Li-Fraumeni Syndrome: TP53 Gene Sequencing

Condition Description

Li-Fraumeni Syndrome (LFS) is an autosomal dominant cancer predisposition syndrome associated with soft-tissue sarcoma, breast cancer, leukemia, osteosarcoma, melanoma, and cancer of the colon, pancreas, adrenal cortex, and brain [1]. Tumors frequently appear in childhood and affected individuals may experience multiple primary tumors during their lifetime. The cancer risk is estimated to be 90% by age 60.

Classic LFS is defined as a proband with a sarcoma before the age of 45 years and a first-degree relative with any cancer before the age of 45 years, and one additional first- or second-degree relative in the same lineage with any cancer before the age of 45 years or a sarcoma at any age.

Li-Fraumeni-Like Syndrome (LFL) is defined alternately as a proband with any childhood cancer, or a sarcoma, brain tumor, or adrenocortical tumor before the age of 45 years, plus a first- or second-degree relative in the same lineage with a typical LFS tumor at any age, and an additional first- or second-degree relative in the same lineage with any cancer before the age of 60 years (Birch [2]); or two first- or second-degree relatives with any LFS-related cancer at any age (Eeles [3]). 

The TP53 gene (17p13.1) has 10 exons and is a tumor suppressor gene. Approximately 70% of LFS cases and 40% of LFL cases contain germline mutations in TP53. 95% of mutations can be detected by sequence analysis. Some genotype-phenotype correlations have been found: brain tumors seem to be associated with missense TP53 mutations located in the DNA-binding loop that contact the minor groove of DNA, whereas adrenal gland carcinomas are associated with missense mutations located in the loops opposing the protein-DNA contact surface. In addition, mutations likely to result in a null phenotype (absence of the protein or loss of function) are associated with earlier onset brain tumors.  A few families with LFS or LFL have been found to have mutations in the CHEK2 gene. The specific contribution of CHEK2 mutations to LFS and LFL-associated cancer risks has yet to be defined.

Sequencing of the TP53 gene is recommended after a clinical diagnosis consistent with Li-Fraumeni syndrome, and provides a complementary method to confirm the presence of mutations in a proband, identify at-risk individuals among the proband's relatives, and provide prenatal diagnosis in families with known mutations.

For patients with suspected LFS or LFL, sequence analysis is recommended as the first step in mutation identification. For patients in whom mutations are not identified by full gene sequencing, deletion/duplication analysis is appropriate.

Please click here for the GeneTests summary on this condition.


  1.  Li FP, Fraumeni JF Jr. Soft-tissue sarcomas, breast cancer, and other neoplasms. A familial syndrome. Ann Intern Med. 1969; 71: 747-752.
  2.  Birch JM, Hartley AL, Tricker KJ, Prosser J, Condie A, Kelsey AM, Harris M, Jones PH, Binchy A, Crowther D. et al. Prevalence and diversity of constitutional mutations in the p53 gene among 21 Li-Fraumeni families. Cancer Res. 1994; 54: 1298-1304.
  3. Eeles RA. Germline mutations in the TP53 gene. Cancer Surv. 1995; 25: 101-124.

Genes (1)


This test is indicated for:

  • Confirmation of a suspected diagnosis of LFS or LFL.
  • Individuals at-risk for LFS or LFL due to family history.


PCR amplification of 10 exons contained in the TP53 gene is performed on patient genomic DNA. Direct sequencing of amplification products is performed in both forward and reverse directions using automated fluorescence dideoxy sequencing methods. The patient's gene sequences are then compared to a normal reference sequence. Sequence variations are classified as mutations, benign variants unrelated to disease, or variations of unknown clinical significance. Variants of unknown clinical significance may require further studies of the patient and/or family members. This assay does not interrogate the promoter region, deep intronic regions, or other regulatory elements, and does not detect large deletions.


An estimated 70% of families with the clinical diagnosis of LFS will have a detectable TP53 mutation. Sequence analysis of the coding region of the TP53 gene detects approximately 95% of disease-causing mutations. Mutations in the promoter region, some mutations in the introns or other regulatory element mutations, and large deletions cannot be detected by this analysis. 

Analytical Sensitivity: ~99%.

Results of molecular analysis should be interpreted in the context of the patient's clinical presentation and family history.

Specimen Requirements

Listed below are EGL's preferred sample criteria. For any questions, please call 470.378.2200 and ask to speak with a laboratory genetic counselor (
Submit only 1 of the following specimen types
Whole Blood (EDTA)

EDTA (Purple Top)
Infants and Young Children (<2 years of age): 2-3 ml
Children > 2 years of age to 10 years old: 3-5 ml
Older Children & Adults: 5-10 ml
Autopsy: 2-3 ml unclotted cord or cardiac blood
Collection and Shipping
Ship sample at room temperature for receipt at EGL within 72 hours of collection. Do not freeze.
DNA, Isolated

Isolation using the Perkin Elmer™Chemagen™ Chemagen™ Automated Extraction method or Qiagen™ Puregene kit for DNA extraction is recommended.
Collection and Shipping
Refrigerate until time of shipment in 100 ng/µL in TE buffer. Ship sample at room temperature with overnight delivery.

Oragene™ Saliva Collection Kit
Orangene™ Saliva Collection Kit used according to manufacturer instructions. Please contact EGL for a Saliva Collection Kit for patients that cannot provide a blood sample.
Collection and Shipping
Please do not refrigerate or freeze saliva sample. Please store and ship at room temperature.

Special Instructions

Please submit copies of pedigree or other family history information along with the sample. Contact the laboratory if further information is needed. Sequence analysis is required before deletion/duplication analysis by targeted CGH array. If sequencing is performed outside of EGL Genetics, please submit a copy of the sequencing report with the test requisition form.

  • Li Fraumeni Syndrome: TP53 Gene Deletion/Duplication (QY) is available for those individuals in whom sequence analysis is negative.
  • Known Mutation Analysis (KM) is available to family members if mutations are identified by sequencing.
  • Prenatal testing is available to individuals who are confirmed carriers of mutations. Please contact the laboratory genetic counselor to discuss appropriate testing prior to collecting a prenatal specimen.

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