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Table 3 Germline LGRs identified in Slovakian HNPCC families.

From: Partial loss of heterozygosity events at the mutated gene in tumors from MLH1/MSH2 large genomic rearrangement carriers

Family code HNPCC criteria Tumor localization
(age at diagnosis)
Gene Deleted or duplicated exons
(systematic nomenclature)
5' deletion MSI IHC LOH
SK-14 AC-I ascendens + sigmoid colon (27) MSH2 del1-7 (c.1-?_1276+?del) 15 kb MSI-H * partial
SK-20 AC-II sigmoid colon (36) MSH2 dup5-6 (c.793-?_1076+?dup) n.a. MSI-H MLH1+, MSH2- partial
SK-21 BG cecum (27) MSH2 del1-3 (c.1-?_645+?del) 15 kb and 27 kb MSI-H MLH1+, MSH2- none
SK-22 AC-I sigmoid colon (36) MLH1 del5-6 (c.381-?_545+?del) n.a. MSI-H MLH1-, MSH2+ partial
SK-23 AC-I cecum + ascendens colon (53) MSH2 del1 (c.1-?_211+?del) - MSI-L * none
SK-25 AC-I cecum (42) MSH2 del1-7 (c.1-?_1276+?del) 15 kb # #  
SK-28 BG ascendens colon + rectum (48) MSH2 del1-3 (c.1-?_645+?del) n.d. MSI-H * n.i.
  1. Fulfillment of HNPCC criteria: AC-I, AC-II, Amsterdam criteria I, II; BG, Bethesda guidelines. Systematic nomenclature: According to the recommendations of the Human Genome Variant Society using reference sequences NM_000249.2 (MLH1) and NM_000251.1 (MSH2). 5' deletion: the probes detecting regions located 15 or 27 kb before MSH2 localized in the TACSTD1 gene; n.a., not applicable; - no reduction of the signal at any of the TACSTD1 probes, n.d., not determined; MSI, microsatellite instability analysis: MSI-H, high level of MSI; MSI-L, low level of MSI; IHC, immunohistochemical analysis, +, a positive staining, -, a negative staining, * staining failed due to fixation problem; #, no FFPE tissue available for analysis; LOH, loss of heterozygosity, n.i. not informative in any LOH marker