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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
...strategies were similarly effective in the chloroplast , resulting in ∼78.5% depletion (Fig. 1C). In contrast, no significant depletion was observed in the mitochondrial (Fig. 1D). In parallel, the sequential depletion strategy achieved a 130% increase in the number of reads mapping to single-copy regions...
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Methods: Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays
- Daisuke Komura,
- Fan Shen,
- Shumpei Ishikawa,
- Karen R. Fitch,
- Wenwei Chen,
- Jane Zhang,
- Guoying Liu,
- Sigeo Ihara,
- Hiroshi Nakamura,
- Matthew E. Hurles,
- Charles Lee,
- Stephen W. Scherer,
- Keith W. Jones,
- Michael H. Shapero,
- Jing Huang,
- and Hiroyuki Aburatani
Genome Res. December 2006 16: 1575-1584; Published in Advance November 22, 2006, doi:10.1101/gr.5629106
..., S. , Tsai, Y.-Y. , Fang, J. , Law, J. , Di, X. , Liu, W.-M. , Yang, G. , Liu, G. , et al. ( 2004b ) Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high density oligonucleotide array . Genome Res. 14 : 414 – 425 . ↵ McCarrol, S.A. , Hadnott, T.N. , Perry, G.H. , Sabeti, P...
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Methods: Parallel Genotyping of Over 10,000 SNPs Using a One-Primer Assay on a High-Density Oligonucleotide Array
- Hajime Matsuzaki,
- Halina Loi,
- Shoulian Dong,
- Ya-Yu Tsai,
- Joy Fang,
- Jane Law,
- Xiaojun Di,
- Wei-Min Liu,
- Geoffrey Yang,
- Guoying Liu,
- Jing Huang,
- Giulia C. Kennedy,
- Thomas B. Ryder,
- Gregory A. Marcus,
- P. Sean Walsh,
- Mark D. Shriver,
- Jennifer M. Puck,
- Keith W. Jones,
- and Rui Mei
Genome Res. March 2004 14: 414-425; doi:10.1101/gr.2014904
...Parallel Genotyping of Over 10,000 SNPs Using a One-Primer Assay on a High-Density Oligonucleotide Array Hajime Matsuzaki 1 , Halina Loi 1 , Shoulian Dong 1 , Ya-Yu Tsai 2 , Joy Fang 1 , Jane Law 1 , Xiaojun Di 1...
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ARTICLE: Genome-wide Detection of Allelic Imbalance Using Human SNPs and High-density DNA Arrays
- Rui Mei,
- Patricia C. Galipeau,
- Cynthia Prass,
- Anthony Berno,
- Ghassan Ghandour,
- Nila Patil,
- Roger K. Wolff,
- Mark S. Chee,
- Brian J. Reid,
- and David J. Lockhart
Genome Res. August 1, 2000 10: 1126-1137; doi:10.1101/gr.10.8.1126
...of additional SNP markers is rapidly advancing, and array-based methods provide a scalable approach to the simultaneous genotyping of thousands of markers in parallel. The availability of more markers and higher capacity array designs will allow efficient, -wide, high-resolution searches for chromosomal changes...
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Methods: Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays
- Christopher W. Wong,
- Thomas J. Albert,
- Vinsensius B. Vega,
- Jason E. Norton,
- David J. Cutler,
- Todd A. Richmond,
- Lawrence W. Stanton,
- Edison T. Liu,
- and Lance D. Miller
Genome Res. March 2004 14: 398-405; doi:10.1101/gr.2141004
...., Foy, M., Ewan, M., et al. 2000 . Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol. 18 : 630 –634. ↵ Cutler, D.J., Zwick, M.E., Carrasquillo, M.M., Yohn, C.T., Tobin, K.P., Kashuk, C., Mathews, D.J., Shah, N.A., Eichler, E.E., Warrington, J...
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Methods: High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis
- Marilyn A.L. West,
- Hans van Leeuwen,
- Alexander Kozik,
- Daniel J. Kliebenstein,
- R.W. Doerge,
- Dina A. St. Clair,
- and Richard W. Michelmore
Genome Res. June 2006 16: 787-795; Published in Advance May 15, 2006, doi:10.1101/gr.5011206
...from microarrays can be leveraged to identify polymorphisms across the genome and can be efficiently developed into genetic markers that are verifiable in a large segregating RIL population. Both marker types also offer opportunities for massively parallel mapping in unsequenced and less studied...
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METHODS: Rapid Mapping of Zebrafish Mutations With SNPs and Oligonucleotide Microarrays
- Heather L. Stickney,
- Jeremy Schmutz,
- Ian G. Woods,
- Caleb C. Holtzer,
- Mark C. Dickson,
- Peter D. Kelly,
- Richard M. Myers,
- and William S. Talbot
Genome Res. December 1, 2002 12: 1929-1934; doi:10.1101/gr.777302
...) The construction of a first generation single nucleotide polymorphism (SNP) map of the zebrafish genome comprising 2035 SNPs and 178 small insertions/deletions, and (2) the development of a method for mapping mutations in which hundreds of SNPs can be scored in parallel with an oligonucleotide microarray. We have...
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METHODS: Oligonucleotide Arrays for High-Throughput SNPs Detection in the MHC Class I Genes: HLA-B as a Model System
- Zhen Guo,
- Mark S. Gatterman,
- Lee Hood,
- John A. Hansen,
- and Effie W. Petersdorf
Genome Res. March 1, 2002 12: 447-457; Published in Advance February 15, 2002, doi:10.1101/gr.206402
...; Sapolsky and Lipshutz 1996 ). With the potential to detect thousands of SNPs in parallel, oligonucleotide arrays offer a cost-effective approach for high-throughput polymorphism analysis. The HLA Class I and II genes encode some of the most complex patterns of SNP substitutions in the human ( So 1994...
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Method: Haplotype-based profiling of subtle allelic imbalance with SNP arrays
- Selina Vattathil and
- Paul Scheet
Genome Res. January 2013 23: 152-158; Published in Advance October 1, 2012, doi:10.1101/gr.141374.112
...a parallel between our approach and two existing methods for slightly different settings. One is the trio-based algorithm of PennCNV (Wang et al. 2007), which uses parental genotypes to validate de novo copy-number variants (CNVs)—within a putative de novo CNV region, it identifies sites at which...
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Method: Copy number variation detection and genotyping from exome sequence data
- Niklas Krumm,
- Peter H. Sudmant,
- Arthur Ko,
- Brian J. O'Roak,
- Maika Malig,
- Bradley P. Coe,
- NHLBI Exome Sequencing Project,
- Aaron R. Quinlan,
- Deborah A. Nickerson,
- and Evan E. Eichler
Genome Res. August 2012 22: 1525-1532; Published in Advance May 14, 2012, doi:10.1101/gr.138115.112
..., Meyerson M, Lander ES. 2008. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods 6: 99–103. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, et al. 2011. Origins and functional impact of copy number variation...

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