# Commercialization of a highly-sensitive, scalable and low-input compatible kit-based solution for discovery of translocations from FFPE tumor biopsies

> **NIH NIH R44** · ARIMA GENOMICS, INC. · 2020 · $999,273

## Abstract

Commercialization of a highly-sensitive, scalable and low-input compatible kit-based solution for
discovery of translocations from FFPE tumor biopsies
Arima Genomics
Project Summary/Abstract
Despite decades of research, cancer takes the lives of nearly 600,000 people every year in the US. The cancer
research community has made key advancements towards improving the precision of cancer diagnosis and
recently substantial efforts have been put forth into the genetic profiling of tumors. Specifically, efforts have
been focused on developing methods to profile genetic alterations such as translocations that are prognostic in
cancer. Knowledge of an individual's translocation profile can be used to uncover the mechanistic basis of
cancer, accelerating cancer research towards development of new precision therapies. Current standard,
including NGS, are limited in their ability to characterize translocations. This is because for NGS (WGS or gene
panel seq.) to profile translocations, breakpoint-spanning reads are needed and NGS does not enrich for such
reads. FISH enriches for breakpoint info by capturing spatial conformation of the genome within cells and but it
has limited utility due to its low-throughput nature and its requirement of apriori info of the translocation
partners. Spectral Karyotyping (SKY) needs living cells and cannot be performed on FFPE samples, which is a
major sample type for cancer samples. Altogether, a method that is (a) high-throughput along the lines of NGS;
(b) enriches translocations along the lines of FISH; (c) not requiring apriori indo of translocating partners to
enable promiscuous translocation detection; and (d) compatible with FFPE samples – would result in a highly
sensitive and scalable solution for translocation discovery. We satisfy the unmet need via a leapfrog solution.
We use HiC to capture conformation on the lines of FISH and couple it with NGS (HiC-Seq) to detect
translocations at high sensitivity, high precision, high PPV and low FP. Our team has unmatchable expertise in
the science of HiC and its commercialization. Specifically, we commercialized Arima-HiC kits in 2018 for
studying conformation in the context of Epigenetics research and generated $1.2M in revenue in the 1st year of
commercialization with 200+ customers, all from 1 sales executive. However, these kits are not compatible to
FFPE, is manual, labor- and time-intensive and cannot handle batches of >10-20 samples at a time – to enable
broad adoption toward cancer research, we have shown the development a boxed kit, the “T-Seq Kit”, based
on enhanced HiC optimized for performance, speed, ease of use that is compatible to low-input FFPE, fresh
and frozen samples. We validate the technology development from sample to insight in a patient-derived FFPE
GIST biopsy and demonstrate that we can sensitively profile translocations even from low tumor purity samples
(or low MAF). As part of this direct-2-phase II program, we propose to further develop our t...

## Key facts

- **NIH application ID:** 9910099
- **Project number:** 1R44CA247185-01
- **Recipient organization:** ARIMA GENOMICS, INC.
- **Principal Investigator:** Siddarth Selvaraj
- **Activity code:** R44 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $999,273
- **Award type:** 1
- **Project period:** 2020-05-01 → 2022-02-28

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9910099

## Citation

> US National Institutes of Health, RePORTER application 9910099, Commercialization of a highly-sensitive, scalable and low-input compatible kit-based solution for discovery of translocations from FFPE tumor biopsies (1R44CA247185-01). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/9910099. Licensed CC0.

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