Peer review of: European polygenic risk score for prediction of breast cancer shows similar performance in (2015)

Reviewers' comments:

Reviewer #1 (Remarks to the Author):

This manuscript presents a very large and fairly comprehensive analysis studying the application of 
a polygenic risk score derived using data from European women to characterize risk in Asian 
women. The components of the paper are well developed but the actual presentation has many 
issues and the paper needs a great deal of revision for clarity. I have many minor comments and 
two more major concerns.
Major question – it is not very clear that genetic analysis to identify 1% of women at polygenic risk 
would have clinical utility or be feasible. If the PRS is set to the top 5% does that provide an Odds 
ratio that is meaningful or a prospective risk that would lead to different management of women?
Some sort of sensitivity analysis considering at least an upper 5% threshold and perhaps an upper 
10% threshold should be included.

What is the AUC when you include versus exclude Family History. Table 3 gives the attenuation in 
OR when including family history but the more interesting element to me would be to evaluate 
what the AUC is when you include markers and Family history.

I think it would be useful to also plot the distribution of risk according to quantiles of risk and 
according to age. This would better illustrate the lack of information from individuals at low PRS 
across all ages.

Minor comments: Line 143. Should read ‘mutations in these genes are rare’ not these genes are 
rare, since almost everyone has two copies of these genes (except rare people with deletions).
Line 157 – this discussion is not very comprehensive. While it may be true that PRS has some 
utility how much does it improve beyond traditional and early collect information like family 
history?

Lines 192-197 it would be helpful to have some information about what the interpretation of the 
PRS mean score would be. Is this score somehow standardized? If not then should it be to make 
the interpretation more straightforward?

Lines 226-230 gives changes in percent attenuation without indicating what is being attenuated or 
what the relevance of this sentence is. Please clarify this section without requiring close perusal of 
the table since the sentence makes no sense as written.

Lines 249-251. The actual AUCs should be cited in the text where it is being highlighted.

These sentences do not make sense. Smaller than what? Since this sentence starts a new 
paragraph there is no referent for that, so the sentence is uninterpretable. ‘The OR per SD was 
significantly smaller (p < 0.05) than that in the Asian studies from Asia, 267 for overall breast 
cancer (1.36, 95% CI = 1.25 – 1.49) and ER-positive breast cancer (1.38, 268 95% CI = 1.25 –
1.53), but significant higher (p < 0.05) for ER-negative breast cancer (1.49,269 95% CI = 1.26 –
1.76, Table 2(b)).’

Around lines 284 – where do the referent risks come from for populations that are being 
described? It does not sound as if population risks for breast cancer are being derived from cohort 
studies but rather from a population database but there is no reference so it is impossible to tell 
how these analyses were conducted.

Line 339 – effect size of PRS - the authors do not define their threshold. Do they mean top 1% of 
Asian PRS as a cut off? Do they mean top 1% of European?

Line 347 – lower predictive accuracy in Asians- the author need to point to a table in this 

discussion and give some values since this information was not previously cited. Or it could be 
moved to the results and described more fully (which would be preferable).

The discussion cites that a screening regimen based on PRS and age could reduce numbers of 
women undergoing screening and cites a prior paper but shouldn’t they also derive these numbers 
from their own analysis?

Line 372 to 375 – this presents some interesting observations that have not been described 
previously and do not cite a figure or table so are uninterpretable.

Lines 381-387- great that simulations were done. Please present the results in a figure and or 
table. Otherwise this is unacceptable presentation of unsupported information.

Lines 406-410. Did the authors check for heterogeneity in the ORs for family history by study? 
Opportunistic control selection could definitely lead to enrichment of FH positive controls. That 
might also be yield a similar frequency of FH in case populations and variability in FH+ controls, 
which could be tested for.

432-435 – the sentence structure in this section is weird and confusing e.g. ‘All three studies are 
population-based case-control studies; and (c) 10,266 women 433 of Chinese ethnicity 
participating in Singapore Chinese Health Study (SCHS)’ In this section you have a period break 
before All so it is not very clear that you are referring to the prior sentence and then you join this 
unclear phrase the next unclear phrase after a semicolon. Please break unrelated phrases into 
sentences and join related clauses to the antecedent sentences.

Line 472 ‘Post-imputation quality of all studies was based on the IMPUTE imputation quality score.’ 
This should not be a guessing game. Please describe what these imputation quality metrics are or 
explain them further in a supplementary methods that are referenced.

Lines 485-490 the English is missing plurals and articles so should be revised. It is great to see a 
reference for how the PRS was standarised, but I think this information should also be placed in 
the text where the means of PRS are presented.

Line 491-495 – the manuscript indicates that the PRS was stratified into quartiles and the middle 
quintile was used for referent but that is not very clearly relevant to the paper where top 1% of 
distribution was used. I think in this section the description is fairly clear but where the 1% cut off 
is described you need to cite that you are using the middle quintile as referent.

Line 507-509 – AUC analyses were adjusted by study where relevant. This needs to be explained 
further.

Lines 515-519 please give a reference for why this formula is appropriate.

The references on line 551 should be cited in the main body of the paper as requested above.

For reproducibility it would be better to specify which modules or R or Stata were used for major 
analyses rather than the very generic reference that is given.

Table 2 needs to cite in the footnote that the cutpoint is top 1% of the PRS in controls if that is 
what was used for stratifying high risk individuals.

Reviewer #2 (Remarks to the Author):

Ho and colleges evaluated the performance of a European-derived polygenic risk score (PRS) in an 
Asian population of 17,262 breast cancer cases and 17,695 controls. Most of these women were 
living in Asian countries, with a smaller population of Asian-Americans (1,507 cases and 1,212 
controls). In addition, they evaluated the PRS performance in 10,255 Chinese women from a 
prospective cohort (413 incident breast cancers). This is a well-conducted study with findings that 
have public health relevance since it provides estimates for polygenic breast cancer risk in Asian 
women that could be used for risk-stratified screening/prevention. The main finding is that the 
European-derived PRS can provide substantial risk stratification of Asian women, however the 
stratification is lower than for European-ancestry women. Although this is the largest study 
conducted in Asians to date, as the authors pointed out, even larger studies are needed to obtain 
precise OR estimates at the extreme of the PRS distribution, or to further improve the performance 
of PRS in Asian women.

Below are some comments/questions for consideration:

Q1: The authors used PRS weights based on estimates from European ancestry populations, rather 
than being re-estimated in Asian populations. This is a reasonable approach as the sample sizes to 
estimate weights are much larger in Europeans and the authors showed evidence of consistent 
effect size for genetic variants between European and Asian populations. However, given that 
previous publications have attempted to derived Asian-specific PRS, it would be of interest to 
directly compare the prediction performance between previous Asian-specific PRS (derived with 
lower sample size) and the European based PRS.

Q2: Did the authors consider incorporating Asian-specific risk variants that are not in the 313-PRSs 
developed for European populations?

Q3. The authors evaluated the PRS based on 313 variants reported in Mavaddat et al. 2019. 
However, 26 of the 313 variants were excluded due to low imputation accuracy score in Asians 
using the 1000 genome reference panel, resulting in a 287-variant PRS. This is a limitation since it 
does not allow direct comparison with the previously published PRS. Did the author consider 
imputing the genotypes based on larger reference panels such as HRC and TopMed ?

Q4: For the Singapore Chinese Health Study (SCHS), only 229 of the 287 variants that were found 
to be polymorphic and imputable. Although this is a valuable study because of its prospective 
nature and information on ancestry, it is a bit confusing to show both the 287-SNP PRS and 229-
SNP PRS as main findings. I suggest moving the 229-SNP PRS findings to supplement or make 
clearer what is the added value of these analyses as main findings. I do not see much value added 
on tables 1 or 2. Findings on Tables 4 and 5 by ancestry are of interest, are PRS means (SD) on 
Table 4 based on the 229 or 287 variant PRS?

Q5. Are the principal components calculated separately for the 10 Asian studies in BCAC and the 
three Asian-American studies?

Q6: The authors find a smaller RR for family history than previously reported in European-ancestry 
studies. Are there previous studies in Asian populations that support this difference?

Q7: The 287-variant PRS was less predictive of breast cancer risk in the three Asian-American 
studies than in the studies conducted in Asian (which found no differences between Asians of 
Chinese, Malay or Indian origin). This is a potentially important finding that requires confirmation 
in larger studies. Could the authors formally test if these differences are statistically significant in 
the current population? Based on these findings, can the authors comment on what needs to be 
done to use PRS in Asian populations in the US? Or other countries?

Minor comments:

Q1: In the imputation for BCAC, the phase of the 1000 genome project should be specified.

Q2: The EM algorithm needs citation

Q3: The version of R and Stata needs to be listed

Q4: Indicate population/sample size included in each table/figure or a reference to a table/figure 
showing the population/sample size.

Q5: Table 1- change format to match Table 2 (with less blank cells).

Q6: Consider adding the European estimates to Figure 2

Q7: Consider adding estimates from American Asians to Figure 3.

Q8: Tables 3 and 4- indicate what PRS is shown – 287-SNP PRS?