Supplementary Figure 1. A - MSH6 p.val282thrfs*10: Endome. Endome. Colon
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1 Supplementary Figure 1 - MSH6 p.val282hrfs*10: C C C C C 1
2 B - MSH6 p.phe1088leufs*5: Rectal Rectal Gastric C C C C C C Rectal C 2
3 C - MSH6 p.rg1172lysfs*5: Ovarian 3
4 D - MSH2 p.yr815*: Gastric Rectal Rectal Families with private mutations. he wild-type allele (black) and haplotype allele linked to the mutation (red) are shown. he genotyped individuals are shown with letters representing the hotspot. Black circles/squares represent cancer cases. Panel shows the family carrying MSH6 p.val282hrfs*10 (C), panel B the family carrying MSH6 p.phe1088leufs*5 (C), panel C the family carrying MSH6 p.rg1172lysfs*5 () and panel D the family carrying MSH2 p.yr815* (). 4
5 Supplementary able 1: Validation of imputation through direct genotyping of imputed heterozygous carriers and imputed wild type homozygotes PMS2 p.pro246cysfs*3 (Freq=0.234%) MSH6 p.leu585pro (Freq=0.08%) PMS2 p.met1? (Freq=0.092%) Imputation Imputation Imputation Direct genotyping wt het wt het wt het wt a 15, het b Freq=population-based carrier frequency; het=heterozygous; wt=wildtype. Counts correspond to individuals where direct genotyping was successful; genotyping success rate was 91% for PMS2 p.pro246cysfs*3, 92% for MSH6 p.leu585pro and 97% for PMS2 p.met1?. a Homozygous wild type carriers b Heterozygous carriers v
6 Supplementary able 2: Patient and tumor characteristics in Lynch syndrome cases Study ID ge, sex Location Histology, grade Stage bsent stains on IHC Germline mutation M R Mucinous, G NK I MLH1/PMS2 MLH1 translocation M R denocarcinoma, G2 IIIB MSH6 MSH6 p.val282hrfs* M L denocarcinoma, G3 IIIC MSH6 MSH6 p.phe1088leufs* M R denocarcinoma, G2 IIIB MSH6 MSH6 p.rg1172lysfs* M R Mucinous, G2 IV PMS2 PMS2 p.glu705lys M R denocarcinoma, G3 IV PMS2 PMS2 p.sn71spfs* F R denocarcinoma, G2 II MSH6 MSH6 p.leu585pro M L Mucinous, G2 II MSH6 MSH6 p.leu585pro M Rec Mucinous, G2 II MSH6 MSH6 p.leu585pro F L denocarcinoma, G3 II MSH6 MSH6 p.leu585pro M R denocarcinoma, G3 II MSH2/MSH6 MSH6 p.leu585pro M Rec denocarcinoma, G2 I Normal (MSH6 5%) MSH6 p.leu585pro 786* 63 M L Mucinous, G2 IIC Normal (MSH6 weak, 1-5%) MSH6 p.leu585pro 30* 57 M L Mucinous, G2 II Normal (MSH6 weak, 5%) MSH6 p.leu585pro 94* 72 F L denocarcinoma, G2 II Normal (MSH6 weak, 20-30%) MSH6 p.leu585pro F R denocarcinoma, G2 II MSH6/PMS2 PMS2 p.pro246cysfs* F Rec denocarcinoma, G2 I PMS2 Presumed PMS2 p.pro246cysfs* M L Mucinous, G NK IIB MSH2/6/PMS2 PMS2 p.pro246cysfs* M R denocarcinoma, G2 I PMS2 PMS2 p.pro246cysfs* M R denocarcinoma, G2 II PMS2 PMS2 p.pro246cysfs* M R denocarcinoma, G2 II PMS2 PMS2 p.pro246cysfs* M R denocarcinoma, G2 I PMS2 PMS2 p.pro246cysfs* M L denocarcinoma, G2 II PMS2 PMS2 p.pro246cysfs*3 6
7 M R denocarcinoma, G2 IIC PMS2 PMS2 p.pro246cysfs* M R denocarcinoma, G2 II PMS2 PMS2 p.pro246cysfs*3 1250* 59 M L denocarcinoma, G2 I Normal PMS2 p.pro246cysfs*3 873* 64 M Rec denocarcinoma, G2 II Normal PMS2 p.pro246cysfs*3 *hese cases had tumor sent for ColoSeq (Results in able 4). F=female; G=grade; IHC=immunohistochemistry; L=left; LS=Lynch syndrome; M=male, NK=not known; R=right; Rec=rectum 7
8 Supplementary able 3: Haplotype analysis in carriers of the PMS2 frameshift mutation rs rs rs rs rs Indel rs rs chr7: chr7: chr7: chr7: chr7: chr7: chr7: chr7: Carrier 1 C G G Yes C Carrier 2 C G G Yes C Carrier 3 C G G Yes C Carrier 4 C G G Yes C Carrier 5 C G G Yes C Carrier 6 C G G Yes C Carrier 7 C G G Yes C Carrier 8 C G G Yes C Carrier 9 C G G Yes C Carrier 10 C G G Yes C Carrier 11 C G G Yes C Carrier 12 C G G Yes C MF* C=3.39% =15.82% =31.16% =15.70% G= % C=15.75% =15.85% Hg38 location displayed. Haplotype obtained from Clendenning *Minor allelic frequency in the Icelandic population. 8
9 Supplementary able 4: Icelandic Lynch syndrome mutations and cancer risks Cancer type Odds ratio 95% CI p-value Cases Controls Info Bladder cancer x , MSH6 p.leu585pro Freq: 0.080% 1) Breast cancer x ,993 Esophageal cancer x ,517 Gallbladder/bile duct cancer x ,076 Gastric cancer x ,521 Liver cancer x ,484 Ovarian cancer x ,299 Pancreatic cancer x ,727 Prostate cancer x ,905 esticular cancer x ,991 Bladder cancer x , Breast cancer x ,993 Brain cancer (glioma) x ,789 PMS2 p.pro246cysfs*3 Freq: 0.234% 2) Esophageal cancer x ,517 Gallbladder/bile duct cancer x ,076 Gastric cancer x ,521 Liver cancer x ,484 Prostate cancer x ,905 esticular cancer x ,991 Bladder cancer x , PMS2 p.met1? Freq: 0.092% 3) Brain cancer (glioma) x ,789 Breast cancer x ,993 9
10 Gallbladder/bile duct cancer > x ,076 Gastric cancer x ,521 Liver cancer x ,484 Pancreatic cancer x ,727 Prostate cancer x ,905 esticular cancer x ,991 CI=confidence interval; Freq=frequency; LS=Lynch syndrome. Info represents the imputation quality of the variant. p-values were obtained by logistic regression analysis. 1) No association seen with adrenal gland, renal pelvis or ureteral cancer. 2) No association seen with adrenal gland, renal pelvis, ureteral and pancreatic cancer. 3) No association seen with adrenal gland, esophageal, renal pelvis and ureteral cancer. In total 16 cancers were tested for each of the mutations. Significant p-value < 3.13x10-3 to correct for multiple tests. 10
11 Supplementary able 5: Primer sequences used for Sanger sequencing of individual variants Gene Protein change Hg38 location Forward Reverse MSH2 p.yr815* chr2: CGCCGGCCCG GGCCGGC MSH6 p.val282hrfs*10 chr2: GCGGGGCCGG CCCGCCGGCC MSH6 p.leu585pro chr2: GGCGCCGCGG GCCGGGCGCCCC MSH6 p.phe1088leufs*5 chr2: GCGCCCCCCG GCCCCGCCC MSH6 p.rg1172lysfs*5 chr2: GCCCGCCCGCCC CGCGGGCCCGC PMS2 Glu705Lys chr7: GGGGGCGGGGC GGCCGGGCCG PMS2 p.pro246cysfs*3 chr7: GGCGGCCG CGGCGCCCC PMS2 p.sn71spfs*4 chr7: CCCGGCCGC GGCGGGCCG PMS2 p.met1? chr7: GCCGGGGCCGG GGGGGCCCCGCC 11
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