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Resource: High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
- Jonas A. Gustafson,
- Sophia B. Gibson,
- Nikhita Damaraju,
- Miranda P.G. Zalusky,
- Kendra Hoekzema,
- David Twesigomwe,
- Lei Yang,
- Anthony A. Snead,
- Phillip A. Richmond,
- Wouter De Coster,
- Nathan D. Olson,
- Andrea Guarracino,
- Qiuhui Li,
- Angela L. Miller,
- Joy Goffena,
- Zachary B. Anderson,
- Sophie H.R. Storz,
- Sydney A. Ward,
- Maisha Sinha,
- Claudia Gonzaga-Jauregui,
- Wayne E. Clarke,
- Anna O. Basile,
- André Corvelo,
- Catherine Reeves,
- Adrienne Helland,
- Rajeeva Lochan Musunuri,
- Mahler Revsine,
- Karynne E. Patterson,
- Cate R. Paschal,
- Christina Zakarian,
- Sara Goodwin,
- Tanner D. Jensen,
- Esther Robb,
- The 1000 Genomes ONT Sequencing Consortium,
- University of Washington Center for Rare Disease Research (UW-CRDR),
- Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium,
- William Richard McCombie,
- Fritz J. Sedlazeck,
- Justin M. Zook,
- Stephen B. Montgomery,
- Erik Garrison,
- Mikhail Kolmogorov,
- Michael C. Schatz,
- Richard N. McLaughlin, Jr.,
- Harriet Dashnow,
- Michael C. Zody,
- Matt Loose,
- Miten Jain,
- Evan E. Eichler,
- and Danny E. Miller
Genome Res. November 2024 34: 2061-2073; Published in Advance October 2, 2024, doi:10.1101/gr.279273.124
.... 2021; Kolmogorov et al. 2023), paving the way for its adoption into clinical settings (Wojcik et al. 2023; Damaraju et al. 2024).Building on the landmark effort of the 1KGP, the 1000 Genomes Project ONT Sequencing Consortium (1KGP-ONT) is leveraging ONT LRS with the goal of generating high-coverage...
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Method: Estimating the size of long tandem repeat expansions from short reads with ScatTR
- Rashid Al-Abri and
- Gamze Gürsoy
Genome Res. December 2025 35: 2701-2713; Published in Advance August 21, 2025, doi:10.1101/gr.280563.125
...the state-of-art with simulated data. We estimated the TR copy number using state-of-the-art methods (ExpansionHunter, GangSTR, and STRling), ScatTR, and a closed-form solution and calculated the root mean square error (RMSE) between the predicted and the true copy number of TRs on simulated data. (A) RMSE...
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Research: Genotype imputation from low-coverage data for medical and population genetic analyses
- Simone Andrea Biagini,
- Sara Becelaere,
- Mio Aerden,
- Tatjana Jatsenko,
- Laurens Hannes,
- Philip Van Damme,
- Jeroen Breckpot,
- Koenraad Devriendt,
- Bernard Thienpont,
- Joris Robert Vermeesch,
- Isabelle Cleynen,
- and Toomas Kivisild
Genome Res. September 2025 35: 1929-1941; Published in Advance July 22, 2025, doi:10.1101/gr.280175.124
...to the genotype called from the high coverage data. This motivated us to carry out systematic revisions of conflicts between the GT and GP values, which could be characteristic only for ultralow coverage data, and to focus our search for optimal solutions in the GDI design on the combination of INFO score, GP...
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Resource: Analysis of 100 high-coverage genomes from a pedigreed captive baboon colony
- Jacqueline A. Robinson,
- Saurabh Belsare,
- Shifra Birnbaum,
- Deborah E. Newman,
- Jeannie Chan,
- Jeremy P. Glenn,
- Betsy Ferguson,
- Laura A. Cox,
- and Jeffrey D. Wall
Genome Res. May 2019 29: 848-856; Published in Advance March 29, 2019, doi:10.1101/gr.247122.118
...and phenotypic effects of both inbreeding and admixture in the wild and in captivity.MethodsSequencing and genotype callingWe extracted DNA from archived buffy coats or liver samples from 100 individuals from the SNPRC colony for high-coverage (>20×) whole- sequencing. These individuals included 33 founders...
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Method: HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies
- Xian Fan,
- Mark Chaisson,
- Luay Nakhleh,
- and Ken Chen
Genome Res. May 2017 27: 793-800; Published in Advance January 19, 2017, doi:10.1101/gr.214767.116
...cancer. Nature 500: 415–421. AlkanC, Coe B, Eichler E. 2011a. Genome structural variation discovery and genotyping. Nat Rev Genet 12: 363–376. Alkan C, Sajjadian S, Eichler EE. 2011b. Limitations of next-generation sequence assembly. Nat Methods 8: 61–65. Au KF, Underwood JG, Lee L, WongWH. 2012...
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Method: Calling amplified haplotypes in next generation tumor sequence data
- Ninad Dewal,
- Yang Hu,
- Matthew L. Freedman,
- Thomas LaFramboise,
- and Itsik Pe'er
Genome Res. February 2012 22: 362-374; Published in Advance November 16, 2011, doi:10.1101/gr.122564.111
...genotype, copy number, and allele-specific read count information beforehand. For any amplicon a with Ca ≥ 3, the amplified alleles that the naive method calls within a are treated as the gold standard for a, as simulation results in Figure 1B reveal the naive method's good performance at high coverage...
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Method: Association studies for next-generation sequencing
- Li Luo,
- Eric Boerwinkle,
- and Momiao Xiong
Genome Res. July 2011 21: 1099-1108; Published in Advance April 26, 2011, doi:10.1101/gr.115998.110
...and their association with common marker alleles. Next-generation sequencing technologies have the potential to discover the entire spectrumof sequence variations in a sample of well-phenotyped individuals. Despite their promise, next-generation sequencing platforms also present challenges. First, the error rate...
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Methods: Rapid whole-genome mutational profiling using next-generation sequencing technologies
- Douglas R. Smith,
- Aaron R. Quinlan,
- Heather E. Peckham,
- Kathryn Makowsky,
- Wei Tao,
- Betty Woolf,
- Lei Shen,
- William F. Donahue,
- Nadeem Tusneem,
- Michael P. Stromberg,
- Donald A. Stewart,
- Lu Zhang,
- Swati S. Ranade,
- Jason B. Warner,
- Clarence C. Lee,
- Brittney E. Coleman,
- Zheng Zhang,
- Stephen F. McLaughlin,
- Joel A. Malek,
- Jon M. Sorenson,
- Alan P. Blanchard,
- Jarrod Chapman,
- David Hillman,
- Feng Chen,
- Daniel S. Rokhsar,
- Kevin J. McKernan,
- Thomas W. Jeffries,
- Gabor T. Marth,
- and Paul M. Richardson
Genome Res. October 2008 18: 1638-1642; Published in Advance September 4, 2008, doi:10.1101/gr.077776.108
...in this improved strain’s entire relative to the reference strain. We generated high-coverage, whole- data sets using single fragment end reads from three next-generation sequencing platforms: 454 Life Sciences (Roche) (∼225-bp reads), Illumina (formerly Solexa sequencing) (32-bp reads), and Applied Biosystems...
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Method: Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation
- Filipe G. Vieira,
- Matteo Fumagalli,
- Anders Albrechtsen,
- and Rasmus Nielsen
Genome Res. November 2013 23: 1852-1861; Published in Advance August 15, 2013, doi:10.1101/gr.157388.113
...priors (random mating and estimated inbreeding coefficients) over two different methods (the probabilistic method by Nielsen et al. 2012 and using calling genotypes). Figure 5 shows that even for high coverage data (;103) (O. s. indica and O. s. japonica in Fig. 5), methods assuming HWE have an excess...
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Resource: A SNP discovery method to assess variant allele probability from next-generation resequencing data
- Yufeng Shen,
- Zhengzheng Wan,
- Cristian Coarfa,
- Rafal Drabek,
- Lei Chen,
- Elizabeth A. Ostrowski,
- Yue Liu,
- George M. Weinstock,
- David A. Wheeler,
- Richard A. Gibbs,
- and Fuli Yu
Genome Res. February 2010 20: 273-280; Published in Advance December 17, 2009, doi:10.1101/gr.096388.109
.... In each set of prior parameters, in bins with fewer than three variant reads at a given locus (i.e., extremely low coverage), the prior SNP probability was set to bemuch smaller than prior error probability; in contrast, in bins with three variant reads or more (i.e., high coverage), the prior SNP...
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