Supplementary Information (doc 863K) - Nature

... (2 times a day), and several lectures and, interactive self-reflection exercises each day. ..... S, Vapnik, V. Gene selection for cancer classification using support vector machines. ... A tutorial on support vector machines for pattern recognition.

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Supplementary Appendix
Supplement to: "Meditation and vacation effects impact disease-associated
molecular phenotypes" Table of Contents Acknowledgements 2
Conflicts of Interest 2
Supplementary Methods 2
Blood collection methods
Assay Methods (Telomerase, Inflammation, Abeta proteins)
Transcriptome Profiling and Analysis
Statistical analyses of survey and biomarker data
Supplementary References
Supplementary Tables
Table S1. Psychological wellbeing during Retreat Week and one month later
Table S2. Psychological wellbeing ten months later
Table S3. Individual Gene Differential expression signatures for baseline
vs. follow up (relaxation
effect) and regular meditators vs. others at follow-up (meditation effect)
see excel file Table S4. The blood weighted coexpression network for the study described
in the main text see excel file
Table S5. Pathway enrichments for coexpression network modules identified
in Table S4 see excel file
Table S6. Gene sets from the MsigDB database enriched for the coexpression
network modules
identified in Table S4 see
excel file
Table S7. Meta-themes from Gene Ontology Tree Maps for vacation network
modules 14
Table S8. Meta-themes from Gene Ontology Tree Maps for meditation network
related to Meditation Signature
Table S9. Biomarker Means (Standard Errors) at baseline, follow up, and
change scores 16
Table S10. Mean Cell type percentage values at baseline and follow up
17 Supplementary Figures
Figure S1. ROC curves for the prediction of vacation and meditation
effects 18
Figure S2. REVIGO Gene Ontology treemap for the meditation-specific,
salmon coexpression 19
Figure S3. Telomerase Activity at baseline and day 5 of retreat network
module 20
Acknowledgements: This study was supported by The Chopra Foundation, and
Marc and Lynn Benioff. The authors gratefully acknowledge the critical
cooperation and assistance of The Chopra Center for Well-being, and The
Mind Body Medical Group, Drs. Deepak Chopra, Sheila Patel, Valencia Porter
and Tim Brieske, and Carolyn Rangel, and the OMNI La Costa Resort and Spa.
We are particularly grateful for Dr. Chopra who opened up the center to
research and supported all aspects of the endeavor. We are also grateful
for the hard work of our research and technical team, Amanda Gilbert, Zoe
Evans, Samantha Schilf, and Rylie Williams from UCSF and Setareh Moghadam
and Louise Monte from UCSD and Lisa Pham from Capella Biosciences Inc. Conflicts of Interest: Dr. Lin is a minor shareholder (< $10K) in Telomere
Diagnostics, a telomere measurement company which had no role in the
current research. Dr. Pek Lum and Lisa Pham are employees of Capella
Biosciences, Inc. (a company focused on monoclonal antibody medicines, with
no relation to outcomes studied here). Dr. Chopra assisted with study
design. The funders (Chopra Foundation, Benioff Foundation) had no role in
data collection, analysis, decision to publish, or preparation of the
manuscript. Dr.'s Epel, Schadt, and Tanzi were past awardees of the
Chopra Foundation's Rustrum Roy Award. Supplementary Methods Study Design and Intervention Protocols
The Retreat and Relaxation Study (RARS), a randomized clinical trial funded
by private foundations (The Chopra Foundation and Marc and Lynn Benioff
Foundation), compared the effects of relaxation at a resort to training in
a meditation/yoga retreat at the same resort (La Costa). Women stayed at
the resort for six days total, all rooms were similar in size and with
similar amenities, and all participants ate the same ayurvedic diet. The
sample included women who were non-meditators and lived in California who
were randomized (computer generated randomization scheme) to a "vacation"
arm or a meditation arm. They did not pay for their stay at the resort. In
addition, a comparison group of non-randomized women was recruited from the
pool of those already registered for the retreat and thus they paid for
their own expenses. While they could live outside of California, all had to
be acclimated to the current time zone by the first day of retreat (using
the one hour per time zone per day criterion). All participants were asked
to not exercise any more than they typically would do each day. Exercise
was recorded in daily diaries. The eligibility criteria for each group were
identical except that prior regular meditation practice was required in the
regular meditator arm. The study was approved by the UCSF and UCSD
Investigational Review Boards, and all participants provided informed
consent. In order to optimize the methods and accurate timing of the data
collection methods, blood draw procedures, sample transport, and assays, an
IRB-approved feasibility pilot study of ten participants was conducted at
an earlier retreat at the same resort (data not included in this study). Power Analysis. Using data from two previous publications[pic]1,2 and G
Power, we calculated required sample size at 31 participants per group with
small effect size of .29 at power = .80 and alpha set at .05 for a total of
93 participants. In greater detail, it was previously demonstrated that
PBMC telomerase activity expressed as natural logarithms increased from
2·00 (SD 0·44) to 2·22 (SD 0·49; p=0·031)[pic]2. Daubenmier's publication
demonstrated that pre-treatment experimental group telomerase levels were
1.67 (SD 0.3) and changed to 1.98 (SD 0.4) post-treatment, whereas control
levels at baseline were 1.84 (SD 0.4) and follow-up were 1.98 (SD
0.3)[pic]1. Assuming the three group model we employed, (vacation, novice
meditator and regular meditator arms), we assumed effect size from t1 to t2
in two groups of meditators to be between .2 and .3 (small effect size)
compared to the vacation arm participants, providing a sample size
calculation was 93 for full sample, so 31 per group. In order to account
for participant attrition throughout the study, we recruited participants
across the groups. Given the many outcomes examined in this study,
including gene expression patterns, we view it as an exploratory trial.
Further, the gene expression methods are inherently exploratory in nature,
a bottom up approach to identifying group differences in genes and gene
Randomized women. Women were recruited mostly from the greater San Diego
area, as well as San Francisco, through many public venues including
flyers, radio and media advertisements. The flyer stated "Participate in a
University of California, San Francisco study examining the effects of a
short meditation retreat on health and wellbeing. This study requires
spending up to six days at La Costa Resort and Spa in Carlsbad, CA in April
2013" and stated basic eligibility criteria. Eligible participants were
healthy women, aged 30-60, English speaking, with no history of chronic
medical conditions and/or diseases. Exclusion criteria included pregnancy,
antidepressants, estrogen or hormone replacement therapy use, smoking, or a
diagnosis of post-traumatic stress disorder. They also could not have a
current or past regular meditation practice.
Women first were screened for eligibility, learned details of study
involvement, and were asked to consider their commitment and availability
before they were enrolled into the study. It was emphasized that this
included a commitment to stay in the study even if they were not randomized
into their preferred group.
The randomization pattern was employed using a permuted block
randomization, allocating a small but equal size group to one then the
other condition. The study coordinator was given the randomization schedule
to follow and this was based on timing of the completion of their
questionnaire. In this way, there was no bias assigned to, for example,
those who enrolled the earliest. Novice meditators were informed of the
group they have been assigned to approximately 2-3 weeks prior to their
arrival at La Costa Resort. Comparison group of regular meditators. An inclusion criterion for "regular
meditators" was to have meditated regularly for at least the past six
months, at least 4 times a week, for at least 15 minutes each time. All of
the women enrolled in the retreat who were within the age range 30-60 years
were invited to learn more about the study. Interested women were screened
on a first come first serve basis until we identified 31 eligible and
interested women (of 44 total screened; 70.5% eligibility). Of the
enrolled women, the average meditation practice was 2.3 years (range from 6
months to 7 years) and more than half (58%) engaged in meditation on a
daily basis.
The intervention groups were not blinded, and site investigators and
study personnel knew to which group participants had been randomized. The
two groups (vacation arm and then novice/regular meditator arms) had
minimal contact with each other during the week and did not know the
details of the daily schedule of the other group. The teachers of the
retreat delivered their standard meditation intervention program to a
larger group of participants, without knowing who among them was enrolled
in this intervention study. Intervention Overview
Meditation Groups program. The Seduction of Spirit Retreat, led by Dr.
Deepak Chopra and colleagues, at the Chopra Center, Carlsbad, CA, over the
past decade, is a meditation retreat attended by several hundred
participants per event. Its goal is to promote an intensive period of
learning and psychological change. The retreat provides training in
meditation (primordial sound meditation, which is similar to mantra