Cancer Genomics and Evolution

Fusion transcripts, tumor structural variation, somatic mosaicism, and developmental origins of cancer cell states.

We study cancer as a genomic and developmental system, combining long-read sequencing, single-cell multi-omics, and integrative regulatory analysis to characterize tumor structural variation, fusion transcripts, clonal architecture, and the cell-state hierarchies that drive disease.

Our work on long-read fusion detection (Qin et al., 2025), somatic SV calling with personal assemblies (Qin et al., 2025), and diploid donor-specific assemblies as cancer reference genomes (Zhang et al., 2025) brings clinical-grade resolution to complex tumor genomes. Single-cell analyses uncover developmental origins of rhabdomyosarcoma and other pediatric tumors (Wei et al., 2022) and define non-genetic transcriptomic programs associated with therapy response and resistance in pediatric cancer models (Yang et al., 2025). Consortium studies characterize somatic mosaicism across normal and diseased tissues (Coorens et al., 2025). Earlier integrative analyses characterized cancer-driver transcription factor programs in oncogenic gene regulation (Xu et al., 2016). These directions connect mechanism-level discovery with translational genomics.

References

2025

Genome Res

Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution

Qian Qin, Victoria Popic, Kirsty Wienand, and 11 more authors

Genome Research, Apr 2025

DOI Bib HTML

@article{Qin2025CTATLRFusion,
  title = {Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution},
  author = {Qin, Qian and Popic, Victoria and Wienand, Kirsty and Yu, Houlin and White, Emily and Khorgade, Akanksha and Shin, Asa and Georgescu, Christophe and Campbell, Catarina D and Dondi, Arthur and Beerenwinkel, Niko and Vazquez, Francisca and Al'Khafaji, Aziz M and Haas, Brian J},
  journal = {Genome Research},
  volume = {35},
  number = {4},
  pages = {967--986},
  month = apr,
  year = {2025},
  doi = {10.1101/gr.279200.124},
}

bioRxiv

Improving long-read somatic structural variant calling with pangenome and de novo personal genome assembly

Qian Qin, Jakob Heinz, and Heng Li

bioRxiv, Oct 2025

DOI Bib HTML

@article{Qin2025LongReadSV,
  title = {Improving long-read somatic structural variant calling with pangenome and de novo personal genome assembly},
  author = {Qin, Qian and Heinz, Jakob and Li, Heng},
  journal = {bioRxiv},
  pages = {2025.10.28.685154},
  month = oct,
  year = {2025},
  doi = {10.1101/2025.10.28.685154},
}

bioRxiv

Diploid donor-specific assembly enhances somatic structural variant detection in cancer genomes

Yuwei Zhang, Han Qu, Qian Qin, and 2 more authors

bioRxiv, Oct 2025

DOI Bib HTML

@article{Zhang2025DSASV,
  title = {Diploid donor-specific assembly enhances somatic structural variant detection in cancer genomes},
  author = {Zhang, Yuwei and Qu, Han and Qin, Qian and Li, Heng and Park, Peter J},
  journal = {bioRxiv},
  pages = {2025.10.28.685155},
  month = oct,
  year = {2025},
  doi = {10.1101/2025.10.28.685155},
}

Nat Commun

The PIK3CA/AKT pathway drives therapy resistance in rhabdomyosarcoma

Q Yang, Y Wang, L A Corchete Sanchez, and 13 more authors

Nature Communications, Dec 2025

DOI Bib HTML

@article{Yang2025RMSResistance,
  title = {The {PIK3CA/AKT} pathway drives therapy resistance in rhabdomyosarcoma},
  author = {Yang, Q and Wang, Y and Corchete Sanchez, L A and Mathavarajah, S and Qin, Qian and Wei, Y and Alpert, E and Whelton, L and Sharma, P and Strom, S and Oultache, I and Iafrate, A J and Pinello, L and Rheinbay, E and Yan, C and Langenau, D M},
  journal = {Nature Communications},
  volume = {17},
  number = {1},
  pages = {65},
  month = dec,
  year = {2025},
  doi = {10.1038/s41467-025-66632-9},
}

Nature

The Somatic Mosaicism across Human Tissues Network

Tim H H Coorens, Ji Won Oh, Yujin Angelina Choi, and 5 more authors

Nature, Jul 2025

DOI Bib HTML

@article{SMaHT2025Network,
  title = {The Somatic Mosaicism across Human Tissues Network},
  author = {Coorens, Tim H H and Oh, Ji Won and Choi, Yujin Angelina and Lim, Nam Seop and Zhao, Boxun and Voshall, Adam and Abyzov, Alexej and others},
  journal = {Nature},
  volume = {643},
  number = {8070},
  pages = {47--59},
  month = jul,
  year = {2025},
  doi = {10.1038/s41586-025-09096-7},
}

2022

Nat Cancer

Single-cell analysis and functional characterization uncover the stem cell hierarchies and developmental origins of rhabdomyosarcoma

Y Wei, Qian Qin, C Yan, and 1 more author

Nature Cancer*Co-first authors , 2022

DOI Bib

@article{Wei2022Rhabdomyosarcoma,
  title = {Single-cell analysis and functional characterization uncover the stem cell hierarchies and developmental origins of rhabdomyosarcoma},
  author = {Wei, Y and Qin, Qian and Yan, C and others},
  journal = {Nature Cancer},
  year = {2022},
  doi = {10.1038/s43018-022-00414-w},
}

2016

Mol Cancer Res

Integrative Analysis Reveals the Transcriptional Collaboration between EZH2 and E2F1 in the Regulation of Cancer-Related Gene Expression

H Xu, K Xu, H H He, and 11 more authors

Molecular Cancer Research, 2016

Bib HTML

@article{Xu2016EZH2E2F1,
  title = {Integrative Analysis Reveals the Transcriptional Collaboration between {EZH2} and {E2F1} in the Regulation of Cancer-Related Gene Expression},
  author = {Xu, H and Xu, K and He, H H and Zang, C and Chen, C H and Chen, Y and Qin, Qian and Wang, S and Wang, C and Hu, S and Li, F and Long, H and Brown, M and Liu, X S},
  journal = {Molecular Cancer Research},
  volume = {14},
  number = {2},
  pages = {163--172},
  year = {2016},
}