Journal List > Lab Med Online > v.8(4) > 1108547

Park, Chang, Kim, and Kim: Germline Variants in MLH1, MSH2, and MSH6 in Korean Patients with Lynch Syndrome

Abstract

Background:

The phenotypic and genetic spectrum of Lynch syndrome (LS) seems to differ according to ethnicity. The aim of this study was to investigate the clinical, pathological, and genetic features of LS in a large sample of Korean patients.

Methods:

We enrolled a total of 232 patients who fulfilled the revised Bethesda criteria (81%, 232/286) from 286 individuals who underwent genetic screening for LS (MLH1, MSH2, and MSH6 sequencing) in the Samsung Medical Center in Korea from 2004 to 2015. Histopathologic findings, microsatellite instability data, and clinical information were collected.

Results:

We identified 61 different pathogenic or likely pathogenic variants (39 in MLH1, 20 in MSH2, and 2 in MSH6), including 4 novel variants, in 101 unrelated Korean patients (101/232, 44%). When multiple tumor manifestations in a single patient were individually considered, there were 285 cancers recorded from 232 cases. A diverse spectrum of tumors, including colorectal cancer, endometrial cancer, stomach cancer, and ovary cancer, was observed. Patients with genetic alterations were more closely associated with a family history of cancers, double primary cancers, and the development of secondary neoplasms than patients without genetic alterations (P<0.0001, P=0.0052, and P=0.0010, respectively).

Conclusions:

We report the distribution of pathogenic variants in MLH1, MSH2, and MSH6, as well as the tumor spectrum, in a large sample of Korean patients with LS. Genetic testing could be an effective stratification strategy for surveillance of LS. This study sheds light on the genetic features of Asian patients with LS

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Table 1.
Baseline characteristics of the study patients
Characteristics Number/total number (%)
No. of patients 232
Male: Female 116:82
Age at onset of first cancer, median (range) 43 (16–82) year
First tumor manifestations  
 Colonic 211/232 (91)
 Extracolonic 21/232 (9)
Total tumor history  
 Colonic 174/232 (75)
 Extracolonic 15/232 (6)
 Both 43/232 (19)
Double primary cancer manifestations 14/232 (6)
Family history of cancers  
 Colonic 69/164 (42)
 Extracolonic 37/164 (23)
 Both 58/164 (35)
Secondary tumor occurrence 37/232 (16)
Immunohistochemistry  
 MLH1 loss 92/168 (55)
 MSH2 loss 47/168 (28)
 MSH6 loss 53/168 (32)
Microsatellite instability  
 High 162/187 (87)
 Stable 25/187 (13)

For the tumor spectrum, multiple tumor manifestations in a single patient were individually considered. ∗Endometrial cancer (N=27), stomach cancer (N=13), ovary cancer (N=7), bladder cancer (N=4), small intestinal cancer (N=4), cervical cancer (N=3), breast cancer (N=3), glioblastoma (N=2), lung cancer (N=2), esophageal cancer (N=1), pheochromocytoma (N=1), and skin cancer (N=1);

The tumor spectrum of family members from 164 cases was as follows: CRC (N=240), stomach cancer (N=28), hepatobiliary cancer (N=22), EC (N=18), lung cancer (N=10), pancreatic cancer (N=7), urinary cancer (N=5), ovary cancer (N=5), breast cancer (N=4), skin cancer (N=2), hematologic cancer (N=2), thyroid cancer (N=2), cervical cancer (N=2), brain cancer (N=1), prostate cancer (N=1), small intestinal cancer (N=1), and pharyngeal cancer (N=1);

Immunohistochemistry and the microsatellite instability assessments were described as the number/total number available.

Table 2.
Pathogenic or likely pathogenic variants identified in Korean patients with Lynch syndrome
Genes NT alterations AA alterations Type N. of probands dbSNP HGMD InSiGHT Clinvar Status§ ACMG-AMP criteria Pathogenicity
MLH1 c.1758dupC p.(Met587Hisfs6) frameshift 15 NA DM Class 5 Pathogenic Known PVS1, PM2, PP1, PS3 P
c.67G> T p.Glu23 nonsense 4 rs63750823 DM Class 5 Pathogenic Known PVS1, PS3, PM2, PP1, PP3 P
c.1918C> T p.Pro640Ser missense 3 rs63749792 DM Class 3 Uncertain significance e Known PM2, PP3, PP1, PP5 LP
c.303_304dupTG p.(Glu102Valfs7) frameshift 3 NA DM NA NA Known PVS1, PM2, PP5 P
c.808_811delACTT p.(Thr270Profs2) frameshift 2 rs267607801 DM Class 5 Pathogenic Known PVS1, PM2, PP5 P
c.440_441insT p.(Thr148Aspfs24) frameshift 2 NA DM NA NA Known PVS1, PM2, PP5 P
c.1975C> T p.(Arg659) nonsense 2 rs63751310 DM Class 5 Pathogenic Known PVS1, PS3, PM2, PP1, PP5 LP
c.1449_1471dup23 p.(Thr491Lysfs8) frameshift 2 NA DM NA NA Known PVS1, PM2, PP5 LP
c.677G> A p.Gln197Argfs8 frameshift ll 2 rs63751711 DM Class 5 Pathogenic Known PVS1, PS3, PM2, PP1, PP3, PP5 P
c.1721T> C p.(Leu574Pro) missense 2 rs63751608 DM Class 4 Likely pathogenic Known PM2, PS3, PP1, PP3, PP5 P
c.884+2dupT NA splicing 2 NA DM NA NA Novel PVS1, PM2 LP
c.678-1G> C p.(Glu227Thrfs7) splicing 2 rs267607784 DM Class 5 Pathogenic Known PVS1, PS3, PM2, PP1 P
c.849T> A p.(Tyr283) nonsense 1 NA NA NA NA Novel PVS1, PM2 LP
c.346dupA p.(Thr116Asnfs6) frameshift 1 rs267607739 DM Class 5 Pathogenic Known PVS1, PM2, PP5 P
c.1984A> C p.Thr662Pro missense 1 NA DM Class 4 Likely pathogenic Known PM2, PS3, PP1, PP3, PP5 LP
c.1668-2A> G NA splicing 1 NA DM NA NA Known PVS1, PM2, PP5 P
c.2104-2A> G NA splicing 1 rs267607889 DM Class 4 Likely pathogenic Known PVS1, PM2, PS3, PP1, PP5 P
c.887dupT p.(Leu296Phefs11) frameshift 1 rs63751620 DM Class 5 NA Known PVS1, PM2, PP5 P
c.791-1G> C p.(His264Leufs2) splicing 1 rs267607795 DM Class 5 Pathogenic Known PVS1, PS3, PM2, PP1 P
c.350C> T p.Thr117Met missense 1 rs63750781 DM Class 5 Pathogenic Known PM2, PS3, PP1, PP3, PP5 LP
c.210_213delAGAA p.(Glu71Ilefs20) frameshift 1 rs267607723 NA Class 5 Pathogenic Known PVS1, PS3, PM2, PP5 P
c.189C> A p.(Asp63Glu) missense 1 NA DM Class 5 Pathogenic Known PM2, PS3, PP1, PP3, PP5 LP
c.2041G> A p.Ala681Thr missense 1 rs63750217 DM Class 5 Pathogenic Known PM2, PS3, PP1, PP3, PP5 LP
c.1333C> T p.(Gln445) nonsense 1 NA NA NA NA Known∗∗ PVS1, PM2 LP
c.2080G> T p.(Glu694) nonsense 1 rs147542208 DM NA NA Known PVS1, PM2, PP5 LP
c.1011dupC p.Asn338Glnfs24 frameshift 1 rs63750677 DM Class 5 NA Known PVS1, PS3, PM2, PP1, PP5 P
c.2142G> A p.(Trp714) nonsense 1 rs63750978 DM NA Pathogenic Known PVS1, PM2, PP5 LP
c.1349delA p.(Asp450Valfs41) frameshift 1 NA DM NA NA Known PVS1, PM2, PP5 LP
c.1758delC p.(Met587Cysfs4) frameshift 1 rs63749863 DM Class 5 NA Known PVS1, PM2, PP5 LP
c.1553_1558+4del10 p.(His518Argfs48) frameshift 1 NA DM NA NA Known PVS1, PM2, PP5 LP
c.503delA p.(Asn168Ilefs34) frameshift 1 NA DM NA NA Known PVS1, PM2, PP5 LP
c.1559-1G> A NA splicing 1 rs267607837 DM Class 4 Pathogenic Known PVS1, PS3, PM2 LP
c.1758dupC p.(Met587Hisfs6) frameshift 1 rs367543283 DM NA NA Known PVS1, PM2, PP5 LP
c.199G> A p.Gly67Arg missense 1 rs63750206 DM Class 5 Pathogenic Known PS3, PM2, PP5, PP1, PP3 LP
c.1546C> T p.(Gln516) nonsense 1 NA DM NA NA Known PVS1, PM2, PP5 LP
c.2181_2182delCA p.(Ile728Serfs4) frameshift 1 NA DM Class 5 NA Known PVS1, PM2, PP5 LP
c.1668-1G> C NA splicing 1 NA DM? NA Likely pathogenic Known PVS1, PM2, PP5 LP
c.790+1G> A p.Glu227_Ser295del splicing 1 rs267607789 DM Class 5 Pathogenic Known PVS1, PS3, PM2, PP5 P
c.19delG p.(Val7Leufs10) frameshift 1 NA DM NA NA Known PVS1, PM2, PP5 LP
MSH2 c.942+3A> T p.Val265_Gln314del splicing 7 rs193922376 DM Class 5 Pathogenic Known PVS1, PS3, PM2, PP1, PP5 P
c.1024delinsAA p.(Val342Asnfs2) frameshift 3 NA DM NA NA Known PVS1, PM2, PP5 P
c.187delG p.(Val63) nonsense 2 rs63750160 DM Class 5 Pathogenic Known PVS1, PM2, PP5 P
c.2038C> T p.Arg680 nonsense 2 rs63749932 DM Class 5 Pathogenic Known PVS1, PS3, PM2, PP1, PP5 P
c.2633_2634delAG p.Glu878Alafs3 frameshift 2 rs63751618 DM Class 5 Pathogenic Known PVS1, PS3, PM2, PP1 P
c.387_388delTC p.(Gln130Valfs2) frameshift 2 rs63750924 DM Class 5 Pathogenic Known PVS1, PM2, PP5 P
c.2089T> C p.Cys697Arg missense 1 rs63750961 DM Class 5 Pathogenic Known PS3, PM2, PP1, PP3, PP5 LP
c.1465G> T p.(Glu489) nonsense 1 NA DM NA NA Known PVS1, PM2, PP1 LP
c.1129C> T p.(Gln377) nonsense 1 rs63750267 DM Class 5 Pathogenic Known PVS1, PM2 LP
c.1552_1553delCA p.Gln518Valfs10 frameshift 1 rs63749930 DM Class 5 Pathogenic Known PVS1, PS3, PM2, PP1, PP5 P
c.1366dupA p.(Thr456Asnfs12) frameshift 1 NA NA NA Pathogenic Known PVS1, PM2 LP
c.1782_1783delAC p.(Leu595Glnfs2) frameshift 1 NA NA NA NA Novel PVS1, PM2 LP
c.1226_1227delAG p.Gln409Argfs7 frameshift 1 rs63750086 DM Class 5 Pathogenic Known PVS1, PS3, PM2, PP1, PP5 P
c.1861C> T p.(Arg621) nonsense 1 rs63750508 DM Class 5 Pathogenic Known PVS1, PM2, PP5 LP
c.1127dupT p.(Leu376Phefs13) frameshift 1 NA DM NA NA Known PVS1, PM2, PP5 P
c.2634+1G> A p.(Gly820Alafs3) splicing 1 rs267608019 DM Class 4 Pathogenic Known PVS1, PS3, PM2, PP1 P
c.881_882del p.(Phe294) frameshift 1 NA NA Class 5 NA Known PVS1, PM2, PP5 LP
c.256G> T p.(Glu86) nonsense 1 NA NA NA NA Novel PVS1, PM2 LP
c.2186_2187insAATG p.(Met729Ilefs22) frameshift 1 NA DM NA NA Known PVS1, PM2, PP5 LP
c.1705_1706delGA p.(Glu569Ilefs2) frameshift 1 rs63750393 DM Class 5 Pathogenic Known PVS1, PM2, PP5 P
MSH6 c.3261dupC p.(Phe1088Leufs5) frameshift 1 rs267608087 DM Class 5 Pathogenic Known PVS1, PM2, PP5 LP
c.873_874delCA p.(Asn291Lysfs20) frameshift 1 rs1060502888 NA NA Pathogenic Known PVS1, PM2, PP5 LP

Abbreviations: NT, nucleotide; AA, amino acid; dbSNP, database of single nucleotide polymorphisms, v150; HGMD, human gene mutation database (professional version, updated in March 2017); InSiGHT, International Society of Gastrointestinal Hereditary Tumors (updated in August 2017 and accessed on January, 2018); ACMG, American College of Medical Genetics and Genomics; DM, disease-causing mutation; NA, not applicable; P, pathogenic; LP, likely pathogenic.

MLH1 (NM_000249.2), MSH2 (NM_000251.1), and MSH6 (NM_000179.2);

Alterations at the amino acid level were deduced from nucleotide alterations in the case of experimental evidence and were filled based on predicted protein sequences in parentheses; Allele frequency of SNPs: rs147542208 (0.000200000 from 1000GP, 0.00002486 from ExAC, 0.000909091 from KRGDB databases), rs63749932 (0.000008244 from ExAC), rs267608087 (0.000057680 from ExAC); § The status of variants was evaluated based on the curated data from InSiGHT, HGMD, and ClinVar (accessed in January 2018) databases; The criteria were applied as follows: PVS1 (nonsense variants, splicing variants and frameshift variants), PS3 (functional evidences by splicing/transcript expression, MMR activity, sub-cellular localization, subunit interaction, protein expression, and stability data from the curated data in In-SiGHT, available at http://insight-group.org/variants/database/ accessed on January, 2018), PM2 (allele frequency less than 0.01 or absent from the databases including the 1000 Genomes Project, Exome Sequencing Project, Exome Aggregation Consortium, or the Korean Reference Genome Database, available at 1000GP, http://browser.1000genomes.org/index.html, http://evs.gs.washington.edu/EVS/, http://exac.broadinstitute.org/, http://152.99.75.168/ KRGDB/, respectively), PP1 (co-segregation data from the curated data in InSiGHT), PP3 (evidence supporting “deleterious” or “damaging” effects was higher than 3 using the in silico tools: functional effects of missense variants were predicted by sorting intolerant from tolerant (SIFT), polymorphism phenotyping-2 (PolyPhen), LRT, FATHMM, MutationTaster, MutationAssesor, and Genomic Evolutionary Rate Profiling (GERP) score), PP5 (a “disease-causing mutation” in the human gene mutation database (HGMD professional, updated on March, 2017, a “pathogenic” mutation in ClinVar (available at http://www.ncbi.nlm.nih.gov/clinvar/ accessed on January, 2018), a “class 4 or class 5 in InSiGHT and Leiden Open Variation Database (LOVD v3.0 Build 19 http://www.lovd.nl/3.0/home), or variants reported from previous studies) [18, 24, 29-31]; ll This pathogenic variant (c.677G> A) is predicted to be a nucleotide substitution at the coding DNA level. However, protein and RNA-based functional studies have consistently found that this variant results in the skipping of exon 8. This variant was classified as a frameshift variant [26-28];

∗∗ This variant (c.1333C> T) was reported in the previous study [35].

Table 3.
Detection rate and distribution of the genetic alterations in mismatch repair genes according to ethnicity
Ethnicity Genetic test Criteria Detection of genetic alterations (%) No. of patients with genetic alterations References
MLH1 MSH2 MSH6 PMS2
Israeli Sequencing, MLPA Genetic diagnosis of LS NA 19/113 (17%) 67/113 (59%) 20/113 (18%) NA [14]
Hungarian Heteroduplex & SSCP, Sequencing, MLPA Amsterdam I-II (n=20) Pedigree suggestive of LS (n=16) 18/36 (50.0) 9/18 (50%) 9/18 (50%) NA NA [13]
Brazilian Sequencing, MLPA Clinical suspicion for LS 45/116 (38.8) 15/45 (33%) 25/45 (56%) 4/45 (9%) 1/45 (2%) [12]
Dutch DGGE, SSCP, Sequencing, Suspected for LS: Amsterdam criteria (n=42) 47/184 (25.5) 28/47 (60%) 19/47 (40%) NA NA [11]
German DHPLC, Sequencing, Southern blot, MLPA Amsterdam criteria 281/574 (49.0) 124/281 (44%) 157/281 (56%) NA NA [10]
Cypriot Sequencing, MLPA Revised Bethesda guideline, Amsterdam criteria 5/77 (6.5) 4/5 (80%) 1/5 (20%) 0 NA [9]
Singapore Sequencing, MLPA Singapore Polyposis Registry 17/59 (28.8) 11/17 (65%) 6/17 (35%) 0 0 [8]
Korean PCR-SSCP Korean Hereditary Tumor Registry 44/164 (26.8) 31/44 (70%) 10/44 (23%) 3/44 (7%) NA [15]
Korean Sequencing Revised Bethesda guideline 101/232 (44.0) 67/101 (66%) 32/101 (32%) 2/101 (2%) NA This study

Abbreviations: MLPA, multiplex ligation-dependent probe amplification; LS, Lynch syndrome; SSCP, single strand conformation polymorphism; DGGE, denaturing gradient gel electrophoresis; DHPLC, denaturing high perfor-mance liquid chromatography; NA, not applicable.

Table 4.
Allele frequency data and in silico analyses of pathogenic or likely pathogenic missense variants
Genes NT alterations AA alterations dbSNP 1000GP ESP6500 ExAC KRGDB SIFT Polyphen2 LRT Mutation Taster Mutation Assessor FATHMM GERP
MLH1 c.1918C> T p.Pro640Ser rs63749792 A A A A D D D D H D 5.81
c.1721T> C p.(Leu574Pro) rs63751608 A A A A D P D D M D 5.44
c.1984A> C p.Thr662Pro NA A A A A T D D D L D 5.49
c.350C> T p.Thr117Met rs63750781 A A A A D D D D H T 5.11
c.189C> A p.(Asp63Glu) NA A A A A D D D D H D 4.98
c.2041G> A p.Ala681Thr rs63750217 A A A A D D D D M D 5.93
c.199G> A p.Gly67Arg rs63750206 A A A A D D D D H D 5.85
MSH2 c.2089T> C p.Cys697Arg rs63750961 A A A A D D D D H D 6.08

Abbreviations: NT, nucleotide; AA, amino acid; 1000GP, 1000 Genomes Project; ESP, Exome Sequencing Project; ExAC, Exome Aggregation Consortium; KRGDB, Korean Reference Genome Database; SIFT, sorting intolerant from tolerant; PolyPhen, polymorphism phenotyping-2; GERP, Genomic Evolutionary Rate Profiling; A, Absent; D, damaging (in PolyPhen)/deleterious (in SIFT, LRT, and FATHMM)/disease-causing (in MutationTaster); P, possibly or probably damaging (in PolyPhen); H, high (functional); M, medium (functional); N, neutral (nonfunctional); L, low(nonfunctional); T, tolerated (in SIFT and FATHMM).

Table 5.
Comparisons of the clinicopathologic and molecular characteristics according to the status of the pathogenic variants
Characteristics Positive for genetic alterations (N=99) Negative for genetic alterations P value
MLH1 MSH2 Positive (N=99) MLH1 alterations (N=67) vs. MSH2 alterations
(N=67) (N=32) (N=131) vs. Negative (N=131) vs. MSH2 alterations (N=32)
Age at onset, median (range) 43 (24–72) 42 (30–81) 43 (16–82) 0.6110 0.8413
Male: Female, Number 36:31 18:14 70:60 0.8620 1.0000
Tumor spectrum       0.0109 0.0840
 Colonic 46/67 (69%) 23/32 (72%) 103/130 (79%)    
 Extracolonic 4/67 (6%) 2/32 (6%) 16/130 (12%)    
 Both 19/67 (28%) 8/32 (24%) 11/130 (8%)    
Family history of cancers 61/67 (91%) 26/32 (74%) 76/130 (58%) <0.0001 0.1071
Double primary cancers 7/67 (10%) 1/32 (3%) 6/130 (5%) 0.0052 0.1320
Secondary malignancy 15/67 (22%) 9/32 (24%) 13/130 (10%) 0.0010 0.7524
Immunohistochemistry          
 MLH1 loss 44/48 (92%) 1/26 (4%) 47/92 (51%) <0.0001 <0.0001
 MSH2 loss 0/48 (0%) 24/26 (92%) 23/92 (25%) 0.2096 <0.0001
 MSH6 loss 2/48 (4%) 23/26 (88%) 26/92 (28%) 0.4982 <0.0001
Microsatellite instability       0.0028 0.5534
 High 57/61 (93%) 28/30 (93%) 79/99 (80%)    
 Stable 4/61 (7%) 2/30 (7%) 20/99 (20%)    
Type of variants     NA NA 0.1179
 Frameshift variants 35/67 (52%) 15/32 (38%)      
 Missense variants 11/67 (16%) 1/32 (3%)      
 Nonsense variants 11/67 (16%) 9/32 (22%)      
 Splicing variants 10/67 (15%) 8/32 (19%)      

Abbreviation: NA, not applicable.

Positive for genetic alterations vs. negative for genetic alterations;

Immunohistochemistry and the microsatellite instability assessments were described as the number/total number available.

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