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1 1 Online Supplemental Material Paleolithic nutrition for metabolic syndrome List of included online supplemental tables RCTs, including outcome data; Supplemental Table 2. Full details of the risk of bias assessment for each included RCT, on each criterion of the Cochrane Risk of Bias instrument; Supplemental Table 3. Characteristics of ongoing RCTs.

2 DATA EXTRACTION FORM Name of study: BOERS 2014 Assessor Initials: EM + EvZ Methods Type of study (e.g., parallel RCT, cross-over RCT, cluster RCT): parallel "randomized controlled single-blinded pilot study" Dates of study (month/year start and end): "Subjects were recruited in September-October 2011 through advertisements..." Duration of follow-up (randomization to end of follow-up): 2 weeks Setting (e.g., outpatient clinic, hospital), including # centers & city/country: Single centre in the Netherlands: "The study took place at the Louis Bolk Institute in Driebergen, the Netherlands, in October-December Laboratory measurements were performed in the Diakonessenhuis, Zeist, the Netherlands." Participants Number of participants randomized: 34 Mean age (+/- SD or range) in each group and/or total (whichever reported): paleo group: 52.0 (SD 10.2); reference group 55.4 (SD 9.0); total: 53.5 (SD 9.7) years Men/Women (n/n): 9/25; 72.2% women in paleo group; 75.0% women in reference group Inclusion criteria: "18 70 years old adults who gave written consent and had at least two of the following characteristics of the MetS [20]: 1. Central obesity (waist circumference 102 cm for men and 88 cm for women) 2. Elevated triglycerides 1.7 mmol/l 3. Reduced HDLcholesterol <1.0 mmol/l for men and <1.3 mmol/l for women) 4. Raised BP 130/85 mmhg or BP medication and 5. Elevated fasting plasma glucose 5.6 mmol/l." Exclusion criteria: "Exclusion criteria were DM2, CVD, smoking, systolic BP > 180 mmhg, hypoglycaemic medication, pregnancy and severe internal or psychiatric disease." Dropouts/Withdrawals (report details in RoB table): "Two subjects (2/16; 12.5%) dropped out from the reference group for personal reasons." None (0/18) dropped out in paleo group Baseline data (report details in RoB table): "Baseline data differed between both groups for BMI and number of characteristics of the MetS." There were also statistically significant differences in baseline values for the individual MetS factors of HDL cholesterol (p=0.00) and fasting glucose (p=0.04) (Table 2), as well as for bodyweight (p=0.04) (Table 3). Interventions: dose/frequency/duration etc Timing of outcome assessments (e.g., 1 week, 1 month, end of study): 2 weeks only, which is also the end of treatment intervention: "The Palaeolithic-type diet intervention...was based on lean meat, fish, fruit, leafy and cruciferous vegetables, root vegetables, eggs and nuts. Dairy products, cereal grains, legumes, refined fats, extra salt and sugar were not part of it." N allocated to paleo diet: 18 Duration of treatment (randomization to end of treatment): 2 weeks Duration of follow-up (randomization to end of follow-up): 2 weeks Number of calories: "an isoenergetic intake of kj" intervention: "The reference diet was based on the guidelines for a

3 BOERS 2014 healthy diet of the Dutch Health Council [23-31]." N allocated to comparator diet: 16 Duration of treatment (randomization to end of treatment): 2 weeks Duration of follow-up (randomization to end of follow-up): 2 weeks Number of calories: "an isoenergetic intake of kj" Dietary advice or provision of foods: "...All meals were delivered at their homes free of charge by a catering service... Both diets were designed as seven consecutive daily menus (breakfast, lunch, dinner and snacks) and provided on the basis of an isoenergetic intake of 8700 kj..." Isocaloric throughout or energy content of diets individually adjusted to maintain stable bodyweight: Diets individually adjusted to maintain stable bodyweight. Quote: "Before the intervention all subjects recorded their usual diet using a food record diary. This diary was used by the dietician to adjust diets to individual energy demand by providing (additional) program-related snacks to prevent weight loss within the intervention period. Bodyweight was measured every second day. A daily bodyweight fluctuation of 2 kg was considered acceptable...this diary was used by the dietician to adjust diets to individual energy demand by providing (additional) program-related snacks to prevent weight loss within the intervention period... For nine subjects extra diet-related snacks were necessary due to over 2 kg weight loss, without being hungry (seven in the Palaeolithic group = 38% versus two in the reference group = 14%)." Restriction vs no restriction of daily caloric intake: Restriction -- meals delivered and participants instructed about "keeping bodyweight stable" -- with the exception of the "program-related snacks to prevent weight loss" Data also on (PMID, Clinical Trials.gov ID): PMID: Outcomes of the study: Glucose tolerance (OGTT) Characteristics of MetS (waist circumference, systolic/diastolic BP, lipids, fasting glucose) intestinal permeability inflammation parameters (hscrp, TNFα) and a stress parameter (salivary cortisol). Tolerability was measured by analysing the adverse events reported during the study and by performing blood tests for haematological indices and liver and kidney functions. Outcome measures according to us, of our review (not from authors of study) Type of analysis follows "", in parentheses, with (ITT)=intention to treat; (PP) = per protocol; (AC) = available case. For values used, (U)=unadjusted; (A)=adjusted. "mean reduction " values obtained by ing RCT authors are enclosed in brackets I. Primary outcome measures: a) Changes of each of the 5 component variables of the metabolic syndrome: 1) waist circumference, 2) triglycerides, 3) HDL-cholesterol, 4) blood pressure, and 5) fasting blood sugar b) Participant-assessed changes in quality of life c) Proportion of participants who reported an adverse event throughout the

4 BOERS 2014 study period What were the results of these outcome measures? Waist circumference (Ia1) 18 (ITT) (A) 16 (ITT) (A) Assessed with cm cm Comment Mean reduction ( Table 3 for baseline and posttreatment means and SDs. SDs of mean changes estimated using Esther's calculator.* Triglycerides (Ia2) Baseline (11.5 At 2 weeks (12.3 Mean change from baseline (7.56 calculated with calculator I sent you 18 (ITT) (A) Assessed with mmol/l mmol/l Baseline (9.4 At 2 weeks (8.7 Mean change ( (ITT) (A) Mean reduction ( Table 3 for baseline and posttreatment means and SDs. SDs of mean changes estimated using Esther's calculator.* HDL Cholesterol (Ia3) Baseline 1.9 (1.4 At 2 weeks 1.0 (0.6 Mean change from baseline ( (ITT) (A) Assessed with mmol/l mmol/l Baseline 1.3 (0.6 At 2 weeks 1.4 (0.6 Mean change 0.10 ( (ITT) (A) (+ means increase in TG in reference group, rather than reduction) Mean reduction ( Table 3 for baseline and posttreatment means and SDs. SDs of mean changes Baseline 1.3 (0.4 At 2 weeks 1.3 (0.4 Mean change from baseline 0.00 (0.25 Baseline 1.6 (0.4 At 2 weeks 1.4 (0.4 Mean change (0.25

5 BOERS 2014 estimated using Esther's calculator.* Systolic blood pressure (Ia4) 18 (ITT) (A) Assessed with mmhg mmhg Mean reduction ( Table 3 for baseline and posttreatment means and SDs. SDs of mean changes estimated using Esther's calculator.* Diastolic blood pressure (Ia4*) Baseline 131 (15 At 2 weeks 122 (10 Mean change from baseline ( (ITT) (A) Assessed with mmhg mmhg Mean reduction ( Table 3 for baseline and posttreatment means and SDs. SDs of mean changes estimated using Esther's calculator.* Fasting blood sugar (Ia5) Baseline 87 (9 At 2 weeks 79 (6 Mean change from baseline (5.53) 18 (ITT) (A) Assessed with mmol/l mmol/l 16 (ITT) (A) Baseline 134 (15 At 2 weeks 129 (14 Mean change ( (ITT) (A) Baseline 86 (13 At 2 weeks 83 (9 Mean change ( (ITT) (A) Mean reduction Table 3 for baseline and posttreatment means and SDs. SDs of mean changes estimated using Baseline 6.1 (0.8 At 2 weeks 5.7 (0.8 Mean change from baseline (0.51 Baseline 5.8 (0.7 At 2 weeks 5.5 (0.8 Mean change (0.48

6 BOERS 2014 Esther's calculator.* Health-related quality of life (Ib) Assessed with Not reported Not reported Mean reduction Not reported Not reported Adverse events (Ic) 18 (ITT) (U) 16 (ITT) (U) Indicate in the 2 rows below whether the numbers extracted from the publication were the numbers of adverse events in each group or the numbers of patients in each group who had adverse events, by following the relevant numbers with (g) or (p). Treatment-related AE (proportion) All AE (proportion) None -- "Among tolerability outcomes the white blood cell count and γ- glutamyltransferase showed a decline in favour of the Palaeolithic group. Blood analysis concerning haematology and liver and kidney function showed no changes in relation to adverse events (Table 4)..." II. Secondary outcome measures 1. Body weight 2. Fasting plasma levels of: a) IGF-1 b) uric acid c) C-reactive protein d) insulin e) total cholesterol Body weight (II-1) None 0/18 1/16 "(nausea and diarrhoea) during the intervention which was not likely related to the intervention)" 18 (ITT) (A) 16 (ITT) (A) Comment

7 BOERS 2014 Assessed with kg kg Table 3 for baseline and posttreatment means and SDs. SDs of mean changes estimated using Esther's calculator.* IGF-1 (II-2a) Baseline 98 (18.2 At 2 weeks 95.3 (17.5 Mean change from baseline (11.31) SD Baseline 86 (14.2 At 2 weeks 84.3 (12.5 Mean change (8.60 Assessed with Not reported Not reported Mean reduction Not reported Not reported Uric acid (II- 2b) Assessed with Not reported Not reported Mean reduction C-reactive protein (II-2c) Not reported 18 (ITT) (A) Assessed with mg/l mg/l Not reported 16 (ITT) (A) Labelled "hscrp" in publication, where "hs" stands for "high sensitivity

8 BOERS 2014 Mean reduction Table 3 for baseline and posttreatment means and SDs. SDs of mean changes estimated using Esther's calculator.* Insulin (II-2d) Baseline 4.4 (3.4 At 2 weeks 4.6 (3.1 Mean change from baseline 0.20 ( (ITT) (A) Assessed with mu/l mu/l Baseline 2.3 (3.1 At 2 weeks 3.0 (4.5 Mean change 0.70 ( (ITT) (A) Mean reduction Table 3 for baseline and posttreatment means and SDs. SDs of mean changes estimated using Esther's calculator.* Total cholesterol (II- 2e) Baseline 11.9 (5.5 At 2 weeks 9.2 (4.9 Mean change from baseline ( (ITT) (A) Assessed with mmol/l mmol/l Baseline 10.2 (6.5 At 2 weeks 9.5 (5.3 Mean change ( (ITT) (A) In this trial, insulin was assessed using mu/l. For entering values into RevMan, mu/l values were converted to pmol/l, which is the SI unit for this clinical lab data. Lindeberg 2007 and Jonsson 2009 assessed with pmol/l. The conversion factor is 1 µiu/ml = pmol/l ( Unitconvert/Insulin.php). Therefore, to convert to pmol/l, I multiplied the means and SDs of change by before entering in RevMan. Hanno confirmed the conversions used are correct. Mean reduction Table 3 for baseline and posttreatment means and SDs. SDs of mean changes estimated using Esther's calculator.* Baseline 5.7 (1.0 At 2 weeks 5.0 (0.9 Mean change from baseline (0.61 Baseline 6.1 (1.4 At 2 weeks 6.0 (1.2 Mean change (0.84

9 BOERS 2014 * SD (changes) calculated using the baseline and post-treatment means and SDs (reported in Table 3), using Esther's Calculator with filename 'Esther Calculator SEM to SD and mean change '.

10 JONSSON 2009 DATA EXTRACTION FORM Name of study: JONSSON 2009 Assessor Initials: EM + EvZ Methods Type of study (e.g., parallel RCT, cross-over RCT, cluster RCT): randomized cross-over trial, with participants initially randomized to either paleo diet or the Diabetes diet, and crossing over to the other diet at the three month time point. We only included the first period data before cross-over (i.e., 3 month time point data) because of the concern about carryover effects. Dates of study (month/year start and end): Quote (page 4, 'Results/Recruitment and participant flow' section): "The study started in January 2005 and the last participant was followed up in September 2007 after which the study was stopped." Duration of follow-up (randomization to end of follow-up): "two consecutive 3-month periods". The duration of follow-up for the trial was 6 months, but the duration of follow-up for the systematic review was 3 months because we only included the first period data before the cross-over at 3 months, and we excluded the post-crossover data. Setting (e.g., outpatient clinic, hospital), including # centers & city/country: Quote (page 2, 'Methods/Patients' section): "three primary health care units in the Lund area in Sweden" Participants Number of participants randomized: 17 Mean age (+/- SD or range) in each group and/or total (whichever reported): paleo group: 66 (6); Diabetes diet group: 63 (6); total: 64 (6) Men/Women (n/n): paleo group: 6/1; Diabetes diet group: 4/2; total: 10/3 Inclusion criteria: Quote (page 2, 'Methods/Patients'): "We included adult patients with type 2 diabetes and a C-peptide value above zero, unaltered medical diabetes treatment and stable weight since three months before start of study, HbA1c above 5.5% by Mono-S standard, creatinine below130 umol/l, liver enzymes below four times their respective upper reference value, no chronic oral or injection steroid treatment and no acute coronary event or change in medication of beta blockers or thyroxin since six months before start of study." Exclusion criteria: Quote (page 2, 'Methods/Patients'): "Exclusion criteria during ongoing study were change in beta blocker or thyroxin medication, chronic oral or injection steroid treatment, warfarin treatment, creatinine above 130 μmol/l or liver enzymes above four times their respective upper reference value, acute coronary event, and physical or psychological illness or changes in personal circumstances which would make further study participation impossible." Dropouts/Withdrawals (including reasons): Of 17 randomized, 4 withdrew (2 in each group), and the reasons for 3/4 of these withdrawals were because the investigators enrolled participants who were later found to be ineligible, and these are justifiable exclusions. Baseline data (including details): "The group starting with the Paleolithic diet differed at baseline only with regard to fasting plasma glucose and AUC glucose being lower and HOMA2 %B being higher compared to the group starting with a Diabetes diet (Table 2)." Interventions: dose/frequency/duration etc Timing of outcome assessments (e.g., 1 week, 1 month, end of study): 3 months and 6 months. Cross-over occurred at 3 months (i.e., at 3 month time point, group initially

11 JONSSON 2009 assigned to paleo crossed over to Diabetes diet and group initially assigned to Diabetes diet crossed over to paleo diet). We only extracted the outcome data at 3 months, and did not extract any post cross-over data because of the concern about carryover effects. intervention: "The information on the Paleolithic diet stated that it should be based on lean meat, fish, fruit, leafy and cruciferous vegetables, root vegetables, eggs and nuts, while excluding dairy products, cereal grains, beans, refined fats, sugar, candy, soft drinks, beer and extra addition of salt. The following items were recommended in limited amounts for the Paleolithic diet: eggs (<2 per day), nuts (preferentially walnuts), dried fruit, potatoes (<1 medium-sized per day), rapeseed or olive oil (<1 tablespoon per day), wine (<1 glass per day). The intake of other foods was not restricted and no advice was given with regard to proportions of food categories (e.g. animal versus plant foods). The evolutionary rationale for a Paleolithic diet and potential benefits were explained [19]." N allocated to paleo diet: 9 (2 were excluded so only 7 analyzed for per protocol analysis) Duration of treatment (randomization to end of treatment): 6 months for trial, 3 months for review (the "treatment" only involved participants receiving oral and written information about their respective initial diets immediately after randomization) Duration of follow-up (randomization to end of follow-up): 6 months (post cross-over data (i.e., data after 3 months) excluded from meta-analysis) Number of calories: Ad libitum consumption of both diets intervention: "...a Diabetes diet in accordance with current guidelines [17]... The information on the Diabetes diet stated that it should aim at evenly distributed meals with increased intake of vegetables, root vegetables, dietary fiber, whole-grain bread and other whole-grain cereal products, fruits and berries, and decreased intake of total fat with more unsaturated fat. The majority of dietary energy should come from carbohydrates from foods naturally rich in carbohydrate and dietary fiber. The concepts of glycemic index and varied meals through meal planning by the Plate Model were explained [18]. Salt intake was recommended to be kept below 6 g per day." N allocated to comparator diet: 8 (2 were excluded so only 6 analyzed for per protocol analysis) Duration of treatment (randomization to end of treatment): 6 months for trial; 3 months for review (the "treatment" only involved participants receiving oral and written information about their respective initial diets immediately after randomization) Duration of follow-up (randomization to end of follow-up): 6 months (post cross-over data (i.e., data after 3 months) excluded from meta-analysis) Number of calories: Ad libitum consumption of both diets Dietary advice or provision of foods: Dietary advice, and also the participants in each group were asked to record their daily food intake -- "Immediately after randomization, all subjects received oral and written information individually (by UCB, GP or AH) in the morning about their respective initial diet...written information with dietary advice and food recipes were similarly formulated for both diets. For increased conformity, the dietary advice and data collection procedure were discussed by all authors except YG at several meetings prior to start of study. Advice about regular physical activity was given equally to all subjects." Isocaloric throughout or energy content of diets individually adjusted to maintain stable bodyweight: Ad libitum food consumption in both groups.

12 JONSSON 2009 Restriction vs no restriction of daily caloric intake: Quote (page 7, section 'Discussion/Possible mechanisms and explanations'): "No advice was given to restrict food intake." Data also on (PMID, Clinical Trials.gov ID): NCT ; PMID: Outcomes of the study: Primary outcomes of study: 1) Changes in the area under the curve (AUC) between 0 and 120 min during OGTT for a) plasma glucose (AUC Glucose0 120) and b) plasma insulin (AUC Insulin0 120) 2) changes in body weight 3) changes in waist circumference 4) serum lipids 5) CRP 6) blood pressure and 7) glycated haemoglobin A1c (HbA1c) by Mono-S standard. Additional outcomes were "beta-cell function (%B) and insulin sensitivity (%S), as percentages of a normal reference population, and insulin resistance (IR, the reciprocal of %S (100/%S))" all assessed using the Homeostatic model assessment (HOMA); insulin sensitivity index; GI based on food diaries. Outcome measures according to us, of our review (not from authors of study) Type of analysis follows "", in parentheses, with (ITT)=intention to treat; (PP) = per protocol; (AC) = available case. For values used, (U)=unadjusted; (A)=adjusted. "mean reduction " values obtained by ing RCT authors are enclosed in brackets I. Primary outcome measures: d) Changes of each of the 5 component variables of the metabolic syndrome: 1) waist circumference, 2) triglycerides, 3) HDL-cholesterol, 4) blood pressure, and 5) fasting blood sugar e) Participant-assessed changes in quality of life f) Proportion of participants who reported an adverse event throughout the study period What were the results of these outcome measures? Waist circumference (Ia1) 7 (AC & PP) (U) 6 (AC & PP) (U) Assessed with cm cm Comment Mean changes from baseline and their SDs calculated using IPD data from Dr. Jonsson* Triglycerides (Ia2) -6.57(3.22) -4.75(6.93) 7 (AC & PP) (U) 6 (AC & PP) (U)

13 JONSSON 2009 Assessed with mmol/l mmol/l Mean changes from baseline and their SDs calculated using IPD data from Dr. Jonsson* HDL Cholesterol (Ia3) (0.48) 0.07 (0.23) 7 (AC & PP) (U) Assessed with mmol/l mmol/l Mean changes from baseline and their SDs calculated using IPD data from Dr. Jonsson* Systolic blood pressure (Ia4) 6 (AC & PP) (U) 0.12 (0.18) (0.12) 7 (AC & PP) (U) Assessed with mmhg mmhg Mean reductions and their SDs calculated using IPD data from Dr. Jonsson* Diastolic blood pressure (Ia4*) 6 (AC & PP) (U) (20.38) 1.33 (17.04) 7 (AC & PP) (U) Assessed with mmhg mmhg Mean reductions and their SDs calculated using IPD data from Dr. Jonsson* Fasting blood sugar (Ia5) 6 (AC & PP) (U) (7.70) (7.60) 7 (AC & PP) (U) Assessed with mmol/l mmol/l 6 (AC & PP) (U) Mean changes from baseline and their SDs calculated using IPD data from Dr. Jonsson* (0.98) (1.11)

14 JONSSON 2009 Health-related quality of life (Ib) Assessed with Not reported Not reported Mean reduction from baseline Adverse events (Ic) Not reported Not reported Treatment-related AE Not reported Not reported (proportion) All AE (proportion) Not reported Not reported f) Body weight (II- 1) 7 (AC & PP) (U) 6 (AC & PP) (U) Assessed with kg kg Mean changes from (3.59) (3.61) baseline and their SDs calculated using IPD data from Dr. Jonsson* IGF-1 (II-2a) Assessed with Not reported Not reported Mean reduction from Not reported Not reported baseline Uric acid (II-2b) Assessed with Not reported Not reported Mean reduction from Not reported Not reported baseline C-reactive protein (II-2c) 7 (AC & PP) (U) 6 (AC & PP) (U) Assessed with mg/l mg/l

15 JONSSON 2009 Mean changes from baseline and their SDs calculated using IPD data from Dr. Jonsson* Insulin (II-2d) (1.36) 1.35 (3.32) 7 (AC & PP) (U) Assessed with pmol/l pmol/l Mean changes from baseline and their SDs calculated using IPD data from Dr. Jonsson* Total cholesterol (II-2e) 6 (AC & PP) (U) (38.88) 3.52 (20.53) 7 (AC & PP) (U) Assessed with mmol/l mmol/l 6 (AC & PP) (U) Mean changes from baseline and their SDs calculated using IPD data from Dr. Jonsson* 0.17 (0.92) (0.84) *Mean and SDs (changes) calculated using the individual patient data Excel file provided by Dr. Jonsson with filename ' Data from study by Jonsson et al 2009 Beneficial effects of a Paleolithic diet (1)v3'. This file provided the outcome value at baseline and at 3 months, for each patient in each group, for all outcomes. The mean changes were calculated by the difference between baseline and 3 months for all 13 participants using the 'Average' function in Excel, and the SDs of these changes were calculated using the 'STDEV' function.

16 LINDEBERG 2007 DATA EXTRACTION FORM Name of study: LINDEBERG 2007 Assessor Initials: EM + EvZ Methods Type of study (e.g., parallel RCT, cross-over RCT, cluster RCT): parallel RCT Dates of study (month/year start and end): Not reported Duration of follow-up (randomization to end of follow-up): 12 weeks, but only the 6 week data was used for the meta-analysis Setting (e.g., outpatient clinic, hospital), including # centers & city/country: "Coronary Care Unit at Lund University Hospital, Sweden" Participants Number of participants randomized: 38 (29 analyzed) Mean age (+/- SD or range) in each group and/or total (whichever reported): paleo: 65 (10); Consensus: 57 (7) [from Table 1]; mean age for both groups combined not reported Men/Women (n/n): 29/0 (only men included) Quote (page 1796, 'Materials and methods/participants'): "The study was a 12 week controlled dietary intervention trial in 29 (out of 38 eligible) male IHD patients..." Inclusion criteria: Quote (page 1796, section 'Materials and methods/participants'): "...male IHD patients with waist circumference >94 cm and increased blood glucose or known diabetes, recruited from the Coronary Care Unit at Lund University Hospital, Sweden. We included patients with any of the following conditions: an ongoing acute coronary syndrome, a history of myocardial infarction diagnosed by creatine kinase MB isoenzyme or troponin elevation, percutaneous coronary intervention or coronary artery bypass surgery or angiographically diagnosed coronary stenosis 30%..." Quote (page 1796, section 'Materials and methods/procedure'): "Patients qualified for the study if they had known type 2 diabetes or, at a screening OGTT with 75 g glucose, a fasting capillary blood glucose 6.1 mmol/l or a 2 h capillary blood glucose 7.8 mmol/l." Exclusion criteria: Quote (page 1796, section 'Materials and methods/participants'): "Exclusion criteria were BMI <20 kg/m2, serum creatinine >130 μmol/l, poor general condition, dementia, unwillingness/inability to prepare food at home, participation in another medical trial, chronic inflammatory bowel disease, type 1 diabetes and treatment with hypoglycaemic agents, warfarin or oral steroids." Dropouts/Withdrawals (including reasons): "In addition to the 29 patients who completed the trial, nine randomised subjects were excluded for the following reasons: worsening general condition (n=4), unwillingness to continue (n=3, all in the Palaeolithic group) or missing OGTT data (one in each group)." Unclear how many were randomized to each group initially. Lindeberg provided the following information: "Of the 38 participants, 20 were randomised to palaeolithic and 18 to mediterranean-like dietary advice." Baseline data (including details): "The two groups differed at baseline only with regard to age being higher (p=0.01) and plasma triacylglycerols being lower (p=0.06) in the Palaeolithic group (Table 1)." See comments Hanno in RoB Interventions: dose/frequency/duration etc Timing of outcome assessments (e.g., 1 week, 1 month, end of study): 6 weeks

17 LINDEBERG 2007 and 12 weeks, with the 6 week outcome data used for our meta-analysis intervention: "(2) a Palaeolithic diet (n=14) based on lean meat, fish, fruits, leafy and cruciferous vegetables, root vegetables (including restricted amounts of potatoes), eggs and nuts." N allocated to paleo diet: 14 analyzed in paleo group but N allocated to paleo group not reported Duration of treatment (randomization to end of treatment): 12 weeks Duration of follow-up (randomization to end of follow-up): 12 weeks Number of calories: Ad libitum consumption -- no restriction on caloric intake and no recommendations for daily caloric intake reported intervention: "(1) a Consensus (Mediterranean-like) diet (n=15) based on whole-grain cereals, low-fat dairy products, potatoes, legumes, vegetables, fruits, fatty fish and refined fats rich in monounsaturated fatty acids and alpha-linolenic acid;" N allocated to comparator diet: 15 analyzed in Consensus diet group but N allocated to Consensus group not reported Duration of treatment (randomization to end of treatment): 12 weeks Duration of follow-up (randomization to end of follow-up): 12 weeks Number of calories: Ad libitum consumption -- no restriction on caloric intake and no recommendations for daily caloric intake Dietary advice or provision of foods: Dietary advice. Quote (page , section 'Materials and methods/diets'): "All subjects were informed individually (by S. Lindeberg, K. Sjöström or E. Borgstrand) during two 1 h sessions and were given written dietary advice and food recipes. Only subjects in the Consensus group were informed of the possible benefits of Mediterranean-like diets rich in whole grains and about the Lyon Diet Heart Study [30]. The Consensus group was also educated by use of a dietary questionnaire for nutrition counselling ( 20 questions ) [31] used in a successful health promotion programme, Live For Life, which led to lowered cardiovascular and total mortality in the Habo municipality, Sweden [32] (Supplementary Table 1). Only subjects in the Palaeolithic group were educated in the concept of evolutionary health promotion [33] and the potential benefits of a Palaeolithic diet. They were advised to increase their intake of lean meat, fish, fruits and vegetables and to avoid all kinds of dairy products, cereals (including rice), beans, sugar, bakery products, soft drinks and beer. The following items were accepted in limited amounts for the Palaeolithic group: eggs (one or fewer per day), nuts (preferentially walnuts), potatoes (two or fewer medium-sized per day), rapeseed or olive oil (one or fewer tablespoons per day). The intake of other foods was not restricted and no advice was given with regard to proportions of food categories (e.g. animal vs plant foods). The type of dietary advice given to the Consensus group was similar to the established programme at the Coronary Care Unit. Since the required increase in education intensity in order to match the Palaeolithic group was rather small, no usual care control group was considered necessary. Advice about regular physical activity was given equally to the two groups. Both groups were advised not to consume more than one glass of wine per day." Isocaloric throughout or energy content of diets individually adjusted to maintain stable bodyweight: Ad libitum food consumption in both groups.

18 LINDEBERG 2007 Restriction vs no restriction of daily caloric intake: no advice was given to restrict daily caloric intake Data also on (PMID, Clinical Trials.gov ID): PMID: NCT Outcomes of the study: Primary outcomes: 1) changes in weight 2) waist circumference 3) plasma glucose AUC (AUC Glucose0 120) 4) plasma insulin AUC (AUC Insulin0 120) in OGTTs. Secondary outcomes: not specified, although multiple additional outcomes compared at baseline, including serum lipids and blood pressure, but the outcome data were not reported for these. Outcome measures according to us, of our review (not from authors of study) Type of analysis follows "", in parentheses, with (ITT)=intention to treat; (PP) = per protocol; (AC) = available case. For values used, (U)=unadjusted; (A)=adjusted. "mean reduction " values obtained by ing RCT authors are enclosed in brackets I. Primary outcome measures: g) Changes of each of the 5 component variables of the metabolic syndrome: 1) waist circumference, 2) triglycerides, 3) HDL-cholesterol, 4) blood pressure, and 5) fasting blood sugar h) Participant-assessed changes in quality of life i) Proportion of participants who reported an adverse event throughout the study period What were the results of these outcome measures? All outcomes reported below are for the 6 week time point. Waist circumference (Ia1) 14 (AC & PP) (U) 15 (AC & PP) (U) Assessed with cm cm Comment Mean reduction from baseline Triglycerides (Ia2) -3.0 ( (2.0 Extracted from Table 2, row "Waist circumference/change 0-6 weeks" 14 (AC & PP) (U) 2015 Jan 2 response from Lindeberg: "Unfortunately, serum lipids were not analysed. (The majority of patients were statin-naive 15 (AC & PP) (U) Quote: "Serum lipids changed to a similar extent in both groups, due to initiation of statin treatment in most patients, and there was no decrease in blood pressure (data not shown)."

19 LINDEBERG 2007 and all of them were prescribed a statin.)" Assessed with mmol/l mmol/l Mean reduction from baseline Provided by Prof. Lindeberg in an e- mail 2015 Jun 27 HDL Cholesterol (Ia3) (0.66) (0.69) Prof Lindeberg 2015 Jun 27 "With regard to serum lipids, I still believe they are difficult to analyse with regard to initiated statin treatment, but here are the changes from baseline to 6 weeks (we don't have HDL):..." Assessed with Not reported Not reported Quote: "Serum lipids changed to a similar extent in both groups, due to initiation of statin treatment in most patients, and there was no decrease in blood pressure (data not shown)." Mean reduction from baseline Systolic blood pressure (Ia4) Not reported Not reported Prof Lindeberg 2015 Jun 27 "With regard to serum lipids, I still believe they are difficult to analyse with regard to initiated statin treatment, but here are the changes from baseline to 6 weeks (we don't have HDL):..." 14 (AC & PP) (U) 15 (AC & PP) (U) Quote: "...there was no decrease in blood pressure (data not shown)." Assessed with mmhg mmhg Mean reduction from baseline Provided by Prof. Lindeberg in an e- mail 2015 Jun (14.26) (8.91) Prof Lindeberg 2015 Jun 27 "A problem with blood pressure is that beta blockers were routinely prescribed to those with a myocardial infarction, irrespective of their blood pressure. Another problem is that blood pressure typically decreases during an acute coronary event

20 LINDEBERG 2007 Diastolic blood pressure (Ia4*) 14 (AC & PP) (U) 15 (AC & PP) (U) (baseline values were 131/78±16/10 mm). Unfortunately, we have not analysed this in detail, so I don't know if there was imbalance between the diet groups in these aspects." Quote: "...there was no decrease in blood pressure (data not shown)." Assessed with mmhg mmhg Mean reduction from baseline Provided by Prof. Lindeberg in an e- mail 2015 Jun (8.95) (8.88) Prof Lindeberg 2015 Jun 27 "A problem with blood pressure is that beta blockers were routinely prescribed to those with a myocardial infarction, irrespective of their blood pressure. Another problem is that blood pressure typically decreases during an acute coronary event (baseline values were 131/78±16/10 mm). Unfortunately, we have not analysed this in detail, so I don't know if there was imbalance between the diet groups in these aspects." 14 (AC & PP) (U) 15 (AC & PP) (U) Fasting blood sugar (Ia5) Assessed with mmol/l mmol/l Mean reduction from baseline Table (1.99) Baseline 6.8 (1.3 to end of 6 weeks 5.2 (1.1 Mean change from baseline (1.99) (2.35) Baseline 7.1 (1.8 to end of 6 weeks 5.8 (1.2 Mean change from baseline (2.35 SDs of change for each group calculated in Excel spreadsheet, assuming p=0.01 for paleo group and p=0.05 for Consensus group, based on footnote of Table 3 (i.e., p-values of paired t test for 0-6 week within group changes: for paleo group: "p<.01"; for Consensus group: "p<0.05"). Because no exact p-values were

21 LINDEBERG 2007 Health-related quality of life (Ib) Assessed with Not reported Not reported reported, I used highest possible p-values (i.e., 0.01 for paleo and 0.05 for Consensus) as conservative assumption. Mean reduction from Not reported Not reported baseline Adverse events (Ic) Indicate in the 2 rows below whether the numbers extracted from the publication were the numbers of adverse events in each group or the numbers of participants in each group who had adverse events, by following the relevant numbers with (g) or (p). Treatment-related AE Not reported Not reported (proportion) All AE (proportion) Not reported Not reported II. Secondary outcome measures 1. Body weight 2. Fasting plasma levels of: g) IGF-1 h) uric acid i) C-reactive protein j) insulin k) total cholesterol Body weight (II- 1) 14 (AC & PP) (U) Assessed with kg kg Mean reduction from baseline IGF-1 (II-2a) 15 (AC & PP) (U) -3.7 ( (2.3 Extracted from 'Table 2 Primary outcome variables', "Weight (kg)", row "Change 0-6 weeks" Assessed with Not reported Not reported Mean reduction from Not reported Not reported baseline Uric acid (II-2b) Assessed with Not reported Not reported Mean reduction from Not reported Not reported baseline C-reactive protein Baseline values reported in

22 LINDEBERG 2007 (II-2c) 14 (AC & PP) (U) 15 (AC & PP) (U) Table 1, but no outcome data for CRP reported. Assessed with mg/l mg/l Mean reduction from baseline Provided by Prof. Lindeberg in an e- mail 2015 Jun 27 Insulin (II-2d) (24.34) (12.5) Prof Lindeberg 2015 Jun 27 "A problem in the interpretation of CRP is that the mean mean±sd was 11.7±19.2 at baseline (when half of the patients had an acute coronary event)." 14 (AC & PP) (U) 15 (AC & PP) (U) Assessed with pmol/l pmol/l Mean reduction from baseline Total cholesterol (II-2e) -11 (21.84) Baseline 102 (36 to end of 6 weeks to 91 (32 Mean change from baseline -11 ( (AC & PP) (U) -23 (41.87) Assessed with mmol/l mmol/l Baseline 123 (68 to at end of 6 weeks 100 (45 Mean change from baseline -23 ( (AC & PP) (U) Table 3 reports baseline and 6 week post-treatment means and SDs, but no p- values or other statistics for calculating SDs of change from 0-6 weeks. Because we only have baseline and post-treatment means and SDs, Esther's spreadsheet was used for this calculation, using baseline and post-tx means and SDs from Table 3, and assuming correlation coefficient=0.08 Quote: "Serum lipids changed to a similar extent in both groups, due to initiation of statin treatment in most patients, and there was no decrease in blood pressure (data not shown)." Mean reduction from baseline Provided by Prof. Lindeberg in an e- mail 2015 Jun (0.80) (0.79) Prof Lindeberg 2015 Jun 27 "With regard to serum lipids, I still believe they are difficult to analyse with regard to initiated statin treatment, but here are the changes from baseline to 6 weeks (we

23 LINDEBERG 2007 don't have HDL):..."

24 MELLBERG 2014 DATA EXTRACTION FORM Name of study: MELLBERG 2014 Assessor Initials: EM + EvZ Methods Type of study (e.g., parallel RCT, cross-over RCT, cluster RCT): parallel RCT Dates of study (month/year start and end): "The subjects were recruited in " Duration of follow-up (randomization to end of follow-up): 2 years Setting (e.g., outpatient clinic, hospital), including # centers & city/country: "baseline tests [were given] at the Clinical Research Center at Umeå University Hospital, Umeå,..." and it is assumed the other aspects of this study (e.g., outcome tests, diet intervention group sessions) were also coordinated through this single center Participants Number of participants randomized: 70 Mean age (+/- SD or range) in each group and/or total (whichever reported): paleo: 59.5 (5.5); NNR: 60.3 (5.9) [from Table 1]; mean age for both groups combined not reported Men/Women (n/n): 0/70 Inclusion criteria: "...postmenopausal non-smoking women with a BMI > 27 kg/m2..." Exclusion criteria: "Exclusion criteria included consumption of a restricted or vegetarian diet, allergy to key components in the intervention diets, history of heart disease, kidney disease, hyperthyreosis or hypothyreosis, osteoporosis or diabetes. Other exclusion criteria were abnormal fasting plasma glucose levels ( > 7mmol/l), blood pressure exceeding 150/90mmHg, hormone replacement therapy, statins, beta-blockers or any medication for psychiatric disorders." Dropouts/Withdrawals (report details in RoB table): For the 6 month time point used for our meta-analysis there were a small number of withdrawals overall (9/70). The 9 withdrawals were not related to knowledge of treatment assignment or effects of the intervention, with one exception who dropped out from NNR group for the reason "disappointed with allocation", and therefore 8/9 of the dropouts would be considered data missing at random. Baseline data (report details in RoB table): No difference in baseline characteristics between the diet groups, with the exception of a baseline imbalance on HDL cholesterol, with higher HDL cholesterol in the paleo group (p=0.01). Spoke to Hanno, no clinically relevant. It is not reported how many variables were tested for baseline imbalance, and it is not clear whether this imbalance in HDL between groups is due to chance or instead indicates a problem with the design or implementation of the randomization. Interventions: dose/frequency/duration etc Timing of outcome assessments (e.g., 1 week, 1 month, end of study): 6, 12, 18, and 24 months; all outcomes except bodyweight and waist circumference were reported only at the 6 month and 24 month time points intervention: "The PD provided 30% of energy intake (E%) from protein, 40 E% fat and 30 E% carbohydrates and included a recommendation for a high intake of MUFA and polyunsaturated fatty acids (PUFA). The diet was based on lean meat, fish, eggs, vegetables, fruits, berries and nuts. Additional fat sources were avocado and oils (rapeseed and olive oil) used in food preparation and dressing. Dairy products, cereals, added salt and refined fats and sugar were excluded."

25 MELLBERG 2014 N allocated to paleo diet: 35 Duration of treatment (randomization to end of treatment): 2 years (the last group session was held at the 24 month time point), although our primary analysis time point is 6 months Duration of follow-up (randomization to end of follow-up): 2 years, although our primary analysis time point is 6 months Number of calories: Ad libitum consumption -- no restriction on caloric intake and no recommendations for daily caloric intake intervention: "The NNR diet was aiming at a daily intake of 15 E% protein, E% fat and E% carbohydrates, with emphasis on low fat dairy products and high-fibre products." N allocated to comparator diet: 35 Duration of treatment (randomization to end of treatment): 2 years (the last group session was held at the 24 month time point), although our primary analysis time point is 6 months Duration of follow-up (randomization to end of follow-up): 2 years, although our primary analysis time point is 6 months Number of calories: Ad libitum consumption -- no restriction on caloric intake and no recommendations for daily caloric intake Dietary advice or provision of foods: Dietary advice and cooking classes: "Each group took part in a total of 12 group sessions held by a trained study dietician (one dietician per diet) throughout the 24-month study period. The group sessions consisted of information on and cooking of the intervention diets, dietary effects on health, behavioral changes and group discussions. The subjects were given recipes and written instructions to facilitate the preparation of meals at home. Eight group sessions (four cooking classes and four follow-up sessions) were held during the first 6 months of the intervention. Additional group meetings were held at 9, 12, 18 and 24 months." Isocaloric throughout or energy content of diets individually adjusted to maintain stable bodyweight: No mention of caloric restriction -- ad libitum caloric consumption in both groups. Restriction vs no restriction of daily caloric intake: "Both diets were consumed ad libitum." Data also on (PMID, Clinical Trials.gov ID): PMID: Outcomes of the study 1) Change in fatmass over a period of 2 years measured by dual-energy X-ray absorptiometry. 2) Anthropometric measurements were made at baseline and after 6, 12, 18 and 24 months 3) The sagittal abdominal diameter 4) Systolic and diastolic blood pressure 5) Fasting blood samples plasma glucose, plasma insulin, serum cholesterol,triglycerides, high-density lipoprotein (HDL) cholesterol, tissue plasminogen activator activity, plasminogen activator inhibitor type 1 (PAI-1) activity and high-sensitivity C-reactive protein (hscrp). Serum low-density lipoprotein (LDL) was calculated as (serum cholesterol_serum HDL_serum triglycerides)/2.2. Outcome measures according to us, of our review (not from authors of study) Type of analysis follows "", in parentheses, with (ITT)=intention to treat; (PP)

26 MELLBERG 2014 = per protocol; (AC) = available case. For values used, (U)=unadjusted; (A)=adjusted. "mean reduction " values obtained by ing RCT authors are enclosed in brackets I. Primary outcome measures: j) Changes of each of the 5 component variables of the metabolic syndrome: 1) waist circumference, 2) triglycerides, 3) HDL-cholesterol, 4) blood pressure, and 5) fasting blood sugar k) Participant-assessed changes in quality of life l) Proportion of participants who reported an adverse event throughout the study period What were the results of these outcome measures? Waist circumference (Ia1) 34 (PP) (A) NNR diet 27 (PP) (A) Assessed with cm cm cm Comment Our outcome is change from baseline All estimated from figure 2 Waist circumference at baseline (N = 35) estimated form fig 2 = cm (SE = 1.67, then SD = 9.82) to 94 cm N =34 (SE 1.67, then SD = 9.68) Mean change would be ( (PP) (A) Triglycerides (Ia2) Assessed with mmol/l mmol/l Waist circumference at baseline (N = 35) estimated form fig 2 = 105 cm (SE = 1.67, then SD = 9.82) to 99 cm N =27 (SE 1.67, then SD = 8.63) Mean change would be ( (PP) (A) Mean reduction Triglycerides, as well as all other outcomes except waist circumference and body weight, were from Table 3. In Table 3, the SEs of the "Change 0-6 months" were converted to SDs before entering in (0.41) (0.36) ok

27 MELLBERG 2014 this table. HDL Cholesterol (Ia3) 34 (PP) (A) Assessed with mmol/l mmol/l 27 (PP) (A) Mean reduction (0.29) (0.21) ok Systolic blood pressure (Ia4) 34 (PP) (A) 27 (PP) (A) Assessed with mm Hg mm Hg Mean reduction (12.83) -8.5 (9.87) ok Diastolic blood pressure (Ia4*) 34 (PP) (A) 27 (PP) (A) Assessed with mm Hg mm Hg Mean reduction -6.6 (6.41) -5.0 (7.79) ok Fasting blood sugar (Ia5) 34 (PP) (A) 27 (PP) (A) Assessed with mmol/l mmol/l Mean reduction (0.87) (1.25) ok Health-related quality of life (Ib) Assessed with Not reported Not reported Mean reduction Not reported Not reported Adverse events (Ic) Report below the numbers of patients in each group who had adverse events. Treatment-related Not reported Not reported AE (proportion) All AE (proportion) Not reported Not reported II. Secondary outcome measures 1. Body weight 2. Fasting plasma levels of: l) IGF-1 m) uric acid n) C-reactive protein o) insulin p) total cholesterol Body weight (II- 1) 34 (PP) (A) 27 (PP) (A)

28 MELLBERG 2014 Assessed with kg kg Our outcome is Mean change from baseline, estimated from Fig 2 IGF-1 (II-2a) Weight at baseline kg (SE = 2, SD = 11.83) Weight at end of study N = 34 is 79 kg (SE 2, SD 11.66) Mean change = kg (7.43 Weight at baseline kg (SE = 2, SD = 11.83) Weight at end of study N = 27 is 84 kg (SE 2, SD 10.39) Mean change = (7.16 Assessed with Not reported Not reported Mean reduction Not reported Not reported Uric acid (II-2b) Assessed with Not reported Not reported Mean reduction Not reported Not reported C-reactive protein (II-2c) 34 (PP) (A) 27 (PP) (A) Assessed with mg/l mg/l

29 MELLBERG 2014 Mean reduction (1.17) (0.88) Insulin (II-2d) 34 (PP) (A) 27 (PP) (A) Assessed with mlu/l mlu/l Mean reduction (5.31) (4.73) In this trial, insulin was assessed using miu/l. For entering values into RevMan, mu/l values were converted to pmol/l, which is = the SI unit for this clinical lab data. Lindeberg 2007 and Jonsson 2009 assessed with pmol/l. The conversion factor is 1 miu/l = pmol/l ( Unitconvert/Insulin.php). Therefore, to convert to pmol/l, I multiplied the means and SDs of change by before entering in RevMan. Hanno confirmed the conversions used are correct. 34 (PP) (A) 27 (PP) (A) Total cholesterol (II-2e) Assessed with mmol/l mmol/l Mean reduction (0.76) (0.78)

30 Supplemental Table 2. Full details of the risk of bias assessment for each included RCT, on each criterion of the Cochrane Risk of Bias instrument BOERS 2014 Bias Random sequence generation (selection bias) Allocation concealment (selection bias) Authors' judgement Low risk Low risk Support for judgement Quote (page 4-5, 'Methods/Statistical methods'): "Subjects were stratified into two groups according to gender and subsequently randomized using separate randomization lists as generated by the Random Allocation Software Program employing a random block size of 6 to guarantee balanced allocation. The study monitor generated the random allocation sequence and assigned subjects to interventions." Comment: Probably done, judged as at low risk of bias. Quote (Page 4-5, 'Methods/Statistical methods'): "The study monitor generated the random allocation sequence and assigned subjects to interventions." Comment: The quote indicates that there was no allocation concealment because the same person (i.e., the "study monitor") had the joint role of generating the random allocation sequence and also assigning subjects to interventions. We judged this as at a high risk of bias. After communication: "The study monitor had no contact with the participants and no role in enrolment. And the investigators enrolling the participants had no role in the assignment and could therefor not foresee it." Comment: Probably done, judged as at low risk of bias. Baseline imbalance (selection bias) High risk Baseline imbalance as the "Other bias" Comment: The paleo group had a higher baseline BMI (33.7 versus 29.8, P = 0.01) (from Table 3) and a greater number of characteristics of the metabolic syndrome at baseline (3.7 versus 2.7, P = 0.02) (from Table 2). In addition, Table 2 shows

31 Supplemental Table 2. Full details of the risk of bias assessment for each included RCT BOERS 2014 Blinding of participants and personnel (performance bias) Blinding of outcome assessment (detection bias) Unclear risk Low risk that the paleo group also had a statistically significantly higher proportion of patients classified as having harmful HDL levels (P = 0.00) at baseline, and Table 3 shows that the paleo group had statistically significantly worse fasting glucose (P = 0.04) and bodyweight (P = 0.04) at baseline. The review authors judged this as at a high risk of bias. Quote (page 2, 'Methods/Study settings'): "It was not known to the subjects whether any of the diets would be superior to the other (single-blinded). After randomization, subjects of the different diet groups could not communicate with each other." Comment: Personnel were not blinded which might lead to performance bias, and the report did not provide sufficient detail about the specific measures used to blind participants from knowledge of which intervention a participant received, to permit a clear judgement. Quote (page 2, 'Methods/Study design'): "single-blinded" No mention of blinding of outcome assessors, and reported as "single-blinded" which suggests only the participants were 'blinded'. Incomplete outcome data (attrition bias) Low risk Comment: Because the outcomes are entirely objective and mostly lab measures, the review authors judge that the outcomes and the outcome measurements are not likely to be influenced by lack of blinding. Quote (page 5, 'Results/First paragraph') "Two subjects (2/16; 12.5%) dropped out from the reference group for personal reasons. There were only a few at random missing cortisol data,..." Comment: The review authors judged this as a low risk of bias because: 1) the small number of withdrawals; 2) no substantial differences in distribution of dropouts across treatment groups; 3) the dropouts were for "personal reasons" and therefore not related to knowledge of treatment assignment or effects of the treatment; 4) the degree of missing data would be unlikely to affect the estimate of