scholarly journals An undifferentiated sarcoma of bone with a round to epithelioid cell phenotype harboring a novel EWSR1 ‐ SSX2 fusion identified by RNA ‐based next‐generation sequencing

2021 ◽  
Author(s):  
Fleur Cordier ◽  
Joni Van der Meulen ◽  
Bram Van Gaever ◽  
Lore Lapeire ◽  
Gwen Sys ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Epithelioid Cell ◽  
Cell Phenotype ◽  
Next Generation ◽  
Undifferentiated Sarcoma ◽  
Generation Sequencing

Clinical benefit of next generation sequencing in soft tissue and bone sarcoma: Rush University Medical Center’s experience.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e22552-e22552
Author(s):  
Mia C. Weiss ◽  
Alan Blank ◽  
Steven Gitelis ◽  
Mary J. Fidler ◽  
Marta Batus
Keyword(s):  
Overall Survival ◽  
Next Generation Sequencing ◽  
Soft Tissue ◽  
Clinical Decision Making ◽  
Soft Tissue Sarcomas ◽  
Bone Sarcoma ◽  
Next Generation ◽  
Undifferentiated Sarcoma ◽  
The Impact ◽  
Generation Sequencing

e22552 Background: The overall survival for metastatic sarcoma has remained at only 18-20%. In the era of next generation sequencing (NGS), much research is ongoing on identifying optimal treatments. The MULTISARC trial aims to determine if NGS can lead to improved overall survival by randomizing patients with metastatic STS to receive NGS (followed by possible NGS-guided therapy) or not. We present our center’s experience with NGS in sarcomas patients. Methods: Patients with soft tissue and bone sarcomas at Rush that had the Foundation Medicine assay sent on tumor samples between August 2017 and August 2018 were analyzed retrospectively. The impact of NGS on clinical decision making was determined based on patients being prescribed off-label FDA-approved therapy targeting identified mutation. Results: Thirty-four patients with bone/soft tissue sarcomas that had NGS sent on specimens were identified. Median age at diagnosis: 43 (18-78 years); 18 males, 16 females. Histologic subtypes: synovial sarcoma, myxofibrosarcoma, leiomyosarcoma, chondrosarcoma, sclerosing epitheloid fibrosarcoma, PEcoma, pleomorphic undifferentiated sarcoma, MPNST, liposarcoma- well and de-differentiated, angiosarcoma, osteosarcoma. 16/34 patients had targetable mutations with approved therapies in tumor types other than sarcoma. Four of these patients had therapy changed based on NGS results, 1 patient with metastatic chondrosarcoma (PTEN mutation, everolimus added), 1 patient with metastatic liposarcoma (CDK4 mutation, palbociclib added), 1 patient with metastatic osteosarcoma (CCD1/CDK4 and a PDGFRA mutation for which palbociclib followed by imatinib was added), and 1 patient with metastatic pleomorphic undifferentiated sarcoma (CDK4 mutation, palbociclib added). Targetable mutations for which clinical trials are available were identified in 25/34 (73%) of the cases. Conclusions: NGS was readily able to identify actionable mutations in close to 50% of patients with clinical trial opportunities in close to 75%. Four patients had therapy changed as a result of NGS testing. Although our study size is small, our data show potential for the use of genomic profiling to identify actionable targets, tailor therapy, and hopefully improve outcomes. [Table: see text]

scholarly journals Prediction of Extended Red Blood Cell Phenotype from Exome Next Generation Sequencing Data

Blood ◽  
2017 ◽  
Vol 130 (Suppl_1) ◽  
pp. 705-705
Author(s):  
Celina Montemayor Garcia ◽  
Spencer E Grissom ◽  
Oscar A Montemayor ◽  
Katie L Lewis ◽  
Panagiota Karagianni ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Blood Cell ◽  
Open Source ◽  
Blood Group ◽  
Red Blood Cell ◽  
African Ancestry ◽  
Ethnic Composition ◽  
Cell Phenotype ◽  
Next Generation ◽  
Generation Sequencing

Abstract Introduction: Accurate typing of patient and donor red blood cell (RBC) antigens is critical for safe transfusion practice. Although blood typing is traditionally accomplished by serology, genotyping methods to predict RBC antigens have proven valuable in a growing number of situations such as recently-transfused patients, scarcity of typing reagents, and indeterminate serologic results. However current RBC genotyping assays address a limited number of blood group genes and associated variants, and may not detect novel genetic changes and certain rare but clinically-significant variants. Next generation sequencing (NGS) technology provides an appealing alternative technology, allowing the user to examine a patient's entire genome or exome in a high-throughput manner. Whereas efforts are underway in multiple fields to apply exome sequencing (ES) for diagnostic, prognostic, and treatment purposes, Transfusion Medicine, with its extensive clinical genomic database, should find ready application from this approach. We describe here the creation of an algorithm to interpret NGS into a predicted extended RBC phenotype, and its application to analyze ES data from 245 participants of the ClinSeq® sequencing cohort. Methods: RyLAN (Red Cell and Lymphocyte Antigen prediction from NGS) was created as an open-source Python application that takes an NGS sorted binary alignment matrix (.bam) file and index as input. The software interacts with a non-relational database that encodes genomic blood group coordinates and phenotype interpretation rules, and yields a predicted extended RBC phenotype and quality parameters. Hard filters for mapping quality, depth, vcf QUAL, and fraction of alternate allele can be modified per individual genomic coordinate. The output is provided as a MongoDB document to facilitate advanced bulk queries and statistical analysis. We employed RyLAN to analyze 245 ES NGS files from the ClinSeq® cohort, using a database of 176 known antigenic, null, and weak blood group single nucleotide variants in 27 blood group genes as input. Results: The cohort consisted of 115 females and 130 males; 89% of participants self-described as white race, non- Hispanic ethnicity. Three percent of participants self-described as Hispanic or Latino, 4% as Asian, 2% with African ancestry, and the remaining as mixed or unknown race. From the total 176 genomic positions analyzed, 160 were not addressed by current commercially-available RBC genotyping platforms. The average read depth for the positions of interest was 78.2, and the average vcf QUAL value was 968. The highest variant nucleotide frequency was observed at the Fya/Fyb and Jka/Jkb loci (275 and 223 total haplotype variant calls, respectively). Among other phenotypes, RyLAN predicted 4 instances of heterozygosity for the KEL*02N.17 allele, 5 heterozygous individuals for the weak FY* X allele, 32 total heterozygous samples for various weak Kidd alleles, 2 homozygous individuals for weak Kidd expression, 1 heterozygosity for Lu6/Lu9, 1 SC:1,2 case, 1 Co(a-b+) predicted phenotype, and a total of 19 RHAG*01.04 and 47 KLF1*BGM12 alleles. Limited areas of the BCAM, KLF1, KEL, FUT7, ERMAP and CR1 genes failed quality filters repeatedly, and careful review indicated that these regions were not captured in the ES libraries. The ACKR1 promoter GATA-binding site variant was present in every sample and predicted all cases of self-reported African ancestry. Conclusions: We describe a new, open-source informatics tool to translate NGS data into a predicted extended RBC phenotype, and demonstrate its application through the analysis of 245 ClinSeq® ES files. Most predicted antigen frequencies were as expected for the ethnic composition of our cohort. We detected a higher frequency of the RHAG p.V270I and KLF1 p.S102P variants than expected, findings that are in agreement with the 1000 Genomes Project and warrant further study. Our analysis also corroborates the relative frequency of the JK*01W.01 allele, and the presence of the JK*01W.03 and JK*01W.04 alleles in the Caucasian population, which can lead to serologic discrepancies in other genotyping platforms. Serologic confirmation of these findings is being conducted. Further study of genomic data across multiple ethnic groups can help refine knowledge of blood group gene polymorphisms and their clinical association. Disclosures No relevant conflicts of interest to declare.

scholarly journals A Tumor Suppressor Role for Bank1 in B-Cell Precursor Acute Lymphoblastic Leukemia

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 1333-1333
Author(s):  
Franziska Auer ◽  
Rodríguez-Hernández Guillermo ◽  
Inés González-Herrero ◽  
Oscar Blanco ◽  
Diego Alonso-López ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Tumor Suppressor ◽  
B Cell ◽  
Cell Phenotype ◽  
Next Generation ◽  
Cell Precursor ◽  
Susceptibility Variant ◽  
Generation Sequencing ◽  
Variable Penetrance

Abstract Introduction: Since the implementation of next generation sequencing techniques, inherited mutations in malignancy-associated susceptibility genes have become of major interest, to identify high-risk individuals, even before an actual disease onset. One challenge in this regard is that germline susceptibility variants often display incomplete or reduced penetrance, which can be influenced by genetic as well as environmental factors (Martin-Lorenzo A. et al., Cancer Discov,, 2015), making it even harder to assess the complete spectrum of the predisposition. Here, we aimed to elucidate the variable penetrance of a family, which harbors the inherited B-cell precursor ALL (BCP-ALL) susceptibility variant PAX5 c.547G>A (Auer F et al., Leukemia, 2014). Methods: We generated a new in vivo model, namely double transgenic Bank1+/-+Pax5+/- mice. Next generation sequencing was used to determine candidate genes influencing the variable penetrance of PAX5 c.547G>A. Pax5+/-+Bank1+/-, as well as Arf-/-+Bank1+/- mouse models were utilized to assess the tumor suppressor potential of Bank1. Murine leukemias were characterized by immune-phenotyping, whole exome sequencing (WES) as well as expression analyses. Results: In a family, harboring PAX5 c.547G>A, 5 out of 7 analyzed children were shown to be mutation carriers, while only 3 out of 5 developed BCP-ALL. In order to assess this variable penetrance further, re-analysis of the WES data revealed an additional rare variant in the B-cell scaffold protein with ankyrin repeats (BANK1) (c.120G>C; rs35978636, minor allele frequency (MAF)<0.01), with a similar transmission spectrum like the heterozygous PAX5 susceptibility variant c.547G>A (Figure 1). BANK1 is primarily expressed in B-cells where it acts as an important adaptor that is involved in B-cell receptor (BCR) induced Ca2+ mobilization from intracellular stores (Yokoyama K et al., EMBO, 2002). Importantly, single nucleotide variants (SNVs) in BANK1 could be linked to confer a susceptibility to a variety of autoimmune diseases, including Systemic Lupus Erythematosus (SLE) (Kozyrev SV et al., Nat. Genet., 2008). The identified BANK1 variant c.120G>C is located in Exon2, the IP3R binding site of BANK1, in proximity to the previously described SLE susceptibility variant c.182G>A, and results in a predicted deleterious protein structure as calculated by SIFT and PolyPhen-2. To test whether Bank1 and Pax5 heterozygosity could cooperate to promote BCP-ALL development, we crossed Bank1+/- mice on a Pax5 heterozygous background and monitored the leukemia incidence of double transgenic Bank1+/-+Pax5+/- mice. Bank1+/-+Pax5+/- mice developed BCP-ALL with clonal blast infiltration in secondary lymphoid organs and an identical leukemia phenotype (CD19-B220+IgM-) and latency like Pax5+/- mice. However, we observed an increase in BCP-ALL disease incidence of 33% compared to the Pax5+/- cohort. These results suggest that Pax5 loss promotes an aberrant B-cell precursor compartment that is susceptible for leukemic transformation, while the combination with Bank1 heterozygosity causes a susceptibility increase in the pre-leukemic population. While these results reflect the variable BCP-ALL penetrance in the human family carrying both PAX5 c.547G>A and BANK1 c.120G>C, it also underlines the multifactorial nature of the disease. Since these results suggest a tumor suppressor function of BANK1 in BCP-ALL, we next explored the effect of Bank1 loss of function on the disease phenotype in a tumor-prone mouse model lacking BCP-ALL susceptibility. Therefore, Bank1-/- mice were crossed back on a p19Arf-deficient background, to obtain the mouse cohorts Bank1+/-p19Arf-/- and Bank1-/-p19Arf-/-. The additional Bank1-deficiency promoted a shift from a T- to mainly B-cell phenotype in the resulting p19Arf-deficient tumors, further supporting a specific tumor suppressor role of Bank1 in BCP-ALL. Conclusion: Taken together, our data underline a tumor suppressor role of Bank1 in the context of BCP-ALL development and supports its involvement in the variable penetrance of BCP-ALL in a family carrying PAX5 c.547G>A. Figure 1. Figure 1. Disclosures No relevant conflicts of interest to declare.

Labordiagnostik bei gastrointestinalen Tumoren

2020 ◽  
Vol 11 (05) ◽  
pp. 232-238
Author(s):  
Marcus Kleber
Keyword(s):  
Next Generation Sequencing ◽  
Kolorektales Karzinom ◽  
Next Generation ◽  
Generation Sequencing

ZUSAMMENFASSUNGDas kolorektale Karzinom (KRK) ist einer der häufigsten malignen Tumoren in Deutschland. Einer frühzeitigen Diagnostik kommt große Bedeutung zu. Goldstandard ist hier die Koloskopie. Die aktuelle S3-Leitlinie Kolorektales Karzinom empfiehlt zum KRK-Screening den fäkalen okkulten Bluttest. Für das Monitoring von Patienten vor und nach Tumorresektion werden die Messung des Carcinoembryonalen Antigens (CEA) und der Mikrosatellitenstabilität empfohlen. Für die Auswahl der korrekten Chemotherapie scheint derzeit eine Überprüfung des Mutationsstatus, mindestens des KRAS-Gens und des BRAF-Gens, sinnvoll zu sein. Eine Reihe an neuartigen Tumormarkern befindet sich momentan in der Entwicklung, hat jedoch noch nicht die Reife für eine mögliche Anwendung in der Routinediagnostik erreicht. Den schnellsten Weg in die breite Anwendung können Next-Generation-Sequencing-basierte genetische Tests finden.

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