Simple Blood Test Could Catch the Most Common Leukemia Gene Error in Kids

DNA index results and conventional karyotyping should be used in tandem to detect high hyperdiploidy (HHD) in children diagnosed with B-cell acute lymphoblastic leukemia (B-ALL) rather than in competition, as each method compensates for the other’s blind spots, according to a new study published in PLOS One.¹

B-ALL is the most common childhood cancer,² so pinpointing the chromosomal makeup of these cancer cells is a top priority, as it shapes prognosis, risk tier, and which chemotherapy protocol to administer, the study authors explained.³ The most telling genetic finding in childhood B-ALL is HHD, a condition seen when leukemic cells carry more than 50 chromosomes, which occurs in roughly 1 in 4 pediatric patients with the blood cancer. Crucially, HHD signals a relatively favorable prognosis. Therefore, missing it or getting the result too late can delay optimal treatment, the study authors emphasized.

Conventional karyotyping is the gold standard to detect HHD, but it is a painstaking process that requires leukemic cells to be cultured, induced into division, and then visually analyzed under a microscope. These cultures regularly fail, the authors noted, with failure rates often exceeding 50% in resource-limited settings, leaving clinicians without a critical piece of the diagnostic picture.

What the Study Did and Found

The new study published in PLOS One evaluated whether the DNA index, a measure of total DNA content in leukemic cells derived from flow cytometry, could reliably substitute for karyotyping when cultures fail and serve as a complementary tool when they succeed. The researchers analyzed data from 210 pediatric patients diagnosed with B-ALL at a specialized children’s hospital in Lima, Peru, between 2017 and 2021. Most patients were aged 1 to 10 years (73.8%). All patients had undergone karyotyping and DNA index analysis. Using karyotype results as the reference standard, the team applied receiver operating characteristic (ROC) curve analysis to identify the optimal DNA index cutoff for flagging HHD.

The results were striking. At a DNA index threshold of at least 1.10, the test demonstrated a sensitivity of 96.6% and a specificity of 89.8%. Its negative predictive value reached 99.1%, meaning a DNA index below the cutoff essentially rules out HHD. The area under the ROC curve was 0.947, placing the DNA index in the “excellent” range for diagnostic performance.

Overall concordance between index and karyotype results was 91.1%, with a Kappa index of 0.75 (95% CI, 0.62-0.87), indicating substantial agreement between the 2 methods. In 25.2% of cases (n = 53), karyotypes failed entirely, a rate the authors attribute primarily to poor sample quality rather than laboratory error. In those cases, the DNA index provided the only available chromosomal estimate.

Notably, not all discordant cases necessarily reflect errors in the index. Eleven of the 13 patients with a diploid karyotype but an elevated index result (≥ 1.16) may represent false negatives from karyotyping, since conventional cytogenetics can miss small or low-frequency aneuploid clones. Without confirmatory fluorescence in situ hybridization or chromosomal microarray testing, the true reference could not be established.

Immunophenotypic Clues

Beyond the chromosomal data, the study identified 2 immunophenotypic markers associated with HHD that clinicians can observe directly from routine flow cytometry panels. Patients with larger blast cell size, measured as a forward scatter ratio of at least 1.35 vs normal lymphocytes, were nearly 5 times more likely (95% CI, 3.0-8.3) to have HHD. Those with aberrant expression of the CD123 antigen were 15 times more likely (95% CI, 2.3-96.6), a finding explained by the gain of extra X chromosomes in hyperdiploid cells, which carry additional copies of the CD123-encoding gene.

These findings suggest that flow cytometry immunophenotyping, already performed at diagnosis, can flag cases warranting closer cytogenetic scrutiny, potentially guiding laboratory prioritization before karyotype results are available.

Why These Findings Matter

For hospitals in Latin America and other regions where cytogenetic infrastructure is limited or unreliable, DNA index testing offers a practical pathway to chromosomal risk stratification. Flow cytometry is faster, requires no cell culture, and can detect aneuploid populations at levels below 1%, far exceeding the sensitivity of conventional karyotyping, the authors explain. Still, the authors emphasize that the 2 methods complement each other and should therefore be used in tandem.

The study does have limitations. It was conducted at a single center, used karyotyping alone as the reference standard, and did not assess whether the DNA index cutoff is capable of predicting clinical outcomes like relapse or event-free survival, which the authors flag for prospective follow-up.

“Longitudinal cohorts would allow to assess whether this cut-off can predict relevant outcomes such as early treatment response, relapse rate, and event-free survival,” the authors concluded. “Moreover, such studies could establish whether the [DNA index] not only facilitates rapid and accessible detection of aneuploidy but also contributes meaningfully to therapeutic decision-making, particularly in settings where conventional cytogenetic testing is not routinely available.”

References

1. Rivera-Orcoapaza C, Rosales-Rimache J. Diagnostic performance of DNA index for detection of high hyperdiploidy in childhood B-cell acute lymphoblastic leukemia. PLoS One. 2026;21(4):e0347201. doi:10.1371/journal.pone.0347201
2. Childhood cancer. American Cancer Society. Accessed April 22, 2026. https://www.cancer.org/cancer/childhood-cancer.html
3. Wan TSK. Cancer cytogenetics: methodology revisited. Ann Lab Med. 2014;34(6):413-425. doi:10.3343/alm.2014.34.6.413