Human whole-genome resequencing (WGS) is the most comprehensive means of dissecting human genetic identity. By reading full coverage of coding and non-coding regions, single nucleotide polymorphisms (SNPs), small insertions/deletions (InDels), copy number variations (CNVs), and large structural variants (SVs) can be mapped with high precision.
1. Sequencing depth configuration: 30X population cohort type, 60X disease screening type, 90X+ ultra-deep tumor type.
2. Standard analysis pipeline: Align to the reference genome (hg19/hg38), apply the GATK Best Practices process to extract mutation sites and perform fine filtering and quality control.
3. Interpretation of clinical notes: Deeply integrated with dbSNP, 1000 Genomes, and ClinVar databases to assist in the ranking of rare mutations, single-gene variants, and pathogenic sites.
Relying on the self-developed T-Series ultra-high-throughput sequencer, it has an extremely low clone amplification duplication rate (Duplication Rate < 3%). The data volume is stable and reliable, and the Q30 base quality assurance rate exceeds 85%, providing higher quality variant calling results.
Bioinformatics analysis delivers rich content and provides a full set of standardized charts, including sequencing quality control reports, alignment coverage distribution charts, and variant calling statistical reports.
| index | industry standard | HST Delivery Metrics |
|---|---|---|
| Base Quality Score (Q30) | ≥ 75% | ≥ 85% |
| Mapping Rate | ≥ 95% | ≥ 98% |
| Duplication Rate | ≤ 10% | ≤ 3% |
| Coverage Uniformity (Fold-80 Penalty) | ≤ 1.8 | ≤ 1.4 |
To ensure smooth sequencing, please follow these guidelines to prepare and submit DNA samples for analysis:
| Sample type | Total quantity requirement | Concentration requirements | Purity requirements (OD 260/280) | Shipping conditions |
|---|---|---|---|---|
| Genomic DNA (blood/tissue extraction) | ≥ 1.0 µg | ≥ 20 ng/µL | 1.8 - 2.0 (no RNA residue and degradation) | Transport on dry ice to avoid repeated freezing and thawing |
| Whole blood samples (EDTA anticoagulant tubes) | ≥ 2.0 mL | - | - | Shipped in ice packs at 4°C, delivered within 24 hours |
| Saliva/mouth swab | According to collection tube standards | - | - | Shipping at room temperature or 4°C with ice packs |
Human whole-exome sequencing (WES) focuses on protein-coding regions that make up approximately 1-2% of the genome. This region is enriched for approximately 85% of known disease-causing mutations in humans, making WES a highly cost-effective approach in clinical genetics and large population-based cohort studies.
HST GENOMICS is deeply compatible with mainstream exon enrichment technologies such as Agilent SureSelect and Roche NimbleGen. At the same time, we provide products optimized for East Asian people. HST-Exome Exon Capture Chip, ensuring a high degree of uniformity of probe hybridization.
1. Single gene genetic disease testing: Combine Trio families (proband and parents) for rapid filtering analysis of recessive, dominant or de novo mutations.
2. Tumor-targeted driver mutations: Perform deep exome sequencing on paired tumor-adjacent tissue to capture somatic mutations.
3. Large sample queue association: Under low budget, realize the construction of deep mutation map of coding regions from thousands to tens of thousands of samples.
The output of exome sequencing bioinformatics analysis includes standard VCF mutation files and is automatically connected to mutation databases such as ClinVar, OMIM and 1000G to assist in clinical pathogenic classification.
| Chip platform | Average sequencing depth | Capture target area coverage (≥10X) | On-target Rate |
|---|---|---|---|
| HST-Exome v2 (58Mb) | ≥ 100X | ≥ 99.0% | ≥ 65% |
| Agilent V8 (36Mb) | ≥ 100X | ≥ 98.5% | ≥ 60% |
Exon capture has high requirements on DNA integrity. Please refer to the following standards when submitting samples:
| Sample type | minimum total amount | Concentration range | OD 260/280 | Shipping advice |
|---|---|---|---|---|
| Highly pure genomic DNA | ≥ 500 ng | ≥ 10 ng/µL | 1.8 - 2.0 (the main band in agarose electrophoresis is clear) | Shipped on dry ice or -20°C ice packs |
| Paraffin section (FFPE) samples | 5-10 pieces (thickness 10 µm) | - | - | Sealed and protected from light for transportation at room temperature |
For complex animal and plant species that are unknown or lack reference genomes, HST GENOMICS integrates mainstream third-generation long-read technology (PacBio Revio) and second-generation high-precision nanopore sequencing, and is supplemented by three-dimensional Hi-C spatial cross-linking technology to assist scientific research teams in completing high-precision de novo assembly (de novo) of chromosome physical levels, whole-genome annotation and comparative evolutionary omics analysis.
1. Long fragment CCS sequencing: Utilize PacBio HiFi mode to produce reads between 15-20Kb in length and >99% single-molecule accuracy, easily spanning highly repetitive and GC-rich genomic regions.
2. Hi-C three-dimensional assembly mount: Capture spatial interactions within chromatin through chemical cross-linking methods, and the algorithm automatically clusters, orients and sorts the assembled Contigs, and mounts them to the corresponding physical chromosomes.
3. Fully automatic letter annotation: Combining homology prediction, de novo prediction and whole-transcriptome splicing to carry out precise gene structure prediction, transposon annotation and multi-gene family phylogenetic tree construction.
Animal and plant De Novo delivery includes assembly quality assessment reports (BUSCO completeness, Contig N50), chromosome mounting heatmaps (Hi-C Heatmap), and fully functional component GFF3 format files.
| Evaluation indicators | Technical specifications | deliver on promise |
|---|---|---|
| Contig N50 length | Third generation HiFi sequencing | ≥ 1.0 Mb (up to 10 trillion levels, depending on the genome heterozygosity of the species) |
| Hi-C mount rate (Scaffold %) | Three-dimensional cross-linking assisted assembly | ≥ 95% The above sequence is mounted to the chromosome physical framework |
| BUSCO Gene Integrity | Assessment of conserved orthologous genes | ≥ 95.0% (Full coverage of eukaryotic conserved pathways) |
| Base Accuracy | Second generation short-read polish correction | ≥ 99.999% (reaching QV50 or above standard) |
Since third-generation macromolecular sequencing has extremely high requirements on DNA molecular weight, please be sure to use pulsed field electrophoresis or gel quality inspection before sending samples:
| species categories | Total DNA requirement | Macromolecule ratio requirements (tape quality inspection) | Sampling recommendations | Transportation form |
|---|---|---|---|---|
| Fresh plant tissue (young leaves/etiolated seedlings) | HMW DNA ≥ 5.0 µg after extraction | Main band molecular weight ≥ 40 Kb Proportion > 70% | Darkroom starvation treatment before sending samples to reduce starch, polyphenols and polysaccharide residues | Liquid nitrogen quick freezing, sealed dry ice transportation |
| Healthy animal muscle/blood | HMW DNA ≥ 3.0 µg after extraction | Main band molecular weight ≥ 30 Kb proportion > 70% | Try to avoid fat, connective tissue and digestive tract samples | Dry ice quick freezing, sealed transportation |
Microbial communities play a key regulatory role in human microecological health, modern soil environment improvement, and industrial fermentation. HST GENOMICS has developed an unbiased meta-omics sequencing and multi-dimensional analysis system that covers complete maps of single microorganisms and complex and diverse communities.
1. Amplicon sequencing (16S/18S/ITS): Perform specific multiplex PCR amplification and sequencing of bacterial 16S V3-V4 region, fungal 18S or ITS, which is extremely cost-effective and can quickly scan the bacterial abundance and diversity ratio in the microecological environment.
2. Metagenomic sequencing (Metagenomics): Unbiased extraction of total environmental DNA from samples (such as soil, feces, water) and high-throughput whole-genome sequencing. It can analyze the classification of bacteria, archaea, viruses, and functional genomic pathways such as carbohydrate enzymes (CAZy) and antibiotic resistance genes (ARG) in the environment without culturing.
3. Complete Genome of a single bacterium: Mixing second-generation short-read (quality control error correction) and third-generation Nanopore long-read sequencing to complete the closed circular assembly of bacterial chromosomes and all plasmids in one step.
Microbial delivery bioinformatics analysis is all-inclusive, providing ASV/OTU partitioning heat maps, Alpha dilution curves, PCA/PCoA spatial dimensionality reduction classification maps, and metagenomic KEGG/EggNOG functional annotation pathway distribution.
| Service subtype | Recommended sequencing data volume | Main delivery results |
|---|---|---|
| Amplicon sequencing (16S/ITS) | ≥ 50k Reads/sample | Bacteria abundance bar chart, Alpha/Beta diversity index, Venn diagram, LEfSe differential marker bacterial screening |
| Environmental metagenomics | ≥ 6 Gb/sample | Species relative abundance profile, CARD resistance gene comparison, CAZy enzyme map, KEGG pathway enrichment analysis |
| Completed diagram of single bacteria (bacteria/fungi) | 0.5 Gb (2nd generation) + 1.5 Gb (3rd generation) | 0 Gap chromosome physical map, plasmid group map, genome map, gene family cluster analysis |
The sample delivery standards for various types of environmental microorganisms are different. Please strictly refer to the following table for pipeline pollution prevention and sealing:
| Sample subcategory | Sample physical quantity requirements | Preservation and pipeline requirements | transport medium |
|---|---|---|---|
| clinical/environmental feces | ≥ 200 mg/sample | Place in a sterile centrifuge tube or use a special stool stabilization tube | Quick freezing with liquid nitrogen or dry ice, sealed transportation with dry ice |
| soil/soil | ≥ 2.0 g/sample | Avoid impurities and dead leaves on the surface of the plant, and use sterile cryopreservation tubes for packaging | Transported on dry ice to prevent direct sunlight and thawing |
| Pure strain (slant/bacteria liquid) | 2.0 mL of fresh bacterial culture liquid, or plate slope | For active strains in the logarithmic growth phase, please do not use tubes containing highly toxic and drug-resistant strains. | Low-temperature transportation in ice packs at 4°C (to ensure the survival of strains) |