Flow Cytometry: Uganda experience and perspective for patients entering cancer care

Dr Carol Achola is the principal pathologist and specialist in hematopathology at Uganda Ministry of Health, Central Public Health Laboratories, Kampala, Uganda.


I'm going to share our story from Uganda about introducing flow cytometry to help support the diagnosis of lymphoma and leukemia.

As we all know, classification of leukemias and lymphomas according to the World Health Organization (WHO) is based on clinical presentation, morphology, and a lot of other tests, but in our setting, we are using morphology and a few cytochemical stains that were available with a limited panel of immunohistochemistry and that is if we had a tissue. If we did not have a tissue, then we would do morphology and the cytochemical stain that was available.

Overall diagnosis took much longer because of the processes involved, right from the referrals from the lower health facilities where patients presented and finally to the Uganda Cancer Institute, which is the only cancer care center in the country. Then there were also delays in diagnosis, which were a big challenge. Flow cytometry was available, but limited to infectious disease research, mainly HIV and malaria. I am going to share a story of how we have leveraged the HIV laboratory systems to functionalize our flow laboratory at the central lab.

Building a Flow Cytometry Lab

With support from Burkitt’s Lymphoma Fund for Africa (BLFA) in December 2018 we launched the Flow Lab, and the testing was also launched at the same time. There was a one-week training that was conducted for technologists in terms of sample processing and sample requirements, and alongside there was also training for pathologists on the analysis of data that was generated. This was done using samples that were submitted from cancer patients at the Uganda Cancer Institute (UCI). Before the BLFA Team left, we had initiated reporting with support from Doctor Steve Kussick.

Introducing a cancer testing service

The initial samples that came from the UCI, were for learning, but they turned out to be tumor cells and some of the patients were started on treatment within 24 hours. When that was launched and because it was a new test, we had Dr Steve Kussick remain in the background to support any difficult cases.

We expanded this because most of our patients come from lower health facilities so by the time, they are referred to the UCI, they have had an experience in the lower health facilities for either a diagnosis or someone thought they had cancer. What we did as a team from the Central Public Health Lab (CPHL) was to embark on a continuing medical education to raise awareness that now we had flow cytometry and to share what the flow cytometry can do, and which patients would require that. We went to all the regional referral hospitals which were 16 in the whole country. Inference of a diagnosis is made from the lower facilities, and we went to the facilities and engaged with the doctors and the laboratory staff.

We focused on the preanalytical considerations when they thought the patient had a leukemia, what they needed to do, how they needed to take the sample and to let them know that now we have the tests and about transporting the sample to the CPHL in Kampala. Then we also distributed our flow request forms and had four people in each of the regional referral hospitals. Whenever a patient needed flow, they would contact this person (a lab personnel) to have the samples drawn and shipped in the shortest time possible.

Overall, the longest time a sample took to come to the CPHL was about 24 hours if samples were coming from up country, but overall, most of them took between 12 -24 hours. Over 95% of the samples that we work on are from the UCI, which takes less than two hours to have the samples brought to the CPHL. Depending on how far the facility was from the lab, we would have the sample in the most feasible time, and we are lucky that the UCI where most of the samples came from is near the facility compared to the other upcountry facilities.

After doing that, we needed to rearrange and consider sample management because we are leveraging the already existing sample transport network. It is a national network which picks samples from about 100 hubs across the country, but these samples are picked together with the HIV viral load samples, samples for early infant diagnosis (EID) and samples for sickle cell. We needed to make certain adjustments to avoid any delay or loss of samples because of the kind of samples that we had.

We made some adjustments for flow samples or samples for flow cytometry, these would not go through the main accession area, which is usually busy and sometimes takes longer than usual. So, all flow samples were accessioning the Flow laboratory on arrival to be processed and run by the on-call technologist. We operate the lab six days a week except for Sunday.

When we generate the files, we can upload it on our portal which is accessed by a pathologist. Usually, it is me because I directly take care of that, but I have other colleagues who also do the analysis depending on the circumstance. We have the files generated, analyzed, and then reported to the treating clinicians via mailing list. This has really improved the turnaround time, reduced the issue of loss of samples and unnecessary delays because all the treating oncologists from the UCI from both the pediatric and adult side are on the mailing list, and we are able to alert them whenever we have an abnormal result.

One other good aspect is that we can do the analysis remotely, so sometimes when you are out of the office on field work, you are able to access via the portal the data that has been generated and you are able to send in the result to the clinicians in time. Then we are also able to obtain real time consults on the difficult cases, initially there were many because it was a new test, but as time has gone on, we have developed capacity to report these cases. We still have Dr Steve Kussick who gives a real time consult whenever necessary.

Also, in the lab we have now developed capacity to do morphological correlation with the flow result on the liquid tumors that come in. We do not have capacity now to process solid tumors and immune-histochemistry (IHC) and other tests on tissue. But we have built capacity within this time to do morphological correlation.

On a few cases that we are unable to arrive at a diagnosis with the stains, we also reach out to the UCI because they have a lab we work very closely with and can run additional IHCs on marrow for cases that we have not yet got a conclusive answer. This has also improved the laboratory-clinician interface which has impacted positively on diagnosis. Often in the lab in this setting because we do not have a lot of electronic systems for managing our patients, we rely a lot on written requests, and often feel the history is not enough. With this we can have a direct consultation with the treating clinicians in the world and this has impacted on the diagnosis.

The sample pathway

This is a summary of the sample pathway that shows the path the samples go through: the EID samples, viral load samples and sickle cell samples.

As we can see, because our health system is organized in a tiered network from the lower facilities up to the national referral, usually the samples come from the lower facilities going towards the national referral. The lab services in the country also mirror that kind of arrangement – there are the lower labs and then you go on to the regional referral labs who have more capacity to conduct certain tests and then more again with the national referral lab.

With flow cytometry the UCI was new, and we are bringing it on board, so we needed to do a lot of communication and engagements to bring on board the sample transport network, the clinicians, and the people at the main laboratory. We introduced the UCI, which was something new we modified in the sample transport network and as I have already alluded to, we had to remove the general accessioning so that we speed the flow of samples to the lab and to dispatch results.


Overall since we launched the flow lab, we have really seen a steady increase in the samples.

In 2020-2021 because of COVID disruption in the patient flow because of the travel restrictions that affected most of our patients who use public transport. But we have seen a steady increment in the number of samples that we are receiving. The males have had slightly more samples sent in.

This data is by age group which shows that a lot of children came, and the Burkitt’s Lymphoma Fund really helped to support pediatric diagnosis. Also, a lot of adults who have leukemia benefited from the service and it is something that we now plan to have support and funding for. We are using this information and data to advocate funding specifically to support the flow lab so that we can have all the patient groups catered for.

As you can see, the adults are benefiting even more than their children that the Burkitt’s Lymphoma Fund set out to support.

Overall, most of the cases we have seen are acute leukemias, which is really the goal from the Burkitt’s Lymphoma Fund. We have a few chronic leukemias, and most of them come, if not all, from the adult population. Multiple myeloma we have a lot of but by design of the panels we were using, we felt it would not benefit a lot, so we engaged the clinicians and we thought we can have a diagnosis of multiple myeloma via morphology and other techniques like immunofixation, so that we really optimize the tests that we the design would really pick out.

This is not representative, it is something deliberate that we did to optimize diagnosis for acute leukemia as we felt that multiple myeloma and other chronic leukemias like the chronic myeloid leukemias (CMLs), unless they were getting more aggressive, we could make a diagnosis without running this flow.

Future areas of focus

We are already completing our ten-color panel validation so we are going to have more robust data and be able to pick more cases that initially we would have to rely on morphology and IFC. This again improves our turnaround time because we do not have to wait for IFC from the marrow that we are not able to do.

Another issue we have had a challenge with, as it was new and then COVID occurred, was that we did not have an electronic information system really developed and supported. Now we are focusing on having clinicians, wherever they are, able to order this test and have real time reporting. Also, this would help in program monitoring and reporting of the information and the data we generate and would be good for advocacy, especially with the ministry.

Currently we are relying on donations and support from partners, but we really feel we need to engage the leadership to also support in diagnosing this. Because of the competing public health priorities, still HIV and TB remain our biggest public health issue, but cancers have been captured as an unfunded priority. We really think this information can be shared with the leadership and have support coming in as this is now the only flow lab in the country and it is supporting the whole country, both the pediatric age group and the adult population.

Lessons Learnt

The cost of establishing a flow laboratory and a cancer diagnostic lab, we really think that countries can leverage the already existing HIV capacity that is already well developed in Sub Saharan Africa to initiate and to improve cancer diagnosis.

We have also learned that it is possible to run a timely cancer diagnostic service from a central point so that we do not have to have flow laboratories distributed all over the country. Uganda and a lot of African countries have very few pathologists, so we would not even have the personnel to run that, and the cost would be higher than we have demonstrated. It is possible to run a flow lab with a central point at a modest cost if we were able to centralize the service. The Laboratory Information Management system (LIMS) is a critical component and considerations need to be put in place as we finish it and develop a flow service.


Our central public lab now also doubles as the National Health Laboratory and Diagnostic Services which was built principally in response to HIV, malaria, and TB. But now the government has really leveraged our needs to improve laboratory diagnosis for a lot of other pathologies, including sickle cell and other cancers.

This is a story that we feel we should share with our counterparts in Africa, that we could set up this expensive cancer diagnostic network at a cheaper price if we leveraged the already well-established HIV infrastructure.

I would like to thank the Burkitt’s Lymphoma Fund for Africa for more fun for starting this in the country and for seeing us this far, and we really hope that we will be supported and able to advance this testing to support the whole country. To Beckman Coulter for supporting with all the supplies and all the HR support that they have given. Doctor Steve Kussick for always being there to provide real time consult. And finally, this the team in Uganda Cancer Institute, the oncologist, both the pediatric and adult oncologist and the team at the Central Public Health Laboratories Laboratory the technologist, the pathologist and importantly, the executive director who doubles as our only senior hematopathologist in the country. Despite her busy schedule, she has always found time to look at the cases whenever called upon.

I thank you all for your attention.

Leukemia and Lymphoma

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