Application of SNaPshot multiplex assays for simultaneous multigene mutation screening in patients with idiopathic sensorineural hearing impairment.
OBJECTIVE
To develop a cost-effective and robust genetic diagnostic tool for patients with idiopathic nonsyndromic sensorineural hearing impairment.


METHODS
Development of a diagnostic tool and validation in a prospective cohort.


METHODS
Twenty common sequence variants in GJB2, SLC26A4, and the mitochondrial 12S rRNA gene were selected based on our previous epidemiological study. These variants were analyzed using the SNaPshot technique. The efficacies of the SNaPshot multiplex assays were determined by using a prospective cohort composed of 214 unrelated Taiwanese patients with idiopathic sensorineural hearing impairment. The results of the assays were compared to the results obtained by direct sequencing.


RESULTS
We developed a diagnostic technique consisting of two consecutive panels of SNaPshot multiplex assays, with each panel screening 10 common sequence variants. Theoretically, this design can detect more than 98% of the known deafness-associated sequence variants in Taiwanese individuals. A total of 126 (58.9%) patients were diagnosed as having at least one sequence variant using the SNaPshot multiplex assays. In total, the SNaPshot assays yielded an accuracy of more than 99%.


CONCLUSIONS
The strengths of SNaPshot multiplex assays include high accuracy, high sensitivity, high flexibility (the examination panel can be easily expanded for additional mutations), low cost (less than US $10 per patient), and easy implementation for any institute with a DNA sequencer. Although only 20 to 30 mutations can be examined in two to three runs of the SNaPshot assay, this technology may be suitable for first-pass screening of deafness-associated mutations in populations with a relatively homogeneous ethnic background.
Wu
Chen-Chi
CC
Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan.
Lu
Ying-Chang
YC
Chen
Pei-Jer
PJ
Liu
Alyssa Yan-Zhen
AY
Hwu
Wuh-Liang
WL
Hsu
Chuan-Jen
CJ
D001692:Biological Transport; D000072259:Connexin 26; D017630:Connexins / Q000235:genetics; D003362:Cost-Benefit Analysis; D004252:DNA Mutational Analysis / Q000191:economics / Q000379:methods*; D003937:Diagnosis, Differential; D005500:Follow-Up Studies; D005820:Genetic Testing / Q000191:economics / Q000379:methods*; D006319:Hearing Loss, Sensorineural / Q000175:diagnosis* / Q000453:epidemiology; D006801:Humans; D026901:Membrane Transport Proteins / Q000235:genetics; D009154:Mutation; D016133:Polymerase Chain Reaction; D015995:Prevalence; D011446:Prospective Studies; D012333:RNA, Messenger / Q000032:analysis* / Q000235:genetics; D015203:Reproducibility of Results; D000076988:Sulfate Transporters; D013624:Taiwan / Q000453:epidemiology
D017630:Connexins; C000607042:GJB2 protein, human; D026901:Membrane Transport Proteins; D012333:RNA, Messenger; C085609:SLC26A4 protein, human; D000076988:Sulfate Transporters; D000072259:Connexin 26