Pediatric Summary Report

Secondary Findings in Pediatric Subjects

Non-diagnostic, excludes newborn screening & prenatal testing/screening

• Status (Pediatric): Passed (Consensus scoring is Complete)
• Curation Status (Pediatric): Released 1.0.3
• Status (Adult): Passed (Consensus scoring is Complete)
• GENE/GENE PANEL: TP53
• Condition: Li-Fraumeni Syndrome
• Mode(s) of Inheritance: Autosomal Dominant

Actionability Assertion

• TP53 ⇔ 0018875 (li-fraumeni syndrome): Strong Actionability

Actionability Rationale

The preliminary assertion was Moderate, but the assertion was changed to Strong given the high tumor risk and effectiveness of surveillance.

Final Consensus Scores

Gene Condition Pairs: TP53 ⇔ 0018875 (OMIM:151623)

Outcome / Intervention Pair	Severity	Likelihood	Effectiveness	Nature of the Intervention	Total Score
Morbidity and mortality from Li Fraumeni syndrome-associated cancers / Cancer surveillance	2	3C	2B	2	9CB
Morbidity and mortality from Li Fraumeni syndrome-associated cancers / Avoidance of radiotherapy	2	3C	0B	3	8CB

1. What is the nature of the threat to health for an individual carrying a deleterious allele?

Prevalence of the Genetic Condition

Li-Fraumeni syndrome (LFS) is a rare cancer syndrome, with 300 to 400 families reported in the literature. [1, 2]

Clinical Features

LFS is an aggressive cancer predisposition syndrome associated with early onset of neoplasms and multiple primary neoplasms within an individual. The most common cancers are soft tissue sarcomas, osteosarcomas, premenopausal breast cancer, brain tumors, and adrenocortical carcinoma, which account for about 70% of LFS-related cancers. Other cancers include colon cancer, gastric cancer, leukemia, lymphoma, cancers of the head and neck, kidney, larynx lung, skin (e.g., melanoma), ovary, pancreas, prostate, testis, and thyroid. To date, male breast cancer has rarely been reported in families with LFS. [1, 3, 4, 5, 6, 2, 7, 8]

Natural History

LFS-related cancers often occur in childhood or young adulthood. Individuals with LFS often develop additional malignancies, with an estimated 40-49% developing a second cancer, or a median 10 years after the first cancer diagnosis. The probability of additional cancers is inversely correlated with younger age at diagnosis of first malignancy. Besides an earlier age of onset, the characteristics of LFS-associated tumors compared to non-LFS are unclear, though there is some evidence that breast cancers in LFS are more likely to be HER2-positive compared to other cases. They are also predominantly estrogen and/or progesterone hormone receptor-positive. The overall prognosis is unknown for LFS and depends on the type and severity of cancers developed. [1, 3, 4, 5, 6, 2, 7, 8]

2. How effective are interventions for preventing harm?

Patient Management

Individuals found to have low-level (e.g, <20%) mosaicism for a TP53 pathogenic variant in leukocytes may require additional follow-up to distinguish between germline variants and postzygotic (acquired) pathogenic variant due to clonal hematopoiesis of indeterminate potential. This is important as the clinical interventions described below are only warranted for those with a diagnosis of LFS. (Tier 3) [3, 5]

Patients should be educated regarding the signs and symptoms of cancer. (Tier 2) [5]

Surveillance

The screening and management of LFS is complex. It is preferred that individuals with LFS be followed at centers with expertise in the management of this syndrome. (Tier 4) [5]

Many of the other cancers associated with germline mutations in TP53 do not lend themselves to early detection. Thus, additional recommendations are general and include:
• Comprehensive physical exams including neurological examination with a high index for suspicion for rare cancers and second malignancies every 3-6 months in children (birth to age 18) and 6-12 months in adults
• Colonoscopy and upper endoscopy every 2-5 years starting at age 18-25 or 5 years before the earliest known colon cancer in the family
• Annual dermatological examination starting at age 18 for melanoma
• Annual full blood count
• Abdominal ultrasound for adrenocortical carcinoma every 3-6 months in children (birth to age 18) and annually for adults
• Annual whole body MRI from birth for soft tissue and osteosarcomas
• Annual brain MRI from birth for brain tumors.
Additional surveillance may be recommended based on family history. One 11-year prospective observational study reported outcomes among 40 TP53 carriers who chose to undergo a surveillance protocol and 49 who declined surveillance (19 crossed over to the surveillance group for a total of 59 undergoing surveillance). Surveillance included biochemical methods and imaging techniques, such as annual mammography, annual brain MRI, annual rapid total-body MRI, ultrasound of the abdomen and pelvis, and colonoscopy. Over a median period of 32 months (IQR: 12-87), surveillance identified 40 asymptomatic neoplasms in 19 of 59 (32%) patients, including both malignant tumors and low-grade or premalignant lesions. Among the 49 individuals who initially declined surveillance, 61 symptomatic tumors were diagnosed in 43 (88%). Of the patients who chose surveillance and were diagnosed with cancer, 84% (16 out of 19) were alive at follow-up (median 38 months, IQR: 12-86) compared to 49% (21 out of 43; median follow-up of 46 months, IQR: 22-72) patients diagnosed with cancer who had not chosen surveillance (p=0.012). All patients who died in the non-surveillance group died of cancer. The 5-year overall survival was greater for the surveillance group (88.8%) compared to the non-surveillance group (59.6%) (p=0.0132). A separate meta-analysis evaluated whole-body MRI among 578 individuals across 13 prospective cohorts where a whole-body MRI was administered as part of a baseline assessment with all participants asymptomatic at the time of the baseline scan and not required to be newly diagnosed. Cancer was identified in 7% of the sample, with 83% of cancers being localized and able to treat with curative intent. (Tier 2) [5, 6, 7, 8]

Circumstances to Avoid

Therapeutic radiotherapy and conventional chemotherapies for cancer treatment should be avoided when possible and diagnostic radiation should be minimized to the extent feasible without sacrificing accuracy. Subsequent primary tumors often develop after the exposure of patients with LFS to radio and/or chemotherapy treatments. (Tier 2) [5, 7]

Carriers of TP53 pathogenic variants are counseled to avoid sun exposure, tobacco use, and other known or suspected carcinogens. (Tier 3) [3]

3. What is the chance that this threat will materialize?

Mode of Inheritance

Autosomal Dominant

Prevalence of Genetic Variants

Germline pathogenic variants in the TP53 gene have been observed in 50-92% of families with features of LFS. (Tier 3) [3, 5, 6]

The frequency of germline TP53 pathogenic variants in the general population is not well established but has been estimated to be as common as 1/3500 to 1/55. (Tier 3) [1, 3, 5, 7]

Penetrance

Estimations of cancer risks associated with LFS are limited to at least some degree by selection bias since dramatically affected kindreds are more likely to be identified and become the subject of further study. (Tier 4) [8]

LFS is highly penetrance with a high lifetime risk for cancer. An analysis from the National Cancer Institute’s LFS study (N=286) showed a cumulative lifetime cancer incidence of nearly 100%. This study also estimated cumulative incidence rates by 70 years:
• Women: breast cancer=54%, soft tissue sarcoma=15%, brain cancer=6%, and osteosarcoma=5%
• Men: soft tissue sarcoma=22%, brain cancer=19%, osteosarcoma=11%. (Tier 3) [5, 8]

Pathogenic variants in TP53 are associated with estimated cancer risks of approximately 22% by age 5, 41% by age 18, 60% by age 45, and 95% by age 70. (Tier 3) [5, 8]

For lifetime risk of developing cancer, women have a 90-100% risk while men have a 73% risk. (Tier 3) [1, 3, 6, 7]

Relative Risk

The relative risk of overall tumor development was not found, however tumor-specific relative risks and 95% confidence intervals are available: bone: 107 (49-203), connective tissue: 61 (33-102), brain: 35 (19-60), pancreas: 7.3 (2-19), breast: 6.4 (4.3-9.3), colon: 2.8 (1-6), liver: 18 (2.1-64). (Tier 3) [3, 6]

Expressivity

LFS patients display high variability in age at onset, tumor locations, and number of types of tumors. (Tier 3) [3]

Phenotypic variability is observed within the same family. (Tier 4) [7]

4. What is the Nature of the Intervention?

Nature of Intervention

Interventions identified in this report include prophylactic surgery to remove target organs, intense surveillance, and medications with potential side effects. Adverse events reported with chemoprevention drugs include headache, hot flushes, vaginal discharge, hypertension, musculoskeletal and vasomotor symptoms, cataracts, endometrial cancer, and thrombotic events.

5. Would the underlying risk or condition escape detection prior to harm in the setting of recommended care?

Chance to Escape Clinical Detection

A study of 116 individuals with LFS (mean age of 37.6 years, range 3-68 years) who had not received cancer therapy at least 6 months prior to screening indicated that 7% had cancer at their baseline cancer screening. (Tier 3) [5]

Further, testing for pathogenic TP53 variants should take place before starting cancer treatment due to the contribution of radiotherapy and conventional chemotherapy to subsequent primary tumors. (Tier 3) [7]

Date of Search: 03.26.2021

Reference List

1. Li-Fraumeni syndrome. Orphanet encyclopedia, http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=524

2. Classification and care of people at risk of familial breast cancer and management of breast cancer and related risks in people with a family history of breast cancer. NICE. (2013) Website: https://www.nice.org.uk/guidance/cg164/chapter/recommendations

3. K Schneider, K Zelley, KE Nichols, J Garber. Li-Fraumeni Syndrome. 1999 Jan 19 [Updated 2013 Apr 11]. In: RA Pagon, MP Adam, HH Ardinger, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024. Available from: http://www.ncbi.nlm.nih.gov/books/NBK1311

4. Online Medelian Inheritance in Man, OMIM®. Johns Hopkins University, Baltimore, MD. LI-FRAUMENI SYNDROME 1; LFS1. MIM: 151623: 2016 Jun 24. World Wide Web URL: http://omim.org.

5. Daly MB, Pilarski R, Berry M, Buys SS, Farmer M, Friedman S, et al. Genetic/Familial High-Risk Asessment: Breast and Ovarian. National Comprehensive Cancer Network (NCCN). (2017) Website: www.nccn.org

6. McBride KA, Ballinger ML, Killick E, Kirk J, Tattersall MH, Eeles RA, Thomas DM, Mitchell G. Li-Fraumeni syndrome: cancer risk assessment and clinical management. Nat Rev Clin Oncol. (2014) 11(5):260-71.

7. Frebourg T, Bajalica Lagercrantz S, Oliveira C, Magenheim R, Evans DG. Guidelines for the Li-Fraumeni and heritable TP53-related cancer syndromes. Eur J Hum Genet. (2020) 28(1476-5438):1379-1386.

8. Kratz CP, Achatz MI, Brugières L, Frebourg T, Garber JE, Greer MC, Hansford JR, Janeway KA, Kohlmann WK, McGee R, Mullighan CG, Onel K, Pajtler KW, Pfister SM, Savage SA, Schiffman JD, Schneider KA, Strong LC, Evans DGR, Wasserman JD, Villani A, Malkin D. Cancer Screening Recommendations for Individuals with Li-Fraumeni Syndrome. Clin Cancer Res. (2017) 23(1557-3265):e38-e45.