Variant Calling

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Variant Calling

Luminous double helix strands of abstract DNA.

Variant calling refers to the sequencing and differential analysis of the genome of an individual or a species population by high-throughput sequencing technology. A large amount of genetic variation information can be obtained, such as single nucleotide polymorphism (SNP), insertion-deletion (InDel), structural variation (SV), copy number variation (CNV), and so forth. This basic information can be further used to develop molecular markers, establish a genetic polymorphism database, and provide data basis for the subsequent revelation of evolutionary relationships and mining of functional genes.

Long-read sequencing technologies, including PacBio SMRT and Oxford Nanopore sequencing, make it possible to detect variants in genomic regions that are proposed difficult to map through typical short-read sequencing methods (such as Illumina sequencing). CD Genomics is a leading global life sciences company. We specialize in the application of third-generation sequencing technologies. With the help of our advanced platform and skilled experts, researchers can detect all variant types from long-read datasets and discover new variants in complex genomic regions.

Overview of Genetic Variants

Genetic variation is a type of variation that can be passed on to offspring as a result of changes in the genetic material of an organism. Genetic variation is always relative. Typically, genetic variants can be divided into two categories, including sequence and structural variants. The former refers to small-scale changes at the nucleotide level affecting the coding sequence of a gene, such as single nucleotide variants (SNVs) and small insertions/deletions (InDels). Structural variants (SVs) are large genomic alterations (>50 bp), mainly including deletions, inversions, duplications, insertions, and translocations. Copy number variations (CNVs), a specific subtype of SVs, mainly manifest as deletions and duplications. These genomic variants have significant phenotypic effects, disrupting gene function and regulating or modifying gene dosage. The importance of SVs for genetic variation among individuals is greater than SNPs and/or InDels. SVs are closely associated with gene regulations, evolution, phenotype, and human diseases.

Main advantages of Long-Read Sequencing Technologies

  • The use of long-reads (>10 kb on average) from a single DNA molecule.
  • Real-time sequencing and analysis with high precision and recall.
  • No PCR amplification is required, simplifying operational processes and avoiding any PCR-related bias.
  • Allow direct sequencing of repeat expansions and regions with extreme GC-content.
  • Allows to resolve variant phasing and distinguish genes of interest from their pseudogene.

Variant Calling at CD Genomics

  • PacBio SMRT sequencing
    By utilizing the SMRT technology of the PacBio Sequel II system, we can generate HiFi reads (median consensus accuracy of >99.9% and long reads up to 30 kb) to help researchers and professionals perform comprehensive and effective variant detection. Our service enables high precision and recalls for SNVs, inDels, SVs, and CNVs even in difficult-to-map repetitive regions.
  • Oxford Nanopore sequencing
    Using the Oxford Nanopore sequencing platform, native DNA strands can be sequenced without PCR. Besides, long nanopore sequencing reads allow for a broader genomic coverage of SNV calls. Our service allows genome-wide variant detection (SNVs/SNPs) with high precision and recall.

Sample Requirements

  1. Sample Type: Genomic DNA, OD260/280=1.8~2.0, no degradation and no contamination
  2. DNA amount:
    -PacBio Sequel ll platform ≥ 10 μg, depending on the desired library insertion size.
    -Nanopore PromethION platform: ≥ 10 μg.

Workflow of Our Service

Workflow of Our Service-CD Genomics.

Analysis Contents

  • Data processing and QC.
  • Map reads to the reference genome.
  • Perform variant calling.
  • Create a summary of the variant calls.
  • Perform Variant feature annotation.
  • Visualize variants on a genome-wide scale.
  • Explore the potential functionality of individual variants.

Our services can be applied to a variety of species, with the advantages of more comprehensive detection of variants and the possibility of detecting new variants. Moreover, expedited services are available. Please feel free to contact us for more details.


  1. Ahsan, M. U., et al. (2021). "NanoCaller for accurate detection of SNPs and indels in difficult-to-map regions from long-read sequencing by haplotype-aware deep neural networks." Genome biology, 22(1), 1-33.
  2. Wenger, A. M., et al. (2019). "Highly-accurate long-read sequencing improves variant detection and assembly of a human genome." bioRxiv 519025. Figure Legends Figure, 1.
For Research Use Only. Not for use in diagnostic procedures.

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