HEREDITARY HEARING LOSS TESTING

The new DNA test is a single assay, which enables comprehensive mutation detection in a number of genes linked to hereditary hearing loss. The test covers 200 mutations in multiple genes that underlie both nonsyndromic (Connexin 26, Connexin 30, Connexin 31, Connexin 43, pendrin, prestin, mitochondrial DNA) and certain syndromic (Connexin 26) causes of hearing loss.

Asper's hereditary hearing loss test has been extensively validated by pre-screened patient DNA samples in a well-designed blind study. As our previous published studies have shown, our tests are able to detect more than 98% of the existing genetic variations, so it's well suited for screening of known mutations related to hereditary hearing loss.



35delG in connexin gene analyzed by APEX. The deletion causes frame shift in protein level.
DNA sample No 2430 is homozygous for 35delG. We have detected in sense strand mutant T allele and in antisense strand mutant A allele (T/A).
DNA sample No 2498 is heterozygous for 35delG. We have detected in sense strand normal G allele and mutant T allele. In antisense strand we have detected normal C allele and mutant A allele (GT/CA).
DNA sample No 2629 has normal genotype for position 35 - in sense strand G allele and in antisense strand C allele (G/C).

Requirements for the DNA samples 

• The DNA quality needs to be ensured (best if isolated with Qiagen kits).

• At least 1,5 mg of genomic DNA is required for HHL chip analysis

• Preferred concentration range of DNA is 100-250 ng/µl.

• DNA samples should be provided in pure sterile water.

DNA sample submitting

• For speedy and secure delivery, international courier services, for example DHL, UPS and FedEx, are recommended; alternatively, you can send samples by air mail as a small parcel. 

• Since high quality DNA samples are stable, there is no need for shipment on dry or wet ice.
  Care should be taken to avoid drying out; please use either screw cap tubes or wrap the caps of each Eppendorf tube with parafilm. 

• In order to avoid damage to the tubes during shipment, a tube storage box made of plastic or cardboard, and doubling it with a padded envelope, is recommended. Please avoid using round containers, such as 50 ml Corning tubes, for tube protection. 

• Send samples to the following address:
         Asper Biotech
         Oru 3
         Tartu 51014
         Estonia
         Ph: +372 7 441 556 

• Please fill in the DNA sample submission form, which improves and accelerates the handling of DNA samples submitted to Asper and include it in the package as you ship samples. Download the form in Microsoft Word or Adobe Acrobat (pdf) format. 

• Notify us by email (info@asperbio.com, or the respective project manager), including the number of samples, which test is to be performed, and shipment tracking data).

• Enclose in the package the list of samples, which test is to be performed and DNA quality data. 

• Please make sure that the declared value for the package in the shipment documents does not exceed 10 EUR (USD).

Additional services

Additional verification by DNA Sequencing
To confirm the results with secondary method, Asper provides verification of the APEX findings by dideoxy sequencing. Sequencing will be performed under strict quality control regulations by professionally trained personnel on Applied Biosystems 3130 Genetic Analyzer.
Hard copies of the reports on official blank
Asper can provide the formatted results on company’s official letter blank upon request. The hard copy will be signed and sealed by head of the lab and sent out by registered mail. 
Storage of DNA samples at Asper's DNA bank
Asper always performs the screening with as limited amount of DNA as possible. If there will be enough remained DNA; it can be storaged in Asper’s DNA bank. The DNA can be used for further analysis by other tests or just for re-screening. The amount of remained DNA will be measured and report will be sent to partner. The data of DNA samples will be recorded in our laboratory information system and stored under strict quality controlled manner. 
Returning of DNA samples
The remained DNA can be also sent back to partners either by regular mail or by courier.  

Turnaround Time

Standard delivery – The results will be delivered approximately in 3 – 6 weeks after the arrival of  samples.
Express delivery – The results will be delivered in 3 – 5  working days from the arrival of samples. Please note that the cost of the express delivery differs from the standard delivery. 

For further information

Payment details
Please contact: info@asperbio.com 
Hereditary Hearing Loss test (pdf, 102 kb)

Publications

1. Development of a Genotyping Microarray for Usher Syndrome
Cremers FP, Kimberling WJ, Kulm M, de Brouwer A, van Wijk E, Te Brinke H, Cremers CW, Hoefsloot LH, Banfi S, Simonelli F, Fleischhauer JC, Berger W, Kelley PM, Haralambous E, Bitner-Glindzicz M, Webster AR, Saihan Z, Debaere E, Leroy BP, Silvestri G, McKay G, Koenekoop RK, Millan JM, Rosenberg T, Joensuu T, Sankila EM, Weil D, Weston MD, Wissinger B, Kremer H.
J Med Genet. 2006 Sep 8

Usher syndrome, a combination of retinitis pigmentosa (RP) and sensorineural hearing loss with or without vestibular dysfunction, displays a high degree of clinical and genetic heterogeneity. Three clinical subtypes can be distinguished, based on the age of onset and severity of the hearing impairment, and the presence or absence of vestibular abnormalities. Thus far, 8 genes have been implicated, which together comprise 347 protein-coding exons. Therefore, sequence analysis and the most routinely used mutation scanning techniques are not cost-effective for molecular diagnostics of Usher syndrome. To improve DNA-diagnostics for patients with Usher syndrome, we developed a genotyping microarray based on the arrayed primer extension (APEX) method. METHODS: Allele-specific oligonucleotides corresponding to 298 Usher syndrome-associated sequence variants known to date, 76 of which are novel, were arrayed. The accuracy of the microarray was analysed using DNAs from 158 patients with known mutations; the efficiency of the microarray was analysed using DNAs from 370 novel European and American patients with Usher syndrome. RESULTS: Validation of the microarray yielded an accuracy of >98%. Among the novel patients, sequence variants were identified in 64/140 (46%) patients with Usher syndrome type I (USH1), 45/189 (24%) patients with Usher syndrome type II (USH2), 6/21 (29%) patients with Usher syndrome type III (USH3), and 6/20 (30%) patients with atypical Usher syndrome. The chip also identified two novel sequence variants, c.400C>T (p.R134X) in PCDH15 and c.1606T>C (p.C536S) in USH2A. DISCUSSION: The Usher genotyping microarray represents a versatile and affordable screening tool for Usher syndrome. Its efficiency will improve with the addition of novel sequence variants with minimal extra costs, making it a very useful first-pass screening tool.

2. Simultaneous multigene mutation detection in patients with sensorineural hearing loss through a novel diagnostic microarray: a new approach for newborn screening follow-up.
Gardner P, Oitmaa E, Messner A, Hoefsloot L, Metspalu A, Schrijver I.
Pediatrics. 2006 Sep;118(3):985-94.

The advent of universal newborn hearing screening in the United States and other countries, together with the identification of genes involved in the process of hearing, have led to an increase in both the need and opportunity for accurate molecular diagnosis of patients with hearing loss. Deafness and hearing impairment have a genetic cause in at least half the cases. The molecular genetic basis for the majority of these patients remains obscure, however, because of the absence of associated clinical features in approximately 70% (ie, nonsyndromic hearing loss) of patients, genetic heterogeneity, and the lack of molecular genetic tests that can evaluate a large number of mutations across multiple genes. DESIGN: We report on the development of a diagnostic panel with 198 mutations underlying sensorineural (mostly nonsyndromic) hearing loss. This panel, developed on a microarray, is capable of simultaneous evaluation of multiple mutations in 8 genes (GJB2, GJB6, GJB3, GJA1, SLC26A4, SLC26A5 and the mitochondrial genes encoding 12S rRNA and tRNA-Ser[UCN]). RESULTS: The arrayed primer extension array for sensorineural hearing loss is based on a versatile platform technology and is a robust, cost-effective, and easily modifiable assay. Because hearing loss is a major public health concern and common at all ages, this test is suitable for follow-up after newborn hearing screening and for the detection of a genetic etiology in older children and adults. CONCLUSIONS: Comprehensive and relatively inexpensive genetic testing for sensorineural hearing loss will improve medical management for affected individuals and genetic counseling for their families.