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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: 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: Proactive functional classification of all possible missense single-nucleotide variants in KCNQ4
- Honglan Zheng,
- Xinhao Yan,
- Guanluan Li,
- Hengwei Lin,
- Siqi Deng,
- Wenhui Zhuang,
- Fuqiang Yao,
- Yu Lu,
- Xin Xia,
- Huijun Yuan,
- Li Jin,
- and Zhiqiang Yan
Genome Res. August 2022 32: 1573-1584; Published in Advance June 27, 2022, doi:10.1101/gr.276562.122
..., Chengdu 610041, China ↵5 These authors contributed equally to this work. Corresponding author: zqyan@szbl.ac.cnAbstractClinical exome sequencing has yielded extensive disease-related missense single-nucleotide variants (SNVs) of uncertain significance, leading to diagnostic uncertainty. KCNQ4 is one...
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Perspective: Challenges and considerations for reproducibility of STARR-seq assays
- Maitreya Das,
- Ayaan Hossain,
- Deepro Banerjee,
- Craig Alan Praul,
- and Santhosh Girirajan
Genome Res. April 2023 33: 479-495; Published in Advance May 2, 2023, doi:10.1101/gr.277204.122
...redelivery into the host. Although in theory any DNA fragment can be tested in any cell line, this recommendation can be advantageous to test cell type–specific effects.Fragment lengthThe length of each candidate enhancer fragment that is compatible with the assay goal, library size, and DNA source (Fig. 1A...
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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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Method: DENT-seq for genome-wide strand-specific identification of DNA single-strand break sites with single-nucleotide resolution
- Juniper J. Elacqua,
- Navpreet Ranu,
- Sarah E. DiIorio,
- and Paul C. Blainey
Genome Res. January 2021 31: 75-87; Published in Advance December 21, 2020, doi:10.1101/gr.265223.120
...be identified for predicting D10A spCas9 nickase activity and the prediction tools could have the option to search for expected wild-type/DSB or D10A nickase off-target activity.DiscussionWe show a method for identifying nicks in human genomic DNA with single-nucleotide resolution and strand specificity using...
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Perspective: Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
- Jung-Wan Mok,
- Shelley B. Gibson,
- Haley A. Dostalik,
- and Shinya Yamamoto
Genome Res. July 2025 35: 1473-1484; Published in Advance June 4, 2025, doi:10.1101/gr.278291.123
...guideline (PS3 and NS3 codes) (Richards et al. 2015), clinical diagnostic laboratories do not carry out these types of studies. For genes in which the functionality of proteins with relevance to disease mechanism can be quantified, MAVE assays based on cell models or recombinant proteins could...
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Method: Fast decoding cell type–specific transcription factor binding landscape at single-nucleotide resolution
- Hongyang Li and
- Yuanfang Guan
Genome Res. April 2021 31: 721-731; Published in Advance March 19, 2021, doi:10.1101/gr.269613.120
...Hongyang Li and Yuanfang Guan Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA Corresponding author: gyuanfan@umich.eduAbstractDecoding the cell type–specific transcription factor (TF) binding landscape at single-nucleotide resolution...
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Resource: Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis
- Chirag Nepal,
- Yavor Hadzhiev,
- Christopher Previti,
- Vanja Haberle,
- Nan Li,
- Hazuki Takahashi,
- Ana Maria M. Suzuki,
- Ying Sheng,
- Rehab F. Abdelhamid,
- Santosh Anand,
- Jochen Gehrig,
- Altuna Akalin,
- Christel E.M. Kockx,
- Antoine A.J. van der Sloot,
- Wilfred F.J. van IJcken,
- Olivier Armant,
- Sepand Rastegar,
- Craig Watson,
- Uwe Strähle,
- Elia Stupka,
- Piero Carninci,
- Boris Lenhard,
- and Ferenc Müller
Genome Res. November 2013 23: 1938-1950; Published in Advance September 3, 2013, doi:10.1101/gr.153692.112
...and its dynamic use during the development of a vertebrate embryo. By using cap analysis of gene expression (CAGE), we mapped transcription initiation events at single nucleotide resolution across 12 stages of zebrafish development. These CAGE-based transcriptome maps reveal -wide rules of core promoter...
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ARTICLE: A genome-wide distribution of 8-oxoguanine correlates with the preferred regions for recombination and single nucleotide polymorphism in the human genome
- Mizuki Ohno,
- Tomofumi Miura,
- Masato Furuichi,
- Yohei Tominaga,
- Daisuke Tsuchimoto,
- Kunihiko Sakumi,
- and Yusaku Nakabeppu
Genome Res. May 2006 16: 567-575; doi:10.1101/gr.4769606
...A -wide distribution of 8-oxoguanine correlates with the preferred regions for recombination and single nucleotide polymorphism in the human Distribution of 8-oxoguanine in human Mizuki Ohno 1 , Tomofumi Miura 1 , 2 , Masato Furuichi 1 , 3 , Yohei Tominaga 1 , Daisuke Tsuchimoto 1 , Kunihiko Sakumi...

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