SDR-seq Connects Genetic Variants to Disease in Single Cells

Researchers at EMBL have developed a single-cell sequencing tool that enables DNA and RNA to be studied together in the same cell, regardless of whether genetic variants occur in coding or non-coding regions. Published in Nature Methods, the method, called SDR-seq, combines high precision with scalability, addressing limitations of earlier technologies.

Lead author Dominik Lindenhofer explained that existing single-cell methods could only capture variants in expressed, coding regions, restricting the scope of analysis. “Our tool works, irrespective of where variants are located, yielding single-cell numbers that enable analysis of complex samples,” he said. This capacity is significant because more than 95% of disease-associated DNA variants are found in non-coding regions, which play a key regulatory role in cell function yet remain incompletely understood.

Non-coding sequences influence processes such as cellular development and regulation. Many variants linked to conditions including congenital heart disease, autism, and schizophrenia are located in these non-coding sections, but current single-cell tools lacked the sensitivity and throughput to investigate them at scale. SDR-seq addresses this gap by allowing direct observation of genetic variation and gene activity from the same cell.

The approach involves encapsulating single cells in oil-water droplets, enabling DNA and RNA to be analyzed side-by-side in thousands of cells simultaneously. The technology integrates several innovations: a cell-fixation method developed by EMBL scientists Judith Zaugg and Kyung-Min Noh to preserve RNA, and a computational decoding system built by Oliver Stegle’s group to interpret complex DNA barcodes. Although tailored for this project, the decoding tool may be applicable to other research.

Analysis of B-cell lymphoma samples revealed that cells with higher numbers of genomic variants displayed more activity in signals that promote cancer growth. These findings showed that variant composition influences cellular states and that increasing variants can correspond with more aggressive lymphoma behavior.

“We have a tool that can link variants to disease,” said Lars Steinmetz, a senior author on the paper. “This capability opens up a wide range of biology that we can now discover. If we can discern how variants actually regulate disease and understand that disease process better, it means we have a better opportunity to intervene and treat it.”