Biochemical HA T FT AD Iceland (1,2) Cohort IM Clinical HA. 10 follicles 2 10 mm or > 10 cc volume. > 63 ng/dl NA >3.8 ng/ml. menses/yr.

Transcription

1 Supplementary Table 1: Defining clinical, biochemical and ultrasound criteria of women with PCOS in contributing cohorts. Abbreviations: IM irregular menses; HA hyperandrogenism; PCOM polycystic ovary morphology; T testosterone; FT free testosterone; AD androstenedione; NA not available. To convert to SI units, multiply testosterone by and androstenedione by Cohort IM Clinical HA Biochemical HA T FT AD PCOM Iceland (1,2) < 9 menses/yr FG > 6 or acne > 63 ng/dl NA >3.8 ng/ml 10 follicles 2 10 mm or > 10 cc volume Boston (1,2) < 9 menses/yr FG > 9 or acne > 63 ng/dl NA >3.8 ng/ml 10 follicles 2 10 mm or > 10 cc volume Chicago (3) < 9 menses/yr FG 9 NA 21.8 pmol/l NA NA 1

2 Supplementary Table 2: Number of subjects with PCOS and controls who manifested one of the Rotterdam criteria for PCOS and the number who fulfilled the Rotterdam or NIH criteria for PCOS. Abbreviations: IM irregular menses; HA hyperandrogenism; PCOM polycystic ovary morphology; NA not available. Cohort Subject Group # IM # HA # PCOM # Rotterdam # NIH Iceland PCOS 404 1, Controls 1 NA NA NA NA NA Boston Chicago PCOS Controls PCOS NA Controls NA NA NA NA NA 1 Control subjects did not report features of PCOS and were not affected participants in the PCOS study. 2 A total of 332 controls had an ultrasound. 2

3 Supplementary Table 3. Odds ratios (OR) and P values for the association of PCOS with seven SNPs identified in a genome wide association study of Chinese women, with no adjustment and adjusted for BMI and age in Iceland and Boston sample sets combined using a Mantel Haenszel model. The association P values are two sided and adjusted for genomic controls in Iceland ( = 1.16). No adjustment SNP OR P OR P Adjusted for age and BMI rs rs rs rs rs rs rs The analysis of the Icelandic samples was restricted to the 13,585 out of 16,976 controls that had BMI available. All the 376 Icelandic PCOS cases had BMI information. 3

4 Supplementary Table 4. Hormone levels as a function of genotype at all seven PCOS risk variants, previously identified in Han Chinese women (5), in women of European ancestry in the combined sample sets from Iceland and Boston. Phenotype data from Chicago subjects was not available. Linear regression using an additive genetic model was used to test for association of PCOS risk variants with 22 log transformed quantitative traits in PCOS cases and controls. Results were adjusted for age and BMI (Boston) and age only (Iceland) and were meta analyzed using a fixed effects inverse variance model. Results are reported as P nominal values. rs was analyzed only in the Icelandic cohort. A p value < 3.2X10 4 was considered significant after Bonferroni correction for 22 traits and 7 SNPs and significant values are highlighted in bold. SNP Trait Effect/other allele N Beta SE P nominal Direction P heterogeneity rs Testosterone a/c E rs Testosterone a/c ? rs Testosterone t/c rs Testosterone a/g rs Testosterone a/g rs Testosterone a/g rs Testosterone t/g rs Androstenedione a/c rs Androstenedione a/c ? rs Androstenedione t/c rs Androstenedione a/g rs Androstenedione a/g rs Androstenedione a/g rs Androstenedione t/g rs DHEAS a/c rs DHEAS a/c ? rs DHEAS t/c rs DHEAS a/g rs DHEAS a/g rs DHEAS a/g

5 rs DHEAS t/g rs OH progesterone a/c rs OH progesterone a/c ? rs OH progesterone t/c rs OH progesterone a/g rs OH progesterone a/g rs OH progesterone a/g rs OH progesterone t/g rs Progesterone a/c rs Progesterone a/c ? rs Progesterone t/c rs Progesterone a/g rs Progesterone a/g rs Progesterone a/g rs Progesterone t/g rs SHBG a/c rs SHBG a/c ? rs SHBG t/c rs SHBG a/g rs SHBG a/g rs SHBG a/g rs SHBG t/g rs LH_FSH a/c rs LH_FSH a/c ? rs LH_FSH t/c rs LH_FSH a/g rs LH_FSH a/g rs LH_FSH a/g rs LH_FSH t/g rs FSH a/c rs FSH a/c ? rs FSH t/c

6 rs FSH a/g rs FSH a/g rs FSH a/g rs FSH t/g rs LH a/c rs LH a/c ? rs LH t/c rs LH a/g rs LH a/g rs LH a/g rs LH t/g rs Prolactin a/c rs Prolactin a/c ? rs Prolactin t/c rs Prolactin a/g rs Prolactin a/g rs Prolactin a/g rs Prolactin t/g rs Maximum Ovarian Volume a/c rs Maximum Ovarian Volume a/c ? rs Maximum Ovarian Volume t/c rs Maximum Ovarian Volume a/g rs Maximum Ovarian Volume a/g rs Maximum Ovarian Volume a/g rs Maximum Ovarian Volume t/g rs Maximum Follicle Number a/c rs Maximum Follicle Number a/c ? rs Maximum Follicle Number t/c rs Maximum Follicle Number a/g rs Maximum Follicle Number a/g rs Maximum Follicle Number a/g rs Maximum Follicle Number t/g

7 rs Maximum Waist Circumference a/c rs Maximum Waist Circumference a/c ? rs Maximum Waist Circumference t/c rs Maximum Waist Circumference a/g rs Maximum Waist Circumference a/g rs Maximum Waist Circumference a/g rs Maximum Waist Circumference t/g rs Maximum Hip Circumference a/c rs Maximum Hip Circumference a/c ? rs Maximum Hip Circumference t/c rs Maximum Hip Circumference a/g rs Maximum Hip Circumference a/g rs Maximum Hip Circumference a/g rs Maximum Hip Circumference t/g rs Waist/Hip Circumference a/c rs Waist/Hip Circumference a/c ? 1 rs Waist/Hip Circumference t/c rs Waist/Hip Circumference a/g rs Waist/Hip Circumference a/g rs Waist/Hip Circumference a/g rs Waist/Hip Circumference t/g rs Systolic Blood Pressure a/c rs Systolic Blood Pressure a/c ? rs Systolic Blood Pressure t/c rs Systolic Blood Pressure a/g rs Systolic Blood Pressure a/g

8 rs Systolic Blood Pressure a/g rs Systolic Blood Pressure t/g rs Diastolic Blood Pressure a/c rs Diastolic Blood Pressure a/c ? rs Diastolic Blood Pressure t/c rs Diastolic Blood Pressure a/g rs Diastolic Blood Pressure a/g rs Diastolic Blood Pressure a/g rs Diastolic Blood Pressure t/g rs Fasting Glucose a/c rs Fasting Glucose a/c ? rs Fasting Glucose t/c rs Fasting Glucose a/g rs Fasting Glucose a/g rs Fasting Glucose a/g rs Fasting Glucose t/g rs Fasting Insulin a/c rs Fasting Insulin a/c ? rs Fasting Insulin t/c rs Fasting Insulin a/g rs Fasting Insulin a/g rs Fasting Insulin a/g rs Fasting Insulin t/g ?+ rs HbA1C a/c rs HbA1C a/c ? rs HbA1C t/c rs HbA1C a/g rs HbA1C a/g rs HbA1C a/g rs HbA1C t/g rs Total Cholesterol a/c rs Total Cholesterol a/c ? 1 8

9 rs Total Cholesterol t/c rs Total Cholesterol a/g rs Total Cholesterol a/g rs Total Cholesterol a/g rs Total Cholesterol t/g rs LDL cholesterol a/c rs LDL cholesterol a/c ? rs LDL cholesterol t/c rs LDL cholesterol a/g rs LDL cholesterol a/g rs LDL cholesterol a/g rs LDL cholesterol t/g rs HDL cholesterol a/c rs HDL cholesterol a/c ? rs HDL cholesterol t/c rs HDL cholesterol a/g rs HDL cholesterol a/g rs HDL cholesterol a/g rs HDL cholesterol t/g rs Triglycerides a/c rs Triglycerides a/c ? rs Triglycerides t/c rs Triglycerides a/g rs Triglycerides a/g rs Triglycerides a/g rs Triglycerides t/g rs Total Cholesterol/HDL a/c rs Total Cholesterol/HDL a/c ? 1 rs Total Cholesterol/HDL t/c rs Total Cholesterol/HDL a/g rs Total Cholesterol/HDL a/g rs Total Cholesterol/HDL a/g

10 rs Total Cholesterol/HDL t/g

11 Supplementary Table 5. Power estimates for detecting association between seven PCOS risk variants, previously identified in Han Chinese women (5), in women of European ancestry in the combined sample sets from Iceland, Boston and Chicago. The power is calculated for the combined effective sample size of 1,349 cases and 1,349 controls, estimated as the sum of the geometric mean of the number of cases and controls for each sample set. The Icelandic effective sample size is further reduced by dividing it by a genomic control factor of 1.16 to adjust for the relatedness of cases and controls. Two sets of power estimates are presented, both assuming seven markers tested and a significance threshold of α = 0.05/ and the minor allele frequency observed in European populations. One set estimates the power assuming the effect estimates observed in the Chinese population (5); the other estimates the effect (OR) detectable with 90% power. SNP Locus OR in Chinese population Minor allele frequency in Europeans Power (α = 0.007) OR detectable with 90% power rs p % 1.57 rs p > 99% 1.25 rs p > 99% 1.37 rs p > 99% 1.24 rs q % 1.64 rs q % 1.57 rs q > 99%

12 Supplementary Table 6. Association with PCOS in the Icelandic samples at the three loci, a) 2p16, b) 2p21 and c) 9q33, for all markers identified in the October 2010 release of the 1000 Genome Project dataset (1GP)(4) and that have correlation r 2 > 0.5 in the 197 Han Chinese samples with any one of the seven reported PCOS risk variants (5). The association is tested using the SNPTEST program (6) and genotypes imputed into the Icelandic samples based on phased haplotypes for the 1094 individuals in the 1GP. Each table includes for each SNP its identifier and NCBI Build 37 position, the effect and non effect allele, the frequency in the Han Chinese (CHB and CHS) and European (CEU, GBR and TSI) samples from 1GP and in the Icelandic samples, and the estimated OR and P value. The tables also included, for each loci, the P value when the association is tested conditional on each of the reported risk variants, and the correlation (r 2 ) between the SNP and corresponding reported risk variant, estimated both for the Han Chinese and European 1GP samples, respectively. All reported P values have been adjusted using the genomic control factor of In each table results for the previously reported risk variants are highlighted in bold. a) 2p16 Allele Frequency Conditional on rs SNP Position Effect Other China Europe Iceland OR P Info China Europe r 2 r 2 P A G C T G T T C A G A C G A T C T A A C T C T C A G C T G A G T

13 rs A G C A T G G A G A A G G A T G T G T C T A T C C A A G C T G A C T G A rs C T G A T C T C G T

14 b) 2p21 Allele Frequency Conditional on Conditional on Conditional on rs rs rs SNP Position Effect Other China Europe Iceland OR P Info China Europe r 2 r 2 P China Europe r 2 r 2 P China Europe r 2 r 2 P A G T C G A rs G A rs A G A T rs C T G C G A C T G A rs G A G A G C rs A G rs G A C T G A T C G A C T G A C A G A C T C T C A C T G A

15 T C T C rs C A A G G A C G C T C T A T T C T C T C A G C T rs A C C T T C T C rs A G C T G A rs A G A C C A G C T C T A rs C T G C T G C G A G G A A G C T C G

16 T C A G C T A G T C rs C T T C G C G C C T T C T C T C C T A G G A C T T G G C G A C G T C A G G C T C C A A G G A T C A G C T T A rs T C G A A G T A

17 T C G T T C T C C T T G G A G A C T A G C A G A A T T C A G G A G C C T A G T C C G T C A T A C C T T C A G C T C T G C G A T A T G C T G A C T

18 C G G A rs C T T C A G T C A G T A C G A C T A T C A G A C T C C G C T A G C T C G rs C T G A T A A G C T C T A T T G C T C A A C C T T C G A A T rs C T

19 C G c) 9q33 Allele Frequency Conditional on Conditional on Conditional on rs rs rs SNP Position Effect Other China Europe Iceland OR P Info China Europe r 2 r 2 P China Europe r 2 r 2 P China Europe r 2 r 2 P A G A G T A T C C A T G G C A G G T A G C A G A C T A G C T C T T C G A C T T C T A G A C T C T G C T G C T G A C G

20 A G A C G T A G A G G C A G G A A C C T G A A C T C C T A C T G A T A G G A A G G A T C G T A G C T C G T A A T T A T A T C A C G A C A A G T C

21 A T A T rs C T C G A G C G A C G A T C C T C T C T rs G A T A T C A G C G G A T C C T T C T C rs A G T C C T T C C G A G A T A G G A rs G A C G G A C A T G

22 C T C G G A C G G A C T C T C A G A T C T A A T G A G T C T C A A G A G T C T C G A C T T C C T A G C T A G T C rs G A G A rs T C T C T C T A A G T C