translation at a specific moment. How should samples for RiboSeq be prepared and sent?

Hendrik: For ribosome profiling, we typically work with cell lines or tissue. If we’re dealing with suspension cell lines, we ask customers to perform a small pretreatment during cultivation involving cycloheximide to stall ribosomal activity. The cells should then be shipped as frozen pellets on dry ice. For adherent cells, we provide a protocol and necessary components for the customer to lyse the cells in-house, provided they have the appropriate infrastructure. If they don’t, we work on alternative solutions. For tissue samples, it’s best to extract and freeze them as soon as possible, ideally using liquid nitrogen, or dry ice if that’s not available.

Joannes: A recent addition to OHMX.bio’s services is single-cell sequencing. How are these samples prepared and shipped?

Hendrik: Parse enables the option of fixating and storing cells prior to library preparation. The protocol of fixating cells takes approximately 30 minutes to an hour. After fixation, samples can be stored for up to 6 months before moving on to barcoding and library preparation, allowing time course experiments and combining samples collected at different timepoints into a single run. Fixed samples need to be stored and shipped at -80°C, it’s important to cool the samples gradually post-fixation to maintain sample integrity and avoid compromising data quality. For controlled cooling, Parse Biosciences offers both tube-based and plate-based fixation workflows.

Joannes: Lastly, how about proteins? Do you often receive extracted proteins, or are you usually expected to handle the extraction?

Hendrik: We typically receive cells from which we perform the protein extraction ourselves. These cells should also be shipped frozen, on dry ice.

Joannes: And a final question: Do you accept samples from all over the world, and can you assist with shipments, particularly for human biological samples?

Hendrik: Yes, we accept samples globally. Human samples usually don’t pose significant transport issues, but when it comes to animal tissue or cells, you’ll need permits from veterinarians. We also arrange import licenses to ensure that shipments aren’t detained at customs. We work with specialized freighters who provide dry ice services, temperature monitoring, and dry ice replenishment during shipment. They also assist with the necessary paperwork, so once everything is in order, we can accept samples from anywhere in the world.

Joannes: Thank you, Hendrik. This has been incredibly informative.

Hendrik: My pleasure, Joannes. Happy to help!