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Human Whole Genome Sequencing

What is 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 6000 platforms, Oxford Nanopore PromethION and PacBio Sequel platforms.

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 of Human Whole Genome Sequencing

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

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

Benefits of Novogene Human Whole Genome Sequencing

  • High-quality data to cover whole human genomes for documentation of SNPs, InDels, SVs, and CNVs.
  • Efficient discovery of repeated sequences through third-generation sequencing long-reads technology.
  • Cost-effective strategy, low-pass sequencing, and imputation services for genome-wide association studies (GWAS) that are available for large cohorts or in complex disease research.
  • Professional bioinformatics pipeline and internationally recognized, best-in-class softwares to provide customers with reliable and publication-ready data.

hWGS Specifications: DNA Sample Requirements

Platform Type Sample Type Amount (Qubit?) Purity
Illumina
NovaSeq 6000
Genomic DNA ≥ 200 ng
OD260/280=1.8-2.0;
no degradation,
no contamination
Genomic DNA
(PCR free)
≥ 1.5 μg
Genomic DNA
from FFPE
≥ 800 ng Fragments should be ≥ 1500 bp
PacBio Sequel II DNA CLR library HMW Genomic DNA ≥ 8 μg A260/280=1.8~2.0;
A260/230=1.5~2.6;
Nc/Qc=0.95~3.00;

Fragments should be ≥ 40k

PacBio sequel II DNA HiFi library HMW Genomic DNA ≥15 μg A260/280=1.8~2.0;
A260/230=1.5~2.6;
Nc/Qc=0.95~3.00;

Fragments should be ≥ 30k

Nanopore
PromethION
HMW Genomic DNA ≥ 8 μg OD260/280=1.8-2.0;
OD260/230=1.5-2.6;

Fragments should be ≥ 30 Kb

Note: Values of sample amount are only listed for your reference. Download the Service Specifications and Sample Requirements to learn more. For detailed information, please contact us with your customized requests.

hWGS Specifications: Sequencing and Analysis

Platform Type Illumina NovaSeq 6000 PacBio Sequel I/II Nanopore PromethION
Read Length Paired-end 150 bp > 15 Kb for Sequel II
(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. Download the Service Specifications to learn more. For detailed information, please contact us for your customized requests.

    Project Workflow of Novogene hWGS Services

    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.

    Error Rate Distribution of hWGS Sequencing Results

    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

    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.


    Sequencing Depth & Coverage Distribution

    Novogene hWGS Sequencing Depth & Coverage Distribution

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

    Novogene hWGS SNP Detection

    Sample Sample_1 Sample_2 Sample_3 Sample_4 Sample_5 Sample_6
    CDS 22318 22343 22271 22702 22654 22418
    Synonymous SNP 11342 11375 11329 11,439.00 11387 11376
    missense SNP 10335 10340 10334 10643 10649 10400
    stopgain 77 81 72 87 87 8.30
    stoploss 14 13 11 12 12 10
    unknown 558 541 536 531 528 501
    intronic 1263778 1261992 1262435 1259099 1262095 1271575
    UTR3 25167 25134 25496 25396 25462 25510
    UTR5 5568 5562 5644 5767 5829 5702
    splicing 84 85 84 86 90 96
    ncRNA exonic 11867 11818 11734 11628 11697 11760
    ncRNA intronic 205360 205028 200363 199813 200397 205018
    ncRNA splicing 66 66 58 61 64 60
    upstream 22383 22339 22230 22648 22744 22708
    downstream 23565 23544 23515 23221 23235 23557
    intergenic 2119447 2115048 2110391 2091107 2098406 2138433
    Total 3700477 3693838 3685038 3662384 3673519 3727684

    Circos Diagram

    Novogene hWGS Circos Diagram

    Note: Novogene shows Circos only when CNV analysis was carried out. The figure consists seven rings from outer to inner.
    (1) The outer circle (the first circle) is chrome information.
    (2) The second ring represents the read coverage in histogram style. A histogram is the average coverage of a 0.5Mbp region.
    (3) The third ring represents indel density in scatter style. A black dot is calculated as indel number in a range of 1Mbp.
    (4) The fourth ring represents snp density in scatter style. A green dot is calculated as snp number in a range of 1Mbp.
    (5) The fifth ring represents the proportion of homozygous SNP (orange) and heterozygous SNP (grey) in histogram style. A histogram is calculated from a 1Mbp region.
    (6) The sixth ring represents the CNV inference. Red means gain, and green means loss.
    (7) The most central ring represents the SV inference in exonic and splicing regions. TRA (orange), INS (green), DEL (grey), DUP (pink) and INV (blue).


    Heatmap of Significantly Mutated Genes

    Novogene hWGS Heatmap of Significantly Mutated Genes


    Linkage Analysis

    Novogene hWGS Linkage Analysis

    Note: The upper x-axis is chromosome number; the lower x-axis is centimorgan (cM). And the y-axis is LOD score.

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