scholarly journals Abstract 4696: High-throughput single-cell targeted DNA sequencing using an updated TapestriTMPlatform reveals rare clones and clonal evolution for multiple blood cancers

2019 ◽  
Author(s):  
Nianzhen Li ◽  
Daniel Mendoza ◽  
Adam Sciambi ◽  
Mani Manivannan ◽  
Jacob Ho ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Single Cell ◽  
High Throughput ◽  
Clonal Evolution ◽  
Multiple Blood

scholarly journals Clonal Evolution of Acute Myeloid Leukemia Revealed by High-Throughput Single-Cell Genomics

2020 ◽  
Author(s):  
Kiyomi Morita ◽  
Feng Wang ◽  
Katharina Jahn ◽  
Jack Kuipers ◽  
Yuanqing Yan ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Dna Sequencing ◽  
Single Cell ◽  
High Throughput ◽  
Myeloid Leukemia ◽  
Clonal Evolution ◽  
Treatment Resistance ◽  
Clonal Diversity ◽  
History Of ◽  
Acute Myeloid

SummaryOne of the pervasive features of cancer is the diversity of mutations found in malignant cells within the same tumor; a phenomenon called clonal diversity or intratumor heterogeneity. Clonal diversity allows tumors to adapt to the selective pressure of treatment and likely contributes to the development of treatment resistance and cancer recurrence. Thus, the ability to precisely delineate the clonal substructure of a tumor, including the evolutionary history of its development and the co-occurrence of its mutations, is necessary to understand and overcome treatment resistance. However, DNA sequencing of bulk tumor samples cannot accurately resolve complex clonal architectures. Here, we performed high-throughput single-cell DNA sequencing to quantitatively assess the clonal architecture of acute myeloid leukemia (AML). We sequenced a total of 556,951 cells from 77 patients with AML for 19 genes known to be recurrently mutated in AML. The data revealed clonal relationship among AML driver mutations and identified mutations that often co-occurred (e.g., NPM1/FLT3-ITD, DNMT3A/NPM1, SRSF2/IDH2, and WT1/FLT3-ITD) and those that were mutually exclusive (e.g., NRAS/KRAS, FLT3-D835/ITD, and IDH1/IDH2) at single-cell resolution. Reconstruction of the tumor phylogeny uncovered history of tumor development that is characterized by linear and branching clonal evolution patterns with latter involving functional convergence of separately evolved clones. Analysis of longitudinal samples revealed remodeling of clonal architecture in response to therapeutic pressure that is driven by clonal selection. Furthermore, in this AML cohort, higher clonal diversity (≥4 subclones) was associated with significantly worse overall survival. These data portray clonal relationship, architecture, and evolution of AML driver genes with unprecedented resolution, and illuminate the role of clonal diversity in therapeutic resistance, relapse and clinical outcome in AML.

scholarly journals Genomic Heterogeneity and Clonal Evolution in Gastroesophageal Junction Cancer Revealed by Single Cell DNA Sequencing

2021 ◽  
Vol 11 ◽  
Author(s):  
Qingke Duan ◽  
Chao Tang ◽  
Zhao Ma ◽  
Chuangui Chen ◽  
Xiaobin Shang ◽  
...  
Keyword(s):  
Lymph Node ◽  
Lymph Node Metastasis ◽  
Lymph Nodes ◽  
Dna Sequencing ◽  
Single Cell ◽  
Single Cells ◽  
Clonal Evolution ◽  
Gastroesophageal Junction ◽  
Common Mutation ◽  
Node Metastasis

Gastroesophageal junction (GEJ) cancer is a tumor that occurs at the junction of stomach and esophagus anatomically. GEJ cancer frequently metastasizes to lymph nodes, however the heterogeneity and clonal evolution process are unclear. This study is the first of this kind to use single cell DNA sequencing to determine genomic variations and clonal evolution related to lymph node metastasis. Multiple Annealing and Looping Based Amplification Cycles (MALBAC) and bulk exome sequencing were performed to detect single cell copy number variations (CNVs) and single nucleotide variations (SNVs) respectively. Four GEJ cancer patients were enrolled with two (Pt.3, Pt.4) having metastatic lymph nodes. The most common mutation we found happened in the TTN gene, which was reported to be related with the tumor mutation burden in cancers. Significant intra-patient heterogeneity in SNVs and CNVs were found. We identified the SNV subclonal architecture in each tumor. To study the heterogeneity of CNVs, the single cells were sequenced. The number of subclones in the primary tumor was larger than that in lymph nodes, indicating the heterogeneity of primary site was higher. We observed two patterns of multi-station lymph node metastasis: one was skip metastasis and the other was to follow the lymphatic drainage. Taken together, our single cell genomic analysis has revealed the heterogeneity and clonal evolution in GEJ cancer.

scholarly journals Longitudinal Monitoring of AML Tumors with High-Throughput Single-Cell DNA Sequencing Reveals Rare Clones Prognostic for Disease Progression and Therapy Response

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 1476-1476
Author(s):  
Dennis J. Eastburn ◽  
Christine M. McMahon ◽  
Robert Durruthy-Durruthy ◽  
Martin Carroll ◽  
Catherine C. Smith ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Single Cell ◽  
Board Of Directors ◽  
High Throughput ◽  
Employment Equity ◽  
Advisory Committees ◽  
Single Cell Sequencing ◽  
Oncogenic Ras ◽  
Flt3 Inhibitor ◽  
Equity Ownership

Abstract AML (acute myeloid leukemia) is increasingly being treated with precision medicine. To better inform treatment, the mutational content of patient samples must be determined. However, current tumor sequencing paradigms are inadequate to fully characterize many instances of the disease. A major challenge has been the unambiguous identification of potentially rare and genetically heterogeneous neoplastic cell populations, capable of critically impacting tumor evolution and the acquisition of therapeutic resistance. Standard bulk population sequencing is unable to identify rare alleles and definitively determine whether mutations co-occur within the same cell. Single-cell sequencing has the potential to address these key issues and transform our ability to accurately characterize clonal heterogeneity in AML. Previous single-cell studies examining genetic variation in AML have relied upon laborious, expensive and low-throughput technologies that are not readily scalable for routine analysis of the disease. We applied a newly developed platform technology to perform targeted single-cell DNA sequencing on over 140,000 cells and generated high-resolution maps of clonal architecture from AML tumor samples. Marrow and/or peripheral blood samples were collected prior to, during treatment, and at clinical progression to the FLT3 inhibitor gilteritinib given on a clinical trial for relapsed/refractory AML with FLT3 mutation. Single-cell sequencing of multiple patient samples demonstrated that relapse clones acquired oncogenic RAS mutations. We utilized the high-throughput and sensitivity of our single-cell approach to more definitively assess where in the course of treatment these RAS mutated clones were acquired. Oncogenic RAS harboring clones, comprising between 0.4%, and 0.1% of tumor populations, were identified in patient samples either prior to or shortly after onset of treatment. Significantly, these RAS variant alleles were not detectable with targeted bulk sequencing. Throughout the course of treatment with the FLT3 inhibitor gilteritinib, the RAS mutant clones selectively expanded and were responsible for resistance to therapy and relapse. These findings point to the presence of underlying genetic heterogeneity in AML and demonstrate the utility of sensitively assaying clonal architecture to better inform patient stratification and therapy selection. Disclosures Eastburn: Mission Bio, Inc.: Employment, Equity Ownership. Durruthy-Durruthy:Mission Bio, Inc.: Employment, Equity Ownership. Smith:Astellas Pharma: Research Funding. Perl:Actinium Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; NewLink Genetics: Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees; Daiichi Sankyo: Consultancy; Arog: Consultancy; Novartis: Membership on an entity's Board of Directors or advisory committees; Astellas: Consultancy; AbbVie: Membership on an entity's Board of Directors or advisory committees.

scholarly journals Clonal evolution and heterogeneity in advanced systemic mastocytosis revealed by single-cell DNA sequencing

2021 ◽  
Vol 5 (6) ◽  
pp. 1733-1736
Author(s):  
Ken-Hong Lim ◽  
Jo-Ning Wu ◽  
To-Yu Huang ◽  
Jie-Yang Jhuang ◽  
Yu-Cheng Chang ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Single Cell ◽  
Systemic Mastocytosis ◽  
Clonal Evolution

scholarly journals Remarkably stable copy-number profiles in osteosarcoma revealed using single-cell DNA sequencing

2021 ◽  
Author(s):  
Sanjana Rajan ◽  
Simone Zaccaria ◽  
Matthew V. Cannon ◽  
Maren Cam ◽  
Amy C. Gross ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Single Cell ◽  
Genomic Instability ◽  
Copy Number ◽  
Fitness Landscape ◽  
Clonal Evolution ◽  
Response To Therapy ◽  
Tumor Evolution ◽  
Sequencing Data ◽  
Recurrent Mutations

AbstractOsteosarcoma is an aggressive malignancy characterized by high genomic complexity. Identification of few recurrent mutations in protein coding genes suggests that somatic copy-number aberrations (SCNAs) are the genetic drivers of disease. Models around genomic instability conflict-it is unclear if osteosarcomas result from pervasive ongoing clonal evolution with continuous optimization of the fitness landscape or an early catastrophic event followed by stable maintenance of an abnormal genome. We address this question by investigating SCNAs in 12,019 tumor cells obtained from expanded patient tissues using single-cell DNA sequencing, in ways that were previously impossible with bulk sequencing. Using the CHISEL algorithm, we inferred allele- and haplotype-specific SCNAs from whole-genome single-cell DNA sequencing data. Surprisingly, we found that, despite extensive genomic aberrations, cells within each tumor exhibit remarkably homogeneous SCNA profiles with little sub-clonal diversification. Longitudinal analysis between two pairs of patient samples obtained at distant time points (early detection, relapse) demonstrated remarkable conservation of SCNA profiles over tumor evolution. Phylogenetic analysis suggests that the bulk of SCNAs was acquired early in the oncogenic process, with few new events arising in response to therapy or during adaptation to growth in distant tissues. These data suggest that early catastrophic events, rather than sustained genomic instability, drive formation of these extensively aberrant genomes. Overall, we demonstrate the power of combining single-cell DNA sequencing with an allele- and haplotype-specific SCNA inference algorithm to resolve longstanding questions regarding genetics of tumor initiation and progression, questioning the underlying assumptions of genomic instability inferred from bulk tumor data.

scholarly journals Author Correction: Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Kiyomi Morita ◽  
Feng Wang ◽  
Katharina Jahn ◽  
Tianyuan Hu ◽  
Tomoyuki Tanaka ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Single Cell ◽  
High Throughput ◽  
Myeloid Leukemia ◽  
Clonal Evolution ◽  
Single Cell Genomics ◽  
Acute Myeloid
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