Searching journal content for articles similar to Hardenbol et al. 15 (2): 269.

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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
...in a single-tube assay (in contrast to fewer than 3100 in the original GoldenGate assay). We perform extensive analyses to demonstrate the power and performance of HD-Marker on various multiplex levels (296, 795, 1293, and 12,472 genic SNPs) across two sequencing platforms in two nonmodel species (the...
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Method: High-fidelity, large-scale targeted profiling of microsatellites
- Caitlin A. Loh,
- Danielle A. Shields,
- Adam Schwing,
- and Gilad D. Evrony
Genome Res. July 2024 34: 1008-1026; Published in Advance July 16, 2024, doi:10.1101/gr.278785.123
...capture approach for targeted profiling of microsatellites, because it is scalable to hundreds of thousands of loci as evidenced by its use in whole-exome sequencing (Majewski et al. 2011). This contrasts with other amplicon-based targeted sequencing approaches, such as molecular inversion probes...
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Methods: Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes
- Katherine Elena Varley and
- Robi David Mitra
Genome Res. November 2008 18: 1844-1850; Published in Advance October 10, 2008, doi:10.1101/gr.078204.108
...: A multiplex pathogen detection assay . PLoS ONE 2 : e223 , doi: 10.1371/journal.pone.0000223 . ↵ Akhras, M.S. , Unemo, M. , Thiyagarajan, S. , Nyren, P. , Davis, R.W. , Fire, A.Z. , Pourmand, N. ( 2007b ) Connector inversion probe technology: A powerful one-primer multiplex DNA amplification system...
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Methods: Multiplex padlock targeted sequencing reveals human hypermutable CpG variations
- Jin Billy Li,
- Yuan Gao,
- John Aach,
- Kun Zhang,
- Gregory V. Kryukov,
- Bin Xie,
- Annika Ahlford,
- Jung-Ki Yoon,
- Abraham M. Rosenbaum,
- Alexander Wait Zaranek,
- Emily LeProust,
- Shamil R. Sunyaev,
- and George M. Church
Genome Res. September 2009 19: 1606-1615; Published in Advance June 12, 2009, doi:10.1101/gr.092213.109
...range, respectively. Alleles at &gt;400,000 target base positions were determined across six subjects and examined for single nucleotide polymorphisms (SNPs), and the concordance with independently obtained genotypes was 98.4%–100%. We detected &gt;500 SNPs not currently in dbSNP, 362 of which were...
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Methods: Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing
- Daniel Summerer,
- Haiguo Wu,
- Bettina Haase,
- Yang Cheng,
- Nadine Schracke,
- Cord F. Stähler,
- Mark S. Chee,
- Peer F. Stähler,
- and Markus Beier
Genome Res. September 2009 19: 1616-1621; Published in Advance July 28, 2009, doi:10.1101/gr.091942.109
...-based sequence capture relying on hybridization. Two studies using solution-phase sequence capture with padlock or molecular inversion probes have been published that targeted large numbers of small genomic regions in a single reaction. Although the multiplexing level of one of these methods was high, low...
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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
...DNA strand of the complex to form a stable “double D-loop.” These joint molecules resist dissociation when both oligonucleotides are completely complementary to the target duplex; however, if the probes are mismatched, the complex is inherently instable and rapidly dissociates. SNPs are identified...
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Research: The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance
- Santosh S. Atanur,
- İnanç Birol,
- Victor Guryev,
- Martin Hirst,
- Oliver Hummel,
- Catherine Morrissey,
- Jacques Behmoaras,
- Xose M. Fernandez-Suarez,
- Michelle D. Johnson,
- William M. McLaren,
- Giannino Patone,
- Enrico Petretto,
- Charles Plessy,
- Kathleen S. Rockland,
- Charles Rockland,
- Kathrin Saar,
- Yongjun Zhao,
- Piero Carninci,
- Paul Flicek,
- Ted Kurtz,
- Edwin Cuppen,
- Michal Pravenec,
- Norbert Hubner,
- Steven J.M. Jones,
- Ewan Birney,
- and Timothy J. Aitman
Genome Res. June 2010 20: 791-803; Published in Advance April 29, 2010, doi:10.1101/gr.103499.109
...different genomic regions by conventional capillary sequencing (C Morrissey, M Johnson, and T Aitman, unpubl.), and, second, against a set of 20,283 SNPs genotyped in multiple rat strains by the STAR consortium using Affymetrix or Illumina SNP genotyping microarrays (The STAR Consortium 2008). Of 108 SNPs...
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Methods: Efficient target-selected mutagenesis in Caenorhabditis elegans: Toward a knockout for every gene
- Edwin Cuppen,
- Eelke Gort,
- Esther Hazendonk,
- Josine Mudde,
- José van de Belt,
- Isaäc J. Nijman,
- Victor Guryev,
- and Ronald H.A. Plasterk
Genome Res. May 2007 17: 649-658; Published in Advance April 6, 2007, doi:10.1101/gr.6080607
.... , Erbilgin, A. , et al. ( 2005 ) Highly multiplexed molecular inversion probe genotyping: Over 10,000 targeted SNPs genotyped in a single tube assay . Genome Res. 15 : 269 – 275 . ↵ Jansen, G. , Hazendonk, E. , Thijssen, K.L. , Plasterk, R.H. ( 1997 ) Reverse genetics by chemical mutagenesis...
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Method: Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing
- Jamie K. Teer,
- Lori L. Bonnycastle,
- Peter S. Chines,
- Nancy F. Hansen,
- Natsuyo Aoyama,
- Amy J. Swift,
- Hatice Ozel Abaan,
- Thomas J. Albert,
- NISC Comparative Sequencing Program,
- Elliott H. Margulies,
- Eric D. Green,
- Francis S. Collins,
- James C. Mullikin,
- and Leslie G. Biesecker
Genome Res. October 2010 20: 1420-1431; Published in Advance September 1, 2010, doi:10.1101/gr.106716.110
...have greatly increased our ability to generate large amounts of sequencing data at a rapid pace. Several methods have been developed to enrich for genomic regions of interest for targeted sequencing. We have compared three of these methods: Molecular Inversion Probes (MIP), Solution Hybrid Selection...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...the Drosophila Genome Nexus (DGN) (Lack et al. 2015). We employed this sample population because it is derived from haploid embryos, thereby mitigating issues related to genotyping. Moreover, the Zambian strains show high levels of interstrain variation. Ignoring the stocks with the In(2L)t inversion, 147 of 197...
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