ONLINE SUPPLEMENTARY MATERIAL FOR: Synergistic interaction of ABCB1 and ABCG2 polymorphisms predicts the prevalence of toxic encephalopathy during anticancer chemotherapy DJ Erdélyi, E Kámory, B Csókay, H Andrikovics, A Tordai, C Kiss, Á Félné-Semsei, I Janszky, A Zalka, G Fekete, A Falus, GT Kovács, C Szalai Hospitals participating in this study: 1st and 2nd Dept. Pediatrics, Semmelweis University, Budapest; Heim Pál Children Hospital, Budapest; Madarász street Children Hospital, Budapest; Markusovszky Hospital, Szombathely; Dept. Pediatrics, University of Pécs, Pécs; Dept. Pediatrics, University of Debrecen, Debrecen; Dept. of Pediatrics, University of Szeged, Szeged; Borsod County Hospital, Miskolc, all in Hungary. Patients were treated according to the same chemotherapy protocols at all institutes (Table S1). Table S1 Flowchart of the intensive chemotherapy phase of the ALL BFM 90 and 95 protocols, low risk and medium risk arms. Induction Prednisone 60mg/m2 orally for 36 days (including tapering at start and end) Vincristine 4 x 1,5 mg/m2 i.v. bolus Daunorubicin 2-4 x 30 mg/m2 / 3 hours infusion i.v.a L-asparaginase 8 x 10.000 U/m2 / 1 hour i.v. infusion Methotrexate 3-5 x 6-12 mg intrathecally (dose depending on age)b Intensification Cyclophosphamide 1-2 x 1 g/m2 / 1 hour infusion c Cytosine arabinoside 8-16 x 75mg/m2 i.v. bolus c Mercaptopurine 60 mg/m2 orally for 14-28 days c Methotrexate 2 x 6-12 mg intrathecally (dose depending on age) Consolidation Methotrexate 4 x 5 g/m2/24 hours infusion Mercaptopurine 25 mg/m2 orally for 56 days Methotrexate 4 x 6-12 mg intrathecally (dose depending on age) Reinduction Dexamethasone 10mg/m2 orally for 30 days (including tapering) Vincristine 4 x 1,5 mg/m2 i.v. bolus Doxorubicin 4 x 30 mg/m2 / 3 hours infusion i.v. L-asparaginase 4 x 10.000 U/m2 / 1 hours i.v. Methotrexate 0-4 x 6-12 mg intrathecally (dose depending on age)b Reintensification Cyclophosphamide 1 x 1 g/m2 / 1 hour infusion Cytosine arabinoside 8 x 75mg/ m2 i.v. bolus Thioguanine 60 mg/m2 orally for 14 days Methotrexate 2 x 6-12 mg intrathecally (dose depending on age) The intensive chemotherapy phase was followed by an oral maintenance chemotherapy period completed 2 or 3 years after the start of intensive therapy. a Patients assigned to the medium risk arm were administered 8 doses of anthracyclines, while 6 doses were given at the low risk arm. In the latter group, two daunorubicin doses were omitted. b Number of doses depending on central nervous system involvement of ALL at diagnosis. c Patients received a shorter protocol in the period of 1995-1999 according to the lower limits of dose number ranges indicated. In the altered protocol in use afterwards, the upper limits of the ranges were applied. Abbreviations: ALL: acute lymphoblastic leukemia; BFM: Berlin-Münster-Frankfurt workgroup; i.v.: intravenous Method for testing ABCB1 polymorphisms ABCB1 3435C/T, 2677G/T,A and 1236C/T genotypes were determined by single base extension method. This method and the primer design were based on the work of Gwee et al.,1 however numerous minor changes were made. Three fragments including exon 12, 21 and 26 were amplified in a single multiplex PCR reaction. The sequences of home made primers are shown in Table S2. We used 20 ng of genomic DNA per sample in a total volume of 20 μl containing 5 mM MgCl2 (Applied Biosystems), 200 μM of each dNTP (Promega), 0.15, 0.075 and 0.3 pmol/μl of the primers, and 1.5 unit of AmpliTaq Gold polymerase (Applied Biosystems) in the PCR buffer (Applied Biosystems). The PCR reaction began with an initial denaturation step at 95 ºC for 10 min, followed by 40 cycles of 95 ºC for 30 s, 58 ºC for 30 s and 72 ºC for 60 s, a final extension at 72 ºC for 5 min was also performed. Electrophoresis was carried out by an Agilent lab-on-chip instrument. Unincorporated dNTPs and primers were degraded by the addition of 1 unit of shrimp alkaline phosphatase (SAP, USB) and 0.5 unit of exonuclease I (USB) to 3 μl of PCR product in a final volume of 5 μl. The mixture was incubated at 37 ºC for 1 hour, and then the enzymes were inactivated at 75 ºC for 15 min. The treated PCR products were subjected to a multiplex minisequencing reaction to interrogate the three simultaneous SNP loci. The reaction contained 1 μl of the treated PCR product 0.4, 0.1 and 0.2 pmol/μl of the minisequencing primers, 2.5 μl of SNaPshot Multiplex Ready Reaction Mix (Applied Biosystems) in a total volume of 5 μl. The reaction contained 25 cycles of 96 ºC for 10 s, 54 ºC for 5 s and 60 ºC for 30 s. The unincorporated fluorescent ddNTPs were degraded by the addition of 1 unit of SAP at 37 ºC for 1 hour, and then the enzyme was inactivated at 75 ºC for 15 min. 0.7 μl of the digested product was added to 9 μl of HiDi formamide and 0.5 μl of GeneScan-120 LIZ size standard (Applied Biosystems). The electrophoresis was performed for 17 min with ABI 310 Genetic Analyzer (Applied Biosystems). The runs were analyzed with Genotyper software (Applied Biosystems) and home made template. The relative position of each peak indicated the SNP locus, and the peak color indicated the specific genotype. Genotype findings were verified for the three ABCB1 polymorphisms on 2 samples for each genotype by single PCR followed by bidirectional sequencing using the BigDye v3.1 kit on an ABI310 sequencer. Table S2 Sequences of oligonucleotides used for genotyping ABCB1 SNPs Forward primer Reverse primer Minisequencing primer 1236C/T tctcaccatcccctctgt tctttgtcacttatccagc ct(c)12gactctgcatcttcaggttcag1 2677G/T,A tagggagtaacaaaataacac tgcaggctataggttccagg (tgac)6ttagtttgactcaccttcccag 3435C/T cttacattaggcagtgac ctcacagtaacttggcag (tgac)12ctcctttgctgccctcac 1 Different from that of Gwee et al., changes made due to hairpin formation Method for testing ABCG2 polymorphisms ABCG2 34G/A and 421C/A genotyping was performed using the LightCycler (Roche Diagnostics) allelic discrimination system. Amplification primers and hybridization probes were designed by the LightCycler Probe Design software (Roche Diagnostics). Table S3 shows the oligonucleotide sequences. Oligonucleotides were synthesized by Integrated DNA Technologies (Coralville, USA). PCR was performed by rapid cycling in glass capillaries in a reaction volume of 10 l with 50 ng genomic DNA, 5 µl 2x PCR Master Mix (Promega), supplemented by 0.7 U Taq DNA polymerase (Finnzyme, Espoo, Finnland), and 1.5 mM MgCl2, and 2.5 pmol of labelled oligonucleotides (sensor and anchor). An asymmetric PCR was used for amplification of the two loci with 5:1.5 pmol forward:reverse amplification oligonuclicleotides and 2:20 F:R amounts for 34G>A and 421C>A SNP-s respectively.2 Cycling conditions were the following: initial denaturation at 94C for 2 min, followed by 70 cycles of denaturation 94C for 0 s, annealing at 50C for 10 s, and extension at 72C for 15 s, with a ramping rate of 20C/s. After amplification, melting curve analysis was performed by cooling the samples to 38C, then gradually heating them to 85C with a ramp rate of 0.1C/s. The decline of fluorescence was continuously monitored. Melting curves were converted to melting peaks with wild type and variant alleles showing distinct melting points. Table S3 Sequences of oligonucleotides used for genotyping ABCG2 SNPs Designation Function Sequence ABCG2-34-F amplification primer 5’atgtattgtcacctagtgtttgc ABCG2-34-R amplification primer 5’agctccttcagtaaatgcc ABCG2-34-ANC hybridization probe 5’gcggggaagccattggtgt/36-FAM/ ABCG2-34-SENS hybridization probe 5’/Bodipy650/ccttgtgacactgggat/3Phos/ ABCG2-421-F amplification primer 5’tatgtatactaaacagtcatggtcttaga ABCG2-421-R amplification primer 5’tggagtctgccactttatccagacct ABCG2-421-ANC hybridization probe 5’gatgatgttgtgatgggcactctgacggtgaga/36-FAM/ ABCG2-421-SENS hybridization probe 5’/Bodipy650/aaacttacagttctcagcagctcttcgg/3Phos/ Nucleotides corresponding to the localization of the investigated sequence variants in the sensor hybridization probes are typed with underline bold face characters. Table S4. CSF methotrexate concentrations (µmol/l) in genotype groups Genotype groups N Median Q25 Q75 Minimum Maximum ABCB1 3435TT 45 (14) 1.95 1.47 3.35 0.76 70.8 ABCB1 3435CC+CT 79 (26) 2.34 1.72 4.82 0.78 81.8 ABCB1 2xTTT 42 (13) 1.94 1.45 3.07 0.76 70.8 ABCB1 non-2xTTT 82 (27) 2.34 1.71 4.83 0.78 81.8 ABCG2 421CC 107 (34) 2.22 1.50 4.59 0.76 81.8 17 (6) 2.33 2.02 2.64 1.12 44.7 ABCG2 421AA+AC N: number of CSF methotrexate concentration data available (number of patients the data are originated from); Q25: 25% quantile; Q75: 75% quantile; 2xTTT: 3435T-2677T-1236T haplotype homozygote. REFERENCES 1. Gwee PC, Tang K, Chua JM, Lee EJ, Chong SS, Lee CG. Simultaneous genotyping of seven single-nucleotide polymorphisms in the MDR1 gene by single-tube multiplex minisequencing. Clin Chem 2003; 49: 672-676. 2. Szilvasi A, Andrikovics H, Kalmar L, Bors A, Tordai A. Asymmetric PCR increases efficiency of melting peak analysis on the LightCycler. Clin Biochem 2005; 38: 727-730.