Gene testing for osteonecrosis of the femoral head in systemic lupus erythematosus using targeted next-generation sequencing: A pilot study

Abstract Background: Pneumocystis jirovecii and Aspergillus fumigatus, are opportunistic pathogenic fungus that has a major impact on mortality in patients with systemic lupus erythematosus. With the potential to invade multiple organs, early and accurate diagnosis is essential to the survival of SLE patients, establishing an early diagnosis of the infection, especially coinfection by Pneumocystis jirovecii and Aspergillus fumigatus, still remains a great challenge.Case presentation: In this case, we reported that the application of next-generation sequencing in diagnosing Pneumocystis jirovecii and Aspergillus fumigatus coinfection in a Chinese girl with systemic lupus erythematosus (SLE). Voriconazole was used to treat pulmonary aspergillosis, besides sulfamethoxazole and trimethoprim (SMZ-TMP), and caspofungin acetate to treat Pneumocystis jirovecii infection for 6 days. On Day 10 of admission, her chest radiograph displayed obvious absorption of bilateral lung inflammation though the circumstance of repeated fever had not improved. Unfortunately, the patient discharged from the hospital since the financial burden, therefore further condition couldn't be tracked.Conclusions: This successful application of the next generation sequencing assisting the rapid diagnosis of Pneumocystis jirovecii and Aspergillus fumigatus coinfection provides a new perspective in the clinical approach against the systematic fungi infections and highlights the potential of this technique in rapid etiological diagnosis.

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Rapid and Precise Diagnosis of Pneumonia Coinfected by Pneumocystis Jirovecii and Aspergillus Fumigatus Assisted by Next-generation Sequencing in a Patient With Systemic Lupus Erythematosus: a Case Report

10.21203/rs.3.rs-154016/v1 ◽

2021 ◽

Author(s):

Yili Chen ◽

Lu Ai ◽

Yingqun Zhou ◽

Yating Zhao ◽

Jianyu Huang ◽

...

Keyword(s):

Systemic Lupus Erythematosus ◽

Next Generation Sequencing ◽

Aspergillus Fumigatus ◽

Lupus Erythematosus ◽

Financial Burden ◽

Pneumocystis Jirovecii ◽

Clinical Approach ◽

Next Generation ◽

Systemic Lupus ◽

Generation Sequencing

Abstract Background: Pneumocystis jirovecii and Aspergillus fumigatus, are opportunistic pathogenic fungus that has a major impact on mortality in patients with systemic lupus erythematosus. With the potential to invade multiple organs, early and accurate diagnosis is essential to the survival of SLE patients, establishing an early diagnosis of the infection, especially coinfection by Pneumocystis jirovecii and Aspergillus fumigatus, still remains a great challenge.Case presentation: In this case, we reported that the application of next-generation sequencing in diagnosing Pneumocystis jirovecii and Aspergillus fumigatus coinfection in a Chinese girl with systemic lupus erythematosus (SLE). Voriconazole was used to treat pulmonary aspergillosis, besides sulfamethoxazole and trimethoprim (SMZ-TMP), and caspofungin acetate to treat Pneumocystis jirovecii infection for 6 days. On Day 10 of admission, her chest radiograph displayed obvious absorption of bilateral lung inflammation though the circumstance of repeated fever had not improved. Unfortunately, the patient discharged from the hospital since the financial burden, therefore further condition couldn't be tracked.Conclusions: This successful application of the next generation sequencing assisting the rapid diagnosis of Pneumocystis jirovecii and Aspergillus fumigatus coinfection provides a new perspective in the clinical approach against the systematic fungi infections and highlights the potential of this technique in rapid etiological diagnosis.

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Rapid and precise diagnosis of pneumonia coinfected by Pneumocystis jirovecii and Aspergillus fumigatus assisted by next-generation sequencing in a patient with systemic lupus erythematosus: a case report

Annals of Clinical Microbiology and Antimicrobials ◽

10.1186/s12941-021-00448-5 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Yili Chen ◽

Lu Ai ◽

Yingqun Zhou ◽

Yating Zhao ◽

Jianyu Huang ◽

...

Keyword(s):

Systemic Lupus Erythematosus ◽

Next Generation Sequencing ◽

Aspergillus Fumigatus ◽

Lupus Erythematosus ◽

Financial Burden ◽

Pneumocystis Jirovecii ◽

Clinical Approach ◽

Next Generation ◽

Systemic Lupus ◽

Generation Sequencing

Abstract Background Pneumocystis jirovecii and Aspergillus fumigatus, are opportunistic pathogenic fungus that has a major impact on mortality in patients with systemic lupus erythematosus. With the potential to invade multiple organs, early and accurate diagnosis is essential to the survival of SLE patients, establishing an early diagnosis of the infection, especially coinfection by Pneumocystis jirovecii and Aspergillus fumigatus, still remains a great challenge. Case presentation In this case, we reported that the application of next -generation sequencing in diagnosing Pneumocystis jirovecii and Aspergillus fumigatus coinfection in a Chinese girl with systemic lupus erythematosus (SLE). Voriconazole was used to treat pulmonary aspergillosis, besides sulfamethoxazole and trimethoprim (SMZ-TMP), and caspofungin acetate to treat Pneumocystis jirovecii infection for 6 days. On Day 10 of admission, her chest radiograph displayed obvious absorption of bilateral lung inflammation though the circumstance of repeated fever had not improved. Unfortunately, the patient discharged from the hospital since the financial burden, and during the follow-up, it was documented the patient died within one week after discharge. Conclusions This successful application of the next generation sequencing assisting the rapid diagnosis of Pneumocystis jirovecii and Aspergillus fumigatus coinfection provides a new perspective in the clinical approach against the systematic fungi infections and highlights the potential of this technique in rapid etiological diagnosis.

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PS2:38 Comparative tissue transcriptome analysis by next-generation sequencing reveals novel pathways that characterise genetic susceptibility and developmental biology in systemic lupus erythematosus (sle)

10.1136/lupus-2018-abstract.86 ◽

2018 ◽

Cited By ~ 1

Author(s):

E Frangou ◽

M Grigorioy ◽

A Banos ◽

G Bertsias ◽

E Dermitzakis ◽

...

Keyword(s):

Systemic Lupus Erythematosus ◽

Developmental Biology ◽

Next Generation Sequencing ◽

Genetic Susceptibility ◽

Transcriptome Analysis ◽

Lupus Erythematosus ◽

Next Generation ◽

Systemic Lupus ◽

Generation Sequencing

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Targeted Next-Generation Sequencing in Men with Metastatic Prostate Cancer: a Pilot Study

Targeted Oncology ◽

10.1007/s11523-018-0576-z ◽

2018 ◽

Vol 13 (4) ◽

pp. 495-500 ◽

Cited By ~ 6

Author(s):

Pedro C. Barata ◽

Prateek Mendiratta ◽

Brandie Heald ◽

Stefan Klek ◽

Petros Grivas ◽

...

Keyword(s):

Prostate Cancer ◽

Next Generation Sequencing ◽

Pilot Study ◽

Metastatic Prostate Cancer ◽

Next Generation ◽

Targeted Next Generation Sequencing ◽

Generation Sequencing

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Targeted Next-Generation Sequencing on Hirschsprung Disease: A Pilot Study Exploits DNA Pooling

Annals of Human Genetics ◽

10.1111/ahg.12076 ◽

2014 ◽

Vol 78 (5) ◽

pp. 381-387 ◽

Cited By ~ 8

Author(s):

Hongsheng Gui ◽

Jessie Yunjuan Bao ◽

Clara Sze-Man Tang ◽

Man-Ting So ◽

Diem-Ngoc Ngo ◽

...

Keyword(s):

Next Generation Sequencing ◽

Pilot Study ◽

Hirschsprung Disease ◽

Next Generation ◽

Dna Pooling ◽

Targeted Next Generation Sequencing ◽

Generation Sequencing

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Analysis of a large cohort of non-small cell lung cancers submitted for somatic variant analysis demonstrates that targeted next-generation sequencing is fit for purpose as a molecular diagnostic assay in routine practice

Journal of Clinical Pathology ◽

10.1136/jclinpath-2018-205319 ◽

2018 ◽

Vol 71 (11) ◽

pp. 1001-1006 ◽

Cited By ~ 3

Author(s):

David Allan Moore ◽

Kevin Balbi ◽

Alexander Ingham ◽

Hendrik-Tobias Arkenau ◽

Philip Bennett

Keyword(s):

Next Generation Sequencing ◽

Single Gene ◽

Small Cell ◽

Molecular Diagnostic ◽

Next Generation ◽

Small Cell Lung ◽

Targeted Next Generation Sequencing ◽

Gene Testing ◽

The Impact ◽

Generation Sequencing

AimsTargeted next-generation sequencing (tNGS) is increasingly being adopted as an alternative to single gene testing in some centres. Our aim was to assess the overall fitness and utility of tNGS as a routine clinical test in non-small cell lung cancer (NSCLC).MethodsAll NSCLC cases submitted to a single laboratory for tNGS analysis over a 3-year period were included. Rejection/failure rates and turnaround times were calculated. For reportable cases, data relating to observed genetic changes likely to be driving tumour growth and/or contributing to therapeutic resistance were extracted. The impact of varied referral site practices (tissue processing and sample format submitted) on analytical outcomes was also considered.ResultsA total of 2796 cases were submitted, of which 217 (7.8%) were rejected and 131 (5.1%) failed. The median turnaround time was seven working days. Of 2448 reported cases, KRAS, EGFR or other recognised driver mutations were observed in 35%, 17% and 5.4%, respectively. Of the remaining cases, 3.5% demonstrated significant incidental evidence of gene amplification. In 15% of EGFR-driven cases, evidence of an EGFR tyrosine kinase inhibitor resistance mechanism was observed. Potential concerns around the provision of slides or precut ‘rolls’ only (cf, formalin fixed paraffin embedded (FFPE) tissue blocks) as standard practice by certain referral sites were identified.ConclusionsA tNGS panel approach is practically achievable, with acceptable success rates and turnaround times, in the context of a routine clinical service. Furthermore, it provides additional clinically and analytically relevant information, which is not available from single gene testing alone.

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