Combinatorial batching of DNA for ultralow-cost detection of pathogenic variants

Ulrik Kristoffer Stoltze*, Christian Munch Hagen, Thomas van Overeem Hansen, Anna Byrjalsen, Anne-Marie Gerdes, Victor Yakimov, Simon Rasmussen, Marie Bækvad-Hansen, David Michael Hougaard, Kjeld Schmiegelow, Henrik Hjalgrim, Karin Wadt, Jonas Bybjerg-Grauholm*

*Corresponding author for this work


BACKGROUND: Next-generation sequencing (NGS) based population screening holds great promise for disease prevention and earlier diagnosis, but the costs associated with screening millions of humans remain prohibitive. New methods for population genetic testing that lower the costs of NGS without compromising diagnostic power are needed.

METHODS: We developed double batched sequencing where DNA samples are batch-sequenced twice - directly pinpointing individuals with rare variants. We sequenced batches of at-birth blood spot DNA using a commercial 113-gene panel in an explorative (n = 100) and a validation (n = 100) cohort of children who went on to develop pediatric cancers. All results were benchmarked against individual whole genome sequencing data.

RESULTS: We demonstrated fully replicable detection of cancer-causing germline variants, with positive and negative predictive values of 100% (95% CI, 0.91-1.00 and 95% CI, 0.98-1.00, respectively). Pathogenic and clinically actionable variants were detected in RB1, TP53, BRCA2, APC, and 19 other genes. Analyses of larger batches indicated that our approach is highly scalable, yielding more than 95% cost reduction or less than 3 cents per gene screened for rare disease-causing mutations. We also show that double batched sequencing could cost-effectively prevent childhood cancer deaths through broad genomic testing.

CONCLUSIONS: Our ultracheap genetic diagnostic method, which uses existing sequencing hardware and standard newborn blood spots, should readily open up opportunities for population-wide risk stratification using genetic screening across many fields of clinical genetics and genomics.

Original languageEnglish
Article number17
JournalGenome Medicine
Issue number1
Pages (from-to)17
Publication statusPublished - 14 Mar 2023


  • Child
  • Infant, Newborn
  • Humans
  • Genetic Predisposition to Disease
  • Genetic Testing/methods
  • Neoplasms/diagnosis
  • Germ-Line Mutation
  • Risk Factors
  • High-Throughput Nucleotide Sequencing
  • DNA


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