Frequently Asked Questions
What starting materials does GeneInsight Informatic Pvt Ltd accept for the services?
We accept total RNA, genomic DNA, amplicon, cell cultures and pellets, tissues, blood, etc.
What kind of DNA/RNA analysis GeneInsight do?
GeneInsight operates a state-of-the-art Next-Generation Sequencing (NGS) facility, equipped with cutting-edge genome sequencing platforms such as Illumina’s NovaSeq X Plus and long-read sequencing technologies like PacBio (Revio/Onso). Our sequencing facility is further supported by PCR and Sanger sequencing, enabling us to offer comprehensive diagnostic solutions to individual customers, researchers, doctors, and hospitals.
What is NGS(Next Generation Sequencing)?
Next-generation sequencing (NGS) is a sequencing technology that offers ultra-high throughput,scalability, and faster DNA and RNA sequencing.
I am interested to do NGS project. How can I reach you?
Please send an email to Project Support with your contact. information. Our sales representative in your region will contact you to take things forward.
Can you help us with the experimental design?
Yes, we will be happy to help you. Our sales representative will contact you to understand your preliminary project requirements. He/She will help (if needed) to have a discussion with a technical expert (Application Scientists with expertise in the relevant area) to give critical inputs to your experimental design. Our support team will also arrange a discussion with our team of experts (Scientists from Wet lab and Bioinformatics) before the project initiation, to review the experimental design so that your aim & goals are aligned with the deliverables promised in the proposal.
How can I get a proposal?
Our sales representative/BD person will provide a proposal after having the initial discussion where your requirements are finalized.
We will have several samples collected in different time points. Should we do sequencing when we collect all samples?
You may send samples to us in several batches. This will allow us to run QC first to check for the sample quality. If sample does not pass QC, this will give you some time to prepare new samples, and we will do the sequencing when we receive all the samples.
Can you recommend any preferred RNA/DNA isolation kits to provide the best quality samples for NGS services?
For RNA-seq, Trizol is more commonly used, you can just use the Chloroform/Phenol method for purification as instructed in the Trizol kit. Another easier method is to use the commercial kit (e.g.Qiagen RNeasy Mini Kit). Moreover, for isolating total RNA from plant samples, we would recommend Qiagen RNeasy Plant Mini Kit. For miRNA sequencing, you may isolate your RNA sample with a mirVana™ miRNA Isolation Kit or Qiagen’s kit. We prefer receiving Total RNA sample however so we can perform the Bioanalyzer QC to check the RNA quality before beginning library construction.For other services, there are generally no preferred DNA/RNA isolation kits as long as minimum requirements for QC are met.
Will the long-distance transport affect the sample condition?
By using proper shipping approaches, the transport will not affect the sample condition. For DNA samples, most DNA are stable in ice for a few days, the dry ice will not require. For RNA samples, RNA is much less stable than DNA, you can send with dry ice, with ethanol precipitate or using RNAstable reagent. For tissue sample, you can send in RNAlater reagents and ship with room temperature. Please seal each vial tube to absolutely prevent leakage and breakage and evaporation, and a secondary container is recommended.
Do you accept FFPE samples for WES and RNA-seq?
Yes. For WES, we can use degraded DNA. For degraded FFPE RNA, we use Ribo-Zero technology to deplete rRNA, as the normal protocol will not work due to loss of the poly-A tails.
How long does GeneInsight keep my samples for? Do you send the left over samples back to me?
Due to limited space in the DNA Sequencing facility freezer we only keep your samples for 3 months,after which time they will be discarded without warning. If you would like your remaining samples returned to you please contact us, we will charge shipping/handling fee.
Technology Platform
Which sequencing platforms do you have?
We have the Illumina sequencing platforms(NovoSeq X plus) and PacBio SMRT. Sequel sequencing platform(Revio/Onso), and we are setting up Sanger. Sequencing platform for confirmatory test.
How do you guarantee the sequencing quality?
We will provide customers with the QC report in every major steps, i.e. QC of the initial input sample, library preparation QC and raw data QC to detect the sequencing quality. Nevertheless, be ensure to do your own quality control before you ship the samples in order to avoid delays or other pitfalls in processing. To monitor sequencing quality control, the PhiX Control will be used. Illumina PhiX Control can be used as a positive control in the clustering process. If a problem occurs in sample preparation, PhiX still generates clusters. These clusters help to discern whether a lack of clusters is due to sample preparation failure or a failure in the cluster generation process. And we will repeat the sequencing step if the failure is due to the sequencing run
What is your service pricing criteria?
Sample pricing criteria depends on the assignments involved: service type, project type, number of samples, data required and mode of data transfer
What will be your payment terms?
Please email to bdgenetics@geneinsights.ai for payment terms
What are the project deliverables for an NGS project?
Standard deliverables in a Sequencing data only project are Sample/Library QC reports, Sequenced Raw Data,Data QC report. Standard deliverables in a bioinformatics analysis alone project is data analysis report (Annexture-1). For any additional details for advanced analysis or customized analysis,you can contact on Project Support projectsupport@geneinsight.ai
How and where do I ship my samples?
Our sale representative in your region will guide you with the shipping of samples. Please refer to our (Annexure 2) for details about shipment protocols.
How will I know that samples reached in your facility?
Our Project support team will acknowledge receipt of your samples over email once they reach our laboratory. Our support team will create a unique project id for your project and share the details with you for tracking the project progress (Figure 1: Overview of the Process from lead to receiving of samples in GeneInsight Informatics Pvt. Ltd).
Can you provide more details on the project management process?
Our Project support team will acknowledge receipt of your samples over email once they reach our laboratory. Our support team will create a unique project id for your project and share the details with you for tracking the project progress (Figure 1: Overview of the Process from lead to receiving of samples in GeneInsight Informatics Pvt. Ltd).
Can you provide more details on the project management process?
Our support team will share reports on completion of each milestone such as quality control (Sample/Library/Sequencing data), sequencing data & analysis. You will be contacted if your feedback & confirmation is needed to proceed from one milestone step to another.
What is the standard turnaround time (TAT) for NGS projects?
Timelines vary depending on the project requirement. Standard TAT for Data only projects are maximum 30-45 days and Data + Analysis (Standard) projects are 90 days. TAT will be counted after samples pass there required QC parameters for processing
What should I do if my starting material is less than what your guidelines specifies?
We have experts with extensive experience with challenging samples and have many low-input protocols in place and our Project support team projectsupport@geneinsight.ai will coordinate with our Lab experts/Application scientist to help you out on low input samples.
What are your quality control steps?
Our wet lab scientist do visual inspection of samples on receipt and move to quality control tests using Agarose Gel Electrophoresis (if DNA), Qubit and/or Nanodrop. Libraries are subjected to analysis by Qubit, Tape station, Bioanalyzer and/or Pippin Pulse. Results/reports generated in each step are shared with you for review. FastQC of Sequencing Data will also be shared for your review.
How long will you keep my samples/library?
Samples are stored at -800C, -200C and 40C based on their type. DNA/RNA samples are retained up to 3 months from the receipt date, Tissue (cells/blood etc.) up to 15 days and libraries up to 2 months. If the project is not initiated within 30 days of receiving the samples, they will be discarded.
How will I know that my project is closed?
Once all QC passed samples are sequenced, data delivered, and Final analysis report shared (if opted for), your project is considered as closed. You will also receive a PCF (project closure form) which identifies the project as closed.
Whole Genome Sequencing
Prokaryotic Whole Genome Analysis Deliverables (Reference-Based)
Standard Analysis: Raw Data QC and Report, Alignment Statistics and Report, Variation Calling Report (SNP, In-Dels), Gene Annotation Table with Variations.
Bacterial Whole Genome Analysis (De-novo)
Standard Analysis: Raw Data QC & Report, Assembly Statistics and Report, Genome Finishing using Closesthomolog, rRNA identification and analysis report,Plasmid Identification and analysis report ProkkaAnnotation.
Eukaryotic Whole Genome Analysis (Reference)
RE-SEQUENCING/TARGETED/EXOME:
Standard Analysis: Raw Data QC and Report, Alignment Report, Variation calling Report (SNP, In-Dels),Basic Variation Annotation and Effect Analysis Report.
Standard Analysis: Raw Data QC and Report, Alignment Report, Variation calling Report (SNP, In-Dels),Basic Variation Annotation and Effect Analysis Report.
Eukaryotic Whole Genome Analysis (De-novo)
Standard Analysis: Raw Data QC and Report, Assembly Statistics and Report, Gene Prediction & Annotation, Report.
Whole Transcriptome Sequencing
Reference Based Standard Analysis:
Raw Data QC and Report, Read Alignment to reference genome and transcript Identifica-tion, Quantification & Expression Profiling of transcripts, Differential Analysis among the conditions, Biolog-ical Significance Analysis of differentials. Gene ontology and Pathway enrichment analysis. Graphs such as Heatmaps, volcano plots, dispersion plot, GO and pathway enrichment graphs.
Denovo Based
Standard Analysis: Raw Data QC & Report, Assembly Statistics and Report, Genome Finishing using Closesthomolog, rRNA identification and analysis report,Plasmid Identification and analysis report ProkkaAnnotation.
Small RNA Sequencing Analysis Deliverables
Standard Analysis: Sample wise Raw Data QC, Unique tags and abundance Report, Known Small RNA analysis report, Identification and Quantitation of Known miRNAs, Expression Profiling and Differential Expression Analysis of Known miRNAs. Mining of Novel miRNAs and Target Prediction
Privacy and Data use
What does your informed consent means?
Your informed consent is essential before we can test you. Obtaining consent involves informing the potential test taker about his or her rights, the purpose of the test, the procedures to be undergone, and the potential risks and benefits of participation. The goal of the informed consent process is to provide sufficient information so that a potential test taker can make an informed decision about whether to take this test and further, to enrol in a study or to continue participation in the same.
What does the consent to store my sample means?
This means that your DNA sample will be stored with the processing lab for a minimum period of 3 months for the purpose of conducting additional tests that you could opt-in for later.
How will my privacy be protected?
GeneInsight values your privacy as paramount. Your demographic and personal medical data will never be shared with a third party. We may use aggregated, anonymous data from our tests as a part of our research – but there is no link to individuals in such a use of data.