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Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
- Ursula Oggenfuss,
- Robert T. Todd,
- Natthapon Soisangwan,
- Bailey Kemp,
- Alison Guyer,
- Annette Beach,
- and Anna Selmecki
Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
...conducted using Canu, quality control was conducted with BUSCO and Quast, and a visual comparison was conducted with MUMmer (see Supplemental Methods; Kurtz et al. 2004; Simão et al. 2015; Koren et al. 2017; Mikheenko et al. 2018; Manni et al. 2021).Genome-wide structural variant and transposable element...
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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
...program that aims to identify disease-causing genetic variants in previously undiagnosed RD families. We utilized 10-fold coverage HiFi long-read sequencing (LRS) for detecting causative structural variants (SVs), single-nucleotide variants (SNVs), insertion-deletions (indels), and short tandem repeat...
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Method: A framework to score the effects of structural variants in health and disease
- Philip Kleinert and
- Martin Kircher
Genome Res. April 2022 32: 766-777; Published in Advance February 23, 2022, doi:10.1101/gr.275995.121
...overcome this problem by using a surrogate training objective, the Combined Annotation Dependent Depletion (CADD) of functional variants. We use human- and chimpanzee-derived SVs as proxy-neutral and contrast them with matched simulated variants as proxy-deleterious, an approach that has proven powerful...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...young ones (Domazet-Lošo and Tautz 2008). However, the underlying mechanism remains unclear. In recent years, medical studies have identified deleterious variants causing rare disorders, “orphan” diseases, and rare forms of common diseases (Richards et al. 2015). Rare diseases are often caused by rare...
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Method: Systematic evaluation of the effect of polyadenylation signal variants on the expression of disease-associated genes
- Meng Chen,
- Ran Wei,
- Gang Wei,
- Mingqing Xu,
- Zhixi Su,
- Chen Zhao,
- and Ting Ni
Genome Res. May 2021 31: 890-899; Published in Advance April 19, 2021, doi:10.1101/gr.270256.120
...resources for discovering distinct genomic features of PAS variants and also develop a credible and convenient experimental tool to validate the effect of PAS variants on expression of disease-associated genes. This approach will greatly accelerate the deciphering of PAS variation-related human diseases.Genome...
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Resource: A platform for curated products from novel open reading frames prompts reinterpretation of disease variants
- Matthew D.C. Neville,
- Robin Kohze,
- Chaitanya Erady,
- Narendra Meena,
- Matthew Hayden,
- David N. Cooper,
- Matthew Mort,
- and Sudhakaran Prabakaran
Genome Res. February 2021 31: 327-336; Published in Advance January 19, 2021, doi:10.1101/gr.263202.120
...human traits and diseases. We then narrow our focus from nORF regions to specific classes of nORF variants (e.g., nORF stop-gained variants) to evaluate potential signals of negative selection, which would be indicative of functional importance. Finally, we move to specific genetic variants...
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Resource: An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants
- Can Yuan,
- Lijing Tang,
- Thomas Lopdell,
- Vyacheslav A. Petrov,
- Claire Oget-Ebrad,
- Gabriel Costa Monteiro Moreira,
- José Luis Gualdrón Duarte,
- Arnaud Sartelet,
- Zhangrui Cheng,
- Mazdak Salavati,
- D. Claire Wathes,
- Mark A. Crowe,
- GplusE Consortium,
- Wouter Coppieters,
- Mathew Littlejohn,
- Carole Charlier,
- Tom Druet,
- Michel Georges,
- and Haruko Takeda
Genome Res. October 2023 33: 1848-1864; Published in Advance September 26, 2023, doi:10.1101/gr.277947.123
.... It is generally believed that knowing the causative variants, or at least those that are more likely to be, may help to further improve the accuracy of genomic selection (Xiang et al. 2019).Causative variants encompass coding and regulatory variants. Coding variants, including missense, nonsense, frameshift...
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Research: Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection
- Konstantin Popadin,
- Stephan Peischl,
- Marco Garieri,
- M. Reza Sailani,
- Audrey Letourneau,
- Federico Santoni,
- Samuel W. Lukowski,
- Georgii A. Bazykin,
- Sergey Nikolaev,
- Diogo Meyer,
- Laurent Excoffier,
- Alexandre Reymond,
- and Stylianos E. Antonarakis
Genome Res. January 2018 28: 1-10; Published in Advance December 13, 2017, doi:10.1101/gr.228411.117
...that an individual bearing an extremely severe deleterious variant (i.e., genetic handicap) might escape embryonic lethality if the -wide burden of SDVs is sufficiently low.ResultsGenomic and transcription variation of genes encoded on Chromosome 21 in T21 individualsFunctionally constrained Chromosome 21 genes...
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Research: Genomic analysis of primordial dwarfism reveals novel disease genes
- Ranad Shaheen,
- Eissa Faqeih,
- Shinu Ansari,
- Ghada Abdel-Salam,
- Zuhair N. Al-Hassnan,
- Tarfa Al-Shidi,
- Rana Alomar,
- Sameera Sogaty,
- and Fowzan S. Alkuraya
Genome Res. February 2014 24: 291-299; Published in Advance January 3, 2014, doi:10.1101/gr.160572.113
...dwarfism disease genes Genome Research 297 www..org Exome sequencing and variant analysis Exome capture was performed using the TruSeq Enrichment kit (Illumina) following the manufacturer’s protocol. Samples were prepared as an Illumina sequencing library, and in the second step, the sequencing libraries...
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Method: De novo mutation rates at the single-mutation resolution in a human HBB gene region associated with adaptation and genetic disease
- Daniel Melamed,
- Yuval Nov,
- Assaf Malik,
- Michael B. Yakass,
- Evgeni Bolotin,
- Revital Shemer,
- Edem K. Hiadzi,
- Karl L. Skorecki,
- and Adi Livnat
Genome Res. March 2022 32: 488-498; Published in Advance January 14, 2022, doi:10.1101/gr.276103.121
...(Inoue et al. 2001; Crow et al. 2009; Dumas et al. 2012; Losos 2017; Kratochwil et al. 2019; Kratochwil and Meyer 2019; Lind 2019; Xie et al. 2019), to its contribution to recurrent genetic disease and cancer (Lupski 1998; McClellan and King 2010; Veltman and Brunner 2012; Shendure and Akey 2015).The...
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