MixHMM: Inferring Copy Number Variation and Allelic Imbalance Using SNP Arrays and Tumor Samples Mixed with Stromal Cells

Zongzhi Liu; Ao Li; Vincent Schulz; Min Chen; David Tuck

doi:10.1371/journal.pone.0010909

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Peer-reviewed

Research Article

MixHMM: Inferring Copy Number Variation and Allelic Imbalance Using SNP Arrays and Tumor Samples Mixed with Stromal Cells

Zongzhi Liu ,

Contributed equally to this work with: Zongzhi Liu, Ao Li

Affiliation Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
⨯
Ao Li ,

Contributed equally to this work with: Zongzhi Liu, Ao Li

Affiliation Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
⨯
Vincent Schulz,

Affiliation Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, United States of America
⨯
Min Chen,

Affiliation Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut, United States of America
⨯
David Tuck

* E-mail: david.tuck@yale.edu

Affiliation Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
⨯

MixHMM: Inferring Copy Number Variation and Allelic Imbalance Using SNP Arrays and Tumor Samples Mixed with Stromal Cells

Zongzhi Liu,
Ao Li,
Vincent Schulz,
Min Chen,
David Tuck

Published: June 1, 2010
https://doi.org/10.1371/journal.pone.0010909

About the Authors

Zongzhi Liu

Contributed equally to this work with: Zongzhi Liu, Ao Li

Affiliation Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America

Ao Li

Contributed equally to this work with: Zongzhi Liu, Ao Li

Affiliation Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America

Vincent Schulz

Affiliation Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, United States of America

Min Chen

Affiliation Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut, United States of America

David Tuck

* E-mail: david.tuck@yale.edu

Affiliation Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: ZL AL VS DT. Performed the experiments: ZL. Analyzed the data: ZL VS. Contributed reagents/materials/analysis tools: MC. Wrote the paper: ZL AL VS MC DT.

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Breast cancer
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Cancers and neoplasms
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Copy number variation
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Single nucleotide polymorphisms
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Variant genotypes
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Stromal cells
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Hidden Markov models
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Normal distribution
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