# Rapid Acute Leukemia Genomic Profiling with CRISPR enrichment and Real-time long-read sequencing

> **NIH NIH R21** · FRED HUTCHINSON CANCER CENTER · 2024 · $187,058

## Abstract

PROJECT SUMMARY/ABSTRACT
Background: Acute myeloid leukemia (AML) continues to have high mortality rates despite a plethora of
available treatments. Variable prognosis, treatment response and survival are largely based on cytogenetic and
molecular aberrations that characterize AML subtypes. Fast and cost-effective methods of detecting AML fusions
and mutations could improve clinical outcomes for patients, as standard next generation sequencing (NGS)
methods are limited by several technical and bioinformatic issues.
Hypothesis: We have developed a CRISPR-based single molecule long-read sequencing assay (CSRL) to
quickly detect clinically relevant mutated genes in AML. This new methodology, combined with new bioinformatic
approaches, allows for same day results of sequencing data. We hypothesize that such technology can be
improved to detect both mutation and translocations common in AML, and that this rapid turn-around-time will
positively impact patient care by allowing swift risk stratification and treatment selection.
Proposal: In this study, we expand the CSRL assay to include more relevant mutations and translocations.
Specifically, we will ask and answer 1) Will the CSRL assay identify all the mutations and fusion in the target
genes seen by NGS and cytogenetics? 2) Do the single molecule reads provide a more accurate assessment of
tumor burden? 3) Do CSRL data allow for determination of phasing of mutations and provide additional
prognostic or predictive significance? 4) Is same-day sample collection and result reporting clinically feasible for
the AML CSRL assay and how will obtaining same-day CSRL results impact clinical decision making? 5) What
improvements can be expected upon the current turnaround time, costs, and assay performance in comparison
to standard NGS? To answer questions 4 and 5, we will conduct a pilot clinical trial to test feasibility of clinical
implementation. Research Design/Specific Aims: Specific aims: SA1) To expand our CSRL sequencing
assay and optimize current bioinformatics workflow to allow for same-day diagnosis (~8 hours). This
development will use a multiplexed CRISPR enrichment library of long nucleic acid molecules on a low cost
Nanopore device. SA2) Validate sensitivity and specificity of the assay developed in SA1 and evaluate
prognostic impact of phasing data provided by long reads and single molecule quantification for more
accurate tumor burden assessment. We will test the proposed method on a set of clinically annotated leukemia
samples with existing molecular data obtained with standard NGS and cytogenetics. SA3) To establish clinical
utility of CSRL sequencing with same-day leukemia molecular diagnosis. The purpose of this specific aim
is to demonstrate the clinical impact of our same day ultrarapid molecular profiling assay through a pilot study
on 10-12 patients at our cancer center. We will test real world feasibility of implementing these methods on
samples from the clinic, ease of same day tes...

## Key facts

- **NIH application ID:** 10815759
- **Project number:** 5R21CA280520-02
- **Recipient organization:** FRED HUTCHINSON CANCER CENTER
- **Principal Investigator:** Cecilia C Yeung
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $187,058
- **Award type:** 5
- **Project period:** 2023-04-01 → 2026-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10815759

## Citation

> US National Institutes of Health, RePORTER application 10815759, Rapid Acute Leukemia Genomic Profiling with CRISPR enrichment and Real-time long-read sequencing (5R21CA280520-02). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10815759. Licensed CC0.

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