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Next generation sequencing leukemia

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https://www.readbyqxmd.com/read/28315400/multicolor-flow-cytometry-and-multi-gene-next-generation-sequencing-are-complementary-and-highly-predictive-for-relapse-in-acute-myeloid-leukemia-following-allogeneic-transplant
#1
Bartlomiej M Getta, Sean M Devlin, Ross L Levine, Maria E Arcila, Abhinita S Mohanty, Ahmet Zehir, Martin S Tallman, Sergio A Giralt, Mikhail Roshal
Minimal Residual disease (MRD) in acute myeloid leukemia (AML) is typically measured using multi-parameter flow cytometry (MFC). Detection of leukemia mutations using multi-gene next generation sequencing (NGS) can potentially be used to measure residual disease. We used a targeted 28-gene NGS panel to detect mutations and different-from-normal 10-colour MFC to measure MRD in AML patients before allogeneic hematopoietic stem cell transplant (HCT). Residual disease was defined when any abnormal blast population was detected using MFC and when any leukemia allele was detected with a variant allele frequency (VAF) ≥5% using NGS...
March 14, 2017: Biology of Blood and Marrow Transplantation
https://www.readbyqxmd.com/read/28314085/targeted-next-generation-sequencing-and-identification-of-risk-factors-in-world-health-organization-defined-atypical-chronic-myeloid-leukemia
#2
Mrinal M Patnaik, Daniela Barraco, Terra L Lasho, Christy M Finke, Kaaren Reichard, Katherine P Hoversten, Rhett P Ketterling, Naseema Gangat, Ayalew Tefferi
Atypical chronic myeloid leukemia (aCML) is an aggressive myeloid neoplasm with overlapping features of myelodysplastic syndromes (prominent granulocytic dysplasia) and myeloproliferative neoplasms (neutrophilic leukocytosis). We studied 25 molecularly-annotated and World Health Organization defined aCML patients; median age 70 years, 84% males. Cytogenetic abnormalities were seen in 36% and gene mutations in 100%. Mutational frequencies were, ASXL1 28%, TET2 16%, NRAS 16%, SETBP1 12%, RUNX1 12%, ETNK1 8% and PTPN11 4%...
March 17, 2017: American Journal of Hematology
https://www.readbyqxmd.com/read/28302711/precision-and-prognostic-value-of-clone-specific-minimal-residual-disease-in-acute-myeloid-leukemia
#3
Pierre Hirsch, Ruoping Tang, Nassera Abermil, Pascale Flandrin, Hannah Moatti, Fabrizia Favale, Ludovic Suner, Florence Lorre, Christophe Marzac, Fanny Fava, Anne-Claire Mamez, Simona Lapusan, Françoise Isnard, Mohamad Mohty, Ollivier Legrand, Luc Douay, Chrystele Bilhou-Nabera, François Delhommeau
The genetic landscape of adult acute myeloid leukemias has been recently unraveled. However, due to their genetic heterogeneity, only a handful of markers are currently used for the evaluation of minimal residual disease. Recent studies using multi-target strategies indicate that detection of residual mutations in less than 5% of cells in complete remission is associated with a better survival. Here, in a series of 69 acute myeloid leukemias with known clonal architecture, we design a clone-specific strategy based on fluorescent in situ hybridization and high-sensitivity next generation sequencing to detect chromosomal aberrations and mutations, respectively, in follow-up samples...
March 16, 2017: Haematologica
https://www.readbyqxmd.com/read/28297626/clinical-applications-of-the-genomic-landscape-of-aggressive-non-hodgkin-lymphoma
#4
Andrea B Moffitt, Sandeep S Dave
In this review, we examine the genomic landscapes of lymphomas that arise from B, T, and natural killer cells. Lymphomas represent a striking spectrum of clinical behaviors. Although some lymphomas are curable with standard therapy, the majority of the affected patients succumb to their disease. Here, the genetic underpinnings of these heterogeneous entities are reviewed. We consider B-cell lymphomas, including Burkitt lymphoma, diffuse large B-cell lymphoma, Hodgkin lymphoma, and primary mediastinal B-cell lymphoma...
March 20, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28255022/molecular-features-of-early-onset-adult-myelodysplastic-syndrome
#5
Cassandra M Hirsch, Bartlomiej P Przychodzen, Tomas Radivoyevitch, Bhumika Patel, Swapna Thota, Michael J Clemente, Yasunobu Nagata, Thomas LaFramboise, Hetty Carraway, Aziz Nazha, Mikkael A Sekeres, Hideki Makishima, Jaroslaw P Maciejewski
Myelodysplastic syndromes are typically diseases of older adults. Early onset patients may have distinct molecular and clinical features or reflect a demographic continuum. The identification of differences between early onset patients and those diagnosed at a traditional age has the potential to advance understanding of the pathogenesis of myelodysplasia and may lead to formation of distinct morphologic subcategories. We studied a cohort of 634 patients with various subcategories of myelodysplastic syndrome and secondary acute myeloid leukemia, stratifying based on age at presentation and clinical parameters...
March 2, 2017: Haematologica
https://www.readbyqxmd.com/read/28212557/using-high-sensitivity-sequencing-for-the-detection-of-mutations-in-btk-and-plc%C3%AE-2-genes-in-cellular-and-cell-free-dna-and-correlation-with-progression-in-patients-treated-with-btk-inhibitors
#6
Adam Albitar, Wanlong Ma, Ivan DeDios, Jeffrey Estella, Inhye Ahn, Mohammed Farooqui, Adrian Wiestner, Maher Albitar
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...
February 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28209658/relevance-of-id3-tcf3-ccnd3-pathway-mutations-in-pediatric-aggressive-b-cell-lymphoma-treated-according-to-the-nhl-bfm-protocols
#7
Marius Rohde, Bettina R Bonn, Martin Zimmermann, Jonas Lange, Anja Möricke, Wolfram Klapper, Ilske Oschlies, Monika Szczepanowski, Inga Nagel, Martin Schrappe, Markus Loeffler, Reiner Siebert, Alfred Reiter, Birgit Burkhardt
Mature B-cell Non-Hodgkin lymphoma is the most common subtype of Non-Hodgkin lymphoma in childhood and adolescence. B-cell Non-Hodgkin lymphoma are further classified into histological subtypes, with Burkitt lymphoma and Diffuse large B-cell lymphoma being the most common subgroups in pediatric patients. Translocations involving the MYC oncogene are known as relevant but not sufficient hit for Burkitt lymphoma pathogenesis. Recently published large-scale next-generation sequencing studies unveiled sets of additional recurrently mutated genes in samples of pediatric and adult B-cell Non-Hodgkin lymphoma patients...
February 16, 2017: Haematologica
https://www.readbyqxmd.com/read/28205134/minimal-residual-disease-in-acute-lymphoblastic-leukemia-how-to-recognize-and-treat-it
#8
REVIEW
Nicholas J Short, Elias Jabbour
In recent years, the identification of minimal residual disease (MRD) that persists after chemotherapy has emerged as the most powerful tool in determining the prognosis of patients with ALL, often superseding historically relevant prognostic factors. Multiple methods to detect MRD exist, each with their own advantages and disadvantages. Multiparameter flow cytometry and quantitative polymerase chain reaction are the most commonly used methods of MRD detection in clinical practice, although there is promise in the use of more sensitive assays utilizing next-generation sequencing that may be able to further refine MRD-based risk stratification...
January 2017: Current Oncology Reports
https://www.readbyqxmd.com/read/28187034/detection-of-novel-t-12-17-p12-p13-in-relapsed-refractory-acute-myeloid-leukemia-by-anchored-multiplex-pcr-amp-based-next-generation-sequencing
#9
Talha Badar, Laura Johnson, Katelyn Trifilo, Helen Wang, Brian A Kudlow, Eric Padron, Peter R Pappenhausen, Mohammad O Hussaini
Although several technologies can be used to detect gene fusions, anchored multiplex PCR next-generation sequencing (AMP-NGS) offers the advantage of novel fusion detection and the ability to multiplex multitudinous genes. We applied AMP-NGS technology in the evaluation of a 56-year-old gentleman with myelodysplastic syndrome transformed acute myeloid leukemia (AML). Patient was initially diagnosed with low-risk myelodysplastic syndrome-refractory cytopenias and multilineage dysplasia (MDS-RCMD), progressed to AML after failing hypomethylating agent therapy...
February 9, 2017: Applied Immunohistochemistry & Molecular Morphology: AIMM
https://www.readbyqxmd.com/read/28179379/rag1-2-induces-genomic-insertions-by-mobilizing-dna-into-rag1-2-independent-breaks
#10
Philipp C Rommel, Thiago Y Oliveira, Michel C Nussenzweig, Davide F Robbiani
The RAG recombinase (RAG1/2) plays an essential role in adaptive immunity by mediating V(D)J recombination in developing lymphocytes. In contrast, aberrant RAG1/2 activity promotes lymphocyte malignancies by causing chromosomal translocations and DNA deletions at cancer genes. RAG1/2 can also induce genomic DNA insertions by transposition and trans-V(D)J recombination, but only few such putative events have been documented in vivo. We used next-generation sequencing techniques to examine chromosomal rearrangements in primary murine B cells and discovered that RAG1/2 causes aberrant insertions by releasing cleaved antibody gene fragments that subsequently reintegrate into DNA breaks induced on a heterologous chromosome...
March 6, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28164543/detection-the-frequency-and-characteristics-of-flt3-internal-tandem-duplication-mutations-by-capillary-electrophoresis-assay-and-next-generation-sequencing-in
#11
Liang Ma, Yongyue Cao, Yongwei Jiang, Xiao Cong, Shuang Lu, Jun Shen, Qian Liu, Chengwu Han, Yuliang Zhan, Yongtong Cao
BACKGROUND: FLT3-internal tandem duplication mutations (ITDs) are found in approximately 30% of patients with acute myeloid leukemia (AML) and are markers of poor prognosis. However, the characteristics of FLT3/ ITDs in Chinese AML patients have rarely been reported. The aim of this study was to analyze the frequency and characteristics of FLT3/ITDs in Chinese AML patients. METHODS: In the selected 152 cases of Chinese AML patients, capillary electrophoresis (CE) was used to analyze the frequency and characteristics of FLT3/ITDs...
October 1, 2016: Clinical Laboratory
https://www.readbyqxmd.com/read/28144274/noonan-syndrome-a-new-survey
#12
Alireza Tafazoli, Peyman Eshraghi, Zahra Kamel Koleti, Mohammadreza Abbaszadegan
Noonan syndrome (NS) is an autosomal dominant disorder with vast heterogeneity in clinical and genetic features. Various symptoms have been reported for this abnormality such as short stature, unusual facial characteristics, congenital heart abnormalities, developmental complications, and an elevated tumor incidence rate. Noonan syndrome shares clinical features with other rare conditions, including LEOPARD syndrome, cardio-facio-cutaneous syndrome, Noonan-like syndrome with loose anagen hair, and Costello syndrome...
February 1, 2017: Archives of Medical Science: AMS
https://www.readbyqxmd.com/read/28137248/multidisciplinary-insight-into-clonal-expansion-of-htlv-1-infected-cells-in-adult-t-cell-leukemia-via-modeling-by-deterministic-finite-automata-coupled-with-high-throughput-sequencing
#13
Amir Farmanbar, Sanaz Firouzi, Sung-Joon Park, Kenta Nakai, Kaoru Uchimaru, Toshiki Watanabe
BACKGROUND: Clonal expansion of leukemic cells leads to onset of adult T-cell leukemia (ATL), an aggressive lymphoid malignancy with a very poor prognosis. Infection with human T-cell leukemia virus type-1 (HTLV-1) is the direct cause of ATL onset, and integration of HTLV-1 into the human genome is essential for clonal expansion of leukemic cells. Therefore, monitoring clonal expansion of HTLV-1-infected cells via isolation of integration sites assists in analyzing infected individuals from early infection to the final stage of ATL development...
January 31, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28122908/wanted-dead-h-or-alive-helicases-winding-up-in-cancers
#14
REVIEW
Wanpei Cai, Zhi Xiong Chen, Grishma Rane, Shikha Satendra Singh, Zhang'e Choo, Chao Wang, Yi Yuan, Tuan Zea Tan, Frank Arfuso, Celestial T Yap, Lorinc S Pongor, Henry Yang, Martin B Lee, Boon Cher Goh, Gautam Sethi, Touati Benoukraf, Vinay Tergaonkar, Alan Prem Kumar
Cancer is one of the most studied areas of human biology over the past century. Despite having attracted much attention, hype, and investments, the search to find a cure for cancer remains an uphill battle. Recent discoveries that challenged the central dogma of molecular biology not only further increase the complexity but also demonstrate how various types of noncoding RNAs such as microRNA and long noncoding RNA, as well as their related processes such as RNA editing, are important in regulating gene expression...
January 2017: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/28115373/the-genetics-and-molecular-biology-of-t-all
#15
REVIEW
Tiziana Girardi, Carmen Vicente, Jan Cools, Kim De Keersmaecker
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy caused by the accumulation of genomic lesions that affect the development of T cells. For many years, it has been established that deregulated expression of transcription factors, impairment of the CDKN2A/2B cell-cycle regulators, and hyperactive NOTCH1 signaling play prominent roles in the pathogenesis of this leukemia. In the past decade, systematic screening of T-ALL genomes by high-resolution copy-number arrays and next-generation sequencing technologies has revealed that T-cell progenitors accumulate additional mutations affecting JAK/STAT signaling, protein translation, and epigenetic control, providing novel attractive targets for therapy...
March 2, 2017: Blood
https://www.readbyqxmd.com/read/28096240/coevolution-of-leukemia-and-host-immune-cells-in-chronic-lymphocytic-leukemia
#16
Noelia Purroy, C J Wu
Cumulative studies on the dissection of changes in driver genetic lesions in cancer across the course of the disease have provided powerful insights into the adaptive mechanisms of tumors in response to the selective pressures of therapy and environmental changes. In particular, the advent of next-generation-sequencing (NGS)-based technologies and its implementation for the large-scale comprehensive analyses of cancers have greatly advanced our understanding of cancer as a complex dynamic system wherein genetically distinct subclones interact and compete during tumor evolution...
January 17, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28091414/acute-myeloid-leukemia-advancements-in-diagnosis-and-treatment
#17
REVIEW
Meng-Ge Yu, Hu-Yong Zheng
OBJECTIVE: Leukemia is the most common pediatric malignancy and a major cause of morbidity and mortality in children. Among all subtypes, a lack of consensus exists regarding the diagnosis and treatment of acute myeloid leukemia (AML). Patient survival rates have remained modest for the past three decades in AML. Recently, targeted therapy has emerged as a promising treatment. DATA SOURCES: We searched the PubMed database for recently published research papers on diagnostic development, target therapy, and other novel therapies of AML...
2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28090092/the-clonal-origins-of-leukemic-progression-of-myelodysplasia
#18
T Kim, M S Tyndel, H J Kim, J-S Ahn, S H Choi, H J Park, Y-K Kim, D-H Yang, J-J Lee, S-H Jung, S Y Kim, Y H Min, J-W Cheong, S K Sohn, J H Moon, M Choi, M Lee, Z Zhang, D D H Kim
The genetics behind the progression of myelodysplasia to secondary acute myeloid leukemia (sAML) is poorly understood. In this study, we profiled somatic mutations and their dynamics using next generation sequencing on serial samples from a total of 124 patients, consisting of a 31 patient discovery cohort and 93 patients from two validation cohorts. Whole-exome analysis on the discovery cohort revealed that 29 of 31 patients carry mutations related to at least one of eight commonly mutated pathways in AML...
February 3, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28079885/mirna182-regulates-percentage-of-myeloid-and-erythroid-cells-in-chronic-myeloid-leukemia
#19
Deepak Arya, Sasikala P Sachithanandan, Cecil Ross, Dasaradhi Palakodeti, Shang Li, Sudhir Krishna
The deregulation of lineage control programs is often associated with the progression of haematological malignancies. The molecular regulators of lineage choices in the context of tyrosine kinase inhibitor (TKI) resistance remain poorly understood in chronic myeloid leukemia (CML). To find a potential molecular regulator contributing to lineage distribution and TKI resistance, we undertook an RNA-sequencing approach for identifying microRNAs (miRNAs). Following an unbiased screen, elevated miRNA182-5p levels were detected in Bcr-Abl-inhibited K562 cells (CML blast crisis cell line) and in a panel of CML patients...
January 12, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28077600/ibrutinib-therapy-increases-t-cell-repertoire-diversity-in-patients-with-chronic-lymphocytic-leukemia
#20
Qingsong Yin, Mariela Sivina, Harlan Robins, Erik Yusko, Marissa Vignali, Susan O'Brien, Michael J Keating, Alessandra Ferrajoli, Zeev Estrov, Nitin Jain, William G Wierda, Jan A Burger
The Bruton's tyrosine kinase inhibitor ibrutinib is a highly effective, new targeted therapy for chronic lymphocytic leukemia (CLL) that thwarts leukemia cell survival, growth, and tissue homing. The effects of ibrutinib treatment on the T cell compartment, which is clonally expanded and thought to support the growth of malignant B cells in CLL, are not fully characterized. Using next-generation sequencing technology, we characterized the diversity of TCRβ-chains in peripheral blood T cells from 15 CLL patients before and after 1 y of ibrutinib therapy...
February 15, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
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