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Genotyping by Sequencing

Service Overview
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Genotyping By SequencingGenotyping by sequencing (GBS) is a rapid and cost-effective approach for comparing genotypes through the mapping of large numbers of SNPs or other markers. A restriction enzyme digestion step reduces genome complexity, so GBS can be applied to large genomes, and the end reads of the restriction fragments allow variants to be compared when no reference genome is available.

Applications of genotyping by sequencing include tracking plant and animal genotypes in breeding programs and conservation projects, examining the diversity of natural populations, discovery of new genetic markers, and screening variants prior to whole genome resequencing.

Novogene provides both GBS and WGS services, and can advise you on the best method for your project and budget goals. GBS provides less sequence data than WGS, but is more cost-effective for some applications, is highly accurate, and can be used in the absence of a reference genome. When a reference genome is available, WGS is recommended for more comprehensive comparisons.

The Novogene Advantage

  • Leader in NGS services: We provide high-quality sequencing, an efficient standard workflow, fast turnaround time, and bioinformatics analyses at a cost-effective price.
  • High quality data: We guarantee that ≥ 80% of bases have a quality score above Q30, exceeding Illumina's official guarantee of ≥ 75%.
  • Verification rate of SNPs: We promise that the verification rate of SNPs is higher than 90%.
  • Ensured sequencing depth and output for every sample: We guarantee the output, sequencing depth, and uniformity for every sample, not just the output of the overall sequencing run.

Project Workflow

Genotyping By Sequencing Project Workflow

Sequencing Strategy

  • 350-420 bp insert DNA library
  • HiSeq platform, paired-end 150 bp

Data Quality Guarantee

  • Novogene guarantees its data quality and output. Our data quality guarantee, as measured by the percentage of bases with a sequencing quality score above Q30 (PE150, ≥ 80%), exceeds Illumina’s official guarantee (PE150, ≥ 75%). See our data example.

Sample Requirements

  • DNA amount: ≥ 600 ng (for two library preparation, quantified by Qubit 2.0)
  • Total volume: ≥ 10 μl
  • Purity: OD260/280 = 1.8-2.0 without degradation and RNA contamination

Turnaround Time

  • Within 15 working days from verification of sample quality (without data analysis)
  • 10 additional working days for data analysis

Recommended Sequencing Depth

  • Tags ≥ 100,000, 8X/Tag on average

Analysis Pipeline

Genotyping By Sequencing Analysis Pipeline

Table. Representative data quality results of Novogene's genotyping by sequencing (GBS) service.
SampleRaw Base (Gb)High-quality rate (%)Error rate (%)Q20 (%)Q30 (%)GC Content (%)
Sample 123.1692.360.0594.9987.5140.60
Sample 227.2391.440.0593.8187.9442.95
Sample 325.1494.860.0495.3288.4741.87
Sample 430.2096.600.0692.4585.7942.87
Sample 531.6196.110.0495.2388.6743.19

Project Example

The following study utilized Novogene's expert genotyping by sequencing service.

Genetic dissection of maize plant architecture with an ultra-high density bin map based on recombinant inbred lines
BMC Genomics, 17: 178 (2016)

In this study, Novogene’s unique GBS strategy was used to construct an ultra-high density maize linkage map for a set of 314 recombinant inbred lines (RILs) and to explore the genetic basis of plant architecture variations using QTL mapping. Using the Illumina HiSeq2000 platform, this study shows that GBS strategy not only is a cost-effective and rapid method for SNP discovery and genotyping, but also is accurate enough to be used for efficient QTL mapping.

GBS figure

Figure. The ultra-high density bin map of the RIL populations using 4183 bin markers inferred from 88,268 high-quality SNPs.


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