Supplementary Table 1 Papers Investigated for Inclusion in Analysis of MLH1 Promoter

Supplementary Table 1 Papers investigated for inclusion in analysis of MLH1 promoter methylation in endometrial cancer tumours. Assays include Methylation-Specific (MS), Polymerase Chain Reaction (PCR), Multiplex Ligand-dependant Probe Amplification (MLPA; ME001 and ME011 are SALSA probemix kits manufactured by MRC-Holland), Restriction Enzyme (RE) digest. Region Tested refers to approximate MLH1 promoter region (as defined by Deng et al.[1]) assayed in paper, further details can be found in appropriate references. Where study samples appeared to overlap, a single representative paper was chosen based on the number of tumours and secondary tumour characteristics (e.g. IHC, MSI) available.

Author / Year / Other Markers Tested / Patient Ages / Methylation Assay / Region Tested / MMR Mutation Testing / Patient Ascertainment / Mutation Status / IHC Status / MMR MSI Status / Tumours / Methylation / Partial Methylation / No Methylation / % Methylated / Study Notes
Esteller [2] / 1998 / Not Reported / MS-RE Digest / A / Unselected / MLH1 Mutation-negative* / Unknown / MSI / 7 / 7 / 0 / 0 / 100 / *Sensitivity of mutation testing methodology to pick up all possible mutations uncertain.
Esteller / 1998 / Not Reported / MS-RE Digest / A / Unselected / MSH2 Mutation-positive* / Unknown / MSI / 2 / 1 / 0 / 1 / 50
Esteller / 1998 / Not Reported / MS-RE Digest / A / Not tested / Unselected / Unknown / Unknown / MSI / 4 / 4 / 0 / 0 / 100
Esteller / 1998 / Not Reported / MS-RE Digest / A / Not tested / Unselected / Unknown / Unknown / MSS / 16 / 1 / 0 / 15 / 6
Gurin [3] / 1999 / Not Reported / MS-RE Digest / B / MLH1, MSH2, SSCP; Sanger validation / Unselected / MLH1 Mutation-negative / Unknown / MSI / 14 / 10 / 0 / 4 / 71 / 1 UV (MLH1 2bp ins -13 ex11) MSI status not clear
Gurin / 1999 / Not Reported / MS-RE Digest / B / MLH1, MSH2, SSCP; Sanger validation / Unselected / MLH1 Mutation-negative / Unknown / MSS / 28 / 0 / 2 / 26 / 0
Esteller [4] / 1999 / LOH, MSH2 meth, MSH6 meth / Not Reported / MS-PCR / A / Not tested / Unselected / Unknown / Unknown / MSI / 12 / 11 / 0 / 1 / 92
Esteller / 1999 / Not Reported / MS-PCR / A / Not tested / Unselected / Unknown / Unknown / MSS / 15 / 0 / 0 / 15 / 0
Salvensen [5] / 2000 / MSH2 meth, p53 IHC / Not Reported / MS-PCR / A / Not tested / Unselected / Unknown / MLH1 present (MLH1 tested only) / MSI / 17 / 1 / 0 / 16 / 6 / Inconclusive methylation samples removed from analysis
Salvensen / 2000 / Not Reported / MS-PCR / A / Not tested / Unselected / Unknown / MLH1 absent (MLH1 tested only) / MSI / 13 / 13 / 0 / 0 / 100
Salvensen / 2000 / Not Reported / MS-PCR / A / Not tested / Unselected / Unknown / MLH1 present (MLH1 tested only) / MSS / 59 / 5 / 0 / 54 / 8
Salvensen / 2000 / Not Reported / MS-PCR / A / Not tested / Unselected / Unknown / MLH1 absent (MLH1 tested only) / MSS / 1 / 1 / 0 / 0 / 100
Whelan [6] / 2002 / Not Reported / MS-PCR / C / Unselected / Unknown / Unknown / MSS / 40 / 2 / 0 / 38 / 5
Strazzullo [7] / 2003 / Not Reported / MS-PCR / A / DHPLC and sanger for MLH1 / No 1st or 2nd Deg rels with HNPCC / Unknown* / MLH1 loss / MSI / 18 / 5 / 0 / 13 / 28 / 4 MLH1 Mutations identified (all MLH1 IHC loss, unmethylated) but not stated if EC or CRC
Strazzullo / 2003 / Not Reported / MS-PCR / A / DHPLC and sanger for MLH1 / No 1st or 2nd Deg rels with HNPCC / Unknown* / MLH1 present / MSI / 3 / 0 / 0 / 3 / 0
Hirasawa [8] / 2003 / Full details available / MS-PCR / A / Not tested / Unselected / Unknown / Unknown / MSI / 12 / 11 / 0 / 1 / 92
Hirasawa / 2003 / Full details available / MS-PCR / A / Not tested / Unselected / Unknown / Unknown / MSS & MSI-L / 16 / 10 / 0 / 6 / 63
Fiegl [9] / 2004 / Full details available / MS-PCR / C / Not tested / Unselected / Unknown / Unknown / Unknown / 15 / 9 / 0 / 6 / 5 / Data available for non-EC cases too (e.g. Cervical cancer, benign disease of the uterus); EC cases include 12 adenocarcinoma, 2 adenosquamous, 1 MMT (not specified which are methylated)
Pijnenborg [10] / 2004 / Not Reported / MS-PCR / A / Not tested / Recurrence (within 3y) and Pathology (FIGO stage 1) / Unknown / MLH1 Present; MSH2 Present / MSI / 4 / 3 / 0 / 1 / 75 / IHC Staining intensity difficult to interpret
Pijnenborg / 2004 / Not Reported / MS-PCR / A / Not tested / Recurrence (within 3y) and Pathology (FIGO stage 1) / Unknown / MLH1 Present; MSH2 Absent / MSI / 1 / 1 / 0 / 0 / 100
Pijnenborg / 2004 / Not Reported / MS-PCR / A / Not tested / Recurrence (within 3y) and Pathology (FIGO stage 1) / Unknown / MLH1 Absent; MSH2 Present / MSI / 1 / 1 / 0 / 0 / 100
Pijnenborg / 2004 / Not Reported / MS-PCR / A / Not tested / Recurrence (within 3y) and Pathology (FIGO stage 1) / Unknown / MLH1 Present; MSH2 Present / MSS / 26 / 12 / 0 / 14 / 46
Pijnenborg / 2004 / Not Reported / MS-PCR / A / Not tested / Recurrence (within 3y) and Pathology (FIGO stage 1) / Unknown / MLH1 Present; MSH2 Absent / MSS / 6 / 2 / 0 / 4 / 33
Pijnenborg / 2004 / Not Reported / MS-PCR / A / Not tested / Recurrence (within 3y) and Pathology (FIGO stage 1) / Unknown / MLH1 Absent; MSH2 Present / MSS / 3 / 1 / 0 / 2 / 33
Pijnenborg / 2004 / Not Reported / MS-PCR / A / Not tested / Recurrence (within 3y) and Pathology (FIGO stage 1) / Unknown / MLH1 Absent; MSH2 Absent / MSS / 1 / 0 / 0 / 1 / 0
Pijnenborg / 2004 / Not Reported / MS-PCR / A / Not tested / Recurrence (within 3y) and Pathology (FIGO stage 1) / Unknown / MLH1 Present; MSH2 Present / MSI / 4 / 4 / 0 / 0 / 100
Pijnenborg / 2004 / Not Reported / MS-PCR / A / Not tested / Recurrence (within 3y) and Pathology (FIGO stage 1) / Unknown / MLH1 Present; MSH2 Absent / MSI / 3 / 3 / 0 / 0 / 100
Pijnenborg / 2004 / Not Reported / MS-PCR / A / Not tested / Recurrence (within 3y) and Pathology (FIGO stage 1) / Unknown / MLH1 Present; MSH2 Present / MSS / 27 / 9 / 0 / 18 / 33
Pijnenborg / 2004 / Not Reported / MS-PCR / A / Not tested / Recurrence (within 3y) and Pathology (FIGO stage 1) / Unknown / MLH1 Present; MSH2 Absent / MSS / 6 / 4 / 0 / 2 / 67
Pijnenborg / 2004 / Not Reported / MS-PCR / A / Not tested / Recurrence (within 3y) and Pathology (FIGO stage 1) / Unknown / MLH1 Absent; MSH2 Present / MSS / 1 / 0 / 0 / 1 / 0
Kanaya [11] / 2005 / PTEN mutation / Full details available / Bisulfite pyrosequencing / A, B, C, D / Not tested / Unselected / Unknown / MLH1 Absent <25% (MLH1 tested only) / MSI-H / 7 / 7 / 0 / 0 / 100 / Full meth >80%, partial meth 10-80%, no meth <10%
Kanaya / 2005 / Full details available / Bisulfite pyrosequencing / A, B, C, D / Not tested / Unselected / Unknown / MLH1 Absent <25% (MLH1 tested only) / MSI-L / 1 / 1 / 0 / 0 / 100
Kanaya / 2005 / Full details available / Bisulfite pyrosequencing / A, B, C, D / Not tested / Unselected / Unknown / MLH1 Absent <25% (MLH1 tested only) / MSS / 4 / 1 / 3 / 0 / 25
Kanaya / 2005 / Full details available / Bisulfite pyrosequencing / A, B, C, D / Not tested / Unselected / Unknown / MLH1 Present >25% (MLH1 tested only) / MSI-H / 11 / 6 / 1 / 4 / 55
Kanaya / 2005 / Full details available / Bisulfite pyrosequencing / A, B, C, D / Not tested / Unselected / Unknown / MLH1 Present >25% (MLH1 tested only) / MSI-L / 9 / 1 / 3 / 5 / 11
Kanaya / 2005 / Full details available / Bisulfite pyrosequencing / A, B, C, D / Not tested / Unselected / Unknown / MLH1 Present >25% (MLH1 tested only) / MSS / 19 / 0 / 4 / 15 / 0
Kanaya / 2005 / Full details available / Bisulfite pyrosequencing / A, B, C, D / Not tested / Unselected / Unknown / Unknown / MSI-H / 1 / 0 / 1 / 0 / 0
Kanaya / 2005 / Full details available / Bisulfite pyrosequencing / A, B, C, D / Not tested / Unselected / Unknown / Unknown / Unknown / 4 / 0 / 2 / 2 / 0
Broaddus [12] / 2006 / Some details Available / MS-PCR / C / Pretty sure no testing, not certain though / Endometrioid / unknown / Unknown; retrospectively tested MLH1 meth were all MLH1 loss / Unknown; retrospectively tested MLH1 meth were all MSI-H / 85 / 25 / 0 / 60 / 29
Broaddus / 2006 / Some details Available / MS-PCR / C / Pretty sure no testing, not certain though / Serous / unknown / Unknown; retrospectively tested MLH1 meth were all MLH1 loss / Unknown; retrospectively tested MLH1 meth were all MSI-H / 19 / 0 / 0 / 19 / 0
Broaddus / 2006 / Some details Available / MS-PCR / C / Pretty sure no testing, not certain though / MMMT / unknown / Unknown; retrospectively tested MLH1 meth were all MLH1 loss / Unknown; retrospectively tested MLH1 meth were all MSI-H / 24 / 1 / 0 / 23 / 4
Helmle [13] / 2005 / Not reported / Bisulfite sequencing / A / Not tested / Unselected / Unknown / MLH1 absent (MLH1 tested only) / MSI-H / 21 / 19 / 0 / 2 / 90
Helmle / 2005 / Not reported / Bisulfite sequencing / B / Not tested / Unselected / Unknown / MLH1 Absent (MLH1 tested only) / MSI-H / 21 / 21 / 0 / 0 / 100
Helmle / 2005 / Not reported / Bisulfite sequencing / C / Not tested / Unselected / Unknown / MLH1 Absent (MLH1 tested only) / MSI-H / 21 / 19 / 0 / 2 / 90
Shibata [14] / 2006 / RAB32 methylation / Minimal data available / MS-PCR / ? / Not tested / Unselected / Unknown / Unknown / MSI-H / 20 / 12 / 0 / 8 / 60
Shibata / 2006 / Minimal data available / MS-PCR / ? / Not tested / Unselected / Unknown / Unknown / MSI-L or MSS / 60 / 4 / 0 / 56 / 7
Fujii [15] / 2006 / BHD (Birt-Hogg-Dube) Mutation / Some details available / MS-PCR / A / Not tested / Unselected / Unknown / Unknown / MSI-H / 39 / 29 / 0 / 10 / 74
Xiong [16] / 2006 / MLH1 mRNA expression; MBD occupancy / Not Reported / MS-PCR / A / Not tested / Low MLH1 mRNA expression / Unknown / Unknown / Unknown / 11 / 7 / 0 / 4 / 64
Xiong / 2006 / Not Reported / MS-PCR / A / Not tested / High MLH1 mRNA expression / Unknown / Unknown / Unknown / 7 / 0 / 0 / 7 / 0
Furlan [17] / 2006 / CDKN2A and MGMT methylation / Full details available / MS-PCR / A / Not tested / Synchronous Cancers (Endo and Ov Cancer) / Unknown / MLH1 IHC found to be absent when 5/5 MLH1 meth retrospectively tested for IHC / MSI-H / 5 / 5 / 0 / 0 / 100
Furlan / 2006 / Full details available / MS-PCR / A / Not tested / Synchronous Cancers (Endo and Ov Cancer) / Unknown / Unknown / MSS / 8 / 0 / 0 / 8 / 0
Hampel [18] / 2006 / Full details available / MS-RE digest / C / MLH1 seq; MLPA all / Unselected / Negative / MLH1 loss/PMS2 loss / MSS / 2 / 2 / 0 / 0 / 100
Hampel / 2006 / Full details available / MS-RE digest / C / MLH1 seq; MLPA all / Unselected / Negative / MLH1 loss/PMS2 present / MSS / 1 / 0 / 0 / 1 / 0
Hampel / 2006 / Full details available / MS-RE digest / C / MLH1, MSH2, MSH6 seq; MLPA all / Unselected / MLH1 positive / MLH1 loss/PMS2 loss / MSI-H / 1 / 0 / 0 / 1 / 0
Hampel / 2006 / Full details available / MS-RE digest / C / MLH1, MSH2, MSH6 seq; MLPA all / Unselected / MSH2 UV / Normal / MSI-H / 1 / 0 / 0 / 1 / 0
Hampel / 2006 / Full details available / MS-RE digest / C / MLH1, MSH2, MSH6 seq; MLPA all / Unselected / MSH2 positive / MSH2 loss/MSH6 loss / MSI-H / 2 / 0 / 0 / 2 / 0
Hampel / 2006 / Full details available / MS-RE digest / C / MLH1, MSH2, MSH6 seq; MLPA all / Unselected / MSH6 positive / Normal / MSI-H / 1 / 0 / 0 / 1 / 0
Hampel / 2006 / Full details available / MS-RE digest / C / MLH1, MSH2, MSH6 seq; MLPA all / Unselected / MSH6 positive / MSH2 loss/MSH6 loss / MSI-H / 2 / 0 / 0 / 2 / 0
Hampel / 2006 / Full details available / MS-RE digest / C / MLH1, MSH2, MSH6 seq; MLPA all / Unselected / MSH6 positive / MSH2 loss/MSH6 loss / MSI-L / 1 / 0 / 0 / 1 / 0
Hampel / 2006 / Full details available / MS-RE digest / C / MLH1, MSH2, MSH6 seq; MLPA all / Unselected / Negative / MLH1 loss/PMS2 loss / MSI-H / 51 / 48 / 0 / 3 / 94
Hampel / 2006 / Full details available / MS-RE digest / C / MLH1, MSH2, MSH6 seq; MLPA all / Unselected / Negative / MLH1 loss/PMS2 loss / MSI-L / 8 / 6 / 0 / 2 / 75
Hampel / 2006 / Full details available / MS-RE digest / C / MLH1, MSH2, MSH6 seq; MLPA all / Unselected / Negative / MLH1 loss/PMS2 present or ND or fail / MSI-H / 19 / 15 / 0 / 4 / 79
Hampel / 2006 / Full details available / MS-RE digest / C / MLH1, MSH2, MSH6 seq; MLPA all / Unselected / Negative / MLH1 loss/PMS2 present or ND or fail / MSI-L / 2 / 0 / 0 / 2 / 0
Hampel / 2006 / Full details available / MS-RE digest / C / MLH1, MSH2, MSH6 seq; MLPA all / Unselected / Negative / MSH2 loss/MSH6 loss / MSI-H / 8 / 1 / 0 / 7 / 13
Hampel / 2006 / Full details available / MS-RE digest / C / MLH1, MSH2, MSH6 seq; MLPA all / Unselected / Negative / MSH6 loss / MSI-H / 4 / 1 / 0 / 3 / 25
Hampel / 2006 / Full details available / MS-RE digest / C / MLH1, MSH2, MSH6 seq; MLPA all / Unselected / Negative / MSH6 loss / MSI-L / 1 / 0 / 0 / 1 / 0
Hampel / 2006 / Full details available / MS-RE digest / C / MLH1, MSH2, MSH6 seq; MLPA all / Unselected / Negative / PMS2 loss / MSI-H / 2 / 0 / 0 / 2 / 0
Hampel / 2006 / Full details available / MS-RE digest / C / MLH1, MSH2, MSH6 seq; MLPA all / Unselected / Negative / PMS2 loss / MSI-L / 1 / 0 / 0 / 1 / 0
Hampel / 2006 / Full details available / MS-RE digest / C / MLH1, MSH2, MSH6 seq; MLPA all / Unselected / Negative / PMS2 loss (MLH1 fail) / MSI-H / 1 / 1 / 0 / 0 / 100
Hampel / 2006 / Full details available / MS-RE digest / C / MLH1, MSH2, MSH6 seq; MLPA all / Unselected / Negative / Normal / MSI-H / 3 / 2 / 0 / 1 / 67
Hampel / 2006 / Full details available / MS-RE digest / C / MLH1, MSH2, MSH6 seq; MLPA all / Unselected / Negative / Normal / MSI-L / 4 / 2 / 0 / 2 / 50
Hampel / 2006 / Full details available / MS-RE digest / C / MLH1, MSH2, MSH6 seq; MLPA all / Unselected / Negative / Normal (MLH1 fail) / MSI-L / 1 / 1 / 0 / 0 / 100
Hampel / 2006 / Full details available / MS-RE digest / C / MLH1, MSH2, MSH6 seq; MLPA all / Unselected / Negative / Normal (MSH6 fail) / MSI-L / 1 / 0 / 0 / 1 / 0
McCourt [19] / 2007 / Some details available / MS-RE Digest / C / Not tested / Unselected* / Unknown / Unknown / MSI-H / 134 / 95 / 0 / 39 / 70.9 / *Unselected = EEC + NEC + Sarcoma