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Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
- W.H. Adrian Tsui,
- Spencer C. Ding,
- Peiyong Jiang,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
...technology in the methylation analysis of long cfDNA (>500 bp), which generally carries more CpG and SNPs than short fragments, and so intrinsically phases these informative loci to augment the power of disease detection (Yu et al. 2021, 2023a). Notably, Choy and colleagues (2022) use the HK model...
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Method: Accurate sequencing of DNA motifs able to form alternative (non-B) structures
- Matthias H. Weissensteiner,
- Marzia A. Cremona,
- Wilfried M. Guiblet,
- Nicholas Stoler,
- Robert S. Harris,
- Monika Cechova,
- Kristin A. Eckert,
- Francesca Chiaromonte,
- Yi-Fei Huang,
- and Kateryna D. Makova
Genome Res. July 11, 2023 ; Published in Advance July 11, 2023, doi:10.1101/gr.277490.122
...kinetics and affect sequencing errors of Pacific Biosciences (PacBio) sequencing (Guiblet et al. 2018). Two major high-throughput sequencing technologies— Illumina and PacBio—are based on synthesis with DNA polymerases. In Illumina sequencing, the Pyrococcus-derived Phusionpolymerase (Quail et al. 2012...
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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
...-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nature Genet. 22 : 239 – 247 . ↵ Germer S. , Holland M.J. , Higuchi R. ( 2000 ) High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR. Genome Res. 10 : 258 – 266 . ↵ Landegren U. , Nilsson M. , Kwok P.Y. ( 1998...
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METHODS: DNA Analysis by Fluorescence Quenching Detection
- Ming Xiao and
- Pui-Yan Kwok
Genome Res. May 1, 2003 13: 932-939; doi:10.1101/gr.987803
..., , 468–470. . ↵ Chen X. , Levine L. , Kwok P.Y. ( 1999 ) Fluorescence polarization in homogeneous nucleic acid analysis. Genome Res. 9 : 492 – 498 . ↵ Germer S. , Holland M.J. , Higuchi R. ( 2000 ) High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR. Genome Res. 10...
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REVIEW: Pyrosequencing Sheds Light on DNA Sequencing
- Mostafa Ronaghi
Genome Res. January 1, 2001 11: 3-11; doi:10.1101/gr.150601
...throughput DNA sequencing. Software for Pyrogram Analysis Specialized software for SNP analysis of pyrograms obtained from liquid-phase pyrosequencing has been developed ( http://www.pyrosequencing.com ). This software enables analyses of selected wells in a microtiter plate and automatically performs...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...methylated or unmethylated molecules based on size fractionation (Weber et al. 2005) followed by either quantitative polymerase chain reaction (qPCR), microarrays or sequencing. In contrast, bisulfite treatment of DNA, as developed by Frommer et al. (1992) and later optimized by Clark et al. (1994), enabled...
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METHODS: Polymorphism Ratio Sequencing: A New Approach for Single Nucleotide Polymorphism Discovery and Genotyping
- Robert G. Blazej,
- Brian M. Paegel,
- and Richard A. Mathies
Genome Res. February 1, 2003 13: 287-293; doi:10.1101/gr.396203
...of mitochondrial DNA mutations in tumors and bodily fluids. Science 287 : 2017 – 2019 . ↵ Germer S. , Holland M.J. , Higuchi R. ( 2000 ) High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR. Genome Res. 10 : 258 – 266 . ↵ Giddings M.C. , Severin J. , Westphall M. , Wu J...
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LETTER: Analysis of allelic differential expression in human white blood cells
- P.V. Krishna Pant,
- Heng Tao,
- Erica J. Beilharz,
- Dennis G. Ballinger,
- David R. Cox,
- and Kelly A. Frazer
Genome Res. March 2006 16: 331-339; Published in Advance February 8, 2006, doi:10.1101/gr.4559106
.... Molecular origins of rapid and continuous morphological evolution. Proc. Natl. Acad. Sci. 101 : 18058 –18063. ↵ Germer, S., Holland, M.J., and Higuchi, R. 2000 . High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR. Genome Res. 10 : 258 –266. ↵ Hinds, D.A., Seymour, A...
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Research: Identifying genomic changes associated with insecticide resistance in the dengue mosquito Aedes aegypti by deep targeted sequencing
- Frederic Faucon,
- Isabelle Dusfour,
- Thierry Gaude,
- Vincent Navratil,
- Frederic Boyer,
- Fabrice Chandre,
- Patcharawan Sirisopa,
- Kanutcharee Thanispong,
- Waraporn Juntarajumnong,
- Rodolphe Poupardin,
- Theeraphap Chareonviriyaphap,
- Romain Girod,
- Vincent Corbel,
- Stephane Reynaud,
- and Jean-Philippe David
Genome Res. September 2015 25: 1347-1359; Published in Advance July 23, 2015, doi:10.1101/gr.189225.115
...L of each primer (10 mM), and 7.5 µL of SYBR Green Supermix 2× (Bio-Rad). A dilution scale made from a pool of all gDNA samples was used for assessing PCR efficiency and quantification. All samples were amplified in triplicates (14 populations × 12 individuals × 3 replicates). After normalization, CNVs were...
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METHODS: Y-Chromosomal SNPs in Finno–Ugric-Speaking Populations Analyzed by Minisequencing on Microarrays
- Mirja Raitio,
- Katarina Lindroos,
- Minna Laukkanen,
- Tomi Pastinen,
- Pertti Sistonen,
- Antti Sajantila,
- and Ann-Christine Syvänen
Genome Res. March 1, 2001 11: 471-482; doi:10.1101/gr.156301
...were immobilized covalently on glass microscope slides as 5 × 5 arrays (Fig. 2 ). The genotyping procedure involves (1) multiplex PCR amplification of the Y-chromosomal DNA regions spanning the SNPs; (2) extension of the immobilized primers with labeled ddNTPs using a DNA polymerase with the multiplex...

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