# Next generation cytogenomics using proximity ligation sequencing

> **NIH NIH R44** · PHASE GENOMICS, INC. · 2020 · $249,984

## Abstract

ABSTRACT
Cytogenetic testing is a cornerstone of clinical genetics diagnostics. However, even with state-of-the-art
methodologies, available clinical cytogenetic methods have a non-overlapping series of limitations. The
resolution of karyotyping is typically estimated to be in the 5-10 megabase pair (Mbp) range, limiting the ability
to definitively localize breakpoints. Fluorescence in situ hybridization (FISH) methods overcome some of these
limitations, but allow only one or in some cases a few loci to be interrogated at a time. Chromosomal microarray
analysis (CMA) offers important advantages over karyotyping and FISH, including applicability to virtually any
tissue, increased resolution, and semiautomated interpretation, but is unable to call balanced translocations,
inversions, complex rearrangements, and changes in ploidy. Thus, several complementary tests are typically
used in parallel or in sequence and this greatly inflates the costs and turnaround times of cytogenetic testing.
Proximity ligation methods such as chromosome conformation capture (3C, Hi-C) can be used to measure
physical and genetic distance between all pairs of loci simultaneously on a full-chromosome scale. This property
has been primarily applied to reconstructing end-to-end chromosome sequences for animals and plants.
However, this technology is extremely well suited to the detection of chromosomal aberrations using relatively
simple and ubiquitous sequencing tools and scalable computational analytics.
We propose to apply proximity ligation as a cytogenomic method to detect the breadth of chromosomal
aberrations at high resolution and low cost. This proposal outlines a path to a commercially available product
and service, which will establish a highly validated method for use in research and eventually in a diagnostic
setting. This will be accomplished by 1) designing an easy to use Hi-C protocol amenable to multiwell plate
handling, 2) building a robust automated platform to reproducibly call chromosomal aberrations from Hi-C data,
and 3) proving the validity and reproducibility of these methods on real world samples. The resulting kit and
software product will be a new cytogenomic method called Karyotyping by SequencingTM (KBS).

## Key facts

- **NIH application ID:** 10140059
- **Project number:** 1R44HG011579-01
- **Recipient organization:** PHASE GENOMICS, INC.
- **Principal Investigator:** Stephen Matthew Eacker
- **Activity code:** R44 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $249,984
- **Award type:** 1
- **Project period:** 2020-09-17 → 2021-02-28

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10140059

## Citation

> US National Institutes of Health, RePORTER application 10140059, Next generation cytogenomics using proximity ligation sequencing (1R44HG011579-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10140059. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*