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Perspective: Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
- Jung-Wan Mok,
- Shelley B. Gibson,
- Haley A. Dostalik,
- and Shinya Yamamoto
Genome Res. July 2025 35: 1473-1484; Published in Advance June 4, 2025, doi:10.1101/gr.278291.123
...human variants can often be studied by investigating the effect of LOF of the orthologous fly gene (Fig. 3A). If similarities between phenotypes of Drosophila mutants and rare disease patients can be identified, such data can be utilized to provide supporting data on pathogenicity (Fig. 2). In addition...
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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
...craniofacial structures, including the external ear (Hildebrand and Soriano 1999). In mice, homozygous loss of function of Shroom3 has been amply described as having variably penetrant neural tube defects (exencephaly, spina bifida), facial clefts, and cardiac and kidney anomalies, among other anomalies...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...reconstructions of the histone locus and the pericentric heterochromatin of the X Chromosome, spanning the Stellate locus to the distal flank of the rDNA cluster. To infer structural changes in these regions where alignments are often not practicable, we introduce landmark anchors based on unique variants...
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Research: Somatic structural variation targets neurodevelopmental genes and identifies SHANK2 as a tumor suppressor in neuroblastoma
- Gonzalo Lopez,
- Karina L. Conkrite,
- Miriam Doepner,
- Komal S. Rathi,
- Apexa Modi,
- Zalman Vaksman,
- Lance M. Farra,
- Eric Hyson,
- Moataz Noureddine,
- Jun S. Wei,
- Malcolm A. Smith,
- Shahab Asgharzadeh,
- Robert C. Seeger,
- Javed Khan,
- Jaime Guidry Auvil,
- Daniela S. Gerhard,
- John M. Maris,
- and Sharon J. Diskin
Genome Res. September 2020 30: 1228-1242; Published in Advance August 13, 2020, doi:10.1101/gr.252106.119
...>200 bp for duplications and inversions and ∼500 bp for deletions. In addition, Complete Genomics technology does not provide information about the allelic fraction at which structural variants are identified. Future studies are warranted to address these issues, ideally using long-read sequencing...
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Research: The human genome contains over a million autonomous exons
- Nicholas Stepankiw,
- Ally W.H. Yang,
- and Timothy R. Hughes
Genome Res. November 2023 33: 1865-1878; Published in Advance November 9, 2023, doi:10.1101/gr.277792.123
..., which would partly explain the existence of lncRNAs. The results clarify several aspects of the human exon complement, identify a large number of previously undocumented exons, and indicate that multiexon lncRNAs are an expected feature of large s.ResultsGenome-wide exon trappingWe used a classical exon...
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Method: Direct determination of diploid genome sequences
- Neil I. Weisenfeld,
- Vijay Kumar,
- Preyas Shah,
- Deanna M. Church,
- and David B. Jaffe
Genome Res. May 2017 27: 757-767; Published in Advance April 5, 2017, doi:10.1101/gr.214874.116
...for thousands of other clones) show a preponderance of errors in low complexity sequence, particularly, near long homopolymers. These errors might be attributable to library construction defects, sequencing defects, algorithmic defects, or possibly errors in the finished sequence (International Human Genome...
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Research: Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism
- Yen-Ju Chen,
- Chia-Ying Chen,
- Te-Lun Mai,
- Chih-Fan Chuang,
- Yu-Chen Chen,
- Sachin Kumar Gupta,
- Laising Yen,
- Yi-Da Wang,
- and Trees-Juen Chuang
Genome Res. March 2020 30: 375-391; Published in Advance March 3, 2020, doi:10.1101/gr.255463.119
...neurodevelopmental disorder that is characterized by limited social communication, restricted and ritualized interests, and repetitive behavior (Chen et al. 2015b; Ansel et al. 2017). Hundreds of genes affected by a variety of genomic variants have been reported to be associated with the etiology of ASD (Xu et al...
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Research: Ranking noncanonical 5′ splice site usage by genome-wide RNA-seq analysis and splicing reporter assays
- Steffen Erkelenz,
- Stephan Theiss,
- Wolfgang Kaisers,
- Johannes Ptok,
- Lara Walotka,
- Lisa Müller,
- Frank Hillebrand,
- Anna-Lena Brillen,
- Michael Sladek,
- and Heiner Schaal
Genome Res. December 2018 28: 1826-1840; Published in Advance October 24, 2018, doi:10.1101/gr.235861.118
...of these introns are delimited by GT-AG dinucleotides. The U2-type spliceosome rarely also recognizes introns flanked by AT-AC dinucleotides (“AT-AC II introns”) (Wu and Krainer 1997). Another rare class of introns (∼0.4%) are removed by the minor U12-type spliceosome (Hall and Padgett 1994, 1996; Turunen et al...
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Research: Targeted resequencing identifies PTCH1 as a major contributor to ocular developmental anomalies and extends the SOX2 regulatory network
- Nicolas Chassaing,
- Erica E. Davis,
- Kelly L. McKnight,
- Adrienne R. Niederriter,
- Alexandre Causse,
- Véronique David,
- Annaïck Desmaison,
- Sophie Lamarre,
- Catherine Vincent-Delorme,
- Laurent Pasquier,
- Christine Coubes,
- Didier Lacombe,
- Massimiliano Rossi,
- Jean-Louis Dufier,
- Helene Dollfus,
- Josseline Kaplan,
- Nicholas Katsanis,
- Heather C. Etchevers,
- Stanislas Faguer,
- and Patrick Calvas
Genome Res. April 2016 26: 474-485; Published in Advance February 18, 2016, doi:10.1101/gr.196048.115
.... To identify novel ODA loci, we conducted targeted high-throughput sequencing of 407 candidate genes in an initial cohort of 22 sporadic ODA patients. Patched 1 ( PTCH1 ), an inhibitor of sonic hedgehog (SHH) signaling, harbored an enrichment of rare heterozygous variants in comparison to either controls...
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Method: Gene discovery by chemical mutagenesis and whole-genome sequencing in Dictyostelium
- Cheng-Lin Frank Li,
- Balaji Santhanam,
- Amanda Nicole Webb,
- Blaž Zupan,
- and Gad Shaulsky
Genome Res. September 2016 26: 1268-1276; Published in Advance June 15, 2016, doi:10.1101/gr.205682.116
...Dictyostelium discoideum . Through genome sequencing, we successfully identified mutant genes with multiple alleles in near-saturation screens, including resistance to intense illumination and strong suppressors of defects in an allorecognition pathway. We tested the causality of the mutations by comparison...

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