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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
...highly specific extension, ligation, and amplification steps. The whole procedure takes place in a single tube and can be finished within 3 d. In HD-Marker, only two probes are needed to genotype a locus, in contrast to the three probes used in the Illumina BeadArray-based GoldenGate assay (Fan et al...
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Methods: Highly multiplexed molecular inversion probe genotyping: Over 10,000 targeted SNPs genotyped in a single tube assay
- Paul Hardenbol,
- Fuli Yu,
- John Belmont,
- Jennifer MacKenzie,
- Carsten Bruckner,
- Tiffany Brundage,
- Andrew Boudreau,
- Steve Chow,
- Jim Eberle,
- Ayca Erbilgin,
- Mat Falkowski,
- Ron Fitzgerald,
- Sy Ghose,
- Oleg Iartchouk,
- Maneesh Jain,
- George Karlin-Neumann,
- Xiuhua Lu,
- Xin Miao,
- Bridget Moore,
- Martin Moorhead,
- Eugeni Namsaraev,
- Shiran Pasternak,
- Eunice Prakash,
- Karen Tran,
- Zhiyong Wang,
- Hywel B. Jones,
- Ronald W. Davis,
- Thomas D. Willis,
- and Richard A. Gibbs
Genome Res. February 2005 15: 269-275; doi:10.1101/gr.3185605
...Highly multiplexed molecular inversion probe genotyping: Over 10,000 targeted SNPs genotyped in a single tube assay Paul Hardenbol 1 , Fuli Yu 2 , John Belmont 2 , Jennifer MacKenzie 1 , Carsten Bruckner 1 , Tiffany Brundage 1...
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LETTER: Parallel Genotyping of Human SNPs Using Generic High-density Oligonucleotide Tag Arrays
- Jian-Bing Fan,
- Xiaoqiong Chen,
- Marc K. Halushka,
- Anthony Berno,
- Xiaohua Huang,
- Thomas Ryder,
- Robert J. Lipshutz,
- David J. Lockhart,
- and Aravinda Chakravarti
Genome Res. June 1, 2000 10: 853-860; doi:10.1101/gr.10.6.853
...extension (SBE) reactions on standardized, generic high-density oligonucleotide probe arrays ( Chee et al. 1996 ; Shoemaker et al. 1996 ; Wang et al. 1998 ; Lipshutz et al. 1999 ). In TAG–SBE, the array is independent of the specific markers genotyped and the assay can be customized for sets of markers...
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METHODS: High-Throughput Genotyping with Single Nucleotide Polymorphisms
- Koustubh Ranade,
- Mau-Song Chang,
- Chih-Tai Ting,
- Dee Pei,
- Chin-Fu Hsiao,
- Michael Olivier,
- Robert Pesich,
- Joan Hebert,
- Yii-Der I. Chen,
- Victor J. Dzau,
- David Curb,
- Richard Olshen,
- Neil Risch,
- David R. Cox,
- and David Botstein
Genome Res. July 1, 2001 11: 1262-1268; Published in Advance June 12, 2001, doi:10.1101/gr.157801
...probes, each labeled with a different fluor, allows one to detect both alleles in a single tube. Moreover, because probes are included in the PCR, genotypes are determined without any post-PCR processing, a feature that is unavailable with most other genotyping methods (for a recent review, see Landegren...
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METHODS: SNP Genotyping by Multiplexed Solid-Phase Amplification and Fluorescent Minisequencing
- Michael H. Shapero,
- Kerstin K. Leuther,
- Anhthu Nguyen,
- Melissa Scott,
- and Keith W. Jones
Genome Res. November 1, 2001 11: 1926-1934; Published in Advance October 15, 2001, doi:10.1101/gr.205001
...effectively limits the extent to which these varied platforms can be modified for highly multiplexed genotyping. The ability to convert hundreds of PCR primer-pairs into a single-tube, multiplexed reaction producing specific, robust products from a complex genomic DNA template would greatly reduce...
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METHODS: Flexible Use of High-Density Oligonucleotide Arrays for Single-Nucleotide Polymorphism Discovery and Validation
- Shoulian Dong,
- Eugene Wang,
- Linda Hsie,
- Yanxiang Cao,
- Xiaogiong Chen,
- and Thomas R. Gingeras
Genome Res. August 1, 2001 11: 1418-1424; Published in Advance July 12, 2001, doi:10.1101/gr.171101
...single-tube sample preparation. Large-Scale Hybridization-Based SNP Validation An alternative sample preparation has been employed to validate the SNPs discovered with the same chip design. Specific DNA fragment targets were selectively enriched from the total pool by use of oligonucleotides bound...
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METHODS: High-Throughput SNP Genotyping by Allele-Specific PCR with Universal Energy-Transfer-Labeled Primers
- Maxim V. Myakishev,
- Yuri Khripin,
- Stella Hu,
- and Dean H. Hamer
Genome Res. January 1, 2001 11: 163-169; doi:10.1101/gr.157901
..., ligase-mediated DNA diagnostic test. Genome Res. 8 : 549 – 556 . ↵ Chen X. , Levine L. , Kwok P.Y. ( 1999 ) Fluorescence polarization in homogeneous nucleic acid analysis. Genome Res. 9 : 492 – 498 . ↵ Germer S. , Higuchi R. ( 1999 ) Single-tube genotyping without oligonucleotide probes. Genome Res. 9...
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Methods: A genotyping system capable of simultaneously analyzing >1000 single nucleotide polymorphisms in a haploid genome
- Hui-Yun Wang,
- Minjie Luo,
- Irina V. Tereshchenko,
- Danielle M. Frikker,
- Xiangfeng Cui,
- James Y. Li,
- Guohong Hu,
- Yi Chu,
- Marco A. Azaro,
- Yong Lin,
- Li Shen,
- Qifeng Yang,
- Manousos E. Kambouris,
- Richeng Gao,
- Weichung Shih,
- and Honghua Li
Genome Res. February 2005 15: 276-283; doi:10.1101/gr.2885205
...of individually amplified PCR products from multiple tubes, followed by column purification. Requirements of specialized probes and detection platforms and long oligonucleotides also limit the flexibility and cost-effectiveness of these systems. In this communication, we describe a simple genotyping system...
REVIEW: An approach to high-throughput genotyping.
- J M Hall,
- C A LeDuc,
- A R Watson,
- and A H Roter
Genome Res. September 1996 6: 781-790; doi:10.1101/gr.6.9.781
....S. and Hartley. J.L. 1990 . Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions. Gene 93 : 125 – 128 . McIndoe, R.A., , Linhardt, M.S. , Hood. L. McIndoe, R.A., Linhardt, M.S. and Hood. L. 1995 . Single-tube genomic DNA isolation from whole blood without pre...
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ARTICLE: A one-step coupled amplification and oligonucleotide ligation procedure for multiplex genetic typing.
- F A Eggerding
Genome Res. June 1995 4: 337-345
...C) in a two-step PCR cycle that employs a 94 degrees C denaturation step and a 72 degrees C anneal-elongation step. In stage II, genotyping of PCR products by competitive oligonucleotide ligation with oligonucleotide probes (Tm values between 51 degrees C and 67 degrees C) located between the PCR...

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