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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...(Coster et al. 2021). The choice of either analysis approach often impacts the experimental design itself (Harvey et al. 2023). Other factors influencing this decision include computational resources, DNA quality and quantity, sequencing depth, and the ability of assembly-based approaches to improve...
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Method: Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs
- Nadin Rohland,
- Swapan Mallick,
- Matthew Mah,
- Robert Maier,
- Nick Patterson,
- and David Reich
Genome Res. November/December 2022 32: 2068-2078; Published in Advance December 14, 2022, doi:10.1101/gr.276728.122
...For the Daicel Arbor “myBaits Expert Human Affinities” reagent, the oligonucleotide bait design is proprietary, and we do not have access to the technical details. Several modules are available (https://arborbiosci.com/genomics...
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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
...with high-density DNA oligonucleotide arrays, offers an optimal solution by providing both SNP genotype information as well as CNV profiling in a single experiment. Methods Experiments 500K EA Arrays and the Whole-Genome Sampling Assay (WGSA) The 500K EA arrays contain 534,500 SNPs on two enzyme...
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LETTER: Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray
- Housheng He,
- Jie Wang,
- Tao Liu,
- X. Shirley Liu,
- Tiantian Li,
- Yunfei Wang,
- Zuwei Qian,
- Haixia Zheng,
- Xiaopeng Zhu,
- Tao Wu,
- Baochen Shi,
- Wei Deng,
- Wei Zhou,
- Geir Skogerbø,
- and Runsheng Chen
Genome Res. October 2007 17: 1471-1477; Published in Advance September 4, 2007, doi:10.1101/gr.6611807
...al. ( 2004 ) Global identification of human transcribed sequences with tiling arrays . Science 306 : 2242 – 2246 . ↵ Bertone, P. , Trifonov, V. , Rozowsky, J.S. , Schubert, F. , Emanuelsson, O. , Karro, J. , Kao, M.-Y. , Snyder, M. , Gerstein, M. ( 2006 ) Design optimization methods for genomic DNA...
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Research: DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity
- Steven R. Eichten,
- Tim Stuart,
- Akanksha Srivastava,
- Ryan Lister,
- and Justin O. Borevitz
Genome Res. November 2016 26: 1520-1531; Published in Advance September 9, 2016, doi:10.1101/gr.205468.116
...respective methylation context (Fig. 1A). The Figure 1. Genomic profiles of DNA methylation of Brachypodium distachyon. (A) Total number of 100-bp genomic tiles (dark gray) are compared to the number of genomic tiles with sequence coverage for all threemethylation sequence contexts. Coverage bar is split...
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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
.... Molecular Inversion Probes (MIPs) In the process of implementing an MIP-based genomic enrichmentmethod,we found that our sequence data included the probe arm sequences that were designed to hybridize to DNA flanking the region of interest (ROI) (data not shown). This occurred when probes were required...
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Methods: Comprehensive high-throughput arrays for relative methylation (CHARM)
- Rafael A. Irizarry,
- Christine Ladd-Acosta,
- Benilton Carvalho,
- Hao Wu,
- Sheri A. Brandenburg,
- Jeffrey A. Jeddeloh,
- Bo Wen,
- and Andrew P. Feinberg
Genome Res. May 2008 18: 780-790; Published in Advance March 3, 2008, doi:10.1101/gr.7301508
...relatively modest: to directly compare methods using the same DNA samples and the same arrays. However, we found significant limitations generally to hybridization-based methylation analysis that could largely be overcome with novel statistical procedures and array design algorithms. As will be described...
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Methods: Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
- Olof Emanuelsson,
- Ugrappa Nagalakshmi,
- Deyou Zheng,
- Joel S. Rozowsky,
- Alexander E. Urban,
- Jiang Du,
- Zheng Lian,
- Viktor Stolc,
- Sherman Weissman,
- Michael Snyder,
- and Mark B. Gerstein
Genome Res. June 2007 17: 886-897; Published in Advance November 21, 2006, doi:10.1101/gr.5014606
...initiation points and can range from the smallest possible distance of one single base up to the length of the probe, or even further. At the design stage it is important to minimize potential cross-hybridization, self-pairing, and other probe sequence artifacts such as DNA secondary structure formation...
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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
...Genome-wide Detection of Allelic Imbalance Using Human SNPs and High-density DNA Arrays Rui Mei 1 , 7 , Patricia C. Galipeau 2 , Cynthia Prass 3 , Anthony Berno 1 , Ghassan Ghandour 4 , Nila Patil 1 , Roger K. Wolff 3...
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Methods: Automatic Identification of Subcellular Phenotypes on Human Cell Arrays
- Christian Conrad,
- Holger Erfle,
- Patrick Warnat,
- Nathalie Daigle,
- Thomas Lörch,
- Jan Ellenberg,
- Rainer Pepperkok,
- and Roland Eils
Genome Res. June 2004 14: 1130-1136; doi:10.1101/gr.2383804
...-tagged cDNAs were expressed in cells transfected on cell arrays (green). Image acquisition is designed in such a way that each image contains only one cell. From top left to bottom right : GFP-tagged NES→cytoplasm (96 images), EGFP→cyto-nuclear (170 images), GFP-tagged cDNA #488→mitochondria (108 images...

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