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Method: Genotype imputation via matrix completion
- Eric C. Chi,
- Hua Zhou,
- Gary K. Chen,
- Diego Ortega Del Vecchyo,
- and Kenneth Lange
Genome Res. March 2013 23: 509-518; Published in Advance December 10, 2012, doi:10.1101/gr.145821.112
...HapMap. TheCHB panel contains only unrelated people, while the YRI panel contains unrelateds plus parent–offspring duos and trios. These two groups also diverge in linkage disequilibrium, with the CHB population exhibiting more and the YRI population exhibiting less. The genotype file merges data from Phase I...
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Method: Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain
- Jenna Kalleberg,
- Jacob Rissman,
- and Robert D. Schnabel
Genome Res. August 2025 35: 1859-1874; Published in Advance June 2, 2025, doi:10.1101/gr.279542.124
...training extension with new data on a SLURM-based computing cluster (Supplemental Fig. S33). Existing trio-based joint-calling companion software (dv-trio; DeepTrio) requires samples with a known pedigree during training and genotyping (Ip et al. 2020; Kolesnikov et al. 2021). In contrast, the curriculum...
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Method: The oligogenic inheritance test GCOD detects risk genes and their interactions in congenital heart defects
- Maureen Pittman,
- Kihyun Lee,
- Franco Felix,
- Yu Huang,
- Adrienne Lam,
- Mauro W. Costa,
- Deepak Srivastava,
- and Katherine S. Pollard
Genome Res. February 2026 36: 330-347; Published in Advance December 12, 2025, doi:10.1101/gr.281141.125
...-occurring damaging variants in probands at a higher rate than expected given parental genotypes. We implement this approach in software called Gene Combinations in Oligogenic Disease (GCOD) and apply it to a cohort of 3377 CHD trios with exome sequencing. This analysis detects 160 gene pairs in which damaging...
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Method: Inferring the mode and strength of ongoing selection
- Gustavo V. Barroso and
- Kirk E. Lohmueller
Genome Res. April 2023 33: 632-643; Published in Advance April 13, 2023, doi:10.1101/gr.276386.121
...generation. It leverages phased sequences from parent–offspring trios to detect signatures of selection in the transmission of single-nucleotide polymorphisms (SNPs) (Meyer et al. 2012) and uses this information to infer dominance and selection coefficients. By exploiting the random shuffling of haplotypes...
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Resource: Assembly and analysis of 100 full MHC haplotypes from the Danish population
- Jacob M. Jensen,
- Palle Villesen,
- Rune M. Friborg,
- The Danish Pan-Genome Consortium,
- Thomas Mailund,
- Søren Besenbacher,
- and Mikkel H. Schierup
Genome Res. September 2017 27: 1597-1607; Published in Advance August 3, 2017, doi:10.1101/gr.218891.116
..., respectively, and the child haplotypes inherited from father and mother, respectively. The variant call sets were then updated to account for changes in variant lengths. We constructed consensus sequences for each parent–offspring haplotype using global alignment between all pairwise sets of phased variants...
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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
...the output of all STR genotyping tools we benchmarked. STRkit can calculate MI in terms of binary “yes/no” copy number inheritance, inheritance ±1 repeat unit, parent–offspring 95% confidence interval overlap, exact sequence inheritance, sequence length, and sequence length ±1 bpr. For MI calculation...
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Method: Secure phasing of private genomes in a trusted execution environment with TX-Phase
- Natnatee Dokmai,
- Kaiyuan Zhu,
- S. Cenk Sahinalp,
- and Hyunghoon Cho
Genome Res. December 2025 35: 2626-2636; Published in Advance November 12, 2025, doi:10.1101/gr.280558.125
...deployment of TEE-based haplotype phasing.TX-Phase provides state-of-the-art phasing accuracyWe first evaluate the phasing accuracy of TX-Phase on 424 parent-offspring trios from the UK Biobank (UKB) and compare with two state-of-the-art phasing tools: SHAPEIT4 (Delaneau et al. 2019) and Eagle2 (Loh et al...
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Research: Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications
- Judith Arres,
- Santosh Elavalli,
- Shalini Behl,
- Daniel Matias Sanchez,
- Ayesha Al Ali,
- Abdelrahman Ahmed Yehia Abdelaziz Saad,
- Azza Attia,
- Cyla Minas,
- Sharika Pariyachery,
- Shariq Ahmed,
- Fatmah Aldhuhoori,
- Nitu Thulasidharan,
- Gurunath Katagi,
- Omar Soliman,
- Shilp Purohit,
- Vinay Kusuma,
- Raony Cardenas,
- Thyago Cardoso,
- Luis F. Paulin,
- Philippe Sanio,
- Joseph Mafofo,
- Haiguo Wu,
- Val Zvereff,
- Albarah El-Khani,
- Fahed Al Marzooqi,
- Tiago R. Magalhães,
- Fritz J. Sedlazeck,
- and Javier Quilez
Genome Res. March 2026 36: 460-471; Published in Advance February 11, 2026, doi:10.1101/gr.280134.124
..., no outliers were observed in any of the PCs, confirming the absence of problematic samples and the robustness of the data set.Performance of SNV, indel, and SV detection across the We used the parent-offspring trio (GM24143, GM24149, and GM24385) to assess SNV/indel variant-calling performance -wide...
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Research: Unraveling undiagnosed rare disease cases by HiFi long-read genome sequencing
- Wouter Steyaert,
- Lydia Sagath,
- German Demidov,
- Vicente A. Yépez,
- Anna Esteve-Codina,
- Julien Gagneur,
- Kornelia Ellwanger,
- Ronny Derks,
- Marjan Weiss,
- Amber den Ouden,
- Simone van den Heuvel,
- Hilde Swinkels,
- Nick Zomer,
- Marloes Steehouwer,
- Luke O'Gorman,
- Galuh Astuti,
- Kornelia Neveling,
- Rebecca Schüle,
- Jishu Xu,
- Matthis Synofzik,
- Danique Beijer,
- Holger Hengel,
- Ludger Schöls,
- Kristl G. Claeys,
- Jonathan Baets,
- Liedewei Van de Vondel,
- Alessandra Ferlini,
- Rita Selvatici,
- Heba Morsy,
- Marwa Saeed Abd Elmaksoud,
- Volker Straub,
- Juliane Müller,
- Veronica Pini,
- Luke Perry,
- Anna Sarkozy,
- Irina Zaharieva,
- Francesco Muntoni,
- Enrico Bugiardini,
- Kiran Polavarapu,
- Rita Horvath,
- Evan Reid,
- Hanns Lochmüller,
- Marco Spinazzi,
- Marco Savarese,
- Solve-RD DITF-ITHACA, Solve-RD DITF-Euro-NMD, Solve-RD DITF-RND, Solve-RD DITF-EpiCARE,
- Leslie Matalonga,
- Steven Laurie,
- Han G. Brunner,
- Holm Graessner,
- Sergi Beltran,
- Stephan Ossowski,
- Lisenka E.L.M. Vissers,
- Christian Gilissen,
- Alexander Hoischen,
- and on behalf of the Solve-RD consortium
Genome Res. April 2025 35: 755-768; Published in Advance March 26, 2025, doi:10.1101/gr.279414.124
...for maximum size of the indels was applied, and all indel calls were used for further analyses. For parent-offspring trios, GLNexus (version 1.3.1) was used to conduct SNV joint genotyping (Yun et al. 2021).Small variants were phased using WhatsHap (version 1.1.0) and variants were annotated using an in...
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Perspective: The impact of long-read sequencing on human population-scale genomics
- Tobias Rausch,
- Tobias Marschall,
- and Jan O. Korbel
Genome Res. April 2025 35: 593-598; doi:10.1101/gr.280120.124
...-read sequencing are further enhanced through the possibility to resolve the haplotype structure of genetic variation through the use of read-based phasing information carried by long reads. In combination with parent–offspring trios or chromosome-wide haplotyping technologies such as Strand-seq, this allows...

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