FlowCytoNews
Flow cytometry, gated weekly.
ISSUE #7 · MONDAY EDITION · THE LITERATURE · NOV 2, 2026
Welcome to the Monday edition of FlowCytoNews. Monday is The Literature: the cytometry papers and preprints that went online in the past two weeks, who did the work, and the number that matters from each. Wednesday is On the Calendar and Friday is Industry Moves. This time: 18 children with end-of-induction B-ALL MRD below 0.01% relapsed at a rate similar to children above that cut-off; St Jude folded a 13-tube pediatric leukemia workup into one 38-parameter spectral tube; and EVE Online players labeled the plots behind a new automated-gating model. Tell us what we missed — hit reply.
■ The Literature
No new OMIP in Cytometry Part A turned up in our search this fortnight. Cytometry Part B did publish a full clinical panel: St Jude's SJIP38, below.
18 children with B-ALL MRD below 0.01% relapsed at a rate similar to those above it
Karthik Bommannan and Shirley Sundersingh (Cancer Institute (W.I.A.), Chennai) analyzed 223 consecutive children with B-ALL diagnosed from 2018 to 2022, grouped by flow MRD at the end of induction: undetectable, detectable below 0.01%, and 0.01% or more. MRD was detectable in 81, of whom 18 were below 0.01%. At 60 months, any detectable MRD was associated with more relapse (cumulative risk 44% vs 22%) and lower relapse-free survival (56% vs 78%) than undetectable MRD. Outcomes were similar for the below-0.01% and the 0.01%-or-more groups (relapse risk 44% vs 44%, relapse-free survival 56% vs 56%, overall survival 66% vs 59%; all p > 0.05). Against undetectable MRD, the below-0.01% group had lower overall survival (66% vs 83%) and relapse-free survival (56% vs 78%). In multivariate analysis, any detectable MRD predicted worse overall survival (HR 2.22, 95% CI 1.30–3.8) and relapse-free survival (HR 2.38, 1.42–3.98). The authors say a prospective trial is needed to know whether intensifying treatment at MRD below 0.01% helps. The abstract does not describe treatment by MRD group, name the panel or say how many cells were acquired. No industry co-authors.
▪ Cytometry Part B · Oct 28 · 10.1002/cyto.b.70088
Why it matters: A child with a small but detectable population is not MRD-negative, and a report that rounds them to "negative" hides a result the clinician needs. Read the comparison with care: many protocols intensify treatment at 0.01% or above, which could pull that group's outcomes toward the lower group's, and the abstract doesn't say how these children were treated. Eighteen patients at one center can't settle treatment, but they are enough to change what a lab writes on the report. See Bench Notes.
St Jude put a 13-tube pediatric leukemia workup into one 38-parameter spectral tube
Peixin Liu and Paul Mead (St Jude Children's Research Hospital, Memphis) built SJIP38, a single-tube, 38-parameter spectral panel for the first workup of suspected new or relapsed acute leukemia in children. It holds the markers their conventional assay spread across 13 tubes, keeps the established diagnostic markers, and reads lineage-defining, maturation-associated and aberrant antigens together. They developed it on a six-laser Sony ID7000, choosing fluorochromes by spillover spread, antigen density and whether a ready-made conjugate was sold. The group says the fluorochrome palette is meant to anchor future spectral assays, including MRD. The abstract does not say how many patient samples were run or how results compared with the 13-tube assay. All authors are from St Jude; no industry co-authors.
▪ Cytometry Part B · Oct 31 · 10.1002/cyto.b.70080
Why it matters: In a child's marrow, thirteen tubes is a real cost in sample, and replacing them with one is the kind of case that moves spectral flow from the research core into the diagnostic lab. The palette is built around one instrument's lasers and detectors, so a lab on another spectral platform can borrow the marker list but will have to redo the unmixing and probably some fluorochrome choices. The number to look for in the full paper is concordance with the old 13 tubes, subtype by subtype.
EVE Online players labeled gates for an AI model; rare populations still lag at 65%
Sebastiano Montante and Ryan Brinkman (BC Cancer, Vancouver) put flow cytometry plots inside the online game EVE Online. Players on 839,199 de-identified accounts gated 52,000 plots, and quality control kept 31,703 consensus annotations to train flowMagic, a machine-learning gating tool. Tested on 92,203 two-parameter plots with standardized reference gates across 79 immune populations, a version given expert template gates reached 90% agreement with the reference for large populations and 65% for low-abundance ones. A general version trained on the players' gates alone, with no template, reached 78% and 42%. Both reproduced known biology, including neutrophil changes in COVID-19 patients and immune development in newborns. The authors conclude that crowd labels add to expert input rather than replace it. Co-authors include staff from CCP Games, the game's developer, Massively Multiplayer Online Science, Eyam Health and Microsoft; Brinkman also lists Dotmatics.
▪ Cytometry Part A · Oct 29 · 10.1002/cyto.a.70074
Why it matters: These numbers show where this crowd-trained model stands: good enough to take the large populations off an analyst's plate, not yet trusted on the rare ones, which tend to be the gates that carry clinical and trial decisions. The 23-point gap between the template and no-template models on rare populations is the price of skipping expert examples. For now the practical split is software on the big gates and a person on the small ones.
In one lab's hands, Sysmex's XF-1600 counted lymphocyte subsets with CVs under 6%
Meritxell Deulofeu Figueras and Maite Serrando Querol (Laboratori Territorial Girona, Hospital Universitari Dr Josep Trueta) tested Sysmex's XF-1600, a flow cytometer with automated sample preparation and volumetric counting, on routine peripheral blood samples. CVs were below 6% for CD3+, CD4+, CD8+, CD19+ and CD16+/CD56+ cells, with no carryover. Leukocyte and lymphocyte counts correlated with Sysmex's XN-series hematology analyzer (Spearman's ρ 0.986 and 0.993), and lymphocyte subsets with a Beckman Coulter Navios (ρ above 0.9 for most parameters). Bland-Altman and Passing-Bablok analyses showed good agreement, though some parameters were not fully interchangeable; the abstract does not say which, or how many samples were run. No industry co-authors, and the abstract does not say who supplied the instrument.
▪ Int J Lab Hematol · Oct 26 · 10.1111/ijlh.70267
Why it matters: An analyzer that prepares the tube and counts absolute numbers itself is aimed at hematology labs that run TBNK without a dedicated flow team, and CVs under 6% on the main subsets is what those labs need. The open question is the parameters that weren't interchangeable with the Navios. If you follow patients over time, find out which ones they were and bridge those before you switch platforms.
BCL-2 by flow flagged marrow involvement in 265 follicular lymphoma patients
Lu-Yang Li and Tao Guan (Shanxi Medical University and Shanxi Provincial Cancer Hospital, Taiyuan) measured BCL-2 by flow in bone marrow aspirates from 265 patients with follicular lymphoma (230 newly diagnosed, 35 relapsed or refractory), split into a BD cohort and a Beckman cohort. Where flow detected clonal B cells, they were CD10+, CD19 dim, CD20 dim, CD22 dim and CD200−. Those marrows had higher BCL-2 by MFI, by percentage and by BCL-2:CD200 ratio than marrows without detectable clonal cells, and those patients had shorter progression-free survival. BCL-2 percentage best separated involved from uninvolved marrows, ahead of the ratio and MFI; the abstract does not give the AUCs. Among involved marrows, higher BCL-2 went with longer PFS. BCL-2 was higher in follicular lymphoma than in other indolent lymphomas, but that comparison had 13 cases (6 CLL, 4 marginal zone, 3 mantle cell). Results were consistent between the two cohorts. No industry co-authors.
▪ Cytometry Part B · Oct 30 · 10.1002/cyto.b.70089
Why it matters: BCL-2 is one intracellular stain added to a staging tube, and it held up in both the BD and the Beckman cohort, which is the first thing a lab would ask. Don't use it to separate follicular from marginal zone lymphoma yet; 13 comparison cases can't carry that. The finding that higher BCL-2 meant longer PFS among involved marrows runs against what most would expect and needs an independent cohort before anyone reads prognosis off it.
Also out
A flow assay finds the IgM behind complement activation in autoimmune hemolytic anemia. Femke Mulder (Leiden University Medical Center) and Richard Pouw (Sanquin Diagnostic Services, Amsterdam) built the Flow IAT: bromelain-treated group O donor red cells are incubated with patient serum, washed, given donor serum as a complement source plus anti-C5 to block lysis, and read for IgM, IgG, C4 and C3. In 48 patients and 21 controls, IgM binding tracked C4 and C3 deposition closely and IgG binding tracked them poorly; the test caught IgM better than conventional diagnostics and IgG less well. Eight of the 11 authors list Sanquin in Amsterdam, including Sanquin Diagnostic Services. — Blood Adv · Oct 30 · 10.1182/bloodadvances.2025019072
Two CLL MRD letters in Leukemia, neither with an abstract online. One is a systematic review and meta-analysis of blood-versus-marrow MRD concordance after first-line treatment with newer agents, from Giuseppe Fiorica (Icahn School of Medicine at Mount Sinai, New York) and Adam Kittai (NYU Grossman Long Island School of Medicine, Mineola). The other, from Yun Wang and Yang Liang (Sun Yat-sen University, Guangzhou), argues in its title that MRD is not a universally reliable surrogate for progression-free survival in trials of new CLL therapies. Titles only. — Leukemia · Oct 22 · 10.1038/s41375-026-03178-9 · Oct 28 · 10.1038/s41375-026-03185-w
A drug sponsor and Teiko make the case for fixing trial blood at the draw site. Michael Lahn (iOnctura, Geneva) and Ramji Srinivasan (Teiko, Salt Lake City) review regulatory T-cell monitoring in global oncology trials: up to 20% of trial samples are excluded for missing transit windows, fixation at the draw kept major population frequencies stable over 72 hours, and serial mass cytometry in the first-in-human study of roginolisib linked falling Tregs to disease control and survival in metastatic uveal melanoma. In the authors' experience, mass-channel assignment cut qualification of a 20-marker panel from about 6 months to about 3 weeks. All authors are from iOnctura and Teiko. — Bioanalysis · Oct 28 · 10.1080/17576180.2026.2744519
PBMC frozen for more than 20 years still stain and survive culture. Typhaine Gris and Paul Toren (CHU de Québec–Université Laval) thawed 22 PBMC samples stored over 20 years in liquid nitrogen and 6 frozen for under 2 months. Recovery was lower in the old samples (54.1% vs 82.4%), but viability stayed at 79% or above, major subsets matched, and viability after 24 hours in culture stayed above 75%; intermediate and non-classical monocytes and memory T cells differed. — Biopreserv Biobank · Oct 29 · 10.1177/19475535261502543
Post-transplant cyclophosphamide slows naive T- and B-cell recovery, most after haploidentical grafts. Michela Ansuinelli and Jerome Ritz (Dana-Farber Cancer Institute, Boston) followed 210 adults with a 37-marker flow panel and TCR sequencing; NK-T and γδ T cells stayed delayed for more than a year after PTCy, and CD8 clonality stayed high after haploidentical PTCy. — Blood Adv · Oct 28 · 10.1182/bloodadvances.2026019683
How you isolate synovial fluid cells decides which patients you can study. Abel Mekonnen Tesfaye and Asbjørn Christophersen (University of Oslo) compared protocols on 48 samples, 19 of them with a 31-marker spectral panel. Density-gradient isolation of mononuclear cells cut the share of usable low-grade inflammatory samples by 50% and shifted composition toward dendritic cells and classical monocytes; repeated centrifugation recovered as many cells as hyaluronidase. — RMD Open · Oct 23 · 10.1136/rmdopen-2026-007291
EBER flow FISH moved to a second lab, in seven patients. Madoka Nishimura and Hirokazu Kanegane (Institute of Science Tokyo) ran the EBV assay on cryopreserved PBMC at two facilities. Where both found at least 5% EBER-positive cells, 6 of 8 data points fell within ±20%; one patient with very few positive cells gave inconsistent results. Three co-authors list LSI Medience Corporation. — Cytometry Part B · Nov 1 · 10.1002/cyto.b.70091
Tisagenlecleucel in 19 patients, phenotyped by flow for 28 days. Sungyu Jee and Jong-Mi Lee (Seoul St. Mary's Hospital, The Catholic University of Korea) found CAR-T cells mostly peaked on day 7, later in several of the 8 B-ALL patients; at peak they were enriched for central memory and carried more HLA-DR and PD-1 than endogenous T cells. In an exploratory analysis, absolute CAR-T counts were higher in patients who developed ICANS. — Cancers · Oct 19 · 10.3390/cancers18203374
Monocyte HLA-DR measured across labs in the PLATINIUM trial. A letter from Robin Jeannet (CHU Limoges) and Guillaume Monneret (Hospices Civils de Lyon), titled as a multicenter proof of concept for inter-laboratory reproducibility of monocyte HLA-DR in whole blood. No abstract online, so title only. — Cytometry Part B · Oct 28 · 10.1002/cyto.b.70087
Preprints
Not peer reviewed.
Super-resolution imaging flow cytometry at up to about 720 cells per second. Y. Luo, corresponding author Tianben Ding (University of Tokyo) and senior author K. Goda combined structured illumination, stroboscopic excitation, hydrodynamic focusing and AI-assisted reconstruction to reach about 118-nm in-plane resolution, roughly twice as fine as the diffraction limit allows. They resolved single lipid droplets in Euglena and mapped mitochondrial remodeling as primary human CD8+ T cells differentiate. — bioRxiv · Oct 20 · 10.64898/2026.10.18.759815
In a reanalyzed food-allergy CyTOF dataset, published differences tracked a staining batch. C. Cherukuri and corresponding author Khodor Abou-Daya (Thomas E. Starzl Transplantation Institute, Pittsburgh) reanalyzed 3.56 million cells from 36 one-year-olds. Peanut-sensitized infants who tolerated peanut had more lineage-negative CD38+ cells (2.26-fold) and HLA-DR+ memory CD4 T cells (1.97-fold) than allergic infants; within one staining batch the dendritic-cell difference held and the T-cell difference weakened. The published naive CD4 T-cell and B-cell differences tracked a staining batch that held half the sensitized-tolerant samples, and CD20 spillover into the TNF channel differed between runs. — bioRxiv · Oct 24 · 10.64898/2026.10.20.760474
B-cell stimulation protocols that look alike by flow don't look alike by RNA. T. D'hamers and corresponding author Celine Everaert (VIB–Ghent University) compared ODN2006, IFN-γ/R-848, anti-CD40 and anti-CD3/CD28 at 8 and 30 hours in 4 donors (81,160 cells); IFN-γ/R-848 and ODN2006 changed the most genes. — bioRxiv · Oct 27 · 10.64898/2026.10.22.760934
■ Bench Notes
MRD below 0.01% is a result. Report it as one.
In the Chennai series above, 18 children with end-of-induction MRD below 0.01% relapsed at a rate similar to those above it. If your report calls them negative, the clinician never sees that result. Four changes make the low end of a flow MRD report mean something:
Put the denominator on every report. State the number of evaluable cells and the detection limit that sample actually reached. In EuroFlow's BCP-ALL MRD study, agreement with PCR rose with the number of cells acquired and reached 93% when more than 4 million cells were acquired (Theunissen et al., Blood 2017, 10.1182/blood-2016-07-726307).
Report three outcomes, not two. Not detected (with that sample's limit), detected below the 0.01% clinical cut-off (with its level, if your assay can quantify it), and at or above the cut-off. The middle category is the one the Chennai data say matters. Keep the clinical cut-off and your lab's quantification limit as separate thresholds on the report.
Set limits in events, then convert for each sample. If your lab needs a 20-event cluster to call MRD, a sample reaches 0.001% only with 2 million evaluable cells, and a 200,000-cell tube can't go below 0.01%. Wood's review sets out how enumeration and cell numbers determine sensitivity (Cytometry B 2016, 10.1002/cyto.b.21239).
Validate the bottom of the range. Dilute known positive samples into normal marrow below 0.01% and measure precision there, not just in the middle of the range. The ICSH/ICCS guidelines set out validation requirements for this kind of assay (Wood et al., Cytometry B 2013, 10.1002/cyto.b.21108).
What did we miss? Hit reply — corrections run at the top of the next edition. If a colleague signs out pediatric leukemia MRD or runs a clinical flow lab, forward this to them.
— Flow Novice