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Modular library preparation
DNA and RNA isolation
Inherited disorders test systems
HLA-typing test system
Servers for genomic data
⠀⠀⠀⠀Parseq Lab has developed its own primer selection algorithms for minimising the number of amplicons for the target regions.
⠀⠀⠀⠀By combining primer panels with Prep&Seq™ modules, you get a complete protocol for targeted sequencing.
⠀⠀⠀⠀By combining primer panels with Prep&Seq™ modules, you get a complete protocol for targeted sequencing.
Customized primer panels Prep&Seq™ U-panel
Manual optimization for "complex" regions
Compatible with Illumina, Thermo Fisher Scientific and MGI
Parseq Lab's own in-house primer selection algorithms for minimising the number of amplicons for the target regions
Panel validation on standard whole genome reference samples
Specifications
Features
Specifications
Analyte
DNA
Reference genome
hg19, hg38, custom references
Regions of interest (ROI)
Coding regions (CDSs), splicing sites, hotspots, untranslated regions (UTRs)
Padding into intronic regions
>= 5 bp
Amplicon length
Short amplicons up to 140 bp (for heavily degraded samples)
Medium amplicons up to 175 bp (for degraded samples)
Long amplicons up to 300 bp (for normal samples)
Any length according to user's request
Medium amplicons up to 175 bp (for degraded samples)
Long amplicons up to 300 bp (for normal samples)
Any length according to user's request
Number of amplicons
Up to 4000 in one pool
Pools
Up to 2
Type of analyzed samples
Blood, leucomass, buccal epithelium, dried blood spots, fresh tissue, FFPE, circulating DNA (cfDNA) or any other
Type of variants analyzed
Germinal, somatic
Platform
Illumina, Thermo Fisher Scientific, MGI
Sequencing mode
Paired-end (PE), single-end (SE)
Recommended read length
Not less than the length of the amplicon to avoid the effect of strand bias
Data analysis software
User's own software, VariFind™ Software for germline variants in the human genome
Identification of contamination, sex, determination of relationship
Inclusion of BIDs - biological identifiers for human samples
In vitro validation
With standard reference or user samples
Databases for design
Taking account of variants from the dbSNP and COSMIC databases (only for somatic variants) to avoid primers annealing on variable regions.
Options
Taking account of hotspots to avoid primers annealing on these sites and to avoid hotspots` location on amplicon ends, the ability to add primers in ready panel
Primer modification
Deoxyuridine
Compatible library preparation
Prep&Seq™ U-target DNA Core Module,
Ion AmpliSeq™ Library Kit 2.0,
Ion AmpliSeq™ Library Kit Plus,
AmpliSeq™ Library PLUS for Illumina
Ion AmpliSeq™ Library Kit 2.0,
Ion AmpliSeq™ Library Kit Plus,
AmpliSeq™ Library PLUS for Illumina
Examples of realized panels
⠀⠀⠀Coordinates of 530 single nucleotide polymorphisms (SNPs). Target amplicon length: 125 – 175 bp for work with degraded DNA samples of plant origin.
Technical requirement №1
Design
Number of amplicons
524
Coverage of regions of interest
98,87%
Amplicon length range, bp
125 - 175
Average amplicon length, bp
163
Size of the region covered by the design, bp
57 973
⠀⠀⠀Coordinates of 530 single nucleotide polymorphisms (SNPs). Target amplicon length: 125 – 175 bp for work with degraded DNA samples of plant origin.
Technical requirement №1
Design
Number of amplicons
524
Coverage of regions of interest
98,87%
Amplicon length range, bp
125 - 175
Average amplicon length, bp
163
Size of the region covered by the design, bp
57 973
⠀⠀⠀⠀All coding regions of 67 genes, padding 20 bp. The maximum length of amplicons after cutting the primers is 200 bp Reference hg38 genome.
Technical requirement №2
Design
Number of amplicons
1472
Coverage of regions of interest
>99,9%
Amplicon length range, bp
125 – 224
Average amplicon length, bp
206,1
Size of the region covered by the design, bp
211 833
⠀⠀⠀⠀All coding regions of 67 genes, padding 20 bp. The maximum length of amplicons after cutting the primers is 200 bp Reference hg38 genome.
Technical requirement №2
Design
Number of amplicons
1472
Coverage of regions of interest
>99,9%
Amplicon length range, bp
125 – 224
Average amplicon length, bp
206,1
Size of the region covered by the design, bp
211 833
Frequently Asked Questions (FAQ)
Which program is used for the selection of primers?
For this purpose, we use our own in-house TORTUGA software. While this is currently available for internal use only, we are actively working on developing a user interface.
Where are the primer panels manufactured?
All panels are manufactured in-house at our premises in St. Petersburg.
What data is needed for the design?
To launch the design, it is necessary to obtain information on the desired characteristics of the panel and target regions in the form of a BED file, a list of transcripts or genes. To make an order, please fill out the form
What does it mean «padding»?
Padding is the range/distance in nucleotides from the exon border deep into the intron. Specifying padding when designing the panel allows you to cover variations in splicing sites. Usually, two to five nucleotides from the border are significant.
How do I know what amplicon length I need?
Pay attention to fragmentation level of the input nucleic acid. Degraded samples have a limited number of long fragments for amplification. You can receive degraded nucleic acid from different kind of samples like FFPE, circulating DNA or remains.
What are the BIDs – «biological identifiers» and why should they be included in the panel?
Biological identifiers (BID) are additional amplicons for highly polymorphic regions of the genome. Each person has unique haplotype by biological identifiers. Biological identifiers can be used for quality control and revealing contamination, parent-child relationship, identical samples with a different identifier, sample sex. These amplicons can optionally be included in any panel.
Why do I need to take account of hotspots for panel design?
Typically, hotspots are understood as clinically significant variants, in a broader sense - any variants of interest. For design we recommend taking account of hotspots to understand if they are covered by panel design; to make sure that they are not on the edges of the amplicons (sequencing errors sometimes occur at the edge positions); to determine whether hotspots fall into regions difficult for sequencing (homopolymers, repeats, regions with a high degree of homology). If hotspots located into such regions, various primer modifications can be added to the design to improve genotyping.
Do you validate primers on real samples?
Yes, we do in vitro validation for every panel. We use international whole genome reference samples for human and user samples for another species.
Related products
A systematic approach to genomic research
Czech Republic, 252 63 Roztoky, Felklova 2014
info@parseq.pro
info@parseq.pro
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