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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
...when genomic data are outsourced to perform analysis tasks, for example, genotype imputation services and federated collaborations genomic analysis. Although numerous cryptographic methods have been developed, these methods may not yet be practical for population-scale tasks in terms of computational...
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Method: Matrix sketching framework for linear mixed models in association studies
- Myson Burch,
- Aritra Bose,
- Gregory Dexter,
- Laxmi Parida,
- and Petros Drineas
Genome Res. September 2024 34: 1304-1311; Published in Advance September 4, 2024, doi:10.1101/gr.279230.124
...sketching to develop a fast and efficient LMM method called Matrix-Sketching LMM (MaSk-LMM) by sketching the genotype matrix to reduce its dimensions and speed up computations. Our framework comes with both theoretical guarantees and a strong empirical performance compared to the current state...
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Resource: Gene expression imputation and cell-type deconvolution in human brain with spatiotemporal precision and its implications for brain-related disorders
- Guangsheng Pei,
- Yin-Ying Wang,
- Lukas M. Simon,
- Yulin Dai,
- Zhongming Zhao,
- and Peilin Jia
Genome Res. January 2021 31: 146-158; Published in Advance December 3, 2020, doi:10.1101/gr.265769.120
...-based approach to impute gene expression on a transcriptome-wide level. After rigorous computational benchmarking, we applied our approach to infer missing data points in the widely used BrainSpan resource and completed the entire grid of spatiotemporal transcriptomics. Next, we conducted deconvolutional...
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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
...the secure processing of users’ data, without requiring complete trust in the SP and their security precautions. For example, recent work (Dokmai et al. 2021) has shown that genotype imputation can be securely and accurately performed within trusted execution environments (TEEs) (Sabt et al. 2015). TEEs...
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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...(Horton et al. 2023). Direct STR genotyping at a scale is thus valuable; STRs cannot always be imputed using SNVs (Gymrek et al. 2016; Saini et al. 2018), as SNV–STR linkage disequilibrium (LD) is lower than SNV–SNV pair LD (Willems et al. 2014; Press et al. 2018). Examination of STR variation...
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Method: Automated interpretable artificial intelligence genomic prediction with AIGP
- Lei Wei,
- Ziqin Jiang,
- Baoliang Fan,
- Yidan Yan,
- Zhenqiang Xu,
- Xiaoxiang Hu,
- and Yuzhe Wang
Genome Res. April 2026 36: 814-826; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
...samples on the MGISEQ-T7 platform (PE150 model). BaseVar version 1.01 (Liu et al. 2018) and STITCH version 2.0 (Davies et al. 2016) were used to impute genotypes. SNPs with minor allele frequency (MAF) < 0.05, call rate (CR) <0.95, and individuals with a CR <0.90 were excluded from further analyses. LD...
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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
...in dimensionality reduction and data simulation. These individual genotype sequences can then be decomposed into latent representations and reconstruction errors (residuals), which provide a sparse representation useful for lossless compression. We show that different populations have differentiated compression...
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Method: Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize
- Shuai Wang,
- Merritt Khaipho-Burch,
- Lynn C. Johnson,
- Zachary R. Miller,
- Peter J. Bradbury,
- Doug Speed,
- William J. Allen,
- M. Cinta Romay,
- Jiquan Xue,
- Edward S. Buckler,
- Guillaume P. Ramstein,
- and Baoxing Song
Genome Res. January 2026 36: 214-225; Published in Advance October 31, 2025, doi:10.1101/gr.280514.125
...mays L.) nested association mapping (NAM) population (McMullen et al. 2009; Gage et al. 2020) provides a valuable resource to link genotypic variation with phenotypic variation using computationally folded protein structures with affordable computing resources. The s of 26 NAM founder lines have been...
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Review: Recent advances in methods to characterize archaic introgression in modern humans
- David Peede,
- Mayra M. Bañuelos,
- Jazeps Medina Tretmanis,
- Miriam Miyagi,
- and Emilia Huerta-Sánchez
Genome Res. February 2026 36: 239-256; Published in Advance January 16, 2026, doi:10.1101/gr.278993.124
...trained on simulated data to detect adaptive introgression by classifying local genotype matrices as adaptively introgressed or not. genomatnn takes a 2D SNP matrix as input (haplotypes x sites), representing the presence or absence of the derived allele at a given site per haplotype (or per unphased...
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Method: Genealogy-based trait association with LOCATER boosts power at loci with allelic heterogeneity
- Xinxin Wang,
- Ryan Christ,
- Erica Young,
- Chul Joo Kang,
- Indraniel Das,
- Edward A. Belter, Jr.,
- Markku Laakso,
- Louis J.M. Aslett,
- David Steinsaltz,
- Nathan O. Stitziel,
- and Ira M. Hall
Genome Res. April 16, 2026 ; Published in Advance April 16, 2026, doi:10.1101/gr.280372.124
...the genotype vector of the LOCATER lead marker (Chr 18: 49,653,146), thus removing signal that can be accounted for by the SMT subtest. Connected dots show the phenotype value of individuals assigned to significant sprigs. (D) Dendrogram generated from the haplotype-level local distance matrix at the lead...
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