Orthodontic treatment can influence the palatal rugae, especially in cases of extraction suggests a study published in the Journal of Dentistry.

Researchers conducted a study to determine the uniqueness and stability of the palatal rugae after orthodontic treatment.
Cast models of untreated subjects (n = 50) were obtained twice at intervals of 8–30 months. Cast models of patients who received non-extraction (n = 50) and extraction (n = 50) orthodontic treatment were obtained before and after treatment at intervals of 11–41 months and 14–49 months, respectively. All 300 cast models were scanned digitally. The palatal rugae were manually extracted and transformed into 3D point clouds using reverse engineering software. An iterative closest point (ICP) registration algorithm based on correntropy was applied, and the minimum point-to-point root mean square (RMS) distances were calculated to analyze the deviation of palatal rugae for scans of the same subject (intrasubject deviation [ISD]) and between different subjects (between-subject deviation [BSD]). Differences in ISD between each group and the deviation between ISD and BSD of all 150 subjects were evaluated.

Results of the study are:
Significant differences were found in the 150 ISD and 1225 BSD in each group, as well as the 150 ISD and 11,175 BSD across all groups. The mean values of ISD in untreated, non-extraction and extraction group were 0.178, 0.229 and 0.333 mm, respectively. When the first ruga was excluded in the extraction group, the mean ISD decreased to 0.241 mm, which was not significantly different from that in the non-extraction group (p = 0.314).
Thus, Orthodontic treatment can influence the palatal rugae, especially in cases of extraction. Furthermore, variation mainly existed in the first ruga in cases of extraction. However, palatal rugae are still unique and may be used as a supplementary tool for individual identification.
Reference:
Evaluation of the stability of the palatal rugae using the three-dimensional superimposition technique following orthodontic treatment by Jiamin Zhao et. al published in the Journal of Dentistry.