Validation of a PCR-Based Next-Generation Sequencing Approach for the Detection and Quantification of Minimal Residual Disease in Acute Lymphoblastic Leukemia and Multiple Myeloma Using gBlocks as Calibrators

Straeten, Jona Van der; Brouwer, Wouter De; Kabongo, Emmanuelle; Dresse, Marie-Françoise; Fostier, Karel; Schots, Rik; Riet, Ivan Van; Bâkkus, Marleen

doi:10.1016/j.jmoldx.2021.01.009

Cited by 6 publications

(4 citation statements)

References 63 publications

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“…The branch-site model was used to detect positive selection on specific branches and affecting a portion of sites by selecting one-to-one orthologous proteins from red clover and its closely related species and using PRANK [ 40 ]. After aligning homologous protein sequences, Gblocks was used to filter the alignment results [ 92 ]. CODEML in PAML was used to evaluate positive selection in specific clades and affecting only certain loci with correction for multiple hypothesis testing using Chi2 [ 88 ].…”

Section: Discussionmentioning

confidence: 99%

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A de novo assembled high-quality chromosome-scale Trifolium pratense genome and fine-scale phylogenetic analysis

Yan

Sang

et al. 2022

BMC Plant Biol

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Background Red clover (Trifolium pratense L.) is a diploid perennial temperate legume with 14 chromosomes (2n = 14) native to Europe and West Asia, with high nutritional and economic value. It is a very important forage grass and is widely grown in marine climates, such as the United States and Sweden. Genetic research and molecular breeding are limited by the lack of high-quality reference genomes. In this study, we used Illumina, PacBio HiFi, and Hi-C to obtain a high-quality chromosome-scale red clover genome and used genome annotation results to analyze evolutionary relationships among related species. Results The red clover genome obtained by PacBio HiFi assembly sequencing was 423 M. The assembly quality was the highest among legume genome assemblies published to date. The contig N50 was 13 Mb, scaffold N50 was 55 Mb, and BUSCO completeness was 97.9%, accounting for 92.8% of the predicted genome. Genome annotation revealed 44,588 gene models with high confidence and 52.81% repetitive elements in red clover genome. Based on a comparison of genome annotation results, red clover was closely related to Trifolium medium and distantly related to Glycine max, Vigna radiata, Medicago truncatula, and Cicer arietinum among legumes. Analyses of gene family expansions and contractions and forward gene selection revealed gene families and genes related to environmental stress resistance and energy metabolism. Conclusions We report a high-quality de novo genome assembly for the red clover at the chromosome level, with a substantial improvement in assembly quality over those of previously published red clover genomes. These annotated gene models can provide an important resource for molecular genetic breeding and legume evolution studies. Furthermore, we analyzed the evolutionary relationships among red clover and closely related species, providing a basis for evolutionary studies of clover leaf and legumes, genomics analyses of forage grass, the improvement of agronomic traits.

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Section: Discussionmentioning

confidence: 99%

“…After aligning homologous protein sequences, Gblocks was used to filter the alignment results [92]. CODEML in PAML was used to evaluate positive selection in specific clades and affecting only certain loci with correction for multiple hypothesis testing using Chi2 [88].…”

Section: Comparative Analysismentioning

confidence: 99%

A de novo assembled high-quality chromosome-scale Trifolium pratense genome and fine-scale phylogenetic analysis

Yan

Sang

et al. 2022

BMC Plant Biol

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“…Currently, mutation profiling using NGS is not routinely performed in the diagnostic work-up of MM, and genetic characterization is still mainly focused on the detection of the above-mentioned cytogenetic alterations. Instead, the use of NGS in clinical practice is directed towards the detection of Measurable Residual Disease (MRD) in MM via the detection of the tumor-specific rearrangements in the IgH, IgK, and/or IgL loci [33,34] It has been shown that obtaining MRD negativity is strongly associated with an improved survival outcome, with the optimal threshold for MRD sensitivity set at 10 −6 [35]. However, with whole-genome sequencing becoming increasingly accessible in clinical practice, there is a growing interest in the characterization of mutations associated with therapy resistance and prognostic impact.…”

Section: Liquid Biopsies: a Comprehensive And Non-invasive Alternativ...mentioning

confidence: 99%

Liquid Biopsies as Non-Invasive Tools for Mutation Profiling in Multiple Myeloma: Application Potential, Challenges, and Opportunities

Heestermans,

Schots,

De Becker

et al. 2024

IJMS

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Over the last decades, the survival of multiple myeloma (MM) patients has considerably improved. However, despite the availability of new treatments, most patients still relapse and become therapy-resistant at some point in the disease evolution. The mutation profile has an impact on MM patients’ outcome, while typically evolving over time. Because of the patchy bone marrow (BM) infiltration pattern, the analysis of a single bone marrow sample can lead to an underestimation of the known genetic heterogeneity in MM. As a result, interest is shifting towards blood-derived liquid biopsies, which allow for a more comprehensive and non-invasive genetic interrogation without the discomfort of repeated BM aspirations. In this review, we compare the application potential for mutation profiling in MM of circulating-tumor-cell-derived DNA, cell-free DNA and extracellular-vesicle-derived DNA, while also addressing the challenges associated with their use.

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“…Up to now(June 2022), thirteen species of mitochondrial genomes sequences [23] of Membracidae have been deposited in the GenBank database, including Leptobelus gazella (JF801955.1) [24], Maurya qinlingensis (NC_044706.1) [25], Leptocentrus albolineatus (NC_044707.1) [25], Tricentrus brunneus (NC_044708.1) [25], Hypsauchenia hardwickii (MK746135.1) [25], Stictocephala bisonia (NC_057522.1) [26],…”

Section: Data Sourcesmentioning

confidence: 99%

Comparative Analysis among 6 Subfamilies of Membracoidea based on the Concatenated Protein-coding Genes of Mitochondrial Genomes

2022

JRSE

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Membracidae belongs to Hemiptera, and is one of the most important insect groups in the world. Insect mitochondrial genes are commonly used and effective molecular markers in insect molecular and evolutionary studies. In this study, the phylogenetic relationships of 28 species in 6 subfamilies of Membracoidea, which most of the species are from the Eastern Hemisphere were discussed based on mitochondrial protein-coding genes. The phylogenetic trees were constructed by the Neighbor-Joining method, maximum likelihood method, and Bayesian method. That is, in 28 species of Membracoidea, Membracidae was usually placed as the sister clade to Cicadellidae, within Membracidae, the 13 species in this study represent two subfamilies, Centrotinae and Smillinae. The inferred relationship was ((E. carinata + S. bisonia) + (H. hardwickii + (((A. yunnanense + A. lineatum) + (L. sp. HL-2012+ L. gazella)) + (L. albolineatus + (T. longivalvulatus+ ((M. qinlingensis+ G. genistae) + (T. sp.EMHAU-15062504+ T. brunneus))))))). The evolutionary status and taxonomic attribution of 28 species of Membracoidea are consistent with the traditional taxonomic results.

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Validation of a PCR-Based Next-Generation Sequencing Approach for the Detection and Quantification of Minimal Residual Disease in Acute Lymphoblastic Leukemia and Multiple Myeloma Using gBlocks as Calibrators

Cited by 6 publications

References 63 publications

A de novo assembled high-quality chromosome-scale Trifolium pratense genome and fine-scale phylogenetic analysis

A de novo assembled high-quality chromosome-scale Trifolium pratense genome and fine-scale phylogenetic analysis

Liquid Biopsies as Non-Invasive Tools for Mutation Profiling in Multiple Myeloma: Application Potential, Challenges, and Opportunities

Comparative Analysis among 6 Subfamilies of Membracoidea based on the Concatenated Protein-coding Genes of Mitochondrial Genomes

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