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Method: Inferring ancestry with the hierarchical soft clustering approach tangleGen
- Klara Elisabeth Burger,
- Solveig Klepper,
- Ulrike von Luxburg,
- and Franz Baumdicker
Genome Res. December 2024 34: 2244-2255; Published in Advance October 21, 2024, doi:10.1101/gr.279399.124
...varying allele frequencies for specific SNPs, which allows conclusions to be drawn about the population structure. This information is often used as a basis to infer ancestries.The development of methods to infer population structure has been part of research for decades, with both model-based (Pritchard...
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Method: Ancestry-agnostic estimation of DNA sample contamination from sequence reads
- Fan Zhang,
- Matthew Flickinger,
- Sarah A. Gagliano Taliun,
- InPSYght Psychiatric Genetics Consortium,
- Gonçalo R. Abecasis,
- Laura J. Scott,
- Steven A. McCaroll,
- Carlos N. Pato,
- Michael Boehnke,
- and Hyun Min Kang
Genome Res. February 2020 30: 185-194; Published in Advance January 24, 2020, doi:10.1101/gr.246934.118
...accurate contamination estimates than the previous methods.New model-based methods accurately estimate genetic ancestryIn the absence of contamination, widely used methods such as LASER and TRACE are known to estimate genetic ancestry accurately. Because we propose using a new model-based approach...
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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
..., compression, classification, and simulation of genomic data with several worldwide whole data sets from both humans and canids, and evaluate the performance of the proposed applications with and without ancestry conditioning. The unsupervised setting of autoencoders allows for the detection and learning...
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Research: Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes
- Diana Lobo,
- Hernán E. Morales,
- Cock Van Oosterhout,
- José Vicente López-Bao,
- Pedro Silva,
- Luis Llaneza,
- Carolina Pacheco,
- Diana Castro,
- Germán Hernández-Alonso,
- George Pacheco,
- John Archer,
- M. Thomas P. Gilbert,
- Nuno Ferrand,
- and Raquel Godinho
Genome Res. March 2025 35: 432-445; Published in Advance February 14, 2025, doi:10.1101/gr.279093.124
...free of recent dog admixture to focus on older introgression events, setting a threshold of -wide dog ancestry below 10%. ADMIXTURE analysis clearly distinguished wolves from dogs at K = 2, with an average -wide proportion attributed to dogs below 1.6% in the wolf (Supplemental Fig. S1A). Similarly...
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Method: BayesRVAT enhances rare-variant association testing through Bayesian aggregation of functional annotations
- Antonio Nappi,
- Liubov Shilova,
- Theofanis Karaletsos,
- Na Cai,
- and Francesco Paolo Casale
Genome Res. December 2025 35: 2682-2690; Published in Advance October 24, 2025, doi:10.1101/gr.280689.125
...Lab resource at https://www.nealelab.is/uk-biobank/. Briefly, we applied filters to remove samples flagged as used in PCA calculations (i.e., unrelated samples) and those with sex chromosome aneuploidy. To restrict the data set to individuals of British ancestry, we utilized the provided principal...
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Resource: A harmonized public resource of deeply sequenced diverse human genomes
- Zan Koenig,
- Mary T. Yohannes,
- Lethukuthula L. Nkambule,
- Xuefang Zhao,
- Julia K. Goodrich,
- Heesu Ally Kim,
- Michael W. Wilson,
- Grace Tiao,
- Stephanie P. Hao,
- Nareh Sahakian,
- Katherine R. Chao,
- Mark A. Walker,
- Yunfei Lyu,
- gnomAD Project Consortium,
- Heidi L. Rehm,
- Benjamin M. Neale,
- Michael E. Talkowski,
- Mark J. Daly,
- Harrison Brand,
- Konrad J. Karczewski,
- Elizabeth G. Atkinson,
- and Alicia R. Martin
Genome Res. May 2024 34: 796-809; Published in Advance May 15, 2024, doi:10.1101/gr.278378.123
..., and genotype QC (Chen et al. 2024), including ancestry outlier removal (Methods) (Supplemental Table S2), we identified 153,894,851 high-quality variants across 4094 individuals, 3400 of whom are inferred to be unrelated (Methods) (Supplemental Table S3). We computed the mean coverage within each population...
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Method: Haplotype and population structure inference using neural networks in whole-genome sequencing data
- Jonas Meisner and
- Anders Albrechtsen
Genome Res. August 2022 32: 1542-1552; Published in Advance July 6, 2022, doi:10.1101/gr.276813.122
...space based on the linear combination of two normal steps.Inference of population structure using PCAWe can also use the NN likelihoods to infer population structure using PCA; however, the approach is not as straightforward as for the model-based ancestry estimation. We use a similar approach...
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Research: Analysis of canine gene constraint identifies new variants for orofacial clefts and stature
- Reuben M. Buckley,
- Nüket Bilgen,
- Alexander C. Harris,
- Peter Savolainen,
- Cafer Tepeli,
- Metin Erdoğan,
- Aitor Serres Armero,
- Dayna L. Dreger,
- Frank G. van Steenbeek,
- Marjo K. Hytönen,
- Heidi G. Parker,
- Jessica Hale,
- Hannes Lohi,
- Bengi Çınar Kul,
- Adam R. Boyko,
- and Elaine A. Ostrander
Genome Res. May 2025 35: 1080-1093; Published in Advance March 24, 2025, doi:10.1101/gr.280092.124
...expected ranges, unlike a competing model based on CDS length (Fig. 1B). These analyses indicate that accumulation of synonymous mutations follows expected mutation probabilities, demonstrating that this framework can be used to determine if genes have significantly fewer nonsynonymous mutations than...
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Research: Inference of selective forces on house mouse genomes during secondary contact in East Asia
- Kazumichi Fujiwara,
- Shunpei Kubo,
- Toshinori Endo,
- Toyoyuki Takada,
- Toshihiko Shiroishi,
- Hitoshi Suzuki,
- and Naoki Osada
Genome Res. March 2024 34: 366-375; Published in Advance March 20, 2024, doi:10.1101/gr.278828.123
...Laboratory Press This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.References ↵Alexander DH, Novembre J, Lange K. 2009. Fast model-based estimation of ancestry in unrelated...
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Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124

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