Lab Med Online.  2022 Jan;12(1):63-67. 10.47429/lmo.2022.12.1.63.

Secondary Germline CDKN2A Mutation Identified using Liquid Biopsy in a Patient with Esophageal Cancer

• Jang H
• Won D
• Shin S
• Park SY
• Kim DJ
• Lee ST
• Choi JR

• KMID: 2538586
• DOI: http://doi.org/10.47429/lmo.2022.12.1.63

Abstract

Liquid biopsy is a non-invasive method for tumor genotyping through detecting the circulating tumor DNA (ctDNA). Here, we describe the case of an esophageal squamous cell cancer patient in which a germline CDKN2A mutation was identified incidentally through liquid biopsy. The preoperative sample analysis revealed a total of five alterations in CDKN2A, TP53, FAT1, and KMT2C genes using next-generation sequencing data. The CDKN2A p.R87W was confirmed as a germline mutation, which is likely a pathogenic variant revealed through peripheral leukocyte DNA analysis. The patient underwent esophagectomy and sequential adjuvant chemoradiation therapy. After the surgery, the variant allele frequencies of somatic variants tended to decrease throughout the treatment. In addition to the detection of somatic variants, ctDNA testing can also provide information on the germline cancer susceptibility variants.

Keyword

Circulating tumor DNA; Germline mutation; CDKN2A; Liquid biopsy; Hereditary cancer syndromes

Figure

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  Fig. 1 Changes in the variant allele frequencies of somatic variants throughout the treatment. The somatic variants identified at the initial liquid biopsy exhibited a decreasing tendency throughout the treatment. The somatic variants were classified based on the 2017 Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists guidelines [26]. The variant allele frequency (VAF, %) was calculated as (read depth count of identified variant/total read depth count at the position)×100. Abbreviations: T, Tier; VAF, variant allele frequency; XP, cisplatin and capecitabine chemotherapy.

Reference

1. Slavin TP, Banks KC, Chudova D, Oxnard GR, Odegaard JI, Nagy RJ, et al. 2018; Identification of incidental germline mutations in patients with advanced solid tumors who underwent cell-free circulating tumor DNA sequencing. J Clin Oncol. JCO1800328. DOI: 10.1200/JCO.18.00328. PMID: 30339520. PMCID: PMC6286162.

2. Veyseh M, Ricker C, Espenschied C, Raymond V, D'Souza A, Barzi A. 2018; Secondary germline finding in liquid biopsy of a deceased patient; case report and review of the literature. Front Oncol. 8:259. DOI: 10.3389/fonc.2018.00259. PMID: 30050867. PMCID: PMC6052887.

3. Shukuya T, Patel S, Shane-Carson K, He K, Bertino EM, Shilo K, et al. 2018; Lung cancer patients with germline mutations detected by next-generation sequencing and/or liquid biopsy. J Thorac Oncol. 13:e17–9. DOI: 10.1016/j.jtho.2017.09.1962. PMID: 28989037. PMCID: PMC5910030.

4. Hu Y, Alden RS, Odegaard JI, Fairclough SR, Chen R, Heng J, et al. 2017; Discrimination of germline EGFR T790M mutations in plasma cell-free DNA allows study of prevalence across 31,414 cancer patients. Clin Cancer Res. 23:7351–9. DOI: 10.1158/1078-0432.CCR-17-1745. PMID: 28947568. PMCID: PMC5712272.

5. Sherr CJ. 2001; The INK4a/ARF network in tumour suppression. Nat Rev Mol Cell Biol. 2:731–7. DOI: 10.1038/35096061. PMID: 11584300.

6. Chan SH, Chiang J, Ngeow J. 2021; CDKN2A germline alterations and the relevance of genotype-phenotype associations in cancer predisposition. Hered Cancer Clin Pract. 19:21. DOI: 10.1186/s13053-021-00178-x. PMID: 33766116. PMCID: PMC7992806.

7. Ruiz A, Puig S, Malvehy J, Lázaro C, Lynch M, Gimenez-Arnau AM, et al. 1999; CDKN2A mutations in Spanish cutaneous malignant melanoma families and patients with multiple melanomas and other neoplasia. J Med Genet. 36:490–3. PMID: 10874641. PMCID: PMC1734379.

8. Puig S, Potrony M, Cuellar F, Puig-Butille JA, Carrera C, Aguilera P, et al. 2016; Characterization of individuals at high risk of developing melanoma in Latin America: bases for genetic counseling in melanoma. Genet Med. 18:727–36. DOI: 10.1038/gim.2015.160. PMID: 26681309. PMCID: PMC4940430.

9. Helsing P, Nymoen DA, Ariansen S, Steine SJ, Maehle L, Aamdal S, et al. 2008; Population-based prevalence of CDKN2A and CDK4 mutations in patients with multiple primary melanomas. Genes Chromosomes Cancer. 47:175–84. DOI: 10.1002/gcc.20518. PMID: 18023021.

10. Kannengiesser C, Brookes S, del Arroyo AG, Pham D, Bombled J, Barrois M, et al. 2009; Functional, structural, and genetic evaluation of 20 CDKN2A germ line mutations identified in melanoma-prone families or patients. Hum Mutat. 30:564–74. DOI: 10.1002/humu.20845. PMID: 19260062.

11. Jenkins NC, Jung J, Liu T, Wilde M, Holmen SL, Grossman D. 2013; Familial melanoma-associated mutations in p16 uncouple its tumor-suppressor functions. J Invest Dermatol. 133:1043–51. DOI: 10.1038/jid.2012.401. PMID: 23190892. PMCID: PMC3594444.

12. Miller PJ, Duraisamy S, Newell JA, Chan PA, Tie MM, Rogers AE, et al. 2011; Classifying variants of CDKN2A using computational and laboratory studies. Hum Mutat. 32:900–11. DOI: 10.1002/humu.21504. PMID: 21462282.

13. Hussussian CJ, Struewing JP, Goldstein AM, Higgins PA, Ally DS, Shea-han MD, et al. 1994; Germline p16 mutations in familial melanoma. Nat Genet. 8:15–21. DOI: 10.1038/ng0994-15. PMID: 7987387.

14. Ranade K, Hussussian CJ, Sikorski RS, Varmus HE, Goldstein AM, Tucker MA, et al. 1995; Mutations associated with familial melanoma impair p16INK4 function. Nat Genet. 10:114–6. DOI: 10.1038/ng0595-114. PMID: 7647780.

15. Yu KK, Zanation AM, Moss JR, Yarbrough WG. 2002; Familial head and neck cancer: molecular analysis of a new clinical entity. Laryngoscope. 112:1587–93. DOI: 10.1097/00005537-200209000-00010. PMID: 12352668.

16. Reymond A, Brent R. 1995; p16 proteins from melanoma-prone families are deficient in binding to Cdk4. Oncogene. 11:1173–8. PMID: 7566978.

17. Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. 2015; Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 17:405–24. DOI: 10.1038/gim.2015.30. PMID: 25741868. PMCID: PMC4544753.

18. Amin MB, Edge SB, editors. 2017. AJCC cancer staging manual. 8th ed. NewYork, NY: Springer International Publishing.

19. Middlebrooks CD, Stacey ML, Li Q, Snyder C, Shaw TG, Richardson-Nelson T, et al. 2019; Analysis of the CDKN2A gene in FAMMM syndrome families reveals early age of onset for additional syndromic cancers. Cancer Res. 79:2992–3000. DOI: 10.1158/0008-5472.CAN-18-1580. PMID: 30967399.

20. Lynch HT, Brand RE, Hogg D, Deters CA, Fusaro RM, Lynch JF, et al. 2002; Phenotypic variation in eight extended CDKN2A germline mutation familial atypical multiple mole melanoma-pancreatic carcinoma-prone families: the familial atypical mole melanoma-pancreatic carcinoma syndrome. Cancer. 94:84–96. DOI: 10.1002/cncr.10159. PMID: 11815963.

21. van der Wilk BJ, Noordman BJ, Atmodimedjo PN, Dinjens WNM, Laheij RJF, Wagner A, et al. 2020; Development of esophageal squamous cell cancer in patients with FAMMM syndrome: Two clinical reports. Eur J Med Genet. 63:103840. DOI: 10.1016/j.ejmg.2020.103840. PMID: 31923587.

22. Daly MB, Pal T, Berry MP, Buys SS, Dickson P, Domchek SM, et al. 2021; Genetic/familial high-risk assessment: breast, ovarian, and pancreatic, version 2.2021, NCCN clinical practice guidelines in oncology. J Natl Compr Canc Netw. 19:77–102. DOI: 10.6004/jnccn.2021.0001. PMID: 33406487.

23. Ratajska M, Koczkowska M, Żuk M, Gorczyński A, Kuźniacka A, Stukan M, et al. 2017; Detection of BRCA1/2 mutations in circulating tumor DNA from patients with ovarian cancer. Oncotarget. 8:101325–32. DOI: 10.18632/oncotarget.20722. PMID: 29254167. PMCID: PMC5731877.

24. Mandelker D, Donoghue M, Talukdar S, Bandlamudi C, inivasan P Sr, Vivek M, et al. 2019; Germline-focussed analysis of tumour-only sequencing: recommendations from the ESMO Precision Medicine Working Group. Ann Oncol. 30:1221–31. DOI: 10.1093/annonc/mdz136. PMID: 31050713. PMCID: PMC6683854.

25. Meric-Bernstam F, Brusco L, Daniels M, Wathoo C, Bailey AM, Strong L, et al. 2016; Incidental germline variants in 1000 advanced cancers on a prospective somatic genomic profiling protocol. Ann Oncol. 27:795–800. DOI: 10.1093/annonc/mdw018. PMID: 26787237. PMCID: PMC4843184.

26. Li MM, Datto M, Duncavage EJ, Kulkarni S, Lindeman NI, Roy S, et al. 2017; Standards and guidelines for the interpretation and reporting of sequence variants in cancer: a joint consensus recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. J Mol Diagn. 19:4–23. DOI: 10.1016/j.jmoldx.2016.10.002. PMID: 27993330. PMCID: PMC5707196.