Colorectal cancer (CRC) is one of the most frequent cancers, especially in well-developed countries and it is one of the major public health concerns worldwide. Hereditary factors are assumed to play a role in approximately 35.0-45.0% of all CRCs [1]. Our understanding of the genetic basis, as well as the guidelines for clinical management of hereditary CRC syndromes continue to evolve rapidly, so it is crucial for clinicians to recognize the unique features in the diagnosis and management of these syndromes. A precise understanding of the genetics of inherited CRCs is important for identifying at-risk individuals, improving cancer surveillance and prevention strategies and developing better diagnostic and therapeutic approaches [2,3].
Approximately 5.0-10.0% of hereditary CRCs develop due to highly penetrant mutations in genes associated with well-characterized inherited Mendelian cancer syndromes. The most commonly affected genes are the MMR genes
Another possible explanation for the aggregation of CRCs in certain families is that the heritability is not due to a single monogenic defect but a multifactorial condition, caused by the conjunction of moderate-risk or low-risk genetic variants, possibly in combination with environmental or lifestyle risk factors. Evidence from recent studies shows that the accumulation of risk variants is associated significantly with an increased risk of CRC in individuals with a family history of the disease [5].
We have previously reported our initial data on the molecular characterization of FAP and HNPCC in our population [6,7]. We now present updated results of the study, which was performed on a larger cohort of patients with a clinical diagnosis of hereditary CRCs using an extended panel of genes related to cancer predispositions.
A total of 107 probands included in this study were recruited from the University Clinics for Digestive Surgery and for Radiology and Oncology, Skopje, RN Macedonia. Sixty- six patients comply with Amsterdam criteria for clinical diagnosis of HNPCC and 41 patients were diagnosed with multiple polyps reminiscent of FAP (>1000 adenomatous polyps through the large bowel, attenuated FAP (<100 adenomatous polyps) or juvenile polyposis (multiple polyps with hemartomatous component). Informed consent was obtained from all participants. The research protocol was approved by the Ethics Committee of the Faculty of Pharmacy in Skopje, RN Macedonia.
Whole blood (3 mL with EDTA as anticoagulant) and fresh frozen tumor tissue or formalin-fixed paraffinembedded (FFPE) blocks were used for DNA isolation. DNA was extracted using the standard phenol/chloroform method and quantified using the spectrophotometer NanoDrop 2000 (Thermo Fisher Scientific, Waltham, MA, USA). Microsatellite instability in tumor samples was analyzed with a multiplex fluorescent polymerase chain reaction (PCR), followed by capillary electrophoresis (CE) on a 3500 Automated Genetic Analyzer (Life Technologies, Carlsbad, CA, USA). Microsatellite instability (MSI) status was determined using nine short tandem repeat (STR) markers: BAT25, BAT26, D2S123, D5S107, D5S346, D17S250,D18S58, D18S61 and D18S535, derived from the panel of microsatellite loci defined by the National Cancer Institute and the protocols described previously [7,8]. The tumor samples were classified as MSI-H (MSI-high) if instability was present at more than 30.0% of the loci screened, MSI-L (MSI-low) if at least one but fewer than 30.0% of the loci showed instability or MSS (microsatellite stable) if all loci were stable.
Four deferent multiplex ligation-dependent probe amplification (MLPA) analyses were used for screening for extended germline rearrangements in the
The presence of methylation in the
Two different platforms were used for NGS: Ion Torrent PGM™ (Thermo Fisher Scientific) and MiniSeq (Illumina Inc., San Diego, CA, USA). For the Ion Torrent PGM platform, two custom AmpliSeq panels were designed using AmpliSeq Designer (Life Technologies). First, analyses of the genes most commonly affected in HNPCC and FAP
All potentially deleterious variants and low coverage regions were validated using standard protocols for Sanger sequencing. In addition, the region spanning exons 10-15 of the
Summary of clinical data and molecular defects detected in 66 patients with hereditary nonpolyposis colorectal cancer.
Sex- Age | History (relatives affected) | Tumor Location | Stage at DX | Extracolonic Cancers G: gastric cancer; P: prostate cancer; Ur: ureteral cancer; E: endometrial cancer; B: breast cancer; O: ovarian cancer; T: thyroid cancer; L: leukemia; R: renal cancer; Br: brain tumor: no mutation detected; [-]: absent; na: not available |
Gene | DNA Sequence Change | Amino Acid Change | ACMG Classification [11] | ||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
MSI Status | MLH1 met | BRAF V600E | ||||||||||
1 | M-42 | 1: 1st; 2: 2nd degree | transversum | na | G; P; Ur | c.896_897insC | p.Pro300SerfsTer7 | pathogenic | [+] | [–] | [–] | |
2 | M-55 | 3: 1st; 1: 2nd degree | transversum | na | none | c.392C>G | p.Ser131Ter | pathogenic | [+] | [–] | [–] | |
3 | F-49 | 1: 1st; 1: 2nd degree | transversum Synchronous: colon + gastric cancer, 5 years before endometrial cancer. |
IIA | G; E | c.392C>G | p.Ser131Ter | pathogenic | [+] | [–] | [–] | |
4 | M-32 | 1: 1st; 2: 2nd degree | transversum | IIA | none | c.392C>G | p.Ser131Ter | pathogenic | [+] | [–] | [–] | |
5 | M-33 | 1: 1st; 2: 2nd degree | ascendens | IIA | none | c.392C>G | p.Ser131Ter | pathogenic | [+] | [–] | [–] | |
6 | F-48 | positive family history; NS | ascendens | na | E | c.1602del | p.Asn535IlefsTer56 | pathogenic | [+] | [–] | [–] | |
7 | F-43 | 2: 1st; 3: 2nd degree | descendens | na | G; P; Ur | c.896_897insC | p.Thr372ThrfsTer7 | pathogenic | [+] | [–] | [–] | |
8 | F-60 | 2: 1st; 2: 2nd degree | caecum | IIA | none | c.392C>G | p.Ser131Ter | pathogenic | [+] | [–] | [–] | |
9 | F-41 | 1: 1st; 2: 2nd degree | caecum | na | E | c.1667+1del | p.? | pathogenic | [+] | [–] | [–] | |
10 | F-29 | 1: 1st; 2: 2nd; 2: 3rd degree | descendens | na | none | c.392C>G | p.Ser131Ter | pathogenic | [+] | [–] | [–] | |
11 | F-24 | 1: 1st; 1: 2nd degree | caecum | IIA | E | c.244A>G | p.Thr82Ala | likely pathogenic | [+] | [–] | [–] | |
12 | M-40 | 1: 1st degree | ascendens | IIA | none | c.244A>G | p.Thr82Ala | likely pathogenic | [+] | [–] | [–] | |
13 | M-55 | 1: 2nddegree | caecum | IIA | none | c.244A>G | p.Thr82Ala | likely pathogenic | [+] | [–] | [–] | |
14 | M-38 | 2: 1st; 2: 2nd; 2: 3rd degree | ascendens | IIA | P; B | c.62C>T | p.Ala21Val | likely pathogenic | [+] | [–] | [–] | |
15 | F-57 | 1: 1st; 2: 2nd degree | ascendens | na | B | c.683T>C | p.Leu228Pro | likely pathogenic | [+] | [–] | [–] | |
16 | M-15 | 1: 1st; 2: 2nd degree | transversum | IIA | E | c.2211-2A>C | p.? | pathogenic | [+] | [–] | [–] | |
17 | F-41 | 2: 1st; 2: 2nd degree | caecum | IIA | E | c.2211-2A>C | p.? | pathogenic | [+] | [–] | [–] | |
18 | M-50 | 1: 1st; 2: 2nd; 2: 3rd degree | transversum | IIA | E | c.2211-2A>C | p.? | pathogenic | [+] | [–] | [–] | |
19 | M-41 | 3: 2nd degree | rectosygma | IIIC | E | c.209_211+11del | p.? | pathogenic | [+] | [–] | [–] | |
20 | M-46 | 1: 1st; 4: 2nd; 2: 3rd degree | rectum | na | G | c.1786-1788del | p.Asn596del | likely pathogenic | [+] | [–] | [–] | |
21 | F-31 | 1: 1st; 2: 2nd degree | ascendens | IVA | none | c.(?_-152)_(260+1_261-1) | p.? | pathogenic | [–] | NA | [–] | |
22 | F-44 | 1: 1st; 2: 2nd degree | rectum | IIIB | E | c.458+1G>T | p.? | pathogenic | [–] | NA | [–] | |
23 | F-44 | 2: 1st; 2: 2nd degree | transversum | IIIA | O | c.2384T>C | p.Ile795Thr | VUS | [–] | NA | [–] | |
24 | M-81 | 1: 1st degree | rectum | IIIC | none | gene inversion | – | pathogenic | [–] | NA | [–] | |
25 | M-61 | 1: 1st degree | sygma | IIIB | none | gene inversion | – | pathogenic | [–] | NA | [–] | |
26 | M-31 | 1: 1st degree | caecum | IIA | none | c.(803+1_804-1)_ (*1_?)del | p.? | pathogenic | [+] | [–] | [–] | |
27 | M-39 | 1: 1st degree | ascendens | IIIC | E | c.(803+1_804-1)_ (*1_?)del | p.? | pathogenic | [+] | [–] | [–] | |
28 | M-68 | 1: 1st; 1: 2nd degree | rectosygma + caecum | IIA | none | c.2192_2196del | p.Leu731CysfsTer3 | pathogenic | [+] | [–] | [–] | |
29 | M-65 | 1: 1st degree | caecum | na | none | c.1327del | p.Pro443ThrfsTer16 | pathogenic | [+] | [+] | [–] | |
30 | M-40 | positive family history; NS | caecum | na | none | c.(803+1_804-1)_ (*1_?)del | p.? | pathogenic | [+] | [–] | [–] | |
31 | F-53 | 2: 2nd degree | caecum + rectum | IIIB | E | c.418G>A | p.Ser128Leu | VUS | [+] | [+] | [–] | |
32 | F-59 | 3: 1st; 1: 2nd degree | rectum | IIA | E; G; T; L | c.934A>G | p.Met312Val | VUS | [–] | NA | [–] | |
33 | F-53 | 2: 1st; 3: 2nd; 3: 3rd degree | sygma | L | c.726G>A | p.Gly207Glu | VUS | [–] | NA | [–] | ||
34 | M-53 | 2: 1st degree | caecum | IIIA | B | c.1100del | p.Thr367fs | pathogenic | [–] | NA | [–] | |
35 | M-52 | positive family history; NS | caecum | na | none | c.470T>G | p.Ile157Ser | likely pathogenic | [+] | [+] | [–] | |
36 | F-51 | 1: 1st; 1: 2nd; 2: 3rd degree | rectum | na | B; P | c.374T>G | p.Phe125Cys | VUS | [–] | NA | [–] | |
37 | F-59 | positive family history; NS | sygma | IV | none | c.1313A>G | p.Asp438Gly | VUS | [–] | NA | [–] | |
38 | M-57 | positive family history; NS | ascendens | IIIB | none | c.2T>C | p.Met1Thr | pathogenic | [+] | [+] | [+] | |
39 | F-43 | 3: 2nd; 1: 3rd degree | transversum | IIA | G; R | c.1111_1114dup ATTA | p.Thr372Asnfs | VUS | [–] | NA | [–] | |
40 | M-64 | 2: 1st degree | rectum | IIIC | none | c. 1111_1114dup ATTA | p.Thr372Asnfs | VUS | [–] | NA | [–] | |
41 | F-42 | 1: 1st degree | caecum | na | E; B | c.2953del | p.Glu985ArgfsTer3 | pathogenic | [–] | NA | [–] | |
42 | M-75 | 2: 1st; 1: 2nd degree | rectum | na | G | c.643G>A | p.Glu215Lys | VUS | [+] | NA | [–] | |
43 | F-53 | 1: 1st; 1: 3rd degree | transversum | I | none | c.2392C>T | p.Arg798Ter | pathogenic | [–] | NA | [–] | |
44 | M-55 | 1 : 1st; 1: 2nd; 2: 3rd degree | ascendens | IIIC | L | c.2392C>T | p.Arg798Ter | pathogenic | [–] | NA | [–] | |
45 | M-50 | 1: 1st; 3: 2nd degree | rectum | IIB | E; G | c.1403C>T | p.Pro468Leu | pathogenic | [–] | NA | [–] | |
46 | F-38 | 1: 1st; 4: 2nd degree | ascendens | na | G; P | c.481G>A | p.Asp161Asn | VUS | [–] | NA | [–] | |
c.4446_4451dup; | p.Glu1482_ | likely | ||||||||||
47 | M-60 | 2: 1st degree | rectum | IIA | O; P | c.545C>T | Thr1483dup; | pathogenic; | [–] | NA | [–] | |
AACAGA | p.Thr182Ile | VUS | ||||||||||
48 | M-44 | 1: 1st; 2: 2nd degree | transversum | IIIB | T | c.4073C>T; | p.Ala1358Val; | VUS; VUS | [–] | NA | [–] | |
c.2792T>G | p.Leu931Arg | |||||||||||
49 | M-55 | 1: 1st; 1: 2nd degree | caecum | IIIB | none | c.1688T>A; | p.Ile563Lys; | VUS; VUS | [–] | NA | [–] | |
c.2792T>G | p.Leu931Arg | |||||||||||
50 | F-70 | 2: 1st degree | sygma | IIB | none | c.1348T>A | p.(Tyr450Asn) | VUS | [–] | NA | [–] | |
51 | M-59 | 1: 1st degree | ascendens | na | none | c.154C>T | p.Arg52Cys | VUS | [–] | NA | [–] | |
52 | F-50 | 2: 1st; 1: 2nd degree | transversum | na | B | c.821G>A | p.Arg274Lys | VUS | [–] | NA | [–] | |
53 | M-17 | 1: 2nd degree | rectum | IIIC | R | c.2484C>T | p.Asn828Asn | VUS | [–] | NA | [–] | |
54 | M-49 | 2: 2nd degree | caecum | na | E | unknown | [–] | [–] | [–] | [–] | NA | [–] |
55 | M-37 | positive family history; NS | caecum | IIB | none | unknown | [–] | [–] | [–] | [+] | [+] | [–] |
56 | M-47 | 2: 1st; 1: 2nd degree | caecum | IIA | none | unknown | [–] | [–] | [–] | [–] | NA | [–] |
57 | M-67 | 3: 1st; 1: 2nd; 2: 3rd degree | caecum | IIIB | E; B | unknown | [–] | [–] | [–] | [–] | NA | [–] |
58 | F-43 | 1: 2nd degree | transversum | na | none | unknown | [–] | [–] | [–] | [–] | NA | [–] |
59 | F-30 | 1: 2nd; 1: 3rd degree | rectum | IIIC | none | unknown | [–] | [–] | [–] | [–] | NA | [–] |
60 | M-49 | 3: 2nd degree | rectum | na | Br | unknown | [–] | [–] | [–] | [–] | NA | [–] |
61 | F-64 | 2: 1st; 2: 2nd degree | rectum | IIB | L; B | unknown | [–] | [–] | [–] | [–] | NA | [–] |
62 | F-62 | 2: 1st; 1: 3rd degree | crassl | na | E | unknown | [–] | [–] | [–] | [–] | NA | [–] |
63 | M-65 | 1: 1st; 3: 2nd degree | rectosygma | IIIC | E | unknown | [–] | [–] | [–] | [–] | NA | [–] |
64 | F-53 | 1: 1st degree | crassl | IV | B; E | unknown | [–] | [–] | [–] | [–] | NA | [–] |
65 | F-38 | 1: 1st degree | caecum | IIA | E | unknown | [–] | [–] | [–] | [+] | [+] | [–] |
66 | F-78 | 2: 1st degree | ascendens Synchronous: colon + gastric cancer. |
na | R; B; Ur | unknown | [–] | [–] | [–] | [–] | NA | [–] |
DX: diagnosis; ACMG: classification according to the American Collage of Medical Genetics [11]; MSI: microsatellite instability; MLH1 met: methylation of the promoter of the
After a detailed review of the clinical/pathological data and familial segregation of CRC and other cancers, we selected 107 unrelated patients for molecular analysis, of which 66 probands complied with the Amsterdam criteria for clinical diagnosis of HNPCC and 41 had multiple polyps reminiscent of FAP or associated syndromes (Figure 1). Of the 66 HNPPC patients, 31 had the MSI+phenotype and 35 had MSS tumors. The disease in HNPCC patients with MSI+ tumors developed predominantly in males, at a younger age (average 42.5 years, range 24-75 years) and with a preponderance for the proximal colon, whereas in HNPCC patients with MSS tumors, the onset of the disease was at an average age of 53 years (range 17-81 years), equally distributed in both genders and localizations. Of the 41 patients with polyposis, 16 patients, predominantly
males (11/16), presented with a classical FAP phenotype (>1000 polyps) at an average age of 38 years (range 9-47 years) at diagnosis, while 25 patients with oligopolyposis (<100 polyps) were diagnosed at an average age of 53 years (range 38-74 years). Extracolonic cancers were present in 17/31 families with MSI+ HNPCC (primarily endometrial and gastric cancers), in 23/35 families with MSS HNPCC (primarily breast/ovarian, endometrial and gastric cancers and leukemias); in 2/16 families with FAP (both with gastric cancer) and in 7/25 families with oligopolyposis (primarily breast and pancreatic cancers). The clinical and pathological data of these patients are summarized in Table 1.
Deleterious variants were detected in 10/35 (28.0%) HNPCC patients with MSS tumors (Figure 2 and Table 1), of which three variants in the MMR genes in four patients (11.4%) [c.(?_-152)_(260+1_261-1)p(?) and c.457+1G>T p.(?) in
Summary of clinical data and molecular defects detected in 41 patients with polyposis syndromes.
Sex- Age | Clinical DX | Number of Polyps | Type of Polypsa | Family History (relatives affected) | Extracolonic Cancersb | Affected Gene | DNA Sequence Change | Amino Acid Change | ACMG Classification [11] | |
---|---|---|---|---|---|---|---|---|---|---|
1 | M-40 | FAP | >100 | AD | 2: 1st; 1: 2nd; 4: 3rd degree | none | c.-19+2475_*2113+34050del | whole gene deletion | pathogenic | |
2 | M-38 | FAP | >100 | AD | positive NS family history; | G | c.-19+5016_*2113+20168del | whole gene deletion | pathogenic | |
3 | F-29 | FAP | >100 | AD | 2: 1st; 1: 2nd degree | none | c.-19+5016_*2113+20168del | whole gene deletion | pathogenic | |
4 | F-33 | FAP | >100 | AD | 2: 1st; 2: 2nd degree | none | c.-19+2475_*2113+34050del | whole gene deletion | pathogenic | |
5 | F-29 | FAP | >100 | AD | 1: 1st; 1: 2nd degree | none | c.1269G>A | p.Trp423Ter | pathogenic | |
6 | M-35 | FAP | >100 | AD | 1: 1st; 5: 2nd degree | none | c.1660C>T | p.Arg554Ter | pathogenic | |
7 | M-32 | FAP | >100 | AD | 2: 1st degree | G | c.3183_3187del | p.Gln1062Terfs | pathogenic | |
8 | F-59 | FAP | >100 | AD | 1: 1st; 1: 2nd degree | none | c.3183_3187del | p.Gln1062Terfs | pathogenic | |
9 | M-38 | FAP | >100 | AD | 1: 1st; 1: 2nd degree | none | c.3199_3202del | p.Ser1068GlyfsTer57 | pathogenic | |
10 | M-52 | FAP | >100 | AD | no family history | none | c.3404_3405del | p.Tyr1135fsTer | pathogenic | |
11 | F-38 | FAP | >100 | AD | 2: 1st; 1: 3rd degree | none | c.3927_3931del | p.Glu1309AspfsTer4 | pathogenic | |
12 | M-44 | FAP | >100 | AD | 1: 1st degree | none | c.3927_3931del | p.Glu1309AspfsTer4 | pathogenic | |
13 | F-39 | FAP | >100 | AD | no family history | none | c.904C>T | p.Arg302Ter | pathogenic | |
c.-152-2A>G; | p.?; | pathogenic; | ||||||||
14 | M-9 | FAP | >100 | JP | 1: 1st degree | none | c.2484C>T | p.Asn828Asn | VUS | |
15 | M-47 | FAP | >100 | AD | 1: 1st; 3: 3rd degree | none | c.1285dupC | p.His429ProfsTer27 | pathogenic | |
16 | M-38 | FAP | >100 | AD | no family history | none | unknown | [–] | [–] | [–] |
17 | M-39 | oligopolyposis | ~30 | AD | 1: 1st degree | none | c.256A>T | p.Lys86Ter | pathogenic | |
18 | M-38 | oligopolyposis | ~10 | AD | no family history | none | c.3920T>A | p.Ile1307Lys | pathogenic | |
19 | F-44 | oligopolyposis | >10 | AD/ HP | 2: 1st; 4: 2nd degree | none | c.1A>G | p.Met1Val | pathogenic | |
p.Arg245His/ | ||||||||||
20 | F-40 | oligopolyposis | ~30 | AD | no family history | none | c.734G>A/c.734G>A | p.Arg245His | pathogenic | |
p.Arg245His/ | ||||||||||
21 | M-47 | oligopolyposis | ~10 | AD | 2: 1st degree | none | c.734G>A/c.734G>A | p.Arg245His | pathogenic | |
22 | M-48 | oligopolyposis | >10 | AD | 1: 1st degree | none | c.536A>G/= | p.Tyr179Cys/= | pathogenic | |
23 | M-55 | oligopolyposis | >10 | AD | 1: 1st degree | none | c.536A>G/= | p.Tyr179Cys/= | pathogenic | |
24 | F-54 | oligopolyposis | ~50 | AD | positive family history; |
none | c.536A>G/=; |
p.Tyr179Cys/=; |
pathogenic | |
25 | M-67 | oligopolyposis | 50-100 | AD | 1: 1st degree | Pa | c.268C>T/c.806G>A | p.p.GlnTrp90269Ter/Ter | pathogenic | |
26 | F-71 | oligopolyposis | 7 | AD | 2: 1st degree | E; Pa | c.268C>T/= | p.Gln90Ter/= | pathogenic | |
27 | M-58 | oligopolyposis | ~10 | AD | 1: 1st; 2: 3rd degree | none | c.268C>T/=; | p.Gln90Ter/=; | VUS | |
c.711G>C | p.Gln237His | |||||||||
28 | M-39 | oligopolyposis | >10 | AD | 1: 1st degree | E | c.1642C>T | p.Gln548Ter | pathogenic | |
29 | F-53 | oligopolyposis | >10 | AD/SE | 1: 1st degree | B | c.902delT | p.Leu301TrpfsTer3 | pathogenic | |
30 | M-53 | oligopolyposis | 21 | AD | no family history | none | c.2149C>T | p.Arg717Trp | VUS | |
31 | M-63 | oligopolyposis | >10 | AD | no family history | none | c.9016G>C | p.Ala3006Pro | VUS | |
32 | F-56 | oligopolyposis | NA | AD | 3: 1st degree | none | c.1462C>T | p.Arg488Cys | VUS | |
33 | M-45 | oligopolyposis | ~10 | AD | no family history | none | c.1462C>T | p.Arg488Cys | VUS | |
c.1462C>T; | p.Arg488Gly; | VUS; | ||||||||
34 | M-46 | oligopolyposis | NA | no data | no family history | none | c.3416G>C; | p.Arg1139Pro; | VUS; | |
c.1447C>G | p.Arg483Gly | VUS | ||||||||
35 | M-57 | oligopolyposis | >10 | AD | 1: 1st degree | none | c.1846G>C | p.Asp616His | VUS | |
36 | F-74 | oligopolyposis | 10 | AD | 2: 1st degree | none | c.2527A>G | p.Ile843Val | VUS | |
37 | M-38 | oligopolyposis | ~10 | AD/ HP | 2: 1st; 2: 2nd degree | Br; L; P; R | c.1431_1433dupAAA | p.Lys477dup | VUS | |
38 | M-54 | oligopolyposis | >30 | AD | 1: 1st degree | none | unknown | [–] | [–] | [–] |
39 | M-58 | oligopolyposis | ~10 | AD | 2: 1st; 7: 2nd degree | none | unknown | [–] | [–] | [–] |
40 | M-67 | oligopolyposis | 20-30 | AD | 2: 1st degree | none | unknown | [–] | [–] | [–] |
41 | F-50 | oligopolyposis | NA | AD | 1: 1st degree | none | unknown | [–] | [–] | [–] |
DX: diagnosis; ACMG: classification according to the American Collage of Medical Genetics [11]; FAP: familial adenomatous polyposis; NA: not available but <100; VUS: variant of unknown significance; [-]: no variant detected.
a AD: adenomatous; JP: juvenile polyps; HP: hyperplastic; SE: sessile.
b G: gastric cancer; Pa: pancreatic cancer; E: endometrial cancer; B: breast cancer; Br: brain tumor; L: leukemia; P: prostate cancer; R: renal cancer.
(93.7%) patients, most of which (13/16; 81.2%) were located in the
The molecular defect in patients with oligopolyposis was extremely heterogeneous (Figure 3, Table 2). Deleterious variants were detected in 13/25 (52.0%) of the patients. In 11/25 (44.0%), the variants were located in genes associated with polyposis syndromes, including
Using the approach described above, we were able to detect clear pathogenic variants (deleterious mutations) in 65/107 (60.7%) patients with hereditary CRCs in our population, of which 54/107 (50.5%) in known well-established CRC susceptibility genes and 11/107 (10.2%) in other genes [Figure 4(A) and Figure 5(A)]. Similar results were obtained in several large studies of patients with a hereditary cancer using whole exome sequencing [13,14], supporting the role of our approach for cascade testing of this disorder.
The majority of these deleterious variants were detected in HNPCC families with MSI+tumors and families expressing the FAP phenotype [Figure 4(B)]. In the HN-PCC group, the Lynch syndrome was confirmed in 25/31 (80.6%) of the MSI+ patients and in 4/35 (11.4%) patients with MSS tumors, indicating the need for Lynch syndrome testing even in MSI- negative cases who fulfill the Amsterdam criteria. Half of the detected MMR mutations in the Lynch syndrome patients were located in the
Deleterious mutations in the
It is worth noting that four mutations, each in the Lynch syndrome and FAP subgroups, were present in >50.0 and >60.0% of patients, respectively, which allowed for the development of specific assays for initial screening and rationale cascade testing for these syndromes in our population (Staninova-Stojovska
In the oligopoliposis group, we detected deleterious mutations in 8/25 (32.0%) patients. In six of these patients, the variants were present in known highly penetrant genes associated with either autosomal dominant (two in
The lowest frequency of pathogenic variants was present in the group of HNPCC patients with MSS tumors (10/35 or 28.5%). As mentioned above, four of these patients had Lynch syndrome due to mutations in the MMR genes (two
In 42/107 (39.2%) patients, we did not detect any deleterious variants in the analyzed genes. Nevertheless, 25 different variants of unknown significance were detected in the majority of these patients (24/42 or 57.1%). Most of these variants had a moderate to low relative risk, as calculated by comparison of their frequency in cancer cases to controls from the Macedonian population or the controls from the GnomAD database (Supplementary Table 2). The VUSs were present predominantly in HNPCC families with MSS tumors (14/42 or 33.3%) and in families with oligopolyposis (8/42 or 19.0%), whereas only two variants were detected in individual patients with the Lynch syndrome [Figure 4(B)]. Most of these variants were present as single variants in individual patients (20/24 or 83.3%), whereas three patients with HNPCC with MSS tumors had two different variants and only one patient with oligopolyposys had three different variants (Tables 1 and 2). In addition, only three patients with deleterious mutations also had a VUS. These data strongly suggest that the polygenic inheritance of low/moderate penetrance variants in the 114 analyzed genes is not a major mechanism responsible for the familial CRC type X (FCCX) and oligopolyposis phenotype in our population. It is worth nothing that the majority of these variants, particularly in patients without deleterious mutations, were located in the DRG genes, further supporting their importance in CRC cancerogenesis [Figure 5(B)]. However, additional evidence from functional analysis is needed in order to accurately classify these variants, which might significantly contribute to the current knowledge on the CRC genetic susceptibility.
We could not detect any variants using this approach in 18/107 (16.8%) patients [Figure 4(A)]. As mentioned above, the majority of these patients (13/18 or 72.2%) were HNPCC patients (11 with MSS tumors and two with MSI due to somatic inactivation of the MMR genes), 4/18 (22%) were patients with oligopylopysis and only one patient had a FAP phenotype. Although we cannot exclude the possibility of the presence of a mutation in deep intronic/ regulatory regions of the analyzed genes that could be missed by our approach, we provide further evidence for the genetic heterogeneity of hereditary CRC, particularly in HNPCC families with MSS tumors and in families with oligopolyposis. However, it is interesting to note that endometrial cancer was present in family members of 5/11 HN-PCC patients with MSS tumors, which indicates that these are Lynch syndrome families with undetected mutations in