scholarly journals Clonality Analysis of Immunoglobulin Gene Rearrangement by Next-Generation Sequencing in Endemic Burkitt Lymphoma Suggests Antigen Drive Activation of BCR as Opposed to Sporadic Burkitt Lymphoma

2015 ◽  
Vol 145 (1) ◽  
pp. 116-127 ◽  
Author(s):  
Teresa Amato ◽  
Francesco Abate ◽  
Pierpaolo Piccaluga ◽  
Michele Iacono ◽  
Chiara Fallerini ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Burkitt Lymphoma ◽  
Gene Rearrangement ◽  
Immunoglobulin Gene ◽  
Next Generation ◽  
Immunoglobulin Gene Rearrangement ◽  
Clonality Analysis ◽  
Generation Sequencing

scholarly journals Immunoglobulin gene rearrangement in Koreans with multiple myeloma: Clonality assessment and repertoire analysis using next-generation sequencing

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0253541
Author(s):  
Miyoung Kim ◽  
Kibum Jeon ◽  
Kasey Hutt ◽  
Alyssa M. Zlotnicki ◽  
Hyo Jung Kim ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Bone Marrow ◽  
Next Generation Sequencing ◽  
Light Chain ◽  
Gene Rearrangement ◽  
Lymphoid Cells ◽  
Immunoglobulin Gene ◽  
Next Generation ◽  
Korean Patients ◽  
Generation Sequencing

Introduction We assessed the applicability of next-generation sequencing (NGS)-based IGH/IGK clonality testing and analyzed the repertoire of immunoglobulin heavy chain (IGH) or immunoglobulin kappa light chain (IGK) gene usage in Korean patients with multiple myeloma (MM) for the first time. Methods Fifty-nine bone marrow samples from 57 Korean patients with MM were analyzed, and NGS-based clonality testing that targeted the IGH and IGK genes was performed using IGH FR1 and IGK primer sets. Results Clonal IGH and IGK rearrangements were observed in 74.2% and 67.7% of samples from Korean patients with kappa-restricted MM, respectively (90.3% had one or both), and in 60.7% and 95.5% of samples from those with lambda-restricted MM, respectively (85.7% had one or both). In total, 88.1% of samples from Koreans with MM had clonal IGH and/or IGK rearrangement. Clonal rearrangement was not significantly associated with the bone marrow plasma cells as a proportion of all BM lymphoid cells. IGHV3-9 (11.63%) and IGHV4-31 (9.30%) were the most frequently reported IGHV genes and were more common in Koreans with MM than in Western counterparts. IGHD3-10 and IGHD3-3 (13.95% each) were the most frequent IGHD genes; IGHD3-3 was more common in Koreans with MM. No IGK rearrangement was particularly prevalent, but single IGKV-J rearrangements were less common in Koreans with kappa-restricted MM than in Western counterparts. IGKV4-1 was less frequent in Koreans regardless of light chain type. Otherwise, the usages of the IGH V, D, and J genes and of the IGK gene were like those observed in previous Western studies. Conclusion NGS-based IGH/IGK clonality testing ought to be applicable to most Koreans with MM. The overrepresentation of IGHV3-9, IGHV4-31, and IGHD3-3 along with the underrepresentation of IGKV4-1 and the differences in IGK gene rearrangement types suggest the existence of ethnicity-specific variations in this disease.

scholarly journals The Mitochondrial Genomes of 18 New Pleurosticti (Coleoptera: Scarabaeidae) Exhibit a Novel trnQ-NCR-trnI-trnM Gene Rearrangement and Clarify Phylogenetic Relationships of Subfamilies within Scarabaeidae

Insects ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1025
Author(s):  
Sam Pedro Galilee Ayivi ◽  
Yao Tong ◽  
Kenneth B. Storey ◽  
Dan-Na Yu ◽  
Jia-Yong Zhang
Keyword(s):  
Next Generation Sequencing ◽  
Gene Order ◽  
Phylogenetic Relationships ◽  
Gene Rearrangement ◽  
Next Generation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Next Generation Sequencing Ngs ◽  
Mt Genome ◽  
Generation Sequencing

The availability of next-generation sequencing (NGS) in recent years has facilitated a revolution in the availability of mitochondrial (mt) genome sequences. The mt genome is a powerful tool for comparative studies and resolving the phylogenetic relationships among insect lineages. The mt genomes of phytophagous scarabs of the subfamilies Cetoniinae and Dynastinae were under-represented in GenBank. Previous research found that the subfamily Rutelinae was recovered as a paraphyletic group because the few representatives of the subfamily Dynastinae clustered into Rutelinae, but the subfamily position of Dynastinae was still unclear. In the present study, we sequenced 18 mt genomes from Dynastinae and Cetoniinae using next-generation sequencing (NGS) to re-assess the phylogenetic relationships within Scarabaeidae. All sequenced mt genomes contained 37 sets of genes (13 protein-coding genes, 22 tRNAs, and two ribosomal RNAs), with one long control region, but the gene order was not the same between Cetoniinae and Dynastinae species. All mt genomes of Dynastinae species showed the same gene rearrangement of trnQ-NCR-trnI-trnM, whereas all mt genomes of Cetoniinae species showed the ancestral insect gene order of trnI-trnQ-trnM. Phylogenetic analyses (IQ-tree and MrBayes) were conducted using 13 protein-coding genes based on nucleotide and amino acid datasets. In the ML and BI trees, we recovered the monophyly of Rutelinae, Cetoniinae, Dynastinae, and Sericinae, and the non-monophyly of Melolonthinae. Cetoniinae was shown to be a sister clade to (Dynastinae + Rutelinae).

scholarly journals Burkitt lymphoma cell line carrying a variant translocation creates new DNA at the breakpoint and violates the hierarchy of immunoglobulin gene rearrangement.

1985 ◽  
Vol 5 (11) ◽  
pp. 3199-3207 ◽  
Author(s):  
C T Denny ◽  
G F Hollis ◽  
I T Magrath ◽  
I R Kirsch
Keyword(s):  
Cell Line ◽  
Burkitt Lymphoma ◽  
Gene Rearrangement ◽  
Lymphoma Cell ◽  
Chromosome 8 ◽  
Immunoglobulin Gene ◽  
Lymphoma Cell Line ◽  
Immunoglobulin Gene Rearrangement ◽  
Burkitt Lymphoma Cell ◽  
Burkitt Lymphoma Cell Line

The Burkitt lymphoma cell line KK124, which contains a reciprocal t(8;22) translocation, was shown to have rearranged in a region 3' to the c-myc proto-oncogene on chromosome 8 and 5' to the lambda constant region on chromosome 22. The breakpoint was cloned and sequenced, revealing that c-myc and a portion of its 3' region abutted a complete lambda variable gene that had undergone V-J recombination. Since this cell line expresses kappa light chain, this lambda rearrangement violates the previously proposed hierarchy of immunoglobulin gene rearrangement. A novel duplication of normal chromosome 8 sequences was also found at the breakpoint. The first exon of c-myc and its flanking sequence from the translocated allele was sequenced and compared with a normal counterpart. Extensive mutation was found within the first exon in contrast to its 3' and 5' flanking regions. S1 nuclease analysis revealed that it was the translocated c-myc being expressed and that there was a promoter shift from P2 to P1. The detailed structural analysis of this cell line provides clues concerning mechanisms of chromosomal translocation and c-myc deregulation in Burkitt lymphomas.

scholarly journals Bioinformatic Clonality Analysis of Next-Generation Sequencing-Derived Viral Vector Integration Sites

2012 ◽  
Vol 23 (2) ◽  
pp. 111-118 ◽  
Author(s):  
Anne Arens ◽  
Jens-Uwe Appelt ◽  
Cynthia C. Bartholomae ◽  
Richard Gabriel ◽  
Anna Paruzynski ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Viral Vector ◽  
Next Generation ◽  
Vector Integration ◽  
Clonality Analysis ◽  
Integration Sites ◽  
Generation Sequencing

scholarly journals Observed Antibody Space: a resource for data mining next generation sequencing of antibody repertoires

2018 ◽  
Author(s):  
Aleksandr Kovaltsuk ◽  
Jinwoo Leem ◽  
Sebastian Kelm ◽  
James Snowden ◽  
Charlotte M. Deane ◽  
...  
Keyword(s):  
Data Mining ◽  
Immune System ◽  
Next Generation Sequencing ◽  
Sequence Diversity ◽  
Immunoglobulin Gene ◽  
Next Generation ◽  
Natural Diversity ◽  
Antibody Repertoires ◽  
Generation Sequencing

AbstractAntibodies are immune system proteins that recognize noxious molecules for elimination. Their sequence diversity and binding versatility have made antibodies the primary class of biopharmaceuticals. Recently it has become possible to query their immense natural diversity using next-generation sequencing of immunoglobulin gene repertoires (Ig-seq). However, Ig-seq outputs are currently fragmented across repositories and tend to be presented as raw nucleotide reads, which means nontrivial effort is required to reuse the data for analysis. To address this issue, we have collected Ig-seq outputs from 53 studies, covering more than half a billion antibody sequences across diverse immune states, organisms and individuals. We have sorted, cleaned, annotated, translated and numbered these sequences and make the data available via our Observed Antibody Space (OAS) resource at antibodymap.org. The data within OAS will be regularly updated with newly released Ig-seq datasets. We believe OAS will facilitate data mining of immune repertoires for improved understanding of the immune system and development of better biotherapeutics.

scholarly journals Nanopore sequencing approach for immunoglobulin gene analysis in chronic lymphocytic leukemia

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Crescenzio Francesco Minervini ◽  
Cosimo Cumbo ◽  
Immacolata Redavid ◽  
Maria Rosa Conserva ◽  
Paola Orsini ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Chronic Lymphocytic Leukemia ◽  
Somatic Hypermutation ◽  
Lymphocytic Leukemia ◽  
Immunoglobulin Gene ◽  
Nanopore Sequencing ◽  
Next Generation ◽  
Sample Number ◽  
Variable Gene ◽  
Generation Sequencing

AbstractThe evaluation of the somatic hypermutation of the clonotypic immunoglobulin heavy variable gene has become essential in the therapeutic management in chronic lymphocytic leukemia patients. European Research Initiative on Chronic Lymphocytic Leukemia promotes good practices and standardized approaches to this assay but often they are labor-intensive, technically complex, with limited in scalability. The use of next-generation sequencing in this analysis has been widely tested, showing comparable accuracy and distinct advantages. However, the adoption of the next generation sequencing requires a high sample number (run batching) to be economically convenient, which could lead to a longer turnaround time. Here we present data from nanopore sequencing for the somatic hypermutation evaluation compared to the standard method. Our results show that nanopore sequencing is suitable for immunoglobulin heavy variable gene mutational analysis in terms of sensitivity, accuracy, simplicity of analysis and is less time-consuming. Moreover, our work showed that the development of an appropriate data analysis pipeline could lower the nanopore sequencing error rate attitude.

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