In one paragraphArticle in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
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 registryThe 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 literatureWho cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
4 · The recordCorrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
5 · Who and what moneyAuthors and funding
24 authors.
Yoshitaka SakamotoDivision of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan.ORCID 0009-0004-2375-2827 Yotaro OchiDepartment of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.ORCID 0000-0001-8472-6164 Yasunori KogureDivision of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.ORCID 0000-0003-1158-5131 Shota KatoDepartment of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.ORCID 0000-0003-3656-2665 Aiko Sato-OtsuboDepartment of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Masahiro SugawaDivision of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan.ORCID 0009-0001-3101-9762 Yosuke TanakaLaboratory of Cancer Target Discovery, National Cancer Center Research Institute, Tokyo, Japan.ORCID 0000-0002-3764-0517 Taro TsujimuraInstitute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.ORCID 0000-0002-3281-0150 Takashi MikamiDivision of Cancer Immune Multicellular System Regulation, Center for Cancer Immunotherapy and Immunobiology (CCII), Graduate School of Medicine, Kyoto University, Kyoto, Japan.ORCID 0000-0003-1846-4500 Genta NagaeGenome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.ORCID 0000-0002-2929-7990 Kenichi ChibaDivision of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan.ORCID 0000-0001-9439-6998 Ai OkadaDivision of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan.ORCID 0000-0002-9782-5900 Yu ItoDivision of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan.ORCID 0000-0002-9047-1919 Hajime SuzukiDivision of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan.ORCID 0009-0004-0727-6824 Takuya YamamotoInstitute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.ORCID 0000-0002-0022-3947 Hiroyuki AburataniGenome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.ORCID 0000-0003-0438-1544 Yuhki KogaDepartment of Pediatrics, Kyushu University, Fukuoka, Japan.
Hiroyuki ManoDivision of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan.ORCID 0000-0003-4645-0181 Seishi OgawaDepartment of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.ORCID 0000-0002-7778-5374 Keisuke KataokaDivision of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.ORCID 0000-0002-8263-9902 Motohiro KatoDepartment of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.ORCID 0000-0001-5145-1774 Yuichi ShiraishiDivision of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan.ORCID 0000-0001-6144-5845 Funding
Data Analysis Center for Somatic Mosaicism Across Human Tissues NetworkUM1DA058230 · NIDA · HARVARD MEDICAL SCHOOL · PI Peter J Park · 2023 to 2026
$6.3MNIDA NIH HHS UM1 DA058230
6 · The paper itselfAbstract
Cancer genome analysis relies on standard human reference genomes, but detecting somatic alterations in highly repetitive or individual-specific regions remains challenging. We developed the Personalized Reference genome-based Cancer Genome Analysis Pipeline (PRCGAP, https://github.com/yos-sk/PRCGAP), to our knowledge, the first comprehensive pipeline integrating haplotype-resolved analyses of somatic point mutations, structural variants, copy number, and DNA methylation on personalized diploid reference genomes, with each variant phased and annotated by genomic features. We applied PRCGAP to eight tumor-normal cell line pairs and three newly collected pediatric B-cell acute lymphoblastic leukemia (B-ALL) clinical samples. PRCGAP recovered most standard reference-based variants (86.7-96.4% across variant types), validated by orthogonal short-read sequencing, while additionally detecting variants that standard references missed (23.4% of SNVs and 32.6% of SVs). Notably, PRCGAP uncovered variants in centromeric and telomeric regions, and somatic single-nucleotide variants were enriched in centromere dip regions, the putative kinetochore formation sites. Using PRCGAP outputs, we identified L1 retrotransposition source sites absent from standard references and showed that a B-ALL IGH::
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PMID42465473
PMCPMC13370941
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