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Research: Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
- Hao Zhu,
- Jiao Zhang,
- Soumya Rao,
- Matthew D. Durbin,
- Ying Li,
- Ruirui Lang,
- Jiqiang Liu,
- Baichuan Xiao,
- Hailin Shan,
- Ziqiu Meng,
- Jinmo Wang,
- Xiaokai Tang,
- Zhenni Shi,
- Liza L. Cox,
- Shouqin Zhao,
- Stephanie M. Ware,
- Tiong Y. Tan,
- Michelle de Silva,
- Lyndon Gallacher,
- Ting Liu,
- Jie Mi,
- Changqing Zeng,
- Hou-Feng Zheng,
- Qingguo Zhang,
- Stylianos E. Antonarakis,
- Timothy C. Cox,
- and Yong-Biao Zhang
Genome Res. May 2025 35: 1065-1079; Published in Advance April 15, 2025, doi:10.1101/gr.280047.124
...(Fig. 4C). We cloned enhancer sequences of EH38E2305115 and EH38E2304970, containing different alleles of rs344131 (A/G, G being the risk allele) and rs61090632 (T/A, A being the risk allele), into firefly luciferase reporter plasmids. Luciferase assays revealed that combinations containing risk...
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Research: Exome sequencing and CRISPR/Cas genome editing identify mutations of ZAK as a cause of limb defects in humans and mice
- Malte Spielmann,
- Naseebullah Kakar,
- Naeimeh Tayebi,
- Catherine Leettola,
- Gudrun Nürnberg,
- Nadine Sowada,
- Darío G. Lupiáñez,
- Izabela Harabula,
- Ricarda Flöttmann,
- Denise Horn,
- Wing Lee Chan,
- Lars Wittler,
- Rüstem Yilmaz,
- Janine Altmüller,
- Holger Thiele,
- Hans van Bokhoven,
- Charles E. Schwartz,
- Peter Nürnberg,
- James U. Bowie,
- Jamil Ahmad,
- Christian Kubisch,
- Stefan Mundlos,
- and Guntram Borck
Genome Res. February 2016 26: 183-191; Published in Advance January 11, 2016, doi:10.1101/gr.199430.115
...compared with wild-type (WT) hindlimbs. Error bars, SD. ZAK mutations in limb defects in humans and mice Genome Research 187 www..org mice with the purpose to test their pathogenicity. This approach holds the promise to contribute to a paradigmatic shift in the investigation ofMendelian disorders. In fact...
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Research: Suppressor mutations in Mecp2-null mice implicate the DNA damage response in Rett syndrome pathology
- Adebola Enikanolaiye,
- Julie Ruston,
- Rong Zeng,
- Christine Taylor,
- Marijke Schrock,
- Christie M. Buchovecky,
- Jay Shendure,
- Elif Acar,
- and Monica J. Justice
Genome Res. April 2020 30: 540-552; Published in Advance April 21, 2020, doi:10.1101/gr.258400.119
...to see an effect. It is also possible that a genetic combination resulted in decreased health or longevity, rather than improvement.View this table: In this window In a new window Table 1. Assessment of Mendelian inheritance of suppressor lociTo identify candidate genes in screen 2, the exome from...
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Perspective: The Mendelian disorders of the epigenetic machinery
- Hans Tomas Bjornsson
Genome Res. October 2015 25: 1473-1481; doi:10.1101/gr.190629.115
...of a subset of target genes is central to the pathogenesis of the Mendelian disorders of the epigenetic machinery (Fahrner and Bjornsson 2014), one should be able to identify downstream target genes, providing a unique window into the pathogenic sequence of these disorders. Given the non-lethality of all...
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Research: Autozygome-guided exome sequencing in retinal dystrophy patients reveals pathogenetic mutations and novel candidate disease genes
- Leen Abu-Safieh,
- May Alrashed,
- Shamsa Anazi,
- Hisham Alkuraya,
- Arif O. Khan,
- Mohammed Al-Owain,
- Jawahir Al-Zahrani,
- Lama Al-Abdi,
- Mais Hashem,
- Salwa Al-Tarimi,
- Mohammed-Adeeb Sebai,
- Ahmed Shamia,
- Mohamed D. Ray-zack,
- Malik Nassan,
- Zuhair N. Al-Hassnan,
- Zuhair Rahbeeni,
- Saad Waheeb,
- Abdullah Alkharashi,
- Emad Abboud,
- Selwa A.F. Al-Hazzaa,
- and Fowzan S. Alkuraya
Genome Res. February 2013 23: 236-247; Published in Advance October 26, 2012, doi:10.1101/gr.144105.112
...to offer a molecular diagnosis to these patients (Koenekoop et al. 2007). Thus, of all Mendelian disorders, this is one disease category where most patients remain unaware of their underlying causative mutation even though such information is critical for informed genetic counseling that aims at prevention...
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Research: Growth disrupting mutations in epigenetic regulatory molecules are associated with abnormalities of epigenetic aging
- Aaron R. Jeffries,
- Reza Maroofian,
- Claire G. Salter,
- Barry A. Chioza,
- Harold E. Cross,
- Michael A. Patton,
- Emma Dempster,
- I. Karen Temple,
- Deborah J.G. Mackay,
- Faisal I. Rezwan,
- Lise Aksglaede,
- Diana Baralle,
- Tabib Dabir,
- Matthew F. Hunter,
- Arveen Kamath,
- Ajith Kumar,
- Ruth Newbury-Ecob,
- Angelo Selicorni,
- Amanda Springer,
- Lionel Van Maldergem,
- Vinod Varghese,
- Naomi Yachelevich,
- Katrina Tatton-Brown,
- Jonathan Mill,
- Andrew H. Crosby,
- and Emma L. Baple
Genome Res. July 2019 29: 1057-1066; Published in Advance June 3, 2019, doi:10.1101/gr.243584.118
.... 2015. The Mendelian disorders of the epigenetic machinery. Genome Res 25: 1473–1481. doi:10.1101/gr.190629.115 ↵Breeze CE, Paul DS, van Dongen J, Butcher LM, Ambrose JC, Barrett JE, Lowe R, Rakyan VK, Iotchkova V, Frontini M, et al. 2016. eFORGE: a tool for identifying cell type-specific signal...
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Resource: Improved exome prioritization of disease genes through cross-species phenotype comparison
- Peter N. Robinson,
- Sebastian Köhler,
- Anika Oellrich,
- Sanger Mouse Genetics Project,
- Kai Wang,
- Christopher J. Mungall,
- Suzanna E. Lewis,
- Nicole Washington,
- Sebastian Bauer,
- Dominik Seelow,
- Peter Krawitz,
- Christian Gilissen,
- Melissa Haendel,
- and Damian Smedley
Genome Res. February 2014 24: 340-348; Published in Advance October 25, 2013, doi:10.1101/gr.160325.113
...candidate genes within a larger multigene locus identified by positional genetic studies. A number of bioinformatic Figure 3. Exomiser querying of an exome containing a known chr10:g.123256215T>G heterozygous mutation associated with Pfeiffer syndrome (MIM:101600), an autosomal dominant Mendelian disease...
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Research: Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis
- Yaniv Erlich,
- Simon Edvardson,
- Emily Hodges,
- Shamir Zenvirt,
- Pramod Thekkat,
- Avraham Shaag,
- Talya Dor,
- Gregory J. Hannon,
- and Orly Elpeleg
Genome Res. May 2011 21: 658-664; Published in Advance April 12, 2011, doi:10.1101/gr.117143.110
...to this work. Abstract Whole exome sequencing has become a pivotal methodology for rapid and cost-effective detection of pathogenic variations in Mendelian disorders. A major challenge of this approach is determining the causative mutation from a substantial number of bystander variations that do...
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Research: Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome
- Gilad D. Evrony,
- Dwight R. Cordero,
- Jun Shen,
- Jennifer N. Partlow,
- Timothy W. Yu,
- Rachel E. Rodin,
- R. Sean Hill,
- Michael E. Coulter,
- Anh-Thu N. Lam,
- Divya Jayaraman,
- Dianne Gerrelli,
- Diana G. Diaz,
- Chloe Santos,
- Victoria Morrison,
- Antonella Galli,
- Ulrich Tschulena,
- Stefan Wiemann,
- M. Jocelyne Martel,
- Betty Spooner,
- Steven C. Ryu,
- Princess C. Elhosary,
- Jillian M. Richardson,
- Danielle Tierney,
- Christopher A. Robinson,
- Rajni Chibbar,
- Dana Diudea,
- Rebecca Folkerth,
- Sheldon Wiebe,
- A. James Barkovich,
- Ganeshwaran H. Mochida,
- James Irvine,
- Edmond G. Lemire,
- Patricia Blakley,
- and Christopher A. Walsh
Genome Res. August 2017 27: 1323-1335; Published in Advance June 19, 2017, doi:10.1101/gr.219899.116
...facilitates the discovery of variants causing Mendelian disease Our study illustrates how transcriptome sequencing (RNA-seq) can provide in vivo functional evidence for rapid identification of pathogenic variants, in particular those that alter gene expression or splicing. While our study identified...
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Method: A novel method for detecting uniparental disomy from trio genotypes identifies a significant excess in children with developmental disorders
- Daniel A. King,
- Tomas W. Fitzgerald,
- Ray Miller,
- Natalie Canham,
- Jill Clayton-Smith,
- Diana Johnson,
- Sahar Mansour,
- Fiona Stewart,
- Pradeep Vasudevan,
- Matthew E. Hurles,
- and the DDD Study
Genome Res. April 2014 24: 673-687; Published in Advance December 19, 2013, doi:10.1101/gr.160465.113
...with sporadic presentation in these families. Although each patient harbored rare, functional variants in known Mendelian disease genes, none of the specific variants we observed had previously been classified as being pathogenic. Therefore, experimental follow-up would be required to definitively implicate...

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