An improved molecular inversion probe based targeted sequencing approach for low variant allele frequency

Biezuner T., Brilon Y., Arye A. B., Oron B., Kadam A., Danin A., ...More

NAR Genomics and Bioinformatics, vol.4, no.1, 2022 (ESCI) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 4 Issue: 1
  • Publication Date: 2022
  • Doi Number: 10.1093/nargab/lqab125
  • Journal Name: NAR Genomics and Bioinformatics
  • Journal Indexes: Emerging Sources Citation Index (ESCI), Scopus, BIOSIS, EMBASE, Directory of Open Access Journals
  • TED University Affiliated: No


© 2022 The Author(s). Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.Deep targeted sequencing technologies are still not widely used in clinical practice due to the complexity of the methods and their cost. The Molecular Inversion Probes (MIP) technology is cost effective and scalable in the number of targets, however, suffers from low overall performance especially in GC rich regions. In order to improve the MIP performance, we sequenced a large cohort of healthy individuals (n = 4417), with a panel of 616 MIPs, at high depth in duplicates. To improve the previous state-of-the-art statistical model for low variant allele frequency, we selected 4635 potentially positive variants and validated them using amplicon sequencing. Using machine learning prediction tools, we significantly improved precision of 10-56.25% (P < 0.0004) to detect variants with VAF > 0.005. We further developed biochemically modified MIP protocol and improved its turn-around-time to ∼4 h. Our new biochemistry significantly improved uniformity, GC-Rich regions coverage, and enabled 95% on target reads in a large MIP panel of 8349 genomic targets. Overall, we demonstrate an enhancement of the MIP targeted sequencing approach in both detection of low frequency variants and in other key parameters, paving its way to become an ultrafast cost-effective research and clinical diagnostic tool.