Low Coverage (aka Low Pass or Shallow) is a type of full-sequencing gaining popularity over microarrays for Genome-Wide Association Studies (GWAS). This is especially true for non-human analysis where microarrays are not developed. This type of sequencing is depicted by an average read depth below 1 over the whole genome; most often characterized as 0.4x or returning around 1.3 gigabases in a human genome sample. A typical WGS with a clinical 30x average read depth returns over 90 gigabases of sequenced base-pairs. Studies have shown that this technique can be as effective as a microarray in GWAS; especially when used in conjunction with Imputation of missing values. It can thus be cost-effective like a microarray as many more samples can be mixed on a flow-cell during a single sequencing run than for a traditional variant-calling, individual-analysis WGS.
Personally, we prefer to not use the term Low Pass as the term "pass" is already used as a quality metric in variant calling for sequencing. This is not to be confused with that aspect.
Historically, Nebula Genomics was offering the 0.4x low coverage sequencing test in addition to a microarray one before introducing their full 30x WGS product. But the reliance on Imputation as a way to get increased coverage for a single sample / tester is a big drawback to its usefulness in Genetic Genealogy or any individual-tester diagnostics.
Personally, we prefer to not use the term Low Pass as the term "pass" is already used as a quality metric in variant calling for sequencing. This is not to be confused with that aspect.
Historically, Nebula Genomics was offering the 0.4x low coverage sequencing test in addition to a microarray one before introducing their full 30x WGS product. But the reliance on Imputation as a way to get increased coverage for a single sample / tester is a big drawback to its usefulness in Genetic Genealogy or any individual-tester diagnostics.
External References
- Low-Coverage Whole Genome Sequencing: Learning From Less Data (NCI)
- Shallow Whole Genome Sequencing (CD Genomics)
- Comparing low-pass sequencing and genotyping for trait mapping in pharmacogenetics (BMC Genomics)
- What is 30x and 0.4x Whole Genome Sequencing? (Sequencing)