Disease Panels & Pathway Genes
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Applied Biological Materials, Inc. is an Illumina Certified Service Provider, dedicated to ensuring the delivery of the highest-quality data available for genetic analysis applications. Click here for more details about the Illumina CSpro program.
  Eliminates the labor-intensive primer design and target selection steps.

Prices are in US dollars. Please contact technical@abmgood.com if you need a quotation in Canadian dollars.
Service/Description Cat. No. Ordered in
Multiples of
Price
TruSight One Sequencing Panel ID50120 3$1095.00*
TruSight Cancer Sequencing Panel ID50150 4$795.00*
TruSight Inherited Disease Sequencing Panel ID50400 4$950.00*
 
Bioinformatics Analysis
Raw data provided in FASTQ format if none of the below services are selected.
Sequencing Panel Analysis
- read mapping (BWA)
- deduplication (Picard)
- local realignment
- base quality recalibration
- variation calling (GATK)
IB00018 1$35.00*
 
Additional Sample Preparation Services
DNA Isolation for NGS IW19001 1$50.00*
 
Data Storage Service
Data Storage (per additional 3 months) IS10001 1$150.00
*Price per Sample
Service Details
Service Details
    The cornucopia of information generated by Next Generation Sequencing (NGS) not only opens avenues for novel scientific explorations but, more importantly, can provide answers to questions that have for long, intrigued scientists across the globe. NGS can provide valuable insights into 'if and how' the genetic material impacts and/or triggers various pathological conditions.

Key Features of abm’s Sequencing Panel Services:
• enable identification of:
  - rare and common single-nucleotide variants (SNV's)
  - small insertion/deletion variants
  - de novo mutations
• guaranteed, high-quality data read-out of sample(s)
• library construction and target capture are performed using Illumina’s comprehensive TruSight Sequencing Panels


TruSight One Sequencing Panel Service - Cat# ID50120
Targeting > 4,800 genes associated with known clinical phenotypes; enabling labs to expand and streamline their assay portfolio and sequencing portfolio. For more information about gene lists and probe manifests, please refer to Illumina’s product files: http://www.illumina.com/products/trusight-one-sequencing-panel.html

With just 50ng of high quality input DNA, the TruSight One panel targets 12Mb of genomic content for Paired-End sequencing on the MiSeq V3 (2x150nt reads) at 200X mean sequencing coverage, which gives up to 8M reads per sample.


TruSight Cancer Sequencing Panel Service - Cat# ID50150
Targeting 94 genes and 284 SNPs previously linked to a predisposition towards both common (e.g. breast, colorectal) and rare cancers. For more information about gene lists and probe manifests, please refer to Illumina’s product files: http://www.illumina.com/products/trusight_cancer.html

With just 50ng of high quality input DNA, the TruSight Cancer panel targets 255Kb of genomic content for Paired-End sequencing on the MiSeq V2 kit (2x150nt reads) at 200X mean sequencing coverage, which gives up to 200,000 reads per sample.


TruSight Inherited Disease Sequencing Panel Service - Cat# ID50400
Focusing on severe, recessive pediatric onset diseases; targeting 552 genes, including coding exons, intron-exon boundaries, and regions known to harbor pathogenic mutations. For more information about gene lists and probe manifests, please refer to Illumina’s product files: http://www.illumina.com/products/trusight_inherited_disease.html

With just 50ng of high quality input DNA, the TruSight Inherited Disease panel targets 2.25Mb of genomic content for Paired-End sequencing on the MiSeq V2 kit (2x150nt reads) at 100X mean sequencing coverage, which gives up to 1 M reads per sample.


For each service, the results are provided in industry standard FASTQ format (default), while the Sequencing Panel Analysis package also delivers the alignment .bam file, as well as the list of detected variants in .vcf format. The kits used for the above target enrichments during library prep are part of the Illumina's TruSight product line. Alternative enrichment kits and panels can be requested at an additional cost.
Sample Requirement Guidelines Click To Open
    Our technical support team will be happy to work on confirming the details of your NGS service. Please contact our specialists at technical@abmgood.com to get your order confirmation number. Any samples shipped to our facility without an order confirmation number in the attention line will be destroyed and disposed immediately upon receipt.
Sample Submission Form Click To Open
Confidentiality
    All customer information is held in strict confidence. All materials and information sent to us and the products produced by us for the order are the property of the customer and will be returned to the customer or discarded in an confidential manner. We only archive customer materials when instructed to.
Project Design/Advice
    Please email NGS@abmgood.com for assistance with starting your sequencing project or for any inquiries relating to our Next Generation Sequencing services.
Product Documents
Product References
FAQs
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Is your company certified as a service provider for Illumina sequencing?
Yes, we are a certified Illumina service provider.
What kind of analysis software do you use for sequence analysis?
The Illumina sequencers come with the integrated software that can perform the regular bioinformatics analysis functions. In addition, we have extensive experience with other open access software such as Galaxy, Adnuril, BioBike, etc. In other words, we are willing to perform additional bioinformatics analysis with different software and tools to satisfy a variety of demands from our customers.
What kind of QC methods do you adopt for the customer's sample(s)?
We will perform QC on your Total RNA samples prior to sequencing them, using the Agilent Bioanalyzer (industry standard) to determine the RNA Integrity Number (RIN). If the RIN is lower than 8, we consider these samples as having failed QC. If the samples do not pass QC, we will ask you to send us new samples. If we do not receive new samples, thereby cancelling the sequencing order, there will be a QC fee of $50/sample. This fee will be waived if you choose to continue with the sequencing order. A strict positive and negative control will be applied to this QC process.

The library QC will also be performed using the Agilent Bioanalyzer to determine library size and purity. Also, prior to loading the libraries on the sequencer, we perform qPCR quantification. The cost for this is included in the sequencing service.

For the QC of the final data from our sequencing service, the integrated software will generally do the job and provide adequate QC information, however, we can also provide additional QC data such as FASTQC upon request.

The data we output will pass our Q30 filter, which means that the error rate in base calls is less than 1 in 1000, or 0.1%. We will get a percentage at the end of the run which states the percentage of bases that have a Q score > 30, and this percentage is usually ≥85%.
What is the lead time for your WGS, WES, and RNA-Seq services?
Our sequencing lead times depend on workload, but are typically 2-4 weeks for sequencing data + 2-3 weeks for standard analysis. Please inquire for lead times for more detailed analysis.
Can you recommend any preferred RNA/DNA isolation kits to provide the best quality samples for these services?
For miRNA sequencing, you may isolate your RNA sample with a mirVana™ miRNA Isolation Kit,
mirVana™ PARIS™ Kit or PureLink® miRNA Isolation kit to enable adequate enrichment of your sample. If preferred, it should be okay to use Qiagen's kit, as long as the RNA Integrity Number (RIN) of the sample is above 8.0 to make sure there is no significant degradation. (Samples with a RIN lower than 8.0 may contain smaller degraded RNA fragments that can be sequenced in addition to the miRNAs). We prefer receiving Total RNA sample however so we can perform the bioanalyzer QC to check the RNA quality before beginning library construction. There will be no extra-charges if you submit Total RNA instead of isolated miRNA.

For miRNA sequencing we require 200ng-2ug of total RNA in 10ul of nuclease free water, as quantified with a fluorometric method. Lower amounts might result in inefficient ligation and low yield. If you are supplying purified miRNA, please submit a minimum of 50-100 ng of purified small RNA in 10ul is required. Purified small RNAs must be in nuclease free water or 10 mM Tris-HCI, pH 8.5.

For other services, there are generally no preferred DNA/RNA isolation kits as long as minimum requirements for QC are met.

Do I need any special software to view the data report files?
You will first need to unzip the fastq.gz files with winrar to view with vim, nano, gedit, Notepad plus plus. Nextgen workbench generally can view the data immediately without unzipping.

The RNASeq_sample_cufflinks_output.tar.gz will also need to be unzipped to see the text files by vim, nano, gedit, or Notepad plus plus. The unzipped data an also be imported as text into the data tab of Excel 2007. Other versions may differ.

To analyze further, Excel can sort, filter, find, match, etc and has many functions for conditional coloring, graphing, etc.
For the data, why are there no "ALT", "POS" and "ID" in your CSV file?
CSV files are meant to be used in conjunction with the raw fastq/bam files by certain commercial bioinformatics software. Many have a proprietary algorithms that takes the ALT POS and ID from the Fastq and indexes them for its own use. They are not meant to be used alone.
Would you let me know the description for the following: Genotype Sample_0, Coverage Sample_0, Coverage By Allele Sample_0, Variant Quality Sample_0, and Genotype Quality Sample_0?
Genotype (Sample Name) = nucleotide. Coverage (Sample Name) = will fail if there are insufficient reads. Coverage by allele (Sample Name) = will fail on one strand (+/-) read if only one side of the pair was sequenced. Variant Quality (Sample Name) = confidence of variant called. Genotype Quality (Sample Name) = confidence of genotype sequenced.
Concerning the column of "CHROM", would you let me know the rules of naming?
type of accession number| actual number| type of sequence| actual curated version used
Does your NGS service including RNA isolation?
We do not provide RNA isolation service by default. However we can provide this service. For more information, please refer to Cat#IR19001.
How many biological replicates do I need for each condition?
To increase confidence and reduce experimental error it is suggested that you submit at least 3 replicates per sample. Note that this is to serve as a guideline only and the final number of replicates and samples is to be determined by the end user based on their final experimental conditions.
What is the current lead time for this service?
Around 6-8 weeks