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Research: T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population
- Daniel Schmitz,
- Adam Ameur,
- and Åsa Johansson
Genome Res. November 2025 35: 2377-2388; Published in Advance September 16, 2025, doi:10.1101/gr.279320.124
...tool, especially for rare diseases, which affect between 3.5% and 5.9% of the population (Nguengang Wakap et al. 2020) and are often caused by a single nucleotide variant (SNV) or a structural variant (SV). However, a minority of the rare disease patients receive a definite diagnosis and often must go...
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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
...for further biomedical and population genetic use, but there is a need to consider each downstream analysis tool individually for its imputation quality thresholds and filtering requirements.Until recently, genotyping arrays were the only cost-effective approach for generating data for medical genomics...
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Review: A systematic review on the biochemical threshold of mitochondrial genetic variants
- Karan K. Smith,
- Jesse D. Moreira,
- Callum R. Wilson,
- June O. Padera,
- Ashlee N. Lamason,
- Liying Xue,
- Deepa M. Gopal,
- David B. Flynn,
- and Jessica L. Fetterman
Genome Res. March 2024 34: 341-365; Published in Advance April 16, 2024, doi:10.1101/gr.278200.123
...Corresponding author: jefetter@bu.eduAbstractMitochondrial DNA (mtDNA) variants cause a range of diseases from severe pediatric syndromes to aging-related conditions. The percentage of mtDNA copies carrying a pathogenic variant, variant allele frequency (VAF), must reach a threshold before a biochemical defect...
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Resource: Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
- Paige A. Byerly,
- Alina von Thaden,
- Evgeny Leushkin,
- Leon Hilgers,
- Shenglin Liu,
- Sven Winter,
- Tilman Schell,
- Charlotte Gerheim,
- Alexander Ben Hamadou,
- Carola Greve,
- Christian Betz,
- Hanno J. Bolz,
- Sven Büchner,
- Johannes Lang,
- Holger Meinig,
- Evax Marie Famira-Parcsetich,
- Sarah P. Stubbe,
- Alice Mouton,
- Sandro Bertolino,
- Goedele Verbeylen,
- Thomas Briner,
- Lídia Freixas,
- Lorenzo Vinciguerra,
- Sarah A. Mueller,
- Carsten Nowak,
- and Michael Hiller
Genome Res. November 2024 34: 2094-2107; Published in Advance November 14, 2024, doi:10.1101/gr.279066.124
...aligned to a reference assembly, informative markers such as -wide single-nucleotide polymorphisms (SNPs) generated via high-throughput genomic data can contribute to the understanding of past and contemporary population demographics (Campana et al. 2016; Gautier et al. 2016; du Plessis et al. 2023; Luo...
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Method: Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change
- Apurva Narechania,
- Dean Bobo,
- Kevin Deitz,
- Rob DeSalle,
- Paul J. Planet,
- and Barun Mathema
Genome Res. October 2024 34: 1651-1660; Published in Advance September 25, 2024, doi:10.1101/gr.278594.123
...that -wide nucleotide diversity (π) of 100 randomly selected daily sequences over the UK pandemic mirrors the KHILL curve but distorts its amplitude. Because π provides a single statistic that averages polymorphism across a population, we deemed it the closest in spirit to KHILL. Still, the time required...
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Research: Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States
- Greta Bellinzona,
- Tiago Nardi,
- Michele Castelli,
- Gherard Batisti Biffignandi,
- Karim Adjou,
- Martha Betson,
- Yannick Blanchard,
- Ioana Bujila,
- Rachel Chalmers,
- Rebecca Davidson,
- Nicoletta D'Avino,
- Tuulia Enbom,
- Jacinto Gomes,
- Gregory Karadjian,
- Christian Klotz,
- Emma Östlund,
- Judith Plutzer,
- Ruska Rimhanen-Finne,
- Guy Robinson,
- Anna Rosa Sannella,
- Jacek Sroka,
- Christen Rune Stensvold,
- Karin Troell,
- Paolo Vatta,
- Barbora Zalewska,
- Claudio Bandi,
- Davide Sassera,
- and Simone M. Cacciò
Genome Res. June 2024 34: 877-887; Published in Advance July 8, 2024, doi:10.1101/gr.278830.123
...LD decay compared with that of population 2 (Fig. 3A), suggesting its more recent origin. We next observed that the distribution of Tajima's D values in population 3 was skewed toward negative values (Fig. 3B), indicating an excess of rare polymorphisms. This skewness was less pronounced...
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Method: Leveraging family data to design Mendelian randomization that is provably robust to population stratification
- Nathan LaPierre,
- Boyang Fu,
- Steven Turnbull,
- Eleazar Eskin,
- and Sriram Sankararaman
Genome Res. July 2023 33: 1032-1041; Published in Advance May 17, 2023, doi:10.1101/gr.277664.123
...statistics for a given significance threshold is a direction for future work. Future work could also improve upon the sibling mode of MR-Twin by using population-based priors to infer parental genotypes with a greater level of accuracy, thereby obtaining superior control of false positives. This approach...
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Method: Haplotype and population structure inference using neural networks in whole-genome sequencing data
- Jonas Meisner and
- Anders Albrechtsen
Genome Res. August 2022 32: 1542-1552; Published in Advance July 6, 2022, doi:10.1101/gr.276813.122
...population size of 10,000 at all points. After filtering for minor allele frequency threshold of 0.05, the data set consists of 2.8 million SNPs.Simulation 2 has the following population split times: t1 = 200, t2 = 120, t3 = 80, and t4 = 40 with an assumed constant population size of 10,000 at all points...
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Method: Highly accurate quantification of allelic gene expression for population and disease genetics
- Anna Saukkonen,
- Helena Kilpinen,
- and Alan Hodgkinson
Genome Res. August 2022 32: 1565-1572; Published in Advance July 6, 2022, doi:10.1101/gr.276296.121
...37 and GRCh38), at multiple different coverage thresholds (across RNA sequencing data from simulated data, population level experiments, and treated cell types) and in different biological settings, showing the potential widespread utility of the tool. Fourth, PAC is only able to correct alignment...
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Method: Optimized sample selection for cost-efficient long-read population sequencing
- T. Rhyker Ranallo-Benavidez,
- Zachary Lemmon,
- Sebastian Soyk,
- Sergey Aganezov,
- William J. Salerno,
- Rajiv C. McCoy,
- Zachary B. Lippman,
- Michael C. Schatz,
- and Fritz J. Sedlazeck
Genome Res. May 2021 31: 910-918; Published in Advance April 2, 2021, doi:10.1101/gr.264879.120
...Corresponding authors: tbenavi1@jhu.edu, mschatz@cs.jhu.edu, fritz.sedlazeck@bcm.eduAbstractAn increasingly important scenario in population genetics is when a large cohort has been genotyped using a low-resolution approach (e.g., microarrays, exome capture, short-read WGS), from which a few individuals...

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