Low Coverage (aka Low Pass or Shallow or Low Read Depth) 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.
Recently, FTDNA has started replacing microarray testing with low pass sequencing. Using a 2x average read depth (6 gigabases) supposedly on an Ultima Genomics sequencer for MyHeritage. And using a Twist Biosciences enrichment panel to get 6 gigabases for their own Family Finder product. Technically, an enrichment panel is more of a WES style test and not low pass sequencing. To date, the BAMs from such testing have not been made available. Only imputed, extracted microarray file format results. For completeness, 23andMe has long offered a WES approach in addition to their microarray panel test.
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.
Recently, FTDNA has started replacing microarray testing with low pass sequencing. Using a 2x average read depth (6 gigabases) supposedly on an Ultima Genomics sequencer for MyHeritage. And using a Twist Biosciences enrichment panel to get 6 gigabases for their own Family Finder product. Technically, an enrichment panel is more of a WES style test and not low pass sequencing. To date, the BAMs from such testing have not been made available. Only imputed, extracted microarray file format results. For completeness, 23andMe has long offered a WES approach in addition to their microarray panel test.
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)
- Petter, Ella; et al, “Relative matching using low coverage sequencing”, (Sep 2020 preprint)
- Rubinacci, Simone, et al, “Efficient phasing and imputation of low-coverage sequencing data using large reference panels” (preprint)
- MyHeritage blog announcement on 2x WGS
- Cheng, Alexandre Pellan, et al, “Paired plus-minus sequencing is an ultra-high throughput and accurate method for dual strand sequencing of DNA molecules” (Aug 2025 preprint) from Ultima Genomics and others
- FamilyTreeDNA “Twist Family Finder FAQ” along with personal communications of RootsTech 2026 presentations and discussions