The new genomes will help scientists explore disease mechanisms and cellular processes

PHOENIX — (April 30, 2026) — A team led by scientists at TGen, part of City of Hope, has generated chromosome-level, diploid genome assemblies of two human cell lines that are widely used in research.

Since the 1960s, the BJ and IMR-90 fibroblast cell lines have been used to study everything from premature aging to chromosome instability in cancer progression. The two new assemblies give researchers additional reference genomes for studying disease mechanisms and fundamental cellular processes.

“A lot of people around the world use these cell lines, but then still rely on the traditional hg38 reference genome to understand their genetics,” said Floris Barthel, M.D., Ph.D., an assistant professor in TGen’s Bioinnovation and Genome Sciences Division and senior author of the study. “We now provide high-quality cell-line-specific references.”

What’s more, the researchers produced these high-quality assemblies—resolving both copies of the genome in each cell line—in a small, independently funded research laboratory. “This is the kind of work that would have required a large consortium effort just a few years ago,” Barthel noted.

The study, published in Nucleic Acids Research, was designated as one of the journal’s “Breakthroughs,” an honor given to the top 1 to 2% of its papers. According to the journal, Breakthrough papers are those that solve long-standing problems in their field or offer exceptional insights likely to shape future research.

Although BJ and IMR-90 appear normal under a microscope, the research team discovered that their DNA sequences differ substantially—both from each other and from the standard reference genome.

Compared to the reference genome, they identified more than 50,000 structural variants across the two cell lines. Structural variants include deletions, insertions, or rearrangements of DNA. These variants likely come from more than one source. Some reflect genetic differences between the two donors, some may be tied to the different tissues the cell lines were derived from (neonatal foreskin for BJ, fetal lung for IMR-90), and others likely accumulated over many generations of growth in culture.

“Many of the variants are small and previously known,” said T. Rhyker Ranallo-Benavidez, Ph.D., a computational scientist in Barthel’s lab and the lead author of the study. “But we also found several novel variants. For example, there’s a previously undetected duplication in the BJ assembly, even though these cell lines have been sequenced extensively for decades.”

The fibroblast cells are diploid, meaning they contain two copies of each chromosome, one from each parent. By assembling both diploid genomes, the researchers were able to see that some variants are on one copy but not the other.

This kind of detailed information is important for experiments such as CRISPR gene editing that pinpoint a specific portion of the genome, Ranallo-Benavidez suggested. “If you’ve designed an experiment for a particular gene locus and you think both copies are the same in the cell line but one is actually different, that changes how you would interpret the results.”

The researchers were even able to assemble the centromeres in both cell lines. The centromere is the “pinched” region that divides each chromosome into a short and long arm.  Some genome assemblies skip these regions because they contain highly repetitive sequences that are hard to assemble, explained Yue Hao, Ph.D., a research assistant professor in the Barthel Lab and co-first author on the paper.

When the researchers took previously published short-read DNA and RNA sequencing data and aligned it to the new assemblies, substantially more of it matched than when aligned to the standard reference genome.

Hao said the study made her optimistic about the near future of assembling individual genomes for personalized medicine. “We just made two almost perfect diploid genomes in one lab. So how far away are we from having an individual genome for each patient? Probably not that far.”

The researchers also developed a genome analysis tool, KaryoScope, that Ranallo-Benavidez describes as a high-resolution “microscope” for sequencing data. “You can use it to see what parts of the genome belong to which chromosome, where genes sit, or where particular types of repeats are located,” he said.

The new tool is already proving useful as the researchers collaborate on new genome assemblies of matched tumor and normal cell lines from a pancreatic cancer patient, Barthel said.

The Lennar Foundation funded this research.

About TGen, part of City of Hope
Translational Genomics Research Institute (TGen) is a Phoenix, Arizona-based nonprofit organization dedicated to conducting groundbreaking research with life-changing results. TGen is part of City of Hope, a world-renowned independent research and treatment center for cancer, diabetes and other life-threatening diseases. This precision medicine affiliation enables both institutes to complement each other in research and patient care, with City of Hope providing a significant clinical setting to advance scientific discoveries made by TGen. TGen is focused on helping patients with neurological disorders, cancer, diabetes and infectious diseases through cutting-edge translational research (the process of rapidly moving research toward patient benefit). TGen physicians and scientists work to unravel the genetic components of both common and complex rare diseases in adults and children. Working with collaborators in the scientific and medical communities worldwide, TGen makes a substantial contribution to help patients through efficiency and effectiveness of the translational process.

TGen
Galen Perry
602-343-8423
gperry@tgen.org

April 30, 2026