Tel: 1-631-275-3058 (USA)   44-208-144-6005 (Europe)       Email: info@cd-genomics.com
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Shallow Whole Genome Sequencing

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CD Genomics provides the accurate and cost-effective shallow whole genome sequencing service using Illumina or BGI DNBseq platforms to achieve genome-wide genetic variation for plants, animals and humans.

Description

Shallow Whole Genome Sequencing (shallow WGS, also known as low pass whole genome sequencing) is a new and high-throughput technology to achieve genome-wide genetic variation accurately and cost-effectively with a broad range of species: cattle, pig, chicken, dog, cat, rat, mice, corn, rice, soybean and pea and humans. Based on shotgun sequencing, shallow WGS can be used to obtain whole genome sequence at a very low coverage (most frequently between 0.4x and 1x) with over 99% accurate variant calls. Shallow WGS returns more data, greater statistical power, and new rare variant discovery capabilities than traditional genotyping arrays and GBS method. Shallow WGS can be used in genome-wide association study (GWAS), evolutionary analysis, pharmacogenomics, molecular breeding, etc. In addition, Shallow WGS can be used to build a custom reference panel for a specific population.

Advantages of Shallow Whole Genome Sequencing

  • More cost-effective than genotyping arrays and regular whole-genome sequencing
  • More data, greater statistical power, and new rare variant discovery capabilities than traditional genotyping arrays
  • Over 99% accurate variant calls across whole genome
  • Flexible setup of new species or custom populations

Shallow Whole Genome Sequencing Workflow

CD Genomics provides the accurate and cost-effective shallow whole genome sequencing and bioinformatics analysis for plants, animals and humans. Our professional expert team executes quality management, following every procedure to ensure confident and unbiased results. The general workflow for shallow whole genome sequencing is outlined below.

Shallow Whole Genome Sequencing

Service Specifications

 

Sample Requirements

  • Sample types for genome DNA, saliva, blood, fresh frozen tissue, cultured cells and FFPE samples.
  • Sample quantity:

Shallow Whole Genome Sequencing

Sequencing

  • Illumina or BGI DNBseq platforms
  • Both PCR and PCR-Free library can be constructed in the library preparation step
  • 100bp and 150bp paired-end sequencing available
  • More than 80% of bases with a ≥Q30 quality score
Bioinformatics Analysis
We provide customized bioinformatics analysis including:

  • Read alignment
  • Variant calling by imputation (reference panel: 1000 Genomes Phase 3)
  • Novel variant discovery
  • Ancestry analysis
  • Microbiome

Analysis Pipeline

CD Genomics provides full shallow whole genome sequencing service package including DNA extraction, library construction, sequencing, raw data quality control, and bioinformatics analysis. We can tailor this pipeline to your research interest. We can offer BAM and VCF data files for you. If you have additional requirements or questions, please feel free to contact us.

Shallow Whole Genome Sequencing

1. How long does it take to get my results back?

Typically, 30-40 working days from sample qualified acceptance to data analysis report availability.

2. Which sequencing machines do you use for low pass whole genome sequencing?

Illumina or BGI DNBseq platforms can be used for sequencing.

3. What are the advantages of low pass whole genome sequencing over traditional genotyping arrays?

Low pass whole genome sequencing can be used to obtain whole genome sequence at a very low coverage (most frequently between 0.4x and 1x) with over 99% accurate variant calls. Over 10x more data than genotyping arrays at a similar or lower cost. Moreover, low pass whole genome sequencing allows to discover new rare variants. All these suggest that low pass whole genome sequencing outperforms genotyping arrays.

* For Research Use Only. Not for use in diagnostic procedures.
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CONTACT CD GENOMICS

45-1 Ramsey Road, Shirley, NY 11967, USA
Tel: 1-631-275-3058 (USA)
       44-208-144-6005 (Europe)
Fax: 1-631-614-7828
Email: info@cd-genomics.com