Stem cells are versatile tools that can potentially be used to treat various disorders, or be directed to grow into much needed organs. The traditional way to obtain embryonic stem cells, the most versatile of them all, has been through fertilizing an egg with a sperm. Unfortunately, this causes some issues for developing treatments, since your immune system will often see these cells (and any organs derived from them) as foreign. Therefore, patients would need to be on immune suppressing drugs for the rest of their lives, which raises the chance of infection and cancer.
Two techniques have recently emerged that can solve this issue: creating induced pluripotent stem (iPS) cells, or cloning via somatic cell nuclear transfer (SCNT).
The first method takes adult cells (such as skin) from the patient, and then exposes them to transcription factors that reprogram them to a stem cell-like state. The second method takes the DNA from the patient, and sticks it into a donor egg, creating a stem cell matching the patient.
Creating stem cells through cloning is more difficult, expensive, and requires donor eggs. However, a new paper in Nature shows that the extra effort is worth it, as cloned stem cells may have fewer abnormalities. When comparing the genomes of iPS and cloned stem cells to IVF generated ones, the researchers found that the iPS cells had more differences in DNA methylation, which controls which genes are turned on. Accordingly, when they profiled the gene expression of all three cell groups, they found that the iPS cells expressed different genes from the cloned or IVF stem cells.
These results need to be confirmed in higher numbers, and it remains to be confirmed whether the genetic differences will have large functional consequences (I would be surprised if they didn't). In all, it suggests that cloned stem cells are the "better" stem cells for now, and hopefully future advances offer easier, cheaper ways to generate stem cells for patients. (Non-fraudulent methods of course...)