Introduction
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List of services
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Schedule
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How to submit
Repeat policy
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How to get results
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Clinical Samples
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Managing your account
Introduction
- To access services you need an account (provide contact info and basic billing info)
- Your samples need to be prepared in a specific way and placed in tubes appropriately
- The process has four possible steps: sample preparation, electronic form submission of sample info, delivery to one of our locations, and sample registration and barcoding
- We then process your samples according to our daily schedule
- Result files for most services are available for download online
- The process is completely automated with no manual pipetting of submitted samples.
List of services
Sequencing service is available for purified plasmids and PCR products. Plasmid miniprep or PCR purification can also be requested before sequencing.
Investigators performing their own sequencing reactions can request terminator removal and injection on the sequencer.
Samples are processed throughout the week usually with next business day turnaround.
Projects with large number of samples are processed on a different schedule and qualify for a discount.
Additional services may also be requested. Click on any of the services below for addition information specific to that service.
You provide a clean PCR product (single band, amplification primers removed) along with a sequencing primer
• Sequencing from plasmids
You provide a clean plasmid (single clone, column purified) along with a sequencing primer
• Injection of user-supplied sequencing reactions
You supply completed sequencing reactions for terminator removal by precipitation and injection on the sequencer
Schedule
Samples are processed Monday through Friday. To ensure next day turnaround of results please adhere to the following schedule:
| SAMPLE TYPE | MUST BE RECEIVED BY |
|---|---|
| Purified plasmid | 11 AM |
| Purified PCR product | 11 AM |
| Sequencing reaction | 3 PM |
| Microbial Isolate for Identification* | Varies |
• We also process samples sent by mail with result delivery one business day from the date of receipt.
• The result delivery turnaround for large scale sequencing projects is dependent upon the size and complexity of the work to be done.
• * Nucleic Acid Purifications for the 16S/18S Microbial Identification Test (Bacteria, Mycobacteria, Yeast or Mould).
How to submit
Sample submission is a four-step process once you have registered an account with the facility. Each step has to be completed before you can go on to the next one.
Step 1: Sample preparation
Depending on the service you are requesting, there are specific instructions to follow for successful sample preparation. Please refer to the list of services for details. In most cases you will prepare only one tube per sequence with DNA template and sequencing oligo mixed together. For best results use the tubes, plates and strips provided at no charge at one of our drop-off locations for all your sample submissions.
Step 2: Electronic form submission of sample information
• Use the username and password we have provided you when you registered your account and log in to the system from any page of the website.
• Select the online submission forms and choose the SEQUENCING submission type.
• The prompts will guide you through the process. You will need to have the following information to fill the electronic form: name of submission, type of sample submitted (plasmid, PCR product, bacterial pellet), type of plasticware in which the samples will be submitted (tubes, strips, plates), names of samples and primers and how many of each you are submitting as well as which samples will receive facility provided universal primers.
• Make sure to hit the ACCEPT button at the end of the process to complete your submission.
• Invoice documents for each submission are available to print for your records, if necessary.
Step 3: Delivery of samples to one of our locations
After making the online submission, bring the samples to one of our 24 hour drop-off locations:
• CCHMC, Research Building (Location R), 1st floor, in front of room R1031
• Samples can also be sent by mail to the following address:
CCHMC DNA Sequencing Facility - Location R1045A
3333 Burnet Avenue
Cincinnati, OH 45229
Step 4: Sample registration and barcoding
This step does not apply to samples sent by mail. In this case, the barcoding is done upon sample receipt by the facility personnel.
The registration process is the assignment of a barcode identifier to a specific tube, strip or plate containing samples submitted for
sequencing. It is done by using the computers with a barcode scanner at each of our drop-off locations.
There is a shortcut on the desktop of these computers called BARCODE REGISTRATION which will take you to the online registration form.
• Use the username and password we have provided you when you registered your account and log in to the system.
• Select the submission name for which you are bringing the samples to register from the list of submissions.
• A complete display of the tubes, strips or plates used in your submission and the name of samples they contain will be shown on screen.
• Proceeding in the order they are displayed, affix a barcode label to each tube, strip, or plate and scan it using the barcode scanner.
• Make sure that each tube, strip or plate in your submission has been assigned the correct barcode before pressing the SUBMIT BARCODE REGISTRATION button.
An alert will confirm that barcodes have been saved.
• Once the all samples are barcoded and registered you can place them inside the refrigerator on any rack available.
Repeat policy and quality control
In the event of a technical failure, it is possible in most cases to repeat the service requested for a particular sample at no charge. The quality of every sequence is checked at the end of a run prior to result delivery and failed sequences are evaluated for the possibility that a technical problem has caused the failure, in which case the sample is automatically scheduled for repeat. These cases are very rare and make up a very small percentage of repeated samples.
Some samples are chosen from every run to be repeated, even without evidence of any sample-specific or run-wide technical failure as a cause. In these cases, we expect very similar results to the original run and utilize these samples for our own internal process quality control. Repeats of this type make up the vast majority of repeated samples.
If you have reasons to believe that some of your samples have failed for a technical reason rather than a template preparation problem and did not get scheduled for repeat please contact us for a reevaluation. We process internal quality control samples (both positive controls and negative controls) on every run to identify systematic problems at each step of the automated process.
Completed sequencing reactions submitted for injection (ABI BigDye terminator v1 chemistry only) are used up during the initial sequence generation and cannot be repeated.
Once your results are available for a particular submission you will receive a notification by email. You can also login through our website to proceed to the result download page of any submission you have made in the past 6 months.
For each sequence, two results files will be generated. The .seq file contains the sequence (base calls) in plain text format. The .ab1 file contains the complete electronic sequence data including the analyzed electropherogram (peaks). In order to view the electrophrerogram on your computer you will need a specific sequence viewer software. We recommend FinchTV from Geospiza. FinchTV has now entered into its 'End of Life phase' and is no longer supported by PerkinElmer.
All the files for a specific submission are placed in a folder and compressed into a .zip file. You can download this .zip file from our website in either PC or MAC format.
If any samples from a particular submission has been repeated they will be placed into the same folder as the original with a naming convention of the name of the sequence from followed by _R.
To maintain the accreditation of our laboratory with the College of American Pathologists (CAP) guidelines, we require that all nucleic acid samples that are destined for clinical testing have been isolated in a CLIA-certified laboratory or a laboratory meeting equivalent requirements for nucleic acid isolation and purification. The CAP standard is referenced below:
If extracted nucleic acid is accepted as a specimen type, the laboratory has a written policy that isolation of nucleic acids for clinical testing occurs in a CLIA-certified laboratory or a laboratory meeting equivalent requirements as determined by the CAP and/or the CMS. This policy is clearly displayed to ordering clients.
User accounts are now linked to your CCHMC network ID and password. For investigators outside of CCHMC, a request for a CCHMC network ID will need to be made by contacting help-cores@bmi.cchmc.org. All IDs must be provisioned for use with our interface by facility administrators. If you are having difficulty in registering, or have an existing account that needs to be inactivated, please contact us at dnacore@cchmc.org or by phone at (513) 636-2801. Currently, user accounts are associated to a single principal investigator (PI), and linked to that PIs available PeopleSoft budget numbers. If you work for more than one PI, please contact us.