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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
...AD [Karczewski et al. 2020] and dbSNP [Sherry et al. 2001]), and for building genotype imputation outsourcing services (Das et al. 2016; Sun et al. 2022). For example, NIH's TOPMed (Kowalski et al. 2019; Taliun et al. 2021) and the Haplotype Reference Consortium (HRC) (McCarthy et al. 2016) serve as reference...
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Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
- Sheila Lutz,
- Megan Lawler,
- Samuel Amidon,
- and Frank W Albert
Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
...High-resolution, genotype-free mapping of genetic 1 variation with CRI-SPA-Map 2 3 Sheila Lutz*, Megan Lawler†, Samuel Amidon†, Frank W. Albert* 4 Department of Genetics, Cell Biology, & Development, 5 University of Minnesota, 6 6-160 Jackson Hall, 321 Church St SE 7 Minneapolis, MN 55455, USA 8...
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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
...and genotyped, in parallel, on Illumina Infinium Global Screening Array-24 v3.0 for ∼700,000 SNPs. The array-based genotype calls were considered as truth.GDI applicationIn light of the success of the GDI filtering approach in minimizing the presence of low-quality variants across the largest possible subset...
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Method: Long-read reconstruction of many diverse haplotypes with devider
- Jim Shaw,
- Christina Boucher,
- Yun William Yu,
- Noelle Noyes,
- and Heng Li
Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
...with an overlap-layout algorithm for reconstruction.We present devider, a new long-read, reference-based haplotyping method for diverse small sequences. Given a set of aligned reads and SNPs, devider models the haplotyping problem as an assembly problem on a positional de Bruijn graph (PDBG). devider is inspired...
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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
...as well as one of the scalable individual genotype-based method (RHE) to real UK Biobank phenotypes measured on N = 291,273 unrelated White British individuals paired with genotypes assayed on 454,207 common array SNPs (we ran SumHer with both GCTA and LDAK SNP taggings for real phenotypes). Here we plot...
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Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
- Meilin Zhang,
- Heng Du,
- Yu Zhang,
- Yue Zhuo,
- Zhen Liu,
- Yahui Xue,
- Lei Zhou,
- Sixuan Zhou,
- Wanying Li,
- and Jian-Feng Liu
Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
...the construction of a feature library. These methods help to efficiently and rapidly evaluate breed diversity and estimate ancestry. However, these feature selection methods were primarily established to select feature SNPs from SNP genotyping array data (Zhao et al. 2023), and developing an effective method...
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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
..., for the cell C3 and the site S6, M[3, 6] = 0.7, which would wrongly call this genotype the wild type (0).Existing cell lineage tree reconstruction methods also differ in high-level computational approaches. Several methods are based on probabilistic inference and use Markov chain Monte Carlo (MCMC) (Jahn et al...
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Research: Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions
- Stacey E.P. Joosten,
- Sebastian Gregoricchio,
- Suzan Stelloo,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Kerim Yavuz,
- Maria Donaldson Collier,
- Tunç Morova,
- Umut Berkay Altintaş,
- Yongsoo Kim,
- Sander Canisius,
- Cathy B. Moelans,
- Paul J. van Diest,
- Gozde Korkmaz,
- Nathan A. Lack,
- Michiel Vermeulen,
- Sabine C. Linn,
- and Wilbert Zwart
Genome Res. April 2024 34: 539-555; Published in Advance May 6, 2024, doi:10.1101/gr.278680.123
...not detect any peaks. Furthermore, as current technologies do not allow for precise single-cell TF profiling in tumor tissues, it remains elusive to what degree intra-tumor heterogeneity of ESR1–chromatin interaction profiles impacts inter-tumor heterogeneity, as we reported in this study.Although inter...
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Method: Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs
- Nadin Rohland,
- Swapan Mallick,
- Matthew Mah,
- Robert Maier,
- Nick Patterson,
- and David Reich
Genome Res. November/December 2022 32: 2068-2078; Published in Advance December 14, 2022, doi:10.1101/gr.276728.122
...of the power of in-solution enrichment, consider studying an ancient individual at a set of about 600,000 single-nucleotide polymorphism (SNP) positions that have been genotyped in diverse modern human populations. Only one in about 100 ancient DNA sequences mapping to the human will overlap these positions...
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Method: A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis
- Daijun Zhang,
- Ren Qi,
- Xun Lan,
- and Bin Liu
Genome Res. August 2025 35: 1794-1808; Published in Advance July 14, 2025, doi:10.1101/gr.280281.124
..., STMSC captures intra- and interstage heterogeneity in cancer development, offering novel insights into the complexity of pathological tissue structures.Spatial transcriptomics (ST) technologies have revolutionized biotechnology by enabling precise localization of gene expression within tissues, offering...

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