Evidence map›Paper›PMID 41722573›Full record

ArticleCell genomics2026

Hi-C for genome-wide detection of enhancer-hijacking rearrangements in routine lymphoid cancer biopsies.

Jamin Wu, Shih-Chun A Chu, Jang Cho, Misha Movahed-Ezazi, Kristyn Galbraith, Camila S Fang, Yiying Yang, Chanel Schroff, Kristin Sikkink, Michelle Perez-Arreola and 21 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Review
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

31 authors.

Jamin WuDepartment of Pathology, NYU Langone Health, New York, NY, USA.
Shih-Chun A ChuDepartment of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
Jang ChoDepartment of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
Misha Movahed-EzaziDepartment of Pathology, NYU Langone Health, New York, NY, USA.
Kristyn GalbraithDepartment of Pathology, NYU Langone Health, New York, NY, USA.
Camila S FangDepartment of Pathology, NYU Langone Health, New York, NY, USA.
Yiying YangDepartment of Pathology, NYU Langone Health, New York, NY, USA.
Chanel SchroffDepartment of Pathology, NYU Langone Health, New York, NY, USA.
Kristin SikkinkArima Genomics, Carlsbad, CA, USA.
Michelle Perez-ArreolaArima Genomics, Carlsbad, CA, USA.
Logan Van MeterArima Genomics, Carlsbad, CA, USA.
Savanna GemusArima Genomics, Carlsbad, CA, USA.
Jon-Matthew BeltonArima Genomics, Carlsbad, CA, USA.
Xue SongDepartment of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
Aishwarya GurumurthyDepartment of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
Hong XiaoDepartment of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
Valentina NardiDepartment of Pathology, Massachusetts General Hospital, Boston, MA, USA.
Abner LouissantDepartment of Pathology, Massachusetts General Hospital, Boston, MA, USA.
Raju K PillaiDepartment of Pathology, City of Hope National Medical Center, Duarte, CA, USA.
Joo Y SongDepartment of Pathology, City of Hope National Medical Center, Duarte, CA, USA.
Dennis ShashaDepartment of Computer Science, New York University, New York, NY, USA.
Aristotelis TsirigosDepartment of Pathology, NYU Langone Health, New York, NY, USA; Department of Medicine, NYU School of Medicine, New York, NY, USA.
Anamarija PerryDepartment of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
Noah BrownDepartment of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
Tatyana GindinDepartment of Pathology, NYU Langone Health, New York, NY, USA.
Lina ShaoDepartment of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
Marcin P CieslikDepartment of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
Minji KimGilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
Anthony D SchmittArima Genomics, Carlsbad, CA, USA.
Matija SnuderlDepartment of Pathology, NYU Langone Health, New York, NY, USA. Electronic address: matija.snuderl@nyulangone.org.
Russell J H RyanDepartment of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA. Electronic address: rjhryan@med.umich.edu.

Funding

Identifying Functional Drivers of MYC Activation via Developmental Enhancers in Diffuse Large B-cell LymphomaR01CA245059 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI RYAN, RUSSELL JAMES HUBBARD · 2020 to 2024
$1.7M
Repeat enhancers as drivers of ETV6-RUNX1+ and ETV6-RUNX1-like B-lymphoblastic leukemiaR01CA289045 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI RUSSELL James Hubbard RYAN · 2025 to 2026
$1000k
NCI NIH HHS R01 CA245059NCI NIH HHS R01 CA289045
6 · The paper itself

Abstract

Standard techniques for detecting genomic rearrangements in formalin-fixed paraffin-embedded (FFPE) biopsies have important limitations. We performed FFPE-compatible Hi-C on 44 clinical biopsies comprising large B cell lymphomas (n = 18), plasma cell neoplasms (n = 14), and other diverse lymphoid cancers, identifying consistent topological differences between malignant B cell and plasma cell states. Hi-C detected expected oncogene rearrangements at high concordance with fluorescence in situ hybridization (FISH) and supported enhancer hijacking in recurrent rearrangements of BCL2, CCND1, and MYC plus unanticipated variants involving homologous loci. Hi-C identified unanticipated non-coding rearrangements involving PD-1 ligand genes and other loci of potential therapeutic relevance, distinguished between functionally divergent classes of BCL6 rearrangements, and provided topological information supporting interpretation of variant MYC rearrangements. Hi-C revealed disease-selective MYC locus topological features that correlated with disease-selective MYC locus enhancers and rearrangement breakpoint distributions. FFPE-compatible Hi-C detects oncogene rearrangements and their topological consequences at genome-wide scale, finding clinically relevant drivers missed by standard approaches.

Indexed as

Enhancer Elements, GeneticGene RearrangementLymphomaBiopsyCyclin D1HumansIn Situ Hybridization, FluorescenceParaffin EmbeddingProto-Oncogene Proteins c-bcl-2Proto-Oncogene Proteins c-mycCyclin D1Proto-Oncogene Proteins c-bcl-2Proto-Oncogene Proteins c-mycenhancer hijackingepigenomicsgenomic rearrangementHi-Cleukemialymphomamolecular diagnosticsmyelomaprecision medicinetranslational research

Identifiers

PMID41722573
PMCPMC13174236

What OpenQuestion holds

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Registered trials

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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.