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Low-Pass Whole Genome Sequencing (lpWGS)

 

Description

Low-pass whole genome sequencing (lpWGS) is commonly defined as sequencing a genome to an average depth less than 1x coverage. lpWGS, combined with genotype imputation, offers an alternative approach to genotyping arrays for trait mapping and calculation of polygenic scores.

Further, it has been reported that low-pass sequencing plus imputation, in addition to providing a substantial increase in statistical power for genome wide association studies (GWAS), provides increased accuracy for polygenic risk prediction (PRS) at effective coverages of 0.5x and higher Applications of lpWGS include genome-wide association studies, biobank profiling, and pharmacogenomics. In addition, lpWGS is easy to set up and customize for specific populations and cases.

 

Low-Pass WGS Advantages

  • Accuracy with less ascertainment bias.
  • 10x more data than genotyping arrays at a similar or lower cost.
  • 10x reduction in cost relative to whole-genome sequencin.
  • 99% accurate whole genome variant calls.
  • Low DNA input required High-throughput and scalable.
  • Less ascertainment bias than genotyping arrays.
  • Complete genomic information to discover novel variation at the population level.
  • Fast and high-volume achieved by multiplexing large numbers of samples.
  • Easy to set up and future-proofed by updating the reference pane.

 

Imputation quality of low-pass sequencing vs genotyping

Low-pass sequencing at 1x coverage consistently yields higher imputation quality than genotyping arrays in European and African populations, but the difference is especially pronounced in African samples.

 

Concordance of low-pass sequencing vs genotyping to the gold-standard

The concordance of imputed low-pass sequencing data to the gold-standard 1000 Genomes data exceeds that of imputed microarray genotypes from the Illumina GSA across all allele frequency bins and is consistently high for both African and European samples.

 

Key Service Details

  • PCR and PCR-free library methods are available.
  • Library construction: DNBSEQ PCR-based/PCR-free library (~350bp insert size).
  • 100bp/150bp Paired end sequencing.
  • Choice of sequencing depth: low pass WGS (1x, 4x, or custom).
  • CAP/CLIA laboratory services available.

 

Sequencing Quality Standard

Guaranteed ≥80% of bases with quality score of ≥Q30.

 

Sample Requirements

We can process your gDNA, saliva, blood, fresh frozen tissue, cell pellets and FFPE samples, with the following general requirements:

  • Regular Samples for PCR Library: Genomic DNA > 1ug (c > 12.5 ng/ul).
  • Low Input Samples for PCR Library: Genomic DNA > 200 ng (c > 2.5 ng/ul).
  • Samples for True PCR-free Library: Genomic DNA > 2 ug (c > 12.5 ng/ul).

 

Turnaround Time

Typically, 18 working days from sample QC acceptance to data analysis report availability

Expedited services are available.