Colony Management

Genotyping and Genetic Analysis

Taconic Biosciences' Genetics Sciences team perform state-of-the-art molecular characterization assays throughout the breeding of every colony to ensure that animal model integrity and quality are maintained.

Reliable results depend on having the right tools and research materials. Taconic helps ensure your mouse or rat models have the desired genetic profile through a variety of assays and techniques.

During your consultation with the Project team, we will create an appropriate genotyping and molecular analysis strategy to support your study.

genotyping machine

Genotyping Services

Inherent to breeding mice and rats is the need for regular genotyping. Accuracy, speed, and access to genotyping data are paramount to proper management of your breeding project. Through an exclusive distributorship with Transnetyx Inc., your Colony Management project has access to all of the services and advantages that Transnetyx offers. In addition to Transnetyx, Taconic also offers genotyping assay design and optimization services, zygosity testing, and transgene characterization. All genotyping services are overseen by PhD molecular biologists and geneticists. Taconic also offers a comprehensive range of single nucleotide polymorphism (SNP) analysis services to allow you to better determine the genetic background of your study animals.

  • Exclusive distributorship with Transnetyx Inc. allows for high-throughput genotyping services with electronic access to data
  • Comprehensive panel of genotyping capabilities which includes conventional and real-time PCR
  • Assay transfer services to optimize existing assays to our platforms, consultation and collaborative assay development and optimization services

To obtain genotyping protocols, please use the Contact Us form or our Live Chat service and provide confirmation of your order. This confirmation could be in the form of a sales order number, purchase order number, or another combination of order details, e.g. organization name, principal investigator, strain quantity, or date received.

Taconic's Terms and Conditions for Models, Products and Services generally restricts breeding and cross-breeding of commercial models, unless additional rights have been granted in writing by Taconic.

Please review the Licensing information listed on the specific web page for your model. Researchers interested in breeding and/or crossing a Taconic model are advised to inquire about limited breeding agreement options.

Taconic is unable to provide technical support for our genotyping protocols.

PCR Genotyping

Traditional PCR

  • Robust method for distinguishing a wide variety of mutant and transgenic lines
  • Ideal for genotyping many types of rodent models including knockouts, knock-ins, and transgenes
  • DNA is extracted from a tail for ear tissue biopsy before amplification, and results are usually available within 5 business days

Real-time PCR

  • Genotyping with this technique can distinguish the presence or absence of specific alleles
  • Best suited for detecting very precise mutations and can also be used to distinguished larger genetic modifications such as gene knockouts, knock-ins, and transgenes
  • DNA is extracted from a tail for ear tissue biopsy before amplification, and results are usually available within 5 business days

Restriction Fragment Length Polymorphism (RFLP)

RFLP genotyping is used to distinguish sequence-specific mutations when the mutation alters a restriction enzyme cut site. This technique is most useful for projects where detecting single base pair changes are essential and real-time PCR is unavailable.

  • Requires extremely specific sequences and used for specialized assays
  • Can be used to identify CRISPR knock-in mutations
  • DNA is extracted from a tail for ear tissue biopsy before amplification, and results are usually available within 5 business


Sequencing is available for analyzing specific nucleotide sequences of one of the alleles in an assay. This service is ideal for projects that have new mutant lines where the sequence of the mutation may be variable due to founder transmission. Sequencing helps to characterize the mutations so that they can be grouped into uniform lines.

  • Can be used to characterize new mutant lines
  • Verifies the exact sequence of an allele
  • DNA is extracted from a tail for ear tissue biopsy before amplification, and results are usually available within 10 to 15 business days

Transgene Characterization

Copy Number Analysis

Copy Number analysis is useful for determining the approximate copy number of a transgene present in a mouse or rat. Transgenes may integrate into the genome in a variable number of copies, and those copies may undergo genetic rearrangements in later generations that alter the copy number in a given locus. Copy number analysis can help identify the initial transgene copy number and help monitor potential rearrangements.

  • In this assay, the relative abundance of the transgene is normalized to a reference gene and compared with a control sample using Taqman based real-time PCR
  • This service has specific sequence and sample requirements and may not be possible in all cases
  • Taconic's project managers and geneticists will be able to determine if this assay is suited for your specific project

Transgene Zygosity Assay

Transgene zygosity genotyping can be used to distinguish heterozygous from homozygous transgenic animals even when the location of the transgene is unknown. This technique is performed by evaluating the relative abundance of a transgene normalized to a reference gene and compared with a reference sample using real-time PCR.

  • Real-time PCR assay with relative quantitative data read-out
  • Appropriate for discerning wild-type, heterozygous and homozygous alleles with gene-targeted modifications
  • DNA is extracted from a tail for ear tissue biopsy before amplification, and results are usually available within 5 business days

Transgene Mapping Analysis (TgMA)

Taconic Biosciences offers Transgene Mapping Analysis in partnership with Cergentis. This service uses targeted locus amplification technology, developed by Cergentis, to identify the exact integration site of a transgene that is randomly integrated into the genome of a mouse or rat via pronuclear injection. Contact us to access this service.

Targeted Locus Amplification (TLA)1,2 is a novel targeted enrichment technology combining the principle of proximity ligation with next generation sequencing to selectively amplify and sequence the transgene and surrounding genomic region of sizes ranging from tens to hundreds of kilobases.

Using only one primer pair, complementary to a short sequence unique to the transgene, crosslinked and ligated DNA fragments surrounding the transgene insertion site are selectively amplified and sequenced. By analyzing the coverage profile of the sequencing reads and the breakpoint sequences, TLA allows the precise identification of the transgene integration site. In addition, it enables the detection of single nucleotide variations, structural variations, and transgene-transgene fusions.

Learn More About

Transgene Mapping Analysis

Taconic Biosciences, Inc. helps you ensure that your mouse or rat models have the desired genetic profile. Learn about consulting with our team, genotyping, pricing, breeding, & ordering.
transgene mapping analysis cover

Transgene Mapping Solutions

Taconic provides an end-to-end solution from sample preparation to final reporting which includes:

  • Precise identification of all transgene integration sites
  • Characterization of any structural changes in the transgene and genomic regions surrounding the transgene
  • Structural changes in the transgene sequence
  • Any Single Nucleotide Variants within the transgene
  • Founder line recommendations and breeding plan optimization as applicable
  • Recommended genotyping protocols that bridge the integration site and allow for genotyping specific integration sites and accurately differentiate homozygous versus heterozygous aniIn some cases, developing genotyping protocols may not be possible due to the nature and the site of transgene integration.

Gene Expression Analysis

Gene Expression Analysis is used to determine whether a gene is expressed and can also determine in which tissues gene expression is turned on. This is important in the initial characterization of genetically engineered mice and rats and can be used as a quality control assay for ongoing monitoring of genetically engineered mice and rats.

Taconic offers the following gene expression services:

Gene Expression Assay Design

  • Design and validation of a real-time PCR assay
  • Used to assess the mRNA levels of a single gene in a particular tissue

Gene Expression Analysis

  • Real-time PCR assay to assess the mRNA levels of single gene in a particular tissue
  • Appropriate for the evaluation of expression of a transgene in tissue(s) of interest and for the evaluation of expression of an endogenous gene in response to a genetic manipulation in tissue(s) of interest

FACS Analysis

  • Evaluation of protein expression in blood samples
  • Appropriate for verification of protein expression on founders and/or breeders for lines that express a transgene in blood

Genetic Profiling (SNP Testing)

High-throughput SNP Testing

Taconic has developed and optimized several custom-designed mouse and rat SNP panels for characterizing strain background, monitoring genetic quality, or developing congenic lines. We offer SNP-based genetic monitoring and genome scanning services using Illumina's Infinium® Beadchips technology and platform. The Infinium® platform is a high-throughput SNP genotyping system based on the direct hybridization of genomic targets to array-bound sequences. Allelic specificity is confirmed by single base extension to incorporate a labeled nucleotide. Upon fluorescent staining, the labeled nucleotide is detected by the Illumina iScan System and subsequently analyzed by the Genome Studio Software which has a 99% call rate and 99.9% reproducibility.

Applications Include:

  • SNP testing when receiving a new GEM line from a collaborator to identify the strain composition
  • Identification of C57BL/6 substrain
  • Before establishing any new breeding colony
  • Evaluating backcrossing to develop congenic lines

SNP Panels

Mouse Genome Scanning Panel

  • Panel of 2,050 SNP markers selected to maximize genetic information across 21 inbred strains ideal for background characterization of most commonly use mouse strains:
    • 129S6/SvEvTac
    • 129X1/SvJ
    • BALB/cAnNTac
    • BALB/cJBomTac
    • BALB/ABomTac
    • BALB/cJ
    • C3H/HeNTac
    • C57BL/6NTac
    • C57BL/6J
    • C57BL/6JBomTac
    • CBA
    • CB17SC
    • CBSCBG
    • DBA/1JBomTac
    • DBA/2NTac
    • FVB/NJ
    • FVB/NTac
    • NOD/MrkTac
    • NOD.Cg-Prkdcscid Il2rgtm1Sug/JicTac
    • NZW
    • SJL/JCrNTac
  • Suitable for accelerated backcrossing (speed congenics) and Quantitative Trait Loci (QTL) analysis

Mouse GenMon Panel

  • Panel of 98 SNP Markers suitable for quality control monitoring of the genetic background of inbred lines, to detect undesired genetic contamination, or to assess genetic variability in some outbred stocks of mice.
  • Not suitable for accelerated backcrossing or Quantitative Trait Loci (QTL) analysis

Mouse C57BL/6 Substrain Panel

  • Panel of 257 SNP markers selected to differentiate C57BL/6 substrains
  • Ideal to differentiate C57BL/6N from C57BL/6J
  • Line should be at least 99.9% in C57BL/6 background prior to utilizing this panel, and if in doubt we recommend to first use the Mouse Genome Scanning Panel to verify the genetic background.

Rat GenMon Panel

  • Panel of 96 SNP markers suitable for routine quality control of inbred rat strains or assessing genetic variability in certain outbred rat stocks.
  • Not suitable for accelerated backcrossing or Quantitative Trait Loci (QTL) analysis

Rat Genome Scanning Panel

  • Panel of 759 SNP markers selected to maximize genetic information across common inbred rat strains:
    • DA/MolTac
    • Lew/MolTac
    • GK/MolTac
    • F344/NTac
    • SHR
  • Suitable for accelerated backcrossing (speed congenics) and Quantitative Trait Loci (QTL) analysis.

We’re Here to Help

Experience & Expertise You Can Trust

Taconic Biosciences' model generation team has produced about 5,000 models in the last 15 years, developing a globally-recognized reputation for advancing the work of in vivo researchers. Our scientific program managers are here to help you navigate the complexities of model generation.

Pricing Guide


De Vree, P. J. P. et al. Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping. Nat. Biotechnol. 32, 1019-1025 (2014)10.1038/nbt.2959.

Cain-Hom, C. et al. Efficient mapping of transgene integration sites and local structural changes in Cre transgenic mice using targeted locus amplification. Nucleic Acids Res. 45, (2017)10.1093/nar/gkw1329.

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