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Research: Genotype imputation from low-coverage data for medical and population genetic analyses
- Simone Andrea Biagini,
- Sara Becelaere,
- Mio Aerden,
- Tatjana Jatsenko,
- Laurens Hannes,
- Philip Van Damme,
- Jeroen Breckpot,
- Koenraad Devriendt,
- Bernard Thienpont,
- Joris Robert Vermeesch,
- Isabelle Cleynen,
- and Toomas Kivisild
Genome Res. September 2025 35: 1929-1941; Published in Advance July 22, 2025, doi:10.1101/gr.280175.124
...genotype imputation from LPS data. Among these, Beagle (Browning et al. 2018) and Gencove's loimpute software (Wasik et al. 2021) have been some of the most popular examples. However, they present limitations in scalability for large cohorts and increased computational costs with large reference panels...
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Method: Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms
- Hongyu Zheng,
- Hirak Sarkar,
- and Benjamin J. Raphael
Genome Res. December 2025 35: 2734-2743; Published in Advance November 17, 2025, doi:10.1101/gr.280555.125
...of the individual technologies, enabling the imputation of expression from unmeasured genes in targeted technologies and/or the deconvolution of admixed expression from technologies with lower spatial resolution. Here, we introduce Spatial Integration for Imputation and Deconvolution (SIID), an algorithm...
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Method: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
- Haotian Zhang,
- Yiming Zhang,
- Teng Gao,
- and Yufeng Wu
Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
...is increasing rapidly. Accurate inference of cell lineage tree from large single-cell data is computationally challenging. In this paper, we present ScisTree2, a fast and accurate cell lineage tree inference and genotype calling approach based on the infinite-sites model. ScisTree2 relies on an efficient local...
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Method: Scalable summary-statistics-based heritability estimation method with individual genotype level accuracy
- Moonseong Jeong,
- Ali Pazokitoroudi,
- Zhengtong Liu,
- and Sriram Sankararaman
Genome Res. September 2024 34: 1286-1293; Published in Advance July 22, 2024, doi:10.1101/gr.279207.124
...of Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA Corresponding authors: bronsonj@cs.ucla.edu, sriram@cs.ucla.eduAbstractSNP heritability, the proportion of phenotypic variation explained by genotyped SNPs, is an important parameter in understanding the genetic...
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Method: Large-scale detection and characterization of inter-chromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets
- Jeanlin Jourdain,
- Harmonie Barasc,
- Thomas Faraut,
- Anne Calgaro,
- Nathalie Bonnet,
- Camille Marcuzzo,
- Amandine Suin,
- Anne Barbat,
- Chris Hozé,
- Florian Besnard,
- Sébastien Taussat,
- Cécile Grohs,
- Claire Kuchly,
- Carole Iampietro,
- Cécile Donnadieu,
- Alain Pinton,
- Didier Boichard,
- and Aurélien Capitan
Genome Res. July 6, 2023 ; Published in Advance July 6, 2023, doi:10.1101/gr.277787.123
...Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets Jeanlin Jourdain,1,2 Harmonie Barasc,3 Thomas Faraut,3 Anne Calgaro,3 Nathalie Bonnet,3 Camille Marcuzzo,4 Amandine Suin,4 Anne Barbat,2 Chris Hozé,1...
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Resource: Discordant calls across genotype discovery approaches elucidate variants with systematic errors
- Elizabeth G. Atkinson,
- Mykyta Artomov,
- Alexander A. Loboda,
- Heidi L. Rehm,
- Daniel G. MacArthur,
- Konrad J. Karczewski,
- Benjamin M. Neale,
- and Mark J. Daly
Genome Res. May 30, 2023 ; Published in Advance May 30, 2023, doi:10.1101/gr.277908.123
...panels for statistical and population genetic efforts. Although such resources are often treated as ground truth, we find that in widely used reference data sets such as the GenomeAggregation Database (gnomAD), some variants pass gold-standard filters, yet are systematically different in their genotype...
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Resource: Comparison and assessment of family- and population-based genotype imputation methods in large pedigrees
- Ehsan Ullah,
- Raghvendra Mall,
- Mostafa M. Abbas,
- Khalid Kunji,
- Alejandro Q. Nato, Jr,
- Halima Bensmail,
- Ellen M. Wijsman,
- and Mohamad Saad
Genome Res. January 2019 29: 125-134; Published in Advance December 4, 2018, doi:10.1101/gr.236315.118
...and challenges from GWAS. Trends Genet 34: 504–517. doi:10.1016/j.tig.2018.03.005 ↵McCarthy S, Das S, Kretzschmar W, Delaneau O, Wood AR, Teumer A, Kang HM, Fuchsberger C, Danecek P, Sharp K, et al. 2016. A reference panel of 64,976 haplotypes for genotype imputation. Nat Genet 48: 1279–1283. doi:10.1038/ng.3643...
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Method: Genotype imputation via matrix completion
- Eric C. Chi,
- Hua Zhou,
- Gary K. Chen,
- Diego Ortega Del Vecchyo,
- and Kenneth Lange
Genome Res. March 2013 23: 509-518; Published in Advance December 10, 2012, doi:10.1101/gr.145821.112
...for predicting the occasionally missing genotypes in a SNP panel but also for combining data from different panels typed on different platforms. Exploiting these in silico genotypes can boost the power of association studies, encourage finer-scale gene mapping, and enable meta-analysis. Several software packages...
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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
...of spatiotemporal transcriptome data in BrainSpan with high accuracy (median: R2 > 0.9). The resulting imputed data provide a reliable resource for downstream analysis. Moreover, our application of deconvolution algorithms (Newman et al. 2015) to recent scRNA-seq data (Bakken et al. 2018; Wu et al. 2019) enabled us...
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Method: Predicting genotype-specific gene regulatory networks
- Deborah Weighill,
- Marouen Ben Guebila,
- Kimberly Glass,
- John Quackenbush,
- and John Platig
Genome Res. March 2022 32: 524-533; Published in Advance February 22, 2022, doi:10.1101/gr.275107.120
...Medical School, Boston, Massachusetts 02115, USA ↵4 Present address: Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Corresponding author: john.platig@channing.harvard.eduAbstractUnderstanding how each person's unique genotype influences...
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