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Method: Proxy panels enable privacy-aware outsourcing of genotype imputation
- Degui Zhi,
- Xiaoqian Jiang,
- and Arif Harmanci
Genome Res. February 2025 35: 326-339; Published in Advance January 10, 2025, doi:10.1101/gr.278934.124
...2009; Im et al. 2012), beacon-type data release mechanisms (Shringarpure and Bustamante 2015; Fiume et al. 2019), and knowledge of haplotype information (Jacobs et al. 2009; Bu et al. 2021). Privacy risks can also impact relatives (Telenti et al. 2014; Branum and Wolf 2015; Ayday and Humbert 2017...
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Method: Assessing transcriptomic reidentification risks using discriminative sequence models
- Shuvom Sadhuka,
- Daniel Fridman,
- Bonnie Berger,
- and Hyunghoon Cho
Genome Res. July 2023 33: 1101-1112; Published in Advance August 4, 2023, doi:10.1101/gr.277699.123
...QTLs; it incorporates necessary calibration for redundancy and correlation among eQTLs to provide a more accurate, sequence-level match score. Our modeling approach helps reveal the full extent of genotypic information in gene expression profiles to better inform privacy risk assessment.DSM incorporates a number...
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Research: Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications
- Judith Arres,
- Santosh Elavalli,
- Shalini Behl,
- Daniel Matias Sanchez,
- Ayesha Al Ali,
- Abdelrahman Ahmed Yehia Abdelaziz Saad,
- Azza Attia,
- Cyla Minas,
- Sharika Pariyachery,
- Shariq Ahmed,
- Fatmah Aldhuhoori,
- Nitu Thulasidharan,
- Gurunath Katagi,
- Omar Soliman,
- Shilp Purohit,
- Vinay Kusuma,
- Raony Cardenas,
- Thyago Cardoso,
- Luis F. Paulin,
- Philippe Sanio,
- Joseph Mafofo,
- Haiguo Wu,
- Val Zvereff,
- Albarah El-Khani,
- Fahed Al Marzooqi,
- Tiago R. Magalhães,
- Fritz J. Sedlazeck,
- and Javier Quilez
Genome Res. March 2026 36: 460-471; Published in Advance February 11, 2026, doi:10.1101/gr.280134.124
...assessed CNV detection with two different variant callers. The Sniffles2 v2.2 SV caller detected the expected drop in coverage corresponding to the deletion but incorrectly classified it as homozygous rather than the expected heterozygous genotype. In contrast, the updated Sniffles2 v2.5.3 correctly...
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Method: Graph-based deep reinforcement learning for haplotype assembly with Ralphi
- Enzo Battistella,
- Anant Maheshwari,
- Barış Ekim,
- Bonnie Berger,
- and Victoria Popic
Genome Res. December 2025 35: 2617-2625; Published in Advance November 14, 2025, doi:10.1101/gr.280569.125
....g., large-scale genotype data sets from The 1000 Genomes Project [The 1000 Genomes Project Consortium 2015] or the UK Biobank [Bycroft et al. 2018]). On the other hand, read-based approaches assemble individual haplotypes using the overlap of read alignments at heterozygous variant loci. Because...
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Method: Haplotype-aware sequence alignment to pangenome graphs
- Ghanshyam Chandra,
- Daniel Gibney,
- and Chirag Jain
Genome Res. September 2024 34: 1265-1275; Published in Advance July 16, 2024, doi:10.1101/gr.279143.124
...75080, USA Corresponding author: chirag@iisc.ac.inAbstractModern pan graphs are built using haplotype-resolved assemblies. When mapping reads to a pan graph, prioritizing alignments that are consistent with the known haplotypes improves genotyping accuracy. However, the existing rigorous formulations...
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Research: Confounding factors in assessing the enriched expression of somatic mutant allele in bulk tumor samples
- Kohei Hagiwara,
- Andrew Thrasher,
- Nadezhda V Terekhanova,
- and Jinghui Zhang
Genome Res. March 4, 2026 gr.281003.125; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
...Confounding factors in assessing the enriched expression of somatic mutant allele in bulk 1 tumor samples 2 3 Running title: 4 Confounders in somatic mutation ASE analysis 5 6 7 Kohei Hagiwara, Andrew Thrasher, Nadezhda V. Terekhanova and Jinghui Zhang* 8 Department of Computational Biology, St...
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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
...the generation of high-quality, contiguous haplotype-resolved assemblies. The pipeline utilizes a custom IGH reference that incorporates several common SVs to enable reference-based phasing of reads. Next, the phased reads are separately assembled de novo. We assessed the accuracy of the initial haplotype...
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Method: Privacy-preserving biological age prediction over federated human methylation data using fully homomorphic encryption
- Meir Goldenberg,
- Loay Mualem,
- Amit Shahar,
- Sagi Snir,
- and Adi Akavia
Genome Res. September 2024 34: 1324-1333; Published in Advance September 5, 2024, doi:10.1101/gr.279071.124
.... 2018; Blatt et al. 2020; Dong et al. 2022)—that is, statistically associating innate variability in single-nucleotide polymorphisms (SNPs) with a risk for a disease or a particular trait—as well as on privacy-preserving classification of DNA and RNA sequences of tumor tissues (Carpov et al. 2022; Hong...
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Method: Accurate short-read alignment through r-index-based pangenome indexing
- Rahul Varki,
- Massimiliano Rossi,
- Eddie Ferro,
- Marco Oliva,
- Erik Garrison,
- Ben Langmead,
- and Christina Boucher
Genome Res. July 2025 35: 1609-1620; Published in Advance June 12, 2025, doi:10.1101/gr.279858.124
...: christinaboucher@ufl.eduAbstractAligning to a linear reference can result in a higher percentage of reads going unmapped or being incorrectly mapped owing to variations not captured by the reference, otherwise known as reference bias. Recently, in efforts to mitigate reference bias, there has been a movement...
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Resource: Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform
- Liubomir Chorbadjiev,
- Murat Cokol,
- Zohar Weinstein,
- Kevin Shi,
- Christopher Fleisch,
- Nikolay Dimitrov,
- Svetlin Mladenov,
- Ivo Todorov,
- Iordan Ivanov,
- Simon Xu,
- Steven Ford,
- Yoon-ha Lee,
- Boris Yamrom,
- Steven Marks,
- Adriana Munoz,
- Alex Lash,
- Natalia Volfovsky,
- and Ivan Iossifov
Genome Res. October 2025 35: 2352-2362; Published in Advance September 16, 2025, doi:10.1101/gr.280356.124
...), as well as analysis tools.The phenotypic and genotypic data are stored in phenotype and genotype storages, respectively. The phenotype storage is implemented as a relational data schema that can be managed by various relational database systems, like DuckDB (https://duckdb.org) or SQLite (https...
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