Shallow Whole Genome Sequencing (sWGS)
What Is Shallow Whole Genome Sequencing (sWGS)?
Shallow Whole Genome Sequencing (sWGS), or “low-pass WGS”, is a low-coverage, cost-effective alternative to deep WGS that surveys the entire genome at just 0.1×–5× coverage. By spreading ~5–20 million reads per sample evenly across all chromosomes, sWGS delivers genome-wide insights—without the cost or data volume of deep WGS. At 0.5×–1× depth, it achieves >99% concordance with common SNP arrays and vastly outperforms Genotyping-By-Sequencing (GBS) in marker density and rare variant discovery. Because sWGS captures broad copy-number variation, aneuploidy, and structural signals, it’s ideal for CNV detection, tumor purity and ploidy estimation, cfDNA liquid biopsies, and biobank QC.
Unlike arrays or species-specific genotyping panels, sWGS works seamlessly across humans, livestock (cattle, pig, chicken), companion animals (dog, cat), model organisms (mouse, rat), and key crops (corn, rice, soybean, pea). Large-scale studies—from GWAS and evolutionary analyses to molecular breeding and pharmacogenomics in under-represented populations—benefit from its low input requirements (as little as 5–10 ng cfDNA), massive multiplexing (hundreds of samples per flow cell), and rapid 7–10 day turnaround.
At AUGenomics, our sWGS workflows are optimized for flexibility, scalability, and affordability—perfect for high-throughput applications and exploratory studies.
Advantages of Shallow WGS
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Genome-Wide Insight: Detect arm-level and focal CNVs, aneuploidy, and large structural changes across all chromosomes.v
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Cost & Data Efficiency: Sequence at ~1/10th the depth of standard WGS—reduce reagent costs and storage requirements by up to 80%.
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High Throughput: Multiplex hundreds of samples per flow cell; ideal for large cohorts or biobank QC.
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Low Input Requirements: Works with as little as 5–10 ng cfDNA or 50 ng gDNA, including FFPE-derived DNA.
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Rapid Turnaround: Standard projects complete in 7–10 business days, with rush options down to 5 days.
Shallow WGS is a powerful tool for:
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Copy-Number Variation (CNV) Detection: Map gains/losses in cancer biopsies, rare disease syndromes, or prenatal screening.
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Tumor Purity & Ploidy Estimation: Quantify tumor cell fraction and genome-wide ploidy shifts in oncology research.
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cfDNA Liquid Biopsy: Screen plasma for broad CNV signals as an early cancer detection or monitoring tool.
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Biobank & QC Screening: Validate sample integrity and detect large-scale genomic artifacts before downstream assays.
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Population-Scale Studies: Perform cost-effective genome-wide surveys in hundreds to thousands of samples.
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Genome-wide screening: for structural abnormalities
If you’re looking for broad insights across the genome at a fraction of the cost of deep sequencing, sWGS offers a valuable starting point
What is Shallow WGS Used For?
Shallow Whole Genome Sequencing (sWGS)
with AUGenomics
Sample Submission
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Accepted Sample Types: Genomic DNA, FFPE-derived DNA, or cell-free DNA (cfDNA) from blood, plasma, or tissue
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Input Requirement: DNA: ≥50–100 ng (≥10 ng for cfDNA workflows)
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Sequencing Recommendations:
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0.1x to 5x coverage depending on analysis goals
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~5–20 million reads per sample
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Supports high multiplexing for large cohorts
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Please refer to our Shipping Guidelines for project-specific guidance.
Turnaround Time
Shallow WGS projects are completed in 7 to 10 business days following sample receipt. Expedited options are available depending on project scope and sequencing depth.
Frequently Asked Questions (FAQs)
Q: What is the difference between shallow and deep WGS?
A: Shallow WGS uses low sequencing depth (typically 0.1x to 5x coverage) to capture broad genome-wide trends, rather than specific variant calls. Deep WGS provides higher resolution for detecting SNVs, indels, and structural variants.
Q: Is sWGS compatible with cfDNA?
A: Yes. Shallow WGS is frequently used to assess CNVs in cell-free DNA from liquid biopsies, especially in oncology applications.
Q: Can I use sWGS for large-scale cohort studies?
A: Absolutely. sWGS is ideal for projects involving dozens to hundreds of samples due to its cost-effectiveness and high-throughput capacity.
Got more questions? Contact our team and get a free consultation anytime. info@augenomics.com
Glossary of Terms
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sWGS: Shallow Whole Genome Sequencing
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CNV: Copy Number Variation
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cfDNA: Cell-Free DNA
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Coverage: The average number of times each base in the genome is sequenced
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Multiplexing: Processing multiple samples in a single sequencing run
