What is the purpose of the International Standards for Cytogenomic Arrays Consortium?

 The ISCA Consortium aims to improve clinical care by providing a large publicly available database and forum where clinicians and researchers can share knowledge to expedite the understanding of copy number variation (CNV) in an abnormal population.

What is the purpose of the ISCA Clinical CNV Database?

The database will serve as a central repository for cytogenetic array data generated in clinical testing laboratories. The very high quality of copy number data (i.e., deletions and duplications) coming from clinical laboratories combined with expert curation will produce an invaluable resource to the clinical and research communities. This large abnormal database will help to classify CNVs of uncertain clinical significance and to translate this knowledge for the improvement of patient care.

Where can I find the ISCA Clinical CNV Database?

The database will be hosted by NCBI in dbGaP (database of Genotypes and Phenotypes) and dbVar (database of genomic structural Variation). The URL for the ISCA study in dbGaP is http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000205.v3.p2

What data is available to the public?

CNV calls with their clinical interpretations will be available to the public in dbVar. In addition, this data will be available through multiple other sources, including the ISCA website, the UCSC Genome Browser, and commercially available array software programs.

For clinical calls submitted to the ISCA database:   http://www.ncbi.nlm.nih.gov/dbvar/studies/nstd37/

For the ISCA list of established pathogenic and benign regions: http://www.ncbi.nlm.nih.gov/dbvar/studies/nstd45/

What data will require controlled access?

 Raw and normalized array data will be deposited into dbGaP and will require controlled access. Access to data in dbGaP must be approved through the Data Access Committee (DAC).

Opt-out Notification:

Is informed consent required from patients using the opt-out notification process?

Informed consent is not required for opt-out notification. The NIH allows clinical laboratories to submit clinical data using an opt-out mechanism, whereby clinicians and patients are informed of the use of de-identified data and patients are provided a means to withdraw participation.

What is the Opt-Out Notification?

This mechanism is based on the following premises: 1) Reasonable effort is made to inform the ordering clinicians of the use of de-identified patient data; and 2) Reasonable effort is made to inform patients of data usage through educational materials and that patients must be provided a means to withdraw participation from the database.

How is the opt-out notification implemented?

The opt-out statement must be placed on the test requisitions and clinical reports. In addition, reasonable attempts to notify the patient of the use of de-identified data should also be made. An example of the opt-out statement can be found on the ISCA website Member page.

How will patients learn about participation in the ISCA Clinical CNV Database?

 All clinical laboratories that would like to contribute prospective data are required to place the opt-out statement on test requisitions and reports. In addition, educational materials should be provided to the patient in the form of lay-oriented web content and fact sheets. The ISCA Consortium is also educating clinicians and genetic counselors of their role in notifying patients of the database and the opt-out notification at scientific conferences and through webinars.

Why use an opt-out mechanism instead of a consent form?

For clinical laboratories that do not obtain full consent for testing, the opt-out process provides another mechanism to collect microarray data for submission to the ISCA Clinical CNV Database.

Is there a time limit on withdrawing participation from the database?

A patient will be able to opt-out at any time.

Is it necessary to notify individuals who had previous testing of the opt-out feature?

No, data obtained prior to implementation of the opt-out feature will be submitted as retrospective data and handled accordingly.

What are the requirements of the opt-out statement?

The opt-out statement provided to ISCA consortium members contains all of the required elements originally set by the NIH and CETT (Collaboration Education and Test Translation Program) collaborative project. An example of the opt-out statement is located in the Member section of the ISCA website.

Where can I find additional information about the opt-out notification?

 Additional FAQ’s on the opt-out mechanism may be found on the CETT website: (http://rarediseases.info.nih.gov/cettprogram/patient_privacy.aspx).

Data Handling:

What types of data does the ISCA database contain?

 The ISCA database accepts raw and normalized array data, CNV calls with clinical interpretations, and phenotype information from the study.

Is patient confidentiality maintained?

The data submitted to the database is de-identified. The database is HIPPA-compliant in maintaining patient privacy and confidentiality. Contributing laboratories are required to certify that adequate precautions are taken to protect patient privacy.

How is confidentiality maintained?

All patient identifiers such as name, date of birth, and unique laboratory accessioning numbers are removed prior to data submission. Data is submitted using a de-identified case number. The submitting laboratory certifies that appropriate protocols for anonymizing data have been followed.


Does an individual need an institutional affiliation to register with the ISCA Consortium?

No. We request that you enter your sponsoring institution in the registration form, but you do not need to be part of a contributing laboratory to register.

Will phenotypic information be the same at the public and controlled-access levels?


At which levels will the raw array data be available?

The raw and normalized array data will be available in dbGaP through controlled access.

What level of access will healthcare providers (clinicians, genetic counselors, etc.) have to the database?

Healthcare providers will have access to the public databases including dbVar. They may also choose to apply for access to the raw and normalized data in dbGaP through the DAC.

What level of access will participating laboratories have to the database?

Clinical laboratories will have access to public data. They may also choose to apply for access to the raw and normalized data in dbGaP through the DAC.


 Does the ISCA Consortium recommend a particular slide format from the four ISCA designs?

 No, laboratories should utilize the slide format appropriate for their needs. Many laboratories prefer the 8x60k for greater efficiencies in cost and through-put.

Do ISCA Consortium laboratories receive a discount for slides?

Some vendors offer a discount for ISCA Consortium members. Please contact your local sales representative for information.

Does the ISCA Consortium share array protocols?

The ISCA Consortium offers troubleshooting tips such as suggested software protocol suggestions in the Members section of the website. Additional information on array protocols and other items can be found within the ISCA forum.