Cancer Risks Associated with Germline Mutations in MLH1, MSH2, and MSH6 Genes in Lynch Syndrome

Supplementary Online Content

Bonadona V, Bonaïti B, Olschwang S, et al. Cancer Risks Associated With Germline Mutations in MLH1, MSH2, and MSH6 Genes in Lynch Syndrome. JAMA. 2011;305(22):2304-2310.

eTable 1. Description of the mutations detected in the 537 families of the study.

eTable 2. Characteristics of family members according to the mutated MMR gene and their cancer status

eTable 3. Number of family members (including index cases) participating to the likelihood for colorectal, endometrial and ovarian cancer risks estimation

eTable 4. Number of family members (including index cases) participating to the likelihood for cancer risks estimation of other HNPCC localizations

eTable 5. Published Studies of Penetrance in Lynch syndrome (from families with an identifed MMR gene mutation): methodological approach and cancer risks estimations (for colorectal and endometrial cancer).

Complementary Analysis Including the 502 Families With Clearly Pathogenic Mutations:

eTable 6. Age-specific cumulative risks of colorectal cancer (CRC), endometrial cancer (EC) and ovarian cancer (OC) according to gene for MMR mutation carriers (n=502)

eTable 7. Cumulative risks of other HNPCC localizations according to the mutated gene (n=502) This supplementary material has been provided by the authors to give readers additional information about their work.

Downloaded From: https://jamanetwork.com/ on 09/27/2021 eTable 1. Description of the mutations detected in the 537 families of the study

Gene Mutation Mutation type No. of pedigrees MLH1 1011dup Asn338GlnfsX24 Frameshift 1 MLH1 1023del Met342CysfsX25 Frameshift 1 MLH1 1085_1086delinsTTG Ser362PhefsX14 Frameshift 1 MLH1 1157_1158del Thr386ArgfsX8 Frameshift 1 MLH1 119del Gly40AlafsX24 Frameshift 1 MLH1 1333del Gln445ArgfsX46 Frameshift 2 MLH1 1348dup Asp450GlyfsX42 Frameshift 1 MLH1 1485dup Leu496IlefsX17 Frameshift 1 MLH1 1489del Arg497GlyfsX11 Frameshift 1 MLH1 1489dup Arg497ProfsX6 Frameshift 1 MLH1 1520_1521del Leu507X Frameshift 1 MLH1 1552del His518MetfsX17 Frameshift 1 MLH1 1597del 6533fsX534 Frameshift 1 MLH1 1690_1693del Leu564PhefsX26 Frameshift 1 MLH1 1717_1718del Val573SerfsX11 Frameshift 1 MLH1 1791del Trp597X Frameshift 1 MLH1 1857dup Glu620X Frameshift 1 MLH1 1877_1883del Phe626TrpfsX9 Frameshift 1 MLH1 1909del Ile637LeufsX6 Frameshift 1 MLH1 1946del Pro649LeufsX12 Frameshift 1 MLH1 1962dup Ile655TyrfsX9 Frameshift 2 MLH1 1978dup Ser627LeufsX5 Frameshift 1 MLH1 20_21del Val7AspfsX23 Frameshift 1 MLH1 2181_2182dup Ile728ThrfsX55 Frameshift 2 MLH1 2184del Leu729CysfsX54 Frameshift 1 MLH1 2191del Pro731LeufsX52 Frameshift 1 MLH1 22_23del Ile8SerfsX22 Frameshift 2 MLH1 2252_2253del Lys751SerfsX3 Frameshift 2 MLH1 277_278del Ser93TyrfsX9 Frameshift 1 MLH1 311del Leu104TrpfsX3 Frameshift 1 MLH1 37_38insCCCA Glu13AlafsX19 Frameshift 1 MLH1 378del Tyr126X Frameshift 1 MLH1 39del Thr14GlnfsX3 Frameshift 1 MLH1 493del Ala165LeufsX2 Frameshift 1 MLH1 503dup Asn168LysfsX4 Frameshift 3 MLH1 55_63delinsT Ile19TrpfsX9 Frameshift 1 MLH1 568del Ile190LeufsX12 Frameshift 1 © 2011 American Medical Association. All rights reserved.

Downloaded From: https://jamanetwork.com/ on 09/27/2021 Gene Mutation Mutation type No. of pedigrees MLH1 574_588+2del Phe192LysfsX29 Frameshift 1 MLH1 620del Leu207HisfsX22 Frameshift 1 MLH1 665del Asn222MetfsX7 Frameshift 1 MLH1 694_695insAGTC Gly232SerfsX4 Frameshift 1 MLH1 768del Cys256delfsX1 Frameshift 2 MLH1 882C>T His264LeufsX2 ou p ? Frameshift 2 MLH1 935_936insCG Glu313ValfsX55 Frameshift 1 MLH1 994del Ser332AlafsX35 Frameshift 1 MLH1 999del Lys333AsnfsX34 Frameshift 2 MLH1 1852_1854del Lys618del In frame small deletion - 30 deleterious MLH1 785_787del Ile262del In frame small deletion - 2 deleterious MLH1 1652_1654del Asn551del In frame small deletion - VUS 1 MLH1 2223_2231del Gln742_Ala744del In frame small deletion - VUS 2 MLH1 990_992del Ile330_Glu331delinsMet In frame small deletion - VUS 1 MLH1 complete deletion Large size rearrangement 2 MLH1 exon 10 deletion Large size rearrangement 1 MLH1 exon 18 deletion Large size rearrangement 1 MLH1 exon 4 deletion Large size rearrangement 1 MLH1 exon 6 deletion Large size rearrangement 1 MLH1 exons 10-11 deletion Large size rearrangement 1 MLH1 exons 12-19 deletion Large size rearrangement 1 MLH1 exons 2-6 deletion Large size rearrangement 2 MLH1 exons 6-8 duplication Large size rearrangement 2 MLH1 109G>A Glu37Lys missense - deleterious 2 MLH1 1919C>T Pro640Leu missense - VUS 2 MLH1 1989G>T Gly663Asp missense - deleterious 1 MLH1 199G>A Gly67Arg missense - deleterious 5 MLH1 199G>T Gly67Trp missense - deleterious 1 MLH1 2T>G Met1? missense - deleterious 1 MLH1 304G>A Glu102Lys missense - VUS 1 MLH1 350C>T Thr117Met missense - deleterious 6 MLH1 677G>A Arg226Gln missense - deleterious 6 MLH1 793C>T Arg265Cys missense - deleterious 1 MLH1 83C>T Pro28Leu missense - deleterious 1 MLH1 112A>G Asn38Asp missense - VUS 1 MLH1 1616C>A Ala539Asp missense - VUS 3 MLH1 1754T>G Leu585Arg missense - VUS 2 © 2011 American Medical Association. All rights reserved.

Downloaded From: https://jamanetwork.com/ on 09/27/2021 Gene Mutation Mutation type No. of pedigrees MLH1 2041G>A Ala681Thr missense - VUS 2 MLH1 731G>T Gly244Val missense - VUS 1 MLH1 86C>G Ala29Gly missense - VUS 1 MLH1 109G>T Glu37X Nonsense 1 MLH1 1144C>T Gln382X Nonsense 1 MLH1 1171C>T Gln391X Nonsense 3 MLH1 1408A>T Arg470X Nonsense 2 MLH1 1459C>T Arg487X Nonsense 7 MLH1 1528C>T Gln510X Nonsense 1 MLH1 1624C>T Gln542X Nonsense 3 MLH1 1672G>T Glu558X Nonsense 3 MLH1 1975C>T Arg659X Nonsense 4 MLH1 2052T>G Tyr684X Nonsense 1 MLH1 2136G>A Trp712X Nonsense 3 MLH1 298C>T Arg100X Nonsense 10 MLH1 37G>T Glu13X Nonsense 3 MLH1 397G>T Gly133X Nonsense 1 MLH1 445C>T Gln149X Nonsense 1 MLH1 497T>A Leu166X Nonsense 1 MLH1 586A>T Lys196X Nonsense 1 MLH1 676C>T Arg226X Nonsense 10 MLH1 753C>G Tyr251X Nonsense 1 MLH1 76C>T Gln26X Nonsense 1 MLH1 889G>T Glu297X Nonsense 1 MLH1 2141G>A Trp714X Nonsense 1 MLH1 1037A>G Spl Splice site 1 MLH1 1038+1G>C Spl Splice site 1 MLH1 1038G>T Spl Splice site 2 MLH1 1039-1G>T Spl Splice site 1 MLH1 1558+1G>T Spl Splice site 1 MLH1 1559-1G>T Spl Splice site 1 MLH1 1559-2A>G Spl Splice site 1 MLH1 1667+1G>T Spl Splice site 1 MLH1 1731G>A Spl Splice site 4 MLH1 1896+1G>T Spl Splice site 1 MLH1 1896G>T Spl Splice site 1 MLH1 207+2T>C Spl Splice site 1 MLH1 2103+1G>A Spl Splice site 1 MLH1 2103+3A>G Spl Splice site 1 © 2011 American Medical Association. All rights reserved.

Downloaded From: https://jamanetwork.com/ on 09/27/2021 Gene Mutation Mutation type No. of pedigrees MLH1 2211-1G>C Spl Splice site 1 MLH1 381-2A>G Spl Splice site 3 MLH1 544A>G Spl Splice site 2 MLH1 546-2A>G Spl Splice site 1 MLH1 588del Spl Splice site 5 MLH1 588dup Spl Splice site 1 MLH1 790+1G>A Spl Splice site 9 MLH1 790+2dup Spl Splice site 1 MLH1 790+3A>T Spl Splice site 1 MLH1 790+5G>T Spl Splice site 1 MLH1 791-2A>G Spl Splice site 1 MLH1 791-5T>G Spl Splice site 1 MLH1 881_884delinsCATTCCT Spl Splice site 1 MLH1 884+4A>G Spl Splice site 1 MSH2 1000_1001insTAA Lys334X Frameshift 1 MSH2 119del Gly40AlafsX24 Frameshift 1 MSH2 1222dup Tyr408LeufsX9 Frameshift 3 MSH2 135_136del His46ArgfsX35 Frameshift 1 MSH2 137dup His46GlnfsX35 Frameshift 1 MSH2 1413dup Pro472ThrfsX3 Frameshift 1 MSH2 1576del Thr526ProfsX17 Frameshift 1 MSH2 166del Glu56ArgfsX8 Frameshift 1 MSH2 1673del Ser558PhefsX2 Frameshift 1 MSH2 1676del Leu559X Frameshift 1 MSH2 1782dup Leu595ThrfsX3 Frameshift 1 MSH2 1783_1787del Leu595MetfsX4 Frameshift 4 MSH2 1897dup Ile633AsnfsX11 Frameshift 2 MSH2 1924_1428delinsTTTC Val642PhefsX43 Frameshift 2 MSH2 20del Glu7GlyfsX57 Frameshift 1 MSH2 2136dup Gly713ArgfsX4 Frameshift 2 MSH2 2166_2173del Ser723TyrfsX20 Frameshift 1 MSH2 2190del Glu731LysfsX14 Frameshift 1 MSH2 2239del Ile747X Frameshift 1 MSH2 229_230del Ser77CysfsX7 Frameshift 1 MSH2 2350_2351insG Phe784ValfsX3 Frameshift 1 MSH2 2361_2364dup Ala789TyrfsX11 Frameshift 1 MSH2 2432del Leu811X Frameshift 1 MSH2 2471_2484dup His829LysfsX16 Frameshift 1 MSH2 2472_2473delinsGAT Ser825MetfsX11 Frameshift 1 © 2011 American Medical Association. All rights reserved.

Downloaded From: https://jamanetwork.com/ on 09/27/2021 Gene Mutation Mutation type No. of pedigrees MSH2 2521del Ile841X Frameshift 2 MSH2 2558del Glu853GlyfsX39 Frameshift 1 MSH2 2595_2610dup Lys871HisfsX16 Frameshift 1 MSH2 2647dup Ile883AsnfsX16 Frameshift 3 MSH2 294_295del Tyr98X Frameshift 1 MSH2 347_350del Asp116GlyfsX57 Frameshift 1 MSH2 388_389del Gln130ValfsX2 Frameshift 4 MSH2 394dup Glu132GlyfsX7 Frameshift 1 MSH2 453_454del Lys151AsnfsX5 Frameshift 1 MSH2 454del Met152CysfsX22 Frameshift 1 MSH2 528_529del Cys176X Frameshift 1 MSH2 574_610del Ile192GlufsX10 Frameshift 1 MSH2 597del Ser233ProfsX13 Frameshift 1 MSH2 687del Ala230LeufsX16 Frameshift 2 MSH2 696_697del Ser233HisfsX22 Frameshift 1 MSH2 746del Lys249ArgfsX5 Frameshift 4 MSH2 804dup Ser269IlefsX10 Frameshift 1 MSH2 82del Glu28ArgfsX36 Frameshift 1 MSH2 839del Phe313PhefsX18 Frameshift 1 MSH2 839dup Leu280PhefsX3 Frameshift 1 MSH2 841del Ser281GlnfsX11 Frameshift 1 MSH2 847del Asp283IlefsX9 Frameshift 2 MSH2 873_876del Thr292LeufsX8 Frameshift 2 MSH2 939del Gln314ArgfsX17 Frameshift 1 MSH2 976_977del Leu326GlyfsX6 Frameshift 1 MSH2 281_282insTTT Val95delinsLeuVal In frame small deletion - 1 deleterious MSH2 1786_1788del Asn596del In frame small deletion - VUS 3 MSH2 2235_2237dup Ile747dup In frame small deletion - VUS 1 MSH2 complete deletion Large size rearrangement 3 MSH2 exon 1 deletion Large size rearrangement 1 MSH2 exon 15 duplication Large size rearrangement 1 MSH2 exon 3 deletion Large size rearrangement 5 MSH2 exon 4 deletion Large size rearrangement 2 MSH2 exon 5 deletion Large size rearrangement 1 MSH2 exon 7 deletion Large size rearrangement 1 MSH2 exon 7 duplication Large size rearrangement 1 MSH2 exon 8 deletion Large size rearrangement 3 MSH2 exon 8 duplication Large size rearrangement 1 © 2011 American Medical Association. All rights reserved.

Downloaded From: https://jamanetwork.com/ on 09/27/2021 Gene Mutation Mutation type No. of pedigrees MSH2 exons 11-14 deletion Large size rearrangement 1 MSH2 exons 1-15 deletion Large size rearrangement 1 MSH2 exons 1-2 deletion Large size rearrangement 8 MSH2 exons 12-13 deletion Large size rearrangement 2 MSH2 exons 1-4 deletion Large size rearrangement 1 MSH2 exons 1-5 deletion Large size rearrangement 2 MSH2 exons 1-6 deletion Large size rearrangement 1 MSH2 exons 1-7 deletion Large size rearrangement 2 MSH2 exons 1-8 deletion Large size rearrangement 1 MSH2 exons 2-5 deletion Large size rearrangement 1 MSH2 exons 2-7 deletion Large size rearrangement 1 MSH2 exons 3-10 deletion Large size rearrangement 1 MSH2 exons 3-11 deletion Large size rearrangement 1 MSH2 exons 3-8 deletion Large size rearrangement 1 MSH2 exons 4-6 duplication Large size rearrangement 1 MSH2 exons 9-10 deletion Large size rearrangement 2 MSH2 exons 9-16 deletion Large size rearrangement 1 MSH2 1022T>C Leu341Pro missense - deleterious 10 MSH2 1759G>C Gly587Arg missense - deleterious 1 MSH2 1906G>C Ala636Pro missense - deleterious 2 MSH2 2039G>C Arg680Pro missense - deleterious 1 MSH2 2089T>C Cys697Arg missense - deleterious 2 MSH2 2245G>A Glu749Lys missense - deleterious 1 MSH2 2651T>G Ile884Ser missense - VUS 2 MSH2 4G>A Ala2Thr missense - deleterious 3 MSH2 1168C>T Leu390Phe missense - VUS 1 MSH2 2558A>G Glu853Gly missense - VUS 1 MSH2 2635-8T>G p.? missense - VUS 1 MSH2 277C>T Leu93Phe missense - VUS 1 MSH2 560T>G Leu187Arg missense - VUS 2 MSH2 775C>T Pro259Ser missense - VUS 2 MSH2 998G>A Cys333Tyr missense - VUS 3 MSH2 1009C>T Gln337X Nonsense 1 MSH2 1012G>T Gly338X Nonsense 1 MSH2 1030C>T Gln344X Nonsense 3 MSH2 1069G>T Glu357X Nonsense 1 MSH2 1075A>T Arg359X Nonsense 1 MSH2 1147C>T Arg383X Nonsense 5 MSH2 1165C>T Arg389X Nonsense 4 © 2011 American Medical Association. All rights reserved.

Downloaded From: https://jamanetwork.com/ on 09/27/2021 Gene Mutation Mutation type No. of pedigrees MSH2 1216C>T Arg406X Nonsense 3 MSH2 1354G>T Glu452X Nonsense 1 MSH2 1447G>T Glu483X Nonsense 2 MSH2 1468A>T Lys490X Nonsense 3 MSH2 1633C>T Gln545X Nonsense 1 MSH2 166G>T Glu56X Nonsense 1 MSH2 1699A>T Lys567X Nonsense 1 MSH2 1710T>G Tyr570X Nonsense 1 MSH2 181C>T Glu61X Nonsense 2 MSH2 1861C>T Arg621X Nonsense 1 MSH2 1968C>G Tyr656X Nonsense 1 MSH2 1984C>T Gln662X Nonsense 1 MSH2 198C>G Tyr66X Nonsense 1 MSH2 2038C>T Arg680X Nonsense 4 MSH2 2092G>T Glu698X Nonsense 3 MSH2 2131C>T Arg711X Nonsense 1 MSH2 2152C>T Gln718X Nonsense 1 MSH2 2228C>A Ser743X Nonsense 1 MSH2 2231T>G Leu744X Nonsense 1 MSH2 226C>T Gln76X Nonsense 1 MSH2 2271C>G Tyr757X Nonsense 1 MSH2 2446C>T Gln816X Nonsense 1 MSH2 2554G>T Glu851X Nonsense 1 MSH2 2581C>T Gln861X Nonsense 1 MSH2 394G>T Glu132X Nonsense 1 MSH2 478C>T Gln160X Nonsense 1 MSH2 508C>T Gln190X Nonsense 1 MSH2 529G>T Glu177X Nonsense 4 MSH2 970C>T Gln324X Nonsense 2 MSH2 1076+1G>A Spl Splice site 1 MSH2 1276+2T>A Spl Splice site 2 MSH2 1277-2A>C Spl Splice site 1 MSH2 1386+1G>T Spl Splice site 3 MSH2 1661+1G>A Spl Splice site 2 MSH2 1661+1G>T Spl Splice site 1 MSH2 1662-2A>G Spl Splice site 1 MSH2 2005+1G>A Spl Splice site 2 MSH2 2005+1G>T Spl Splice site 1 MSH2 2005+2del Spl Splice site 2 © 2011 American Medical Association. All rights reserved.

Downloaded From: https://jamanetwork.com/ on 09/27/2021 Gene Mutation Mutation type No. of pedigrees MSH2 2633dup Spl Splice site 1 MSH2 2634+1G>A Spl Splice site 1 MSH2 2634+1G>T Spl Splice site 1 MSH2 2635-3C>A Spl Splice site 2 MSH2 646+1G>C Spl Splice site 1 MSH2 646-2A>G Spl Splice site 1 MSH2 793-2A>C Spl Splice site 1 MSH2 942+1A>C Spl Splice site 1 MSH2 942+2T>G Spl Splice site 1 MSH2 942+3A>T Spl Splice site 15 MSH6 1123dup Glu375GlyfsX7 Frameshift 2 MSH6 1596dup Ser532X Frameshift 1 MSH6 1738del Ser580ArgfsX6 Frameshift 1 MSH6 2062_2063del Val688LeufsX9 Frameshift 1 MSH6 2804_2805del Ser935X Frameshift 1 MSH6 311del Leu104TrpfsX3 Frameshift 1 MSH6 3261del Phe1088SerfsX2 Frameshift 2 MSH6 3261dup Phe1088LeufsX5 Frameshift 5 MSH6 3312dup Gly1105TrpfsX3 Frameshift 1 MSH6 3320del Asp1107ValfsX8 Frameshift 1 MSH6 3407del Asn1136IlefsX9 Frameshift 1 MSH6 3699_3702del Lys1233AsnfsX6 Frameshift 2 MSH6 388_389del Gln130ValfsX2 Frameshift 1 MSH6 3927_3938dup Glu1310_Ile1313dup Frameshift 1 MSH6 2234T>A Ile745Asn missense - VUS 1 MSH6 1453C>T Gln485X Nonsense 1 MSH6 1483C>T Arg495X Nonsense 1 MSH6 1835C>A Ser612X Nonsense 1 MSH6 212T>A Tyr709X Nonsense 1 MSH6 2764C>T Arg922X Nonsense 1 MSH6 2983C>G Tyr994X Nonsense 1 MSH6 3477C>A Tyr1159X Nonsense 1 MSH6 3991C>T Arg1331X Nonsense 1 MSH6 755C>A Ser252X Nonsense 1 MSH6 3802_3806del Spl Splice site 2

Downloaded From: https://jamanetwork.com/ on 09/27/2021 eTable 2. Characteristics of family members according to the mutated MMR gene and their cancer status Total MLH1 MSH2 MSH6 Number of informative participants (current age* (years): median, min-max) 10 283 4962 4630 691 (46, 1-108) (46, 1-100) (46, 1-108) (53, 6-100) Males 5164 2512 2307 345 Females (46, 1-100) (46, 1-99) (45, 1-108) (51, 17-95) 5119 2450 2323 346 (47, 1-100) (46, 1-100) (46, 1-99) (53, 6-100) Number of genotyped participants (% of total) 2 622 (25.5%) 1219 (24.6%) 1220 (26.3%) 183 (26.5%) Mutation carriers (% of genotyped individuals) 1 633 (62.3%) 761 (62.4%) 759 (62.2%) 113 (61.7%) Number of unaffected participants or participants with non-HNPCC cancer (% of total)# 8 496 (82.6%) 4077 (82.2%) 3826 (82.6%) 593 (85.8%) Genotyped Mutation carriers 1766 802 825 139 789 351 369 69 Number of participants with cancer of the HNPCC spectrum (% of total) 1787 (17.4%) 885 (17.8%) 804 (17.4%) 98 (14.2%) Genotyped Mutation carriers 856 417 395 44 844 410 390 44

* age at the inclusion in the study or if dead, age at death #with an average age at censoring of 45 years (range: 2-107)

Downloaded From: https://jamanetwork.com/ on 09/27/2021 eTable 3. Number of family members (including index cases) participating to the likelihood for colorectal, endometrial and ovarian cancer risks estimation (the numerator is the number of affected individuals within the given age class and the denominator is the number of individuals, not yet censored or not yet affected, in the middle of the age class) * CRC (number of affected individuals / number EC (number of affected individuals / number OC (number of affected individuals / number of individuals not yet censored or affected) of individuals not yet censored or affected) of individuals not yet censored or affected) Age, y All MLH1 MSH2 MSH6 All MLH1 MSH2 MSH6 All MLH1 MSH2 MSH6 carriers carriers carriers carriers carriers carriers carriers carriers carriers carriers carriers carriers 11-20 13 / 6468 8 / 3062 5 / 2979 0 / 427 0 / 3240 0 / 1496 0 / 1520 0 / 224 1 / 3240 0 / 1496 1 / 1520 0 / 224

21-30 125 / 73 / 2692 50 / 2622 2 / 406 2 / 2910 1 / 1332 1 / 1365 0 / 213 4 / 2909 0 / 1332 4 / 1364 0 / 213

5720

31-40 412 / 210 / 194 / 8 / 347 28 / 2383 11 / 1088 16 / 1108 1 / 187 19 / 2382 9 / 1087 9 / 1110 1 / 185

4440 2052 2041

41-50 474 / 243 / 211 / 20 / 263 66 / 1652 29 / 760 33 / 743 4 / 149 41 / 1683 15 / 774 22 / 762 4 / 147

2931 1351 1317

51-60 282 / 135 / 781 129 / 737 18 / 167 58 / 961 22 / 457 23 / 408 13 / 96 13 / 988 6 / 469 5 / 423 2 / 96

1685

61-70 118 / 884 60 / 421 43 / 368 15 / 95 11 / 543 4 / 265 6 / 222 1 / 56 0 / 561 0 / 273 0 / 232 0 / 56

71-80 35 / 440 23 / 205 8 / 186 4 / 49 5 / 279 3 / 127 0 / 118 2 / 34 0 / 288 0 / 131 0 / 123 0 / 34

*Warning: the simple ratio of the numerator divided by the denominator does not allow the calculation of cancer risks estimations (see statistical analysis)

Downloaded From: https://jamanetwork.com/ on 09/27/2021 eTable 4. Number of family members (including index cases) participating to the likelihood for cancer risks estimation of other HNPCC localizations (the numerator is the number of affected individuals within the given age class and the denominator is the number of individuals, not yet censored or not yet affected, in the middle of the age class) *

Stomach (number of affected Urothelium (number of affected Small bowel (number of affected Biliary tract (number of affected individuals / number of individuals / number of individuals / number of individuals / number of Age, y individuals not yet censored or individuals not yet censored or individuals not yet censored or individuals not yet censored or affected) affected) affected) affected) MLH1 MSH2 MSH6 MLH1 MSH2 MSH6 MLH1 MSH2 MSH6 MLH1 MSH2 MSH6 carriers carriers carriers carriers carriers carriers carriers carriers carriers carriers carriers carriers 11-20 0 / 3064 0 / 2979 0 / 428 0 / 3064 0 / 2979 0 / 428 0 / 3064 0 / 2979 0 / 428 0 / 3064 0 / 2979 0 / 428

21-30 1 / 2736 1 / 2665 0 / 408 0 / 2737 0 / 2665 1 / 408 0 / 2737 2 / 2665 0 / 408 0 / 2737 1 / 2665 0 / 408

31-40 5 / 2223 2 / 2181 0 / 353 1 / 2223 2 / 2181 0 / 352 7 / 2222 6 / 2177 0 / 353 1 / 2223 0 / 2180 0 / 353

41-50 9 / 1625 7 / 1562 1 / 285 0 / 1625 5 / 1560 0 / 285 8 / 1616 7 / 1557 0 / 285 2 / 1626 0 / 1563 0 / 285

51-60 9 / 1015 8 / 911 0 / 192 1 / 1018 20 /903 0 / 192 10 / 1006 10 / 901 0 / 192 1 / 1018 1 / 914 0 / 192

61-70 7 / 555 3 / 493 0 / 115 2 / 558 6 / 488 3 / 115 8 / 553 4 / 485 3 / 114 1 / 559 1 / 495 0 / 115

71-80 3 / 266 4 / 232 0 / 58 0 / 269 2 / 233 1 / 58 1 / 265 0 / 2979 0 / 57 0 / 270 0 / 235 0 / 58

*Warning: the simple ratio of the numerator divided by the denominator does not allow the calculation of cancer risks estimations (see statistical analysis)

Downloaded From: https://jamanetwork.com/ on 09/27/2021 eTable 5. Published studies of penetrance in Lynch syndrome (from families with an identified MMR gene mutation): methodological approach and cancer risks estimations (for CCR and CE)

Reference Nb of Country of Recruitment of Statistical Method Correction for Specific Studied 70 y cumulative 70 y cumulative families origin families selection bias data genes risk for CRC (IC risk for EC (IC censoring 95%) 95%) Dunlop 1997 6 Scotland Relatives of early- Survival analysis Yes --- MLH1 M: 74% (NA) 42% (NA) onset CRC cases (maximum likelihood MSH2 W: 30% (NA) (<35y) with MSI principle) with phenotype identified exclusion of index from population-based cases cancer registry Aarnio 1999 50 Finland Non-specified Cumulative incidence No --- MLH1 82% (NA) 60 % (NA) Members of HNPCC (person-years of MSH2 families with known follow-up) mutations Vasen 2001 79 The Dutch HNPCC Kaplan-Meier analysis No --- MLH1 MLH1: MLH1: Netherlands registry and Clinical MSH2 M: # 65% (NA) # 25% (NA) Norway Genetic Centre MSH6 W: # 54% (NA) MSH2: Radium Hospital (multiple-case MSH2: # 37% (NA) families) M: # 72% (NA) (from figure) W: # 54% (NA) (from figures) Green 2002 12 Canada Medical Genetics Kaplan-Meier analysis Inappropriate For CRC Founder M: 92% (NA) 79% (NA) (Newfoundla Clinic (multiple-case (exclusion of risk: age at MSH2 W: 64% (NA) nd) families) sibships in whom entry in mutation mutation status screening was known for colonoscopy <50% of siblings) program For EC risk: age at hysterectom y Hendriks 20 The The Netherlands Kaplan-Meier analysis No --- MSH6 M: 69% (42-83) 71% (50-83) 2004 Netherlands Foundation for the W: 30% (12-44) Norway Detection of Hereditary Tumors Italy and Clinical Genetics Departments (Multiple-case families) Plaschke 27 Germany German HNPCC Kaplan-Meier analysis No --- MSH6 Both sexes: # ND 2004 registry (multiple-case 80% (NA) (from families) figure) Hampel 70 Finland Multiple-case families Kaplan-Meier analysis Inappropriate --- MLH1 M: 69% (59-79) 54% (42-66) 2005 (n = 45) and (exclusion of the MSH2 W: 52% (38-67) © 2011 American Medical Association. All rights reserved.

Downloaded From: https://jamanetwork.com/ on 09/27/2021 Reference Nb of Country of Recruitment of Statistical Method Correction for Specific Studied 70 y cumulative 70 y cumulative families origin families selection bias data genes risk for CRC (IC risk for EC (IC censoring 95%) 95%) population-based probands) CCR with MSI phenotype (n = 25) Quehenberg 84 The Dutch HNPCC family Modified segregation Yes For CRC MLH1 M: 27% (13-51) 32% (11-70) er 2005 Netherlands registry (multiple-case analysis / conditioned risk: age at MSH2 W: 22% (11-44) families) likelihood on observed first phenotypes and on colonoscopy the event that at least one CRC, EC or MC case in the family was a carrier Jenkins 2006 17 Australia FD and SD relatives Modified segregation Yes For CRC MLH1 All genes: ND of early-onset CRC analysis / conditioned risk: age at MSH2 M: 45% (29-62) cases (<45y) likelihood on surgery for MSH6 W: 38% (19-51) unselected for family phenotype and polypectomy PMS2 MLH1/MSH2: history and mutated genotype of the For EC risk: for MMR genes proband age at M: 56% (37-75) hysterectom W: 48% (26-65) y Alarcon 2007 36 France Family cancer clinics Genotype restricted Yes --- MLH1 All genes: 14% (6-20) (multiple-case likelihood (conditioned MSH2 M: 47% (12-98) families) on all observed W: 33% (24-54) phenotypes and the genotype of index case) Barrow 121 UK (North Clinical Genetics Kaplan-Meier analysis Inappropriate --- MLH1 M: 54% (51-58) 28% (25-32) 2008, 2009 West of Service (multiple-case (exclusion of MSH2 W: 46% (43-50) England) families) index cases, MSH6 assignation of carrier status to untested unaffected FD relatives of proven carriers based on observed proportion in families) Baglietto 113 Australia Family cancer clinics Modified segregation Yes For CRC MSH6 M: 22% (14-32) 26% (18-36) 2009 United (n=65) and analysis / conditioned risk: age at W: 10% (5-17) States population-based likelihood on genotype polypectomy Canada cancer registries and phenotype of the For EC risk: (n=48) proband +/- age at The phenotype of all Netherlands hysterectom relatives (according y Scotland recruitment) New Zealand © 2011 American Medical Association. All rights reserved.

Stoffel 2009 147 United Cancer genetics Modified segregation Partly --- MLH1 All genes: All genes: States clinics (multiple-case analysis / conditioned MSH2 M: 66% (59-76) 39% (31-47) families) likelihood on genotype MSH6 W: 43% (37-53) MLH1: and phenotype of the proband and MLH1: 33% (NA) phenotype of FD M: 97% (NA) MSH2: relatives affected with W: 53% (NA) 45% (NA) CRC MSH2: M: 52% (NA) W: 40% (NA) In supplementary Yes --- MLH1 All genes: 38% (15-54) material: most MSH2 M: 34% (3-54) conservative form of MSH6 W: 32% (0-38) ascertainment correction: conditioning on proband’s genotype and phenotype and on the phenotypes of all relatives Choi 2009 32 Canada FD and SD relatives Modified segregation Partly --- MLH1 All genes: ND of incident CRC cases analysis / conditioned MSH2 M: 60% (35-73) identified from likelihood on MSH6 W: 47% (27-60) population-based phenotype of the cancer registry (cases proband and FD MLH1: without family history relatives M: 67% (27-89) of CRC excluded) and W: 35% (10-59) mutated for MMR MSH2: genes M: 55% (2-75) W: 53% (2-70)

CRC: colorectal cancer; EC: endometrial cancer; NA: Not Available; M: men; W: women; MC: cancer at minor HNPCC site (small bowel, stomach, ovary, urinary tract); FD: first degree; SD: second degree; ND: not done;

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Reference list of the studies listed in eTable 5: Dunlop MG, Farrington SM, Carothers AD et al: Cancer risk associated with germline DNA mismatch repair gene mutations. Hum Mol Genet. 1997;6(1):105-110. Aarnio M, Sankila R, Pukkala E et al: Cancer risk in mutation carriers of DNA-mismatch-repair genes. Int J Cancer. 1999;81(2):214-218. Vasen HF, Stormorken A, Menko FH et al: MSH2 mutation carriers are at higher risk of cancer than MLH1 mutation carriers: a study of hereditary nonpolyposis colorectal cancer families. J Clin Oncol. 2001;19(20):4074-4080. Green J, O'Driscoll M, Barnes A et al: Impact of gender and parent of origin on the phenotypic expression of hereditary nonpolyposis colorectal cancer in a large Newfoundland kindred with a common MSH2 mutation. Dis Colon Rectum. 2002;45(9):1223-1232. Hendriks YM, Wagner A, Morreau H et al: Cancer risk in hereditary nonpolyposis colorectal cancer due to MSH6 mutations: impact on counseling and surveillance. Gastroenterology. 2004;127(1):17-25. Plaschke J, Engel C, Kruger S et al: Lower incidence of colorectal cancer and later age of disease onset in 27 families with pathogenic MSH6 germline mutations compared with families with MLH1 or MSH2 mutations: the German Hereditary Nonpolyposis Colorectal Cancer Consortium. J Clin Oncol. 2004;22(22):4486-4494. Hampel H, Stephens JA, Pukkala E et al: Cancer risk in hereditary nonpolyposis colorectal cancer syndrome: later age of onset. Gastroenterology. 2005;129(2):415-421. Quehenberger F, Vasen HF, van Houwelingen HC: Risk of colorectal and endometrial cancer for carriers of mutations of the hMLH1 and hMSH2 gene: correction for ascertainment. J Med Genet. 2005;42(6):491-496. Jenkins MA, Baglietto L, Dowty JG et al: Cancer risks for mismatch repair gene mutation carriers: a population-based early onset case-family study. Clin Gastroenterol Hepatol. 2006;4(4):489-498. Alarcon F, Lasset C, Carayol J et al: Estimating cancer risk in HNPCC by the GRL method. Eur J Hum Genet. 2007;15(8):831-836. Barrow E, Alduaij W, Robinson L et al: Colorectal cancer in HNPCC: cumulative lifetime incidence, survival and tumour distribution. A report of 121 families with proven mutations. Clin Genet. 2008;74(3):233-242. Barrow E, Robinson L, Alduaij W et al: Cumulative lifetime incidence of extracolonic cancers in Lynch syndrome: a report of 121 families with proven mutations. Clin Genet. 2009;75(2):141-149. Baglietto L, Lindor NM, Dowty JG et al: Risks of Lynch syndrome cancers for MSH6 mutation carriers. J Natl Cancer Inst. 2010;102(3):193-201. Stoffel E, Mukherjee B, Raymond VM et al: Calculation of risk of colorectal and endometrial cancer among patients with Lynch syndrome. Gastroenterology. 2009;137(5):1621-1627. Choi YH, Cotterchio M, McKeown-Eyssen G et al: Penetrance of colorectal cancer among MLH1/MSH2 carriers participating in the colorectal cancer familial registry in Ontario. Hered Cancer Clin Pract. 2009;7(1):14

Downloaded From: https://jamanetwork.com/ on 09/27/2021 Complementary analysis including the 502 families with clearly pathogenic mutations.

eTable 6. Age-specific cumulative risks of colorectal cancer (CRC), endometrial cancer (EC) and ovarian cancer (OC) according to gene for MMR mutation carriers (n=502)

Cumulative risk of CRC, % (95% CI) Cumulative risk of EC, % (95% CI) Cumulative risk of OC, % (95% CI)

Age, All MLH1 MSH2 MSH6 All MLH1 MSH2 MSH6 All MLH1 MSH2 MSH6

20 0 (0-1) 0 (0-1) 0 (0-1) 0 (0-0) 0 (0-0) 0 (0-0) 0 (0-0) 0 (0-0) 0 (0-0) 0 (0-0) 0 (0-0) 0 (0-0)

30 2 (1-3) 1 (0-3) 2 (1-5) 0 (0-1) 0 (0-1) 0 (0-1) 0 (0-1) 0 (0-0) 0 (0-0) 0 (0-0) 0 (0-1) 0 (0-0)

40 6 (4-9) 7 (3-11) 9 (5-14) 1 (0-3) 2 (1-4) 1 (0-4) 2 (0-7) 1 (0-2) 1 (0-1) 0 (0-2) 1 (0-3) 0 (0-0)

50 14 (10-20) 19 (13-32) 21(14-31) 3 (2-6) 8 (4-15) 9 (3-19) 8 (3-21) 3 (1-8) 3 (1-5) 4 (0-11) 4 (1-9) 0 (0-1)

60 27 (20-38) 36 (22-55) 36 (23-54) 7 (5-13) 22 (12-38) 32 (12-55) 17 (8-52) 9 (5-19) 7 (2-21) 16 (1-45) 11 (2-28) 1 (0-2)

70 38 (28-52) 49 (33-78) 47 (29-76) 12 (8-22) 32 (16-58) 57 (23-83) 19 (8-76) 15 (8-31) 8 (2-37) 21 (1-65) 23 (3-52) 1 (0-3)

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eTable 7. Cumulative risks of other HNPCC localizations according to the mutated gene (n=502)

Cumulative cancer risk at 70 years, % (95% CI)

Localization MLH1 MSH2 MSH6 Total

Stomach 6% (0.2-17) 0.02% (0-10) 0 0.7% (0.08-4.4)

Urothelium 0.1% (0-2.6) 1.8% (0.6-8) 0.7% (0-2.1) 2.3 % (0.6-5.7)

Small bowel 0.3% (0.1-3) 1.0% (0-5) 0 0.6 % (0.1-1.3)

Biliary tract 2.0% (0-15) 0.05% (0-0.3) 0 0.6 % (0.07-2.5)

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