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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
...by sequencing (GBS) (Elshire et al. 2011), restriction site-associated DNA sequencing (RAD-Seq) (Baird et al. 2008; Davey et al. 2011), and double-digest RAD-Seq (ddRADseq) (Peterson et al. 2012; Truong et al. 2012). These methods concentrate sequencing data on regions adjacent to restriction sites...
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Method: HD-Marker: a highly multiplexed and flexible approach for targeted genotyping of more than 10,000 genes in a single-tube assay
- Jia Lv,
- Wenqian Jiao,
- Haobing Guo,
- Pingping Liu,
- Ruijia Wang,
- Lingling Zhang,
- Qifan Zeng,
- Xiaoli Hu,
- Zhenmin Bao,
- and Shi Wang
Genome Res. December 2018 28: 1919-1930; Published in Advance November 8, 2018, doi:10.1101/gr.235820.118
....g., Illumina iScan System). With the rapid development of sequencing technologies, it is conceivable that switching GoldenGate from BeadArray to NGS platforms would revive this powerful methodology by addressing array-related issues and achieve the goal of cost-effective targeted genotyping of transcriptome...
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Method: Multiplexed shotgun genotyping for rapid and efficient genetic mapping
- Peter Andolfatto,
- Dan Davison,
- Deniz Erezyilmaz,
- Tina T. Hu,
- Joshua Mast,
- Tomoko Sunayama-Morita,
- and David L. Stern
Genome Res. April 2011 21: 610-617; Published in Advance January 13, 2011, doi:10.1101/gr.115402.110
...used next-generation sequencing to combine marker discovery and genotyping in a single step (Baird et al. 2008; Huang et al. 2009). Bothmethods can generate a large number of -wide markers and can accommodate multiplexing of individuals. However, the restrictionsite associated DNA (RAD) approach...
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Methods: Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays
- Baochuan Lin,
- Zheng Wang,
- Gary J. Vora,
- Jennifer A. Thornton,
- Joel M. Schnur,
- Dzung C. Thach,
- Kate M. Blaney,
- Adam G. Ligler,
- Anthony P. Malanoski,
- Jose Santiago,
- Elizabeth A. Walter,
- Brian K. Agan,
- David Metzgar,
- Donald Seto,
- Luke T. Daum,
- Russell Kruzelock,
- Robb K. Rowley,
- Eric H. Hanson,
- Clark Tibbetts,
- and David A. Stenger
Genome Res. April 2006 16: 527-535; Published in Advance February 15, 2006, doi:10.1101/gr.4337206
...and influenza A viruses For sensitivity assessments, real-time PCR assays were conducted on an iCycler instrument (Bio-Rad Laboratories) or R.A.P.I.D. LightCycler (Idaho Technology Inc.) to determine the number of adenovirus s in each sample. The findings for the samples were compared with those for 10-fold...
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Method: Mutation mapping and identification by whole-genome sequencing
- Ignaty Leshchiner,
- Kristen Alexa,
- Peter Kelsey,
- Ivan Adzhubei,
- Christina A. Austin-Tse,
- Jeffrey D. Cooney,
- Heidi Anderson,
- Matthew J. King,
- Rolf W. Stottmann,
- Maija K. Garnaas,
- Seungshin Ha,
- Iain A. Drummond,
- Barry H. Paw,
- Trista E. North,
- David R. Beier,
- Wolfram Goessling,
- and Shamil R. Sunyaev
Genome Res. August 2012 22: 1541-1548; Published in Advance May 3, 2012, doi:10.1101/gr.135541.111
..., Cresko WA, Johnson EA. 2008. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3: e3376 doi: 10.1371/journal.pone.0003376. Botstein D, White RL, Skolnick M, Davis RW. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum...
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Methods: Rapid identification of homologous recombinants and determination of gene copy number with reference/query pyrosequencing (RQPS)
- Zhenyi Liu,
- Anna C. Obenauf,
- Michael R. Speicher,
- and Raphael Kopan
Genome Res. November 2009 19: 2081-2089; Published in Advance October 1, 2009, doi:10.1101/gr.093856.109
...-primer PCR reaction system (Fakhrai-Rad et al. 2002; Royo et al. 2007) was used for the amplification of the DNA fragments containing an SNV in a PCR reaction mixture containing 2 mL of DNA template, 12.5 mL of Bullseye Taq DNA Polymerase Mix (Midsci), 1 mL of untailed gene-specific primer, 0.2mL of tailed...
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Methods: Fluorescent Detection and Isolation of DNA Variants Using Stabilized RecA-Coated Oligonucleotides
- Michael C. Rice,
- Brandy M. Heckman,
- Yi Liu,
- and Eric B. Kmiec
Genome Res. January 2004 14: 116-125; Published in Advance December 12, 2003, doi:10.1101/gr.1386204
...for the in situ detection of tissue samples. Oligonucleotide-mediated detection could provide a rapid, cost-effective in situ method for more precise staging of tumors and choosing the appropriate chemotherapeutic regimen. METHODS Oligonucleotides and DNA Substrates Double D-loop intermediates have been formed...
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Method: Sequence-based physical mapping of complex genomes by whole genome profiling
- Jan van Oeveren,
- Marjo de Ruiter,
- Taco Jesse,
- Hein van der Poel,
- Jifeng Tang,
- Feyruz Yalcin,
- Antoine Janssen,
- Hanne Volpin,
- Keith E. Stormo,
- Robert Bogden,
- Michiel J.T. van Eijk,
- and Marcel Prins
Genome Res. April 2011 21: 618-625; Published in Advance February 1, 2011, doi:10.1101/gr.112094.110
...restriction enzyme digestion and consecutive adapter-ligated restriction fragment amplification, without the need for prior sequence information. These features are sharedwith the restrictionsite associated DNA (RAD) technique which has been described as an integrated platform for SNP discovery and genotyping...
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Review: Population genetic inference from genomic sequence variation
- John E. Pool,
- Ines Hellmann,
- Jeffrey D. Jensen,
- and Rasmus Nielsen
Genome Res. March 2010 20: 291-300; Published in Advance January 12, 2010, doi:10.1101/gr.079509.108
..., as restriction fragment length polymorphisms, microsatellites, and small-scale DNA sequencing (e.g., Kreitman 1983) broadened the range of questions open to empirical investigation. With the recent flood of -wide single nucleotide polymorphism (SNP) data, and now the advent of fully sequenced population samples...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...clinical practice.A hallmark of cancer is widespread genetic and epigenetic instability (Hanahan and Weinberg 2011). Cancer often originates through somatic mutations that accumulate throughout an individual's lifetime due to exposure to carcinogens, DNA replication errors, and other factors, thereby...
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