Reviewer's report
Title:Association of an NF-kappaB1 intron SNP (rs4648068) with gastric cancer
patients in Chinese Han population
Version: 2Date:16 January 2012
Reviewer: Megan Hitchins
Reviewer's report:
Lu and colleagues have performed a straight forward case-control study
exploring the SNP genotype and allele frequencies in a gastric cancer cohort and
appropriately matched healthy control population of Chinese Han individuals to
test for associations with particular SNP alleles within the NF-kB1 gene and
gastric cancer. This study, although simple in concept, design and execution, has
yielded an exciting finding worthy of reporting. Lu et al. demonstrate an
association between gastric cancer incidence, as well as particular
clinico-pathologic features among gastric cancers, and an intronic SNP genotype
within NF-kB1. They tested 4 SNPs in a subset of their individuals (30 cases and
30 controls) and demonstrate that the homozygous genotype for the minor allele
(among healthy controls) of intronic SNP rs4648086 is associated with an
increased risk for gastric cancer. They then extended their study for this SNP
alone to the rest of their cases and controls. This seems logical and
cost-effective. However, it is interesting to note that even among the initial test
case-control group studied, another SNP (rs4648065) showed a trend but did not
reach statistical significance. It is plausible that with inclusion of additional
individuals, and hence an increase in the power this would have afforded, this
SNP may also have reached significance. Since these 2 SNPs have distinct
SNP-tags (ie may or may not be in particularly close linkage disequilibrium) the
authors may have missed some important information.
Therefore, the paper should provide (minor essential revisions):
1. A better justification for selecting only the one SNP for extended study ie
provide projected power calculations for the extended cohort on the basis of the
initial test study to warrant the strategy they employed in only studying one SNP
further.
2. Provide an assessment of the haplotypes they identified among the 4 closely
located SNPs in the 30 cases and 30 controls. This should include the possible
combinations (43 = 12), and which ones they are likely to have observed on a
probablistic level by calculating R2 values among their observed genotypes. This
would certainly be possible by studying homozygotes. Otherwise, programs such
as PHASE could be used for this. Then, if they re-calculate their associations
based on these likely haplotype frequencies as well, they may explain why each
of the SNPs showed a trend towards significance. It is likely that the lower the P
value among the other 3 SNPs, the closer it is located to the intronic SNP
rs4648086. There is always a danger with SNP association studies that any one
SNP is tagging another site. By studying the haplotypes in total, this would
provide greater evidence that the rs4648086 SNP may indeed be causally
related to the phenotype (not just linked to something close by that is functional).
A recent study on VHL in clear cell renal carcinoma provides a good model for
the extra statistical work this would entail.
This study is worthy of publication if the issues above are adequately addressed.
This would require no further lab work, but additional data mining.
The authors should also take into consideration some minor points for inclusion
in their paper, which should improve the overall content (discretionary revisions):
1. A scaled map (as supplementary information if not in the actual text) should be
drawn to provide an overview of the SNP locations with respect to their position
within the gene, with respect to one-another, and if possible, also their tag-SNPs.
2. Odd Ratios and CIs should be provided in all the Tables, where relevant, not
just the frequencies and P values. One OR is referred to in the Discussion, but is
no-where in the Results. The Adjusted odds ratios could be provided as ‘AOR’.
3. A sentence or two should be added to the Discussion to explain why, although
the P values are significant, the ORs are low, to provide an interpretation of the
degree of contribution.
4. The potential functional role of the intronic SNP could be speculated upon
further so the paper is hypothesis-forming as well as merely reporting a simple
finding. For instance, some interrogation of the databases might reveal
something worthy of further investigation: cross-species conservation analysis of
the non-coding region where the key SNP is located might reveal it is located in a
conserved region, which would provide supportive evidence for a functional role
eg within an enhancer element for example. The Encode database could also be
examined at this location to determine if this SNP might be located within a
regulatory element eg is it associated with increased levels of H3K9me1
(monomethylation) that is typically located at enhancer elements.
Level of interest: An article of importance in its field
Quality of written English: Needs some language corrections before being
published
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I have no competing interests to declare.
Reviewer's report
Title:Association of an NF-kappaB1 intron SNP (rs4648068) with gastric cancer
patients in Chinese Han population
Version: 2Date:16 January 2012
Reviewer: Megan Hitchins
Reviewer's report:
Lu and colleagues have performed a straight forward case-control study
exploring the SNP genotype and allele frequencies in a gastric cancer cohort and
appropriately matched healthy control population of Chinese Han individuals to
test for associations with particular SNP alleles within the NF-kB1 gene and
gastric cancer. This study, although simple in concept, design and execution, has
yielded an exciting finding worthy of reporting. Lu et al. demonstrate an
association between gastric cancer incidence, as well as particular
clinico-pathologic features among gastric cancers, and an intronic SNP genotype
within NF-kB1. They tested 4 SNPs in a subset of their individuals (30 cases and
30 controls) and demonstrate that the homozygous genotype for the minor allele
(among healthy controls) of intronic SNP rs4648086 is associated with an
increased risk for gastric cancer. They then extended their study for this SNP
alone to the rest of their cases and controls. This seems logical and
cost-effective. However, it is interesting to note that even among the initial test
case-control group studied, another SNP (rs4648065) showed a trend but did not
reach statistical significance. It is plausible that with inclusion of additional
individuals, and hence an increase in the power this would have afforded, this
SNP may also have reached significance. Since these 2 SNPs have distinct
SNP-tags (ie may or may not be in particularly close linkage disequilibrium) the
authors may have missed some important information.
Therefore, the paper should provide (minor essential revisions):
1. A better justification for selecting only the one SNP for extended study ie
provide projected power calculations for the extended cohort on the basis of the
initial test study to warrant the strategy they employed in only studying one SNP
further.
2. Provide an assessment of the haplotypes they identified among the 4 closely
located SNPs in the 30 cases and 30 controls. This should include the possible
combinations (43 = 12), and which ones they are likely to have observed on a
probablistic level by calculating R2 values among their observed genotypes. This
would certainly be possible by studying homozygotes. Otherwise, programs such
as PHASE could be used for this. Then, if they re-calculate their associations
based on these likely haplotype frequencies as well, they may explain why each
of the SNPs showed a trend towards significance. It is likely that the lower the P
value among the other 3 SNPs, the closer it is located to the intronic SNP
rs4648086. There is always a danger with SNP association studies that any one
SNP is tagging another site. By studying the haplotypes in total, this would
provide greater evidence that the rs4648086 SNP may indeed be causally
related to the phenotype (not just linked to something close by that is functional).
A recent study on VHL in clear cell renal carcinoma provides a good model for
the extra statistical work this would entail.
This study is worthy of publication if the issues above are adequately addressed.
This would require no further lab work, but additional data mining.
The authors should also take into consideration some minor points for inclusion
in their paper, which should improve the overall content (discretionary revisions):
1. A scaled map (as supplementary information if not in the actual text) should be
drawn to provide an overview of the SNP locations with respect to their position
within the gene, with respect to one-another, and if possible, also their tag-SNPs.
2. Odd Ratios and CIs should be provided in all the Tables, where relevant, not
just the frequencies and P values. One OR is referred to in the Discussion, but is
no-where in the Results. The Adjusted odds ratios could be provided as ‘AOR’.
3. A sentence or two should be added to the Discussion to explain why, although
the P values are significant, the ORs are low, to provide an interpretation of the
degree of contribution.
4. The potential functional role of the intronic SNP could be speculated upon
further so the paper is hypothesis-forming as well as merely reporting a simple
finding. For instance, some interrogation of the databases might reveal
something worthy of further investigation: cross-species conservation analysis of
the non-coding region where the key SNP is located might reveal it is located in a
conserved region, which would provide supportive evidence for a functional role
eg within an enhancer element for example. The Encode database could also be
examined at this location to determine if this SNP might be located within a
regulatory element eg is it associated with increased levels of H3K9me1
(monomethylation) that is typically located at enhancer elements.
Level of interest: An article of importance in its field
Quality of written English: Needs some language corrections before being
published
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I have no competing interests to declare.
Please review this paper.
user
Reviewer's report
Title:Association of an NF-kappaB1 intron SNP (rs4648068) with gastric cancer
patients in Chinese Han population
Version: 2Date:16 January 2012
Reviewer: Megan Hitchins
Reviewer's report:
Lu and colleagues have performed a straight forward case-control study
exploring the SNP genotype and allele frequencies in a gastric cancer cohort and
appropriately matched healthy control population of Chinese Han individuals to
test for associations with particular SNP alleles within the NF-kB1 gene and
gastric cancer. This study, although simple in concept, design and execution, has
yielded an exciting finding worthy of reporting. Lu et al. demonstrate an
association between gastric cancer incidence, as well as particular
clinico-pathologic features among gastric cancers, and an intronic SNP genotype
within NF-kB1. They tested 4 SNPs in a subset of their individuals (30 cases and
30 controls) and demonstrate that the homozygous genotype for the minor allele
(among healthy controls) of intronic SNP rs4648086 is associated with an
increased risk for gastric cancer. They then extended their study for this SNP
alone to the rest of their cases and controls. This seems logical and
cost-effective. However, it is interesting to note that even among the initial test
case-control group studied, another SNP (rs4648065) showed a trend but did not
reach statistical significance. It is plausible that with inclusion of additional
individuals, and hence an increase in the power this would have afforded, this
SNP may also have reached significance. Since these 2 SNPs have distinct
SNP-tags (ie may or may not be in particularly close linkage disequilibrium) the
authors may have missed some important information.
Therefore, the paper should provide (minor essential revisions):
1. A better justification for selecting only the one SNP for extended study ie
provide projected power calculations for the extended cohort on the basis of the
initial test study to warrant the strategy they employed in only studying one SNP
further.
2. Provide an assessment of the haplotypes they identified among the 4 closely
located SNPs in the 30 cases and 30 controls. This should include the possible
combinations (43 = 12), and which ones they are likely to have observed on a
probablistic level by calculating R2 values among their observed genotypes. This
would certainly be possible by studying homozygotes. Otherwise, programs such
as PHASE could be used for this. Then, if they re-calculate their associations
based on these likely haplotype frequencies as well, they may explain why each
of the SNPs showed a trend towards significance. It is likely that the lower the P
value among the other 3 SNPs, the closer it is located to the intronic SNP
rs4648086. There is always a danger with SNP association studies that any one
SNP is tagging another site. By studying the haplotypes in total, this would
provide greater evidence that the rs4648086 SNP may indeed be causally
related to the phenotype (not just linked to something close by that is functional).
A recent study on VHL in clear cell renal carcinoma provides a good model for
the extra statistical work this would entail.
This study is worthy of publication if the issues above are adequately addressed.
This would require no further lab work, but additional data mining.
The authors should also take into consideration some minor points for inclusion
in their paper, which should improve the overall content (discretionary revisions):
1. A scaled map (as supplementary information if not in the actual text) should be
drawn to provide an overview of the SNP locations with respect to their position
within the gene, with respect to one-another, and if possible, also their tag-SNPs.
2. Odd Ratios and CIs should be provided in all the Tables, where relevant, not
just the frequencies and P values. One OR is referred to in the Discussion, but is
no-where in the Results. The Adjusted odds ratios could be provided as ‘AOR’.
3. A sentence or two should be added to the Discussion to explain why, although
the P values are significant, the ORs are low, to provide an interpretation of the
degree of contribution.
4. The potential functional role of the intronic SNP could be speculated upon
further so the paper is hypothesis-forming as well as merely reporting a simple
finding. For instance, some interrogation of the databases might reveal
something worthy of further investigation: cross-species conservation analysis of
the non-coding region where the key SNP is located might reveal it is located in a
conserved region, which would provide supportive evidence for a functional role
eg within an enhancer element for example. The Encode database could also be
examined at this location to determine if this SNP might be located within a
regulatory element eg is it associated with increased levels of H3K9me1
(monomethylation) that is typically located at enhancer elements.
Level of interest: An article of importance in its field
Quality of written English: Needs some language corrections before being
published
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I have no competing interests to declare.
assistant