Low-Pass Whole Genome Sequencing Frequently Asked Questions

General Questions

1. What is low-pass whole genome sequencing (LP-WGS)?

Low-pass whole genome sequencing (also referred to as LP-WGS or shallow whole genome sequencing) is an inexpensive, high-throughput, DNA-sequencing technology used to accurately detect genetic variation within the genomes of a multitude of species. Using imputation algorithms, this technology offers a high accuracy of variant call detection at a very low sequence coverage.

2. What are the advantages of LP-WGS over other techniques?

LP-WGS has the following advantages:

  • Inexpensive alternative compared to exome, WGS, and genotyping arrays
  • Higher statistical power, discovery of new rare variants, provides significantly more data compared to genotyping arrays
  • Up to 99% accurate detection of variant calls
  • Low DNA input required

3. What is the LP-WGS Plus solution?

In some cases, e.g. clinical applications, it may be beneficial to receive additional coverage of specific regions of interest using deep sequencing approaches. GENEWIZ’s LP-WGS Plus service is a unique solution that combines LP-WGS with our exome sequencing or targeted sequencing services, enabling researchers to gain additional coverage of particular genomic regions or variants while still remaining cost-effective.

4. How does GENEWIZ utilize imputation for LP-WGS and LP-WGS Plus?

Imputation based analyses have become a key tool for analyzing human genetic data. Imputation is a technique that uses the sequence data generated alongside publicly available reference data to bioinformatically “fill in the gaps” allowing researchers to accurately evaluate the association of genetic markers that are not directly sequenced.

5. Can GENEWIZ assist with experimental design?

Absolutely! GENEWIZ's NGS team is comprised of a group of dedicated technical experts that are available to assist with designing your experiment and answering any questions you may have. You can either submit your questions using the quote request form to your left, or you can submit an inquiry through the button above.

6. How do I contact GENEWIZ for a technical consultation about my project?

GENEWIZ's NGS team is composed of Ph.D. scientists who can help you optimize your project design and provide consultation. Contact us here.

7. What is the price for LP-WGS?

Please submit a quote request to receive accurate pricing information, as cost varies depending on the details of the project.

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Sample Preparation

8. How should I prepare my samples?

Please submit at least 500 ng of normalized genomic DNA at a concentration of 20 ng/µL in 96 well plates. We do not perform sample QC in order to provide the most cost-effective service possible.

9. Does the starting material need to be normalized to 20 ng/µL?

Yes, you must normalize your starting material as GENEWIZ does not adjust the concentration prior to library preparation. For optimal results, please adjust your sample concentrations to 20 ng/µL prior to submission. We recommend using a dsDNA quantification assay such as Qubit or PicoGreen.

10. What are the sample submission guidelines?

  • Sample Type: Genomic DNA
  • Sample Purity (OD260/280): 1.8-2.0
  • Minimum Amount: 500 ng (We recommend using a dsDNA quantification assay such as Qubit or PicoGreen.)
  • Concentration: Normalized to 20 ng/µL
  • Resuspension Buffer: Water, EB, or low TE (<0.1 mM EDTA)
  • Shipment Method: Dry Ice

11. Do you accept other sample types besides Genomic DNA?

Yes, for complete sample details, see the Sample Submission Guidelines.

12. What happens if my samples do not meet your starting material requirements?

GENEWIZ's NGS team is composed of Ph.D. scientists who can help you optimize your project design and provide consultation. Contact us here.

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Sequencing & Data Analysis

13. Which sequencing platform should I choose?

The answer is highly dependent on many factors, including the goals of your experiment, the organism of interest, and the amount of material available. In most cases, standard Illumina® platforms with 2x150 bp chemistries are used for LP-WGS projects.

14. Which organisms are available for imputation?

Human, mouse, rat, dog, soy, maize, domestic cat, chicken, and cattle.

15. Am I out of luck if my species of research is not on your list?

Absolutely not! We may be able to build a reference genome for you. We can perform deep sequencing on a select number of individuals and assemble a reference genome for imputation. Please contact us for more details.

16. What reference database(s) are used for each species?

We use 1000 Genomes Phase 3 for our human imputation reference panel. For more information on reference panels from other species, contact our NGS team at NGS@genewiz.com.

17. What bioinformatics analysis does GENEWIZ offer for LP-WGS?

Standard deliverables for LP-WGS (human, mouse, rat, dog, soy, maize, domestic cat, chicken, and cattle) include the following:

  • Sample QC, includes raw data QC & alignment metrics.
  • FASTQ files
  • Aligned BAM file: BAM file with reads aligned to the target genome, includes all reads from original FASTQ files
  • Imputed VCF file

Human LP-WGS deliverables:
In addition to the standard deliverables for all species, human LP-WGS data analysis also includes the following:

  • Copy number variant analysis
  • Ancestry analysis
  • Calculated polygenic risk scores files

Custom bioinformatics analysis and reports are available. Please contact us for details on customizing your analysis to answer your biological question(s).

18. How is data delivered?

GENEWIZ will recommend the best data delivery option based on the platform and project details. Data delivery options include:

  • Secure File Transfer Protocol (sFTP
  • Customer cloud account
  • Hard drive (additional charges may apply)

Please note in the “Additional Comments” section of your quote request if you have any specific preference for the above data delivery options.

19. How will my data be delivered?

If your results are being shipped to you via hard drive, you can track its shipment using the tracking number provided to you in the delivery email sent from GENEWIZ.

If your results are being delivered via another data delivery method, such as AWS S3, Aspera, or other cloud-based methods, please refer to the delivery email sent from GENEWIZ for detailed information on the transfer, and consult with your IT department to ensure compliance with your institution’s policies.

If your results are being sent via a secure File Transfer Protocol (sFTP), please refer to GENEWIZ’s sFTP Data Download Guide for instructions on how to download your data and troubleshooting tips.

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Order & Processing

20. How do I request a quote?

Please fill out a quote requestand our NGS team will follow up with you shortly.

21. What happens after I submit a quote request form?

Our NGS team will review your inquiry, follow up with a quote, and guide you through the next steps.

22. How do I confirm a quote?

For a quick tutorial, watch the video below.

23. How do I submit the GENEWIZ Sample Submission Form to provide detailed information about my samples?

Upon project confirmation, our NGS team will share our Sample Submission Form. Please complete the Form and send it back to NGS@genewiz.com. Our team will update the details of the project on your behalf.

24. How can I monitor the progress of my project?

The status of your order, including an estimated date of delivery, can be viewed anytime through your GENEWIZ account. Visit the Order Summary page of your project to find the current order status. Watch the video below for a brief tutorial.

25. How long does GENEWIZ hold samples?

We hold samples for 1 year after project completion. Please contact us if you would like samples retained for a longer period or shipped back to you.

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Have a specific question? Contact us!

Email | 877-436-3949, Ext. 1

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