A new study has revealed the case for more extensive gene mapping in disease research, with whole genome sequencing offering an unprecedented look at the makeup and behavior of Hodgkin lymphoma that could lead to better understanding of this and other cancers' development and treatment.
The current standard exome sequencing, which is a detailed look at protein-coding genes, detects some mutations and variants that advance cancers. But researchers at Sylvester Comprehensive Cancer Center in the University of Miami Miller School of Medicine found that whole-genomic sequencing paints a bigger, broader picture and detects other changes related to cancer development. The study also noted that whole genome sequencing identified other key events such as chromothripsis, the chromosomal rearrangement that plays a role in many cancers.
“We found that, by using whole genome sequencing, we can read virtually all the mutations in both protein coding and noncoding regions of the genome, as well as structural and copy number variations,” said Dr Craig Moskowitz of the Oncology Service Line at Sylvester, professor of medicine at the Miller School, and a co-author on the study. “We found many genomic events that had never been recorded before. It’s the best technology we’ve found to identify new cancer drivers.”
The team’s research, published in journal Blood Cancer Discovery, involved the creation of a sorting system to isolate and enlarge the difficult-to-study and rare Hodgkin and Reed Sternberg (cHL) cells, the hallmarks of the lymphatic system cancer. The research on these abnormal white blood cells, when combined with whole genome sequencing, will provide the scientists with the template to now take a similar, more detailed look at other cancers.
“Cancers are incredibly complex diseases, and we still have a long way to go before we fully understand them,” said Dr C. Ola Landgren, director of the Myeloma Research Institute, co-leader of Translational and Clinical Oncology Research Program, and co-author on the study. “By leveraging whole genome sequencing, we can better assess tumor evolution, identify structural issues, and hopefully gain new therapeutic insights.”
This comes after news that National Institutes of Health has developed an innovative software tool that can assemble a whole genome sequence in just days. Verkko (“network” in Finnish) was created by the Telomere-to-Telomere (T2T) consortium, the collaborative project funded by NIH’s National Human Genome Research Institute (NHGRI) that was behind the world’s first complete human genome sequenced in 2022.
“We took everything we learned in the T2T project and automated the process,” said NHGRI associate investigator Sergey Koren, who spearheaded the Verkko project and is senior author on the paper. “Now with Verkko, we can essentially push a button and automatically get a complete genome sequence.”
It took two decades to shift the needle from 92% to 100% in human genome mapping, following on from the Human Genome Project’s ambitious plan to ID more than three billion base pairs that form DNA, and nearly three years for the T2T consortium to manually assemble the difficult final fragments to complete the very first gapless genome. Now, Verkko can complete the task in just days.
“Verkko can democratize generating gapless genome sequences,” said Adam Phillippy, an NHGRI senior investigator who worked on the T2T project and Verkko. “This new software will make assembling complete genome sequences as affordable and routine as possible.”
Newly mapped regions of the human genome are likely to lead to much better understanding and in turn treatment of disease. Scientists also hope Verkko will speed up efforts to map complete genomes of common research species such as mice, fruit flies and zebrafish, in an effort to better understand these complementary animals. Mapping species further afield will also aid in comparative genomics, and potentially lead to new genetic links between seemingly diverse species.
Verkko is still a work in progress, with the software in beta-testing stage but available now. The research behind Verkko's creation was published in journal Nature Biotechnology.
