PIXUL-ChIP: Platform for High Throughput Epigenetic Chromatin Immunoprecipitation (ChIP) Assays


To develop a tool for rapid sample preparation for chromatin immunoprecipitation (ChIP) assays

Anticipated Impact: 

Improved efficiency and reliability of ChIP assays, and enhanced understanding of the biology of major diseases


Most diseases (including cancer, heart disease, and neurological disorders) are associated with abnormal gene expression. This abnormal expression is often caused by changes in the physical association of proteins with DNA. Chromatin immunoprecipitation (ChIP) assay is a powerful laboratory technique that allows researchers to identify which proteins are bound to specific DNA regions. This knowledge can improve understanding of how diseases develop (i.e., the mechanisms by which normal gene expression is altered), and, in the longer term, enable the development of new strategies to prevent, diagnose, or treat disease (i.e., a protein that alters the expression of a disease-associated gene may be a useful target for a diagnostic test or drug). It currently takes several hours to prepare DNA samples for ChIP analysis, and this long preparation time is associated with sample degradation and poor reproducibility of results. This grant supports the development and validation of PIXUL, a novel ultrasound tool for rapid DNA preparation that is expected to enhance the speed, sensitivity, and reliability of ChIP assays.  Formation of a new company to commercialize this technology is planned.

Rapid Sample Preparation for Genomic Assays

Grant Update

Principal Investigator:
Karol Bomsztyk
Grantee Organization:
University of Washington
Grant Title:
PIXUL-ChIP: Platform for high throughput epigenetic chromatin immunoprecipitation (ChIP) assays
Grant Cohort and Year:
2014 Proof of Concept (03)
Grant Period:
06/16/2014 - 06/15/2016 (Completed)
Grant Amount:
Virtually every disease involves abnormal expressions of certain genes which can be determined through analyzing epigenetic markers. Identification of detrimentally expressed genes for targeted drug delivery is the hallmark of personalized medicine. Chromatin ImmunoPrecipitation (ChIP) is the most powerful tool used in epigenetics. In ChIP assays it is necessary to shear or fragment chromatin. We have previously developed a powerful high throughput platform for analysis of epigentics marks, Matrix ChIP. However, the pre-analytical chromatin shearing steps remain a major bottleneck. The goal of this LSDF funded project is to develop a microprocessor for high throughput chromatin preparation, PIXUL, where dozens and eventually hundreds of samples are prepared at a time. Since the LSDF grant started 24 months ago we designed, engineered and tested a unique transducer array to shear DNA and chromatin samples that includes a proprietary amplifier to drive the transducer system.

Impact in Washington

Location of LSDF Grantee
Locations of Collaborations/Areas of Impact

Legislative Districts:
11, 34, 36, 37, 43, 46

Health Impacts

Rapid Sample Preparation for Genomic Assays