BELARDINILLI FRANCESCA^1,#, MICHELA DE MEO^1,#, FRANCESCO DEL GIUDICE², CARLO MARIA SCORNAJENGHI², PAOLA GAZZANIGA¹, ETTORE DE BERARDINIS², LUCA MARINO³, FABIO MASSIMO MAGLIOCCA⁴, BENJAMIN INBEH CHUNG⁵, JAN ŁASZKIEWICZ⁶, VALENTINA MAGRI⁴, GIUSEPPE GIANNINI^1,7, CHIARA NICOLAZZO^1,*

Oncology Research, Vol.33, No.3, pp. 723-731, 2025, DOI:10.32604/or.2024.056282 - 28 February 2025

Abstract Objectives: Intravesical Bacillus Calmette-Guérin (BCG) therapy is a gold standard for patients with high-risk non-muscle invasive bladder cancer (NMIBC). Although a long-lasting therapeutic response is observed in most patients, BCG failure occurs in 30%–50% of patients and a progression to muscle-invasive disease is found in 10%–15%. Therefore, predicting high-risk patients who might not benefit from BCG treatment is critical. The purpose of this study was to identify, whether the presence of specific oncogenic mutations might be indicative of BCG treatment response. Methods: Nineteen high-grade NMIBC patients who received intravesical BCG were retrospectively enrolled and divided… More > Graphic Abstract

YAN ZHANG, HEYANG ZHANG, JING WANG, XIN WEI, YI QU, FENG XU, LIJUN ZHANG^*

Oncology Research, Vol.32, No.5, pp. 955-963, 2024, DOI:10.32604/or.2023.043922 - 23 April 2024

Abstract Background: Bortezomib results in peripheral neuropathy (PN) in approximately 50% of patients, during multiple myeloma (MM) treatment, a complication known as Bortezomib-induced peripheral neuropathy (BIPN). The drug response varies among individuals. Genetic factor may play an important role in BIPN. Methods: A next-generation sequencing (NGS) panel containing 1659 targets from 233 genes was used to identify risk variants for developing BIPN in 204 MM patients who received bortezomib therapy. mRNA expression of MTHFR and ALDH1A1 in 62 peripheral blood samples was detected by real-time quantitative PCR (RT-qPCR). Serum homocysteine (Hcy) levels were detected in 40 samples… More > Graphic Abstract

JIYU WANG^1,2, HUIXIA LI^1,2, DEYUAN ZHOU^1,2, LIHONG BAI^1,2, KEJING TANG^1,2,3,*

BIOCELL, Vol.48, No.4, pp. 623-637, 2024, DOI:10.32604/biocell.2024.030420 - 09 April 2024

Abstract Background: For patients with lung cancer, timely identification of new lung lesions as infectious or non-infectious, and accurate identification of pathogens is very important in improving OS of patients. As a new auxiliary examination, metagenomic next-generation sequencing (mNGS) is believed to be more accurate in diagnosing infectious diseases in patients without underlying diseases, compared with conventional microbial tests (CMTs). We designed this study to find out whether mNGS has better performance in distinguishing infectious and non-infectious diseases in lung cancer patients using bronchoalveolar lavage fluid (BALF). Materials and Methods: This study was a real-world retrospective review… More >

Paul H. Chung¹, Joon Yau Leong¹, Jared J. Wallen², Whitney Stanton³, Niccole Diaz³, Caleb D. Phillips⁴, Gerard D. Henry⁵

Canadian Journal of Urology, Vol.29, No.6, pp. 11348-11354, 2022

Abstract Introduction: Traditional culture is the current standard-of-care to determine therapeutic antibiotics for patients suffering from penile prostheses (PP) infections. However, approximately 50% of PPs removed for infection are culture negative. Next-generation sequencing (NGS) compares DNA sequences to reference sequences with known microbial taxonomies to identify isolates and report relative abundances. We aim to compare the ability for standard culture and NGS techniques to identify microorganisms and biofilm composition on PPs.
Materials and methods: Ninety-one PPs explanted for mechanical malfunction were included in this study. Devices removed for infection or erosion were excluded. During revision surgery, two specimens… More >

Mary Aksa¹, Junaid Rashid^2,*, Muhammad Wasif Nisar¹, Toqeer Mahmood³, Hyuk-Yoon Kwon⁴, Amir Hussain⁵

CMC-Computers, Materials & Continua, Vol.68, No.3, pp. 3931-3946, 2021, DOI:10.32604/cmc.2021.016081 - 06 May 2021

Abstract Advancements in next-generation sequencer (NGS) platforms have improved NGS sequence data production and reduced the cost involved, which has resulted in the production of a large amount of genome data. The downstream analysis of multiple associated sequences has become a bottleneck for the growing genomic data due to storage and space utilization issues in the domain of bioinformatics. The traditional string-matching algorithms are efficient for small sized data sequences and cannot process large amounts of data for downstream analysis. This study proposes a novel bit-parallelism algorithm called BitmapAligner to overcome the issues faced due to… More >

Paul H. Chung, Joon Yau Leong, Seth Teplitsky, Patrick J. Shenot, Akhil K. Das, Leonard G. Gomella

Canadian Journal of Urology, Vol.27, No.5, pp. 10418-10423, 2020

Abstract Infection of artificial urinary sphincters or inflatable penile prostheses is one of the most devastating complications after prosthetic surgery and can have a significant impact on a quality of life. Patients undergoing revision surgery with or without device replacement may have increased risk for infection when compared to initial primary surgery. As such, surgeons may utilize traditional culture results to direct antimicrobial therapy for these patients. Unfortunately, culture results can be inconclusive in up to one-third of the time even in the setting of active device infection. Next-generation sequencing (NGS) of DNA is an emerging More >

Tarek A ATIA

BIOCELL, Vol.43, No.4, pp. 253-262, 2019, DOI:10.32604/biocell.2019.08180

Abstract Recurring miscarriage (RM) is a frustrating reproductive complication with variable etiology. Numerous genetic defects have been known to play a crucial role in the etiology of RM. Chromosomal abnormalities are frequently detected, while other genetic defects cannot be diagnosed through routine research, such as cryptic chromosomal anomalies, single nucleotide polymorphism, single-gene defect, and gene copy number variation. Diagnostic laboratories have recently used variable advanced techniques to detect potential genetic abnormalities in couples with RM and/or in products of conception. Here we aim to summarize the known genetic causes of RM, with a focus on the More >

Nelly Sabbaghian¹, Maria C. Digilio², Gillian M. Blue^3,4, Timothée Revil⁵, David S. Winlaw^3,4, William D. Foulkes^1,6

Congenital Heart Disease, Vol.13, No.3, pp. 401-406, 2018, DOI:10.1111/chd.12578

Abstract Objective: We previously identified a pathogenic germline DICER1 variant in a child with transposition of the great arteries who was a member of a family with DICER1 syndrome. In view of a report linking DICER1 knockout in murine cardiomyocytes to cardiac outflow defects, we investigated the involvement of DICER1 in transposition of the great arteries.
Design: We used Fluidigm access array followed by next generation sequencing to screen for variants in the coding exons, their exon/intron boundaries and the 30 untranslated region of DICER1 in patient DNA.
Cases: Germline DNA was collected from 129 patients with either sporadic or familial More >