Automated, absolute quantification of MRD in ALL patients by droplet microfluidics, single DNA copy barcoding and IG/TR amplicon NGS

In this project FRRB finances partner number 4: Fondazione Matilde Tettamanti e Menotti de Marchi ONLUS (Fondazione Tettamanti), Milano. The Principal Investigator responsible of the project is Dr. Giovanni Cazzaniga.

FRRB also finances partner number 5: ASST Papa Giovanni XXIII, Bergamo. The Principal Investigator is Dr. Alessandro Rambaldi.

Pathology of interest:

Childhood and adult acute lymphoblastic leukemia

Area of research:


Start date:

May 2019

End date:

April 2022


€ 499.860,00

Project partners:

University of Freiburg – leading partner

University Hospital Schleswig-Holstein

Centre for Research and Technology Hellas (CERTH), Institute of Applied Biosciences (INAB)

Fondazione Matilde Tettamanti e Menotti de Marchi ONLUS (Fondazione Tettamanti), Milano

ASST Papa Giovanni XXIII, Bergamo


The assessment of minimal residual disease (MRD) during first-line therapy is regarded as most important prognostic factor in adult and childhood acute lymphoblastic leukemia (ALL). However, current methods used for MRD assessment have major drawbacks.

Multiparameter flow cytometry is not fully standardized and requires expert skills. Allele specific PCR of clonal immunoglobuline (IG) and T-cell receptor (TR) gene rearrangements is time consuming and needs patient-specific reagents, thus making it ineligible for IVD-guided analytical validation. In this context amplicon based IG/TR NGS was introduced, which allows for the characterization of millions of IG/TR rearrangements in parallel without the need for patient specific reagents, thus allowing IVD-guided analytical validation. The downside of this method is that it is prone to amplification biases that hamper correct quantification. Also, contamination of libraries leading to false positive results constitutes a severe problem in diagnostic routine. The goal and hypothesis of Quant-ALL is to eliminate these disadvantages by a combination of innovative high throughput molecular tools.

Aims and methods: (1) Establishment of an amplicon based IG/TR NGS approach using single DNA copy barcoding and droplet microfluidics for IG/TR based MRD quantification in ALL. (2) Optimization of existing bioinformatics tools used for IG/TR NGS to quantify index IG/TR sequences. (3) Transfer of this technology to a pre-existing centrifugal microfluidic platform for full automation and standardization. (4) Validation of technology for childhood and adult ALL using biobanked follow-up samples that are MRD quantified with standard technologies.

Expected results are the full automation of a high throughput technology for MRD quantification in ALL. This technology will be standardized and validated to allow a wide distribution to ALL MRD reference laboratories and fundamentally improve MRD quantification in childhood and adult ALL.