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Resource: Proactive functional classification of all possible missense single-nucleotide variants in KCNQ4
- Honglan Zheng,
- Xinhao Yan,
- Guanluan Li,
- Hengwei Lin,
- Siqi Deng,
- Wenhui Zhuang,
- Fuqiang Yao,
- Yu Lu,
- Xin Xia,
- Huijun Yuan,
- Li Jin,
- and Zhiqiang Yan
Genome Res. August 2022 32: 1573-1584; Published in Advance June 27, 2022, doi:10.1101/gr.276562.122
...are linked to an autosomal dominant form of nonsyndromic progressive hearing impairment: DFNA2 in humans, a late-onset disease, with high-frequency hearing loss (Coucke et al. 1994; Van Camp et al. 1997; Kubisch et al. 1999). The KCNQ4 gene is one of the most commonly responsible genes for autosomal dominant...
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Research: Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps
- Kristine Bilgrav Saether,
- Jesper Eisfeldt,
- Jesse D. Bengtsson,
- Ming Yin Lun,
- Christopher M. Grochowski,
- Medhat Mahmoud,
- Hsiao-Tuan Chao,
- Jill A. Rosenfeld,
- Pengfei Liu,
- Marlene Ek,
- Jakob Schuy,
- Adam Ameur,
- Hongzheng Dai,
- Undiagnosed Diseases Network,
- James Paul Hwang,
- Fritz J. Sedlazeck,
- Weimin Bi,
- Ronit Marom,
- Josephine Wincent,
- Ann Nordgren,
- Claudia M.B. Carvalho,
- and Anna Lindstrand
Genome Res. November 2024 34: 1785-1797; Published in Advance November 1, 2024, doi:10.1101/gr.279346.124
...region missing in GRCh38 shaded in blue.View this table: In this window In a new window Table 2. Junction characteristics of identified inversions (T2T-CHM13)Case P4855_501 suffered hearing impairment, intellectual disability, autistic features, diplopia, anosmia as well as hypogonadism and had a 43 Mbp...
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Research: Deciphering the largest disease-associated transcript isoforms in the human neural retina with advanced long-read sequencing approaches
- Merel Stemerdink,
- Tabea Riepe,
- Nick Zomer,
- Renee Salz,
- Michael Kwint,
- Jaap Oostrik,
- Raoul Timmermans,
- Barbara Ferrari,
- Stefano Ferrari,
- Alfredo Dueñas Rey,
- Emma Delanote,
- Suzanne E. de Bruijn,
- Hannie Kremer,
- Susanne Roosing,
- Frauke Coppieters,
- Alexander Hoischen,
- Frans P.M. Cremers,
- Peter A.C. ‘t Hoen,
- Erwin van Wijk,
- and Erik de Vrieze
Genome Res. April 2025 35: 725-739; Published in Advance March 4, 2025, doi:10.1101/gr.280060.124
...used for genomic DNA capture. This method facilitated the successful capture and sequencing of ADGRV1 transcripts as well as full-length 18.9 kb USH2A transcripts. By combining algorithmic analysis with detailed manual curation of sequenced reads, we identified novel isoforms characterized...
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ARTICLE: An autosomal recessive nonsyndromic form of sensorineural hearing loss maps to 3p-DFNB6.
- K Fukushima,
- A Ramesh,
- C R Srisailapathy,
- L Ni,
- S Wayne,
- M E O'Neill,
- G Van Camp,
- P Coucke,
- P Jain,
- and E R Wilcox
Genome Res. October 1995 5: 305-308; doi:10.1101/gr.5.3.305
...) is the most common form of congenitally acquired inherited hearing impairment. Although numerous loci are believed to exist, only five have been identified. Using a pooled genomic DNA screening strategy, we have identified a sixth locus, DFNB6, on 3p in the interval bounded by D3S1619 and D3S1766. Footnotes...
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Resource: Mitochondrial DNA variation across 56,434 individuals in gnomAD
- Kristen M. Laricchia,
- Nicole J. Lake,
- Nicholas A. Watts,
- Megan Shand,
- Andrea Haessly,
- Laura Gauthier,
- David Benjamin,
- Eric Banks,
- Jose Soto,
- Kiran Garimella,
- James Emery,
- Genome Aggregation Database Consortium,
- Heidi L. Rehm,
- Daniel G. MacArthur,
- Grace Tiao,
- Monkol Lek,
- Vamsi K. Mootha,
- and Sarah E. Calvo
Genome Res. March 2022 32: 569-582; Published in Advance January 24, 2022, doi:10.1101/gr.276013.121
...Kristen M. Laricchia1,2,8, Nicole J. Lake3,4,8, Nicholas A. Watts1,2, Megan Shand1, Andrea Haessly1, Laura Gauthier1, David Benjamin1, Eric Banks1, Jose Soto1, Kiran Garimella1, James Emery1, Genome Aggregation Database Consortium7, Heidi L. Rehm1,2, Daniel G. MacArthur1,4,5, Grace Tiao1...
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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
...-specificity of regulatory elements and genes. Further, the putatively different mechanisms of phenotypic effects of deletions compared to insertions or duplications complicates a generalized approach for variant effect prediction, as the effect can be mediated by copy number alterations of redundant or unique genomic...
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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
.....org Results Identification of ZAK mutations in split-foot malformation with mesoaxial polydactyly We studied an autosomal recessive disorder characterized by a split-foot phenotype, nail abnormalities of the hands, and hearing impairment. In a multiplex consanguineous Pakistani family with four affected...
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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
...Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Exeter, EX2 5DW, United Kingdom; 2Genetics Research Centre, Molecular and Clinical Sciences Institute, St. George's University of London, London SW17 0RE, United Kingdom; 3Human Genetics and Genomic Medicine, Faculty of Medicine...
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Research: Translational plasticity facilitates the accumulation of nonsense genetic variants in the human population
- Sujatha Jagannathan and
- Robert K. Bradley
Genome Res. December 2016 26: 1639-1650; Published in Advance September 19, 2016, doi:10.1101/gr.205070.116
...in a homozygous state in healthy individuals. It is unknown why these common variants are well tolerated, even though some affect essential genes implicated in Mendelian disease. Here, we combine genomic, proteomic, and biochemical data to demonstrate that many common nonsense variants do not ablate protein...
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Research: Quantitative analysis of Y-Chromosome gene expression across 36 human tissues
- Alexander K. Godfrey,
- Sahin Naqvi,
- Lukáš Chmátal,
- Joel M. Chick,
- Richard N. Mitchell,
- Steven P. Gygi,
- Helen Skaletsky,
- and David C. Page
Genome Res. June 2020 30: 860-873; Published in Advance May 27, 2020, doi:10.1101/gr.261248.120
...sequence (Skaletsky et al. 2003). Other MSY genes have been amplified into multicopy gene families, with genes in these families showing upwards of 99.9% nucleotide sequence identity. In an RNA-seq experiment, many short reads from these genes will map to multiple genomic locations. These multimapping...

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