Rapid Genetic Diagnosis for Okinawan Patients with Enlarged Vestibular Aqueduct Using Single-Stranded Tag Hybridization Chromatographic Printed-Array Strip

Overview

Journal J Clin Med

Specialty General Medicine

Date 2022 Feb 25

PMID 35207372

Authors

Akira Ganaha

Eiji Hishinuma

Tadashi Kaname

Masahiro Hiratsuka

Shunsuke Kondo

Tetsuya Tono

Affiliations

Soon will be listed here.

Abstract

Both Pendred syndrome (PS) and nonsyndromic hearing loss with an enlarged vestibular aqueduct (EVA) are autosomal recessive disorders caused by pathogenic variants. The spectrum of pathogenic variants varies with the ethnic background. Among the patients with EVA in Okinawa, 94% had some combination of NM_000441.2(SLC26A4):c.1707+5G>A and NM_000441.2(SLC26A4):c.2168A>G(p.His723Arg), the two pathogenic variants that are the most common in this population. We identified these two pathogenic variants using a novel genotyping method that employed an allele-specific polymerase chain reaction (PCR) from a gDNA and single-stranded tag hybridization chromatographic printed-array strip (STH-PAS) in DNA samples obtained from 48 samples in Okinawa, including 34 patients with EVA and 14 carriers of c.1707+5G>A or c.2168A>G. In addition, whole blood and saliva samples were used for analysis in this genotyping method with direct PCR. The results of STH-PAS genotyping were consistent with those obtained using standard Sanger sequencing for all samples. The accuracy of the STH-PAS method is 100% under the optimized conditions. STH-PAS genotyping provided a diagnosis in 30 out of 34 patients (88%) in Okinawan patients with EVA in under 3 h. The turn-around time for STH-PAS genotyping used with direct PCR was 2 h as a result of the omission of the DNA extraction and purification steps. Using information about the ethnic distribution of pathogenic variants in the gene, STH-PAS genotyping performs a rapid genetic diagnosis that is simple and has a considerably improved efficiency.

References

Fujii K, Matsubara Y, Akanuma J, Takahashi K, Kure S, Suzuki Y . Mutation detection by TaqMan-allele specific amplification: application to molecular diagnosis of glycogen storage disease type Ia and medium-chain acyl-CoA dehydrogenase deficiency. Hum Mutat. 2000; 15(2):189-96. DOI: 10.1002/(SICI)1098-1004(200002)15:2<189::AID-HUMU8>3.0.CO;2-H. View

Tsukada K, Nishio S, Hattori M, Usami S . Ethnic-specific spectrum of GJB2 and SLC26A4 mutations: their origin and a literature review. Ann Otol Rhinol Laryngol. 2015; 124 Suppl 1:61S-76S. DOI: 10.1177/0003489415575060. View

Nakagawa O, Ito S, Hanyu O, Yamazaki M, Urushiyama M, Tani N . Female siblings with Pendred's syndrome. Intern Med. 1994; 33(6):369-72. DOI: 10.2169/internalmedicine.33.369. View

Miyagawa M, Nishio S, Usami S . Mutation spectrum and genotype-phenotype correlation of hearing loss patients caused by SLC26A4 mutations in the Japanese: a large cohort study. J Hum Genet. 2014; 59(5):262-8. PMC: 4521295. DOI: 10.1038/jhg.2014.12. View

Choi B, Stewart A, Nishimura K, Cha W, Seong M, Park S . Efficient molecular genetic diagnosis of enlarged vestibular aqueducts in East Asians. Genet Test Mol Biomarkers. 2009; 13(5):679-87. PMC: 2953255. DOI: 10.1089/gtmb.2009.0054. View

Looi M, Zakaria H, Osman J, Jamal R . Quantity and quality assessment of DNA extracted from saliva and blood. Clin Lab. 2012; 58(3-4):307-12. View

Newton C, Graham A, Heptinstall L, Powell S, Summers C, Kalsheker N . Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res. 1989; 17(7):2503-16. PMC: 317639. DOI: 10.1093/nar/17.7.2503. View

Yamaguchi-Kabata Y, Nakazono K, Takahashi A, Saito S, Hosono N, Kubo M . Japanese population structure, based on SNP genotypes from 7003 individuals compared to other ethnic groups: effects on population-based association studies. Am J Hum Genet. 2008; 83(4):445-56. PMC: 2561928. DOI: 10.1016/j.ajhg.2008.08.019. View

Pastinen T, Raitio M, Lindroos K, Tainola P, Peltonen L, Syvanen A . A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays. Genome Res. 2000; 10(7):1031-42. PMC: 310927. DOI: 10.1101/gr.10.7.1031. View

10.

Kwiatkowski R, Lyamichev V, de Arruda M, Neri B . Clinical, genetic, and pharmacogenetic applications of the Invader assay. Mol Diagn. 2000; 4(4):353-64. DOI: 10.1016/s1084-8592(99)80012-5. View

11.

Albert S, Blons H, Jonard L, Feldmann D, Chauvin P, Loundon N . SLC26A4 gene is frequently involved in nonsyndromic hearing impairment with enlarged vestibular aqueduct in Caucasian populations. Eur J Hum Genet. 2006; 14(6):773-9. DOI: 10.1038/sj.ejhg.5201611. View

12.

Singer V, Lawlor T, Yue S . Comparison of SYBR Green I nucleic acid gel stain mutagenicity and ethidium bromide mutagenicity in the Salmonella/mammalian microsome reverse mutation assay (Ames test). Mutat Res. 1999; 439(1):37-47. DOI: 10.1016/s1383-5718(98)00172-7. View

13.

Rah Y, Kim A, Koo J, Lee J, Oh S, Choi B . Audiologic presentation of enlargement of the vestibular aqueduct according to the SLC26A4 genotypes. Laryngoscope. 2014; 125(6):E216-22. DOI: 10.1002/lary.25079. View

14.

Usami S, Abe S, Weston M, Shinkawa H, Van Camp G, Kimberling W . Non-syndromic hearing loss associated with enlarged vestibular aqueduct is caused by PDS mutations. Hum Genet. 1999; 104(2):188-92. DOI: 10.1007/s004390050933. View

15.

Bu Y, Huang H, Zhou G . Direct polymerase chain reaction (PCR) from human whole blood and filter-paper-dried blood by using a PCR buffer with a higher pH. Anal Biochem. 2008; 375(2):370-2. DOI: 10.1016/j.ab.2008.01.010. View

16.

Zhao F, Lan L, Wang D, Han B, Qi Y, Zhao Y . Correlation analysis of genotypes, auditory function, and vestibular size in Chinese children with enlarged vestibular aqueduct syndrome. Acta Otolaryngol. 2013; 133(12):1242-9. DOI: 10.3109/00016489.2013.822555. View

17.

Tsukamoto K, Suzuki H, Harada D, Namba A, Abe S, Usami S . Distribution and frequencies of PDS (SLC26A4) mutations in Pendred syndrome and nonsyndromic hearing loss associated with enlarged vestibular aqueduct: a unique spectrum of mutations in Japanese. Eur J Hum Genet. 2003; 11(12):916-22. DOI: 10.1038/sj.ejhg.5201073. View

18.

Kumondai M, Ito A, Hishinuma E, Kikuchi A, Saito T, Takahashi M . Development and application of a rapid and sensitive genotyping method for pharmacogene variants using the single-stranded tag hybridization chromatographic printed-array strip (STH-PAS). Drug Metab Pharmacokinet. 2018; 33(6):258-263. DOI: 10.1016/j.dmpk.2018.08.003. View

19.

Ganaha A, Kaname T, Yanagi K, Naritomi K, Tono T, Usami S . Pathogenic substitution of IVS15 + 5G > A in SLC26A4 in patients of Okinawa Islands with enlarged vestibular aqueduct syndrome or Pendred syndrome. BMC Med Genet. 2013; 14:56. PMC: 3664218. DOI: 10.1186/1471-2350-14-56. View

20.

Reyes S, Wang G, Ouyang X, Han B, Du L, Yuan H . Mutation analysis of SLC26A4 in mainland Chinese patients with enlarged vestibular aqueduct. Otolaryngol Head Neck Surg. 2009; 141(4):502-8. PMC: 3309400. DOI: 10.1016/j.otohns.2009.07.004. View