Animal Program: Genotyping of Mice and Rats

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Policy Number:
UW-4096
Old Policy Number:
2010-038-v
Responsible Office:
Research Animal Resources and Compliance

University Policy

Rationale/​Purpose:

The purpose of this policy is to establish consistent standards for genotyping of mice and rats in the UW–Madison animal program.

Genotyping animals in a litter is critical to the efficient pursuit of research and in reducing the number of animals involved in a research project. Most often the genotype is determined by analysis of DNA extracted from samples collected from young rodents. Analysis by Polymerase Chain Reaction (PCR) requires the least amount of DNA and is commonly used.  Other genotyping or genetic analysis methods may require larger amounts of DNA.  Genotyping prior to weaning allows genetically desirable animals to be promptly identified and facilitates more efficient use of cage space.

Historically, tissue biopsies (e.g., ear, tail, toe) have been commonly used to obtain DNA for genotyping, but biopsies must be carefully performed as they have the potential to result in some level of pain or distress.

Definitions:
Distal Phalanx Biopsy
Refined method of toe clipping that refers to the removal of the distal (3rd) phalanx of a digit that may be used for genotyping or identification.
Ear Punch
Application of a specific combination of small hole punches or notches to the outside edges of a rodent’s ear (pinna) for tissue collection (biopsy) or identification.
Genotyping
The process through which an animal’s genetic make-up is determined using a sample taken from the animal.
Identification
The process of uniquely marking an animal so it can be differentiated from other animals within a group.
Momentary Pain
Brief, transient pain that typically does not require analgesia.
Policy:
  1. Principal investigators should use the least invasive method of genotyping available and collect the smallest sample that will meet scientific needs.
  2. Whenever genotyping and identification of an individual is required, a method should be chosen that meets both goals.
  3. Genotyping procedures that cause more than momentary pain or distress should be performed with appropriate sedation, analgesia, or anesthesia.
  4. Genotyping and identification procedures must be described and approved in an Animal Care and Use Protocol.
  5. Principal investigators must ensure sufficient training for individuals performing these procedures.
  6. Procedures
    1. Ear Punching
      1. Ear punching is the preferred method if it allows for scientific needs to be met.1
      2. Ear punching can be used for genotyping and identification.
      3. Anesthesia and analgesia are not required for the collection of small (e.g., 2 mm) ear punches.
      4. Ear punching can be repeated if additional genotyping is necessary.
    2. Tail Biopsy
      1. Tail biopsies performed in mice and rats ≤ 21days of age may be performed without anesthesia or analgesia.
      2. Tail biopsies performed on mice and rats > 21 days of age requires anesthesia and analgesia.
      3. For most procedures, a 2 mm biopsy provides an adequate tissue sample. If necessary, up to 5 mm can be removed at one time.
      4. Repeat tail biopsies require the use of anesthesia and analgesia and must be justified in the Animal Care and Use Protocol and approved by the Institutional Animal Care and Use Committee (IACUC).
    3. Distal Phalanx Biopsy
      1. Distal phalanx biopsy can be used for genotyping and identification.
      2. As a method of identification, distal phalanx biopsy should only be used when no other method of individual identification is feasible and must be justified in the Animal Care and Use Protocol.2
      3. Distal phalanx biopsy may be a preferred method if it is used both for genotyping and identification.2
      4. Mice and rats should be 7 days old or less at the time of distal phalanx biopsy.4
      5. Distal phalanx biopsy may be performed between post-natal days 8-17 if the tissue is used for genotyping and identification.3
      6. Anesthesia and/or analgesia is required and must be described in the approved Animal Care and Use Protocol as it is considered to cause more than momentary pain or distress at this age.2
      7. Limitations
        1. No more than one toe per front foot may be biopsied; the front feet should not be sampled if future experimental use could include behavioral tests such as grip strength.
        2. Up to two toes may be biopsied from rear feet.
        3. No more than four toes total per animal may be biopsied.
      8. If repeat genotyping is necessary, another method must be utilized for DNA collection.
External References:

1 Taitt KT, Kendall LV. Physiologic stress of ear punch identification compared with restraint only in mice. J Am Assoc Lab Anim Sci. 2019 Jul 1;58(4):438-442. doi: 10.30802/AALAS-JAALAS-18-000120. Epub 2019 May 10. PMID: 31076022; PMCID: PMC6643090.

2 ILAR guide for the care and use of laboratory animals. National Academy Press, Washington D.C. 2011.

3 Castelhano-Carlos MJ, Sousa N, Ohl F, Baumans V. Identification methods in newborn C57BL/6 mice: A developmental and behavioural evaluation. Lab Animal 2010; 4:88-103.

4 Paluch LR, Lieggi CC, Dumont M, Monette S, Riedel ER, Lipman NS. Developmental and behavioral effects of toe clipping on neonatal and preweanling mice with and without vapocoolant anesthesia. J Am Assoc Lab Anim Sci. 2014 Mar;53(2):132-40. PMID: 24602538; PMCID: PMC3966268.

Policy Administration

Approval Authority:
Attending Veterinarian
Policy Manager:
IACUC Administrator
Contact:
IACUC Administrator -- IACUC Administrator, iacuc_administrator@rarc.wisc.edu, (608) 262-1238
Effective Date:
06-08-2010
Date Issued:
06-08-2010
Revised Dates:

03-01-2011, 08-01-2017, 02-01-2018, 12-23-2025

Reviewed Dates:

02-01-2018, 04-1-2025

Retrieved:
01-01-2026 02:15:34