Abstract B029: Feasibility of Low-Cost Genomic Newborn Screening for Pediatric Cancers via Targeted NGS Pooling

Abstract Purpose: Very early onset rare pediatric cancers such as retinoblastoma are not included in current public health newborn screening (NBS), even though early detection can prevent serious health problems. Currently, babies are screened for retinoblastoma using the “red-reflex” eye test, but this method often misses cancers, leading to delayed diagnoses and poor outcomes. Modern genomic technologies such as targeted Next-Generation Sequencing (tNGS) can detect causal variants in the RB1 gene and other cancer predisposition syndrome (CPS) genes, but applying tNGS individually to every newborn remains cost-prohibitive for NBS implementation. We propose that DNA pooling strategies can further reduce per-sample costs, making CPS gene testing feasible for NBS enabling earlier detection and monitoring of high-risk infants. Methods: As part of a proof-of-concept cancer predisposition screening study, we obtained tNGS data from archived dried blood spots (DBS) — the standard NBS sample — from the Michigan BioTrust for Health, from 1,948 children diagnosed with CPS before age eight. To evaluate the pooling approach, we organized DBS DNA extracted from 28 different newborns into groups: a 4×4 grid of 16 samples and one additional row and column of 10 samples overlapping with the 4 x 4 grid. The samples were pooled across rows and columns (16 samples in 4 x 4 grid resulted in 8 pools) and the remaining two row and column sample pools were in pools of 10. We performed custom tNGS and bioinformatics processing for these 10 pools (with either 4- or 10-sample pools) targeting RB1 and other cancer-associated genes (TP53, WT1, APC, SMARCB1, DICER1, PTCH1, SUFU, RET). A custom algorithm deconvoluted the pooled sequencing data to pinpoint which individual DBS sample carried a causal rare (pathogenic) variant. Results: Among the 28 samples, two carried pathogenic RB1 variants (c.751C>T [p.Arg251Ter] and c.1333C>T [p.Arg454Ter]). Both variants were within the 4 x 4 grid and were correctly assigned to the appropriate individual. Within the larger 10-sample pools, only one RB1 variant was pinpointed (as anticipated), highlighting the success of both pooling approaches. This approach preserved sensitivity and specificity while demonstrating an estimated 2–5-fold library prep cost reduction versus individual tNGS. Preliminary testing across additional algorithm settings, CPS genes and cohorts will be presented. Conclusions: Pooling DBS for tNGS in public health NBS is feasible, accurate, and more cost-effective for detecting rare early-onset pediatric cancer risks. This supports a transformative “cancer-risk NBS” paradigm, enabling proactive surveillance and earlier intervention for at-risk infants. These findings provide a strong basis for pilot implementation in real-world NBS programs, with potential to expand to additional actionable conditions. Citation Format: Arindam Bhattacharjee, Mads C Nielsen, Ulrik K Stoltze, Lisa Diller, Richard B Parad. Feasibility of Low-Cost Genomic Newborn Screening for Pediatric Cancers via Targeted NGS Pooling [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Discovery and Innovation in Pediatric Cancer— From Biology to Breakthrough Therapies; 2025 Sep 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(18_Suppl_2):Abstract nr B029.