Acampora D, Merlo GR, Paleari L, Zerega B, Postiglione MP, Mantero S, Bober E, Barbieri O, Simeone A, Levi G (1999) Craniofacial, vestibular and bone defects in mice lacking the Distal-less-related gene Dlx5. Development 126:3795–3809. https://doi.org/10.1242/dev.126.17.3795

Article  CAS  PubMed  Google Scholar 

Ambrosetti I, Bernardini L, Pollazzon M, Giuffrida MG, Guida V, Peluso F, Baroni MC, Polizzi V, Napoli M, Rosato S, Trimarchi G, Gelmini C, Caraffi SG, Wischmeijer A, Frattini D, Novelli A, Garavelli L (2023) Split Hand-Foot and Deafness in a Patient with 7q21.13-q21.3 Deletion Not Including the DLX5/6 Genes. Genes (Basel) 14. https://doi.org/10.3390/genes14081526

Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22:195–201. https://doi.org/10.1093/bioinformatics/bti770

Article  CAS  PubMed  Google Scholar 

Arundel P, Borg SA (2023) Early Life Management of Osteogenesis Imperfecta. Curr Osteoporos Rep 21:779–786. https://doi.org/10.1007/s11914-023-00823-5

Article  PubMed  PubMed Central  Google Scholar 

Azaiez H, Booth KT, Ephraim SS, Crone B, Black-Ziegelbein EA, Marini RJ, Shearer AE, Sloan-Heggen CM, Kolbe D, Casavant T, Schnieders MJ, Nishimura C, Braun T, Smith RJH (2018) Genomic landscape and mutational signatures of deafness-associated genes. Am J Hum Genet 103:484–497. https://doi.org/10.1016/j.ajhg.2018.08.006

Article  CAS  PubMed  PubMed Central  Google Scholar 

Baek JI, Oh SK, Kim DB, Choi SY, Kim UK, Lee KY, Lee SH (2012) Targeted massive parallel sequencing: the effective detection of novel causative mutations associated with hearing loss in small families. Orphanet J Rare Dis 7:60. https://doi.org/10.1186/1750-1172-7-60

Article  PubMed  PubMed Central  Google Scholar 

Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 14:708–715. https://doi.org/10.1101/gr.1933104

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bluhm A, Viceconte N, Li F, Rane G, Ritz S, Wang S, Levin M, Shi Y, Kappei D, Butter F (2019) ZBTB10 binds the telomeric variant repeat TTGGGG and interacts with TRF2. Nucleic Acids Res 47:1896–1907. https://doi.org/10.1093/nar/gky1289

Article  CAS  PubMed  PubMed Central  Google Scholar 

Brown KK, Reiss JA, Crow K, Ferguson HL, Kelly C, Fritzsch B, Morton CC (2010) Deletion of an enhancer near DLX5 and DLX6 in a family with hearing loss, craniofacial defects, and an inv(7)(q21.3q35). Hum Genet 127:19–31. https://doi.org/10.1007/s00439-009-0736-4

Article  CAS  PubMed  PubMed Central  Google Scholar 

Brownstein Z, Friedman LM, Shahin H, Oron-Karni V, Kol N, Abu Rayyan A, Parzefall T, Lev D, Shalev S, Frydman M, Davidov B, Shohat M, Rahile M, Lieberman S, Levy-Lahad E, Lee MK, Shomron N, King MC, Walsh T, Kanaan M, Avraham KB (2011) Targeted genomic capture and massively parallel sequencing to identify genes for hereditary hearing loss in Middle Eastern families. Genome Biol 12:R89. https://doi.org/10.1186/gb-2011-12-9-r89

Article  CAS  PubMed  PubMed Central  Google Scholar 

Castiglione A, Moller C (2022) Usher Syndrome Audiol Res 12:42–65. https://doi.org/10.3390/audiolres12010005

Article  PubMed  Google Scholar 

Choi BY, Park G, Gim J, Kim AR, Kim BJ, Kim HS, Park JH, Park T, Oh SH, Han KH, Park WY (2013) Diagnostic application of targeted resequencing for familial nonsyndromic hearing loss. PLoS ONE 8:e68692. https://doi.org/10.1371/journal.pone.0068692

Article  CAS  PubMed  PubMed Central  Google Scholar 

Christmas MJ, Kaplow IM, Genereux DP, Dong MX, Hughes GM, Li X, Sullivan PF, Hindle AG, Andrews G, Armstrong JC, Bianchi M, Breit AM, Diekhans M, Fanter C, Foley NM, Goodman DB, Goodman L, Keough KC, Kirilenko B, Kowalczyk A, Lawless C, Lind AL, Meadows JRS, Moreira LR, Redlich RW, Ryan L, Swofford R, Valenzuela A, Wagner F, Wallerman O, Brown AR, Damas J, Fan K, Gatesy J, Grimshaw J, Johnson J, Kozyrev SV, Lawler AJ, Marinescu VD, Morrill KM, Osmanski A, Paulat NS, Phan BN, Reilly SK, Schaffer DE, Steiner C, Supple MA, Wilder AP, Wirthlin ME, Xue JR, Zoonomia Consortium section s, Birren BW, Gazal S, Hubley RM, Koepfli KP, Marques-Bonet T, Meyer WK, Nweeia M, Sabeti PC, Shapiro B, Smit AFA, Springer MS, Teeling EC, Weng Z, Hiller M, Levesque DL, Lewin HA, Murphy WJ, Navarro A, Paten B, Pollard KS, Ray DA, Ruf I, Ryder OA, Pfenning AR, Lindblad-Toh K, Karlsson EK, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, et al. (2023) Evolutionary constraint and innovation across hundreds of placental mammals. Science 380: eabn3943. https://doi.org/10.1126/science.abn3943

de Geus CM, Free RH, Verbist BM, Sival DA, Blake KD, Meiners LC, van Ravenswaaij-Arts CMA (2017) Guidelines in CHARGE syndrome and the missing link: Cranial imaging. Am J Med Genet C Semin Med Genet 175:450–464. https://doi.org/10.1002/ajmg.c.31593

Article  PubMed  PubMed Central  Google Scholar 

Depew MJ, Liu JK, Long JE, Presley R, Meneses JJ, Pedersen RA, Rubenstein JL (1999) Dlx5 regulates regional development of the branchial arches and sensory capsules. Development 126:3831–3846. https://doi.org/10.1242/dev.126.17.3831

Article  CAS  PubMed  Google Scholar 

Dougherty GW, Mizuno K, Nothe-Menchen T, Ikawa Y, Boldt K, Ta-Shma A, Aprea I, Minegishi K, Pang YP, Pennekamp P, Loges NT, Raidt J, Hjeij R, Wallmeier J, Mussaffi H, Perles Z, Elpeleg O, Rabert F, Shiratori H, Letteboer SJ, Horn N, Young S, Strunker T, Stumme F, Werner C, Olbrich H, Takaoka K, Ide T, Twan WK, Biebach L, Grosse-Onnebrink J, Klinkenbusch JA, Praveen K, Bracht DC, Hoben IM, Junger K, Gutzlaff J, Cindric S, Aviram M, Kaiser T, Memari Y, Dzeja PP, Dworniczak B, Ueffing M, Roepman R, Bartscherer K, Katsanis N, Davis EE, Amirav I, Hamada H, Omran H (2020) CFAP45 deficiency causes situs abnormalities and asthenospermia by disrupting an axonemal adenine nucleotide homeostasis module. Nat Commun 11:5520. https://doi.org/10.1038/s41467-020-19113-0

Article  CAS  PubMed  PubMed Central  Google Scholar 

Downie L, Halliday J, Burt R, Lunke S, Lynch E, Martyn M, Poulakis Z, Gaff C, Sung V, Wake M, Hunter MF, Saunders K, Rose E, Lewis S, Jarmolowicz A, Phelan D, Rehm HL, Melbourne Genomics Health A, Amor DJ (2020) Exome sequencing in infants with congenital hearing impairment: a population-based cohort study. Eur J Hum Genet 28:587–596. https://doi.org/10.1038/s41431-019-0553-8

Article  CAS  PubMed  Google Scholar 

Francey LJ, Conlin LK, Kadesch HE, Clark D, Berrodin D, Sun Y, Glessner J, Hakonarson H, Jalas C, Landau C, Spinner NB, Kenna M, Sagi M, Rehm HL, Krantz ID (2012) Genome-wide SNP genotyping identifies the Stereocilin (STRC) gene as a major contributor to pediatric bilateral sensorineural hearing impairment. Am J Med Genet A 158A:298–308. https://doi.org/10.1002/ajmg.a.34391

Article  CAS  PubMed  Google Scholar 

Fujiwara T, Shin JM, Yamaguchi A (2022) Advances in the development of PubCaseFinder, including the new application programming interface and matching algorithm. Hum Mutat 43:734–742. https://doi.org/10.1002/humu.24341

Article  PubMed  PubMed Central  Google Scholar 

Fujiwara T, Yamamoto Y, Kim JD, Buske O, Takagi T (2018) PubCaseFinder: a case-report-based, phenotype-driven differential-diagnosis system for rare diseases. Am J Hum Genet 103:389–399. https://doi.org/10.1016/j.ajhg.2018.08.003

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gelb BD, Cave H, Dillon MW, Gripp KW, Lee JA, Mason-Suares H, Rauen KA, Williams B, Zenker M, Vincent LM, ClinGen RWG (2018) ClinGen’s RASopathy Expert Panel consensus methods for variant interpretation. Genet Med 20:1334–1345. https://doi.org/10.1038/gim.2018.3

Article  PubMed  PubMed Central  Google Scholar 

Gottlieb MM, Arenillas DJ, Maithripala S, Maurer ZD, Tarailo Graovac M, Armstrong L, Patel M, van Karnebeek C, Wasserman WW (2015) GeneYenta: a phenotype-based rare disease case matching tool based on online dating algorithms for the acceleration of exome interpretation. Hum Mutat 36:432–438. https://doi.org/10.1002/humu.22772

Article  PubMed  Google Scholar 

Guan J, Li J, Chen G, Shi T, Lan L, Wu X, Zhao C, Wang D, Wang H, Wang Q (2021) Family trio-based sequencing in 404 sporadic bilateral hearing loss patients discovers recessive and De novo genetic variants in multiple ways. Eur J Med Genet 64:104311. https://doi.org/10.1016/j.ejmg.2021.104311

Article  CAS  PubMed  Google Scholar 

Haberlandt E, Loffler J, Hirst-Stadlmann A, Stockl B, Judmaier W, Fischer H, Heinz-Erian P, Muller T, Utermann G, Smith RJ, Janecke AR (2001) Split hand/split foot malformation associated with sensorineural deafness, inner and middle ear malformation, hypodontia, congenital vertical talus, and deletion of eight microsatellite markers in 7q21.1-q21.3. J Med Genet 38:405–409. https://doi.org/10.1136/jmg.38.6.405

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ideura M, Nishio SY, Moteki H, Takumi Y, Miyagawa M, Sato T, Kobayashi Y, Ohyama K, Oda K, Matsui T, Ito T, Suzumura H, Nagai K, Izumi S, Nishiyama N, Komori M, Kumakawa K, Takeda H, Kishimoto Y, Iwasaki S, Furutate S, Ishikawa K, Fujioka M, Nakanishi H, Nakayama J, Horie R, Ohta Y, Naito Y, Kakudo M, Sakaguchi H, Kataoka Y, Sugahara K, Hato N, Nakagawa T, Tsuchihashi N, Kanda Y, Kihara C, Tono T, Miyanohara I, Ganaha A, Usami SI (2019) Comprehensive analysis of syndromic hearing loss patients in Japan. Sci Rep 9:11976. https://doi.org/10.1038/s41598-019-47141-4

Article  CAS  PubMed  PubMed Central