Feasibility and limitations of cultured skin fibroblasts for germline genetic testing in hematologic disorders

• Published in: Human mutation Vol. 43; no. 7; pp. 950 - 962
• Main Authors: DeRoin, Lia, Cavalcante de Andrade Silva, Marcela, Petras, Kristin, Arndt, Kelly, Phillips, Nathaniel, Wanjari, Pankhuri, Subramanian, Hari Prasanna, Montes, David, McElherne, James, Theissen, Megan, Briese, Renee, Das, Soma, Godley, Lucy A., Segal, Jeremy, Gaudio, Daniela, Fitzpatrick, Carrie, Churpek, Jane E.
• Format: Journal Article
• Language: English
• Published: United States John Wiley & Sons, Inc 01.07.2022
• Subjects: Biopsy; Cell culture; Feasibility Studies; Fibroblasts; Gene frequency; Genetic Predisposition to Disease; Genetic screening; Genetic Testing; Germ Cells; Germ-Line Mutation; germline genetics; Hematologic Diseases; Hematological diseases; Humans; inherited; leukemia; lymphoma; Malignancy; myelodysplastic syndrome; Myelodysplastic syndromes; Retrospective Studies; skin fibroblasts; Skin tests; Stem cell transplantation; Telomeres; leukemia; myelodysplastic syndrome; inherited; skin fibroblasts; lymphoma; germline genetics
• ISSN: 1059-7794; 1098-1004; 1098-1004
• DOI: 10.1002/humu.24374

To avoid acquired variants found in the blood, cultured skin fibroblasts are a recommended DNA source for germline genetic testing in patients with hematologic disorders, but data are lacking regarding practicality and limitations. We conducted a retrospective cohort study of 350 subjects with hematologic disorders who underwent skin fibroblast culture for germline genetic testing. We analyzed next‐generation sequencing data from the targeted capture of 144 inherited cancer and bonemarrow failure genes to identify variants at heterozygous and subclonal variant allele frequencies. Sixteen (5%) biopsies failed to culture. Culture failure was more likely in samples with delays in culture initiation (OR = 4.3; p < 0.01) or a pathogenic variant in a telomere gene (OR = 42.6; p < 0.01). Median culture time was 28 days (IQR 22−29 days). Culture time was longer for subjects with prior allogeneic stem cell transplantation (+10.7%; p = 0.02) and shorter in subjects with a heterozygous pathogenic variant (−11.9%; p < 0.01), larger biopsy size (−10.6%; p < 0.01), or lymphoid malignancy (−8.4%; p < 0.01). Subclonal variants were identified in 10 (4%) and confirmed in five (56%) of eight with alternate samples available. Subclonal and discordant variants illustrate that germline testing from cultured skin fibroblasts requires phenotypic correlation and, in rare cases, follow‐up studies for optimal interpretation.