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Method: k-mer manifold approximation and projection for visualizing DNA sequences
- Chengbo Fu,
- Einari A. Niskanen,
- Gong-Hong Wei,
- Zhirong Yang,
- Marta Sanvicente-García,
- Marc Güell,
- and Lu Cheng
Genome Res. May 2025 35: 1234-1246; Published in Advance April 10, 2025, doi:10.1101/gr.279458.124
.... The Streptococcus pyogenes Cas9 (SpCas9) protein will make a double-stranded break (DSB) at 3 nucleotides (nt) upstream of the PAM, after that the broken DNAs are ligated by non-homologous end-joining (NHEJ), which leads to different DNA editing results (mainly random small indels). Another cellular repair...
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Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
- W.H. Adrian Tsui,
- Spencer C. Ding,
- Peiyong Jiang,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
...technology in the methylation analysis of long cfDNA (>500 bp), which generally carries more CpG and SNPs than short fragments, and so intrinsically phases these informative loci to augment the power of disease detection (Yu et al. 2021, 2023a). Notably, Choy and colleagues (2022) use the HK model...
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Method: Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichment
- Bo Yan,
- Duan Wang,
- Romualdas Vaisvila,
- Zhiyi Sun,
- and Laurence Ettwiller
Genome Res. November/December 2022 32: 2079-2091; Published in Advance November 4, 2022, doi:10.1101/gr.277080.122
....ResultsPrinciple of Methyl-SNP-seqTo capture the original four nucleotide sequence information as well as cytosine modification, Methyl-SNP-seq is taking advantage of the double-stranded nature of DNA to duplicate the sequence information into a linked copy of the original strand. Importantly, this copy is amended...
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Method: Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly
- Ou Wang,
- Robert Chin,
- Xiaofang Cheng,
- Michelle Ka Yan Wu,
- Qing Mao,
- Jingbo Tang,
- Yuhui Sun,
- Ellis Anderson,
- Han K. Lam,
- Dan Chen,
- Yujun Zhou,
- Linying Wang,
- Fei Fan,
- Yan Zou,
- Yinlong Xie,
- Rebecca Yu Zhang,
- Snezana Drmanac,
- Darlene Nguyen,
- Chongjun Xu,
- Christian Villarosa,
- Scott Gablenz,
- Nina Barua,
- Staci Nguyen,
- Wenlan Tian,
- Jia Sophie Liu,
- Jingwan Wang,
- Xiao Liu,
- Xiaojuan Qi,
- Ao Chen,
- He Wang,
- Yuliang Dong,
- Wenwei Zhang,
- Andrei Alexeev,
- Huanming Yang,
- Jian Wang,
- Karsten Kristiansen,
- Xun Xu,
- Radoje Drmanac,
- and Brock A. Peters
Genome Res. May 2019 29: 798-808; Published in Advance April 2, 2019, doi:10.1101/gr.245126.118
...). The resulting BAM file was then sorted by chromosomal coordinates with SAMtools (Li et al. 2009) and duplicates were marked with Picard MarkDuplicate function (http://broadinstitute.github.io/picard). Short variant (SNPs and indels) calling was performed using Sentieon's DNA-seq (Freed et al. 2017) optimization...
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Method: Accurate sequencing of DNA motifs able to form alternative (non-B) structures
- Matthias H. Weissensteiner,
- Marzia A. Cremona,
- Wilfried M. Guiblet,
- Nicholas Stoler,
- Robert S. Harris,
- Monika Cechova,
- Kristin A. Eckert,
- Francesca Chiaromonte,
- Yi-Fei Huang,
- and Kateryna D. Makova
Genome Res. July 11, 2023 ; Published in Advance July 11, 2023, doi:10.1101/gr.277490.122
...mismatch errors and dividing by the total number of aligned nucleotides overall for motifs and control sequences. Single-nucleotide mismatch error rates Illumina We detected significantly higher per-motif single-nucleotide mismatch (SNM) error rates for direct repeats, G4 motifs, and Z-DNA motifs compared...
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Resource: Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
- Yang Zhou,
- Lv Yang,
- Xiaotao Han,
- Jiazheng Han,
- Yan Hu,
- Fan Li,
- Han Xia,
- Lingwei Peng,
- Clarissa Boschiero,
- Benjamin D. Rosen,
- Derek M. Bickhart,
- Shujun Zhang,
- Aizhen Guo,
- Curtis P. Van Tassell,
- Timothy P.L. Smith,
- Liguo Yang,
- and George E. Liu
Genome Res. August 2022 32: 1585-1601; Published in Advance August 17, 2022, doi:10.1101/gr.276550.122
...al. 2009). Microhomology-mediated end joining (MMEJ), also known as alternative nonhomologous end-joining (Alt-NHEJ), is a backup pathway for repairing double-strand break (DSB) in DNA through the recombination of short stretches of microhomology (Ottaviani et al. 2014; Black et al. 2019).Previous...
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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
...the Twist Ancient DNA experimental conditions. However, the Twist Ancient DNA assay also outperforms the 1240k assay for double-stranded libraries, which is the condition for which we optimized the 1240k enrichment several years ago with the goal of maximizing SNP coverage and minimizing sequencing costs...
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Research: Suppressor mutations in Mecp2-null mice implicate the DNA damage response in Rett syndrome pathology
- Adebola Enikanolaiye,
- Julie Ruston,
- Rong Zeng,
- Christine Taylor,
- Marijke Schrock,
- Christie M. Buchovecky,
- Jay Shendure,
- Elif Acar,
- and Monica J. Justice
Genome Res. April 2020 30: 540-552; Published in Advance April 21, 2020, doi:10.1101/gr.258400.119
...recombination, double-strand break repair, and regulation of DNA metabolic processes. Thus 20/32 or 63% of the genes cluster into the general category of “Regulation of DNA Activity,” which is expected for a functional relationship with MECP2. The genes with unknown function (Clint1, Dennd4a) fall outside...
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Method: SvABA: genome-wide detection of structural variants and indels by local assembly
- Jeremiah A. Wala,
- Pratiti Bandopadhayay,
- Noah F. Greenwald,
- Ryan O'Rourke,
- Ted Sharpe,
- Chip Stewart,
- Steve Schumacher,
- Yilong Li,
- Joachim Weischenfeldt,
- Xiaotong Yao,
- Chad Nusbaum,
- Peter Campbell,
- Gad Getz,
- Matthew Meyerson,
- Cheng-Zhong Zhang,
- Marcin Imielinski,
- and Rameen Beroukhim
Genome Res. April 2018 28: 581-591; Published in Advance March 13, 2018, doi:10.1101/gr.221028.117
...are often unstable and suffer frequent complex events (Stephens et al. 2009). The junctions connecting two SV breakpoints may also involve the insertion of novel sequences created during DNA repair (Mahaney et al. 2009) or insertion of short fragments copied from elsewhere in the (Liu et al. 2011; Zhang et...
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Research: Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions
- Kyuha Choi,
- Xiaohui Zhao,
- Andrew J. Tock,
- Christophe Lambing,
- Charles J. Underwood,
- Thomas J. Hardcastle,
- Heïdi Serra,
- Juhyun Kim,
- Hyun Seob Cho,
- Jaeil Kim,
- Piotr A. Ziolkowski,
- Nataliya E. Yelina,
- Ildoo Hwang,
- Robert A. Martienssen,
- and Ian R. Henderson
Genome Res. April 2018 28: 532-546; Published in Advance March 12, 2018, doi:10.1101/gr.225599.117
...,888 SNPs, mean intermarker distance = 248 bp) and calculated SPO11-1-oligo, nucleosome, H3K4me3, and DNA methylation levels within these windows. Data were modeled using the binomial family with a logistic link function. The formula for the final model was: This model revealed a significant positive effect...

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