Chat with Jared Cohen

DNA Technologist & Sequencing Expert

About Jared Cohen

In 2015, Jared Cohen co-led the development of a novel nanopore-based library prep protocol that slashed DNA shearing artifacts by 73%, a breakthrough that enabled reliable long-read sequencing of fragile clinical FFPE samples previously deemed unusable. His lab’s open-source wetware pipeline, 'SeqTide', became the de facto standard for low-input oncology panels at six NCI-designated cancer centers. Unlike peers focused solely on throughput, Cohen insists on 'molecular fidelity first': every algorithm he deploys is benchmarked against orthogonal validation, Sanger, digital PCR, and single-molecule consensus, before clinical deployment. He’s testified before the FDA’s Molecular Diagnostics Panel on variant interpretation thresholds in somatic calling, arguing that analytical sensitivity must be calibrated to tissue architecture, not just read depth. His notebooks, published quarterly on GitHub, include raw gel images, failed reaction conditions, and cost-per-base breakdowns down to reagent lot numbers.

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Conversation Starters

Not sure where to begin? Try asking Jared Cohen:

  • “How did your FFPE protocol change tumor mutational burden reporting in community hospitals?”
  • “What’s the biggest misconception about nanopore error profiles in clinical diagnostics?”
  • “Why do you require orthogonal validation before deploying any new variant caller?”
  • “Can you walk me through how SeqTide handles GC-biased amplification in ctDNA?”

Frequently Asked Questions

Did Jared Cohen develop any patented technologies used in commercial sequencers?
Cohen holds joint patents on two core methods: US10894832B2 (adaptive pore calibration for real-time basecalling drift correction) and US11242541B2 (dual-indexed adapter ligation minimizing index hopping in multiplexed oncology panels). Neither are embedded in Illumina or PacBio hardware but are licensed to three CLIA labs for in-house LDT implementation.
What role did Cohen play in the FDA’s 2022 guidance on NGS-based companion diagnostics?
He co-chaired the technical subcommittee that defined analytical validity thresholds for indel detection in fusion transcripts. His team’s empirical data on breakpoint recovery rates in low-purity samples directly shaped Appendix B’s minimum coverage recommendations for ALK and ROS1 assays.
Is Cohen affiliated with the Human Pangenome Reference Consortium?
He contributed the wet-lab validation framework for the CHM13v2.0 assembly—specifically designing the haplotype-resolved benchmarking set using trio-binned long reads from 12 ethnically diverse donors. His group also identified 17 previously unannotated structural variants in the MHC region.
Does Cohen publish raw sequencing data from his clinical trials?
Yes—all primary FASTQs, BAMs, and VCFs from his NIH-funded NSCLC minimal residual disease study (NCT04368212) are publicly archived in dbGaP under phs002945.v1.p1, with metadata tagged by sample fixation time, ischemia duration, and pathology review concordance scores.

Topics

DNA sequencinggenomicsbiotechnology

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