Responses to Reviewers
February 3, 2010
Title: Association and Interaction of PPAR-complex Gene Variants with Latent Traits of
Left Ventricular Diastolic Function-a case control study
Version: 1 Date: 12 October 2009
Reviewer: Venkatesan Radha
Reviewer's report: The manuscript entitled "Association and Interaction of PPAR-complex
Gene Variants with Latent Traits of Left Ventricular Diastolic Function-a case control study
"describes an interesting and important study. The study is well designed, the clinical sample
size is adequate and the presentation of the results is also good. The authors probably need to
address the following issues.
Critique #1. The authors have shown that SNPs have independent association but after
correction for multiple testing the significance is lost. However gene-gene interaction is
significant. This result can be presented in the context of the complex nature of the
inheritance of the disease.
Response #1: This a very insightful comment. We revised the discussion as suggested and
added a reference to the important “missing heritability” problem (see paragraph #1, page
11).
Critique #2. The functional role of PPAR ALPHA, GAMMA AND PPARGC needs to
be spelt out in the discussion thus bringing out the rationale of the genetic study design.
Response #2: As suggested by the reviewer, the authors have reorganized the discussion
section (pages 11-12) to better highlight the important roles played by PPARA, PPARG, and
PPARGC1A in regulating the molecular mechanisms underlying hypertensive heart
disease-related traits, all of which have been repeatedly shown in transgenic models.
Critique #3. PGC 1A to be replaced as PPARGC1A
Response #3: Throughout the revised manuscript, the genes are now referenced using the
official symbol names approved by HGNC (Human Genome Organization Gene
Nomenclature Committee) .
Reviewer: Chao-Qiang Lai
Reviewer's report: This study was to examine the association between 64 SNPs in the
three-PPAR gene complex and derived latent LVDF traits in 403 White subjects. The latent
LVDF traits were extracted from 14 endophenotypes using independent component analysis.
The results showed that seven SNPs were significantly associated with the latent LVDF
traits based on linear regression. However, no association is significant after correction for
multiple testing based on FDR. Further, ridge analysis was employed to examine the
interaction between genetic variants within the complex. Eight-pair SNP-SNP interactions
were found, mainly at the PGC-1a locus. The findings are interesting and the writing is clear.
But several questions need to be addressed:
Critique #1: The title: Obviously, this is not a case-control study.
Response #1: The authors’ intention was to highlight a novel use of the ICA-extracted latent
trait to define “case” and “control” groups. However, we acknowledge that this is not a
typical case-control design and the original title may cause some confusion. We deleted “a
case-control study” from the title.
Critique #2: As this is a three-gene complex, LD pattern among all SNPs should be
presented. This will help readers to understand the association and interaction between
variants on the latent LVDF traits based on ridge analysis and other outcomes reported
in previous studies based on haplotype analysis.
Response #2: This is an excellent suggestion. Since the three genes reside on different
chromosomes, LD between SNPs in different genes is not defined. Therefore, we included
LD patterns produced by Haploview analysis for each of the three genes in the Online
Supplement (Figures S4-S6).
Critique #3: What are the correlations between the traditional risk factors, such as
LDL-C, TG, HDL-C and the latent LVDF traits and its individual components? This
should be addressed in this study. Table S6 should be provided in the text if space is
allowed.
Response #3: As suggested, the original Table S6 is now included in the main body of the
revised manuscript as Table 3. We also extracted and present below the (Spearman’s)
correlation coefficients between several traditional risk factors and the latent LVDF trait
as requested. This table is now included as Supplementary Table S3 (also shown below).
Table S3. Spearman’s correlation coefficients between traditional cardiovascular
risk factors and the latent LVDF trait.
Latent LVDF trait
Correlation Coefficient
P value
Systolic blood pressure
0.178
0.0003
Diastolic blood pressure
0.205
<0.0001
Body mass index
0.405
<0.0001
Insulin
0.148
0.006
Total cholesterol
-0.025
0.61
Triglyceride
0.169
0.0007
LDL-C
0.008
0.88
HDL-C
-0.215
<0.0001
Critique #4: Based on the power calculation (results), which SNP’s association can be
detected at the 80% power? What is the power to detect gene-gene (SNP-SNP)
interaction in this population?
Response #4: The expected power was estimated under the assumption that an associated
SNP has minor allele frequency of 0.2 and a locus-specific heritability of at least 2%. Since
this is not a familial study, we do not have information to estimate the heritability. The
power of detecting SNP-SNP interactions is generally lower, and much more dependent on
the underlying genetic model (multi-loci penetrances). Therefore, the power estimates are
meant to be used as corroborative evidence, not as proof of the findings. We now stated the
assumption of the power analysis in the text for clarity.
Critique #5: Check ref5.
Response #5: This reference appears in PubMed as follows: How to diagnose diastolic
heart failure. European Study Group on Diastolic Heart Failure. Eur Heart J 1998,
19(7):990-1003. However, we will leave it to the discretion of the editors to modify the
citation to be consistent with the style of the journal.