Confounding factors affecting analysis of germline structural variants in pediatric solid tumors

Area of Science:

• Genetics
• Oncology
• Bioinformatics

Background:

• Germline structural variants (SV) are implicated in pediatric solid tumors.
• Previous studies reported SVs involving MYCN and RAF1::TMEM40.
• The clinical relevance of these findings requires validation.

Purpose of the Study:

• To investigate potential confounders in germline predisposition studies for pediatric solid tumors.
• To assess the impact of circulating tumor DNA (ctDNA) and population stratification on reported SVs.
• To provide recommendations for improving the accuracy of future germline studies.

Main Methods:

• Analysis of germline DNA samples from pediatric solid tumor cases.
• Assessment of tumor-in-normal contamination using non-polymorphic markers.
• Examination of population stratification using polymorphic markers.
• Bioinformatic analysis of SVs involving MYCN and RAF1::TMEM40.

Main Results:

• Germline predisposition SVs involving MYCN were confounded by ctDNA.
• Germline predisposition SVs involving RAF1::TMEM40 were confounded by enrichment for Hispanic or Latino ancestry.
• These confounders impact the reliability of reported germline findings.

Conclusions:

• Circulating tumor DNA and population stratification can lead to false positives in germline predisposition studies.
• Future germline studies must rigorously control for tumor contamination and population structure.
• Ensuring clinical relevance requires careful methodological validation in genetic studies of pediatric cancers.