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Human Whole Genome Sequencing

Human whole genome sequencing (hWGS) enables researchers to describe the full genetic composition of individuals and characterize entire human genomes. It allows the identification of genomic variation information, including single-nucleotide polymorphisms (SNPs), insertions and deletions (InDels), structural variations (SVs), and copy number variations (CNVs) in a single and cost-efficient assay.

With extensive experience and well-developed bioinformatics know-how, Novogene delivers high-quality data, publication-ready analysis figures, and personalized results to meet different research objectives and customer needs. Novogene offers ultra-fast turnaround time, even for large projects: equipped with numerous Illumina NovaSeq X Plus /NovaSeq6000 platforms, Oxford Nanopore PromethION and PacBio Revio/Sequel II system.

Novogene is capable of sequencing up to 200,000 human genomes per year at a competitive cost. Novogene hWGS service can provide data across a broad range of applications, including studies on genetic diseases, cancers, pathogenesis mechanisms, or population genetics. Multiple DNA sequencing technologies available at Novogene can identify the highly polymorphic and highly repetitive regions within the genome of interest, thereby providing a complete and accurate human genome characterization [1].

Applications

Human genome sequencing has been assisting researchers in the following research areas:

  • Genetic diseases
  • Cancers
  • Pathogenesis mechanisms
  • Human population origins

Advantages

 
Short-read sequencing

  • Efficient discovery and documentation of genomic variants such as SNPs, InDels, SVs and CNVs.
  • Cost-effective strategy, low-pass sequencing, and imputation services for genome-wide association studies (GWAS) for larger cohorts or complex disease research.

 
Long-read sequencing

  • Efficient discovery of repeated sequences and large structural variants.
  • Direct detection of methylation information (5mC in CpG sites).

Specifications: DNA Sample Requirements

Platform Type Sample Type Amount (Qubit®) Purity
Illumina
NovaSeq X Plus /NovaSeq6000
 Genomic DNA ≥ 200 ng
A260/280=1.8-2.0;
no degradation,
no contamination
Genomic DNA
(PCR free)		 ≥ 1.2 μg
Genomic DNA
from FFPE tissue		 ≥ 400 ng Fragments longer than 1,000 bp
PacBio Revio/ Sequel II system HiFi library HMW Genomic DNA ≥5 μg A260/280=1.75-2.0;
A260/230=1.4-2.6;
*NC/QC=0.95-3.00

Fragments should be ≥ 30 kb
Nanopore
PromethION		 HMW Genomic DNA ≥ 8.5 μg A260/280=1.75-2.0;
A260/230=1.4-2.6;

Fragments should be ≥ 30 kb

*NC/QC: NanoDrop concentration/Qubit concentration

Specifications: Sequencing and Analysis

Platform Type Illumina NovaSeq X Plus /NovaSeq6000 PacBio Revio/ Sequel II system Nanopore PromethION
Read Length Paired-end 150 bp > 15 kb
(Average)		 > 17 kb (Average)
Sequencing Depth
 For rare diseases:
30-50×		 For genetic diseases:
10-20×		 For genetic diseases:
10-20×
For tumor tissues: 50×;
For adjacent normal tissues and blood: 30×		 For tumor tissues:
≥20×		 For tumor tissues:
≥20×
Standard Data
Analysis
  • Data quality control
  • Alignment with reference genome
  • SNP/InDel/SV/CNV detection
  • Somatic SNP/InDel/SV/CNV detection (For tumor-normal paired samples)
  • Data quality control
  • Sequence alignment
  • Structural variant (SV) detection
  • Variation annotation

Note: Values of sequencing depths are only listed for your reference. For more information, please contact us.

Project Workflow

From sample preparation, library preparation, DNA sequencing and data quality control, to bioinformatics analysis, Novogene provides high-quality products and professional services. Each step is performed in agreement with a high scientific standard and meticulous design to ensure high-quality research results.



[1] https://www.genome.gov/about-genomics/fact-sheets/Sequencing-Human-Genome-cost

Publications of Human Whole Genome Sequencing

Human whole-genome sequencing (WGS) allows researchers to identify inherited disorders, characterize mutations that drive cancer progression, track disease outbreaks, and achieve many other research goals. Here we have summarized some outstanding academic publications that have been using novogene hWGS services.

Data Quality Control

Sequencing Error Rate Distribution

The sequencing error rate is the major confounding factor of precise detection of low-frequency variations by deep sequencing. It determines the quality of the sequencing data. The sequencing error rate is highly associated with the sequencing cycle, escalating towards the end of each read because of the consumption of chemical reagents, which is a common feature of the Illumina high throughput sequencing platform.

Novogene hWGS Error Rate Distribution

Note: The x-axis represents position in reads, and the y-axis represents the average error rate of bases of all reads at a position.

GC Content Distribution

GC content distribution aims to check the potential of AT/GC separation. Sample contamination, sequencing bias, and errors during library preparation can impact on the sequencing results.

Novogene hWGS GC Content Distribution

Note: The x-axis is position in reads, and the y-axis is percentage of each type of bases (A, T, G, C); different bases are distinguishable by different colors.

Alignment to Reference Genome

Sequencing Depth & Coverage Distribution

Sequencing depth and coverage illustrate the average number of pair-end clean reads which are aligned to the known reference nucleotides. The sequencing coverage distribution determines whether the identification of variations can be done with a certain degree of confidence at specific base positions.

Novogene hWGS Sequencing Depth & Coverage Distribution

Average sequencing depth (bar plot) and coverage (dot-line plot) in each chromosome.

Note: The x-axis represents chromosome;the left y-axis is the average depth; the right y-axis is the coverage (proportion of covered bases).

SNP/InDel/SV/CNV Calling

Single nucleotide polymorphisms (SNPs), also known as single nucleotide variants (SNVs), constitute the largest class of genetic variants in the genome. Another class of genetic variations includes small insertions and deletions (InDels) which are <50 bp in length. The InDels present in the coding region or splicing sites may cause changes in mRNA transcripts and proteins.

Novogene hWGS SNP Detection

The number of SNPs/InDels in various genomic regions

Novogene hWGS SNP Detection

The number of different types of SNPs/InDels in the coding region

Structural variants (SVs) are genetic variants with relatively larger sizes (>50 bp), and they include deletions, duplications, insertions, inversions, and translocations. SVs form the underlying genetic basis of individual differences and have potential effects on the disease and cancer susceptibility.

 

Novogene hWGS Circos Diagram

The number of different types of SV in each sample

Note: The x-axis represents samples, and the y-axis indicates the number of each type of SV.

Copy number variants (CNVs) are genetic variants that lead to variations in copy number of relatively larger fragments (longer than 50 bp) among individuals. There are two types of CNVs, i.e. gain and loss of copies. CNVs may form the underlying genetic basis of individual differences and cancers.

https://www.novogene.com/amea-en/wp-content/uploads/sites/4/2021/10/535.png

The size of genomic regions affected by CNVs in each sample

Note:The x-axis represents samples name, and the y-axis indicates the total size of genomic regions affected by gain or loss (Mb)

Advanced Analysis

Driver Gene Analysis

Heatmap of Significantly Mutated Genes

Only a few mutations related to cancer can drive tumorigenesis by affecting genes. Significantly mutated genes (SMGs) refer to those mutations that show a significantly higher mutation rate than the background mutation rate (BMR), thus indicating a positive selection during tumorigenesis. Analysis of SMGs helps us pinpoint the key genes that are critical for cancer initiation and progression.

Novogene hWGS Heatmap of Significantly Mutated Genes

Heatmap of significantly mutated genes (SMGs) across samples

 Note:
The bar plot at the top shows the mutation rate of each sample (Mutations/Mb). The heatmap in the center shows the types of mutations of each SMG across samples. The horizontal axis represents samples, and the vertical axis represents SMGs. Different types of mutations are distinguished by different colors. The bar plot on the left side of the heatmap shows the percentage of samples affected by mutations in each SMG, and the plot on the right side shows p values of SMGs.

Tumor Heterogeneity Analysis

Intra-tumor Heterogeneity Analysis

Intra-tumor heterogeneity refers to the heterogeneous composition of tumor cells. Deciphering the intra-tumor heterogeneity and clonal architecture may contribute towards the understanding of therapeutic resistance.
The number and content (subclonal somatic mutations) of tumor subclones were identified by analyzing the variant allele frequencies of somatic mutations.

Novogene hWGS Linkage Analysis

Inferred clonal architecture

Note:
The horizontal axis of each panel represents variant allele frequency (VAF). A cluster of mutations with relatively low VAF represents a subclonal population. The top panel shows kernel density of VAFs across regions with copy number one, two, or three, posterior predictive densities summed over all clusters for copy number neutral variants, and posterior densities for each cluster/component. The panels below the top panel show read depth versus VAFs for each class of copy number regions.

*Please contact us to get the full demo report.

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