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Methods: Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays
- Georg Zeller,
- Richard M. Clark,
- Korbinian Schneeberger,
- Anja Bohlen,
- Detlef Weigel,
- and Gunnar Rätsch
Genome Res. June 2008 18: 918-929; Published in Advance March 6, 2008, doi:10.1101/gr.070169.107
...-characterized plant, Arabidopsis thaliana . Nonredundantly, 27% of the was included within the boundaries of PRs predicted at high specificity (≈97%). The resulting data set provides a fine-scale view of polymorphic sequences in A. thaliana ; patterns of polymorphism not apparent in SNP data were readily detected...
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Method: Secure discovery of genetic relatives across large-scale and distributed genomic data sets
- Matthew M. Hong,
- David Froelicher,
- Ricky Magner,
- Victoria Popic,
- Bonnie Berger,
- and Hyunghoon Cho
Genome Res. September 2024 34: 1312-1323; Published in Advance August 7, 2024, doi:10.1101/gr.279057.124
...to the same bucket index. For this purpose, we devised a novel encoding scheme that splits and subsamples genotypes into k-SNPs (similar to k-mers, but noncontiguous; single-nucleotide polymorphism [SNP]), such that the similarity between k-SNPs reflects extended runs of identical genotypes, typically...
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Methods: PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
- Kai Wang,
- Mingyao Li,
- Dexter Hadley,
- Rui Liu,
- Joseph Glessner,
- Struan F.A. Grant,
- Hakon Hakonarson,
- and Maja Bucan
Genome Res. November 2007 17: 1665-1674; Published in Advance October 5, 2007, doi:10.1101/gr.6861907
...segmental duplication regions from the UCSC Genome Browser ( Kuhn et al. 2007 ) and consolidated them into a list of 8546 non-overlapping regions encompassing 154 Mb ( Bailey et al. 2001 ). We found that 604/2633 CNVs (30 Mb/125 Mb) in HapMap individuals overlap with these regions, suggesting that fine-scale...
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RESOURCE: PolyScan: An automatic indel and SNP detection approach to the analysis of human resequencing data
- Ken Chen,
- Michael D. McLellan,
- Li Ding,
- Michael C. Wendl,
- Yumi Kasai,
- Richard K. Wilson,
- and Elaine R. Mardis
Genome Res. May 2007 17: 659-666; Published in Advance April 6, 2007, doi:10.1101/gr.6151507
.... Nat. Genet. 36 : 861 – 866 . ↵ Gordon, D. , Abajian, C. , Green, P. ( 1998 ) Consed: A graphical tool for sequence finishing . Genome Res. 8 : 195 – 202 . ↵ Gunderson, K.L. , Steemers, F.J. , Lee, G. , Mendoza, L.G. , Chee, M.S. ( 2005 ) A -wide scalable SNP genotyping assay using microarray...
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Method: Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits
- Carlos Ruiz-Arenas,
- Alejandro Cáceres,
- Marcos López,
- Dolors Pelegrí-Sisó,
- Josefa González,
- and Juan R. González
Genome Res. December 2020 30: 1802-1814; Published in Advance November 17, 2020, doi:10.1101/gr.258301.119
...recombClust, a method that uses SNP-phased data to detect differences in historic recombination in a chromosome population. We validated our method by performing simulations and by using real data to accurately predict the alleles of well-known recombination modifiers, including common inversions...
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Method: Identifying crossovers and shared genetic material in whole genome sequencing data from families
- Kelley Paskov,
- Brianna Chrisman,
- Nathaniel Stockham,
- Peter Yigitcan Washington,
- Kaitlyn Dunlap,
- Jae-Yoon Jung,
- and Dennis P. Wall
Genome Res. October 2023 33: 1747-1756; Published in Advance October 25, 2023, doi:10.1101/gr.277172.122
...sequencing data is spurious crossover calls caused by variant calling errors. This issue is exacerbated in WGS owing to its higher error rate compared with microarray data, paired with the existence of error-prone regions of the (low complexity regions, microsatellites, etc.) where errors occur across...
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Research: Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
- Aitor Serres-Armero,
- Brian W. Davis,
- Inna S. Povolotskaya,
- Carlos Morcillo-Suarez,
- Jocelyn Plassais,
- David Juan,
- Elaine A. Ostrander,
- and Tomas Marques-Bonet
Genome Res. May 2021 31: 762-774; Published in Advance April 16, 2021, doi:10.1101/gr.266049.120
...), but other forms of genomic variation have rarely been studied systematically. In fact, there is still a lack of fine-scale, -wide analyses of any variants other than SNPs across dog breeds, a notable exception when compared to humans and other model organisms (Yalcin et al. 2011; Brown et al. 2012; Sudmant...
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Research: Pedigree-based estimation of human mobile element retrotransposition rates
- Julie Feusier,
- W. Scott Watkins,
- Jainy Thomas,
- Andrew Farrell,
- David J. Witherspoon,
- Lisa Baird,
- Hongseok Ha,
- Jinchuan Xing,
- and Lynn B. Jorde
Genome Res. October 2019 29: 1567-1577; doi:10.1101/gr.247965.118
...at its 5′ flanking region, which may have occurred during the insertion event, and thus does not have a TSD. Alu #4 is de novo in individual 8327 (NA07355) but is also present at low levels by IGV and PCR in sibling 8439 (NA07351) (Supplemental Fig. S1). Amplification of a nearby SNP indicates...
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Research: Ultra-long-range interactions between active regulatory elements
- Elias T. Friman,
- Ilya M. Flyamer,
- Davide Marenduzzo,
- Shelagh Boyle,
- and Wendy A. Bickmore
Genome Res. August 2023 33: 1269-1283; Published in Advance July 14, 2023, doi:10.1101/gr.277567.122
.... 2009). More fine-scale mapping revealed “subcompartments” within these larger domains (Rao et al. 2014; Spracklin et al. 2023), with extremely high sequencing depths revealing compartments of sizes down to a few kilobases (Goel et al. 2023; Harris et al. 2023). What drives compartment interactions...
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Resource: Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies
- Mingzhou Li,
- Lei Chen,
- Shilin Tian,
- Yu Lin,
- Qianzi Tang,
- Xuming Zhou,
- Diyan Li,
- Carol K.L. Yeung,
- Tiandong Che,
- Long Jin,
- Yuhua Fu,
- Jideng Ma,
- Xun Wang,
- Anan Jiang,
- Jing Lan,
- Qi Pan,
- Yingkai Liu,
- Zonggang Luo,
- Zongyi Guo,
- Haifeng Liu,
- Li Zhu,
- Surong Shuai,
- Guoqing Tang,
- Jiugang Zhao,
- Yanzhi Jiang,
- Lin Bai,
- Shunhua Zhang,
- Miaomiao Mai,
- Changchun Li,
- Dawei Wang,
- Yiren Gu,
- Guosong Wang,
- Hongfeng Lu,
- Yan Li,
- Haihao Zhu,
- Zongwen Li,
- Ming Li,
- Vadim N. Gladyshev,
- Zhi Jiang,
- Shuhong Zhao,
- Jinyong Wang,
- Ruiqiang Li,
- and Xuewei Li
Genome Res. May 2017 27: 865-874; Published in Advance September 19, 2016, doi:10.1101/gr.207456.116
..., Paudel Y, Semiadi G, Meijaard E, Li N, Crooijmans RP, et al. 2013. Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus. Genome Biol 14: R107. Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan...
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