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Method: Secure discovery of genetic relatives across large-scale and distributed genomic data sets
- Matthew M. Hong,
- David Froelicher,
- Ricky Magner,
- Victoria Popic,
- Bonnie Berger,
- and Hyunghoon Cho
Genome Res. September 2024 34: 1312-1323; Published in Advance August 7, 2024, doi:10.1101/gr.279057.124
...often becomes infeasible. Developing a privacy-preserving solution for this task is challenging owing to the burden of estimating kinship between all the pairs of individuals across data sets. We introduce SF-Relate, a practical and secure federated algorithm for identifying genetic relatives across...
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Method: Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases
- Prashant S. Emani,
- Maya N. Geradi,
- Gamze Gürsoy,
- Monica R. Grasty,
- Andrew Miranker,
- and Mark B. Gerstein
Genome Res. December 2023 33: 2156-2173; Published in Advance December 14, 2023, doi:10.1101/gr.278322.123
...rare ones) to identify individuals has been repeatedly shown, the availability of small sets of noisy genotypes, from environmental DNA samples or functional genomics data, motivated us to quantify their informativeness. We present a computational tool suite, termed Privacy Leakage by Inference across...
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Method: A privacy-preserving solution for compressed storage and selective retrieval of genomic data
- Zhicong Huang,
- Erman Ayday,
- Huang Lin,
- Raeka S. Aiyar,
- Adam Molyneaux,
- Zhenyu Xu,
- Jacques Fellay,
- Lars M. Steinmetz,
- and Jean-Pierre Hubaux
Genome Res. December 2016 26: 1687-1696; Published in Advance October 27, 2016, doi:10.1101/gr.206870.116
.... The compromise of position information also leads to potential threats for the content encrypted by SE. For example, if positions are known and coverage can be inferred from the encrypted content size, CNV (copy number variation) analysis can identify deletions/insertions without the need for the sequence itself...
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Method: Secure phasing of private genomes in a trusted execution environment with TX-Phase
- Natnatee Dokmai,
- Kaiyuan Zhu,
- S. Cenk Sahinalp,
- and Hyunghoon Cho
Genome Res. December 2025 35: 2626-2636; Published in Advance November 12, 2025, doi:10.1101/gr.280558.125
...in restrictive regulatory environments owing to data privacy concerns. Although privacy-preserving analysis tools have been developed to broaden access to these servers, none of the existing methods support haplotype phasing, a critical component of the imputation workflow. The complexity of phasing algorithms...
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Method: Autoencoders for genomic variation analysis
- Margarita Geleta,
- Daniel Mas Montserrat,
- Xavier Giro-i-Nieto,
- and Alexander G. Ioannidis
Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
..., predominantly composed of individuals with non-European ancestry, are reluctant to participate in genetic studies due to privacy concerns or apprehensions about potential misuse, as seen in prior cases (Maher 2015; Guglielmi 2019). To circumvent these challenges, data simulation tools can be used to augment...
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Method: A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples
- Shuai Guo,
- Xiaoqian Liu,
- Xuesen Cheng,
- Yujie Jiang,
- Shuangxi Ji,
- Qingnan Liang,
- Andrew Koval,
- Yumei Li,
- Leah A. Owen,
- Ivana K. Kim,
- Ana Aparicio,
- Sanghoon Lee,
- Anil K. Sood,
- Scott Kopetz,
- John Paul Shen,
- John N. Weinstein,
- Margaret M. DeAngelis,
- Rui Chen,
- and Wenyi Wang
Genome Res. January 2025 35: 147-161; Published in Advance November 25, 2024, doi:10.1101/gr.278822.123
...the technological discrepancy, and then develop a deconvolution framework called DeMixSC using this well-matched, that is, benchmark, data. Built upon a novel weighted nonnegative least-squares framework, DeMixSC identifies and adjusts genes with high technological discrepancy and aligns the benchmark data...
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Insight/Outlook: The ethics of conducting molecular autopsies in cases of sudden death in the young
- Amy L. McGuire,
- Quianta Moore,
- Mary Majumder,
- Magdalena Walkiewicz,
- Christine M. Eng,
- John W. Belmont,
- Salma Nassef,
- Sandra Darilek,
- Katie Rutherford,
- Stacey Pereira,
- Steven E. Scherer,
- V. Reid Sutton,
- Dwayne Wolf,
- Richard A. Gibbs,
- Roger Kahn,
- Luis A. Sanchez,
- and the Molecular Autopsy Consortium of Houston (MATCH)
Genome Res. September 2016 26: 1165-1169; Published in Advance July 13, 2016, doi:10.1101/gr.192401.115
...investigation but then used as the foundation for public health and research programs.Although concerns about individual autonomy and privacy are either attenuated or absent in the context of post-mortem genetic testing, the results of an autopsy may be relevant to living biological relatives, with potential...
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Method: Multikernel linear mixed models for complex phenotype prediction
- Omer Weissbrod,
- Dan Geiger,
- and Saharon Rosset
Genome Res. July 2016 26: 969-979; Published in Advance June 14, 2016, doi:10.1101/gr.201996.115
...prediction. MKLMM is as computationally efficient as standard LMMs and does not require storage of genotypes, thus achieving state-of-the-art predictive power without compromising computational feasibility or genomic privacy. [Supplemental material is available for this article.] One of the principal aims...
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Perspective: Can I be sued for that? Liability risk and the disclosure of clinically significant genetic research findings
- Amy L. McGuire,
- Bartha Maria Knoppers,
- Ma’n H. Zawati,
- and Ellen Wright Clayton
Genome Res. May 2014 24: 719-723; Published in Advance March 27, 2014, doi:10.1101/gr.170514.113
...to privacy with regard to their health information during the informed consent process (Richardson andCho 2012). However, this theory has been criticized because research does not aim to promote individual health, and creating obligations of ancillary care would compromise the central mission of researchers...

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