Selection of patients with germline MLH1 mutated Lynch syndrome by determination of MLH1 methylation and BRAF mutation

Bouzourène, Hanifa; Hutter, Pierre; Losi, Lorena; Martin, Patricia; Benhattar, Jean

doi:10.1007/s10689-009-9302-4

Cited by 45 publications

(39 citation statements)

References 42 publications

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“…In agreement with previous reports, the sensitivity of the absence of BRAF mutation is very high in identifying MLH1 mutation carriers 16,18,21,39 (Table 3 and Supplementary Data Table 5). A single false-negative was identified adding to the increasing number of LS tumors harboring a BRAF mutation.…”

Section: Discussionsupporting

confidence: 92%

“…First, the low prevalence of BRAF mutations observed in our selected population (11% of MSI tumors and 20% of those lacking MLH1 protein expression). This is in the lower range of reported series 16,18,21,39 but likely to reflect the experience of referral centers. 21 Second, the significant number of LS cases and MLH1 germline carriers analyzed allows more accurate estimates.…”

Section: Discussionmentioning

confidence: 69%

“…The lack of MLH1 promoter hypermethylation showed a sensitivity of 66% for LS depiction. Again, this is in the lower range (57-100%) of reported series 12,18,21,39 (Table 3 and Supplementary Data Table 5) and maybe linked to the low prevalence of hypermethylation observed (42%). This low prevalence may well reflect the demographics of a Cancer Genetics Unit and/or the technique used and the conservative threshold cutoff chosen.…”

Section: Discussionmentioning

confidence: 75%

“…Also, we have confirmed that considering only C-and D-regions of MLH1 promoter, 36,40 yields the best performance in the diagnostic setting. 18,21,39 Quantitative assessment obtained by pyrosequencing is attractive, but its application to FFPE samples is not straightforward.…”

Section: Discussionmentioning

confidence: 99%

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MLH1 promoter hypermethylation in the analytical algorithm of Lynch syndrome: a cost-effectiveness study

et al. 2012

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The analytical algorithm of Lynch syndrome (LS) is increasingly complex. BRAF V600E mutation and MLH1 promoter hypermethylation have been proposed as a screening tool for the identification of LS. The aim of this study was to assess the clinical usefulness and cost-effectiveness of both somatic alterations to improve the yield of the diagnostic algorithm of LS. A total of 122 colorectal tumors from individuals with family history of colorectal cancer that showed microsatellite instability and/or loss of mismatch repair (MMR) protein expression were studied. MMR germline mutations were detected in 57 cases (40 MLH1, 15 MSH2 and 2 MSH6). BRAF V600E mutation was assessed by single-nucleotide primer extension. MLH1 promoter hypermethylation was assessed by methylation-specific multiplex ligation-dependent probe amplification in a subset of 71 cases with loss of MLH1 protein. A decision model was developed to estimate the incremental costs of alternative case-finding methods for detecting MLH1 mutation carriers. One-way sensitivity analysis was performed to assess robustness of estimations. Sensitivity of the absence of BRAF mutations for depiction of LS patients was 96% (23/24) and specificity was 28% (13/47). Specificity of MLH1 promoter hypermethylation for depiction of sporadic tumors was 66% (31/47) and sensitivity of 96% (23/24). The cost per additional mutation detected when using hypermethylation analysis was lower when compared with BRAF study and germinal MLH1 mutation study. Somatic hypermethylation of MLH1 is an accurate and cost-effective pre-screening method in the selection of patients that are candidates for MLH1 germline analysis when LS is suspected and MLH1 protein expression is absent.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 69%

Section: Discussionmentioning

confidence: 75%

Section: Discussionmentioning

confidence: 99%

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MLH1 promoter hypermethylation in the analytical algorithm of Lynch syndrome: a cost-effectiveness study

et al. 2012

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“…The somatic BRAF V600E (c.1799T>A mutation hotspot) mutation is highly associated with MLH1 promoter methylation in colorectal tumours (not endometrial), but not all methylated tumours have the BRAF mutation 71,78,255,256 . It has been suggested that colorectal tumours with MLH1 promoter methylation and/or the BRAF V600E mutation should not be screened for MMR mutations [256][257][258] . Furthermore, testing for MLH1 methylation and the BRAF V600E mutation appears to have become increasingly utilised in molecular and genetic testing algorithms in clinical practice to discriminate sporadic MSI-H CRC from MSI-H CRC in LS.…”

Section: Mlh1 Promoter Methylation and Braf V600ementioning

confidence: 99%

Interpreting the clinical significance of mismatch repair gene sequence variants

Thompson¹

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The clinical classification of inherited nucleotide sequence variants identified in disease-related genes has a direct impact on the clinical management of patients and their families. Lynch syndrome is an autosomal dominant cancer predisposition syndrome caused by germline mutations in the mismatch repair (MMR) genes (MLH1, MSH2, MSH6 and PMS2). However, ~30% of MMR gene variants identified in suspected Lynch cases are of uncertain clinical significance, which constitutes a challenge for genetic counselling and clinical management of families. In the past there has been no uniform system to tackle these variants, and mainly ad hoc methods have been utilized to determine if they are disease causing. The multifactorial likelihood model approach was initially developed for the evaluation of sequence variants in the BRCA1/2 cancer predisposition genes. It was adapted for MMR gene variants to provide a quantitative measure of risk in the form of probability of pathogenicity. Estimates of prior probability of pathogenicity based on evolutionary sequence conservation and physicochemical characteristics of predicted alterations were combined with variant segregation information and tumour features. Microsatellite instability (MSI) and somatic BRAF V600E tumour data for unselected colorectal cancer probands of known pathogenic variant status were used to derive likelihood ratios (LR) for tumour characteristics using the Colon Cancer Family Registry resource.The LR in favour of pathogenicity was estimated to be ~12-fold for a MSI and BRAF V600E mutation-negative colorectal tumour. Our findings provide a working multifactorial likelihood model for classifications that carefully considers mode of ascertainment for gene testing.

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Contribution of MLH1 constitutional methylation for Lynch syndrome diagnosis in patients with tumor MLH1 downregulation

Pinto

Guerra

et al. 2018

Cancer Medicine

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Constitutional epimutation of the two major mismatch repair genes, MLH1 and MSH2, has been identified as an alternative mechanism that predisposes to the development of Lynch syndrome. In the present work, we aimed to investigate the prevalence of MLH1 constitutional methylation in colorectal cancer (CRC) patients with abnormal expression of the MLH1 protein in their tumors. In a series of 38 patients who met clinical criteria for Lynch syndrome genetic testing, with loss of MLH1 expression in the tumor and with no germline mutations in the MLH1 gene (35/38) or with tumors presenting the BRAF p.Val600Glu mutation (3/38), we screened for constitutional methylation of the MLH1 gene promoter using methylation‐specific multiplex ligation‐dependent probe amplification (MS‐MLPA) in various biological samples. We found four (4/38; 10.5%) patients with constitutional methylation in the MLH1 gene promoter. RNA studies demonstrated decreased MLH1 expression in the cases with constitutional methylation when compared with controls. We could infer the mosaic nature of MLH1 constitutional hypermethylation in tissues originated from different embryonic germ layers, and in one family we could show that it occurred de novo. We conclude that constitutional MLH1 methylation occurs in a significant proportion of patients who have loss of MLH1 protein expression in their tumors and no MLH1 pathogenic germline mutation. Furthermore, we provide evidence that MLH1 constitutional hypermethylation is the molecular mechanism behind about 3% of Lynch syndrome families diagnosed in our institution, especially in patients with early onset or multiple primary tumors without significant family history.

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Selection of patients with germline MLH1 mutated Lynch syndrome by determination of MLH1 methylation and BRAF mutation

Cited by 45 publications

References 42 publications

MLH1 promoter hypermethylation in the analytical algorithm of Lynch syndrome: a cost-effectiveness study

MLH1 promoter hypermethylation in the analytical algorithm of Lynch syndrome: a cost-effectiveness study

Interpreting the clinical significance of mismatch repair gene sequence variants

Contribution of MLH1 constitutional methylation for Lynch syndrome diagnosis in patients with tumor MLH1 downregulation

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