Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR (2010) A method and server for predicting damaging missense mutations. Nat Methods 7:248–249. https://doi.org/10.1038/nmeth0410-248
CAS
Article
PubMed
PubMed Central
Google Scholar
Arumilli M, Layer RM, Hytönen MK, Lohi H (2020) webGQT: a shiny server for genotype query tools for model-based variant filtering. Front Genet 11:152. https://doi.org/10.3389/fgene.2020.00152
CAS
Article
PubMed
PubMed Central
Google Scholar
Bai X, Zhang C, Zhang F, Xiao Y, Jin Y, Wang H, Xu L (2020) Five novel mutations in LOXHD1 gene were identified to cause autosomal recessive nonsyndromic hearing loss in four Chinese families. Biomed Res Int 2020:1685974. https://doi.org/10.1155/2020/1685974
CAS
Article
PubMed
PubMed Central
Google Scholar
Bateman A, Sandford R (1999) The PLAT domain: a new piece in the PKD1 puzzle. Curr Biol 9:588
Article
Google Scholar
Broeckx BJ, Hitte C, Coopman F, Verhoeven GE, De Keulenaer S, De Meester E, Derrien T, Alfoldi J, Lindblad-Toh K, Bosmans T, Gielen I, Van Bree H, Van Ryssen B, Saunders JH, Van Nieuwerburgh F, Deforce D (2015) Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes. Sci Rep 5:12810. https://doi.org/10.1038/srep12810
CAS
Article
PubMed
PubMed Central
Google Scholar
Buniello A, MacArthur JAL, Cerezo M, Harris LW, Hayhurst J, Malangone C, McMahon A, Morales J, Mountjoy E, Sollis E, Suveges D, Vrousgou O, Whetzel PL, Amode R, Guillen JA, Riat HS, Trevanion SJ, Hall P, Junkins H, Flicek P, Burdett T, Hindorff LA, Cunningham F, Parkinson H (2019) The NHGRI-EBI GWAS catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res 47:D1005–D1012. https://doi.org/10.1093/nar/gky1120
CAS
Article
PubMed
Google Scholar
Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ (2015) Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4:7–8. https://doi.org/10.1186/s13742-015-0047-8
CAS
Article
PubMed
PubMed Central
Google Scholar
Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall IM (2015) SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Methods 12:966–968. https://doi.org/10.1038/nmeth.3505
CAS
Article
PubMed
PubMed Central
Google Scholar
Choi Y, Chan AP (2015) PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics 31:2745–2747. https://doi.org/10.1093/bioinformatics/btv195
CAS
Article
PubMed
PubMed Central
Google Scholar
Choi Y, Sims GE, Murphy S, Miller JR, Chan AP (2012) Predicting the functional effect of amino acid substitutions and indels. PLoS ONE 7:e46688. https://doi.org/10.1371/journal.pone.0046688
CAS
Article
PubMed
PubMed Central
Google Scholar
Comito B, Knowles KE, Strain GM (2012) Congenital deafness in Jack Russell terriers: prevalence and association with phenotype. Vet J 193:404–407. https://doi.org/10.1016/j.tvjl.2012.02.018
CAS
Article
PubMed
Google Scholar
Coppens AG, Kiss R, Heizmann CW, Deltenre P, Poncelet L (2001) An original inner ear neuroepithelial degeneration in a deaf Rottweiler puppy. Hear Res 161:65–71
CAS
Article
Google Scholar
De Risio L, Freeman J, Lewis T (2016) Prevalence, heritability and genetic correlations of congenital sensorineural deafness and coat pigmentation phenotype in the English bull terrier. BMC Vet Res 12:146–156. https://doi.org/10.1186/s12917-016-0777-6
CAS
Article
PubMed
PubMed Central
Google Scholar
Edvardson S, Jalas C, Shaag A, Zenvirt S, Landau C, Lerer I, Elpeleg O (2011) A deleterious mutation in the LOXHD1 gene causes autosomal recessive hearing loss in Ashkenazi Jews. Am J Med Genet A 155A:1170–1172. https://doi.org/10.1002/ajmg.a.33972
CAS
Article
PubMed
Google Scholar
Gardner EJ, Lam VK, Harris DN, Chuang NT, Scott EC, Pittard WS, Mills RE, 1000 Genomes Project Consortium, Devine SE (2017) The mobile element locator tool (MELT): population-scale mobile element discovery and biology. Genome Res 27:1916–1929. https://doi.org/10.1101/gr.218032.116
CAS
Article
PubMed
PubMed Central
Google Scholar
Golosova O, Henderson R, Vaskin Y, Gabrielian A, Grekhov G, Nagarajan V, Oler AJ, Quinones M, Hurt D, Fursov M, Huyen Y (2014) Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses. PeerJ 2:e644. https://doi.org/10.7717/peerj.644
Article
PubMed
PubMed Central
Google Scholar
Grillet N, Schwander M, Hildebrand MS, Sczaniecka A, Kolatkar A, Velasco J, Webster JA, Kahrizi K, Najmabadi H, Kimberling WJ, Stephan D, Bahlo M, Wiltshire T, Tarantino LM, Kuhn P, Smith RJ, Muller U (2009) Mutations in LOXHD1, an evolutionarily conserved stereociliary protein, disrupt hair cell function in mice and cause progressive hearing loss in humans. Am J Hum Genet 85:328–337. https://doi.org/10.1016/j.ajhg.2009.07.017
CAS
Article
PubMed
PubMed Central
Google Scholar
Guevar J, Olby NJ, Meurs KM, Yost O, Friedenberg SG (2018) Deafness and vestibular dysfunction in a Doberman Pinscher puppy associated with a mutation in the PTPRQ gene. J Vet Intern Med 32:665–669. https://doi.org/10.1111/jvim.15060
Article
PubMed
PubMed Central
Google Scholar
Hytönen MK, Arumilli M, Sarkiala E, Nieminen P, Lohi H (2019) Canine models of human amelogenesis imperfecta: identification of novel recessive ENAM and ACP4 variants. Hum Genet 138:525–533. https://doi.org/10.1007/s00439-019-01997-8
CAS
Article
PubMed
PubMed Central
Google Scholar
Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL (2008) NCBI BLAST: a better web interface. Nucleic Acids Res 36:5. https://doi.org/10.1093/nar/gkn201
CAS
Article
Google Scholar
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J (2005) Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110:462–467
CAS
Article
Google Scholar
Karlsson EK, Baranowska I, Wade CM, Salmon Hillbertz NH, Zody MC, Anderson N, Biagi TM, Patterson N, Pielberg GR, Kulbokas EJ, Comstock KE, Keller ET, Mesirov JP, von Euler H, Kämpe O, Hedhammar A, Lander ES, Andersson G, Andersson L, Lindblad-Toh K (2007) Efficient mapping of mendelian traits in dogs through genome-wide association. Nat Genet 39:1321–1328. https://doi.org/10.1038/ng.2007.10
CAS
Article
PubMed
Google Scholar
Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ, Zody MC, Mauceli E, Xie X, Breen M, Wayne RK, Ostrander EA, Ponting CP, Galibert F, Smith DR, DeJong PJ, Kirkness E, Alvarez P, Biagi T, Brockman W, Butler J, Chin CW, Cook A, Cuff J, Daly MJ, DeCaprio D, Gnerre S, Grabherr M, Kellis M, Kleber M, Bardeleben C, Goodstadt L, Heger A, Hitte C, Kim L, Koepfli KP, Parker HG, Pollinger JP, Searle SM, Sutter NB, Thomas R, Webber C, Baldwin J, Abebe A, Abouelleil A, Aftuck L, Ait-Zahra M, Aldredge T, Allen N, An P, Anderson S, Antoine C, Arachchi H, Aslam A, Ayotte L, Bachantsang P, Barry A, Bayul T, Benamara M, Berlin A, Bessette D, Blitshteyn B, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Brown A, Cahill P, Calixte N, Camarata J, Cheshatsang Y, Chu J, Citroen M, Collymore A, Cooke P, Dawoe T, Daza R, Decktor K, DeGray S, Dhargay N, Dooley K, Dooley K, Dorje P, Dorjee K, Dorris L, Duffey N, Dupes A, Egbiremolen O, Elong R, Falk J, Farina A, Faro S, Ferguson D, Ferreira P, Fisher S, FitzGerald M, Foley K, Foley C, Franke A, Friedrich D, Gage D, Garber M, Gearin G, Giannoukos G, Goode T, Goyette A, Graham J, Grandbois E, Gyaltsen K, Hafez N, Hagopian D, Hagos B, Hall J, Healy C, Hegarty R, Honan T, Horn A, Houde N, Hughes L, Hunnicutt L, Husby M, Jester B, Jones C, Kamat A, Kanga B, Kells C, Khazanovich D, Kieu AC, Kisner P, Kumar M, Lance K, Landers T, Lara M, Lee W, Leger JP, Lennon N, Leuper L, LeVine S, Liu J, Liu X, Lokyitsang Y, Lokyitsang T, Lui A, Macdonald J, Major J, Marabella R, Maru K, Matthews C, McDonough S, Mehta T, Meldrim J, Melnikov A, Meneus L, Mihalev A, Mihova T, Miller K, Mittelman R, Mlenga V, Mulrain L, Munson G, Navidi A, Naylor J, Nguyen T, Nguyen N, Nguyen C, Nguyen T, Nicol R, Norbu N, Norbu C, Novod N, Nyima T, Olandt P, O’Neill B, O’Neill K, Osman S, Oyono L, Patti C, Perrin D, Phunkhang P, Pierre F, Priest M, Rachupka A, Raghuraman S, Rameau R, Ray V, Raymond C, Rege F, Rise C, Rogers J, Rogov P, Sahalie J, Settipalli S, Sharpe T, Shea T, Sheehan M, Sherpa N, Shi J, Shih D, Sloan J, Smith C, Sparrow T, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Stone S, Sykes S, Tchuinga P, Tenzing P, Tesfaye S, Thoulutsang D, Thoulutsang Y, Topham K, Topping I, Tsamla T, Vassiliev H, Venkataraman V, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Yang S, Yang X, Young G, Yu Q, Zainoun J, Zembek L, Zimmer A, Lander ES (2005) Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438:803–819. https://doi.org/10.1038/nature04338
CAS
Article
PubMed
Google Scholar
Maekawa K, Nishio SY, Abe S, Goto SI, Honkura Y, Iwasaki S, Kanda Y, Kobayashi Y, Oka SI, Okami M, Oshikawa C, Sakuma N, Sano H, Shirakura M, Uehara N, Usami SI (2019) Mutational spectrum and clinical features of patients with LOXHD1 variants identified in an 8074 hearing loss patient cohort. Genes (Basel). https://doi.org/10.3390/genes10100735.E735
Article
Google Scholar
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303. https://doi.org/10.1101/gr.107524.110
CAS
Article
PubMed
PubMed Central
Google Scholar
Meyermans R, Gorssen W, Buys N, Janssens S (2020) How to study runs of homozygosity using PLINK? A guide for analyzing medium density SNP data in livestock and pet species. BMC Genomics 21:94–x. https://doi.org/10.1186/s12864-020-6463-x
CAS
Article
PubMed
PubMed Central
Google Scholar
Mori K, Moteki H, Kobayashi Y, Azaiez H, Booth KT, Nishio SY, Sato H, Smith RJ, Usami S (2015) Mutations in LOXHD1 gene cause various types and severities of hearing loss. Ann Otol Rhinol Laryngol 124(Suppl 1):135S–41S. https://doi.org/10.1177/0003489415574067
Article
PubMed
PubMed Central
Google Scholar
Morton CC, Nance WE (2006) Newborn hearing screening–a silent revolution. N Engl J Med 354:2151–2164
CAS
Article
Google Scholar
Okonechnikov K, Golosova O, Fursov M, UGENE team (2012) Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28:1166–1167. https://doi.org/10.1093/bioinformatics/bts091
CAS
Article
PubMed
Google Scholar
Papadopoulos JS, Agarwala R (2007) COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics 23:1073–1079
CAS
Article
Google Scholar
Platt S, Freeman J, di Stefani A, Wieczorek L, Henley W (2006) Prevalence of unilateral and bilateral deafness in border collies and association with phenotype. J Vet Intern Med 20:1355–1362. https://doi.org/10.1892/0891-6640(2006)20[1355:pouabd]2.0.co;2
Article
PubMed
Google Scholar
Plevova P, Paprskarova M, Tvrda P, Turska P, Slavkovsky R, Mrazkova E (2017) STRC deletion is a frequent cause of slight to moderate congenital hearing impairment in the Czech Republic. Otol Neurotol 38:e393–e400. https://doi.org/10.1097/MAO.0000000000001571
Article
PubMed
Google Scholar
Purfield DC, Berry DP, McParland S, Bradley DG (2012) Runs of homozygosity and population history in cattle. BMC Genet 13:70. https://doi.org/10.1186/1471-2156-13-70
CAS
Article
PubMed
PubMed Central
Google Scholar
Rausch T, Zichner T, Schlattl A, Stutz AM, Benes V, Korbel JO (2012) DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28:i333–i339. https://doi.org/10.1093/bioinformatics/bts378
CAS
Article
PubMed
PubMed Central
Google Scholar
Riazuddin SA, Parker DS, McGlumphy EJ, Oh EC, Iliff BW, Schmedt T, Jurkunas U, Schleif R, Katsanis N, Gottsch JD (2012) Mutations in LOXHD1, a recessive-deafness locus, cause dominant late-onset Fuchs corneal dystrophy. Am J Hum Genet 90:533–539. https://doi.org/10.1016/j.ajhg.2012.01.013
CAS
Article
PubMed
PubMed Central
Google Scholar
Rose R, Golosova O, Sukhomlinov D, Tiunov A, Prosperi M (2019) Flexible design of multiple metagenomics classification pipelines with UGENE. Bioinformatics 35:1963–1965. https://doi.org/10.1093/bioinformatics/bty901
CAS
Article
PubMed
Google Scholar
Shen N, Wang T, Li D, Liu A, Lu Y (2019) Whole-exome sequencing identifies a novel missense variant within LOXHD1 causing rare hearing loss in a Chinese family. BMC Med Genet 20:30–2. https://doi.org/10.1186/s12881-019-0758-2
Article
PubMed
PubMed Central
Google Scholar
Strain GM (1996) Aetiology, prevalence and diagnosis of deafness in dogs and cats. Br Vet J 152:17–36
CAS
Article
Google Scholar
Strain GM (2004) Deafness prevalence and pigmentation and gender associations in dog breeds at risk. Vet J 167:23–32
Article
Google Scholar
Strain GM (2015) The genetics of deafness in domestic animals. Front Vet Sci 2:29. https://doi.org/10.3389/fvets.2015.00029
Article
PubMed
PubMed Central
Google Scholar
Webb AA, Ruhe AL, Neff MW (2019) A missense mutation in MYO7A is associated with bilateral deafness and vestibular dysfunction in the Doberman pinscher breed. Can J Vet Res 83:142–148
CAS
PubMed
PubMed Central
Google Scholar
Wesdorp M, Schreur V, Beynon AJ, Oostrik J, van de Kamp JM, Elting MW, van den Boogaard MH, Feenstra I, Admiraal RJC, Kunst HPM, Hoyng CB, Kremer H, Yntema HG, Pennings RJE, Schraders M (2018) Further audiovestibular characterization of DFNB77, caused by deleterious variants in LOXHD1, and investigation into the involvement of Fuchs corneal dystrophy. Clin Genet 94:221–231. https://doi.org/10.1111/cge.13368
CAS
Article
PubMed
Google Scholar
Yokoyama JS, Lam ET, Ruhe AL, Erdman CA, Robertson KR, Webb AA, Williams DC, Chang ML, Hytönen MK, Lohi H, Hamilton SP, Neff MW (2012) Variation in genes related to cochlear biology is strongly associated with adult-onset deafness in border collies. PLoS Genet 8:e1002898. https://doi.org/10.1371/journal.pgen.1002898
CAS
Article
PubMed
PubMed Central
Google Scholar
Zhang C, Hao S, Liu Y, Zhou B, Liu F, Zheng L, Ma P, Liu Q, Lin X, Yan Y, Zhang Q (2019) A novel LOXHD1 variant in a Chinese couple with hearing loss. J Int Med Res 47:6082–6090. https://doi.org/10.1177/0300060519884197
Article
PubMed
PubMed Central
Google Scholar