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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
...structure analyses, genetic diversity evaluation, and ancestry estimation (Kennedy et al. 2003; Zimmerman et al. 2020). Simultaneously, the latest advances in SNP high-throughput arrays and WGS facilitate the SNPs applied in the usual genetic analyses. However, compared with WGS, SNP arrays were primarily...
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Method: CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes
- Marzia Rossato,
- Luca Marcolungo,
- Luca De Antoni,
- Giulia Lopatriello,
- Elisa Bellucci,
- Gaia Cortinovis,
- Giulia Frascarelli,
- Laura Nanni,
- Elena Bitocchi,
- Valerio Di Vittori,
- Leonardo Vincenzi,
- Filippo Lucchini,
- Kirstin E. Bett,
- Larissa Ramsay,
- David James Konkin,
- Massimo Delledonne,
- and Roberto Papa
Genome Res. May 2023 33: 787-797; Published in Advance May 1, 2023, doi:10.1101/gr.277628.122
...that the same homologous regions are examined in each individual (Peterson et al. 2012).High-throughput low-cost genotyping has largely been achieved by the analysis of single-nucleotide polymorphisms on microarray-based platforms (SNP arrays). These allow up to several thousand SNPs to be tested simultaneously...
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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
...approaches. In particular, germline adaptive immune system genes, like immunoglobulin (IG) and T cell receptor (TR) genes, are particularly hard to genotype using classic reference-based methods owing to their highly repetitive and homologous nature. In this paper, we present ImmunoTyper2, a new...
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Research: Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
- Nora Zidane,
- Carla Rodrigues,
- Valérie Bouchez,
- Martin Rethoret-Pasty,
- Virginie Passet,
- Sylvain Brisse,
- and Chiara Crestani
Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124
...Institut Pasteur, National Reference Center for Corynebacteria of the Diphtheriae Species Complex, 75015 Paris, France Corresponding author: chiara.crestani@pasteur.fr Abstract High-throughput massive parallel sequencing has significantly improved bacterial pathogen genomics, diagnostics, and epidemiology...
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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
...at the upstream and downstream edges of the right-shifted variants where zero is the red line in A. Small polymorphisms occur most frequently 1 bp inside the right-shifted insertion sequence (red arrow).To better understand the origin of these polymorphisms, we were able to confidently genotype 71 SNVs found...
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Research: High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity
- Kaia Mattioli,
- Pieter-Jan Volders,
- Chiara Gerhardinger,
- James C. Lee,
- Philipp G. Maass,
- Marta Melé,
- and John L. Rinn
Genome Res. March 2019 29: 344-355; Published in Advance January 25, 2019, doi:10.1101/gr.242222.118
...that is responsible for this genetic association.DiscussionHere, we have characterized the differences between lncRNA, mRNA, and eRNA core promoter sequences by combining computational predictions and experimental testing using high-throughput assays. Because many lncRNAs are thought to arise from enhancers (Marques...
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Method: Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data
- Li Song,
- Gali Bai,
- X. Shirley Liu,
- Bo Li,
- and Heng Li
Genome Res. May 11, 2023 gr.277585.122; Published in Advance May 11, 2023, doi:10.1101/gr.277585.122
...V, Sauter J, Norman PJ, Hollenbach JA. 2021. High-throughput Interpretation of Killer-cell Immunoglobulin-like Receptor Short-read Sequencing Data with PING. PLoS Comput Biol 17: e1008904. Migliorini F, Torsiello E, Spiezia F, Oliva F, Tingart M, Maffulli N. 2021. Association between HLA genotypes...
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Method: Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors
- Nitan Shalon,
- David A. Relman,
- and Eitan Yaffe
Genome Res. May 2022 32: 986-1003; Published in Advance April 12, 2022, doi:10.1101/gr.275894.121
.... The recovery of MGE s will allow the field to conduct high-throughput computational surveys of mobile elements, strengthening the understanding of the evolution and spread of mobile elements and their genetic cargo in natural environments.The goal of this work was to develop a tool (DomCycle) that reliably...
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Methods: High-throughput genotyping by whole-genome resequencing
- Xuehui Huang,
- Qi Feng,
- Qian Qian,
- Qiang Zhao,
- Lu Wang,
- Ahong Wang,
- Jianping Guan,
- Danlin Fan,
- Qijun Weng,
- Tao Huang,
- Guojun Dong,
- Tao Sang,
- and Bin Han
Genome Res. June 2009 19: 1068-1076; Published in Advance May 6, 2009, doi:10.1101/gr.089516.108
...-based mapping approach with -based high-throughput strategies. The availability of sequences opened the door to high-throughput genotyping. This was initially accomplished by adopting microarray technology, which detects single nucleotide polymorphisms (SNPs) through hybridizing genomic DNA to oligonucleotides...
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Method: Targeted genotyping of variable number tandem repeats with adVNTR
- Mehrdad Bakhtiari,
- Sharona Shleizer-Burko,
- Melissa Gymrek,
- Vikas Bansal,
- and Vineet Bafna
Genome Res. November 2018 28: 1709-1719; Published in Advance October 23, 2018, doi:10.1101/gr.235119.118
..., Ma C, Fontanillas P, Moutsianas L, McCarthy DJ, et al. 2016. The genetic architecture of type 2 diabetes. Nature 536: 41–47. ↵Gelfand Y, Hernandez Y, Loving J, Benson G. 2014. VNTRseek—a computational tool to detect tandem repeat variants in high-throughput sequencing data. Nucleic Acids Res 42: 8884...

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