Mutation-specific Assays Research Articles

Identification of Various Recombinants in a Patient Coinfected With the Different SARS-CoV-2 Variants.

Viral recombination that occurs by exchanging genetic materials between two viral genomes coinfecting the same host cells is associated with the emergence of new viruses with different virulence. Herein, we detected a patient coinfected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta and Omicron variants and identified various recombinants in the SARS-CoV-2 full-length spike gene using long-read and Sanger sequencing. Samples from five patients in Japan with household transmission of coronavirus disease 2019 (COVID-19) were analyzed using molecular assays for detection and identification of SARS-CoV-2. Whole-genome sequencing was conducted using multiplex PCR with short-read sequencing. Among the five SARS-CoV-2-positive patients, the mutation-specific assay identified the Delta variant in three, the Omicron variant in one, and an undetermined in one. The undermined patient was identified as Delta using whole-genome sequencing, but samples showed a mixed population of Delta and Omicron variants. This patient was analyzed for viral quasispecies by long-read and Sanger sequencing using a full-length spike gene amplicon. In addition to the Delta and Omicron sequences, the viral quasispecies analysis identified nine different genetic recombinant sequences with various breakpoints between Delta and Omicron sequences. The nine detected recombinant sequences in the spike gene showed over 99% identity with viruses that were detected during the Delta and Omicron cocirculation period from the United States and Europe. This study demonstrates that patients coinfected with different SARS-CoV-2 variants can generate various viral recombinants and that various recombinant viruses may be produced during the cocirculation of different variants.

Detection of SARS-CoV-2 Variants Mu, Beta, Gamma, Lambda, Delta, Alpha, and Omicron in Wastewater Settled Solids Using Mutation-Specific Assays Is Associated with Regional Detection of Variants in Clinical Samples.

ABSTRACTChanges in the circulation of SARS-CoV-2 variants of concern (VOCs) may require changes in the public health response to the COVID-19 pandemic, as they have the potential to evade vaccines and pharmaceutical interventions and may be more transmissive than other SARS-CoV-2 variants. As such, it is essential to track and prevent their spread in susceptible communities. We developed digital reverse transcription (RT)-PCR assays for mutations characteristic of VOCs and used them to quantify those mutations in samples of wastewater settled solids collected from a publicly owned treatment works (POTW) during different phases of the COVID-19 pandemic. Wastewater concentrations of single mutations characteristic of each VOC, normalized by the concentration of a conserved SARS-CoV-2 N gene, correlate with regional estimates of the proportion of clinical infections caused by each VOC. These results suggest that targeted RT-PCR assays can be used to detect variants circulating in communities and inform the public health response to the pandemic.IMPORTANCE Wastewater represents a pooled biological sample of the contributing community and thus a resource for assessing community health. Here, we show that emergence, spread, and disappearance of SARS-CoV-2 infections caused by variants of concern are reflected in the presence of variant genomic RNA in wastewater settled solids. This work highlights an important public health use case for wastewater.

Droplet digital polymerase chain reaction for detection and quantification of cell-free DNA TP53 target somatic mutations in oral cancer.

BACKGROUND: TP53 mutation is a driver mutation of oral carcinogenesis. This study investigated cancerous and cell-free DNA (cfDNA) in patients with oral squamous cell carcinoma (OSCC) to detect the target hotspot somatic mutation of TP53.OBJECTIVE: TP53 target hotspot mutations were determined in surgically resected primary tumor samples from 107 OSCC patients.METHODS: Cancerous and cfDNA samples were examined for mutations through droplet digital polymerase chain reaction (ddPCR) by using mutation-specific assays. The ddPCR results were evaluated alongside clinicopathological data.RESULTS: In total, 23 cases had target TP53 mutations in varying degrees. We found that OSCC had relatively low cfDNA shedding, and mutations were at low allele frequencies. Of these 23 cases, 13 had target TP53 mutations in their corresponding cfDNA. Target somatic mutations in cancerous DNA and cfDNA are related to cervical lymph node metastasis. The cfDNA concentration is related to primary tumor size, lymph node metastasis, and OSCC stage.CONCLUSIONS: Our results show that the detection of TP53 target somatic mutations in OSCC patients by using ddPCR is technically feasible. Low levels of cfDNA may produce different results between cancerous tissue and cfDNA analyses. Future research on cfDNA may quantify diagnostic biomarkers in the surveillance of OSCC patients.

EMQN best practice guidelines for molecular genetic testing and reporting of 21-hydroxylase deficiency

Molecular genetic testing for congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency (21-OHD) is offered worldwide and is of importance for differential diagnosis, carrier detection and adequate genetic counseling, particularly for family planning. In 2008 the European Molecular Genetics Quality Network (EMQN) for the first time offered a European-wide external quality assessment scheme for CAH (due to 21-OH deficiency). The interest was great and over the last years at about 60 laboratories from Europe, USA and Australia regularly participated in that scheme. These best practice guidelines were drafted on the basis of the extensive knowledge and experience got from those annually organized CAH-schemes. In order to obtain the widest possible consultation with practicing laboratories the draft was therefore circulated twice by EMQN to all laboratories participating in the EQA-scheme for CAH genotyping and was updated by that input. The present guidelines address quality requirements for diagnostic molecular genetic laboratories, as well as criteria for CYP21A2 genotyping (including carrier-testing and prenatal diagnosis). A key aspect of that article is the use of appropriate methodologies (e.g., sequencing methods, MLPA (multiplex ligation dependent probe amplification), mutation specific assays) and respective limitations and analytical accuracy. Moreover, these guidelines focus on classification of variants, and the interpretation and standardization of the reporting of CYP21A2 genotyping results. In addition, the article provides a comprehensive list of common as well as so far unreported CYP21A2-variants.

Abstract A66: Analytical validation of 7 droplet digital PCR assays detecting TERT, BRAF, and NRAS hotspot mutations in plasma-derived circulating tumor DNA (ctDNA)

Abstract Introduction: Serial monitoring of sensitive and specific blood-based biomarkers of disease burden in cancer patients could enable clinicians to adjust treatments at the earliest signs of disease progression when the likelihood of improved outcomes is probably greatest. Such assays require preanalytical, analytical, and clinical validation prior to use. We conducted analytical validation studies of 7 droplet digital PCR (ddPCR) assays to determine their performance characteristics in detecting mutant TERT, BRAF, and NRAS ctDNA. Methods: Probe-based ddPCR assays (Bio-Rad) detecting BRAF V600E, K, NRAS Q61K, R, L, and TERT C228T, C250T were studied. Preanalytical validation experiments using plasma collected in EDTA tubes investigated processing variables including plasma volumes, centrifugation speeds, and DNA extraction efficiencies, and evaluated the necessity of internal controls using spike-in experiments. Analytical validation studies assessed accuracy using plasma from healthy donors spiked with known amounts of mutant nucleosomal DNAs from control cell lines. Potentially interfering substances were evaluated using the AcroMetrix inhibition panel (Thermo Scientific). Precision/reproducibility was assessed using combinations of multiple reagent lots and operators. Assay specificity was determined using templates with different mutations to check cross-reactivity. Limits of Blank (LoB) and Limits of Detection (LoD) were calculated for each assay using 8 replicate wells of healthy donor plasma or mutant cell line DNA, respectively. Three-phase inter-laboratory harmonization was conducted using: 1) extracted DNA, 2) plasmas spiked with control DNAs, and 3) melanoma patient samples shipped in PAXgene Blood ccfDNA tubes (Qiagen). Results: Preanalytical validation yielded a double centrifugation protocol to reduce contaminating large DNA. Assays were highly accurate and precise with 80-90% recovery of spiked-in mutant templates and coefficients of variation (CVs) <10%, respectively. BRAF and NRAS mutation-specific assays also detected alternative specific mutations in their respective targets that were easily discernible from the perfect-match mutation as discrete clusters in the ddPCR output software. The LoBs ranged from 0.24 to 1.68 copies/mL and 0.016% to 0.058% fractional abundance; LoDs ranged from 0.01% to 0.05%. Inter-laboratory harmonization demonstrated CVs ranging from 1.5% to 15%. Conclusion: This ddPCR-based plasma analysis platform demonstrates low background levels in normal plasma, yielding high sensitivities to detect small amounts of ctDNAs with these mutations. The assays also demonstrate highly reproducible results between laboratories. These assays could be integrated into biomarker-driven clinical trials to evaluate their potential to inform more personalized clinical decision-making. Citation Format: Mahrukh M. Syeda, Broderick Corless, Iman Osman, Cindy Spittle, George Karlin-Neumann, David Polsky. Analytical validation of 7 droplet digital PCR assays detecting TERT, BRAF, and NRAS hotspot mutations in plasma-derived circulating tumor DNA (ctDNA) [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A66.

Detection of Loss of Heterozygosity in cfDNA of Advanced EGFR- or KRAS-Mutated Non-Small-Cell Lung Cancer Patients.

Liquid biopsy is currently approved for management of epidermal growth factor receptor (EGFR)-mutated non-small-cell lung cancer (NSCLC) patients. However, one unanswered question is whether the rate of cell-free DNA (cfDNA)-negative samples is due to technical limitations rather than to tumor genetic characteristics. Using four microsatellite markers that map specific chromosomal loci often lost in lung cancer, we conducted a pilot study to investigate whether other alterations, such as loss of heterozygosity (LOH), could be detected in EGFR-negative cfDNA. We analyzed EGFR-mutated NSCLC patients (n = 24) who were positive or negative for EGFR mutations in cfDNA and compared the results with a second cohort of 24 patients bearing KRAS-mutated cancer, which served as a representative control population not exposed to targeted therapy. The results showed that in EGFR-negative post-tyrosine-kinase-inhibitor (TKI) cfDNAs, LOH frequency was significantly higher than in both pre- and post-TKI EGFR-positive cfDNAs. By contrast, no association between KRAS status in cfDNA and number of LOH events was found. In conclusion, our study indicates the feasibility of detecting LOH events in cfDNA from advanced NSCLC and suggests LOH analysis as a new candidate molecular assay to integrate mutation-specific assays.

Circulating tumor DNA in patients with colorectal adenomas: assessment of detectability and genetic heterogeneity

Improving early detection of colorectal cancer (CRC) is a key public health priority as adenomas and stage I cancer can be treated with minimally invasive procedures. Population screening strategies based on detection of occult blood in the feces have contributed to enhance detection rates of localized disease, but new approaches based on genetic analyses able to increase specificity and sensitivity could provide additional advantages compared to current screening methodologies. Recently, circulating cell-free DNA (cfDNA) has received much attention as a cancer biomarker for its ability to monitor the progression of advanced disease, predict tumor recurrence and reflect the complex genetic heterogeneity of cancers. Here, we tested whether analysis of cfDNA is a viable tool to enhance detection of colon adenomas. To address this, we assessed a cohort of patients with adenomas and healthy controls using droplet digital PCR (ddPCR) and mutation-specific assays targeted to trunk mutations. Additionally, we performed multiregional, targeted next-generation sequencing (NGS) of adenomas and unmasked extensive heterogeneity, affecting known drivers such as APC, KRAS and mismatch repair (MMR) genes. However, tumor-related mutations were undetectable in patients’ plasma. Finally, we employed a preclinical mouse model of Apc-driven intestinal adenomas and confirmed the inability to identify tumor-related alterations via cfDNA, despite the enhanced disease burden displayed by this experimental cancer model. Therefore, we conclude that benign colon lesions display extensive genetic heterogeneity, that they are not prone to release DNA into the circulation and are unlikely to be reliably detected with liquid biopsies, at least with the current technologies.

Droplet digital PCR for detection and quantification of circulating tumor DNA in plasma of head and neck cancer patients

BackgroundDuring posttreatment surveillance of head and neck cancer patients, imaging is insufficiently accurate for the early detection of relapsing disease. Free circulating tumor DNA (ctDNA) may serve as a novel biomarker for monitoring tumor burden during posttreatment surveillance of these patients. In this exploratory study, we investigated whether low level ctDNA in plasma of head and neck cancer patients can be detected using Droplet Digital PCR (ddPCR).MethodsTP53 mutations were determined in surgically resected primary tumor samples from six patients with high stage (II-IV), moderate to poorly differentiated head and neck squamous cell carcinoma (HNSCC). Subsequently, mutation specific ddPCR assays were designed. Pretreatment plasma samples from these patients were examined on the presence of ctDNA by ddPCR using the mutation-specific assays. The ddPCR results were evaluated alongside clinicopathological data.ResultsIn all cases, plasma samples were found positive for targeted TP53 mutations in varying degrees (absolute quantification of 2.2–422 mutational copies/ml plasma). Mutations were detected in wild-type TP53 background templates of 7667–156,667 copies/ml plasma, yielding fractional abundances of down to 0.01%.ConclusionsOur results show that detection of tumor specific TP53 mutations in low level ctDNA from HNSCC patients using ddPCR is technically feasible and provide ground for future research on ctDNA quantification for the use of diagnostic biomarkers in the posttreatment surveillance of HNSCC patients.

Detecting circulating tumor DNA in renal cancer: An open challenge

BackgroundDetection of circulating tumor DNA (ctDNA) in blood of cancer patients is regarded as an important step towards personalized medicine and treatment monitoring. In the present study, we investigated the clinical applicability of ctDNA as liquid biopsy in renal cancer. MethodsctDNA in serum and plasma samples derived from ccRCC and colon cancer patients as well as ctDNA isolated from RCC xenografts with known VHL mutation status was investigated using next generation sequencing (NGS). Additionally, a Taqman mutation specific assay was used for specific VHL mutation detection in blood. ResultsIn our study, we successfully identified KRAS mutation in colon cancer patients. We also confirmed the presence of specific VHL mutations in ctDNA derived from RCC xenografts indicating the capability of renal tumors to release DNA into the blood circulation. However, we could not detect any VHL mutation in plasma or serum samples derived from nine ccRCC patients. To increase the sensitivity, a VHL mutation specific Taqman assay was tested. With this approach, the pVHL mutation p.Val130Leu in exon 2 in one patient was successfully detected. ConclusionThese data suggest a reduced tumor DNA shedding and an increased clearance of the tumor DNA from the circulation in renal cancer patients independently of tumor size, metastases, and necrosis. This implies that highly sensitive detection methods for mutation calling and prior knowledge of the mutation are required for liquid biopsies in ccRCC.

Universal Haplotype-Based Noninvasive Prenatal Testing for Single Gene Diseases.

Researchers have developed approaches for the noninvasive prenatal testing of single gene diseases. One approach that allows for the noninvasive assessment of both maternally and paternally inherited mutations involves the analysis of single nucleotide polymorphisms (SNPs) in maternal plasma DNA with reference to parental haplotype information. In the past, parental haplotypes were resolved by complex experimental methods or inferential approaches, such as through the analysis of DNA from other affected family members. Recently, microfluidics-based linked-read sequencing technology has become available and allows the direct haplotype phasing of the whole genome rapidly. We explored the feasibility of applying this direct haplotyping technology in noninvasive prenatal testing. We first resolved the haplotypes of parental genomes with the use of linked-read sequencing technology. Then, we identified SNPs within and flanking the genes of interest in maternal plasma DNA by targeted sequencing. Finally, we applied relative haplotype dosage analysis to deduce the mutation inheritance status of the fetus. Haplotype phasing and relative haplotype dosage analysis of 12 out of 13 families were successfully achieved. The mutational status of these 12 fetuses was correctly classified. High-throughput linked-read sequencing followed by maternal plasma-based relative haplotype dosage analysis represents a streamlined approach for noninvasive prenatal testing of inherited single gene diseases. The approach bypasses the need for mutation-specific assays and is not dependent on the availability of DNA from other affected family members. Thus, the approach is universally applicable to pregnancies at risk for the inheritance of a single gene disease.

Abstract 3968: Comparison of NGS and digital PCR for the detection of point mutations in breast tumor and plasma samples

Abstract Background Over the past years, tumor derived alterations in plasma has emerged as a promising cancer biomarker. The clinical applications envisioned with liquid biopsies range from monitoring of treatment response to disease progression and acquired resistance. However, the analysis of circulating tumor DNA (ctDNA) is challenging owing to the small fraction of tumor specific DNA relative to background levels of non-tumor derived DNA and therefore requires highly specific and sensitive techniques. Experimental procedures The Ion AmpliSeqTM Cancer Hotspot Panel v2, covering 2,800 COSMIC mutations from 50 cancer genes was used to analyze 31 primary tumor and metastatic lesions along with 19 matched plasma samples from 13 breast cancer (BC) patients receiving neoadjuvant treatment and 6 advanced stage metastatic BC patients. Digital PCR (dPCR) experiments were set up using mutation-specific assays (Biorad) for the detection of 13 hotspot mutations in PIK3CA, TP53, PTEN, AKT1, CDKN2A and STK11 genes previously identified in the solid tumor samples using next generation sequencing (NGS). Results The specificity and sensitivity of the mutation-specific dPCR assays were tested in dilution curves using synthetic oligonucleotides and tumor samples bearing the mutation of interest. Mutations could be robustly detected in plasma samples using dPCR with a sensitivity as low as 0.1% and a sensitivity of 0.5% using NGS. All mutations previously identified using NGS were validated using dPCR in tumor (n = 27) as well as in plasma samples (n = 5). Moreover, dPCR identified 4 additional mutations in 4 plasma samples in the neoadjuvant setting and 4 in the metastatic setting, 2 in tumor and 2 in plasma samples. The mutant allelic frequencies (MAF) of these newly identified mutations were very low (range 0.2%-1.8%) close to the detection limit of the technology. Through the use of dPCR, the detection rate of plasma ctDNA increased from 8% using NGS to 38% in the neoadjuvant setting and from 67% using NGS to 100% in the metastatic setting thereby highlighting the greater sensitivity of the dPCR technology. The MAF assessed by NGS and dPCR were highly correlated both in the neoadjuvant and metastatic (Spearman ρ = 0.84 and ρ = 0.97) settings, a higher concordance between NGS and dPCR being observed when the MAF are high. Conclusions The use of dPCR allows the detection of low-frequency tumor-specific mutations in plasma with a greater sensitivity compared to NGS providing the high accuracy and sensitivity essential for liquid biopsies. Citation Format: Françoise Rothé, Ghizlane Rouas, Michelle Coureau, Marion Maetens, David Brown, Christos Sotiriou, Michail Ignatiadis. Comparison of NGS and digital PCR for the detection of point mutations in breast tumor and plasma samples. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3968.

Abstract A31: Association between TERT promoter mutations and BRAF/NRAS mutations in patients with primary and metastatic melanoma tumors

Abstract Background: BRAF and NRAS are well-established driver oncogenes in melanoma. Mutations in the promoter region of the telomerase reverse transcriptase gene (TERT) increase gene expression and have been identified at high rates in metastatic melanoma, and rarely in familial melanoma. One recent study found an association between TERT mutations and BRAF or NRAS mutations. We developed mutation-specific assays to detect BRAF V600 and NRAS Q61 mutations along with TERT C228T and C250T promoter mutations to identify the prevalence of these mutations in melanoma tumor samples, association with BRAF/NRAS mutations, and potential use of TERT as a biomarker for blood-based monitoring. Methods: We analyzed 316 primary and metastatic tumors from 114 patients with unresectable stage III/IV melanoma, enrolled and followed in the NYU Melanoma Biorepository program. Each patient had >1 tumor samples available for analysis. We used a combination of allele-specific PCR (Taqman) and SNaPshot assays to identify BRAF V600E/K/R, NRAS Q61L/K/R and TERT promoter C228T and C250T mutations in tumors from 114 patients. We tested the association between TERT promoter mutations and BRAF or NRAS mutations using Fisher's Exact Test. We also analyzed plasma for TERT promoter mutations using samples from a separate group of 20 stage IV patients with stable or active disease at the time of blood draw. Results: Among the 114 patients, 49, 40 and 22 had 2, 3 or 4 tumors available for analysis respectively. There were 3 patients from whom we analyzed only 1 tumor. We amplified the TERT promoter in 304/316 (96%) samples, and detected mutations in 177/304 (58%) tumors. We found C228T or C250T mutations in 39/77 (51%) primaries and 138/227 (61%) metastases. C228T and C250T mutations were present in 86/304 (28%) and 87/304 (29%) tumors respectively. Among patients with >2 tumor samples we found that 40/111 (36%) had tumors that were discordant for TERT mutations (e.g. >1 TERT mutant and >1 TERT wild-type). Six patients had tumors with both C228T and C250T mutations, present either within different individual tumors (n=2 patients) or within the same tumor (n=4 patients). We amplified BRAF and NRAS in 307/316 (97%) tumor samples. We detected BRAF mutations in 95/307 (31%) tumors. BRAF V600E/K/R mutations were found in 22/77 (29%) primaries and 73/227 (32%) metastases. We detected NRAS mutations in 54/307 (18%) tumors. NRAS Q61K/L/R mutations were found in 7/77 (9%) primaries and 47/227 (21%) metastases. Among 177 tumors with TERT mutations, we found BRAF V600 mutations in 72/177 (41%) and NRAS Q61 mutations in 34/177 (19%). There was a statistically significant association between the occurrence of TERT mutations and BRAF or NRAS mutations for both primary (OR=4.32, p<0.01, 95% CI 1.57-11.91) and metastatic tumors (OR=3.16, p<0.01, 95% CI 1.79-5.56). Overall, 21/74 (28%) primaries and 85/222 (38%) metastases had mutations in both TERT and BRAF or NRAS. On a per-patient basis, 64/114 (56%) patients had at least 1 NRAS-mutant tumor or 1 BRAF-mutant tumor; 86/114 (75%) had at least 1 TERT mutant tumor. Overall, 98/114 (86%) patients had either a TERT mutation or a BRAF/NRAS mutation. We detected a TERT mutation in the plasma of 1/20 (5%) patients with an available sample. Conclusions: C228T/C250T TERT promoter mutations occur more frequently than BRAF mutations in primary and metastatic melanomas. TERT mutations preferentially associated with BRAF or NRAS mutations suggesting a possible cooperative role with these oncogenes. The high frequency of TERT tumor mutations on a per-patient basis combined with the presence of inter-tumor heterogeneity and the detection of mutated TERT DNA in the plasma suggest that TERT may be a useful disease biomarker in a large proportion of patients. Citation Format: Gregory A. Chang, Jyothirmayee S. Tadepalli, Nathaniel H. Fleming, Kevin Lui, Yongzhao Shao, Farbod Darvishian, Anna Pavlick, Russell Berman, Richard Shapiro, Iman Osman, David Polsky. Association between TERT promoter mutations and BRAF/NRAS mutations in patients with primary and metastatic melanoma tumors. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Melanoma: From Biology to Therapy; Sep 20-23, 2014; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(14 Suppl):Abstract nr A31.

Droplet Digital PCR for DNMT3A and IDH1/2 Mutations to Improve Early Diagnosis of Acute Myeloid Leukemia Relapse after Allogeneic HSCT

INTRODUCTION:Despite the considerable improvement documented over the last two decades in the outcome of allogeneic Hematopoietic Stem Cell Transplantation (allo-HSCT) for Acute Myeloid Leukemia (AML), primary disease relapse still represents the main cause of mortality in transplanted patients. Since most of the available therapies for post-transplantation relapse display very limited activity when enacted in overt hematologic recurrence, efforts are aimed to anticipate relapse detection and treatment to the Minimal Residual Disease (MRD) stage. Still, the genetic heterogeneity and extensive clonal evolution which are distinctive features of AML hinder the identification of reliable MRD markers. Recent studies demonstrated that mutations in the DNMT3A and IDH1/2 genes occur very early during the step-wise process of leukemogenesis, possibly representing disease founder mutations, shared by all disease subclones and maintained throughout the patient longitudinal history. Moreover, by being present both in full-fledged transformed cells and their progenitors, their tracking might provide a wider scope on the efficacy of allo-HSCT in eradicating preleukemic stem cells.METHODS: We took advantage of ultra-sensitive droplet digital PCR (ddPCR) to test a total of 52 bone marrow samples collected longitudinally over time from 17 patients who received myeloablative allo-HSCT for AML. All patients carried at least one mutation amongst DNMT3A R882H, IDH1 R132C, IDH1 R132H, IDH2 R140Q and IDH2 R172K, documented at diagnosis by conventional Sanger sequencing. As controls, we tested bone marrow samples collected at diagnosis from 7 patients typing negative for the mutations, and peripheral blood samples from 8 healthy individuals. ddPCR assays were performed using the Bio-Rad QX100 system: each sample was tested in duplicates, employing 25 ng of genomic DNA in each reaction well and using as reference for each mutation-specific assay the respective wild-type allele. Samples with a mutant-to-wild-type ratio above 0.1% were considered positive. ddPCR results were compared to those obtained testing the same samples by quantitative PCR (qPCR) assessment of the WT1 gene transcript (considering as threshold for relapse prediction 250 copies of WT1/104 copies of ABL) and by qPCR-based hematopoietic chimerism assessment (employing the AlleleSEQR Chimerism Assay and considering as threshold for relapse prediction a host-specific signal above 1%).RESULTS:All the 17 samples collected at diagnosis and typing positive for the mutations of interest by conventional Sanger sequencing resulted positive also for the corresponding ddPCR assay. None of the samples from healthy individuals or from patients typing negative for the mutations resulted positive by ddPCR. All the samples tested at post-transplantation relapse remained positive for the mutations present at diagnosis, except for one case, originally carrying both DNMT3A and IDH2 mutations and typing negative for the latter at relapse. This observation might argue against the putative role of IDH mutations as leukemia-founder events, and suggests that, when present, DNMT3A could represent a more reliable MRD marker. In samples harvested in overt leukemia, the population carrying the mutant allele, quantified by ddPCR, consistently exceeded the morphological count of leukemic blasts. When post-transplantation remission samples were tested, 32/32 (100%) of those harvested from patients who remained long-term leukemia-free (median follow-up after allo-HSCT: 19 months) resulted negative for the mutations of interest, whereas 3/5 (60%) of those from patients who subsequently relapsed resulted positive. Of notice, only 1 of those 5 samples displayed WT1 transcript overexpression and host chimerism above the 1% threshold, whereas the remaining 4 resulted negative by both qPCR-based techniques.CONCLUSIONS: Although the very small number of patients included in this preliminary analysis warrants for caution, ddPCR for DNMT3A and IDH1/2 mutations appears extremely promising, displaying optimal specificity and very high sensitivity in relapse prediction, and comparing favorably with our present and historical results obtained by qPCR-based post-transplantation monitoring techniques. DisclosuresBonini:MolMed S.p.A.: Consultancy.

Establishing optimal quantitative-polymerase chain reaction assays for routine diagnosis and tracking of minimal residual disease in JAK2-V617F-associated myeloproliferative neoplasms: a joint European LeukemiaNet/MPN&MPNr-EuroNet (COST action BM0902) study

Reliable detection of JAK2-V617F is critical for accurate diagnosis of myeloproliferative neoplasms (MPNs); in addition, sensitive mutation-specific assays can be applied to monitor disease response. However, there has been no consistent approach to JAK2-V617F detection, with assays varying markedly in performance, affecting clinical utility. Therefore, we established a network of 12 laboratories from seven countries to systematically evaluate nine different DNA-based quantitative PCR (qPCR) assays, including those in widespread clinical use. Seven quality control rounds involving over 21 500 qPCR reactions were undertaken using centrally distributed cell line dilutions and plasmid controls. The two best-performing assays were tested on normal blood samples (n=100) to evaluate assay specificity, followed by analysis of serial samples from 28 patients transplanted for JAK2-V617F-positive disease. The most sensitive assay, which performed consistently across a range of qPCR platforms, predicted outcome following transplant, with the mutant allele detected a median of 22 weeks (range 6–85 weeks) before relapse. Four of seven patients achieved molecular remission following donor lymphocyte infusion, indicative of a graft vs MPN effect. This study has established a robust, reliable assay for sensitive JAK2-V617F detection, suitable for assessing response in clinical trials, predicting outcome and guiding management of patients undergoing allogeneic transplant.

EGFR Exon 19 Insertions: A New Family of Sensitizing EGFR Mutations in Lung Adenocarcinoma

Epidermal growth factor receptor (EGFR) genotyping is now standard in the management of advanced lung adenocarcinoma, as this biomarker predicts marked benefit from treatment with EGFR tyrosine kinase inhibitors (TKI). EGFR exon 19 insertions are a poorly described family of EGFR mutations, and their association with EGFR-TKI sensitivity in lung adenocarcinoma is uncertain. Patients with lung cancers harboring EGFR exon 19 insertions were studied. The predicted effects of the insertions on the structure of the EGFR protein were examined, and EGFR exon 19 insertions were introduced into Ba/F3 cells to assess oncogenicity and in vitro sensitivity to EGFR-TKIs. In patients receiving TKI, response magnitude was assessed with serial computed tomographic (CT) measurement. Twelve tumors harboring EGFR exon 19 insertions were identified; patients were predominately female (92%) and never-smokers (75%). The 11 specimens available for full sequencing all showed an 18-bp insertion that resulted in the substitution of a Pro for Leu at residue 747. The mutant EGFR transformed the Ba/F3 cells, which were then sensitive to EGFR-TKI. Six patients with measurable disease received TKI and five had a response on serial CT. EGFR exon 19 insertions are a newly appreciated family of EGFR-TKI-sensitizing mutations, and patients with tumors harboring these mutations should be treated with EGFR-TKI. While these mutations may be missed through the use of some mutation-specific assays, the addition of PCR product size analysis to multigene assays allows sensitive detection of both exon 19 insertion and deletion mutations.

Prevalence of BRCA1 and BRCA2 mutations in unselected breast cancer patients from Greece

BackgroundInheritance of a mutation in either BRCA1 or BRCA2 accounts for approximately 5% of all breast cancer cases, but varies by country. Investigations into the contribution of BRCA mutations to breast cancer incidence in Greece have been, for the most part, limited by small sample sizes and by the use of cases selected for their family history of cancer. The aim of the current study was to estimate BRCA mutation frequencies in breast cancer patients unselected for family history.MethodsTo do so, we enrolled 127 unselected women with breast cancer from the Alexandra Hospital in Athens, Greece, a large public hospital in the city. Mutations in BRCA1 and BRCA2 were detected using a combination of techniques and were confirmed by direct sequencing. Two large genomic deletions were sought using mutation-specific assays. A detailed family history of cancer was obtained from each patient.ResultsWe were able to successfully complete testing on samples from 127 women. Among these, six mutations were identified (four in BRCA1 and two in BRCA2) representing 4.7% of the total or 9.5% of cases diagnosed before age forty. None of the mutation carriers had a family history of breast or ovarian cancer. Three of the four BRCA1 mutations were in exon 20: two were a G5331A mutation and the third was a 3.2 kb deletion. The fourth BRCA1 mutation was the 3819delGTAAA in exon 11. The two BRCA2 mutations were in exon 11 (3782del10 and 4512insT).ConclusionsThe G5331A mutation in BRCA1 appears to be a founder mutation in the Greek population.

A Non-Synonymous Mutation in the Canine Pkd1 Gene Is Associated with Autosomal Dominant Polycystic Kidney Disease in Bull Terriers

Polycystic Kidney Disease is an autosomal dominant disease common in some lines of Bull Terriers (BTPKD). The disease is linked to the canine orthologue of human PKD1 gene, Pkd1, located on CFA06, but no disease-associated mutation has been reported. This study sequenced genomic DNA from two Bull Terriers with BTPKD and two without the disease. A non-synonymous G>A transition mutation in exon 29 of Pkd1 was identified. A TaqMan® SNP Genotyping Assay was designed and demonstrated the heterozygous detection of the mutation in 47 Bull Terriers with BTPKD, but not in 102 Bull Terriers over one year of age and without BTPKD. This missense mutation replaces a glutamic acid residue with a lysine residue in the predicted protein, Polycystin 1. This region of Polycystin 1 is highly conserved between species, and is located in the first cytoplasmic loop of the predicted protein structure, close to the PLAT domain and the second transmembrane region. Thus, this change could alter Polycystin 1 binding or localization. Analytic programs PolyPhen 2, Align GVGD and SIFT predict this mutation to be pathogenic. Thus, BTPKD is associated with a missense mutation in Pkd1, and the application of this mutation specific assay could reduce disease transmission by allowing diagnosis of disease in young animals prior to breeding.

Detection of Drug-Resistant Clones in Chronic Myelogenous Leukemia Patients during Dasatinib and Nilotinib Treatment

Imatinib effectively inhibits the tyrosine kinase activity conferred by the BCR-ABL gene [fusion gene of BCR (breakpoint cluster region) and ABL1 (c-abl oncogene 1, receptor tyrosine kinase)] and thereby appreciably improves outcomes for chronic myelogenous leukemia (CML). A small percentage of patients relapse because of the proliferation of escape clones; such relapses can be treated with second-generation drugs. Early detection and monitoring of resistant clones may provide clinical benefit. We describe the development and testing of a new approach for quantitative monitoring of CML resistance. We designed mutation-specific assays that use hydrolysis probes and an array of allele-specific primers containing nucleotides mismatched at various positions. All assays were tested with plasmids containing corresponding mutant or wild-type sequences, allowing identification of optimal assays for specific and effective amplification of the target template. Clinical samples were then used to compare the results of selected assays with those of standard genotyping. We used a modified amplification refractory mutational system approach and testing with plasmid constructs to design assays that allowed highly selective detection of resistance for all target mutations. By taking advantage of single-step performance and high PCR efficiency, we were able to quantitatively track the absolute amount of resistance conferred by a specific mutation over 4 orders of magnitude. Moreover, we designed an integrated test for dasatinib resistance that uses multiple primers simultaneously. These single-step, closed-tube assays specifically target mutations associated with resistance to dasatinib or nilotinib. Compared with standard genotyping, such biased genotyping improves the detection of resistance or alternative features via quantitative analysis of the absolute amount of resistance.

High Frequency of BRCA1 Founder Mutations in the Bahamas.

Abstract The frequency of mutations in the BRCA1 and BRCA2 genes differs among ethnic groups, due to regional founder effects. The Bahamas is an island nation of 305,000 people, with a complex history of immigration from the 1600s-1800s including English, Americans and African slaves. An initial survey by our group demonstrated that 48% of breast cancers in the Bahamas are diagnosed in women under 50 suggesting an inherited cause for many. In a follow up study, we identified four distinct BRCA1 mutations in 9 of 19 high risk Bahamian breast and ovarian cancer families (47.36%). A fifth mutation has been previously published in a Bahamian family and is a confirmed African founder mutation. In the current study, we sought to estimate the prevalence of these mutations among unselected breast and ovarian cancer patients from the Bahamas. We have enrolled 135 unrelated women with breast (n = 133) or ovarian cancer (n=2) attending public and private clinics in the Bahamas and Miami. A detailed family history was obtained from each patient and a saliva sample was obtained for DNA analysis. DNA samples were tested by mutation specific assay for the presence of five BRCA1 mutations (IVS13+1G>A, M1775R, IVS16+6A>C, 4730insG and 943ins10). Twenty-three mutations were detected, representing 17% mutation prevalence in this population, including IVS13+1G>A (14 times), IVS16+6A>C (two times), M1775R (three times), 4730insG (three times) and 943ins10 (once). This reflects a very high rate of genetic breast cancer in this population with a strong founder effect. This important finding raises the possibility of developing an inexpensive genetic screen for inherited susceptibility to breast cancer in the Bahamas and the need to mount an effective cancer prevention strategy for this population at high risk. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 4078.

PCR-Based MRD Detection in AML with Normal Karyotype or Other intermediate Risk Aberrations by the Use of FLT3-LM, NPM1-Mutations, MLL-PTD or WT1-Overexpression.

The prognostic value of MRD detection in AML has been shown for PML-RARA, AML1-ETO, and CBFB-MYH11positive AML, a group which accounts for only 20–25% of AML. The largest group of AML is represented by cases with normal karyotype or unbalanced intermediate risk group karyotypes. In this group different molecular mutations occur, which are associated with heterogeneous clinical outcome. Thus, different MRD patterns can be anticipated. To expand the spectrum of molecular targets in intermediate risk AML, we used MLL-PTD, FLT3-LM, and NPM1 which are detectable in 45–50% of all intermediate risk group pts for MRD detection. In addition, overexpression of WT1 for MRD detection was used to even include pts. without detectable mutations. In total 996 samples (spl) of 234 patients (pts) were analysed by quantitative real time PCR. For MLL-PTD (321 spl of 78 pt), and WT1 (336 spl of 66 pts) universal assays were used. For NPM1 mutation specific assays (182 spl of 54 pts (42 x type A, 2 x type B, 7 x type D, 3 x rare not yet defined types)) and for FLT3-LM (161 spl of 18 selected pts) patient specific assays were used. All assays were RNA based. Sensitivity of the assays were between 1:100.000 to 1:1.000.000 for the FLT3-LM and NPM1, depending on pts specific assay. Sensitivity was 1:10.000 to 1:100.000 for MLL-PTD due to low background levels detectable in healthy controls. The sensitivity of WT1 was relatively low with 1:100 at most, as there was no high WT1 expressor at diagnosis in this cohort. With all markers the clinical course of the disease was clearly be reflected and all 84 relapses were detectable due to recurring high expression rates. In 17 cases, were samples 2–4 months before clinical relapse were available relapses were predictable based on increasing transcript levels. Five different follow up intervals (int) were defined: up to day 21; days 22–60; days 61–120; day 121–365, later. The log change from diagnosis to defined follow up intervals was analyzed. A rapid decline of median transcript ratios in the NPM1 group (int 1: 2 log; int 2 to 4: 4 log) was observed. Relapses in the NPM1 group occurred earliest after one year. AML with FLT3-LM similarly showed good responses with 1–2 log decreases in int 1 and 2 and 3 log in int 3 and 4. Also this group revealed the first relapses in int 5. The MLL-PTD group was characterized by slow response rates with only 0.2 log reduction in int 1 and 2 and hardly 3 log in int 3. In this group many relapses occurred in int 4 and 5. These data reflect the biological differences of these molecular subgroups: NPM1 as a favourable group, FLT3-LM as a slightly unfavourable group with good response rates but high relapse rates, and MLL-PTD as an entity with bad prognosis due to poor response rates and high relapse rates. Due to low sensitivity WT1 reflected only 0.2 log in interval 1 up to 2 log in interval 3. Seven cases were analyzed in parallel for WT1 and MLL-PTD, 6 for WT1 and FLT3-LM, and one for FLT3-LM and MLL-PTD. Although the correlation of parallel assessment was high (R=0.993) the median differences of log changes of FLT3-LM and NPM1 was one log larger than for MLL-PTD and three log larger than for WT1, depending on the initial sensitivity of the assays. In conclusion: MRD detection is feasible in the karyotypically intermediate risk group. it nicely reflects biological difference in this group NPM1, MLL-PTD and FLT3-LM are better MRD-markers than WT1, which may only be investigated in cases without any other available marker.