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PONE-D-22-29477Genetic scores for predicting longevity in the Croatian oldest-old populationPLOS ONE

Dear Dr. Šetinc,

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Reviewer #1: Partly

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Reviewer #1: No

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Reviewer #1: Yes

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Reviewer #1: Yes

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Reviewer #1: Šetinc and colleagues present results from a study of long-lived Croatian’s using targeted genotyping methods. Of the 43 variants genotyped – each with strong a priori evidence from the literature – two (2) were associated with survival to age 90+ in the multivariate model with p<0.01. In the univariate analyses, only one variant (rs2267723, GHRHR) was associated with p<0.01.

Major comments:

1. The selection of the 43 variants includes many key longevity loci from the field (APOE, SH2B3, CDKN2A, etc.) but is missing some key references. In particular the Timmers et al. 2019 meta-analysis of 500,000 people for parents lifespan (https://pubmed.ncbi.nlm.nih.gov/30642433) which identified several variants not included in the targeted genotyping panel. I am of course not asking you to re-do genotyping, but please acknowledge/justify this omission.

2. Table 1 (and 2) present results from a multivariate model where the genotype specification is chosen based on the best model fit parameters. This has resulted in some surprising results, for example participants heterozygous for rs1042522 located in the TP53 gene (i.e., the CG genotype group) are reported to have 1.7x likelihood of reaching 90 years, compared to the common genotype groups (CC + GG combined). Whilst there is a lot in the Discussion on p53 role in ageing/longevity the authors do not comments on why the heterozygotes only would experience lifespan benefit – a result in contract to the previous literature (which saw an additive effect with increasing G alleles).

2.1. I suspect that these borderline associations (p=0.04) should not be read into much, given the sample size and therefore power to detect the published effect sizes. The authors report substantially larger effects than seen in prior literature, after a running multiple iterations of the model to get the best prediction. I am not sure on the biological validity of including variants coded as HET vs HOM+HOM – normally in genetic epidemiology this format would be used to test for deviation from an additive model (i.e., justifying whether to use a recessive or dominant model).

3. I personally put more belief in the univariate results available in Supplementary Table 2, where 5 SNPs were associated (p<0.05) with survival to 90+ (and one for 95+). I suggest more emphasis it put on these results in the paper as this seems better “replication” of the published effect of these SNPs. Whilst the p-values are quite borderline, each SNP has a priori evidence meaning multiple testing correction would be too conservative, and using p<0.05 is appropriate, given the analysis.

4. I am actually surprised that the polygenic score is predictive of 5-year survival, given all the participants by definition reached 85 years to be eligible for the study, and the main outcome was survival to 90 years. Many of the studied “longevity” variants are actually more “disease risk” variants likely affecting mortality risk at ages below 85. There even reaching 85+ is a selected group, and this may explain why some “longevity” variants from the literature do not appear to have an effect in your study (i.e., the people who experienced the negative effects were not included?). Please discuss this point in the manuscript (what effect the participant selection had on power etc).

Minor comments:

1. Please include sample size in the abstract (N in study, % reached 90+/95+, etc)

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Reviewer #1: No

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Genetic scores for predicting longevity in the Croatian oldest-old population

PONE-D-22-29477R1

Dear Dr. Šetinc,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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Kind regards,

David M. Ojcius

Academic Editor

PLOS ONE