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Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
- Li-Ting Chen,
- Myrthe Jager,
- Dàmi Rebergen,
- Geertruid J. Brink,
- Tom van den Ende,
- Willem Vanderlinden,
- Pauline Kolbeck,
- Marc Pagès-Gallego,
- Ymke van der Pol,
- Nicolle Besselink,
- Norbert Moldovan,
- Nizar Hami,
- Wigard P. Kloosterman,
- Hanneke van Laarhoven,
- Florent Mouliere,
- Ronald Zweemer,
- Jan Lipfert,
- Sarah Derks,
- Alessio Marcozzi,
- and Jeroen de Ridder
Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
...) can be determined through digital droplet polymerase chain reaction (ddPCR) or targeted sequencing (panels) (Diaz and Bardelli 2014; Wan et al. 2017; Corcoran and Chabner 2018; Lustberg et al. 2018; Bronkhorst et al. 2019a; Husain et al. 2022). However, tumor detection from small sample volumes (∼10 m...
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Method: MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals
- Keisha D. Carlson,
- Peter H. Sudmant,
- Maximilian O. Press,
- Evan E. Eichler,
- Jay Shendure,
- and Christine Queitsch
Genome Res. May 2015 25: 750-761; Published in Advance February 6, 2015, doi:10.1101/gr.182212.114
...amplification (i.e., amplification stutter). Although traditional Sanger sequencing accurately assesses STR genotypes, this costly method is severely limited in throughput. Hence, it is not well suited for genotyping STRs across many individuals. Nevertheless, when researchers compared the three Sanger...
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Methods: High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping
- Daniel A. Peiffer,
- Jennie M. Le,
- Frank J. Steemers,
- Weihua Chang,
- Tony Jenniges,
- Francisco Garcia,
- Kirt Haden,
- Jiangzhen Li,
- Chad A. Shaw,
- John Belmont,
- Sau Wai Cheung,
- Richard M. Shen,
- David L. Barker,
- and Kevin L. Gunderson
Genome Res. September 2006 16: 1136-1148; Published in Advance August 9, 2006, doi:10.1101/gr.5402306
...of aberrations using HL-60 on the 109K BeadChip. The human promyelocytic leukemia cell line (HL-60) contains several well-characterized chromosomal aberrations. ( A ) An example of several discrete monoallelic amplifications across an ∼4.5-Mb region on chromosome 8 (green bar). The monoallelic amplification...
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METHODS: Whole Genome Analysis of Genetic Alterations in Small DNA Samples Using Hyperbranched Strand Displacement Amplification and Array–CGH
- José M. Lage,
- John H. Leamon,
- Tanja Pejovic,
- Stefan Hamann,
- Michelle Lacey,
- Deborah Dillon,
- Richard Segraves,
- Bettina Vossbrinck,
- Antonio González,
- Daniel Pinkel,
- Donna G. Albertson,
- Jose Costa,
- and Paul M. Lizardi
Genome Res. February 1, 2003 13: 294-307; doi:10.1101/gr.377203
...found evidence of moderate distortion of the ratios, but fewer instances of markedly over-represented or under-represented clusters of loci (Fig. 3 , panel in lower left). We then performed an experiment in which the amplification reaction with φ29 DNA polymerase was limited to 2 h, to generate ∼250...
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Methods: Parallel Genotyping of Over 10,000 SNPs Using a One-Primer Assay on a High-Density Oligonucleotide Array
- Hajime Matsuzaki,
- Halina Loi,
- Shoulian Dong,
- Ya-Yu Tsai,
- Joy Fang,
- Jane Law,
- Xiaojun Di,
- Wei-Min Liu,
- Geoffrey Yang,
- Guoying Liu,
- Jing Huang,
- Giulia C. Kennedy,
- Thomas B. Ryder,
- Gregory A. Marcus,
- P. Sean Walsh,
- Mark D. Shriver,
- Jennifer M. Puck,
- Keith W. Jones,
- and Rui Mei
Genome Res. March 2004 14: 414-425; doi:10.1101/gr.2014904
...). As a demonstration of the utility of the genotyping platform in whole-genome scans, we have replicated and refined a linkage region on chromosome 2p for chronic mucocutaneous candidiasis and thyroid disease, previously identified using a panel of microsatellite (STR) markers. Footnotes [Supplemental...
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RESOURCE: Chromosome-Specific Single-Locus FISH Probes Allow Anchorage of an 1800-Marker Integrated Radiation-Hybrid/Linkage Map of the Domestic Dog Genome to All Chromosomes
- Matthew Breen,
- Sophie Jouquand,
- Corinne Renier,
- Cathryn S. Mellersh,
- Christophe Hitte,
- Nigel G. Holmes,
- Angélique Chéron,
- Nicola Suter,
- Françoise Vignaux,
- Anna E. Bristow,
- Catherine Priat,
- E. McCann,
- Catherine André,
- Sam Boundy,
- Paul Gitsham,
- Rachael Thomas,
- Wendy L. Bridge,
- Helen F. Spriggs,
- Ed J. Ryder,
- Alistair Curson,
- Jeff Sampson,
- Elaine A. Ostrander,
- Matthew M. Binns,
- and Francis Galibert
Genome Res. October 1, 2001 11: 1784-1795; doi:10.1101/gr.189401
..., has been constructed using the RHDF5000-2 whole-genome radiation hybrid panel. Meiotic linkage analysis was performed, with at least one microsatellite marker from each dog autosome on a panel of reference families, allowing one meiotic linkage group to be anchored to all 38 dog autosomes. We present...
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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
...and epigenetics using short- and long-read sequencing. (A) Performance comparison of structural variant detection across sequencing technologies, evaluated against the GIAB Tier1 V0.6 benchmark (Kolmogorov et al. 2023). (B) Reinterpretation of a germline recurrent event using long-read sequencing. (Upper panel...
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Method: Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases
- Prashant S. Emani,
- Maya N. Geradi,
- Gamze Gürsoy,
- Monica R. Grasty,
- Andrew Miranker,
- and Mark B. Gerstein
Genome Res. December 2023 33: 2156-2173; Published in Advance December 14, 2023, doi:10.1101/gr.278322.123
...rare ones) to identify individuals has been repeatedly shown, the availability of small sets of noisy genotypes, from environmental DNA samples or functional genomics data, motivated us to quantify their informativeness. We present a computational tool suite, termed Privacy Leakage by Inference across...
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Research: Genetic analysis of complex traits in the emerging Collaborative Cross
- David L. Aylor,
- William Valdar,
- Wendy Foulds-Mathes,
- Ryan J. Buus,
- Ricardo A. Verdugo,
- Ralph S. Baric,
- Martin T. Ferris,
- Jeff A. Frelinger,
- Mark Heise,
- Matt B. Frieman,
- Lisa E. Gralinski,
- Timothy A. Bell,
- John D. Didion,
- Kunjie Hua,
- Derrick L. Nehrenberg,
- Christine L. Powell,
- Jill Steigerwalt,
- Yuying Xie,
- Samir N.P. Kelada,
- Francis S. Collins,
- Ivana V. Yang,
- David A. Schwartz,
- Lisa A. Branstetter,
- Elissa J. Chesler,
- Darla R. Miller,
- Jason Spence,
- Eric Yi Liu,
- Leonard McMillan,
- Abhishek Sarkar,
- Jeremy Wang,
- Wei Wang,
- Qi Zhang,
- Karl W. Broman,
- Ron Korstanje,
- Caroline Durrant,
- Richard Mott,
- Fuad A. Iraqi,
- Daniel Pomp,
- David Threadgill,
- Fernando Pardo-Manuel de Villena,
- and Gary A. Churchill
Genome Res. August 2011 21: 1213-1222; Published in Advance March 15, 2011, doi:10.1101/gr.111310.110
...across a range of perturbations, and have the added benefit of known population structures (Churchill 2007). However, existing RIL panels have limitations such as large regions 13These authors have contributed equally to this work. 14Corresponding authors. E-mail dpomp@unc.edu. E-mail threadgill...
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Methods: Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays
- Georg Zeller,
- Richard M. Clark,
- Korbinian Schneeberger,
- Anja Bohlen,
- Detlef Weigel,
- and Gunnar Rätsch
Genome Res. June 2008 18: 918-929; Published in Advance March 6, 2008, doi:10.1101/gr.070169.107
...) The corresponding polymorphic region (PR) label sequence for Bor-4 and resulting PR predictions (color coding is as shown at bottom ). Light gray shading that extends across panels C and D corresponds to PR labels (red). Plotted data are from Nordborg et al. (2005) and Clark et al. (2007) . Despite the obvious...
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