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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
...to map genomic regions shaping quantitative traits with high spatial resolution 306 and statistical power sufficient to detect subtle effect sizes typical of natural genetic variation. 307 Incorporation of sequence data improves mapping resolution 308 We incorporated our WGS data to determine...
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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
...tool for -scale STRs genotyping and potentially for detecting the most common category of de novo STR mutation events: ±1 repeat unit changes. However, without a more complete mutation detection procedure with statistical confidence measures to control for false discovery, we cannot claim that all loci...
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Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
- Michael K.B. Ford,
- Ananth Hari,
- Meredith Yeager,
- Lisa Mirabello,
- Stephen Chanock,
- Ibrahim Numanagić,
- COVNET Consortium,
- and S. Cenk Sahinalp
Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
....98; and TRDV, 1.0. IG loci showed more variation in concordance rates: IGLV, 0.94; IGKV, 0.88; and IGHV, 0.74. The lower concordance rate observed for IGHV is consistent with the known complexity and prevalence of duplications in this region, which makes the problem of resolving ambiguous read mappings more...
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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
...this enhancer. These results demonstrate the power of caQTLs to characterize regulatory mechanisms at GWAS loci.Chromatin accessibility quantitative trait loci (caQTLs) have successfully identified functional variants and regulatory elements at a subset of gene expression QTLs (eQTLs) and -wide association...
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Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
...-based assemblies (Brawand et al. 2014), limiting its ability to detect more complex genomic variation.There is currently limited insight into SVs in cichlids via a -wide approach, especially within individual radiations like Lake Malawi, which harbors an estimated more than 800 species predominantly from...
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Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
..., TF binding for each factor is highly variable across genotypes, as shown for two loci for Twist and Mef2 occupancy (Fig. 1F).Effects of genetic variation on TF binding are extensive and preferably detected in genomic regions with less bufferingTo disentangle the impact of genetic variation on TF...
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Method: A scalable adaptive quadratic kernel method for interpretable epistasis analysis in complex traits
- Boyang Fu,
- Prateek Anand,
- Aakarsh Anand,
- Joel Mefford,
- and Sriram Sankararaman
Genome Res. September 2024 34: 1294-1303; Published in Advance August 29, 2024, doi:10.1101/gr.279140.124
...thresholds needed to account for the number of tests performed. As a result, successful detection of epistasis requires examining a large number of individuals to obtain adequate power.An alternative approach to identify trait-relevant genetic variants focuses on grouping variants into “sets” and jointly...
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Research: Identification and validation of supervariants reveal novel loci associated with human white matter microstructure
- Shiying Wang,
- Ting Li,
- Bingxin Zhao,
- Wei Dai,
- Yisha Yao,
- Cai Li,
- Tengfei Li,
- Hongtu Zhu,
- and Heping Zhang
Genome Res. January 2024 34: 20-33; Published in Advance December 12, 2023, doi:10.1101/gr.277905.123
...loci associated with white matter microstructure. However, GWASs suffer from limited reproducibility and difficulties in detecting multi-single-nucleotide polymorphism (multi-SNP) and epistatic effects. In this study, we adopt the concept of supervariants, a combination of alleles in multiple loci...
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Research: Major impacts of widespread structural variation on sorghum
- Zhihai Zhang,
- Joao Paulo Gomes Viana,
- Bosen Zhang,
- Kimberly K.O. Walden,
- Hans Müller Paul,
- Stephen P. Moose,
- Geoffrey P. Morris,
- Chris Daum,
- Kerrie W. Barry,
- Nadia Shakoor,
- and Matthew E. Hudson
Genome Res. February 2024 34: 286-299; Published in Advance March 13, 2024, doi:10.1101/gr.278396.123
...-type variations.SV data allow detection of new GWAS associationsTo further investigate the causative genomic loci associated with the increased heritability gained by adding SVs to the polymorphism data set, we performed GWAS based on the whole- SNP, SV, and combined SNP and SV data sets. First, we investigated...
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Resource: Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle
- Alexander S. Leonard,
- Xena M. Mapel,
- and Hubert Pausch
Genome Res. February 2024 34: 300-309; Published in Advance February 14, 2024, doi:10.1101/gr.278267.123
...quantitative trait loci (e/sQTL) are large contributors to phenotypic variability. Achieving sufficient statistical power for e/sQTL mapping requires large cohorts with both genotypes and molecular phenotypes, and so, the genomic variation is often called from short-read alignments, which are unable...

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