During chronic partial sleep deprivation, PER35/5 subjects exhibited slightly but reliably higher slow-wave activity and slow-wave energy than PER34/4 subjects. All three PER3 VNTR genotypes, however, demonstrated robust and equivalent cumulative decreases in cognitive performance and physiological alertness, and cumulative increases in sleepiness across chronic PSD, with increasing daily inter-subject variability. The genotypes showed no differences at baseline in habitual sleep, physiological sleep structure, circadian phase, physiological sleepiness, cognitive performance, or subjective sleepiness. Thus, collectively, we conclude the PER3 VNTR polymorphism is not associated with differential vulnerability to the neurobehavioral effects of chronic PSD, although it is related to sleep homeostatic responses. Consequently, this polymorphism may be critical to behavioral performance only when sleep is entirely absent at a specific circadian phase in the early morning hours (i.e., from 6–8 am). Moreover—since the genotypes were comparable at baseline and showed equivalent inter-individual vulnerability to partial sleep deprivation—PER3 does not contribute to the cumulative neurobehavioral effects of chronic partial sleep loss.
Our chronic PSD protocol produced robust changes in cognitive performance, standard sleepiness and wakefulness measures, and physiological sleep measures characteristic of cumulative sleep loss studies conducted in various laboratories 
, thus validating our experimental approach. We detected poorer performance on the DS working memory capacity test, the first study to report such a cumulative change, and on the PVT, with variability of lapses increasing for all genotypes across PSD days, and greater self-rated and physiological sleepiness across the five days of PSD—but not differentially so—in PER35/5
subjects had slightly but reliably better cognitive throughput than their PER34/4
counterparts, as indicated by significantly higher DSST scores across all 5 PSD nights. Our data contrast with two TSD studies which found that PER35/5
individuals showed poorer outcomes on a waking performance composite 
and on specific executive function tasks, but did not differ on the DSST 
. Since our version of the DSST contained nine symbols and digits instead of eight, and it was longer, as determined from mean data presented in 
, the reasons for this discrepancy remain unclear, but may be methodological or due to differences produced by TSD versus chronic PSD conditions.
SWA and SWE—putative markers of sleep homeostasis—were higher after chronic PSD. In contrast to Viola et al.'s TSD study 
, however, we found no evidence for differential responses to chronic PSD between PER35/5
subjects; this may be due to the nature of such PSD paradigms, in which mitigation of homeostasis occurs via partial daily sleep recuperation 
. Since overall homeostatic differences were small between PER35/5
subjects during chronic PSD, and there were no differential increases as a result of sleep loss, PER3
is not the exclusive genetic determinant of the homeostatic response to chronic PSD. In addition, because homeostatic differences occurred during the biological night, other genetic polymorphisms—including clock gene polymorphisms 
—may influence differential vulnerability to SWA and SWE changes resulting from chronic PSD.
Our study suggests that PER35/5
subjects may have higher sleep need under chronic PSD conditions, but not at baseline, in contrast to data from Viola et al. 
. The baseline discrepancies may be explained by a sleep debt factor inherent to a difference in design between studies. In our study, for the first two nights (baseline), all subjects received 10 h time in bed from 2200–0800 h to reduce any pre-existing sleep debt prior to chronic PSD. Baseline was preceded by average pre-study sleep durations of approximately 8 h in both groups; thus, our examination of baseline sleep was completed under fully-rested homeostatic pressure conditions. By contrast, since subjects in the Viola et al. 
study had on average .5–1 h less sleep prior to entry (7–7.5 h sleep duration), they were not given any saturation nights, and their baseline sleep was curtailed to between 6.78–7.45 h time in bed (for PER35/5
, respectively), they likely still harbored a significant lingering sleep debt. As such, protocol artifact and differential preexisting sleep debt—rather than true endogenous variations—may explain reported baseline differences in sleep propensity and sleep homeostatic measures between the PER35/5
subjects showed higher homeostatic pressure during sleep chronic PSD, but not poorer cognitive, executive functioning or subjective sleepiness responses to chronic PSD. Such a separation of responses has been noted in other studies in which the homeostatic sleep responses to chronic PSD and TSD have not been reflected in waking neurobehavioral or cognitive responses 
. These findings suggest that distinct genetic polymorphisms mediate differential vulnerability to cognitive and subjective sleepiness changes resulting from chronic PSD.
Despite prior studies showing that the PER3
VNTR polymorphism is associated with diurnal preference and delayed sleep phase syndrome 
, we found no significant genotype differences in circadian phase as measured by chronotype. Similarly, we found no differences in our other measure of circadian phase, the actigraphic sleep midpoint. Our results concur with more recent reports that utilized both physiological and self-rated circadian measures 
, and they may be due to a lack of power to detect such differences in smaller sample size studies, or may highlight false positives in earlier studies 
Notably, we found no differences in executive functioning following five nights of chronic PSD. The COWAT, which measures verbal fluency and orthographic lexical retrieval, and involves the dorsolateral and prefrontal cortex, showed no differences in word production 
. The genotypes showed no differences in performance on the Hayling and Brixton tests, which measure basic task initiation speed and response suppression performance, and detection of and ability to follow rules, respectively. Poor performance on these tests is associated with frontal lobe dysfunction and dysexecutive symptoms 
. Moreover, all groups performed equivalently on various performance outcomes of the TOL, which measures executive planning and problem solving abilities, and involves the prefrontal cortex 
. Thus, across a variety of executive function tasks, PER35/5
subjects performed at par with PER34/4
subjects, in contrast to results from a previous study indicating executive functioning impairment in this group 
In the Groeger et al. study 
, the performance deficits posited to be mediated by the PER3
VNTR polymorphism occurred selectively only at two time points—2–4 h after the midpoint of the circadian melatonin rhythm—approximately from 6–8 am. We could not collect data after the 0200 h test bout, since our subjects were asleep from 0400–0800 h on each of the PSD nights. Thus, our results cannot be directly compared with the findings of Groeger et al. 
. However, such selective findings—both in terms of time of day and executive tests affected—indicate that other genetic polymorphisms may influence executive function and cognitive performance deficits resulting from TSD.
In summary, the PER34/4, PER34/5 and PER35/5 genotypes demonstrated comparable cumulative increases in sleepiness and cumulative decreases in cognitive performance and physiological alertness, across five nights of chronic PSD, with all genotypes showing increasing daily inter-subject variability. During chronic PSD, PER35/5 subjects exhibited slightly but reliably higher SWA and SWE than PER34/4 subjects. In contrast to published data in TSD paradigms, PER3 polymorphism variants did not differ on baseline sleep measures or in their physiological sleepiness, cognitive, executive functioning or subjective responses to chronic PSD. Thus, the PER3 VNTR polymorphism is not a genetic marker of differential vulnerability to the cumulative neurobehavioral effects of chronic PSD. We propose that other genes—both circadian and non-circadian—regulate neurobehavioral responses to chronic PSD. Our study is the first to characterize the role of any genetic polymorphism in response to chronic PSD, a condition experienced by millions of individuals persistently and daily due to work, travel and social obligations, and one associated with a wide range of serious health consequences. As such, this study provides a foundation for future studies using a candidate gene approach to investigate neurobehavioral and homeostatic responses to chronic partial sleep deprivation.