ALBERT

Description: BCR-ABL measurement by real-time quantitative PCR (RQ-PCR) has become an essential component for assessing treatment response for CML. A major molecular response (MMR) has prognostic significance and can be used to guide therapeutic decisions. However, the various methods are not standardized and the value representing MMR varies, which may lead to misinterpretation of molecular response. To align data, an international reporting scale (IS) was proposed where MMR is 0.10%. Conversion to the IS is achieved by applying laboratory (lab) specific conversion factors (CF). We aimed to calculate CF for diverse RQ-PCR methods by reference of patient BCR-ABL values to those generated in a reference lab with an established CF; validate the CF by subsequent patient sample exchange; examine the concordance of BCR-ABL values after IS conversion; determine if manufactured reference material is suitable for CF calculation. 34 labs from 13 countries (Australia/New Zealand 11, North/South America 9, Asia 8, Europe 6) sent 615 patient samples to the Adelaide reference lab to determine their specific CF. The RQ-PCR methods varied by the control gene (ABL 17, BCR 12, GUSβ 4, G6PDH 2, β2M 1, GAPDH 1; 3 labs used 2 controls therefore 37 methods), instrument, probe technology and standards. The CF for each method was calculated from the bias of patient BCR-ABL values between the originating lab and the reference lab, providing the bias was consistent across the dynamic range (Bland and Altman, Lancet,1986;1:307). CF were determined for 33 methods, 1 failed due to inconsistencies in the bias and 3 labs sent insufficient samples. CF were validated by sending subsequent sets of patient samples to the reference lab. The validation process is complete for 12 methods using 384 samples. The specific CF remained valid for each method. The mean bias between the reference and originating lab values was negligible after conversion. The limits of agreement indicated that 95% of values were within ±4.6-fold of the reference value. In contrast, prior to conversion 95% of values were within ±13-fold. Importantly after conversion the concordance in the range representing MMR was 87% (154/178 samples). In the future, conversion to the IS will be achieved using certified reference material, however this is currently not available. In order to mimic the patient bias CF calculation we prepared prototype reference material using BCR-ABL positive cells diluted to 4 levels using volunteer cells. The material was distributed to 29 labs and analysis completed for 24 methods. For 12 of the 24 the CF calculated using the reference material was consistent with the patient bias CF. This indicates that CF calculation is achievable using manufactured reference material but optimization is required before widespread distribution. In summary, alignment of BCR-ABL data generated from diverse methods is achievable using an international standardisation approach, and differences between laboratories are small enough to allow consistent interpretation of results and clinical decision-making.

Description: Molecular analysis is recommended for monitoring patients (pts) with CML. For imatinib treated pts in chronic phase (CP), molecular analysis provides important prognostic information. A major molecular response (MMR, BCR-ABL ≤0.1% IS (international scale)) is associated with favourable progression free survival and is a primary endpoint of clinical trials. The 3 month (m) BCR-ABL level is predictive of MMR and almost all de-novo pts with values ≤1.0% IS subsequently achieve MMR. The second generation tyrosine kinase inhibitors nilotinib and dasatinib (2TKI) have demonstrated efficacy for CP pts who fail imatinib therapy due to resistance or intolerance. However, treatment failure associated with the presence of a limited spectrum of resistant mutations is evident. Furthermore, it has recently been suggested that failure to achieve a major cytogenetic response (MCR) by 12m defines inadequate response and these pts should be considered for alternative therapies (Cortes et al, Blood,2008,112,516). Pts in minor cytogenetic response or complete hematologic response at 12m had a projected 1 year progression rate of 17% compared to 3% for those with MCR at 12m. The value of molecular monitoring in the setting of 2TKI has not been defined in terms of the early prediction of response or emergence of resistant mutations. We monitored BCR-ABL levels and mutation status in 155 CP pts treated with nilotinib (n=73; 400mg BD) or dasatinib (n=82; ≥100mg (76/82 70mg BD)) after imatinib failure for a median of 18m (range (r) 3–36). The BCR-ABL level at 3m of 2TKI was highly predictive of subsequent MMR, P10% IS rather than upon a significant rise. The rise associated with emergent mutations when BCR-ABL was ≤10% IS was significantly higher: median 7.3-fold, P10% IS are at risk of acquiring 2TKI resistant mutations and would benefit from regular mutation screening until BCR-ABL falls below 10% IS. Thereafter, a significant rise of 〉5-fold in BCR-ABL should trigger mutation screening. Figure Figure

Description: Background: Molecular monitoring by the measurement of major BCR-ABL mRNA levels is important for the evaluation of the therapeutic efficacy of TKI in CML patients. However, there is no commercial kit easily available in each laboratory or hospital, which can estimate deeper responses below MR4.5that is 4.5-log reduction by the international scale (IS) 0.0032%. Methods: An ODK-1201 kit (Otsuka Pharmaceutical Co. Japan) is based on a HawkZ05 Fast One-Step RT-PCR Kit (Roche, Indianapolis, IN, USA). In this kit, reverse transcription and quantitative PCR (RT-qPCR) are performed in one tube, of which products are measured by ABI 7500 fast Dx (Life Technologies Japan, Japan). To isolate enough amount of RNA for the evaluation of molecular responses below MR4.5in CML patients, 7 ml of peripheral blood is required for this kit. To get the conversion factor (CF) for the IS, the panel of WHO International Standard was obtained from NIBSC, which comprises four ampoules each containing freeze-dried BCR-ABL-positive and -negative cells at various ratios from 0.01% to 10%. RNAs were isolated from each ampoule with a QIAamp RNA Blood Mini Kit (QIAGEN) and were subjected to the measurement of major BCR-ABL and ABL mRNAs with an ODK-1201 kit. Since %BCR-ABL/ABL in the WHO standard panel was already defined, CF was calculated by comparing the values of %BCR-ABL/ABL obtained by ODK-1201 with those of WHO standard panel. To validate the results obtained by ODK-1201, we collected 267 peripheral blood samples from CML patients as a multicenter study, and 120 samples in these were measured by ODK-1201 and in the international reference laboratory (Adelaide Lab), respectively. In addition, we conducted another multicenter study to compare ODK-1201 with an Ipsogen BCR-ABL1 Mbcr IS-MMR DX Kit (QIAGEN) and a One-Step qRT-PCR BCR-ABL Kit (Molecular MD), in which we measured the samples from 201 CML patients, 25 patients with non-CML hematologic malignancies and 25 healthy volunteers by these methods. All of the samples were obtained after the written informed consent was given. Results: The CF of ODK-1201 determined by the WHO standard panel was 1.12. After conversion to the IS by this CF, %BCR-ABL/ABLIS determined by ODK-1201 ranged from 0.0007% to 144.6867% in CML patients. In contrast, all of the values were below 0.0007% in the samples from patients with non-CML hematologic malignancies and healthy volunteers. The overall correlation between ODK-1201 and Adelaide Lab system was very good (94% within 3-fold bias) and the evaluation of MMR was concordant in 84% of CML samples. As for 46 CML samples with %BCR-ABL/ABL IS between 0.0032% and 0.1%, IS values by ODK-1201 were similar to the ones by Adelaide Lab system (with MR4.5; 0.0032%) with 89% within 3-fold and high correlation coefficient (r=0.89). Also, the correlation between ODK-1201 and Ipsogen was r = 0.97 (n = 224) and that between ODK-1201 and Molecular MD kit was r = 0.97 (n = 221), indicating that ODK-1201 was as accurate as Ipsogen and Molecular MD kits. Together, these results indicate that ODK-1201 was capable of measuring at least MR4.5 with the lowest value detected as 0.0007% (calculated sensitivity of less than MR5.0) by the IS. Conclusions: We developed a major BCR-ABLmRNA kit, ODK-1201 with CF for the IS and confirmed its high sensitivity (0.0007%) and accuracy. The procedure is very simple and takes only 2.5 h, and it needs a small amount of blood because RT-qPCR is performed in a single tube. It will enable us to evaluate deeper molecular responses in any laboratories. Conflict of interest :received research fundinand and honoraria from Otsuka I.M. received honoraria from Otsuka during the conduct of the study. H.N. received research funding from Otsuka during the conduct of the study and received research funding and honoraria from otsuka outside the submitted work. C.Y. received research funding from Otsuka during the conduct of the study and honoraria from Novartis and Bristol Myers Squibb. S.B. received research funding and honoraria from Novartis, Bristol Myers Squibb, Otsuka and Ariad. L.F. has no conflict of interest. K.D. and T.S. are employee of Otsuka. Y.K. received honoraria from Otsuka during the conduct of the study. T.N. received grants and personal fees from Otsuka during the conduct of the study, and grants and personal fees from Otsuka outside the submitted work. Disclosures Matsumura: Otsuka: Consultancy, Honoraria. Nakamae:Otsuka : Research Funding. Yoshida:Otsuka: Research Funding. Branford:Otsuka: Research Funding. Koga:Otsuka: Employment. Sogabe:Otsuka: Employment. Kanakura:Otsuka: Consultancy. Naoe:Otsuka: Consultancy.

Description: In many parts of the world, diagnosis and monitoring of CML patients is limited by the availability and cost of molecular testing. In countries without molecular diagnostic capabilities, blood samples can be shipped to central labs, but this is both hampered by sample degradation, and the high costs of shipping. This study explores the method of directly spotting peripheral blood onto a paper template (dried blood spots), with subsequent shipping, RNA extraction, and BCR-ABL testing. Methods: Blood Spots and Shipment. We received dried blood spots from Australia and African countries by mail or courier, and blood from CML patients from our institution were also used for these experiments. 200μL of blood (PB) was pipetted onto Whatman 503 Protein Saver Cards (PSC; Sigma-Aldrich), where each card contains four 50μL spots. Cards were allowed to dry for at least 24 hours at room temperature. For mailing, PSCs were sealed into glassine envelopes with a packet of desiccant, and then placed inside a mailing envelope following DOT and IATA regulation for shipping non-regulated, exempt human specimens. RNA Extraction from Cards and %BCR-ABL determination. Blood spots were incubated with proteinase K followed by RNA isolation using RNeasy Mini Kits (Qiagen). Extracted RNA was quantified using a NanoDrop spectrometer (Thermo Scientific). %BCR-ABL was determined using the automated Cepheid GeneXpert platform or manual two-step quantitative RT-PCR on the 7900HT Fast Real-Time PCR System (Applied Biosystems). Results: Bench top time course: To test for effects of long transit times on RNA quality, we performed a time course study of cards at room temperature (RT) with 5 samples. For each sample, multiple cards were spotted with PB. The cards were then allowed to sit at RT for predetermined amounts of time, up to 42 days, before extracting RNA. We measured RNA integrity for one of the specimens (CML # 5) and found rapid degradation with the RIN number going from 8.7 for the fresh blood to 2.8 after 28 days on the card. However the amplification for both BCR-ABL and ABL differed less than one cycle between the fresh blood and the last time point by manual qRT-PCR (BCR-ABL Ct = 23.63 for fresh blood and 24.06 for day 28 PSC; ABL Ct = 26.69 for fresh blood and 27.64 for day 28 PSC). Figure 1 shows the results of the time course experiment for the 5 samples as a plot of ΔCt versus time in days. BCR-ABL qRT-PCR concordance studies: We compared the %BCR-ABL results obtained in fresh specimen at the institution sending the sample with the %BCR-ABL results we obtained from RNA extracted from PSC using the Cepheid GeneXpert. Paired evaluable results were available for 9 samples with a median WBC = 9.8 x 109/L (range: 3.37x109/L – 85.5x109/L). Samples were 8 to 49 days old at the time of extraction. The amount of RNA input into the GeneXpert reaction ranged from 38.75ng to 1μg. The %BCR-ABL detected ranged from 0.37% to 27% (see Table). The mean absolute difference between fresh blood and PSC BCR-ABL% is 2%; the relative mean percent change for BCR-ABL, using fresh blood as the reference is 13.1% (S.D., 31.2), P = 0.24. Conclusions and future directions: Dried blood spots are relatively inexpensive method to transport blood that preserves enough RNA stability to allow highly accurate BCR-ABL detection, when compared to results performed on an identical platform using fresh peripheral blood samples. Further studies are undergoing to accurately determine the sensitivity of this method and the feasibility of using regular mail for inexpensive transport of specimens. Table 1IDWBC (1000/μL)Sample Age at Spotting (Days)Sample Age at RNA extraction (Days)RNA ng/μlVolume GeneXPert (μL)Paper %BCR-ABL (IS)GeneXpertFresh Blood % BCR-ABL (IS) GeneXpertI1na010426349naI224.101311092745I38009181544naI47.4285102.4*3.1I55.50495241.92I63.61307.4225912I785.5130102102439I812.212912.415128.8I9na1281.5250.37*0.71I103.370273257.85.7I1115.912731102325I126.612714.415na2.3 *%BCR-ABL was manually calculated due to late ABL Cts because of low starting material. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

Description: RQ-PCR provides an appropriate method to monitor CML. However methods are not standardized leading to differences in reported BCR-ABL values. An International Scale (IS) was proposed to generate comparable values when tested in any laboratory, Blood,2006,108,28. The scale is fixed to a major molecular response (MMR), a value with established prognostic significance. We distributed BCR-ABL reference standards to 12 laboratories (labs) to establish lab specific conversion factors (CF) for the IS. The IS MMR value is 0.1%. The Adelaide reference laboratory (ref lab) has an established MMR value (0.08%) and the CF is 1.25 (0.1/0.08). Multiplying by 1.25 converts the ref lab values to the IS. The ref lab prepared standards with 3 BCR-ABL levels (L1, L2, L3) by diluting K562 cells in cells of normal volunteers. Trizol stabilized cells were sent frozen to labs in Europe (2), USA (3), Asia (5) and Australia (2) that use various methods and controls (ABL 7, BCR 3, GUS 1, ABL and GUS 1). Each lab determined mean BCR-ABL/control% values for each level, which were correlated with those of the ref lab. CF were calculated from regression equations using the formulae: Log y=(slope×(log 0.1))+intercept, CF=0.1/antilog y, where y=lab equivalent MMR value and 0.1=IS MMR. 11 of 12 labs showed a linear relationship across the standards and were included in the analysis. Prior to IS conversion there was a wide range between the lowest and highest values; L1 22-fold (r0.01–0.31); L2 48-fold (r0.06–3.0); L3 10-fold (r10–101). After IS conversion using lab specific CF the agreement was substantially improved; L1 1.8-fold (r0.07–0.13), L2 2.4-fold (r0.33–0.77), L3 3.9-fold (r19–76). CF have been validated for 5 labs by patient sample exchange. The ref lab tested up to 20 samples per lab and values compared before and after conversion. Conversion failed to align data in 1 lab and the reason is not yet established. In the other 4 labs there was a significant difference in the median values before conversion (p=0.01) but not after (p=0.49). 75% were within 2-fold and 98% within 5-fold after conversion, a significant improvement compared to pre conversion (45% p=0.005, 72% p=0.0001). The preliminary data suggest the approach is a reasonable process to achieve standardization, which is anchored to a critical BCR-ABL value. It allows for differences generated by various RQ-PCR methods and controls. The on-going validity of conversion is reliant on maintaining performance of analysis within a lab. We anticipate the project will lead to preparation of certified reference standards available to all labs and that standardized molecular monitoring will facilitate more consistent adherence to treatment guidelines.

Description: Abstract 2742 Molecular monitoring of BCR/ABL transcripts by real time quantitative reverse transcription PCR (qRT-PCR) is an essential technique for clinical management of patients with BCR/ABL-positive CML and ALL. Though quantitative BCR/ABL assays are performed in hundreds of laboratories worldwide, results among these laboratories cannot be reliably compared due to heterogeneity in test methods, data analysis, reporting, and lack of quantitative standards. Recent efforts towards standardization have been limited in scope. Aliquots of RNA were sent to clinical test centers worldwide in order to evaluate methods and reporting for e1a2, b2a2, and b3a2 transcript levels using their own qRT-PCR assays. Total RNA was isolated from tissue culture cells that expressed each of the different BCR/ABL transcripts. Serial log dilutions were prepared, ranging from 100 to 10−5, in RNA isolated from HL60 cells. Laboratories performed 5 independent qRT-PCR reactions for each sample type at each dilution. In addition, 15 qRT-PCR reactions of the 10−3 b3a2 RNA dilution were run to assess reproducibility within and between laboratories. Participants were asked to run the samples following their standard protocols and to report cycle threshold (Ct), quantitative values for BCR/ABL and housekeeping genes, and ratios of BCR/ABL to housekeeping genes for each sample RNA. Thirty-seven (n=37) participants have submitted qRT-PCR results for analysis (36, 37, and 34 labs generated data for b2a2, b3a2, and e1a2, respectively). The limit of detection for this study was defined as the lowest dilution that a Ct value could be detected for all 5 replicates. For b2a2, 15, 16, 4, and 1 lab(s) showed a limit of detection at the 10−5, 10−4, 10−3, and 10−2 dilutions, respectively. For b3a2, 20, 13, and 4 labs showed a limit of detection at the 10−5, 10−4, and 10−3 dilutions, respectively. For e1a2, 10, 21, 2, and 1 lab(s) showed a limit of detection at the 10−5, 10-4, 10-3, and 10-2 dilutions, respectively. Log %BCR/ABL ratio values provided a method for comparing results between the different laboratories for each BCR/ABL dilution series. Linear regression analysis revealed concordance among the majority of participant data over the 10-1 to 10-4 dilutions. The overall slope values showed comparable results among the majority of b2a2 (mean=0.939; median=0.9627; range (0.399 – 1.1872)), b3a2 (mean=0.925; median=0.922; range (0.625 – 1.140)), and e1a2 (mean=0.897; median=0.909; range (0.5174 – 1.138)) laboratory results (Fig. 1–3)). Thirty-four (n=34) out of the 37 laboratories reported Ct values for all 15 replicates and only those with a complete data set were included in the inter-lab calculations. Eleven laboratories either did not report their copy number data or used other reporting units such as nanograms or cell numbers; therefore, only 26 laboratories were included in the overall analysis of copy numbers. The median copy number was 348.4, with a range from 15.6 to 547,000 copies (approximately a 4.5 log difference); the median intra-lab %CV was 19.2% with a range from 4.2% to 82.6%. While our international performance evaluation using serially diluted RNA samples has reinforced the fact that heterogeneity exists among clinical laboratories, it has also demonstrated that performance within a laboratory is overall very consistent. Accordingly, the availability of defined BCR/ABL RNAs may facilitate the validation of all phases of quantitative BCR/ABL analysis and may be extremely useful as a tool for monitoring assay performance. Ongoing analyses of these materials, along with the development of additional control materials, may solidify consensus around their application in routine laboratory testing and possible integration in worldwide efforts to standardize quantitative BCR/ABL testing. Disclosure: Sher: Invivoscribe Technologies Inc: Employment. Miller:Invivoscribe Technologies Inc: Employment. Huang:Invivoscribe Technologies Inc: Employment. Shaw:Invivoscribe Technologies Inc: Employment.

Description: Introduction: Major Molecular Response (MMR) is defined as a three-log reduction from a standardized baseline of BCR-ABL/control gene transcript ratio in CML patients at diagnosis. MMR has prognostic significance for progression-free survival for patients on Imatinib® therapy. Day-to-day monitoring of the MMR value in clinical laboratories is challenging due to the absence of a commercially available standardized MMR control RNA. To improve the reliability of BCR-ABL quantitation, MolecularMD has evaluated the feasibility of a single MMR control RNA valid for blood samples drawn in EDTA or PAXgene™ tubes. Material and Methods: Patient sample RNAs were interchanged between our laboratory and an International Randomized Interferon versus STI571 study (IRIS) laboratory, which had established an MMR value and international scale reporting. This exchange enabled our laboratory to establish an MMR value and reporting on an international scale using a validated conversion factor. A serial dilution of a BCR-ABL positive cell line into a human BCR-ABL negative cell line was prepared. These dilutions were tested in IRIS laboratories with established MMR value and international scale reporting and at our laboratory by QRT-PCR to determine the BCR-ABL/control gene ratio using respectively BCR and ABL control genes. We compared the BCR-ABL/ABL ratio in 104 paired PB CML patient samples drawn either in EDTA and PAXgene tubes and the BCR-ABL/BCR ratio in 32 patient samples. Stability studies were performed to evaluate the degradation of liquid and dried forms of the MMR RNA. Results: We established a conversion factor (CF) of 0.81 with an MMR value of 0.123%. Using this CF and MMR value, we created appropriate RNA dilutions that matched the MMR value using ABL as a control gene. Repeated analyzes of this MMR control RNA confirmed the accuracy of the sample with a median value of 0.124%, very close to the MMR value defined previously (0.123%). Stability studies demonstrated that the dried RNA samples could be stored several days at 37°C and freeze-thawed up-to 10 times without significant degradation. These RNA samples once reconstituted with water could also be used several times for BCR-ABL monitoring without any significant degradation. Comparison of BCR-ABL/ABL ratio between EDTA and PAXgene tubes revealed differences unlikely to have clinical impact on disease management suggesting that the MMR RNA created would be suitable under both EDTA and PAXgene extraction methodologies. Conclusions: We produced a stable MMR control RNA in large quantity for accurate monitoring of the MMR value. This MMR control RNA is now be tested in several laboratories to confirm the stability and reliability of this reagent. The MMR control RNA will be an important tool for standardizing MMR value in laboratories, and an integral part of a BCR-ABL QRT-PCR diagnostic kit.