Research involving the DNA inside tumors furthers the understanding of cancers at their deepest roots: the cellular level. Scientists researching tumor samples use a process known as DNA sequencing in which they look at the specific order, or arrangement, of the cell’s genetic components, or they may investigate genetic mutations in the cell.
Researchers utilize different methods of obtaining the genetic code of tumors: sequencing smaller fragments from a large number of cells versus sequencing larger samples from a small number of cells. Sequencing smaller fragments is more common in today’s research world, but has a disadvantage that tumor mutations that occur together within a cell are unlikely to be sequenced together. Additionally, researchers can adjust the sequencing “coverage”, which is the number of times a particular site in a genome is sequenced.
Variations in sequencing methods prompted researchers led by Max Shpak, Ph.D., to study scientists’ ability to accurately estimate the amount of genetic variation in biological populations, such as among cells in a tumor, from smaller sequencing fragments.
The results of the study conducted by Dr. Shpak and his co-investigators imply that, all else being equal, low coverage sequencing and genome pooling provide improved estimates of genetic variation. However, the cost for better variation estimates is reduced information about mutations that occur together within the same cell. The study utilized cells from a malignant lung tumor, and its findings may be applied to active research involving the genetics of cancer cells.
TO LEARN MORE:
Shpak M., Y. Ni, J. Lu, P. Mueller 2017. Variance in estimated pairwise genetic distance under high vs. low coverage sequencing: the contribution of linkage disequilibrium. Theoretical Population Biology 117: 51-63