Viability Primary Screen IMPC_VIA_002

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Purpose

To assess the postnatal viability, sub-viability, and lethality of mice of each zygosity and sex during cohort production.

Experimental Design

  • Monitor genotypes of at least 28 live offspring from a specified breeding strategy (i.e. HetXHet). A single breeding strategy should be used per procedure so that totals of pups can be grouped together. If another breeding strategy is used for some litters, please submit a separate procedure, distinguished by sequence id. 
  • Record age of pups at genotype (P1-P28).
  • (Optional) Record the age of the youngest and oldest female parents when cohort breeding starts.
  • Record raw numbers of live pups of each sex/zygosity combination.
  • Identify viability/subviability/lethality of zygosities/sexes by application of a percentage-based derivations. 
  • The viability calls are only made where the parental cross is Het x Het for autosomal genes and Het x Hemi for the X-linked genes. Hemizygous male viability is also calculated from WT x Hemi cross.
  • If homozygous lethal: perform the embryonic lethal pipeline (if available). 

Procedure

  1. Determine gene category (see Notes below).
  2. Select breeding strategy to generate phenotyping cohort for a colony.
  3. Genotype all live pups and record numbers of each sex/zygosity for a minimum of 28 pups. If possible, record pups grouped by litter, along with the parental IDs and date of birth for each litter. Record all three parents for trio matings. Where litter data is not available, group these pups together as the “noLitter” group.
  4. Submit numbers to seriesParameters. Include zeros for all categories where no pups were recorded, even if they were not expected. Do not submit values to the derived total or outcome parameters (see example submission file).
    1. Where litter data is available, submit each litter as a single increment of all “Number of…” parameters. Include parental IDs and dates of birth where possible. Use a unique identifier for each litter as the incrementValue. Trios matings are indicated by the presence of a second female parentID; otherwise, omit this ID.
    2. Where litter data is not available, submit pups grouped together as a single increment of all “Number of…” parameters, using incrementValue=”noLitter”. Omit the litter date of birth for this group. “unknown” can be submitted for parentalIDs for this group (or any litter where the parent cannot be identified).
  5. Identify strains that produce no homozygous/hemizygous male or female pups. 
    1. Homozygous animal viability call is calculated for both sexes of autosomal genes and females of X-linked genes.
    2. Heterozygous animal viability call is calculated for both sexes of autosomal genes.
    3. Hemizygous male viability call is calculated for males for X-linked genes based on the total number of pups.
    4. For sex specific homozygous viability calls, 28 pups of that particular sex are required.
  6. Strains that produce <25% expected (#totalpups * 0.125 (3 for 28) (4 for 29-36) (5 for 37-52) homozygous pups will be considered SUBVIABLE (partial preweaning lethality [MP: 0011110]). 

Notes

Anzygous is a term to describe the zygosity of a female animal for a gene on the Y-chromosome i.e. no copies of the gene expected. As with all sex/zygosity categories, please report zeros for all litters/colonies where no animals of this type were found, even if they were not expected from that breeding strategy.

Gene category should be available from production labs at each centre. It can be ascertained for most genes by searching NCBI gene. Any gene on a numbered chromosome is autosomal. Contact production labs or DCC data wranglers for assistance.

Parameters & Metadata

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Name Version Type Description Req. Upload Req. Analysis Annotation Increment Options Ontology Options Unit Data Type Derived History Key Group ID
Name Version Type Description Req. Upload Req. Analysis Annotation Increment Option Ontology Options Unit Data Type Derived History Key Group ID