A domestic cat whole exome sequencing resource for trait discovery.
作者： Karen M. Vernau , Catrina Fronick , Christopher R. Helps , John S. Munday , Wesley C. Warren
DOI: 10.1038/S41598-021-86200-7
关键词: Exome 、 Gene 、 Biology 、 Genome 、 Deep sequencing 、 Exome sequencing 、 Whole genome sequencing 、 Allele 、 Sequence assembly 、 Computational biology
摘要: Over 94 million domestic cats are susceptible to cancers and other common rare diseases. Whole exome sequencing (WES) is a proven strategy study these disease-causing variants. Presented 35.7 Mb capture design based on the annotated Felis_catus_9.0 genome assembly, covering 201,683 regions of cat genome. was conducted 41 with known unknown genetic diseases traits, which ten had matching whole sequence (WGS) data available, used validate WES performance. At 80 × mean depth coverage, 96.4% on-target base coverage > 20-fold, while over 98% single nucleotide variants (SNVs) identified by WGS were also WES. Platform-specific SNVs restricted sex chromosomes small number olfactory receptor genes. Within cats, we 31 previously causal discovered new gene candidate variants, including novel missense variance for polycystic kidney disease atrichia in Peterbald cat. These results show utility identify alleles traits first time feline model.
nature.com
sci-hub.st 参考文章(70)
Sonia Clavero, David F. Bishop, Urs Giger, Mark E. Haskins, Robert J. Desnick, Feline congenital erythropoietic porphyria: two homozygous UROS missense mutations cause the enzyme deficiency and porphyrin accumulation. Molecular Medicine. ,vol. 16, pp. 381- 388 ,(2010) , 10.2119/MOLMED.2010.00038
A I Zhigachev, I Ia Katser, M V Vladimirova, Phenotypic and genotypic characteristics of russian hairless cats Genetika (Moskva). ,vol. 36, pp. 538- 544 ,(2000)
D. F. Patterson, M. E. Haskins, P. F. Jezyk, Models of Human Genetic Disease in Domestic Animals Advances in human genetics. ,vol. 12, pp. 263- 339 ,(1982) , 10.1007/978-1-4615-8315-8_4
Alison J. Pearks Wilkerson, Terje Raudsepp, Tina Graves, Derek Albracht, Wesley Warren, Bhanu P. Chowdhary, Loren C. Skow, William J. Murphy, Gene discovery and comparative analysis of X-degenerate genes from the domestic cat Y chromosome. Genomics. ,vol. 92, pp. 329- 338 ,(2008) , 10.1016/J.YGENO.2008.06.012
Peter Walter, Michael Richard Green, Joseph Sambrook, Keith Roberts, Molecular Cloning A Laboratory Manual Fourth Edition ,(2015)
Bart J.G. Broeckx, Christophe Hitte, Frank Coopman, Geert E.C. Verhoeven, Sarah De Keulenaer, Ellen De Meester, Thomas Derrien, Jessica Alfoldi, Kerstin Lindblad-Toh, Tim Bosmans, Ingrid Gielen, Henri Van Bree, Bernadette Van Ryssen, Jimmy H. Saunders, Filip Van Nieuwerburgh, Dieter Deforce, Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes. Scientific Reports. ,vol. 5, pp. 12810- 12810 ,(2015) , 10.1038/SREP12810
Yael Shilo-Benjamini, Kathryn L. Good, Robert A. Grahn, Danielle D. Splawski, Leslie A. Lyons, Ron Ofri, Christopher M. Reilly, David J. Maggs, Paul G. Fitzgerald, Characterization of an Early-Onset, Autosomal Recessive, Progressive Retinal Degeneration in Bengal Cats. Investigative Ophthalmology & Visual Science. ,vol. 56, pp. 5299- 5308 ,(2015) , 10.1167/IOVS.15-16585
Geraldine A. Auwera, Mauricio O. Carneiro, Christopher Hartl, Ryan Poplin, Guillermo del Angel, Ami Levy‐Moonshine, Tadeusz Jordan, Khalid Shakir, David Roazen, Joel Thibault, Eric Banks, Kiran V. Garimella, David Altshuler, Stacey Gabriel, Mark A. DePristo, From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline Current protocols in human genetics. ,vol. 43, ,(2013) , 10.1002/0471250953.BI1110S43
C. Drögemüller, S. Rüfenacht, B. Wichert, T. Leeb, Mutations within the FGF5 gene are associated with hair length in cats. Animal Genetics. ,vol. 38, pp. 218- 221 ,(2007) , 10.1111/J.1365-2052.2007.01590.X
Sonia Clavero, Yuri Ahuja, David F. Bishop, Brittany Kwait, Mark E. Haskins, Urs Giger, Robert J. Desnick, Diagnosis of feline acute intermittent porphyria presenting with erythrodontia requires molecular analyses Veterinary Journal. ,vol. 198, pp. 720- 722 ,(2013) , 10.1016/J.TVJL.2013.10.008