How do I know if I fill-up the NGS Order Form correctly? There are some parts that I don’t have the information.
Our NGS Order Form is designed to be comprehensive for different type of NGS applications. You only need to fill-in the portion that is relevant to the accepted NGS inquiry. For your kind information, all accepted NGS inquiries by 1st BASE will be provided a specific NGS ID.
We will check through your ordering information with the specific NGS ID before proceeding the order. Shall we need further clarification, we will give you a call or email you as soon as we can to minimize delay in processing the order.
How do I know if I fill-up the Bioinformatics Analysis (BI) Form correctly? There are some parts that I’m not too sure about the options to choose.
In each of our BI Analysis Form, there is additional Tab within the same Excel File to give an example to our customers. We also prepared specific guideline for different type of BI analysis and elaborated the available options. Please contact us if you need further clarification. Alternatively, we can always setup the webchat or teleconference to guide you step-by-step.
What kind of sample are accepted and its requirement for my NGS inquiry?
We only accept biological samples categorized under WHO Risk Group 1 and Risk Group 2. Upon confirmation of acceptance for your NGS inquiry, we shall send you the sample submission guideline & sample requirements, which specified to the library construction or NGS application that you ordered.
Should I quantify my NGS sample before order submission? And how to quantify?
Yes, you are recommended to quantify your NGS sample before submitting the order.
All 1st BASE NGS Order inclusive of 1x Sample Quality Control (Sample QC) as default to assure only QC passed original sample to proceed to library construction before sequencing. It is important to know your NGS sample quality before submitting the order.
If your laboratory didn’t equip with fluorescent quantification (e.g. Qubit™) for nucleic acid according to our sample submission guideline, you shall run an agarose gel to access the nucleic acid quality and measure the concentration using Nanodrop™ or spectrophotometer. Email us your gel photo by (i) indicating the volume of nucleic acid that loaded into each well, (ii) the total volume (in µL) you have for each sample, and (iii) concentration that you measured using Nanodrop or spectrophotometer; so that we could help to give preliminary assessment of your sample quality & quantity before order submission.
Alternatively, 1st BASE offers NGS Grade DNA/ RNA Extraction as add-on services.
If I send raw sample for 1st BASE NGS Grade DNA/ RNA extraction, can I have the information about the name of the extraction kit that you use with my sample?
Yes, it is only applicable when such information is available.
Not all nucleic acid extraction can be successfully completed using commercial extraction kit. Commercial nucleic acid extraction kit can give high purity, but in most applications, you forced to repeat the extraction a few times to reach the total amount of DNA/ RNA required for NGS. In some research projects, the sample preparation prefers to be extracted from 1 individual sample rather than pooled of different extraction. At 1st BASE, we had developed a few proprietary extraction methods to breakthrough such limitations.
On the other hand, if the DNA/ RNA extraction is completed by well-developed commercial kit, we will be able to share the kit information in the final report of your NGS Order.
My samples do not meet your minimum requirements, can I still submit my order?
If you are not able to prepare fresh new samples due to nature of samples, you could submit your order by giving us the acknowledgement to accept the risks.
Typically, NGS is less forgiven to sub-optimal samples due to the relative high cost of library preparation and sequencing for each sample. Occasionally, there will be sample QC falls within the borderline of our sample requirements. Such samples could have insufficient amount of nucleic acid or contaminated with impurities.
1st BASE offers DNA/ RNA Purification as add-on services. Additional sample purification may improve the sample quality to some context. However, it will reduce the amount of the nucleic acid greatly after purification.
If we have certain level of confident to process the sub-optimal samples, we will advise you the successful rate of processing such samples directly to library construction. However, one must take note that success in library construction doesn’t mean the Bioinformatics (BI) Analysis is optimal. You could only know the impacts of processing such samples to NGS after the BI is completed and compare their data with the good samples. We believe only the project owner will be able to evaluate the acceptance of such risk(s). For example: if the samples are highly degraded (e.g. FFPE samples or nucleic acid extracted from environmental water), you have certain understanding and expectation to process the degraded nucleic acid to sequencing and you don’t expect any better samples to be compared in your BI analysis; then such cases are good to go.
On the other hand, if we don’t think it is worth of trying to proceed to library construction after access the project information, we will advise you to resend new samples. Typically, processing bad samples to library construction will generate bad libraries (fragmented libraries). If the libraries were asked to join run with other order, it will jeopardize the quality of the entire run. At such context, you may ask to pay for the entire lane or flow cell sequencing only for your order. At 1st BASE, we could process such custom run readily once you give us the greenlight to accept the new project cost assessment.
How to interpret my Bioinformatics Analysis result?
Most of 1st BASE Standard Bioinformatics (BI) Analysis accompany a summary report to assist customers to interpret the BI analysis results. You should firstly read the summary report before open any result folder. Most of the explanation of the analysis and references are available in the summary report.
Shall you need further assistance on the BI analysis, please contact us to arrange a teleconference with our assigned Bioinformatician for your Order.
Can 1st BASE keep my NGS data more than a month?
All result link in FTP or Illumina BaseSpace is only accessible for 30 days. Alternatively, you could order the data to be released in physical storage device like flash drive or external hard disk at a separate fee.
What should I do if I lost my NGS data? Can you help to retrieve my NGS data?
If the NGS data had been released within the past 3 months, we will try to look for it within our existing Cloud server. We have no guarantee that we will be able to retrieve the information. If the information is no longer available, we are afraid that you will need to rerun your Order.