| Literature DB >> 34407413 |
Irene Alfaras1, Keisuke Ejima2, Camila Vieira Ligo Teixeira1, Clara Di Germanio1, Sarah J Mitchell1, Samuel Hamilton1, Luigi Ferrucci1, Nathan L Price1, David B Allison3, Michel Bernier1, Rafael de Cabo4.
Abstract
We assess the degree of phenotypic variation in a cohort of 24-month-old male C57BL/6 mice. Because murine studies often use small sample sizes, if the commonly relied upon assumption of a normal distribution of residuals is not met, it may inflate type I error rates. In this study, 3-20 mice are resampled from the empirical distributions of 376 mice to create plasmodes, an approach for computing type I error rates and power for commonly used statistical tests without assuming a normal distribution of residuals. While all of the phenotypic and metabolic variables studied show considerable variability, the number of animals required to achieve adequate power is markedly different depending on the statistical test being performed. Overall, this work provides an analysis with which researchers can make informed decisions about the sample size required to achieve statistical power from specific measurements without a priori assumptions of a theoretical distribution.Entities:
Keywords: Kaplan-Meier; aging phenotypes; gate speed; mouse aging; mouse phenotypes; plasmode; power calculation; respiratory exchange ratio; survival; type I error
Mesh:
Year: 2021 PMID: 34407413 PMCID: PMC8449850 DOI: 10.1016/j.celrep.2021.109560
Source DB: PubMed Journal: Cell Rep Impact factor: 9.423
Figure 1.Contribution of phenotypic heterogeneity to longevity of 24-month-old male C57BL/6 mice
(A) Kaplan-Meier survival curve for male C57BL/6 mice fed a standard ad libitum diet. Red arrow depicts the age at which baseline measurements were collected (e.g., 104 weeks or 2 years of age), and black arrow shows the median survival. n = 366.
(B) Morphometric analysis and body temperature. Percentages of fat mass, fluid, and lean body mass were determined by nuclear magnetic resonance (NMR) and normalized to body weight (BW). n = 366 mice.
(C) Circulating levels of glucose, insulin, and lactate in animals fasted for 6 h, and calculation of the homeostatic model assessment of insulin resistance (HOMA2-IR). n = 355 mice (n = 57 for lactate).
(D) Physical performance as assessed by wire hang (n = 66), cage top (n = 68), grip strength (n = 101), and rotarod (n = 104) tests. The values were normalized to body weight.
(E) Mice were placed into metabolic cages for the measure of the rates of oxygen consumption (VO2) and CO2 production (VCO2), respiratory exchange ratio (RER), energy expenditure as heat, and voluntary locomotor activity during two light (L) and dark (D) cycles. n = 64 mice.
The data in (B)–(E) represent median with interquartile range (IQR).
(F) Trajectories of VO2, VCO2, and RER during 48 h (two light/dark cycles). Each point represents mean ± SEM. n = 64.
See also Table S1.
Analysis of metabolic and behavioral readouts during continuous 48-h measurements (two light and two dark sessions) in the CLAMS monitoring system
| Light sessions (mean ± SD) | Dark sessions (mean ± SD) | t (df) | p value | n | |
|---|---|---|---|---|---|
| VO2 (mL/h) | 116.4 ± 16.66 | 133.3 ± 19.27 | 7.21 (126) | <0.0001 | 64 |
| VCO2 (mL/h) | 101.1 ± 14.65 | 120.0 ± 17.87 | 7.456 (119.3) | <0.0001 | 64 |
| RER | 0.8677 ± 0.0045 | 0.8998 ± 0.0046 | 5.014 (126) | <0.0001 | 64 |
| Heat (kcal/h) | 0.5611 ± 0.0072 | 0.6454 ± 0.0086 | 7.545 (126) | <0.0001 | 64 |
| Total activity (counts) | 684.2 ± 31.17 | 1715 ± 73.2 | 12.96 (85.12) | <0.0001 | 64 |
Paired t test with two-tailed p value. The normality hypothesis was not rejected for metabolic outputs and locomotor activity between light and dark cycles.
Figure 2.Computed type I error rates and power from plasmode-based simulation
(A) Computed type I error rates for body weight from the plasmode-based simulation and the five different statistical tests with nominal significance level set at 0.05. Filled blue circles are type I error rates and bars are the 95% confidence interval (CI), respectively. A horizontal dotted line corresponds to the significance level.
(B) Computed power for body weight using the Welch’s test when outcome of the treatment group was increased by 10%–50%. A horizontal dotted line denotes an 80% cutoff and corresponds to a significance level of 0.05.
(C) Cumulative distributions of empirical data (black dots and lines) and the normal distributions (red lines) of body weight with the same means and variances. p values from Shapiro-Wilk test (test for normality), skewness, and excess kurtosis are listed.
(D) Heatmap depicting the sample size required to attain 80% power among the indicated outcome measures using the Welch’s test. Similar analyses were carried out for all outcome measures and are illustrated in Figure 2 and Figures S1-S3.
See also Figures S1-S3 and Tables S2-S4.
Figure 3.Illustration of a plasmode-based simulation aimed at computing type I error rate
In this simulation, our original data (body weight) was used to create a treatment group by maintaining the same mean of the population distribution but with the variance in the treatment group (k) set at 1-, 5-, or 10-fold larger than that in the control group.
KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Chemicals, peptides, and recombinant proteins | ||
| AIN-93G diet | Dyets, Inc. | Cat #110700 |
| Teklad Global 18% Protein Extruded Rodent Diet | Envigo | Cat #2018SX |
| Critical commercial assays | ||
| Mouse insulin ELISA kit | Crystal Chem, Inc. | Cat# 90080; RRID:AB_2783626 |
| Deposited Data | ||
| Data sets and original codes |
| |
| Experimental models: Organisms/strains | ||
| Male C57BL/6J mice | The Jackson Laboratory | JAX 000664 |
| Male C57BL/6JN mice | NIA Aged Rodent Colony | N/A |
| Software and algorithms | ||
| Prism 6.0 | GraphPad | |
| Microsoft Excel 2019 | Microsoft Corp. | |
| Canvas Draw 6 for macOS | Canvas GFX | RRID:SCR_014288 |
| R programming language v.4.0.1 | R Development Core Team | RRID:SCR_001905 |
| Other | ||
| Rotarod | Med Associates, Inc. | Cat#ENV-574M |
| Minispec LF90 | Bruker Optics |
|
| Oxymax Open Circuit Indirect Calorimeters | Columbus Instruments |
|
| Breeze2 Glucometer | Bayer | |