ArticleJournal of clinical laboratory analysis2026
Not Missing the Notch: Detection Challenges of Juxtamembrane NOTCH1 Variant Detection in T-Cell Acute Lymphoblastic Leukemia.
Article in Journal of clinical laboratory analysis, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundActivating mutations in NOTCH1 are frequent in T-cell acute lymphoblastic leukemia (T-ALL) and, in the absence of alterations in RAS or PTEN, are associated with favorable prognosis. Besides classical heterodimerization and PEST domain mutations, juxtamembrane internal tandem duplications (JME-ITDs) represent a third class of activating variants. Their intermediate size and sequence composition can challenge short-read next-generation sequencing and variant calling algorithms, leading to underdetection in routine diagnostics.
methodsAn index case of newly diagnosed T-ALL harboring a NOTCH1 juxtamembrane insertion that was discordantly detected by variant callers during routine targeted NGS (Hematology OncoKitDx v2) prompted further analysis. The variant was evaluated using VarDict and VarScan2, followed by manual inspection with IGV and orthogonal confirmation by Sanger sequencing. To further assess variability in the detection of JME-ITDs, six additional BAM files from patients with previously confirmed variants were reanalyzed using VarDict, VarScan2, Mutect2, and Pindel.
resultsIn the index case, VarDict detected a 51-bp NOTCH1 JME-ITD (c.5168-2_5216dup) that was missed by VarScan2 and confirmed by Sanger sequencing. Reanalysis of the seven cases showed that Mutect2 and VarDict detected all JME-ITDs (100%), VarScan2 identified only three (42.8%), and Pindel detected six mutations (85.7%). These results reflect differences in algorithmic strategies where haplotype-based callers incorporate soft-clipped and split reads, whereas pileup-based discard them.
conclusionDetection of NOTCH1 JME-ITDs depends strongly on variant-calling strategy. Combining haplotype-based callers with split-read structural variant tools may reduce false negatives and improve detection of clinically relevant insertions in diagnostic NGS pipelines.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.