Monitoring Bone Marrow Transplant Recipients

Hello everyone, it’s been quite some time since my last post. I hope everyone has remained safe and healthy during these times!

My last post dived into short tandem repeat (STR) analysis for bone marrow engraftment monitoring. Today is a presentation of a patient who was transplanted for treatment of acute myeloid leukemia (AML). With all patients (with minor exceptions), donor and pre-transplant recipient samples are taken before transplant. Their informative alleles are then identified and used to determine the percent of donor and any recipient cells in subsequent post-transplant samples.

This patient was unique in that we were not able to obtain the donor sample (they were transplanted outside of our system), and therefore we used a buccal swab for their pre-transplant recipient informatives.

Buccal swabs are chosen because they are a non-invasive way to obtain squamous epithelial cells. These cells are important because they are of the recipient origin and will not change. With this technique, it is essential that the patient has no mucosal inflammation or is not too rough when swabbing their cheek. Otherwise, the buccal sample may become contaminated with blood which would contain donor cells.

We then inferred the donor informatives from the data of a mixed sample and the buccal swab.

Calculation of recipient and donor percentage in a post-transplant sample is determined on specific formulas that utilize these informative alleles. But what happens when a patient relapses and new mutations or deletions are introduced into their genome, causing a change in these informative alleles?

In this case, the patient had a loss of allele at two loci (CSF1PO – allele 11 and D5S818 – allele 13) after having previously obtained full engraftment (Figure 1).

Figure 1. The pre-sample was acquired through a buccal swab. There was no donor sample that was acquirable, and therefore the donor informative alleles were inferred through available data. In September of 2019, the patient was at 100% donor. Almost a year later, the patient is now at 4% donor and missing previously identified recipient alleles, indicating a loss of allele/mutation. Brown box with “R” stands for recipient. Blue box with “D1” stands for donor. Green box with D1R stands for shared.

The importance here is that the true percent donor is 4% (Figure 2). If we take a look at the affected informative alleles, we see an erroneous result of 100% donor and NI (which means the locus is non-informative, eliminating it from the calculations). This expands on the importance of an analyst to be attentive to the results presented. While this case was clearly evident and was caught by our error measurements, it is theoretically possible to cause an issue, especially in cases where the recipient percentages may be smaller. Furthermore, this phenomenon stresses the importance of including multiple informative alleles in our analysis, which increases our measurement of confidence.1

Figure 2. CSF1PO and D5S818 are incorrectly representing the patient’s status. CSF1PO is representing the patient at 100% donor and D5S818 is automatically identified as a non-informative by our software. After automatic and manual loci ignores, the total percent donor was 4%

We know that a loss of allele (loss of heterozygosity) is the likely explanation because both loci are in locations specific to the disease. Looking at Figure 3 below, the two alleles were affected because they were both present on the long arm of chromosome 5. Further, this chromosome is known to be involved in AML, and is also, of course, associated with other disorders like MDS.2 Additionally, the patient had cytology testing that identified this as an affected chromosome.

Figure 3. CSF1PO and D5S818 are both located on the long arm of chromosome 5. CSF1PO’s location is 5q33.1 and D5S818’s location is 5q23.2.

This is an interesting phenomenon and one that shows in measurable terms how a patient’s status can affect their molecular results. It’s further an expression of the molecular mechanisms of a disease, one of my first measurable experiences of how a disease affects the physical molecular constituents of another human.

To me, this encounter was an expression of how complicated, and yet connected, the entire genome has been designed. I am continuously amazed and look forward to expanding my understanding of molecular science.


  1. Crow J, Youens K, Michalowski S, et al. Donor cell leukemia in umbilical cord blood transplant patients: a case study and literature review highlighting the importance of molecular engraftment analysis. J Mol Diagn. 2010;12(4):530-537. doi:10.2353/jmoldx.2010.090215
  2. Crow J, Youens K, Michalowski S, et al. Donor cell leukemia in umbilical cord blood transplant patients: a case study and literature review highlighting the importance of molecular engraftment analysis. J Mol Diagn. 2010;12(4):530-537. doi:10.2353/jmoldx.2010.090215

-Ben Dahlstrom is a recent graduate of the NorthShore University HealthSystem MLS program. He currently works as a molecular technologist for Northwestern University in their transplant lab, performing HLA typing on bone marrow and solid organ transplants. His interests include microbiology, molecular, immunology, and blood bank.

How We Can Make a Clinical Difference Despite Not Seeing Patients

People assume that I chose pathology because I didn’t like patients but this couldn’t be further from the truth. During medical school, I was a Schweitzer Fellow and volunteered at two free health clinics in the Philadelphia Asian community where I helped start hepatitis B screening and vaccination programs in populations with a high prevalence of this disease. I also served as the student director of my school’s migrant farm worker health clinic where we provided screenings and care to farm workers every summer. In fact, I often was asked to speak with patients because I could convince reluctant patients to comply with care.

But this doesn’t mean that I was the best medical student on the wards or in the clinics; in fact, far from it. Now that I look back, I was often too stressed to quickly triage what was most important to do clinically. But being a trained critical thinker, I could often reason out the answers. A couple of my residents thought that I wasn’t made for clinical medicine because I thought things out in a different way than most.

For an artistic and introspective person like me, I found my home in pathology. I need work that visually stimulates me and provides variety, challenges, and most importantly, enough time to take a breath, gather my facts, and think things through. Sometimes, even my physician friends joke that we are introverts who don’t like patients. They think that we sit at microscopes all day, can’t write prescriptions, make diagnoses in isolation, and prefer to release reports with the words “recommend clinical correlation”  so that other doctors can provide the actual care. All of these things are so untrue.

On my molecular pathology rotation, I was reminded how the pathologist and the clinical lab are integral to the complete clinical care of the patient. A transplant patient on anti-CMV prophylaxis was admitted for diarrhea. His labs were positive for both C.difficile and a very high CMV viral load. He was given antibiotics and an increased anti-CMV medication dosage before being subsequently discharged. He was again admitted a few days later with worsening diarrhea despite medication compliance. He was again C.difficile positive and his CMV load was now three times higher than his previous result. He was put on IV gancyclovir and a repeat CMV load ordered to assess therapeutic response before discharge with a prescription for the same dosage of valgancyclovir he was given on his previous recent admission.

Our techs always compare abnormal results with previous values, so my attending and I were notified of the elevated CMV viral loads. The techs in my facility cannot access patient medical records so I was responsible to work up this case. I’m often amazed at how often they pick up a serious issue even without access to clinical records– more than just looking at the number, they know that something is not quite right.

I noted that the patient had been on valgancyclovir with dosage increases for CMV prophylaxis since discharge from his transplant. His CMV load was previously undetectable prior to the recent admissions. I called the transplant surgeon and suggested CMV resistance genotyping based on the clinical history and blood was sent that day. As the experts in diagnostic medicine, we can impact clinical care even when we don’t physically examine the patient. We must serve as the bridge between the clinical lab and primary physician – both informing them of available diagnostics as well as suggesting appropriate tests – because care is more than just the numbers.

-Betty Chung