scholarly journals Old questions, new tools: does next-generation sequencing hold the key to unraveling intestinal B-cell responses?

2014 ◽  
Vol 8 (1) ◽  
pp. 29-37 ◽  
Author(s):  
O Pabst ◽  
H Hazanov ◽  
R Mehr
2017 ◽  
Vol 23 (4) ◽  
pp. 691-696 ◽  
Author(s):  
Olga Sala Torra ◽  
Megan Othus ◽  
David W. Williamson ◽  
Brent Wood ◽  
Ilan Kirsch ◽  
...  

2017 ◽  
Vol 35 (7_suppl) ◽  
pp. 72-72
Author(s):  
Mustafa H. Syed ◽  
Caleb Ho ◽  
Kseniya Petrova-Drus ◽  
JinJuan Yao ◽  
Wayne Yu ◽  
...  

72 Background: Clonality testing is an integral part of the initial assessment of B and T cell malignancies. The further use of conventional clonality assays for monitoring of disease post treatment is limited by low assay sensitivity and inability to track clones based on their unique sequences. Clonality assessment by next generation sequencing (NGS) provides increased diagnostic capabilities, allowing the tracking of disease specific clones as well as the full spectrum of clonal sequences that arise in response to therapy. Here we describe our initial experience using an NGS based assay for monitoring and our comparison to conventional clonality assays and flow cytometry. Methods: DNA was extracted from hematologic samples received for routine clonality assessment including diagnostic (DS) and follow-up post therapy (PT) samples. Clonality testing was performed by conventional PCR-based assays using biomed II primers and by NGS utilizing Lymphotrack IGH FR1 and TRG kits (Invivoscribe). The amplified products were sequenced on Illumina MiSeq. For MRD assessment, we created dedicated laboratory protocols as well as in-house developed software, MSK-LymphoClone (LC), containing a data analysis pipeline, analytical tools for clonality assessment and a signout portal for easy search and retrieval of pertinent clones. Results: Samples from 48 patients were included (48 DS and 60 PT) encompassing 12 plasma cell neoplasms, 11 acute lymphoblastic leukemias, 16 mature B-cell and 9 T-cell lymphomas. All diagnostic samples showed clonal rearrangement with 100% concordance between conventional and NGS assays. Residual disease was detected in 27/60 (45%) PT samples using conventional fragment size based assays, 27/57 (47%) using flow and 38/60 (63%) using NGS. Diagnostic clonal sequences were detected in as low as 0.0019% of total reads in PT samples tested by NGS. 18/60 (30.0%) PT samples (17 patients) were disease negative by all assays; 16 patients remained disease-free (median follow-up - 2.4 months). Conclusions: NGS clonality testing is a valuable tool for monitoring patients with B and T cell neoplasms showing higher sensitivity and specificity than conventional assays.


2021 ◽  
Vol 10 (Supplement_2) ◽  
pp. S1-S1
Author(s):  
Fatima Al Dhaheri ◽  
Ann T MacIntyre ◽  
Alicia M Johnston

Abstract Background X-linked agammaglobulinemia is a primary immunodeficiency associated with mutations in the B cell tyrosine kinase (BTK) gene leading to failure in B cell maturation and defective antibody production. Campylobacter and closely related Helicobacter species can cause persistent bacteremia, enteritis and cellulitis in patients with XLA and are difficult to diagnose and eradicate. In this context, detection of circulating microbial cell-free DNA (mcfDNA) by next-generation sequencing (NGS) can be used to identify infectious agents in susceptible immunocompromised hosts. Methods We report 4-year-old fraternal twins with XLA presenting with disparate clinical manifestations due to C. upsaliensis and coinfection with C. upsaliensis and H. canis respectively. Results Patient #1 was diagnosed with XLA at 11 months-old and was started on weekly immunoglobulin replacement. At 2.5 yo he developed recurrent fever, abdominal pain and diarrhea. Endoscopy/colonoscopy revealed focal ileocolitis without ulceration or granulomas. Stool infectious workup, including bacterial stool cultures, was negative. At 3 yo he developed gram- rod bacteremia that was not further identified but successfully treated with ceftriaxone. He presented 2 months later with fever and diarrhea; blood cultures were negative, but stool culture grew C. jejuni. His symptoms recrudesced after two months and he was treated for presumed recurrent Campylobacter infection. Intermittent fevers and diarrhea recurred, and repeat stool culture grew C. upsaliensis identified by MALDI-TOF resulting in a 3-month course of azithromycin. Stool PCR remained positive for Campylobacter species after one month of therapy. Fever and diarrhea recurred after completion of therapy and stool culture again grew C. upsaliensis but sensitivities could not be obtained. McfDNA testing confirmed C. upsaliensis and therapy with ertapenem, ciprofloxacin, amoxicillin and doxycycline was initiated. He remained symptom free three months into therapy. Patient #2 was diagnosed with XLA at 1 yo and started weekly immunoglobulin replacement. At 3.5 yo he developed fever, erythema nodosum (EN) and arthritis. Given his twin’s diagnosis of Campylobacter enteritis with likely bacteremia, a presumptive diagnosis of Campylobacter related reactive arthritis and EN was made. Treatment with Naprosyn and 14 days of azithromycin failed to prevent the return of EN post therapy. He had multiple courses of azithromycin each followed by return of EN rash. Following completion of therapy, he presented with high fevers, worsening rash, leukocytosis and elevated ESR. Blood and stool cultures were obtained and returned negative. Despite completion of a 3 month course of azithromycin, stool PCR remained positive for Campylobacter species and his symptoms persisted. The recrudescence of fevers and worsening rash 2 months after completion of therapy prompted repeat blood and stool cultures that returned negative. McfDNA testing was obtained in that context and identified Helicobacter canis and Campylobacter upsaliensis. Treatment with ertapenem, ciprofloxacin, amoxicillin and doxycycline was initiated and he remained symptom free three months into therapy. Conclusions Physicians should be aware of the varied presentations of chronic Campylobacter and Helicobacter infection in XLA patients. Plasma NGS for circulating mcfDNA in immunocompromised patients offers a rapid, non-invasive means of detecting these fastidious organisms that can be difficult to diagnose using more conventional means.


Blood ◽  
2013 ◽  
Vol 122 (5) ◽  
pp. 726-733 ◽  
Author(s):  
Hakim Bouamar ◽  
Saman Abbas ◽  
An-Ping Lin ◽  
Long Wang ◽  
Daifeng Jiang ◽  
...  

Key Points Targeted capture/next-generation sequencing is a powerful tool for the diagnosis of known and discovery of new IGH fusions in DLBCL. IGH-mediated deregulation of IRF8 and EBF1 in DLBCL is characterized by induction of AID and BCL6, suppression of PRDM1, and antiapoptosis.


2016 ◽  
Vol 5 (7) ◽  
pp. e93 ◽  
Author(s):  
Vladimir Vigdorovich ◽  
Brian G Oliver ◽  
Sara Carbonetti ◽  
Nicholas Dambrauskas ◽  
Miles D Lange ◽  
...  

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