Order Solid Tumor Fusion/Expression. It can detect all fusions described in sarcoma, in addition it also detects mutations in most relevant genes. This helps in diagnosis, classification and determining therapy of sarcoma.
Which test should we order for Sarcoma?
Which test should we order for diffuse large B-cell Lymphoma (DLBCL)?
Order Hematology Fusion/Expression test. This test will classify the DLBCL into ABC vs GCB and gives you all mutations and help in selecting therapy and predicting outcome. Our test is the only test on the market that give you GCB vs ABC classification by expression profiling, which is significantly more accurate than IHC, and at the same time gives you mutation profile.
What should I order for acute lymphoblastic leukemia (ALL) to distinguish between Ph-positive vs Ph-like, vs average ALL?
Order Hematology Fusion/Expression test
Which test should I order for lung cancer?
Order the GTC Solid tumor profile. This test will give results of mutations amplification of 434 genes (including EGFR, RAS, BRAF…), but in addition, it will give results on microsatellite instability (MSI) testing and Tumor Mutation Burdon (TMB). However, if you wants information on translocation of ALK, ROS1, and RET, you need to order the GTC Solid Tumor PLUS.
Mutations in cell free DNA (cfDNA) or cells in the peripheral blood along with anemia or thrombocytopenia are the whole mark of myelodysplastic syndrome (MDS). The incidence of MDS is 3-4 per 100,000 per year but increases significantly above the age of 50 and it is at 30 per 100,000 per year in patients above the age of 70. The diagnosis of MDS is confirmed when mutations in hematopoietic cells are detected at relatively high levels (>40% of cells). However, mutations at low levels in few cells can be detected in normal individuals. In general, random somatic mutations occur in normal cells, but rarely these cells evolve into viable clone, but with aging, the possibility of a clone to accumulate increases. Clonal hematopoiesis of indeterminate potential (CHIP) is defined by the presence of low-level mutations in the peripheral blood in clinically normal individuals. CHIP is detected in 3-5% of normal individuals above the age of 50 and in approximately 10% of people aged 70 to 80. The most common mutation is on the DNMT3A gene, followed by TET2 and ASXL1. The rate of transformation to a hematological neoplasia is 0.5–1% per year. Clonal cytopenias of undetermined significance (CCUS) is defined by the presence of cytopenia (anemia, low platelets or white cells) along with low level mutations but does not meet World Health Organization (WHO)-defined criteria for MDS and the mutations are detected in <40% of cells. Approximately 25% to 65% of patients with cytopenia will have mutation in one or more genes. These patients with mutations have significantly higher probability of developing MDS or other hematopoietic neoplasms (AML, MPN, lymphoma,…) within 5 years. In addition, recent studies linked mutations in peripheral blood to cardiovascular disease (CVD). Recent data show that patients with CHIP have 4.0-times greater risk of myocardial infarction as compared to individuals without such clone. The prevalence of CHIP in patients with coronary artery disease is reported to be at 18.2%. In contrast, the prevalence of CHIP in centenarians is only at 2.5%. It has been shown that mutations in TET2 gene, which is one of the commonly mutated genes in CHIP, are pro-inflammatory and lead to the development of atherosclerotic plaques. Based on that it has been suggested that anti-inflammatory agents might slow the progression of cardiovascular disease in patients with low level mutations in peripheral blood. Therefore, testing the peripheral blood for the presence of mutations provides information for: Diagnosis of myelodysplastic syndrome (MDS). Detecting the presence of mutations in the presence of cytopenia and confirming the diagnosis of clonal cytopenias of undetermined (CCUS) Detecting the presence of CHIP to monitor the development of hematologic neoplasms, especially MDS Detecting CHIP and predicting increased risk of cardiovascular disease (CVD) Additional studies are needed to determine the clinical relevance of anti-inflammatory agents in reducing CVD or to determine the relationship between duration of the presence of CHIP or level of the mutated clone with progression of CVD or hematologic neoplasms. References: The shadowlands of MDS: idiopathic cytopenias of undetermined significance (ICUS) and clonal hematopoiesis of indeterminate potential (CHIP). Malcovati L, Cazzola M. Hematology Am Soc Hematol Educ Program. 2015;2015:299-307. doi: 10.1182/asheducation-2015.1.299. PMID: Clonal hematopoiesis of indeterminate potential and its distinction from myelodysplastic syndromes. Steensma DP, Bejar R, Jaiswal S, Lindsley RC, Sekeres MA, Hasserjian RP, Ebert BL. 2015 Jul 2;126(1):9-16. doi: 10.1182/blood-2015-03-631747. PMID: 25931582. Deep Sequencing of Cell-Free Peripheral Blood DNA as a Reliable Method for Confirming the Diagnosis of Myelodysplastic Syndrome. Albitar F, Ma W, Diep K, De Dios I, Agersborg S, Thangavelu M, Brodie S, Albitar M. Genet Test Mol Biomarkers. 2016 Jul;20(7):341-5. doi: 10.1089/gtmb.2015.0278. Epub 2016 Jun 1. Age-related clonal hematopoiesis associated with adverse outcomes. Jaiswal S1, Fontanillas P, Flannick J, Manning A, Grauman PV, Mar BG, Lindsley RC, Mermel CH, Burtt N, Chavez A, Higgins JM, Moltchanov V, Kuo FC, Kluk MJ, Henderson B, Kinnunen L, Koistinen HA, Ladenvall C, Getz G, Correa A, Banahan BF, Gabriel S, Kathiresan S, Stringham HM, McCarthy MI, Boehnke M, Tuomilehto J, Haiman C, Groop L, Atzmon G, Wilson JG, Neuberg D, Altshuler D, Ebert BL. N Engl J Med. 2014 Dec 25;371(26):2488-98. doi: 10.1056/NEJMoa1408617. Clonal Hematopoiesis and Its Impact on Cardiovascular Disease. Sano S, Wang Y, Walsh K. Circ J. 2018 Sep 4. doi: 10.1253/circj.CJ-18-0871. PMID: 30185689. Clinical Implications of Clonal Hematopoiesis. Steensma DP. Mayo Clin Proc. 2018 Aug;93(8):1122-1130. doi: 10.1016/j.mayocp.2018. PMID: 30078412. Myeloid cell contributions to cardiovascular health and disease. Nahrendorf M. Nat Med. 2018 Jun;24(6):711-720. doi: 10.1038/s41591-018-0064-0. PMID: 29867229. Atherosclerosis and clonal hematopoyesis: A new risk factor. Páramo Fernández JA. Clin Investig Arterioscler. 2018 May - Jun;30(3):133-136. doi: 10.1016/j.arteri.2018.03.001. Tet2-Mediated Clonal Hematopoiesis Accelerates Heart Failure Through a Mechanism Involving the IL-1β/NLRP3 Inflammasome. Sano S, Oshima K, Wang Y, MacLauchlan S, Katanasaka Y, Sano M, Zuriaga MA, Yoshiyama M, Goukassian D, Cooper MA, Fuster JJ, Walsh K. J Am Coll Cardiol. 2018 Feb 27;71(8):875-886. doi: 10.1016/j.jacc.2017.12.037. Somatic Mutations and Clonal Hematopoiesis: Unexpected Potential New Drivers of Age-Related Cardiovascular Disease. Fuster JJ, Walsh K. Circ Res. 2018 Feb 2;122(3):523-532. doi: 10.1161/CIRCRESAHA.117.312115. Clonal Hematopoiesis and Evolution to Hematopoietic Malignancies. Bowman RL, Busque L, Levine RL. Cell Stem Cell. 2018 Feb 1;22(2):157-170. doi: 10.1016/j.stem.2018.01.011. Risk and timing of cardiovascular death among patients with myelodysplastic syndromes. Brunner AM, Blonquist TM, Hobbs GS, Amrein PC, Neuberg DS, Steensma DP, Abel GA, Fathi AT. Blood Adv. 2017 Oct 18;1(23):2032-2040. doi: 10.1182/bloodadvances.2017010165. eCollection 2017 Oct 24. The maturation of a 'neural-hematopoietic' inflammatory axis in cardiovascular disease. Stiekema LCA, Schnitzler JG, Nahrendorf M, Stroes ESG. Curr Opin Lipidol. 2017 Dec;28(6):507-512. doi: 10.1097/MOL.0000000000000457. Clonal Hematopoiesis and Risk of Atherosclerotic Cardiovascular Disease. Jaiswal S, Natarajan P, Silver AJ, Gibson CJ, Bick AG, Shvartz E, McConkey M, Gupta N, Gabriel S, Ardissino D, Baber U, Mehran R, Fuster V, Danesh J, Frossard P, Saleheen D, Melander O, Sukhova GK, Neuberg D, Libby P, Kathiresan S, Ebert BL. N Engl J Med. 2017 Jul 13;377(2):111-121. doi: 10.1056/NEJMoa1701719. Clonal hematopoiesis associated with TET2 deficiency accelerates atherosclerosis development in mice. Fuster JJ, MacLauchlan S, Zuriaga MA, Polackal MN, Ostriker AC, Chakraborty R, Wu CL, Sano S, Muralidharan S, Rius C, Vuong J, Jacob S, Muralidhar V, Robertson AA, Cooper MA, Andrés V, Hirschi KK, Martin KA, Walsh K. 2017 Feb 24;355(6327):842-847. doi: 10.1126/science.aag1381. Clonal hematopoiesis. Jan M, Ebert BL, Jaiswal S. Semin Hematol. 2017 Jan;54(1):43-50. doi: 10.1053/j.seminhematol.2016.10.002. Epub 2016 Oct 20. Review. Clonal Hematopoiesis Associated With Adverse Outcomes After Autologous Stem-Cell Transplantation for Lymphoma. Gibson CJ, Lindsley RC, Tchekmedyian V, Mar BG, Shi J, Jaiswal S, Bosworth A, Francisco L, He J, Bansal A, Morgan EA, Lacasce AS, Freedman AS, Fisher DC, Jacobsen E, Armand P, Alyea EP, Koreth J, Ho V, Soiffer RJ, Antin JH, Ritz J, Nikiforow S, Forman SJ, Michor F, Neuberg D, Bhatia R, Bhatia S, Ebert BL. J Clin Oncol. 2017 May 10;35(14):1598-1605. doi: 10.1200/JCO.2016.71.6712.
Chronic Lymphocytic Leukemia Prognostic Indicator
Circulating Ki-67 index in plasma as a biomarker and prognostic indicator in chronic lymphocytic leukemia. Ki-67 is a nuclear antigen that is expressed in all stages of the cell cycle, except G(0), and is widely used as a marker of cellular proliferation in human tumors. We recently showed that elevated levels of Ki-67 circulating in plasma (cKi-67) are associated with shorter survival in patients with acute lymphoblastic leukemia. The current study included 194 patients with CLL and 96 healthy control subjects. cKi-67 levels in plasma were determined using an electrochemiluminescent immunoassay. We normalized the cKi-67 level to the absolute number of lymphocytes in the patient's peripheral blood to establish the plasma cKi-67 index. The cKi-67 index showed significant correlation with lymph node involvement and Rai stage (P=0.05). Higher cKi-67 index values were significantly associated with shorter survival. Multivariate Cox proportional hazards regression analysis demonstrated that the association of the cKi-67 index with shorter survival was independent of IgV(H) mutation status. In a multivariate model incorporating the cKi-67 index with B2M and IgV(H), only cKi-67 index and B2M levels remained as independent predictors of survival. The results of this study suggest that the plasma cKi-67 index, along with B2M level, is a strong predictor of clinical behavior in CLL. Links to more resources Full Text Sources Elsevier Science ClinicalKey Europe PubMed Central - Author Manuscript PubMed Central - Author Manuscript Other Literature Sources COS Scholar Universe Medical Chronic Lymphocytic Leukemia - Genetic Alliance Miscellaneous NCI CPTAC Assay Portal
Patients with Myeloproliferative Disorders
MPL mutation profile in JAK2 mutation-negative patients with myeloproliferative disorders. Mutations in the thrombopoietin receptor gene (myeloproliferative leukemia, MPL) have been reported in patients with JAK2 V617F-negative chronic myeloproliferative disorders (MPDs). We evaluated the prevalence of MPL mutations relative to JAK2 mutations in patients with suspected MPDs. A total of 2790 patient samples submitted for JAK2 mutation analysis were tested using real-time polymerase chain reaction and bidirectional sequencing of plasma RNA. JAK2 V617F-negative samples were tested for JAK2 exons 12 to 14 mutations, and those with negative results were then tested for mutations in MPL exons 10 and 11. Of the 2790 patients, 529 (18.96%) had V617F, 12 (0.43%) had small insertions or deletions in exon 12, and 7 (0.25%) had other JAK2 mutations in exons 12 to 14. Of the 2242 JAK2 mutation-negative patients, 68 (3.03%) had MPL mutations. W515L was the predominant MPL mutation (n=46; 68%), and 10 (15%) patients had other W515 variants. The remaining MPL mutations (n=12, 17%) were detected at other locations in exons 10 and 11 and included 3 insertion/deletion mutations. The S505N mutation, associated with familial MPD, was detected in 3 patients. Overall, for every 100 V617F mutations in patients with suspected MPDs, there were 12.9 MPL mutations, 2.3 JAK2 exon 12 mutations, and 1.3 JAK2 exons 13 to 14 mutations. These findings suggest that MPL mutation screening should be performed before JAK2 exons 12 to 14 testing in JAK2 V617F-negative patients with suspected MPDs.
Chimerism Analysis of Cell-Free DNA
Chimerism Analysis of Cell-Free DNA in Patients Treated with Hematopoietic Stem Cell Transplantation May Predict Early Relapse in Patients with Hematologic Malignancies. BACKGROUND: We studied DNA chimerism in cell-free DNA (cfDNA) in patients treated with HSCT. METHODS: Chimerism analysis was performed on CD3+ cells, polymorphonuclear (PMN) cells, and cfDNA using 16 small tandem repeat loci. The resulting labeled PCR-products were size-fractionated and quantified. RESULTS: Analyzing samples from 191 patients treated with HSCT for nonneoplastic hematologic disorders demonstrated that the cfDNA chimerism is comparable to that seen in PMN cells. Analyzing leukemia patients (N = 126) showed that, of 84 patients with 100% donor DNA in PMN, 16 (19%) had evidence of clinical relapse and >10% recipient DNA in the plasma. Additional 16 patients of the 84 (19%) showed >10% recipient DNA in plasma, but without evidence of relapse. Eight patients had mixed chimerism in granulocytes, lymphocytes, and plasma, but three of these patients had >10% recipient DNA in plasma compared to PMN cells and these three patients had clinical evidence of relapse. The remaining 34 patients showed 100% donor DNA in both PMN and lymphocytes, but cfDNA showed various levels of chimerism. Of these patients 14 (41%) showed laboratory or clinical evidence of relapse and all had >10% recipient DNA in cfDNA. CONCLUSION: Monitoring patients after HSCT using cfDNA might be more reliable than cellular DNA in predicting early relapse. Reference Image A: Copyright © 2016 Mahmoud Aljurf et al. Comparing percent of donor DNA in plasma cfDNA with polymorphonuclear (PMN) and lymphocytes. (a) cfDNA versus PMN DNA in patients with nonneoplastic diseases; (b) cfDNA versus Lymphocytes DNA in patients with nonneoplastic diseases; (c) cfDNA versus PMN in patients with hematologic neoplasms; (d) cfDNA versus lymphocyte DNA in patients with hematologic neoplasms. Reference Image B: Copyright © 2016 Mahmoud Aljurf et al. Chimerism pattern in a patient with CML treated with HSCT. Pretransplant and donor patterns are shown in the left panel. The middle and right panels show the patterns in PMN, lymphocytes, and plasma at two different points. The BCR-ABL fusion level as detected by RT/PCR is shown on top. The middle sample shows mixed chimerism in plasma only as well as residual BCR-ABL1 fusion RNA. The right panel shows the disappearance of the recipient DNA and fusion BCR-ABL1. Published Online: http://dx.doi.org/10.1155/2016/8589270 References E. D. Thomas, R. Storb, R. A. 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Waldmann, “Immune reconstitution at 6 months following T-cell depleted hematopoietic stem cell transplantation is predictive for treatment outcome,” Transplantation, vol. 74, no. 11, pp. 1551–1559, 2002. View at Publisher · View at Google Scholar · View at Scopus J. Storek, R. P. Witherspoon, and R. Storb, “T cell reconstitution after bone marrow transplantation into adult patients does not resemble T cell development in early life,” Bone Marrow Transplantation, vol. 16, no. 3, pp. 413–425, 1995. View at Google Scholar · View at Scopus W. Frankel, A. Chan, R. E. T. Corringham, S. Shepherd, A. Rearden, and J. Wang-Rodriguez, “Detection of chimerism and early engraftment after allogeneic peripheral blood stem cell or bone marrow transplantation by short tandem repeats,” American Journal of Hematology, vol. 52, no. 4, pp. 281–287, 1996. View at Publisher · View at Google Scholar · View at Scopus A. H. Elmaagacli, D. W. Beelen, H. W. Becks et al., “Molecular studies of chimerism and minimal residual disease after allogeneic peripheral blood progenitor cell or bone marrow transplantation,” Bone Marrow Transplantation, vol. 18, no. 2, pp. 397–403, 1996. View at Google Scholar · View at Scopus S.-J. Choi, K.-H. Lee, J.-H. Lee et al., “Prognostic value of hematopoietic chimerism in patients with acute leukemia after allogeneic bone marrow transplantation: a prospective study,” Bone Marrow Transplantation, vol. 26, no. 3, pp. 327–332, 2000. View at Publisher · View at Google Scholar · View at Scopus J. Serrano, J. Roman, J. Sanchez et al., “Molecular analysis of lineage-specific chimerism and minimal residual disease by RT-PCR of p210BCR-ABL and p190BCR-ABL after allogeneic bone marrow transplantation for chronic myeloid leukemia: increasing mixed myeloid chimerism and p190BCR-ABLdetection precede cytogenetic relapse,” Blood, vol. 95, no. 8, pp. 2659–2665, 2000. View at Google Scholar· View at Scopus A. H. Elmaagacli, K. Runkel, N. Steckel et al., “A comparison of chimerism and minimal residual disease between four different allogeneic transplantation methods in patients with chronic myelogenous leukemia in first chronic phase,” Bone Marrow Transplantation, vol. 27, no. 8, pp. 809–815, 2001. View at Publisher · View at Google Scholar · View at Scopus M. Lawler, P. Humphries, and S. R. McCann, “Evaluation of mixed chimerism by in vitro amplification of dinucleotide repeat sequences using the polymerase chain reaction,” Blood, vol. 77, no. 11, pp. 2504–2514, 1991. View at Google Scholar · View at Scopus I. Buño, P. Nava, A. Simón et al., “A comparison of fluorescent in situ hybridization and multiplex short tandem repeat polymerase chain reaction for quantifying chimerism after stem cell transplantation,” Haematologica, vol. 90, no. 10, pp. 1373–1379, 2005. View at Google Scholar · View at Scopus M. Adamek, G. Opelz, K. Klein, C. Morath, and T. H. Tran, “A fast and simple method for detecting and quantifying donor-derived cell-free DNA in sera of solid organ transplant recipients as a biomarker for graft function,” Clinical Chemistry and Laboratory Medicine, vol. 53, pp. 1434–6621, 2015. View at Publisher · View at Google Scholar J. Beck, M. Oellerich, U. Schulz et al., “Donor-derived cell-free DNA is a novel universal biomarker for allograft rejection in solid organ transplantation,” Transplantation Proceedings, vol. 47, no. 8, pp. 2400–2403, 2015. View at Publisher · View at Google Scholar R. Sachidanandam, D. Weissman, S. C. Schmidt et al., “A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms,” Nature, vol. 409, no. 6822, pp. 928–933, 2001.View at Publisher · View at Google Scholar · View at Scopus J. R. Gomez, J. Serrano, A. Jiménez et al., “Myeloid mixed chimerism is associated with relapse in bcr-abl positive patients after unmanipulated allogeneic bone marrow transplantation for chronic myelogenous leukemia,” Haematologica, vol. 85, no. 2, pp. 173–180, 2000. View at Google Scholar · View at Scopus P. Bader, J. Beck, A. Frey et al., “Serial and quantitative analysis of mixed hematopoietic chimerism by PCR in patients with acute leukemias allows the prediction of relapse after allogeneic BMT,” Bone Marrow Transplantation, vol. 21, no. 5, pp. 487–495, 1998. View at Publisher · View at Google Scholar ·View at Scopus
High-Sensitivity Sequencing for the Detection of Mutations
Using high-sensitivity sequencing for the detection of mutations in BTK and PLCγ2 genes in cellular and cell-free DNA and correlation with progression in patients treated with BTK inhibitors. Patients with chronic lymphocytic leukemia (CLL) that develop resistance to Bruton tyrosine kinase (BTK) inhibitors are typically positive for mutations in BTK or phospholipase c gamma 2 (PLCγ2). We developed a high sensitivity (HS) assay utilizing wild-type blocking polymerase chain reaction achieved via bridged and locked nucleic acids. We used this high sensitivity assay in combination with Sanger sequencing and next generation sequencing (NGS) and tested cellular DNA and cell-free DNA (cfDNA) from patients with CLL treated with the BTK inhibitor, ibrutinib. We also tested ibrutinib-naïve patients with CLL. HS testing achieved 100x greater sensitivity than Sanger. HS Sanger sequencing was capable of detecting < 1 mutant allele in background of 1000 wild-type alleles (1:1000). Similar sensitivity was achieved with HS NGS. No BTK or PLCγ2 mutations were detected in any of the 44 ibrutinib-naïve CLL patients. We demonstrate that without the HS testing 56% of positive samples would have been missed for BTK and 85% of PLCγ2 would have been missed. With the use of HS, we were able to detect multiple mutant clones in the same sample in 37.5% of patients; most would have been missed without HS testing. We also demonstrate that with HS sequencing, plasma cfDNA is more reliable than cellular DNA in detecting mutations. Our studies indicate that wild-type blocking and HS sequencing is necessary for proper and early detection of BTK or PLCγ2 mutations in monitoring patients treated with BTK inhibitors. Furthermore, cfDNA from plasma is very reliable sample-type for testing. Reference Image A: Increase in sensitivity with the addition of BNA/LNA oligonucleotides to sequencing (A) Sanger Sequencing. Genomic DNA positive for a BTK C481S (g>c) mutation is serially diluted with WT DNA to determine the limit of detection for the conventional and high-sensitivity (HS) Sanger based assays. Limit of detection is approximately 20% mutant allele in a background of WT by the conventional assay compared with 0.1% in the HS assay. (B) Next Generation Sequencing. The lower panel shows the high sensitivity testing of a sample which clearly demonstrates three different DNA strands with three different mutations: c.1442G>C (C481S), c.1441T>C (C481R) and c.1441T>A (C481S). The upper panel shows the same sample tested in conventional NGS without the high sensitivity approach. The three mutations were detectable but at a lower frequency. Reference Image B: Testing DNA derived from peripheral blood plasma is more sensitive than serum and even cells Temporally matched samples from the same patient (Patient # 4) reveals both a BTK C481R (t>c) and a PLCγ2 L845F (a>t) mutation in plasma. The BTK mutation is not detected in cells and both mutations are absent in serum.
Deep Sequencing of Cell-Free Peripheral Blood DNA as a Reliable Method for Confirming the Diagnosis of Myelodysplastic Syndrome. BACKGROUND: Demonstrating the presence of myelodysplastic syndrome (MDS)-specific molecular abnormalities can aid in diagnosis and patient management. We explored the potential of using peripheral blood (PB) cell-free DNA (cf-DNA) and next-generation sequencing (NGS). MATERIALS AND METHODS: We performed NGS on a panel of 14 target genes using total nucleic acid extracted from the plasma of 16 patients, all of whom had confirmed diagnoses for early MDS with blasts <5%. PB cellular DNA from the same patients was sequenced using conventional Sanger sequencing and NGS. RESULTS: Deep sequencing of the cf-DNA identified one or more mutated gene(s), confirming the diagnosis of MDS in all cases. Five samples (31%) showed abnormalities in cf-DNA by NGS that were not detected by Sanger sequencing on cellular PB DNA. NGS of PB cell DNA showed the same findings as those of cf-DNA in four of five patients but failed to show a mutation in the RUNX1 gene that was detected in one patient's cf-DNA. Mutant allele frequency was significantly higher in cf-DNA compared with cellular DNA (p = 0.008). CONCLUSION: These data suggest that cf-DNA, when analyzed using NGS, is a reliable approach for detecting molecular abnormalities in MDS and should be used to determine if bone marrow aspiration and biopsy are necessary. Published Online:14 Jul 2016 https://doi.org/10.1089/gtmb.2015.0278 Links to more resources Medical Myelodysplastic syndromes - Genetic Alliance Myelodysplastic Syndromes - MedlinePlus Health Information Miscellaneous NCI CPTAC Assay Portal NCI CPTC Antibody Characterization Program
Press Release – Genomic Testing Cooperative
Genomic Testing Cooperative, a Limited Cooperative Association, Launches a New Platform for Affordable Genomic Cancer Profiling Irvine, California-November 1, 2018 - Genomic Testing Cooperative (GTC), a Limited Cooperative Association, announced today that it will offer multiple laboratory-developed genomic profiling tests for hematologic and solid tumors using next-generation sequencing (NGS) technology. The co-op provides a first of its kind platform for cooperation between commercial, hospital-based, and academic laboratories. This co-op structure allows the member laboratories to share resources and to participate in technological innovation and determining the type of tests being developed. In addition, the co-op provides economies of scale that reduce costs of innovation in NGS. The co-op model is ideal for standardizing testing, obtaining FDA-clearance, and working with pharmaceutical companies on clinical trials. Complete molecular profiling including comprehensive interpretation, therapeutic options, and clinical trials are offered to co-op member laboratories at an affordable price. “This co-op platform aims to revolutionize the next-gen sequencing cancer testing approach. Cooperation is critical for clinical laboratories to keep pace with the rapid advances in NGS technology, chemistry, bio-informatics, and clinical applications.” said founder Dr. Maher Albitar, the CEO and CMO at GTC. “In the era of precision medicine, we at the Genomic Testing Cooperative, believe that every patient with cancer has the right to affordable molecular profiling of their cancer so clear treatment options can be explored.” At this time, 8 different cancer genomic profiling tests are available. -Liquid biopsy for hematologic neoplasms is offered covering abnormalities in 177 genes. Bone marrow biopsy, which is a very painful procedure, can potentially be avoided in more than 50% of patients if the liquid biopsy is used to profile molecular abnormalities in cell-free DNA. -The hematology profiling covers the coding sequence of 177 genes and provides complete information on diagnosis, prognosis, and heterogeneity in hematologic neoplasms. Screening for fusion and translocation in hematologic neoplasms is also available covering fusions and expression profiles of 65 different genes. Complete DNA and RNA evaluation of hematologic neoplasms (GTC Hematology Profile PLUS) provide a comprehensive molecular evaluation of mutation, expression, and fusion/translocation of various types of hematologic neoplasms including diagnosis of Ph-like acute lymphoblastic leukemia and distinguishing between GCB and ABC diffuse large B-cell lymphoma. -The solid tumors molecular profile evaluates mutations and fusions in the entire coding sequence of 434 genes and provides information on Tumor Mutation Burden (TMB) and Microsatellite Instability (MSI). A test for various fusions detected in solid tumors is also offered covering translocations involving 55 genes, including ALK, ROS1, RET, NTRK1, NTRK2, NTRK3 and sarcoma translocations. Generated molecular data is curated and checked for accuracy with the aid of proprietary software based on multiple algorithms and deep learning/machine learning approaches. About Genomic Testing Cooperative, LCA Genomic Testing Cooperative (GTC) is a privately-owned molecular testing company located in Irvine, CA. The company operates based on a cooperative (co-op) business model. Members of the co-op hold type A shares with voting rights. The company offers its patron members a full suite of comprehensive genomic profiling based mainly on next-generation sequencing. Molecular alterations are identified based on rigorous testing with the aid of specially developed algorithms to increase accuracy and efficiency. The clinical relevance of the detected alterations is pulled from numerous databases using an internally developed software. Relevance of findings to diagnosis, prognosis, selecting therapy, and predicting outcome are reported to members. The co-op model allows GTC to make the testing and information platform available to members at a lower cost because of a lower overhead. GTC depends on the co-op members for marketing, sales, and billing. For more information, please visit https://genomictestingcooperative.com/. Forward Looking Statements All of the statements, expectations, and assumptions contained in this press release are forward-looking statements. Such forward-looking statements are based on the GTC management’s current expectations. A number of risks and uncertainties, including the ability of the company to recruit members for the co-op or to obtain adequate volume to reduce cost per test may differ from these expectations. Actual results and events may differ materially and adversely from these expectations. All information in this press release is as of the date of the release, and GTC undertakes no duty to update this information unless required by law. Company contact: Jennifer Varca Genomic Testing Cooperative. Jvarca@genomictestingcooperative.com
Acute Myeloid Leukemia | ASH Annual Meeting Abstract
Session: 613. Acute Myeloid Leukemia: Clinical Studies: Poster I Molecular Epidemiologic Associations in Acute Myeloid Leukemia (AML) and Myelodysplastic Syndromes (MDS) within the United States Dr. Albitar’s molecular work is presented at the ASH meeting in oral and poster presentations Saturday, December 1, 2018, 6:15 PM-8:15 PM | Hall GH (San Diego Convention Center) Background: Acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) are heterogeneous groups of disorders with a spectrum of clinical presentations and outcomes. Prognosis depends on various factors including age, karyotype, performance status, previous treatments, and mutation status. Genetic profiling with next generation sequencing (NGS) is increasingly being used at diagnosis to detect presence of somatic mutations for prognostic risk stratification, and identification of therapeutic targets. Here we seek to identify epidemiologic differences in genetic mutations based on population and demographic data in patients with a preliminary diagnosis of AML or MDS. Methods: NGS mutation data were collected for 62 genes related to AML/MDS on a total of 10,934 patient samples submitted for testing for suspected AML/MDS. Samples were run on either the 54-gene NeoType Myeloid Disorders Profile (Neogenomics) or the 37-gene OnkoSight Myeloid Malignancies Panel (Genpath). The frequency of gene mutations (i.e., the number of patient samples with mutations for each gene) was identified for 58 counties in the USA. Counties in which fewer than 50 patient samples were tested were excluded from the dataset to minimize sampling bias. The counties were then grouped into 3 categories ranging from most urban to most rural based on a modified version of the 2013 National Center for Health Statistics classification system G-1 – > 1,000,000 (N=34), G2 - 250,000 – 1,000,000 (N=16) and G3 < 250,000 (N=8). One-way ANOVA and subsequent T-tests were performed for all genes based on the 3 urban-rural groupings to determine if significant differences in frequency of mutations exist between the 3 groupings. Difference of proportions tests were performed to identify variations in the patterns of frequency between counties. Results: The top 10 most frequent mutations were TET2, ASXL1, DNMT3A, SRSF2, TP53, RUNX1, SF3B1, U2AF1, NRAS, and NPM1(highest to lowest). The three mutations with the widest range of variability across counties were DNMT3A, TET2, and ASXL1 (DTA mutations). The median age across all counties was 68 (range 44-77). The county with the youngest and highest median age was Montgomery, CA and Pinellas, FL, with ASXL1 and TET2 as the most frequent mutation, respectively. Sacramento, CA had an unusually high rate of ASXL1 mutations (> 24%). ASXL1 was also significantly higher than TET2 in Essex, NJ; Montgomery, MD; and Sacramento, CA. (p=0.0287, p < 0.0001, p < 0.0001, respectively). IDH1was higher than IDH2 for Martin, FL (p= 0.0481). The highest frequency of TP53 mutation (24%) was in Bexar, TX compared to Montgomery, MD which had the lowest (2%). When counties were grouped based on population density, the frequency of RUNX1 and SF3B1 were statistically different across the counties, highest in G2 compared to G1 and G3 (p= 0.0294 and 0.0010 respectively). Conclusion: Our retrospective observational study is the first of its kind to look at genetic mutations in AML/MDS patients across the United States using commercially available NGS platforms. In general, patients had analogous combinations and frequencies of mutations commonly seen in AML and MDS, and the wide variation in frequency of DTA mutations is consistent with information known about age-related clonal hematopoiesis. In counties that showed a higher rate of ASXL1 > TET2, there may be a potential environmental factor accounting for this difference as the reverse is more commonly seen. Likewise, IDH1 mutations are typically seen at a lower frequency compared to IDH2, and it is interesting to note the reverse in Martin, FL (G2) despite the mutation frequency of all other genes being similar compared to the median for all counties. Our data analysis also showed a significant difference in frequency of mutations for TP53, RUNX1, and SF3B1. These variations have important implications in regard to prognosis, and the approach to treatment. Our observations suggest further investigation is warranted to explore potential environmental exposures related to somatic mutational patterns in patients with AML and MDS. Read more about the poster on ASH site: 60th Annual Meeting and Exposition (December 1-4, 2018) Disclosures: McCloskey: Jazz Pharmaceuticals: Consultancy, Speakers Bureau; Celgene Pharmaceuticals: Honoraria, Speakers Bureau; Amgen Pharmaceuticals: Speakers Bureau; Pfizer: Consultancy; Takeda Pharmaceuticals: Consultancy, Speakers Bureau; COTA: Equity Ownership. Koprivnikar: Amgen: Speakers Bureau; Otsuka: Consultancy; Alexion: Consultancy, Speakers Bureau. Program: Oral and Poster Abstracts Session: 613. Acute Myeloid Leukemia: Clinical Studies: Poster I Hematology Disease Topics & Pathways: AML, Adult, Diseases, Technology and Procedures, Study Population, Clinically relevant, Myeloid Malignancies, NGS Saturday, December 1, 2018, 6:15 PM-8:15 PM Hall GH (San Diego Convention Center) Adam Zrinski Albitar, BS1*, Neil Shah, MD2, James K McCloskey, MD3, Jamie L. Koprivnikar, MD4, Jianhua Zhao, PhD5*, Chirag Desai, MS, MBA5*, Sucha Sudarsanam, MS6*, Maher Albitar, MD7 and Catherine E. Lai, MD8 1Georgetown University School of Medicine, Washington, DC 2Georgetown University Hospital, Washington, DC 3John Theurer Cancer Center, Hackensack, NJ 4John Theurer Cancer Center at Hackensack University Medical Center, Hackensack Medical Center, NJ 5Bioreference Laboratory, Elmwood Park, NJ 6NeoGenomics, Inc., Aliso Viejo, CA 7 Former: NeoGenomics, Valley Center, CA - Now: Genomic Testing Cooperative, Irvine, CA 8Lombardi Comprehensive Cancer Center, Georgetown University Hospital, Washington, DC
Venetoclax in Combination with FLAG-IDA Chemotherapy (FLAG-V-I) for Fit | ASH ANNUAL MEETING ABSTRACT
Dr. Albitar’s molecular work is presented at the ASH meeting in oral and poster presentations Program: Oral and Poster Abstracts | Monday, December 3, 2018, 6:00 PM-8:00 PM Session: 616. Acute Myeloid Leukemia: Novel Therapy, excluding Transplantation: Poster III Background: Venetoclax (VEN) is a potent and selective small molecule BCL2 inhibitor, with activity both as a single agent in relapsed/refractory AML, and in frontline combinations with hypomethylating agents and low-dose cytarabine. The ability of VEN to reduce the apoptotic threshold indicates it may be effective in combination with genotoxic agents which induce apoptosis, such as the FLAG-IDA regimen. Objectives: A Phase 1b/2 clinical trial was designed to assess the safety and efficacy of VEN in combination with FLAG-IDA induction/consolidation. The primary safety endpoint was the overall incidence and severity of adverse events by CTCAE criteria. The primary efficacy endpoint was ORR by modified IWG AML criteria, and defined as CR, CRi, and PR. Secondary analyses include duration of response (DOR) and overall survival (OS), and exploratory analyses include gene expression signatures by RNA sequencing. Methods: Eligibility for the Phase 1b portion includes medically fit, relapsed/refractory (R/R) AML patients of any age with adequate organ function and ECOG PS ≤ 2. Patients receive FLAG-IDA induction/consolidation, in combination with VEN orally daily. FLAG-IDA induction for R/R AML consists of fludarabine 30 mg/m2 IV days 2-6, cytarabine 2 g/m2 IV days 2-6, idarubicin 6 mg/m2 IV days 4-6, and filgrastim 5 mcg/kg daily days 1-7 (or peg-filgrastim 6 mg after day 5 to replace remaining injections). The first cohort (dose -1) received FLAG-IDA with VEN 200 mg on days 1-21 of induction, incorporating a 2-day VEN dose ramp up. After the observation of gram-negative bacteremia and/or sepsis in 5 of the first 6 patients during cycle 1 nadir, an amended dose level -1 induction was designed with VEN 200 mg on days 1-14 and cytarabine 1.5 g/m². After completion of induction/consolidation, single-agent VEN at 400 mg orally continuously is provided as maintenance for patients not proceeding to SCT. The data cutoff for this analysis was 7.26.2018. Results: Twelve patients with a median age of 49 years (range 32 - 72) have been enrolled. All patients had relapsed/refractory AML with a median of 2 (range 1 - 4) prior treatments, and four (33%) patients had received ≥1 prior allogeneic SCT. Six patients (50%) had complex cytogenetics, 3 (25%) were intermediate risk, and 3 (25%) were favorable risk. Additional demographics including molecular annotation at study enrollment are provided in Table 1. The median number of FLAG-IDA + VEN cycles received is 2 (0.5 – 3). Severe adverse events regardless of causality were neutropenic fever/bacteremia (n=5), pneumonia/lung infection (n=4), sepsis (n=4), typhlitis (n=1), and hypotension (n=2). All cases of sepsis occurred in the original dose -1 cohort. No early mortality was observed on study (30-d and 60-d mortality 0%). Of 12 patients, one remains too early for response assessment. Of 11 patients, 8 patients (73%) achieved a best response of CR/CRi (7 CR, 1 CRi). Seven patients attained a best response within the first induction cycle, and one attained blast reduction after cycle 1 followed by CR after re-induction. Median time to ANC recovery > 500/ul in responding patients was 28 days (range 23 to 33 days). Of the 8 responding patients, three patients proceeded to allogeneic SCT, 2 remain on study, 2 patients relapsed, and 1 patient died in CR. Figure 1 depicts OS and DOR. With a median follow-up time of 4 months to date, median DOR has not been reached and the 6-month OS is 67%. NGS evaluation of RNA at pre-treatment and end of cycle 1 (EOC1) timepoints demonstrated no significant difference in BCL2 expression, either before/after therapy per patient, or based on clinical response. In patients who failed to achieve CR/CRi, significantly lower EOC1 expression (p=0.05) of BAX, BCLXL, BCL10, BCL2A1, BCL3, BCL9, TRS1, and TP53 was identified. Additionally, increased MCL1 expression at EOC1 was significantly (p=0.04) associated with relapse. Conclusion: FLAG-IDA chemotherapy with venetoclax demonstrates notable activity in a heavily pre-treated and R/R yet medically fit patient population. Neither prolonged cytopenias nor early mortality was observed. The ongoing Phase 1b portion aims to establish the best VEN dose in combination with intensive chemotherapy, to be followed with a Phase 2 portion with treatment arms for both newly diagnosed and R/R AML patients. Courtney D. DiNardo, MD, MSc1, Maher Albitar, MD2*, Tapan M. Kadia, MD3, Kiran Naqvi, MD, MPH4, Kenneth Vaughan, RN4*, Antonio Cavazos, MSc5*, Sherry A. Pierce, BSN, BA4*, Koichi Takahashi, MD6, Steven M. Kornblau, MD7, Farhad Ravandi, MBBS8, Jorge E. Cortes, MD4, Hagop M. Kantarjian, MD9 and Marina Y. Konopleva, MD, PhD4 1Department of Leukemia, UT MD Anderson Cancer Center, Houston, TX 2Former: NeoGenomics, Valley Center, CA - Now: Genomic Testing Cooperative, Irvine, CA 3Department of Leukemia, M.D. Anderson Cancer Center, Houston, TX 4Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 5Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX 6Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX 7Department of Leukemia, MD Anderson Cancer Center, Houston, TX 8Department of Leukemia, University of Texas- MD Anderson Cancer Center, Houston, TX 9Department of Leukemia, University of Texas M.D. Anderson Cancer Center, Houston, TX
Validation of Clinical Prognostic Models and Integration of Genetic Biomarkers | ASH ANNUAL MEETING ABSTRACT
Dr. Albitar’s molecular work is presented at the ASH meeting in oral and poster presentations. Validation of Clinical Prognostic Models and Integration of Genetic Biomarkers of Drug Resistance in CLL Patients Treated with Ibrutinib Program: Oral and Poster Abstracts | Monday, December 3, 2018: 11:45 AM Type: Oral Session: 642. CLL: Therapy, excluding Transplantation: Advances in CLL Using Novel Combination Therapy Introduction: We previously reported a prognostic scoring system in CLL using pre-treatment factors in patients treated with ibrutinib [Ahn et al, 2016 ASH Annual Meeting]. Here we present long-term follow-up results and validation of the prognostic models in a large independent cohort of patients. We also determine the incidence of resistance-conferring mutations in BTK and PLCG2 genes in different clinical risk groups. Methods and Patients: The discovery cohort comprised 84 CLL patients on a phase II study with either TP53 aberration (deletion 17p or TP53 mutation) or age ≥65 years (NCT01500733). The validation cohort comprised 607 patients pooled from four phase II and III studies for ibrutinib in treatment-naïve or relapsed/refractory CLL (NCT01105247; NCT01578707; NCT01722487; NCT01744691). All patients received single-agent ibrutinib 420mg once daily. We used Cox regression models to identify independent predictors of PFS, Kaplan-Meier method to estimate probabilities of PFS, log-rank test to compare PFS, and Cochran-Armitage trend test to compare the incidence of mutation among subgroups. We used R version 3.5.0 or SAS® version 9.3 for statistical analyses. For biomarker correlation, we tested cellular DNA or cell-free DNA collected from patients in the discovery cohort with the targeted sequencing of BTK and PLCG2 genes. Result: At a median follow-up of 5.2 years, 28 (33.3%) of 84 patients in the discovery cohort progressed or died. 52 (61.9%) patients had treatment-naïve CLL. Independent factors of PFS on univariate analysis were; TP53 aberration, prior treatment, and β-2 microglobulin (B2M) >4mg/L (P<0.05 for all tests). Unmutated IGHV and advanced Rai stage (III/IV) showed a trend toward inferior outcome without reaching statistical significance. Because higher levels of B2M were associated with relapsed/refractory CLL, we performed two multivariate Cox regression models to assess B2M and prior treatment status separately. Risk groups were determined by the presence of TP53 aberration, advanced Rai stage, and B2M >4mg/L for Model 1, and TP53 aberration, advanced Rai stage, and relapsed/refractory CLL for Model 2 (Table 1). The high-risk group had all three adverse risk factors; the intermediate-risk group had two risk factors; and the low-risk group, none or one. The median PFS of the high-risk group was 38.9 months for Model 1 and 38.4 months for Model 2, and was significantly shorter than those of intermediate and low-risk groups. In the validation cohort, 254 (41.8%) of 607 patients progressed or died at a median follow-up of 4.2 years. 167 (27.5%) patients had treatment-naïve CLL. Both models showed statistically significant differences in PFS by risk groups (Table 1). For the high-risk group, 4-year PFS was 30.2% in Model 1 and 30.5% in Model 2, which were inferior to those of intermediate (53.4 and 52.4%) and low-risk groups (68.7 and 73.7%). Model 1 classified 20% of patients and Model 2 classified 28% of patients to the high-risk group. BTK and PLCG2 mutations are common genetic drivers of ibrutinib resistance in CLL. To determine whether the incidence of these mutations correlates with prognostic risk groups, we performed targeted sequencing of BTK and PLCG2 of samples collected from patients in the discovery cohort. We used cell-free DNA for patients who received long-term ibrutinib (≥3 years) and had low circulating tumor burden, and cellular DNA, for samples collected within 3 years on ibrutinib or at progression. Of 84 patients, 69 (82.1%) were tested at least once, and 37 (44.0%) were tested at least twice. The frequency of testing was similar across the risk groups by two models (P>0.05). The cumulative incidences of mutations at 5 years in the low-, intermediate-, and high-risk groups were: 21.4%, 44.8% and 50%, respectively, by Model 1 (P=0.02); and 22.6%, 41.4% and 66.7%, respectively, by Model 2 (P=0.01). Conclusion: We developed and validated prognostic models to predict the risk of disease progression or death in CLL patients treated with ibrutinib. Risk groups classified by three commonly available pre-treatment factors showed statistically significant differences in PFS. The clinically-defined high-risk disease was linked to higher propensity to develop clonal evolution with BTK and/or PLCG2 mutations, which heralded ibrutinib resistance. Inhye E. Ahn, MD1, Xin Tian2*, Maher Albitar, MD3*, Sarah E. M. Herman, PhD4*, Erika M. Cook4*, Susan Soto4*, Wanlong Ma5*, David Ipe6*, L. Claire Tsao6*, Mei Cheng6*, James P. Dean6 and Adrian Wiestner, MD7 1Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD 2Office of Biostatistics Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 3Former: NeoGenomics, Valley Center, CA - Now: Genomic Testing Cooperative, Irvine, CA 4Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 5NeoGenomics Laboratories, Irvine, CA 6Pharmacyclics LLC, an AbbVie Company, Sunnyvale, CA 7NIH, NHLBI, Bethesda, MD
Eltrombopag Improves Hematopoiesis
Dr. Albitar’s molecular work is presented at the ASH meeting in oral and poster presentations Eltrombopag Improves Hematopoiesis in Patients with Low to Intermediate-2 Risk Myelodysplastic Syndrome(MDS) Program: Oral and Poster Abstracts | Saturday, December 1, 2018: 4:00 PM Session: 637. Myelodysplastic Syndromes—Clinical Studies: Novel Therapeutics I Eltrombopag (EPAG), a thrombopoietin receptor agonist, has been shown to improve hematopoiesis in patients with aplastic anemia (AA), but in MDS patients the effect of thrombopoietin mimetics in bone marrow function is still unclear. In this phase-2 dose escalation study, we investigated the safety and effectiveness of EPAG treatment in low to intermediate-2 risk MDS patients (NCT 00961064). Thirty patients were enrolled from March 2011 to July 2017. Preceding enrollment the majority of patients were either diagnosed with AA (n=13) or hypoplastic MDS (n=5). EPAG was started at 50 mg/day, up to a maximal dose of 150 mg/day, increasing the dose by 25mg every 2 weeks. The primary endpoint was hematologic response at 16 or 20 weeks, defined as either: (1) an increase in platelet counts ≥20.000/uL or transfusion independence for a minimum of 8 weeks; (2) hemoglobin (Hb) increase of ≥1.5g/dL from baseline, or a reduction in red blood cells (RBC) transfusion of at least 50%; or (3) an increase in absolute neutrophil counts (ANC) of ≥0.5x109/L or by at least 100% in patients with a baseline ANC <0.5x109/L. Responding patients could continue EPAG treatment on an extension arm. The primary endpoint of hematological response was met in 14/30 patients (47%). All responders continued EPAG on the extension arm. In 3 patients, peripheral blood cell counts declined on EPAG after the initial response. One patient withdrew from the study. Ten of the 14 responding patients achieved a robust response (RR) after a median treatment duration of 15 months (range 7-27 months). Robust response was defined as stable hematopoiesis with at least a hemoglobin >10g/dl, and thrombocytes >50.000/L, and ANC>1000/L. However, peripheral blood cell counts significantly declined in 5/10 RR and EPAG was restarted per protocol. In 4 of these patients, peripheral blood cell counts recovered. One patient did not achieve a second response. Based on International Prognostic Score System (IPSS), 4/30 (13%) patients progressed on study, including 3 non-responders and 1 responder, at a median follow-up of 4 months (3-35 months). The responding patient was diagnosed with increased bone marrow myeloblast 7 months after discontinuation of EPAG for robust response and 35 months after enrolling in the study. New cytogenetic abnormalities determined progression in non-responding patients (Figure). Novel dose-limiting toxicities were not observed. Three patients developed CTCAE grade III hepatic toxicities. One of them discontinued EPAG at 3 months. Elevated transaminases returned to baseline after EPAG discontinuation in 2 patients. In both cases, EPAG was resumed either at the same (150mg/day) or reduced dose (50mg/day) level. There were no treatment-related death cases. One patient died on study before the primary endpoint from acute respiratory distress syndrome. Sequential acquisition of genomic aberrations has been associated with malignant transformation. Targeting next-generation sequencing for somatic variants in genes previously associated with myeloid malignancies (Myeloid cancer genes, MCG) was performed in 29/30 patients with sufficient material (bone marrow mononuclear cells) available from baseline, primary endpoint, and at time of progression. At baseline, 22/29 (76%) patients were found with at least one mutation:TET2 (14.5%), ASXL1 (12.5%), SF3B1 (8.3%), SETBP1 (8.3%), ATM (8.3%), and ZRSR2 (8.3%). After EPAG, additional somatic variants in different genes were detected in 4/14 responders and 7/16 non-responders. Variants present at baseline were no longer detected in post EPAG samples from 4 responding and 6 non-responding patients. The VAF of variants detected at both time points were similar, indicating no selective expansion of clones with EPAG in neither responder, non-responder nor patients with progression based on IPSS. In conclusion, our results suggest that EPAG is well-tolerated and effective in restoring hematopoiesis in patients with low to intermediate-2 risk MDS, particular with a prior history of hypoplastic bone marrow failure syndromes. EPAG was discontinued for robust response in the majority of responders but declining blood cell counts were observed in about 50% of them. Variants in MCG were more common at study entry compared to patients with aplastic anemia (Yoshizato, NEJM, 2015). However, EPAG appears not to selectively promote expansion of clones harboring MCGs in this patient population. Alana Vicente, MD1*, Fernanda Gutierrez-Rodrigues, PhD2*, Valentina Giudice, MD2*, Zhijie Wu, MD, PhD2*, Sachiko Kajigaya, PhD2*, Maria del Pilar Fernandez Ibanez2*, Maher Albitar, MD3, Barbara Weinstein, RN2*, Katherine R. Calvo, MD, PhD2, Danielle M. Townsley, MD, MSc2, Phillip Scheinberg, MD4, Cynthia E. Dunbar, MD5, Neal S. Young, MD2 and Thomas Winkler, MD2 1Hematology Branch, Hematology Branch,National heart,Lung,and Blood Institute(NHLBI),NIH,Bethesda,Maryland, Bethesda, MD 2Hematology Branch, National Heart, Lung, and Blood Institute, National Institute of Health, Bethesda, MD 3Former: NeoGenomics, Valley Center, CA - Now: Genomic Testing Cooperative, Irvine, CA 4Division of Hematology, Hospital A Beneficencia Portuguesa, São Paulo, Brazil 5Hematology Branch, NIH, Bethesda, MD
Acute Lymphoblastic Leukemia | Just published: A consensus of North American experts
Recommendations for the assessment and management of measurable residual disease in adults with acute lymphoblastic leukemia: A consensus of North American experts The vast majority of adults with acute lymphoblastic leukemia (ALL) achieve remission with standard chemotherapy regimens, but many of these patients ultimately relapse and die from leukemia. In these patients, relapse occurs despite achievement of morphologic remission (ie, bone marrow blasts <5%), suggesting that low levels of measurable residual disease (MRD), also called “minimal residual disease,” persist in the remission bone marrow (Figure 1). Compared with morphologic assessment alone, sensitive methods of MRD quantification can better estimate the reduction in posttreatment disease burden and provide information about the leukemia biology and treatment response of individual patients. Posttreatment MRD status is a powerful prognostic factor in all subtypes of ALL and, in many studies, supersedes historically relevant prognostic factors, including age, white blood cell count, and cytogenetics.4–7 Given the significant impact of MRD on survival outcomes in adults with ALL, many authorities suggest that MRD status can be used to inform postremission strategies, such as allogeneic hematopoietic stem cell transplantation (HSCT) in first remission. The development of novel approaches (eg, blinatumomab, inotuzumab ozogamicin, and chimeric antigen receptor [CAR] T cells) that are highly effective in eradicating residual disease has further increased the complexity of decision-making regarding MRD. Download the paper: Measurable Residual Disease in ALL, paper,11,18 A consice description of Acute lymphoblastic leukemia Acute lymphoblastic leukemia (ALL) is a cancer of the lymphoid line of blood cells characterized by the development of large numbers of immature lymphocytes. Symptoms may include feeling tired, pale skin color, fever, easy bleeding or bruising, enlarged lymph nodes, or bone pain. As an acute leukemia, ALL progresses rapidly and is typically fatal within weeks or months if left untreated. In most cases, the cause is unknown.Genetic risk factors may include Down syndrome, Li-Fraumeni syndrome, or neurofibromatosis type 1. Environmental risk factors may include significant radiation exposure or prior chemotherapy. Evidence regarding electromagnetic fields or pesticides is unclear. Some hypothesize that an abnormal immune response to a common infection may be a trigger. The underlying mechanism involves multiple genetic mutations that results in rapid cell division. The excessive immature lymphocytes in the bone marrow interfere with the production of new red blood cells, white blood cells, and platelets. Diagnosis is typically based on blood tests and bone marrow examination.
CSI Laboratory is the first to offer 177 gene liquid biopsy for hematology
-a step forward to precision in cancer diagnostics- CSI LABORATORIES ADVANCES BY PARTNERING WITH DR. MAHER ALBITAR OF GENOMICS TESTING COOPERATIVE (GTC) Membership in the Co-op also makes CSI Laboratory the first to offer 177 gene liquid biopsy for hematology ALPHARETTA – CSI Laboratories, nationally renowned for its quality cancer diagnostics, goes a step forward to precision cancer diagnostics. Today announces its partnership with Genomic Testing Cooperative (GTC) in order to provide a new level of Next Generation Sequencing to the market. This partnership combines the gold standard in quality cancer diagnostics with advanced genomics technology - giving pathologists and oncologists access to the most comprehensive and detailed cancer data. This information also enables physicians to gauge prognosis and recommend more personalized patient treatments as needed. The partnership’s focus on quality and technology has already made CSI Laboratories the first in the market to offer 177 gene panel liquid biopsy for hematology – accelerating cancer diagnostic speed and accuracy. The combined menu of CSI Laboratories and GTC tests represents the most comprehensive and innovative offering in cancer patient profiling on the market. “CSI Laboratories is continuously leveraging state-of-the-art technology and medical experience to give pathologists and oncologists the information they need to provide the best patient care.” Dr. Maher Albitar, founder of GTC and former Senior Vice President, Chief Medical Officer, and Director of R & D at NeoGenomics Laboratories, will be hosting a webinar alongside CSI Laboratories’ esteemed Medical Director, Dr. Lawrence Hertzberg, M.D., to discuss the partnership’s goals and forthcoming capabilities regarding cancer diagnostics. “I am very pleased to be working with the team at CSI Laboratories and we are excited about enabling them to offer the most innovative and comprehensive molecular profiling for hematologic and solid tumors.” _Dr. Albitar “When combined with the innovative, comprehensive and affordable molecular profiling of GTC, the patient-centered personalized pathology services offered at CSI will enable physicians to make the right decision for their patients with more accuracy than ever before,” he added. CSI Laboratories’ clients benefit from having access to an experienced medical team, highly trained technologists and expert scientific advisors dedicated to ensuring the details of every test result are understood in order to personalize patient treatment plans. According to Dr. Hertzberg “CSI is very excited about offering next generation sequencing (NGS) services to all of our clients at a reasonable price by partnering with GTC. We anticipate enhanced diagnostic capability - including possible referral of patients to clinical trials based upon NGS results. “ ABOUT CSI LABORATORIES CSI Laboratories is specialized in precision cancer diagnostics laboratory focused specifically on meeting the unique needs and challenges of pathologists and community hospitals. CSI Laboratories offers flow cytometry, cytogenetic analysis, fluorescence in-situ hybridization (FISH), immunohistochemistry, molecular genetics, and consultations in the areas of hematopathology and surgical pathology. CSI Laboratories is a CLIA-certified and CAP-accredited laboratory located in Alpharetta, GA. CSI Laboratories is independently owned and operated by medical professionals and has provided expert diagnostic testing to pathologists across the United States since 1997. For more information, please visit www.csilaboratories.com. About Genomic Testing Cooperative Genomic Testing Cooperative (GTC) is a privately-owned molecular testing company located in Irvine, CA. The company offers its patron members a full suite of comprehensive genomic profiling based mainly on next-generation sequencing. Molecular alterations are identified based on rigorous testing with the aid of specially developed algorithms to increase accuracy and efficiency. The co-op model allows GTC to make the testing and information platform available to members at a lower cost because of a lower overhead. For more information, please contact us. Read the press release on Business Wire
Looking for an answer quickly from your NGS provider?
Time Matters on Health Tests When dealing with cancer, clinicians and patients need to know the results of molecular testing as soon as possible. Are you waiting 21-28 days to receive your NGS results? Genomic Testing Cooperative (GTC) is using disruptive technology and will report results within 7 days of receiving the sample. GTC tests all coding sequence of 434 genes for solid tumors and 177 genes for hematology and provides a comprehensive report within 7 days from receiving a sample. Despite this extensive testing and comprehensive reporting, GTC manages to offer these panels at an affordable price. For more information on these two tests and others, check out our test menu
INTERVIEW: Introduction to Genomic Testing Cooperative by Dr. Maher Albitar
A quick interview from Genomic Testing Cooperative founder, CEO/CMO, Dr. Albitar, introducing Genomic Testing Cooperative answering questions about it... Get all the answers by watching the following video: What is a precision diagnosis? What makes GTC different? What is the co-op model? How does GTC deliver value in genomic testing? How does GTC use artificial intelligence? How does GTC disrupt the genomic testing market? What will be reported from GTC testing? How do you support community-based labs? How does GTC model contribute to companion testing?
Sarcoma Diagnosis and Classification
Order GTC Solid Tumor Expression/Fusion Profile Sarcoma Diagnosis and Classification. The GTC Solid Tumor Expression/Fusion Profiling provides highly informative and actionable data for patients with sarcoma. Sarcomas are heterogeneous group of cancer that arises in the connective tissue. Diagnosis and subclassification of sarcoma can be very difficult due to overlapping in histological and immunohistological features. Determining the molecular abnormalities, especially fusion genes and chromosomal translocations in a specific sarcoma can be very helpful in diagnosis, subclassification and determining therapy. Sarcoma is a rare cancer type, but it is relatively more common in pediatric patients. In general, the presence of a specific translocation in one sarcoma type does not occur in any other types of sarcoma, thus it is very helpful to test for the driver abnormality in subclassification of sarcomas. Using NGS is the most comprehensive and cost-effective approach to determine the driver molecular abnormality in a cancer expected to be a sarcoma. Our NGS assay analyzes the most common genes involved in translocations reported in sarcoma and covers all partner genes in a fashion similar to break apart probes in FISH testing. Below is a list of the most common translocations in sarcoma. Additional translocations can also be detected with our assay. In addition, mutations in various genes can also be detected and will be reported. Specimen Requirements: -FFPE: 1 H&E slide and 8-10 unstained slides, 5-7 microns of tissue fixed with 10% NBF fixative.. Shipping: Ship using cold pack. Ship with overnight delivery. Turn Around Time: 7 Days Download the PDF about Sarcoma Diagnosis and Classification Read more about the Test
Diffuse Large B-Cell Lymphoma (DLBCL)
Order GTC Hematology Expression/Fusion Profile GTC Hematology Expression/Fusion Profiling provides highly informative and actionable data for patients with DLBCL as follows: 1) B-cell Markers: This assay provides data on the expression of markers specific to B-cell. It will report the levels of expression of B-cell markers, including CD19, CD79A, CD79B, PAX5, CD22, and others. The levels of CD274 (PD-L1) will also be determined and reported. After confirming that the case is B-cell neoplasm, multiple algorithms and deep learning are used to determine the following: 2) Cell of Origin (COO): Diffuse large B-cell lymphomas (DLBCLs) are clinically heterogeneous group and outcome varies significantly between patients irrespective of treatment protocol. However, determining the cell of origin (COO) in DLBCL has been reported by multiple studies to be helpful in distinguishing lymphoma arising from germinal center cells (GBC) with relatively less aggressive clinical course and non-GCB or activated B-cell (ABC). ABC DLBCL has significantly more aggressive clinical course and poor outcome. Both NCCN guideline and the World Health Organization (WHO) classification recommend subclassification of DLBCL into GCB and ABC, either using IHC or expression profiling. The current recommendations and various clinical trials suggest that therapy should be different for ABC subtype. Ibrutinib , lenalidomide or bortezomib should be considered in addition to R-CHOP therapy in patients with DLBCL and ABC subtype. Immunohistochemistry using antibodies for Bcl-6, CD10, and MUM-1 (Hans algorithm) are currently the most widely used method for determining COO or predicting outcome. However, the concordance rate between the expression profiling assay and the Hans algorithm has been reported to be around 73.6%. Therefore, we developed our expression profiling using NGS and validated it against other expression profiling and IHC. Our COO classification is highly reliable. It is based on using artificial intelligence (AI) to analyze the expression data and predict COO. Furthermore, based on analyzing more than 400 cases of lymphoma, this algorithm can further point out more aggressive features if detected within the GCB and the ABC groups. 3) Determining Double Hit Lymphoma (DHL) Double hit lymphoma occurs in about 10% of DLBCL it is defined by translocations involving MYC and BCL2 or BCL6. Double hit DLBCL is almost always in GCB subtype. In principle, all translocations lead to overexpression, but when IHC is used, double-expressor lymphoma can be seen in higher percentage of patients. Different cut-off points for MYC and BCL2/BCL6 IHC-positive cells have been used to define double-expressor leading to controversy and variation in clinical relevance. The expression profiling allows us to determine the RNA expression levels of BCL2, MYC, and BCL6. Therefore, after determining the COO, we can determine if the case is double hit or not. 4) Determining the levels of Ki67 expression: Levels of Ki67 will be determined to rule out the potential diagnosis of Burkitt lymphoma. High Diffuse Large B-Cell Lymphoma (DLBCL) expression of Ki67 mRNA is associated with poor outcome. Specimen Requirements: -FFPE: 1 H&E slide and 8-10 unstained slides, 5-7 microns of tissue fixed with 10% NBF fixative. Shipping: Ship using a cold pack. Ship with overnight delivery. Turn Around Time: 7 days Read more about the Test >>
23rd Annual International Congress on Hematologic Malignancies 2019
23rd Annual International Congress on Hematologic Malignancies 2019: Focus on Leukemias, Lymphomas and Myeloma The annual International Congress on Hematologic Malignancies is dedicated to providing clinicians access to emerging data in treating hematologic malignancies. Providing practical tools to optimize therapy and personalize care. Our Chief Medical Officer Dr. Maher Albitar will be presenting Beyond Genomics: Integrating Molecular Medicine in Our Practice on Friday March 1st, 8:40am. Few words about the Congress Now in its 23rd year, the annual International Congress on Hematologic Malignancies®: Focus on Leukemias, Lymphomas, and Myeloma provides practitioners who manage hematologic malignancies the practical tools to translate emerging data into the best therapy for patients with these tumors, personalize care based upon patient and tumor characteristics, and apply novel management strategies to their practices to improve outcomes for their patients. Back by popular demand! This 3.5-day meeting will be held from Thursday through mid-afternoon Sunday. As always, agenda topics will focus on methods to apply state-of-the-art strategies to your clinical practice settings. This engaging and highly interactive meeting will provide ample opportunity to interact with internationally renowned experts in the management of leukemias, lymphomas, myeloma, myelodysplastic syndromes, myeloproliferative neoplasms, and benign hematologic malignancies. Our faculty will distill practice-changing evidence and recommend methods to place this information in its proper clinical context so it can be applied to the real-world care scenarios you encounter. In doing so, a focus will be placed on how to proactively mitigate and manage treatment-related toxicities associated with new treatment strategies. The well-known and highly interactive Medical Crossfire® discussion panels interspersed throughout the meeting will allow attendees to explore some of the most challenging clinical situations in the management of hematologic malignancies, many of which have multiple potential approaches to care. This dynamic Congress will challenge participants to apply new information they have learned, reflect on new practices they can bring back to their clinics to share with their peers, and ultimately improve patient outcomes in their practice settings. Acknowledgement of Commercial Support This activity is supported by educational grants from AbbVie Inc., Acerta Pharma – A member of the AstraZeneca Group, Adaptive Biotechnologies, Celgene Corporation, Daiichi Sankyo, Inc., Gilead Sciences, Inc., Jazz Pharmaceuticals, Inc., NewLink Genetics, Novartis Pharmaceuticals Corporation, Rigel Pharmaceuticals, Inc., Seattle Genetics, Inc., and Takeda Oncology. Target Audience This educational activity is directed toward community-based hematologists and medical oncologists, as well as fellows involved in the treatment and management of patients with hematologic malignancies. Nurse practitioners, nurses, physician assistants, pharmacists, researchers, and other healthcare professionals interested in the treatment of hematologic malignancies may also participate. Hot Topics for 2019: The expanding role of new immunologic approaches, including CAR T cells and checkpoint inhibitors, in hematologic malignancies The emergence of molecular-based therapies and new cytotoxic formulations in patients with acute leukemias Effective utilization of the increasing therapeutic armamentarium in multiple myeloma New clinical considerations for frontline and subsequent strategies for Hodgkin and non-Hodgkin lymphomas Patient, disease, and drug characteristics will inform sequencing decisions in patients with chronic lymphocytic leukemia New approaches for treatment and duration of therapy among patients with myeloproliferative neoplasms The Congress will take part in: Thursday, February 28, 2019 – Sunday, March 3, 2019 Eden Roc Miami 4525 Collins Avenue Miami Beach, FL, 33140 https://www.gotoper.com/
Acute Lymphoblastic Leukemia
Order GTC Hematology Expression/Fusion Profile The GTC Hematology Expression/Fusion test provides actionable information for: 1) Determining Fusion and classification (Ph-Positive or Ph-Like) Acute lymphoblastic leukemia (ALL) is a heterogeneous disease with genomic alterations dominated by structural chromosomal abnormalities, particularly translocations. Most of the reported chromosomal translocations in ALL lead to the expression of fusion RNAs and proteins that frequently upregulate expression of oncoproteins or the expression of more potent oncoprotein. Philadelphia chromosome-positive (Ph1) ALL is one of the subtypes of ALL that is characterized by t(9;22)(q34;q11) and produces constitutively active BCR-ABL1 fusion oncoprotein. Ph-positive ALL is common in adults and detected in almost 25% of patients but rare in pediatric ALL, only detected in 3% to 5% of patients. Ph-positive ALL is associated with significantly more aggressive disease with poor outcome. However, with the advent of tyrosine kinase inhibitor (TKI), significant improvement in outcomes can be achieved. More recent studies demonstrated that some patients with ALL may not have PH-positive ALL but have a disease just as aggressive called Philadelphia chromosome (Ph)-like ALL. This new subtype is now recognized by the WHO 2016 classification and should be distinguished from other types of ALL and Ph-positive ALL because of its implication on therapy and prognosis. Ph-like ALL has been reported in 24% of adult ALL and in 15% of pediatric ALL. CRLF2 overexpression, resulting from rearrangement, is the most common abnormality in Ph-like ALL. Abnormalities involving ABL-class genes (ABL1, ABL2, PDGFRB, and CSF1R), JAK2 and EPOR are the second most prevalent abnormalities after CRLF2 overexpression. The table below list the abnormalities in Ph-like ALL and the potential targeted therapy. Testing acute lymphoblastic leukemia and precise classification as Ph-like is very important not only for prognosis but also for considering the various kinase inhibitors in the therapy. 2) Detecting mutation: Mutations in various related genes will also be reported including: JAK2, JAK1, NRAS, KRAS, ABL1, IKZF1, Pax5, TP53, ATM, BRAF, and others. 3) Determining Expression levels of B-cell markers: The assay will provide information on the levels of expression of the following genes: ABL1 CD36 CD79B BCR CD44 CD8A CD19 CD58 CRLF2 CD22 CD70 MYC CD274 CD74 PAX5 CD28 CD79A Fusions mRNA that can be detected in Ph-like ALL and potential therapy (check PDF for details) Specimen Requirements: -Fresh Bone marrow or peripheral blood if it contains an adequate number of circulating blasts (>15%). -FFPE: 1 H&E slide and 8-10 unstained slides, 5-7 microns of tissue fixed with 10% NBF fixative.. Shipping: Ship using a cold pack. Ship with overnight delivery. Turn Around Time: 7 days Download the PDF about Acute Lymphoblastic Leukemia Read more about the Test>>
Cellgen Diagnostics and Genomic Testing Cooperative Partner
CELLGEN DIAGNOSTICS AND GENOMIC TESTING COOPERATIVE PARTNER TO ESTABLISH A NEW STANDARD IN CO-DEVELOPMENT OF COMPANION DIAGNOSTICS FOR CANCER THERAPIES Alliance will enable a faster and more rigorous approach to biomarker discovery and companion diagnostic co-development Irvine, CA—April 3, 2019—Cellgen Diagnostics, a leading precision diagnostics company, and Genomic Testing Cooperative (GTC), a pioneer in molecular testing, today announced a strategic collaboration to help accelerate global development of companion tests for various oncology therapeutics. The collaboration, between GTC’s Next Generation Sequencing (NGS), artificial intelligence (AI) based biomarker discovery service and Cellgen’s integrated companion diagnostics platform will provide the pharmaceutical industry a seamless integration of biomarker discovery, validation and development of in vitro diagnostic companion assays (IVD). Companion diagnostics (CDx) enables precision medicine by making sure the correct person is taking the correct therapies. The companies expect the first application of their collaboration will be in immuno-oncology (I-O). “This collaboration integrates GTC’s extensive experience in biomarker identification and companion diagnostics development with Cellgen’s ground-breaking technology to bring unparalleled technical harmonization to the precision oncology industry,” said Lavance Northington, Founder and CEO of Cellgen Diagnostics. “Through this industry-leading partnership, we believe we can improve the pace and pathway of drug development by showcasing the transformative potential of immuno-oncology therapies to patients around the world with an offering that will be unmatched in the industry.” Cellgen will provide a fully automated companion diagnostic platform that can be leveraged across multiple drug pipelines. Cellgen Immune Panel assays will allow pharma groups in R&D to use a standard approach to patient stratification and therapeutic response monitoring during clinical trials and into the clinic. Genomics Testing Cooperative combines next generation sequencing, machine learning and deep-learning to comprehensively profile the tumor microenvironment and create unique patient phenotypic profiles. Synergies between both companies will enable biopharmaceutical companies to make more informed decisions regarding their immuno-oncology pipelines. “Genomic Testing Cooperative was established as a diagnostic company focused on innovation and democratizing the advances in medical diagnostics through a co-op business model,” said Dr. Maher Albitar, founder and CEO of GTC. “Cellgen will provide an amplification-free platform for measuring RNA and testing DNA abnormalities in under 2 hours. We believe in the transformative potential of this collective approach for our pharmaceutical partners because it will reduce the cost and timeframe of pivotal clinical trials by guaranteeing better patient classification throughout the drug development continuum.” The collaboration will initially focus on next generation sequencing applications in early-stage clinical programs to allow researchers comprehensive information from a single sample for molecular classification. Terms of the agreement have not been disclosed. About Cellgen Diagnostics Headquartered in Irvine, California with R&D lab facilities located in San Diego, California, Cellgen is focused on developing and commercializing a non-invasive precision medicine platform that can detect circulating nucleic acids, such mRNA in white blood cells in under 2 hours. Running on its proprietary platform, Cellgen’s disposable cartridge assays will essentially function as a diagnostic memory stick that measures the genetic expression of a patient’s immune system to determine if their immune profile is a match for a particular targeted treatment. Cellgen’s world class team consists of experienced diagnostic, clinical and entrepreneurial executives that have unique insights into the development of a successful start-up enterprise through initial product launch and venture exit. To learn more about Cellgen Diagnostics, please visit www.cellgendx.com About Genomic Testing Cooperative, LCA Genomic Testing Cooperative (GTC) is a privately-owned molecular testing company located in Irvine, CA. The company operates based on a cooperative (co-op) business model. The company offers its patron members a full suite of comprehensive genomic profiling based mainly on next-generation sequencing. Molecular alterations are identified based on rigorous testing with the aid of specially developed algorithms to increase accuracy and efficiency. The clinical relevance of the detected alterations is pulled from numerous databases using an internally developed software. Relevance of findings to diagnosis, prognosis, selecting therapy, and predicting outcomes are reported to members. The co-op model allows GTC to make the testing and information platform available to members at a lower cost because of a lower overhead. GTC depends on the co-op members for marketing, sales, and billing. For more information, please visit www.genomictestingcooperative.com Contact Cellgen Diagnostics Lavance Northington, MBA CEO Lavance@cellgendx.com O: (949) 285-6888 Genomic Testing Cooperative Maher Albitar, M.D. CEO/CMO email@example.com O: (949) 540-9421
Study shows that RNA Plus DNA profiling significantly enhanced Drug Matching
Recent study published in Nature Medicine (Rodon et al, Nature Medicine volume 25, pages 751–758, 2019) showed that molecular profiling using both DNA and RNA significantly enhanced therapy recommendation and patient outcome. A third of the studied patients got drug therapy recommendation when both RNA and DNA testing was performed. Genomic testing cooperative (GTC) offers combined RNA and DNA profiling without significant increase in cost. Order GTC Solid Tumor PLUS or GTC Hematology PLUS for proper RNA and DNA profiling. In addition to DNA profiling (SNV, indels, TMB, and MSI), thorough molecular profiling requires RNA profiling. GTC RNA testing provides important information on fusion/translocation (ALK, ROS1, RET, NTRK, BCR-ABL1, EWRS1, ..), expression levels (MYC, Ki67, PDL1…) and exon skipping (MET exon 14, NTRK…). • Reference: - Rodon J, et al "Genomic and transcriptomic profiling expands precision cancer medicine: The WINTHER trial" Nature Med 2019; 25:751-758.
GTC Presents at the 2019 ASCO Annual Meeting
Genomic Testing Cooperative (GTC) and Collaborators to Present data Resulting from its Proprietary DNA and RNA Profiling of Diffuse Large B-cell Lymphoma at the 2019 ASCO Annual Meeting Irvine, California – May 22, 2019 – Genomic Testing Cooperative, LCA. today announced that data using its unique DNA and RNA profiling will be presented at the American Society of Clinical Oncology (ASCO) annual meeting. In collaboration with University of California San Francisco, Fresno, CA and The University of Texas MD Anderson Cancer Center, Houston, TX, Genomic Testing Cooperative (GTC) used its proprietary DNA- and RNA-based profiling of diffuse large B-cell lymphoma (DLBCL) to study primary brain lymphoma. While DLBCL is common, primary brain lymphoma, also called Primary Central Nervous System Lymphoma (PCNSL), is rare, difficult to treat and poorly studied. Using its proprietary algorithm and modeling of DNA and RNA data, GTC provides important information on the biology of DLBCL that can predict clinical behavior and help clinicians decide proper therapeutic approaches. Data will be presented at ASCO meeting comparing PCNSL with DLBCL to provide information on the biology of the PCNSL that might help in better understanding this type of lymphoma and perhaps improve selection of therapy. Dr. Maher Albitar, GTC Chief Executive Officer and Chief Medical Officer, stated “It is no longer adequate to provide only DNA-based mutation profiling of cancer. RNA profiling using NGS is becoming very important in providing complementary information and comprehensive profiling.” He added “RNA profiling using NGS does not only provide reliable and reproducible quantitative data, but also provides information on splicing abnormalities that are important in understanding the oncogenic potentials of genes”. The number of new DLBCL diagnosed in the US is estimated to be 18,300/year. The number of new PCNSL diagnosed in the US 1,600/year. Presentations details: 1) Abstract # 7549: Title: Molecular profiling of primary central nervous system lymphoma as compared to activated B-cell subtype of diffuse large B-cell lymphoma. Authors: Mohamad Barakat, Maher Albitar, Zijun Xu-Monette, Ken H Young, Haifaa Abdulhaq; University of California San Francisco, Fresno, CA; Genomic Testing Cooperative, Irvine, CA; The University of Texas MD Anderson Cancer Center, Houston, TX; UCSF Fresno, Fresno, CA Presented Monday, June 3, 2019 2) Abstract # 7535 Title: Diversity of genetic alterations of primary central nervous system lymphoma in Hispanic versus non-Hispanic population. Authors: Mohamad Barakat, Maher Albitar, Robin L. Whitney, Calvin Chen, Yu-Hung Kuo, William Silveira, Mohammed SANI Bukari, Subramanyeswara Rao Arekapudi, Karamjit Dhaliwal-Binning, Haifaa Abdulhaq; UCSF Fresno, Fresno, CA; Genomic Testing Cooperative, Irvine, CA; University of California San Francisco, Fresno, CA; Clovis Community Medical Center, Clovis, CA; UCSF Fresno, Clovis, CA; UCSF Fresno, VA, Fresno, CA Presented Monday, June 3, 2019 About Genomic Testing Cooperative, LCA Genomic Testing Cooperative (GTC) is a privately-owned molecular testing company located in Irvine, CA. The company operates based on a cooperative (co-op) business model. Members of the co-op hold type A shares with voting rights. The company offers its patron members a full suite of comprehensive genomic profiling based mainly on next generation sequencing. Molecular alterations are identified based on rigorous testing with the aid of specially developed algorithms to increase accuracy and efficiency. The clinical relevance of the detected alterations is pulled from numerous databases using internally developed software. Relevance of findings to diagnosis, prognosis, selecting therapy, and predicting outcome are reported to members. The co-op model allows GTC to make the testing and information platform available to members at a lower cost because of a lower overhead. GTC depends on the co-op members for marketing, sales, and billing. For more information, please visit https://genomictestingcooperative.com/. Forward Looking Statements All of the statements, expectations and assumptions contained in this press release are forward-looking statements. Such forward-looking statements are based on the GTC management’s current expectations. A number of risks and uncertainties, including ability of the company to recruit members for the co-op or to obtain adequate volume to reduce cost per test may differ from these expectations. Actual results and events may differ materially and adversely from these expectations. All information in this press release is as of the date of the release, and GTC undertakes no duty to update this information unless required by law. Company contact: Jennifer Varca Genomic Testing Cooperative. Jvarca@genomictestingcooperative.com
The FDA has Approved Drugs for FGFR Abnormalities
The FDA has approved Balversa (erdafitinib) as a treatment for adult patients with locally advanced or metastatic bladder cancer that have FGFR3 or FGFR2 abnormalities and that has progressed during or following prior platinum-containing chemotherapy. Urothelial tumors have been reported to show abnormalities in FGFR3 (22%), FGFR1 (8%), and FGFR2 (2%). These abnormalities involve mutations, fusion and amplification/overexpression. Abnormalities in FGFR can also be seen in various tumor types including lung (20%), breast (10%), melanoma (20%) rhabdomyosarcoma (7%), and cervical cancer (5%). Genomic Testing Cooperative (GTC) offers comprehensive testing of FGFR(1, 2, 3, and 4) covering mutations in all coding sequence, various fusions and expression levels. However, mutations studied in the FDA approval process are four point mutations in FGFR3 (FGFR3 gene (p.R248C, p.S249C, p.G370C and p.Y373C) and two fusions (FGFR2:BICC1 and FGFR2:CASP7). Specimen Requirements: FFPE: 1 H&E slide and 6-8 unstained slides, 5-7 microns of tissue fixed with 10% NBF fixative. Please circle tumor for microdissection. Alternatively, the FFPE block can be sent for tumor circling and cutting at our laboratory. Shipping: Ship using cold pack. The cold pack should not directly contact specimen. Ship as soon as sample collected with overnight delivery. Turn Around Time: 7 days DOWNLOAD the PDF
Comprehensive PIK3CA Mutation Analysis
When you order GTC Breast Cancer Profile The FDA has approved Piqray (alpelisib) tablets, to be used in combination with the FDA-approved endocrine therapy fulvestrant, to treat postmenopausal women, and men, with hormone receptor (HR)-positive, human epidermal growth factor receptor 2 (HER2)-negative, PIK3CA-mutated, advanced or metastatic breast cancer following progression on or after an endocrine-based regimen. FDA approval of the drug was based on detecting one of 11 frequent mutations in PIK3CA. Based on our data, these 11 mutations constitute only 62.83% of the mutation we detect when Next Generation Sequencing (NGS) is used. Abnormalities in PIK3CA have been reported in approximately 30% of patients with breast cancer. Most of the reported mutations are gain of function. In addition to mutations, PIK3CA gene amplification has been reported in 10% of breast cancers. Based on our database more than 126 different mutations can be seen in PIK3CA gene when NGS is used for testing. Genomic Testing Cooperative (GTC) offers comprehensive PIK3CA mutation profiling as a part Breast Cancer profiling. GTC Breast Cancer Molecular profile includes mutations analysis and copy number variation testing of 40 different genes. In addition tumor mutation burden (TMB) and microsatellite instability (MSI) testing results are also reported with this profile. Tested Genes: AKT1 APCATM ATR ATRX BRAF BRCA1 BRCA2 CDH1 CDKN2A EGFR EPCAM ERBB2 ERBB3 ERBB4 ESR1 IDH1 IDH2 KIT KMT2A KMT2C KMT2D KRAS MAP2K4 MAP3K1 MLH1 MSH2 MSH6 MTOR NF1 NOTCH1 NOTCH2 NRAS PDGFRA PIK3CA PIK3R1 PMS2 PTEN RB1 SF3B1 TP53 + (MSI) + (TMB) Specimen Requirements: FFPE: 1 H&E slide and 6-8 unstained slides, 5-7 microns of tissue fixed with 10% NBF fixative. Please circle tumor for microdissection. Alternatively, the FFPE block can be sent for tumor circling and cutting at our laboratory. Shipping: Ship using cold pack. The cold pack should not directly contact specimen. Ship as soon as sample collected with overnight delivery. Turn Around Time: 5-7 days >> See the tests
Genomic Testing Cooperative Receives Medicare (Palmetto GBA) Coverage for two NGS Hematology Molecular Profiling Tests Including Liquid Biopsy for Hematologic Neoplasms
GTC Receives Medicare Coverage for 2 NGS Hematology Molecular Profiling Tests Including Liquid Biopsy for Hematologic Neoplasms Irvine, California– June 19, 2019 – Genomic Testing Cooperative, LCA announced that the Medicare Administrative Contractor Palmetto GBA (MolDx®) has finalized its review and has established coverage for two Genomic Testing Cooperative (GTC) hematology profiles: GTC-Hematology (177 gene DNA profiling) and GTC-Hematology Plus (177 gene DNA and 1408 gene RNA profiling). The two Comprehensive Genomic Profile (CGP) tests are designed to help Pathologists and Hematologists/Oncologists in establishing the precise diagnosis, prognosis and determine therapy in hematologic neoplasms. The GTC Hematology test (177 gene DNA Profile) can be performed on cell-free DNA (cf-DNA) from peripheral blood samples representing the first Palmetto GBA covered liquid biopsy for hematology. A liquid biopsy for suspected hematologic neoplasms or monitoring patients with hematologic neoplasms can be highly useful and practical as a replacement to the painful bone marrow biopsy, which can be a deterrent for some patients. Dr. Maher Albitar, GTC Chief Executive Officer and Chief Medical Officer, stated “We are delighted that Palmetto GBA sees the value of GTC hematologic profiling testing and thrilled they are making this testing available to appropriate patient populations. Proper diagnosis, classification and clinical management of hematologic malignancies require in-depth molecular profiling, which saves the healthcare systems money over the long run. Our testing also provides information on the molecular heterogeneity within the neoplasm, which is very important for precise planning of the therapeutic approach”. Laboratories and hospitals that are members of the cooperative group as well as non-member medical professionals will have immediate access to these Medicare-covered Hematology Profiling tests. It is estimated that approximately 1,399,180 people in the US are either living with the diagnosis of hematologic neoplasm or in remission. Approximately 175,200 new cases of hematologic neoplasms are diagnosed annually in the US. Chronic Myeloproliferative neoplasm, acute myeloid leukemia, and myelodysplastic syndrome are the major diseases in myeloid neoplasms. HEMATOLOGY PROFILE HEMATOLOGY PROFILE PLUS About Genomic Testing Cooperative, LCA Genomic Testing Cooperative (GTC) is a privately-owned molecular testing company located in Irvine, CA. The company operates based on a cooperative (co-op) business model. Members of the co-op hold type A shares with voting rights. The company offers its patron members a full suite of comprehensive genomic profiling based mainly on next-generation sequencing. Molecular alterations are identified based on rigorous testing with the aid of specially developed algorithms to increase accuracy and efficiency. The clinical relevance of the detected alterations is pulled from numerous databases using internally developed software. Relevance of findings to diagnosis, prognosis, selecting therapy, and predicting outcome are reported to members. The co-op model allows GTC to make the testing and information platform available to members at a lower cost because of a lower overhead. GTC depends on the co-op members for marketing, sales, and billing. For more information, please visit https://genomictestingcooperative.com/. Forward Looking Statements All of the statements, expectations and assumptions contained in this press release are forward-looking statements. Such forward-looking statements are based on the GTC management’s current expectations and includes statements regarding the value of comprehensive genomic profiling, RNA profiling, DNA profiling, algorithms, therapy, the ability of testing to provide clinically useful information. All information in this press release is as of the date of the release, and GTC undertakes no duty to update this information unless required by law. >> Read more about Liquid Biopsy Hematology Profile
Myelodysplastic Syndrome (MDS)
MDS is defined as ineffective hematopoiesis characterized by adequate or increased hematologic elements in bone marrow with peripheral cytopenia. Therefore, the presence of cytopenia in one or more hematologic lines is necessary for the diagnosis of MDS. However, numerous reactive conditions other than MDS can cause cytopenia and these conditions must be distinguished from MDS. While dysplasia in hematologic cells is an indication of the diagnosis of MDS, the presence of mutations along with cytopenia is the most conclusive evidence for the diagnosis of MDS. Normal individuals above the age of 50 may show mutation in some genes (ASXL1, TET2, DNMT3, and TP53), however, the level (Variant allele frequency, VAF) is low (<10%). If there is no evidence of cytopenia, the presence of mutation is called clonal hematopoiesis of indeterminate potential (CHIP) and in the presence of cytopenia, it is called Clonal cytopenia of undetermined significance (CCUS). Patients with CHIP may develop hematologic neoplasms at later time and patients with CCUS most likely will develop overt neoplasm within 5 years. Developing overt MDS increases significantly if the VAF is above 10%. Download PDF Practically, cytopenia with a mutation between 10% and 20% should be considered early MDS. In the presence of mutations in two or more genes and VAF >10%, diagnosis of MDS can be made. Mutation in FLT3 and NPM1 should be considered an indication of acute myeloid leukemia, which can be de novo or secondary. Below are the most commonly mutated genes in MDS based on our database: TET2 Frequency: 31% Prognosis: Neutral Action: Hypomethylating agents, Vitamin C may activate TET2 function. Most of TET2 mutations lead to termination and loss of function and expression. Loss of function in TET2 leads to DNA hypermethylation and silencing the expression of important genes. DNMT3A Frequency: 28% Prognosis: Poor Action: Hypomethylating agents Mutations in DNMT3A lead to significant hypermethylation. ASXL1 Frequency: 21% Prognosis: Poor Action: bromodomain and extraterminal (BET) Inhibitors ASXL1 gen is involved in chromatin modification. ASXL1 mutations can be gain of function or truncation and perhaps loss of function. lead to loss of function and significant hypermethylation. SRSF2 Frequency: 17% Prognosis: Poor Action: Spliceosome modifiers (H3B-8800, sudemycins, spliceostatin A, and meayamycin) SRSF2 gene is involved in RNA splicing. SF3B1 Frequency: 1 5% Prognosis: Favorable Action: Spliceosome modifiers (H3B-8800, sudemycins, spliceostatin A, and meayamycin) SF3B1 gene is involved in RNA splicing and almost always associated with ring sideroblasts. When detected with JAK2, CALR or MPL, MDS/MPN-RARS-T should be considered. RUNX1 Frequency: 11% Prognosis: Poor Action: RUNX1 Inhibitors RUNX1 is a transcription factor, also called core-binding factor subunit alpha-2 (CBFA2). TP53 Frequency: 10% Prognosis: Poor Action: " MDM2 inhibitors, Hypomethylation agents, Wee1 inhibitors, Chk1 inhibitors, kevetrin, APR-246, nutlins, gene therapy" TP53 mutations imply defect checkpoint/cell cycle mechanism and indicate very aggressive disease. NRAS Frequency: 8% Prognosis: Poor Action: MEK Inhibitors Presence of NRAS mutation is an indication of monocytic lineage involvement and chronic myelomonocytic (CMML) disease rather than pure MDS. U2AF1 Frequency: 6% Prognosis: Poor Action: Spliceosome modifiers (H3B-8800, sudemycins, spliceostatin A, and meayamycin) U2AF1 is involved in RNA splicing IDH2 Frequency: 5% Prognosis: Neutral Action: IDH2 inhibitors IDH2 is involved in DNA methylation JAK2 Frequency: 5% Prognosis: Neutral Action: JAK2 inhibitors ( ruxolitinib, fedratinib, Pacritinib, Momelotinib) JAK2 is involved as a tyrosine kinase involved in cytokine pathway. The presence of JAK2 mutation in MDS should always raise the possibility of MPN/MDS with ring sideroblasts and thrombocytosis. SETBP1 Frequency: 5% Prognosis: Poor Action: No targeted therapy SETBP1 protein is a nuclear oncoprotein forms a complex involved in cell proliferation. ZRSR2 Frequency: 5% Prognosis: Poor Action: Spliceosome modifiers (H3B-8800, sudemycins, spliceostatin A, and meayamycin) ZRSR2 is located on X chromosome and more frequently mutated in males. CBL Frequency: 4% Prognosis: Poor Action: No targeted therapy CBL protein is E3 ubiquitin ligase involved in RAS pathway, therefore, more commonly mutated in CMML. IDH1 Frequency: 4% Prognosis: Neutral Action: IDH1 inhibitors IDH1 mutations lead to hypermethylation. Download PDF Specimen Requirements: -Liquid Biopsy: 5 mL. Peripheral blood in EDTA tube. -Bone Marrow Cells: 2 mL. EDTA tube. -Peripheral Blood Cells: 5 mL. EDTA tube. -FFPE: 1 H&E slide and 6-8 unstained slides, 5-7 microns of BM clot or tissue Shipping: Ship using cold pack. The cold pack should not directly contact Blood or BM specimen. Ship As soon as sample collected with overnight delivery. Turn Around Time: 5-7 days >> See HEMATOLOGY PROFILE