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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
...and genotyped, in parallel, on Illumina Infinium Global Screening Array-24 v3.0 for ∼700,000 SNPs. The array-based genotype calls were considered as truth.GDI applicationIn light of the success of the GDI filtering approach in minimizing the presence of low-quality variants across the largest possible subset...
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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...genotypes proximate SNVs, whose locations are extracted from a user-provided VCF catalog file from, for example, dbSNP (Sherry et al. 2001). For diploid alleles, depending on what SNV data are present, STRkit either uses a Gaussian mixture model (GMM) allele-calling approach with copy numbers, segregates...
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Method: CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes
- Marzia Rossato,
- Luca Marcolungo,
- Luca De Antoni,
- Giulia Lopatriello,
- Elisa Bellucci,
- Gaia Cortinovis,
- Giulia Frascarelli,
- Laura Nanni,
- Elena Bitocchi,
- Valerio Di Vittori,
- Leonardo Vincenzi,
- Filippo Lucchini,
- Kirstin E. Bett,
- Larissa Ramsay,
- David James Konkin,
- Massimo Delledonne,
- and Roberto Papa
Genome Res. May 2023 33: 787-797; Published in Advance May 1, 2023, doi:10.1101/gr.277628.122
..., Garrick D, Gao H, Wang L, Zhao F. 2022. Comparison of genotype imputation for SNP array and low-coverage whole- sequencing data. Front Genet 12: 704118. doi:10.3389/fgene.2021.704118 ↵Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C, Orchard R, et al. 2016...
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Method: Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and otter
- Niccoló Tesi,
- Alex Salazar,
- Yaran Zhang,
- Sven van der Lee,
- Marc Hulsman,
- Lydian Knoop,
- Sanduni Wijesekera,
- Jana Krizova,
- Anne-Fleur Schneider,
- Maartje Pennings,
- Kristel Sleegers,
- Erik-Jan Kamsteeg,
- Marcel Reinders,
- and Henne Holstege
Genome Res. November 2024 34: 1942-1953; Published in Advance October 15, 2024, doi:10.1101/gr.279351.124
...exclude that we have missed some expanded genotypes due to allele dropouts, the centenarians that we included were previously shown to be enriched with the protective alleles in the majority of SNPs associated with AD (Tesi et al. 2024).In summary, otter and TREAT are flexible and accurate bioinformatics...
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Research: Targeted and complete genomic sequencing of the major histocompatibility complex in haplotypic form of individual heterozygous samples
- Taishan Hu,
- Timothy L. Mosbruger,
- Nikolaos G. Tairis,
- Amalia Dinou,
- Pushkala Jayaraman,
- Mahdi Sarmady,
- Kingham Brewster,
- Yang Li,
- Tristan J. Hayeck,
- Jamie L. Duke,
- and Dimitri S. Monos
Genome Res. October 2024 34: 1500-1513; Published in Advance September 26, 2024, doi:10.1101/gr.278588.123
...-based SNPs, restricted to microarray sites, instead of relying on the known sequences. Regarding the trios, while two methods were initially considered, ultimately the haploid sequences of the probands used phase-estimated genotyping data of the proband alone to generate the scaffold for the assembly (i...
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Method: Detection of simple and complex de novo mutations with multiple reference sequences
- Kiran V. Garimella,
- Zamin Iqbal,
- Michael A. Krause,
- Susana Campino,
- Mihir Kekre,
- Eleanor Drury,
- Dominic Kwiatkowski,
- Juliana M. Sá,
- Thomas E. Wellems,
- and Gil McVean
Genome Res. August 2020 30: 1154-1169; Published in Advance August 19, 2020, doi:10.1101/gr.255505.119
...effect of each variant, we transferred existing 3D7 gene models and performed ab initio gene prediction on each parental via the Companion (Steinbiss et al. 2016) annotation server. We then concatenated gene models for each cross and annotated all variants with SnpEff (Cingolani et al. 2012). Taking...
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Resource: Low-coverage sequencing: Implications for design of complex trait association studies
- Yun Li,
- Carlo Sidore,
- Hyun Min Kang,
- Michael Boehnke,
- and Gonçalo R. Abecasis
Genome Res. June 2011 21: 940-951; Published in Advance April 1, 2011, doi:10.1101/gr.117259.110
...+JPT, and YRI for SNPs with MAF 1%–2%. Low-coverage versus high-coverage sequencing designs We have so far shown that low-coverage sequencing of many individuals can be used to detect polymorphic sites and infer genotypes when many individuals are sequenced, each at 23–63 depth. This capability has important...
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Research: Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
- William T. Harvey,
- Peter Ebert,
- Jana Ebler,
- Peter A. Audano,
- Katherine M. Munson,
- Kendra Hoekzema,
- David Porubsky,
- Christine R. Beck,
- Tobias Marschall,
- Kiran Garimella,
- and Evan E. Eichler
Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
...: their limitation in detecting large insertions compared to ONT reads, likely because of increased ONT sequence read length, and their increased recall when assembled even at low coverages. HiFi reads consistently lag behind their ONT counterparts for large insertions, recovering only half of the insertions...
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Method: Targeted genotyping of variable number tandem repeats with adVNTR
- Mehrdad Bakhtiari,
- Sharona Shleizer-Burko,
- Melissa Gymrek,
- Vikas Bansal,
- and Vineet Bafna
Genome Res. November 2018 28: 1709-1719; Published in Advance October 23, 2018, doi:10.1101/gr.235119.118
...and risk for type 1 diabetes (OR = 2.2) (Durinovic-Belló et al. 2010). Notwithstanding these examples, the advent of -wide SNP genotyping arrays led to VNTRs being largely ignored. They have been called “the forgotten polymorphisms” (Brookes 2013).View this table: In this window In a new window Table 1...
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Resource: Accurate detection and genotyping of SNPs utilizing population sequencing data
- Vikas Bansal,
- Olivier Harismendy,
- Ryan Tewhey,
- Sarah S. Murray,
- Nicholas J. Schork,
- Eric J. Topol,
- and Kelly A. Frazer
Genome Res. April 2010 20: 537-545; Published in Advance February 11, 2010, doi:10.1101/gr.100040.109
...that represent artifacts of systematic sequencing errors. Additionally, once a SNP has been identified in an individual, relaxed criteria can be used to assign genotypes (detect SNPs at low coverage) in other individuals. Population sequence data can be used for SNP detection even in the absence of accurate base...

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