De Novo DNA assembler for third generation sequencers’ reads based on BLASR algorithm

Author(s):  
Robert M. Nowak ◽  
Michał Winiarski ◽  
Wiktor Kuśmirek
Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 3904-3904
Author(s):  
Nadia El Khawanky ◽  
Amy Hughes ◽  
Wenbo Yu ◽  
Sanaz Taromi ◽  
Jade Clarson ◽  
...  

Chimeric antigen receptor T-cells (CAR Tc) have yielded impressive remission rates in treatment-refractory B-cell malignancies (B-ALL and B-lymphomas) by targeting CD19, resulting in the first FDA approved CAR Tc therapies, Kymriah and Yescarta. However, the translation of these results for other cancer entities remains a challenge. Pre-clinical studies using second-generation CAR Tc against the interleukin-3 receptor alpha chain (CD123) engendered strong anti-leukemic activity. CD123 CAR Tc clinical studies resulted in transient responses, or complete remission but at the expense of on-target off-tumor toxicities. Our studies employing third-generation anti-CD123 CAR Tc demonstrate strong anti-leukemic activity with no adverse effects in vivo. However, the leukemia was not completely eradicated. Combining anti-CD123 CAR Tc with DNA hypomethylating (HMA) agents may enhance the anti-leukemic effect and survival. HMAs such as azacytidine (Aza) activate key epigenetically silenced pathways in AML cells, inhibiting cell proliferation while enhancing cell immunogenicity. We hypothesized that Aza will increase the expression of CD123 on AML cells resulting in long-term disease eradication by anti-CD123 CAR Tc. The anti-leukemic efficacy, survival advantage, safety and feasibility of the combination treatment with Aza and anti-CD123 CAR Tc were evaluated in vivo. HL-60 (CD123med), MLL-2 (CD123lo), MOLM-13 (CD123hi), primary de novo and relapsed/refractory (r/r) AML cells were cultured for 0-8 days in the presence of Aza (0µM-5µM) and analysed for their CD123 expression by flow cytometry, quantitative western blot and RNAseq. The anti-CD123 CAR was constructed with the humanized CSL362-based ScFv and the CD28-OX40-CD3ζ signaling domain, encoded in a third-generation lentiviral vector and expressed in CD3+ Tc from healthy donors. Rag2γc-/- mice (n=12-16/ group) were engrafted with 1x105 MOLM13/ffLuc AML cells and treated with PBS, 5x106 Non-transduced (NTD) Tc orCAR Tc, 4x 2.5mg/kg Aza, or 5x106 CAR Tc following 4x Aza (2.5mg/kg). Leukemic burden was assessed weekly by bioluminescence imaging. Tc activity and immunophenotyping was performed using flow cytometry at day 35 post engraftment, and survival was monitored. HL-60, MLL-2 and MOLM-13 cells showed significant increases in HLA-DR, PD-L1, STAT1 and IRF7 expression, as well as CD123 when exposed to Aza (Fig 1A,B). Interestingly, the increased effect was seen from day one regardless of concentration. This was similarly reflected in AML patient cells. Aza treatment also arrested cell proliferation and decreased viability in both cell lines and patient cells suggesting Aza can aid in the anti-leukemic effect. Rag2γc-/- mice engrafted with MOLM-13 and treated with Aza and CD123 CAR Tc demonstrated suppressed growth, and eradication of MOLM-13 cells compared to mice treated with CD123 CAR Tc or Aza alone. Additionally, a significant decrease in residual CD123+ cells in the bone marrow (BM) of dual treated mice was seen (Fig 1C). A higher frequency of residual CD8+ T-cells in the BM, and CD4+ Tc in the peripheral blood (PB) and BM of dual treated mice was observed compared to CAR Tc only treated mice. Most prominently, we found a significantly higher mean number of stem cell-like and central memory CD8+ Tc in the BM of dual treated mice (232 cells/µl and 208cells/µl, respectively) compared to the CAR Tc only group (55 cells/µl and 23 cells/µl, respectively). Assessment of immune checkpoint markers on residual CAR Tc of dual treated mice revealed significantly decreased levels of CTLA-4, PD-1 and TIM-3 in the BM, and CTLA-4 in the PB compared to the CAR Tc only group. While CAR Tc treatment alone demonstrated a survival advantage compared to PBS, NTD or Aza treated mice, Aza and CAR Tc treatment had a significantly higher survival rate compared to the CAR Tc only group (92% vs. 46% at day 50, p<.01). Our findings indicate that Aza increases immunogenicity and augments the cell surface expression of CD123 on AML cells, allowing enhanced recognition and elimination of malignant cells by CD123 CAR Tc. This is the first demonstration that HMAs and CAR Tc immunotherapy can be used synergistically to treat AML. Considering HMAs are currently under clinical investigation in AML, our data encourage further clinical evaluation of this dual treatment in r/r AML, including high-risk patients that are chemotherapy or allogeneic transplantation ineligible. Disclosures Hughes: Novartis, Bristol-Myers Squibb, Celgene: Research Funding; Novartis, Bristol-Myers Squibb: Consultancy, Other: Travel. White:BMS: Honoraria, Research Funding; AMGEN: Honoraria, Speakers Bureau. Yong:Novartis: Honoraria, Research Funding; Celgene: Research Funding; BMS: Honoraria, Research Funding.


2019 ◽  
Vol 15 (8) ◽  
pp. 685-687 ◽  
Author(s):  
Stefan Verheye ◽  
Ricardo A. Costa ◽  
Joachim Schofer ◽  
John A. Ormiston ◽  
Michael Maeng ◽  
...  

2021 ◽  
Author(s):  
Víctor García-Olivares ◽  
Adrián Muñoz-Barrera ◽  
José Miguel Lorenzo-Salazar ◽  
Carlos Zaragoza-Trello ◽  
Luis A. Rubio-Rodríguez ◽  
...  

AbstractThe mitochondrial genome (mtDNA) is of interest for a range of fields including evolutionary, forensic, and medical genetics. Human mitogenomes can be classified into evolutionary related haplogroups that provide ancestral information and pedigree relationships. Because of this and the advent of high-throughput sequencing (HTS) technology, there is a diversity of bioinformatic tools for haplogroup classification. We present a benchmarking of the 11 most salient tools for human mtDNA classification using empirical whole-genome (WGS) and whole-exome (WES) short-read sequencing data from 36 unrelated donors. Besides, because of its relevance, we also assess the best performing tool in third-generation long noisy read WGS data obtained with nanopore technology for a subset of the donors. We found that, for short-read WGS, most of the tools exhibit high accuracy for haplogroup classification irrespective of the input file used for the analysis. However, for short-read WES, Haplocheck and MixEmt were the most accurate tools. Based on the performance shown for WGS and WES, and the accompanying qualitative assessment, Haplocheck stands out as the most complete tool. For third-generation HTS data, we also showed that Haplocheck was able to accurately retrieve mtDNA haplogroups for all samples assessed, although only after following assembly-based approaches (either based on a referenced-based assembly or a hybrid de novo assembly). Taken together, our results provide guidance for researchers to select the most suitable tool to conduct the mtDNA analyses from HTS data.


2017 ◽  
Author(s):  
Łukasz Neumann ◽  
Robert M. Nowak ◽  
Wiktor Kuśmirek
Keyword(s):  
De Novo ◽  

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1322
Author(s):  
Christian Wever ◽  
David L. Van Tassel ◽  
Ralf Pude

The emerging bioeconomy will increase the need for plant biomass. We call for a third-generation of bioenergy crops, or biomass crops, to help move society towards a sustainable bioeconomy and global food security. Third-generation biomass crops should be capable of producing both food and raw materials. Such flexibility would allow farmers to respond to global markets and buffer global food security. At the same time, third-generation biomass crops need to increase the sustainability of agriculture. To reach such ambitious goals, new biomass crops have to develop de novo from promising perennial wild species.


BIOspektrum ◽  
2012 ◽  
Vol 18 (5) ◽  
pp. 524-526
Author(s):  
Tobias Paprotka ◽  
Daniel Monne Parera ◽  
Yadhu Kumar ◽  
Kerstin A. Stangier
Keyword(s):  
De Novo ◽  

2020 ◽  
Author(s):  
Abdulqader Jighly

AbstractIndexing of DNA sequences is the art of sorting massive genomic data in a user-friendly structure to enable rapid accessing and comparing of different patterns in the data. Current genome assemblers use general algorithms for string indexing that do not exploit the special structural arrangement of genomes. Here, I am proposing a new algorithm that indexes only the configuration of microsatellite motifs along reads assuming that the order of microsatellites will be the same in overlapped sequences. The index size is >1000 times smaller than currently used indices and it has higher tolerance to the high error rates produced by third generation sequencing platforms. The results showed that the proposed algorithm can rapidly detect overlaps among considerable proportion of uncorrected long reads (~50% of all simulated base pairs with average read size of 8.16 kb and total error rates of 14.4%) to build large initial contigs. Unassembled reads can be then mapped to these contigs or can be assembled with them with currently used algorithms. Thus, the proposed algorithm can efficiently be used as an initial stage to significantly reduce the number of pairwise sequence comparisons among reads and/or references and improve the performance of different software but not replacing them. The algorithm was also useful for comparative genomics and detect large locally colinear blocks and structural variations among ten saccharomyces cerevisiae strains. The proposed algorithm has the power to make de novo assembly of individuals as routine activity which can lead to more accurate variant calling and pan genomics.


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