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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...transfer) affects stability. Age-matched cohorts of 12 ART-derived and 16 naturally conceived C57BL/6J inbred mice were reared in a controlled setting and whole--sequenced to ∼50× coverage. Using a rigorous pipeline for de novo single-nucleotide variant (dnSNV) discovery, we observe a ∼30% (95% CI: 4...
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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
..., China ↵3 These authors contributed equally to this work. Corresponding author: liujf@cau.edu.cnAbstractAs the scale of deep whole- sequencing (WGS) data has grown exponentially, hundreds of millions of single nucleotide polymorphisms (SNPs) have been identified in livestock. Utilizing these massive SNP...
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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
...disease and complex traits but can be difficult to resolve with short-read sequencing. We present STRkit, a software package for genotyping STRs using long-read sequencing (LRS) that uses proximate single-nucleotide variants to improve genotyping accuracy without a priori haplotype information. We show...
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Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
- Hsin-Yen Larry Wu,
- Isaiah D. Kaufman,
- and Polly Yingshan Hsu
Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
...-seq/RNA-seq data sets from different conditions for comparison. It also contains functions for plotting single-transcript views, reading-frame decomposition, and RNA-seq coverage alone. Importantly, ggRibo supports the visualization of other omics data sets that could also be presented with single-nucleotide...
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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
...to significantly and directly affect the strength of the ERE and thereby ESR1 binding, we used the in silico prediction tool SNP2TFBS (Kumar et al. 2017), which compares the position weight matrix of a TF binding motif in reference format and when including the rSNP/indel variant. This resulted in a short list...
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Research: Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement
- Peter A. Audano and
- Christine R. Beck
Genome Res. January 2024 34: 7-19; Published in Advance January 4, 2024, doi:10.1101/gr.278203.123
...confirm that SNP and indel polymorphisms are enriched at shifted breakpoints and are also absent from variant callsets. Breakpoint homology increases the likelihood of imprecise SV calls and the distance they are shifted, and tandem duplications are the most heavily affected SVs. Because graph methods...
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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
...@genetics.med.harvard.eduAbstractThe strategy of in-solution enrichment for hundreds of thousands of single-nucleotide polymorphisms (SNPs) has been used to analyze >70% of individuals with -scale ancient DNA published to date. This approach makes it economical to study ancient samples with low proportions of human DNA and increases the rate...
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Research: Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations
- Anu Toropainen,
- Lindsey K. Stolze,
- Tiit Örd,
- Michael B. Whalen,
- Paula Martí Torrell,
- Verena M. Link,
- Minna U. Kaikkonen,
- and Casey E. Romanoski
Genome Res. March 2022 32: 409-424; Published in Advance February 22, 2022, doi:10.1101/gr.276064.121
...were either present as the sole variant nucleotide, when no other variants in the 198-bp window were present (30% of oligos), or in existing European haplotypes when additional polymorphic variants (5% minor allele frequency [MAF]) were located within the window (63% of oligos; up to the top five most...
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Method: Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine
- Bo Yan,
- Duan Wang,
- and Laurence Ettwiller
Genome Res. June 2024 34: 904-913; Published in Advance June 10, 2024, doi:10.1101/gr.278294.123
...ratio, RIMS-seq2 is attuned to variations from the reference . Thus, we also investigated the effect of single-nucleotide polymorphism (SNP) on methylation calls. We observed an increase in methylation call accuracy if the publicly available NA12878 SNP positions were to be removed prior to methylation...
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Method: Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N
- Yun Zhang,
- Chanhee Park,
- Christopher Bennett,
- Micah Thornton,
- and Daehwan Kim
Genome Res. July 2021 31: 1290-1295; Published in Advance June 8, 2021, doi:10.1101/gr.275193.120
...and REF-RC-3N indexes (Methods) are sufficient for unifying alignment of all known NC sequencing data types. HISAT-3N also allows for incorporation of splice sites, single-nucleotide polymorphisms, and small insertions/deletions using a graph index structure available in the HISAT2 program. Like most...

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