SALSA MS-MLPA KIT ME011-A1 Mismatch Repair genes (MMR) Lot 0609, 0408, 0807, 0407

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1 SALSA MS-MLPA KIT ME011-A1 Mismatch Repair genes (MMR) Lot 0609, 0408, 0807, 0407 The Mismatch Repair (MMR) system is critical for the maintenance of genomic stability. MMR increases the fidelity of DNA replication by identifying and excising single-base mismatches and insertion-deletion loops that may arise during DNA replication. Cells with MMR deficiency may lead to the accumulation of mutations resulting in the initiation of cancer. The MMR genes are involved in one of the most prevalent cancer syndromes in humans known as hereditary nonpolyposis colon cancer (HNPCC). There are several proteins required for the complete MMR system. Mutations in the MLH1 and MSH2 have been found in about 90% of HNPCC cases. Mutations in other MMR genes have been less frequent in HNPCC patients. In many sporadic colon cancers, hypermethylation of the MLH1 gene promoter resulting in its transcriptional silencing has been observed more than mutations. This ME011-A1 MMR mix has been developed to detect aberrant CpG islands methylation of six MMR genes and includes 5 s for MLH1, 3 s MSH2, 3 s for MHSH6, 3 s for MSH3, 1 for MLH3, 3 s for PMS2 and 3 s specific for the MGMT promoter region. MGMT plays a role in removing O(6)-alkylguanine which is the major mutagenic and carcinogenic lesion induced by alkylating mutagens. The MLH1 gene is located at chromosome 3p22.1, MLH3 at chromosome 14q24.3, MSH2 at 2p21, MSH3 at 05q14.1, MSH6 gene at 2p16, PMS2 at 7p22 and the MGMT gene is located at chromosome 10q26. This kit includes 21 s containing a recognition, which yields information about the methylation status of a target sequences. In addition, 11 reference s are present which are not influenced by the digestion. Besides the detection of aberrant methylation, all s present will give information on copy number changes in the analysed sample. More information about MS-MLPA can be found on page 6. This SALSA MS-MLPA kit can be used to detect aberrant methylation of one or more sequences of the MMR genes. Methylation levels can be different for different tissues. Please use DNA derived from the same type of tissue and purified by the same method as reference sample. This SALSA MS-MLPA kit can be used to detect deletions and duplications of one or more sequences of the MMR genes. Heterozygous deletions of recognition sequences should give a 35-50% reduced relative peak area of the amplification product of that. However, mutations and/or polymorphisms very close to the ligation may also result in a reduced relative peak area. Therefore, apparent deletions detected by a single always require confirmation by other methods. We have no information on what percentage of defects in these genes is caused by deletions/duplications of complete exons. Please note that most defects in these genes are expected to be small (point) mutations, most of which will not be detected by this MLPA test. SALSA MS- kits are sold by for research purposes and to demonstrate the possibilities of the MLPA technique. This kit is not CE/FDA certified for use in diagnostic procedures. kits are supplied with all necessary buffers and enzymes. Purchase of the test kits includes a limited license to use these products for research purposes. The use of this SALSA kit requires a thermocycler with heated lid and sequence type electrophoresis equipment. Different fluorescent PCR primers are available. The MLPA technique has been first described in Nucleic Acid Research 30, e57 (2002). The MS-MLPA method for the detection of both copy numbers and methylation changes was described in Nucleic Acid Research 33, e128 by Nygren et al Related kits P003 MLH1/MSH2: Hereditary nonpolyposis colon cancer (HNPCC) genes included: MSH2, MLH1 P248 MLH1/MSH2: HNPCC confirmation genes included: MSH2, MLH1 P008 MSH6/PMS2: HNPCC genes included: MSH6, PMS2, MUTYH More information Web : info@mlpa.com; Fax : Mail : bv; Willem Schoutenstraat 6, 1057 DN Amsterdam, the Netherlands SALSA MS- kit ME011 MMR Page 1 of 8

2 References of kit ME011 Jeuken JW et al. (2007). MS-MLPA: an attractive alternative laboratory assay for robust, reliable, and semiquantitative detection of MGMT promoter hypermethylation in gliomas. Lab Invest Aug 13. Please note During testing on various tumour samples, we have observed that many s undergo significant methylation changes. However, as we have little access to patient samples, it is unfortunately not possible for to validate each on samples with known decreased mrna levels and of which the methylation status of the sequences has been confirmed by independent methods. The MS-MLPA s are in promoter regions which are unmethylated in normal blood-derived control samples, and they do not generate a signal after digestion in normal controls. We have tested each by in vitro methylation of sample DNAs with Hha1 methylase, and found each signal indeed remains intact after Hha1 digestion. Methylation-specific MLPA Please note that each MS-MLPA reaction generates two samples that need analysis by capillary electrophoresis: one undigested sample for copy number detection and one digested sample for methylation detection. A modification of the MLPA technique, MS-MLPA allows the detection of both copy number changes and unusual methylation levels of different sequences in one simple reaction. MLPA s for methylation quantification are similar to normal MLPA s, except that the sequence detected by the MS-MLPA contains the sequence recognized by the methylation-sensitive restriction enzyme. Similar to ordinary MLPA reactions, the MS-MLPA protocol starts with sample DNA denaturation and overnight hybridization. The reaction then is split into two tubes. One tube is processed as a standard MLPA reaction. This reaction provides information on copy number changes. The other tube of the MLPA hybridization reaction is incubated with the methylation-sensitive endonuclease while simultaneously, the hybridized s are ligated. Hybrids of (unmethylated) oligonucleotides and unmethylated sample DNA are digested by the enzyme. Digested s will not be exponentially amplified by PCR and hence will not generate a signal when analyzed by capillary electrophoresis. In contrast, if the sample DNA is methylated, the hemimethylated -sample DNA hybrids are prevented from being digested by and the ligated s will generate a signal. More information about MS-MLPA can be found in the MS-MLPA protocol. Please note that this product can not be used with an alternative protocol in which the genomic DNA is first digested with Hha1, followed by MLPA reactions on both digested and undigested genomic DNA. Data analysis The ME011-A1 MMR mix contains 32 different s with amplification products between 136 and 400 nt. In addition, it contains 7 control fragments generating an amplification product smaller than 120 nt: four DNA Quantity fragments (Q-fragments) at nt and three DNA denaturation control fragments (Dfragments) at nt. More information on how to interpret observations on these control fragments can be found in the MLPA protocol. Intra-sample data normalisation (all samples) For analysis of MLPA results, not the absolute fluorescence values but intra-normalized data are used (relative peak areas). The data generated in the digested and undigested sample should first be normalized intra-sample by comparing the signal of each target-specific against every single reference separately, thereby creating as many ratios per as there are reference s. The median of all produced ratios per gives an estimate of the final ratio of the sample s targetspecific sequences. This median can then be used for sample to reference comparison, both in the copy number determination and in the digestion determination. Copy numbers determination (comparison between undigested samples) The final ratio, or ploidy status, of each is calculated by comparing a) the intra-normalized ratio of each obtained on the undigested patient sample with b) the average intra-normalized ratio of each obtained on the undigested reference samples. When copy number changes have a low coincidence in SALSA MS- kit ME011 MMR Page 2 of 8

3 your samples (20% or lower) you may also use the median of all intra-normalized signals of all undigested samples per. Methylation analysis (comparing digested and undigested samples) Methylation status of MS-MLPA s* is calculated by dividing a) the intra-normalized ratio of each MS- MLPA obtained on the digested sample with b) the intra-normalized ratio of each MS-MLPA obtained on the undigested sample. Multiplying this value with 100 gives an estimation of the percentage methylation. Aberrant methylation can than be identified by a changed methylation status of one or more MS-MLPA s in a patient sample when compared to results obtained on DNA reference samples. *Note: An MS-MLPA targets a single specific in a CpG island; if methylation is absent for a particular CpG-, this does not necessarily mean that the whole CpG island is unmethylated! For samples containing both tumour and normal cells, MLPA experiments will indicate the average copy number of genes. When only small numbers of samples are tested, visual comparison of peak profiles should be sufficient to easily identify exon deletions and methylation status. Comparison of results should preferably be performed within one experiment. Only samples from the same tissue and purified by the same method should be compared. Note that Coffalyser, the MLPA analysis tool developed at, can be downloaded free of charge from our web This mix was developed by A. Errami & J.P. Schouten at. In case the results obtained with this mix lead to a scientific publication, it would be very much appreciated if the first mix designer could be made a coauthor. Info/remarks/suggestions for improvement: info@mlpa.com. SALSA MS- kit ME011 MMR Page 3 of 8

4 SALSA MS-MLPA ME011-A1 MMR mix Hha1 Chromosomal position reference MMR Q-fragments: DNA quantity; only visible with less than 100 ng sample DNA D-fragments: Low signal of 88 or 96 nt fragment indicates incomplete denaturation 136 Reference (CREM) 0981-L p PMS L p MLH L1265-3p PMS L p MSH L p MLH L p Reference (TNFRSF1A) 0554-L p MSH L p MGMT 5670-L q MLH L p MLH L q MSH L p MSH L q Reference (PAH) 2334-L q MLH L p MSH L0499-2p Reference (BCL2) 0587-L q * MLH L p MSH L p MSH L q MLH L p MSH L p Reference (CDK6) 3184-L2523-7q * MGMT 7188-L q PMS L p Reference (CDH1) 2416-L q * MSH L q MLH L q Reference (AI651963) 1234-L p MGMT 2239-L q Reference (TSPAN15) 0973-L q MSH L p21 * More variable and might be replaced in future lots. This contains a but is not completely digested when normal blood-derived DNA is used! Note: Please notify us of any mistakes. The identity of the genes detected by the reference s is available on request: info@mlpa.com. SALSA MS- kit ME011 MMR Page 4 of 8

5 MMR s arranged according to chromosomal location The Hha1 s are marked with grey. s are marked with - MLH1 s L7710 MLH L1265 MLH1-265* 6221-L1747 MLH L7712 MLH L1266 MLH L1745 MLH1 + * More variable. (distance to ATG start) (Deng, A-region) (Deng, B-region) Reverse (Deng, B-region) (Deng, C-region) - 13 (Deng, D-region) (intron 1, 93 nt after exon 1) TCCGCCACATACCGCTCGTAGTAT- TCGTGCTCAGCCTCGTAGTGGCGCCTGAC GGGTCCACTCGGGCCGGAAAACT- AGAGCCTCGTCGACTTCCATCTTGCTTCTTT CTGCTGAGGTGATCTGGCGCAGA- GCGGAGGAGGTGCTTGGCGCTTCTCAGGC AGAGCGGACAGCGATCTCTAACGCGCAA- GCGCATATCCTTCTAGGTAGCGGGCAGTA CGTTGAGCATCTAGACGTTTCCTTGGCTCT- TCTGGCGCCAAAATGTCGTTCGTGGCAGG CGGACACGCCTCTTTGCCCGGGCAGA- GGCATGTACAGCGCATGCCCACAACGGCG Distance to next 0.2 kb 0.2 kb The most important methylation region for MLH1 expression, the Deng C-region, is from -248 to -178 nt before the transcription. The transcription that Deng uses for reference lies 21 nt before the startcodon. The second most important region, the Deng D-region, is from -9 to +15 nt (Deng G. et al (1999) Cancer Research 59, and Capel, E. et al (2007) Oncogene advance online publ.). For this reason, methylation of the 198 and 166 nt s will be most important for mrna expression. It is not possible for us to design extra MLPA s in these regions as there are no other s. MSH2 s L7711 MSH2 + AY reverse L2162 MSH L0599 MSH * 0911-L0499 * More variable MSH2 exon CGAAACCCGCAGACGCGCATCCT- TAGTAGAGCTCCTTTCTGTGTTTACTCAGCT AGTAGCTAAAGTCACCAGCGTGCGCGGGA- AGCTGGGCCGCGTCTGCTTATGATTGGTTG CCTTTTCGACCGGGGCGACTTCT- ATACGGCGCACGGCGAGGACGCGCTGCTG CGTCGATTCCCAGATCTTAACCGACT- TGCCAAGAAGTTTCAAAGACAAGCAGCAAA Distance to next 0.3 kb 26.5 kb The MSH2 ATG startcodon is at in this AY sequence. MSH6 s U L5732 MSH CCAGCCCCGCGGCGTGAGGGA - AGGGGAGCTCAGCAGTTCCCCGCGCGGGG L5733 MSH CGAGGCGCCTGTTGATTGGCCACT-GGGG CCCGGGTTCCTCCGGCGGAGCGCGCCT L5731 MSH CGTTCTGTCGGACGGAGCTCCTAAAAreverse GCACCGCATCTACCGCGCGGCTCCTGCTG Distance to next 0.2 kb The MSH6 ATG startcodon is at in this U sequence. One more methylation for MSH6 is available in kit ME002 Tumor suppressor-2. SALSA MS- kit ME011 MMR Page 5 of 8

6 MLH3 s NM_ L7722 MLH L0793 MLH3, exon CGTGGGCACGCACGAGCCTCA- AGATCCAAGGTGCGCGCGTCGGCGTCCGAG GCGACCTTGTTCTTCCTTTCCTTCCGA- GAGCTCGAGCAGAGAGGACTGTGATGAGAC Distance to next 9.0 kb The MLH3 ATG startcodon is at in this NM_ sequence (startcodon in exon 2). PMS2 s Genbank AC L7715 PMS L7716 PMS L4043 PMS GCAAAAGGGGGTAGCGCGTGCCAAAG- GCCAACGCTCAGAAACCGTCAGAGGTCACG CCAATGGGAGTTCAGGAGGCGGA- GCGCCTGTGGGAGCCCTGGAGGGAACTTT GGAGGTGAGCGGGGCTCGCAGTCT- TCCGGTGTCCCCTCTCGCGCGCCCTCTTTG Distance to next 0.2 kb The PMS2 ATG startcodon is at in this AC sequence. MSH3 s L7721 MSH3 + Genbank AY reverse 346* 7939-L7720 MSH ** 7938-L7719 MSH GGGCTGCTGCGCGGGAGGCCCAGT-TGCTG ATTTCTGCCCGGATTCTGCTGCCCGGTGAG GTGGGCAGCCTGCGCCCGTTT- GGGTCCCATCGCCCCGGCCCGGCAGATACC GACAGCAGCGGGAGGACCTCCGA-GCCCG CTCGTTACAGCAGAACGCGCGGTCAAGTTT Distance to next * More variable The MSH3 ATG startcodon is at in this AY sequence. ** This contains a but is not digested completely when normal blood-derived DNA is used!!! MGMT s Genbank X L1261 MGMT L5146 MGMT * 7188-L5144 MGMT * More variable Transcript NM_ starts at CCAGCGTAGCCGCCCCGAGCA-GGACCGGG ATTCTCACTAAGCGGGCGCCGTC GGCAAACTAAGGCACAGAGCCTCA-GGCGG AAGCTGGGAAGGCGCCGCCCGGCTTGTAC GTCCTCGCGGTGCGCACCGTT-TGCGA CTTGGTGAGTGTCTGGGTCGCCTCGCTCC Distance to next 0.4 kb Complete sequences are available on request: info@mlpa.com. SALSA MS- kit ME011 MMR Page 6 of 8

7 Reference s Partial sequence L0781 AI CAATTGCCATTTTTTCCTGACATTCACTGT- GGAAATTTGGTGCACGACACTGTTAGGGGA L0382 BCL2 - CTTCTCCTGGCTGTCTCTGAAGACTC- TGCTCAGTTTGGCCCTGGTGGGAGCTTGCA L1862 CDH1 - CTATGAAGGAAGCGGTTCCGAAGCTGCTA- GTCTGAGCTCCCTGAACTCCTCAGAGTCAG L2523 CDK6 - CGTGATTGGACTCCCAGGAGAAGAAGACT- GGCCTAGAGATGTTGCCCTTCCCAGGCAGG L0566 CREM - GGAGCTCCTCCACCAGGTGCTACAAT-TGTA CAGTACGCAGCACAATCAGCTGATGGCACA L0560 TSPAN15 - GGGGTGGAGGACATCATCATGGA-GCACT CTGTCACTGATGGGCTCCTGGGGCCCGGTG L1820 PAH - CAGTGCCCTGGTTCCCAAGAA-CCATTCAAG AGCTGGACAGATTTGCCAATCAGATTCTCA L0123 TNFRSF1A - GCCACACTGCCCTGAGCCCAA-ATGGG GGAGTGAGAGGCCATAGCTGTCTGGC The Hha1 s are marked with grey. s are marked with - Chromosomal location 10p14 18q q22.1 7q p q22 12q23 12p13.31 Complete sequences are available on request: info@mlpa.com. SALSA MS- kit ME011 MMR Page 7 of 8

8 kit ME011 MMR sample picture ,63 158,16 238, ,39 166,35 133,77 153,11 246,50 263,58 318,83 96,10 208, ,61 91,16 195,37 183,12 228, ,81 190,12 201,08 219,36 256,30 281,69 291,57 353,21 396,21 272,35 308,78 326,88 336,91 381,74 364, ,53 344,39 300, Dye Signal Size Figure 1. Capillary electrophoresis pattern from a sample of approximately 50 ng human male control DNA analyzed with kit ME011 MMR (lot 0609) undigested control DNA Dye Signal Size Figure 2. Capillary electrophoresis pattern from a sample of approximately 50 ng human male control DNA analyzed with kit ME011 MMR (lot 0407) digested with Hha1. The MSH3 at length 282 nt contains a but is not completely digested when blood-derived DNA is used! Please note an aspecific product may be present at 350 nt. SALSA MS- kit ME011 MMR Page 8 of

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