Novogene Corporation

We are currently running a $199 promotion including library preparation and sequencing (20 million paired-end 150bp reads).

For projects with 24 or more samples, we are offering:

• $189 per sample mRNA-seq (20M PE150 reads on the Illumina NovaSeq platform.)

• $199 per sample mRNA-seq with bioinformatics including differential gene expression analysis. Full content of free analysis described in bolded text below.

Service Details:

• 250-300 bp insert cDNA library, non strand-specific. Stranded option available.
• Illumina HiSeq PE150 standard, SE50 option available.
• Q30≥80% for PE150, Q30≥90% for SE50

Comprehensive analysis available with a low package price, or can be ordered independently for analysis only projects.

Bioinformatics Analysis Content:

With Reference Genome
• Data Quality Control: filtering reads containing adapter or with low quality
• Statistics Analysis of Data Production and Quality
• Mapping Reads to Reference Genome
• Correlation analysis (For biological replicates only)
• Differential Expression Analysis (two or more groups of samples)
• GO Enrichment Analysis of Differentially Expressed Genes (DEGs) (two or more groups of samples)
• KEGG Pathway Enrichment Analysis of Differentially Expressed Genes (DEGs) (two or more groups of samples)
• Protein Protein Interaction Analysis
• Functional Annotation of Transcription Factors
• Functional Annotation of Oncogene
• Alternative Splicing (AS) Quantification and Differential Expression Analysis
• Identification of anti－Transcript (Strand Specific Library Only)
• TSS and TSS Prediction (Strand Specific Library Only)
• SNP/InDel Analysis
• Fusion Gene Analysis (for tumor sample and cancer cell line)

Without Reference Genome
• Data quality control: filtering reads containing adapter or with low quality
• Statistics analysis of data production and quality
• De novo transcriptome assembly
• Gene functional annotation using seven databases (NR, NT, KOG, KO, Swiss-Prot, GO and PFAM)
• GO, COG, KEGG classification
• SNP&InDel analysis
• SSR analysis
• Gene expression analysis
• Correlation analysis (For biological replicates only)
• Differential expression analysis (two or more groups of samples)
• GO enrichment analysis of differentially expressed genes (DEGs) (two or more groups of samples)
• KEGG pathway enrichment analysis of differentially expressed genes (DEGs) (two or more groups of samples)
• Protein-protein interaction analysis

Promotional pricing valid through 30 November 2018

We are currently running a promotion for human Whole-Exome Sequencing (hWES):

$299 (50X coverage) and $399 (100X coverage) for full-service exome capture with the industry-standard Agilent SureSelect Human All Exon V6 Kit, library preparation, and sequencing.

Service Details:

• Agilent SureSelect Human All Exon V6 Kit (58M)
• Illumina HiSeq PE150
• Q30≥80%
• 6G raw data guaranteed (50X on-target coverage)
• Turnaround time 22 working days after samples pass QC (for ≤ 20 samples)

Comprehensive Analysis Available at an Additional $49/Sample

Bioinformatics Analysis Content, Standard:

• Data quality control
• Alignment with reference, statistics of sequencing depth and coverage
• SNP and InDel calling, annotation and statistics
• Somatic SNP/InDel/CNV calling, annotation and statistics (For paired tumor samples)

*Promotion valid through 31 March 2019

Sequencing Strategy
• 350 bp insert DNA library
• HiSeq X platform or NovaSeq 6000 platform, paired-end 150 bp

10X Genomics Chromium is also available for whole genome sequencing.

Turnaround Time
• 15 working days after verification of sample quality (without data analysis)
• Additional 8 working days for data analysis

Recommended Sequencing Depth
• For tumor tissues: 50×, adjacent normal tissues and blood 30×
• For rare diseases: 30~50×

Bioinformatics Analysis includes:
• Data quality control: filtering out reads containing adapters or with low quality
• Alignment with reference genome, statistics of sequencing depth and coverage
• SNP/InDel/SV/CNV calling, annotation and statistics
• Somatic SNP/InDel/SV/CNV calling, annotation and statistics (paired tumor samples)

Whole Genome Sequencing on HiSeq X Ten

Service Details:
• Available for human, plants and animals
• Illumina HiSeq X Ten (PE150)
• 350 bp insert DNA library
• Q30≥80%
• Recommended coverage: 30X-50X for rare diseases; 50X for tumor tissues and 30X for adjacent normal tissues and blood

Comprehensive analysis available at a low package price.

Bioinformatics Analysis Content includes:
• Data quality control: filtering reads containing adapters or with low quality
• Alignment with reference genome

• Statistics of sequencing depth and coverage
  • SNP/InDel/SV/CNV calling, annotation and statistics
  • Somatic SNP/InDel/SV/CNV calling, annotation and statistics (for paired tumor samples)

Novogene is one of the first few companies in the world employing the powerful Illumina HiSeq X Ten for whole genome sequencing. We possess one of the largest NGS capacities in the world with two sets of HiSeq X Ten systems at our California and China labs. Our extensive experience and bioinformatics capabilities enable us to expertly meet customer needs with timely turn-around at highly competitive prices.

We are offering heavily-discounted rates on NovaSeq sequencing when purchasing by lane or flow cell. TWO-WEEK service turnaround time.

We are able to offer the following sequencing options on the Illumina NovaSeq platform:
• S2 Flow Cell, PE150. Expected data output: 1000 Gigabases
• S4 Lane sequencing, PE150. Expected data output: 800 Gigabases
• S4 Flow Cell, PE150. Expected data output: 3200 Gigabases

System specifications: 167Gb – 6Tb output range, 1.6 – 20 B reads per run, and 2 x 150 bp max read length

Introduced by Illumina in January 2017, the NovaSeq Series provides tremendous scalability and flexibility to accommodate diverse applications and project sizes, for virtually any sequencing method, genome, and scale of project. The NovaSeq system extends services previously unavailable on HiSeq X Ten, such as expression profiling, whole transcriptome analysis, microbial genome, exome, low pass WGS, etc., while accommodating rapid turnaround, flexible configurations and cost effectiveness. The addition of 25 NovaSeq sequencers not only expands Novogene’s sequencing capacity, but also greatly reduces our sequencing cycle times. With NovaSeq, we are able to sequence up to 48 human whole genomes and produce 6Tb of data per single run as short as 40 hours. We also upgraded our data storage and computing power to match NovaSeq’s high capacity and efficiency.

System specifications: 1.6 – 1.8 Tb output range, 5.3 – 6 B reads per run, and 2 x 150 bp max read length

Acceptable sample types: WGS library

The HiSeq X System is the world’s first to break the $1000 genome barrier for human whole genome sequencing (WGS). By providing ultra-high throughput and a low price point per genome, the HiSeq X System provides an opportunity to reshape the economics and scale of WGS for both human and non-human species. The HiSeq X System is especially powerful for population-scale WGS. Equipped with 30 powerful Illumina HiSeq X systems, Novogene is capable of sequencing up to 54,000 human genomes per year. Being one of the first few companies adopting HiSeq X Ten since early 2014, we have extensive experience providing whole genome sequencing service on this powerful system, having successfully sequenced tens of thousands of genomes with high quality results.

Whole Genome Sequencing on HiSeq X Ten

Service Details:
• Available for human, plants and animals
• Illumina HiSeq X Ten (PE150)
• 350 bp insert DNA library
• Q30≥80%
• Recommended coverage: 30X-50X for rare diseases; 50X for tumor tissues and 30X for adjacent normal tissues and blood

Comprehensive analysis available at a low package price.

Bioinformatics Analysis Content includes:
• Data quality control: filtering reads containing adapters or with low quality
• Alignment with reference genome

• Statistics of sequencing depth and coverage
  • SNP/InDel/SV/CNV calling, annotation and statistics
  • Somatic SNP/InDel/SV/CNV calling, annotation and statistics (for paired tumor samples)

Novogene is one of the first few companies in the world employing the powerful Illumina HiSeq X Ten for whole genome sequencing. We possess one of the largest NGS capacities in the world with two sets of HiSeq X Ten systems at our California and China labs. Our extensive experience and bioinformatics capabilities enable us to expertly meet customer needs with timely turn-around at highly competitive prices.

At Novogene, We are pleased to offer customers SMRT Sequencing using Pacbio Sequel.

Please contact us for more detail regarding the service.

Basic Data Analysis and Advanced Data Analysis are both offered by our professional bioinformatics team.

Bioinformatics Analysis Content Includes:
With Reference Genome
• Data quality control: filtering reads containing adapter or with low quality
• Statistics analysis of data production and quality
• Mapping reads to reference genome
• Novel gene prediction
• Alternative splicing analysis
• SNP/InDel analysis
• Identification of anti-transcript (strand-specific library only)
• TSS and TSS prediction (strand-specific library only)
• Gene expression quantification
• Correlation analysis (for biological replicates only)
• Differential expression analysis (two or more groups of samples)
• GO enrichment analysis of differentially expressed genes (DEGs) (two or more groups of samples)
• KEGG pathway enrichment analysis of differentially expressed genes (DEGs) (two or more groups of samples)
• Protein-protein interaction analysis
• Transcription factor analysis of differentially expressed genes(DEGs) (two or more groups of samples)

Without Reference Genome
• Data quality control: filtering reads containing adapter or with low quality
• Statistics analysis of data production and quality
• De novo transcriptome assembly
• Gene functional annotation using seven databases (NR, NT, KOG, KO, Swiss-Prot, GO and PFAM)
• GO, COG, KEGG classification
• SNP&InDel analysis
• SSR analysis
• Gene expression analysis
• Correlation analysis (For biological replicates only)
• Differential expression analysis (two or more groups of samples)
• GO enrichment analysis of differentially expressed genes (DEGs) (two or more groups of samples)
• KEGG pathway enrichment analysis of differentially expressed genes (DEGs) (two or more groups of samples)
• Protein-protein interaction analysis

Service Details
• 130-470 bp insert DNA library
• Illumina HiSeq PE250
• Data guarantee: Each sample not less than 30,000 tags, 50,000 tags or 100,000 tags.
• Recommend strategy: 30,000 tags, 50,000 tags, or 100,000 tags

Bioinformatics Analysis Content
• Data split and reads merging
• Data quality control: data filtration and chimera removal
• OTUs cluster and phylogenetic relationship construction
• Species annotation
• Alpha diversity analysis (Observed species, Goods coverage, Chao1, ACE, Shannon, Simpson Index)
• Beta diversity analysis (Unifrac distance heatmap, PCA, PCoA, UPGMA)

Service Details:
• 250~300 bp insert strand specific library with rRNA removal (Ribo-ZeroTM Magnetic Kit)
• Illumina HiSeq PE150
• Q30>=80%
• Recommended data amount: ≥10 Gb/sample

Bioinformatics Analysis Content:
• Data quality control: filtering reads containing adapter or with low quality
• Statistics of data production and quality
• Alignment with reference genome
• Reference based reconstruction of transcripts
• Filtering of candidate lncRNA
• Alternative splicing analysis
• SNP/Indel calling
• LncRNA target gene prediction
• Expression quantification analysis
• LncRNA mRNA comparative analysis

Service details:
• 18-24 bp insert cDNA Library
• Illumina HiSeq SE50
• Q30>=90%
• Recommend data amount: ≥10M reads/sample

Bioinformatics Analysis Content:
• Data quality control: filtering reads containing adapter or with low quality
• Summarize the length distribution of small RNA
• Analyze common and specific sequences between two samples
• Align small RNA to reference genome
• Identify known miRNA
• Identify rRNA, tRNA, snRNA, snoRNA and Non-coding RNA
• Identify repeat associated small RNAs (repeat annotation information of the reference genome should be • provided)
• Align small RNA to mRNA, exon and intron
• Predict novel miRNAs and their secondary structures by Mireap from unannotated small RNAs
• Analyze the expression pattern of known miRNAs
• Analyze the base bias of miRNA
• Classify and annotate of small RNAs

We offer different NGS service with different outputs.

Please contact us to learn more about our NGS service on our X ten, Novaseq, and HiSeq 4000.

Service Details
• 300 bp insert DNA library
• Illumina HiSeq PE150
• Q30 ≥ 80%.
• Data Guarantee: Each sample generates at least 5-10 Gb raw data
• Recommended Strategy: 6 Gb raw data or 12 Gb raw data

Bioinformatics Analysis Content
• Data quality control: filtering reads containing adapter or with low quality, filtering host genome sequences
• Assembly
• Species annotation (microorganic sequences extracted from NCBI NR database 2014-10-19)
• Gene prediction
• Gene annotation（KEGG, eggNOG, CAZy database）
• Species/Gene/Function abundance statistics and cluster analysis
• Comparative analysis (among samples)

Service Details:
• 250~300-bp insert bisulfite treated DNA library
• Illumina HiSeq PE150
• Q30≥80%
• Recommend sequencing depth: ≥ 30X

Bioinformatics Analysis Content:
• Data quality control (filtering reads containing adapter or with low quality; Q20, Q30, error rate distribution, GC distribution, total bases)
• Mapping to reference genome (mapping rate, duplication rate, sequencing depth, reads coverage)
• mCs detection, methylation level calculation.
• Methylation level and frequency distribution in different sequence context (CG, CHG, CHH)
Methylation level and frequency distribution in different chromosomes
• Methylation level and frequency distribution in different functional elements (promoter, 5'UTR, exon, intron, 3'UTR)
• Differentially methylated regions (DMRs) detection and annotation
• Function enrichment (Gene Ontology and KEGG Pathway) of DMR-associated genes
• Visualization of BS Seq data

Service Details
• 100-50 bp insert DNA library (depending on peak distribution)
• Illumina HiSeq SE50
• Q30≥80%
• Recommend sequencing depth: ≥ 20 M reads

Bioinformatics Analysis Content:
• Data quality control (get rid of reads containing adapter or with low quality; Q20, Q30, error rate distribution, GC distribution, total bases)
• Mapping onto reference genome (mapping rate, reads distribution)
• Peak calling
• Motif prediction
• Peak annotation (downstream or overlapping gene, TSS)
• Functional analysis of peak-associated genes (Gene Ontology, pathway)
• Visualization of ChIP-seq data

Service Details:
• Illumina HiSeq PE150
• Data quality guarantee:
o Simple genome: Contig N50 ≥ 30 Kb, Scaffold N50 ≥ 1 Mb
o Mammal (except Chiroptera) or bird genome: Contig N50 ≥ 30 Kb, Scaffold N50 ≥ 3 Mb
o Complex genome: Contig N50 ≥ 20 Kb, Scaffold N50 ≥ 300 Kb

Bioinformatics Analysis Content:
• Genome survey
• Genome assembly
• Genome annotation
• Comparative genome analysis
• Personalized analysis

Sequencing Strategy

3 libraries: 1-2K, 2-3K and 3-6K OR customized according to your species of interest

PacBio Sequel system

Data Quality Guarantee
Guaranteed 5G, 10G, or 20G data package, based on project design
Sample Requirements

Total RNA amount: ≥ 10 μg; RNA concentration: ≥ 200 ng/μl
RIN value ≥ 8.0
OD260/280 ≥ 1.8, OD260/230 ≥ 1.8, without degradation and DNA contamination

Turnaround Time
Within 12 weeks from verification of sample quality with data analysis

Service Details
• 200bp insert cDNA library
• HiSeq PE150
• 20 M clean reads for general depth
• 40 M clean reads for high depth
• Q30≥80%
• Recommended data amount: >=20M reads/sample
• Bioinformatics analysis content same as regular RNA Seq

Service Details:
• 350bp insert DNA library
• Illumina HiSeq PE150
• Q30≥80%
• Bioinformatics analysis content same as regular whole genome or whole exome sequencing

We offer different NGS service with different outputs.

Please contact us to learn more about our NGS service on our X ten, Novaseq, and HiSeq 4000.

Hereditary Cancer Risk Assessment-NovoCR

About NovoCR

NovoCR, a product of genetic testing for hereditary cancer by novogene, utilizes next-generation sequencing technology to classify genetic information and provides cancer risk assessment. Through comparing genetic information to authoritative latest database, NovoCR analyzes more than one hundred genes in sixteen types of cancer in one test and provides a comprehensive report, which helps our customers to understand their risk for cancer and make important decisions about intervention.

Products

Advantages:

1. High coverage: A variety of gene mutation types, including single nucleotide mutation, insertions, deletions and repeats, can be effectively detected by a single test in more than one hundred genes related to sixteen types of cancer.

• High accuracy: more than 99% accuracy is guaranteed by sequence capture and NGS.
• Professional: Comprehensive and latest cancer risk database.
• Short turnaround time: Automated test and analysis, reporting in 15 working days.

What can I expect from NovoCR?
Complete, fast and accurate test result of the genetic testing.

1. Diagnose the cause of cancer at an early stage and provide guidance for personal medicine.

• Support the evidence used to predict the risk of developing cancer and provide guidance for healthcare.
• If you have high cancer risk, you may increase the surveillance frequency, and your relatives need the genetic testing also.
• Support life-time health management by updating database constantly.

Services procedure:

Send samples (blood or saliva) -Check your report after 15 working days online or ask for a paper report.

Newborn Screening is testing carried out on newborn babies to detect a wide variety of disorders. Typically, testing is performed on a blood sample obtained from a heel prick when the baby is two or three days old to identify infants at increased risk for a specific genetic disorder so that treatment can begin as soon as possible; when a Newborn Screening result is positive, further diagnostic testing is usually required to confirm or specify the results and counseling is offered to educate the parents, thus could help to alleviate the mental and physical damage.

Why is the Newborn Screening needed?

Phenylketonuria (PKU) and Congenital hypothyroidism (CH) are two commonly seen inherited disorders. Phenylalanine is a building block of proteins (an amino acid) that is obtained through the diet. It is found in all proteins and in some artificial sweeteners. If PKU is not treated, phenylalanine can build up to harmful levels in the body, causing intellectual disability and other serious health problems. Congenital hypothyroidism occurs when the thyroid gland fails to develop or function properly. In 80 to 85 percent of cases, the thyroid gland is absent, abnormally located, or severely reduced in size (hypoplastic). In the remaining cases, a normal-sized or enlarged thyroid gland is present, but production of thyroid hormones is decreased or absent. If untreated, congenital hypothyroidism can lead to intellectual disability and abnormal growth.
The Nest Generation Sequencing (NGS)-based Newborn Screening that NovoHope provides could detect nearly 70 inherited disorders in a single test. Through analysis of the NGS data, you could get a full profile of your children’s healthy status. NovoHope dedicated to guide your children a healthy life.

Everyone has two copies of each gene which are inherited in pairs, one from each parent. Being a carrier means that one copy of a gene has a change, called a mutation, which causes it to not work properly. Carriers still have one working copy of the gene, so they typically do not have any health problems associated with carrying a mutation. Therefore, many people can be carriers of a disease-causing mutation without even knowing it. Being a carrier, however, means there is an increased chance that your child could be born with a genetic disease. If you and your partner are both carriers of the same autosomal recessive disease, there is a 25% chance your child will inherit the mutation from each of you and therefore have that disease. There is a 50% chance your child will inherit a single mutation from either you or your partner, which would make your child a carrier. There is a 25% chance that no mutations will be passed on to your child.

The test just uses a little saliva to look for genetic markers linked to more than 100 kinds of inherited diseases. If you and your partner are both carriers for the same genetic disease, you should discuss your test results and next steps with your doctor or a genetic counselor, to choose one reproductive options to protect your future children. You could to do the prenatal testing by chorionic villus sampling (CVS) at 10-12 weeks of pregnancy or amniocentesis at 15-18 weeks of pregnancy, or go through in vitro fertilization and preimplantation genetic diagnosis (PGD) of the embryos prior to pregnancy, or go for the egg or sperm donation.

Carrier Screening is applicable to:

1. Prepare for birth;

• Have a family history of a genetic disorder
• Are at increased risk for a specific condition based on ethnicity (Beta-Thalassemia, Glucose-6-Phosphate Dehydrogenase Deficiency)
• Would like additional information about your reproductive risks

With the development of NGS technology, whole genome sequencing has become an important tool for bacterial and fungal genome research with reasonable cost and short turnaround time.

Novogene provides different types of services based on diverse research requirements.

Bacterial/Fungal genome draft map

With the construction of short insertion library followed by Miseq deep sequencing and primary assembly, bacterial and fungal genome draft map can fulfill basic research requirement with low cost.

Bacterial/Fungal genome resequencing

For strains that already have reference genome sequences, bacterial and fungal genome resequencing adapt short insertion library construction and HiSeq sequencing followed by variation analysis (including SNP and InDel calling), which is the best choice for population study.

Technical Parameters

Sample Requirements

• DNA amount: for < 800 bp insertion Library, ≥3 μg; for PCR-free Library, ≥5 μg; for 2-6 kb insertion Library, ≥5 μg
• DNA concentration: ≥50 ng/μL
• Purity: OD 260/280= 1.8-2.0 without degradation and RNA contamination

Long non-coding (Lnc) RNAs refer to RNAs of which length is greater than 200 nt and not involved in protein coding. LncRNAs have been characterized to be associated with important cellular processes such as X-chromosome inactivation, imprinting, maintainance of pluripotency, lineage commitment and apoptosis in mammalian system.

Sequencing Strategy

• 200 bp insertion strand-specific cDNA library
• HiSeq 2500 Platform V4 reagent, Paired-end 125 bp

Sample Requirements

• Total RNA amount: ≥6 μg
• RNA concentration: ≥100 ng/μL
• RIN value ≥6.5 for plants and fungi; RIN value≥7.0 for animals
• Purity: OD260/280 = 1.8-2.2, OD260/230 ≥ 2.0 without degradation and DNA contamination

Turnaround Time

• Within 60 days from sample verification

Recommended Data Amount

• 10 Gb clean data for general depth
• 20 Gb clean data for high depth

With a stable alternation of gene expression in cells during cell proliferation and differentiation process, DNA methylation plays a crucial role in the development of most types of cancer, neurodegenerative diseases and neurological diseases. Therefore, to characterize methylation of bases is critical to understand regulation of genes at epigenetic level. Sequencing of bisulfite-converted DNA provides a useful whole epigenome analysis tool for researchers to focus on specific tissues or dynamic developmental processes.

Sequencing Strategy

• 300 bp insertion DNA library
• HiSeq 2500 Platform V4 reagent, Paired-end 125 bp

Sample Requirements

• Total DNA amount: ≥5 μg
• DNA concentration: ≥50 ng/μL
• Purity: OD 260/280= 1.8-2.0 without degradation and RNA contamination

Turnaround Time

• Within 50 days from sample verification

Recommended Sequencing Depth

• Effective sequencing depth above 30X

With the rapid development of next-generation sequencing technology，de novo sequencing enables the construction of the first genome map of specific species and lay the foundation for subsequent research, including identification the origin of species, evolution, and adaptation to specific environment, etc.

Simple Genome

Simple genome refers to the genome of haploid with low repeat content (lower than 50%) or diploid with low heterozygous rate (lower than 0.5%), such as most of the mammals, birds, and cultivated crops.

Complex Genome

Complex genome refers to the genome of diploid or polyploidy with high repeat content (higher than 50%) or high heterozygous rate (higher than 0.5%), such as most of the arbor, aquatic and insects, etc.

• Moderately heterozygous genome (diploid)
• High heterozygous genome (diploid)
• Highly repetitive genome (diploid)

Sample Requirements

• DNA amount for survey: ≥10 µg
• DNA amount for RAD-seq: ≥3 µg
• DNA amount for genome de novo sequencing: ≥500 µg
• DNA concentration: ≥50 ng/μL
• Purity: OD 260/280= 1.8-2.0 without degradation and RNA contamination

Technical Parameters

Publications

1. Huang S, Li R, Zhu H, et al. The genome of the cubumber Cucumis sativus L. Nature genetics.
   2009. 41: 1275-1281.

• Li R, Zhu H, Zhou G, et al. Building the sequence map of the human pan-genome. Nature
  Biotechnology. 2009. 28: 57-63.
• Li R, et al. The sequence and de novo assembly of the giant panda genome. Nature. 2010. 463:
  311-317.
• Li R, et al. The genome of the mesohexaploid crop species Brassica rapa. Nature. 2011. 8: 1035-
  1039.
• Qu Y, Zhao H, Li R and Lei F. Ground tit genome reveals avian adaptation to living at high altitudes
  in the Tibetan plateau. Nature communications. 2013. 4: 2071.
• Li M, Tian S, Li R. Genomic analyses identify distinct patterns of selection in domesticated pigs and
  Tibetan wild boars. Nature genetics. 2013. 45(12): 1431-1438.

RNA Sequencing Services