Article
Neurosciences
Johra Khan, Lubna Al Asoom, Ahmad Al Sunni, Nazish Rafique, Rabia Latif, Majed Alabdali, Azhar Alhariri, Majed Aloqaily, Sayed AbdulAzeez, Sadaf Jahan, Saeed Banawas, J. Francis Borgio
Summary: This study identified 17 functional variants in 12 genes associated with higher migraine risk among Saudi female migraineurs of Arab ancestry using whole-exome sequencing. Half of the significant genes were expressed in the temporal lobe, expanding our understanding of migraine pathophysiology and the potential for personalized genetic research using biomarkers for early identification.
Article
Rheumatology
Yiming Luo, Marcela A. Ferrada, Keith A. Sikora, Cameron Rankin, Hugh D. Alessi, Daniel L. Kastner, Zuoming Deng, Mengqi Zhang, Peter A. Merkel, Virginia B. Kraus, Andrew S. Allen, Peter C. Grayson
Summary: This study suggests that rare variants in the DCBLD2 gene may play a role in the development of RP. These findings should be further validated in a larger sample and supported by functional experiments.
ANNALS OF THE RHEUMATIC DISEASES
(2023)
Article
Medicine, General & Internal
Nourah H. Al Qahtani, Sayed AbdulAzeez, Noor B. Almandil, Norah Fahad Alhur, Hind Saleh Alsuwat, Hatoon Ahmed Al Taifi, Ahlam A. Al-Ghamdi, B. Rabindran Jermy, Mohamed Abouelhoda, Shazia Subhani, Lubna Al Asoom, J. Francis Borgio
Summary: Family trio next-generation sequencing was used to analyze genetic variations in a Saudi Arabian family with a history of unexplained recurrent pregnancy loss (RPL). A novel homozygous exonic variation in the ASIC5 gene was identified in the dead fetus, confirmed through Sanger sequencing, and found to be highly pathogenic. This rare autosomal recessive mutation in ASIC5 gene was associated with RPL and potentially fatal to the fetus.
FRONTIERS IN MEDICINE
(2021)
Article
Medicine, General & Internal
Taylor B. Cavazos, Linda Kachuri, Rebecca E. Graff, Jovia L. Nierenberg, Khanh K. Thai, Stacey Alexeeff, Stephen Van den Eeden, Douglas A. Corley, Lawrence H. Kushi, Regeneron Genetics Center, Thomas J. Hoffmann, Elad Ziv, Laurel A. Habel, Eric Jorgenson, Lori C. Sakoda, John S. Witte
Summary: This study conducted whole-exome sequencing of individuals from two large multi-ancestry populations to characterize genetic susceptibility to multiple cancers, identifying variants and genes that may play a fundamental role in the development of multiple primary cancers. The results suggest shared mechanisms underlying carcinogenesis and highlight previously undiscovered variant-phenotype associations significantly overrepresented among individuals with multiple cancers.
Article
Genetics & Heredity
Marguerite R. Irvin, Praful Aggarwal, Steven A. Claas, Lisa de Las Fuentes, Anh N. Do, C. Charles Gu, Andrea Matter, Benjamin S. Olson, Amit Patki, Karen Schwander, Joshua D. Smith, Vinodh Srinivasasainagendra, Hemant K. Tiwari, Amy J. Turner, Deborah A. Nickerson, Dabeeru C. Rao, Ulrich Broeckel, Donna K. Arnett
Summary: This study conducted an exome-wide association study in African Americans, identifying three genes (MYRIP, TRAPPC11, and SLC27A6) that may be associated with LV hypertrophy. Functional validation of these genes provided new insights into hypertrophic pathways.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Adeline Germain, Jeanne-Marie Perotin, Gonzague Delepine, Myriam Polette, Gaetan Deslee, Valerian Dormoy
Summary: A comparative whole-exome sequencing analysis was performed on bronchial epithelia from COPD and non-COPD subjects, revealing genetic alterations and copy number variations in remodelled epithelia, mainly in COPD patients. Functional analysis highlighted cilia-associated processes, indicating a greater genetic alteration in remodelled epithelia.
Article
Surgery
Erina Takai, Hiromi Nakamura, Suenori Chiku, Emi Kubo, Akihiro Ohmoto, Yasushi Totoki, Tatsuhiro Shibata, Ryota Higuchi, Masakazu Yamamoto, Junji Furuse, Kyoko Shimizu, Hideaki Takahashi, Chigusa Morizane, Toru Furukawa, Shinichi Yachida
Summary: The study aimed to identify novel genes that increase the risk of familial pancreatic cancer (FPC) in the Japanese population. The findings revealed potentially harmful germline variants in tumor suppressor genes in FPC patients, and somatic loss of heterozygosity of certain FPC susceptibility genes may contribute to FPC development. Genetic testing for a wider range of FPC predisposition genes could improve screening methods for high-risk groups of pancreatic cancer.
Article
Biochemistry & Molecular Biology
Lance P. Doucette, Nicole C. L. Noel, Yi Zhai, Manlong Xu, Oana Caluseriu, Stephanie C. Hoang, Alina J. Radziwon, Ian M. MacDonald
Summary: This study focused on inherited retinal dystrophies (IRDs) in ten families from Alberta, Canada, using novel gene discovery methods. The genetic causes of IRDs in three families were identified as variants in known disease-associated genes, while two potential new associations were also found. The research provided interesting insights into blinding conditions and unsolved cases, offering valuable information for further investigation.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Oncology
Weifeng Liu, Renxian Wang, Yanrui Zhang, Huina Wang, Zhen Huang, Tao Jin, Yongkun Yang, Yang Sun, Shanbo Cao, Xiaohui Niu
Summary: In this study, the genomic profiles of 33 osteosarcoma patients were analyzed, revealing the potential roles of the MAPK and PI3K-Akt signaling pathways in determining prognosis. Significant differences in somatic copy number alterations and mutation sites and frequencies were observed between patients with good and poor prognosis. Patients with poor prognosis may have access to a larger number of treatment options based on the frequency of potentially actionable alterations.
Article
Biochemistry & Molecular Biology
Peng-Fei Xu, Cong Li, Shao-Yan Xi, Fu-Rong Chen, Jing Wang, Zhi-Qiang Zhang, Yan Liu, Xin Li, Zhong-Ping Chen
Summary: Branching evolution is widespread in the recurrent process of gliomas, and recurrent tumors continue to evolve independently with chemoradiotherapy, harboring multiple recurrenceselected genetic alterations. Truncal variants within partial driver genes among primary and recurrent gliomas may be ideal therapeutic targets.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Pediatrics
Sonal Gupta, Praveen Mathur, Ashwani Kumar Mishra, Krishna Mohan Medicherla, Obul Reddy Bandapalli, Prashanth Suravajhala
Summary: The aim of this study was to identify de novo heterozygous missense variants associated with Congenital Pouch Colon (CPC) and discover variants of unknown significance. Whole exome sequencing (WES) was performed on individuals admitted to J.K. Lon Hospital in India between 2011 and 2017. Comparison of affected proband exomes with unaffected family members revealed rare variants associated with CPC. RNA-Seq was also performed to investigate differential gene expression. The study identified rare variants (TAF1B, MUC5B, and FRG1) that may contribute to CPC development, providing potential targets for intervention.
Article
Genetics & Heredity
Zekiye Altun, Hongling Yuan, Burcin Baran, Safiye Aktas, Esra Esmeray Sonmez, Can Kucuk, Nur Olgun
Summary: This study aimed to investigate genetic aberrations in neuroblastoma (NB) by comparing high and low-risk NB patients using whole-exome sequencing (WES) and to reveal the heterogeneity and association between somatic variants and clinical features. Seven NB patients with clinical data were included (4 in the low-risk group and 3 in the high-risk group). Somatic variants associated with NB genes were identified and analyzed using bioinformatics methods. Several gene variations were found in both groups, including oncogenes and tumor suppressor genes. Candidate gene variations were associated with chromatin remodeling complexes, the RAS pathway, cell proliferation, and DNA repair mechanism. Some variations were specific to high-risk patients or low-risk patients. Comparisons with the cBioportal cancer genomic database identified common gene variants in high-risk patients but not in low-risk patients. GO/KEGG enrichment analysis was performed to explore relevant biological processes and molecular pathways related to gene variants, which can help unravel the molecular mechanisms of NB tumorigenesis and the phenotypic differences between high-risk and low-risk patients.
Article
Oncology
Lanlan Wang, Yali Ma, Wenjie Han, Qiumin Yang, Muhammad Jamil
Summary: By performing Whole Exome Sequencing (WES) on Pakistani lung cancer patients, this study identified clinically important pathogenic mutations in 6 DNA repair genes and revealed their potential implications on prognosis. Down-regulation of these mutated genes and hypermethylation in their promoters were observed, indicating a potential convergence of genetic and epigenetic factors driving genomic instability in lung cancer cells. These findings contribute to our understanding of lung cancer susceptibility and offer potential avenues for targeted therapeutic interventions in Pakistani patients.
AMERICAN JOURNAL OF CANCER RESEARCH
(2023)
Article
Clinical Neurology
Rainer Malik, Nathalie Beaufort, Simon Frerich, Benno Gesierich, Marios K. Georgakis, Kristiina Rannikmae, Amy C. Ferguson, Christof Haffner, Matthew Traylor, Michael Ehrmann, Cathie L. M. Sudlow, Martin Dichgans
Summary: The study identified associations between genetic variants in GBE1 and decreased white matter burden, while variants in HTRA1 were linked to increased WMH volume. Rare variants in the protease domain of HTRA1 were found to play a significant role in determining WMH burden in the general population, affecting carriers' WMH volume and potentially leading to various neurological and non-neurological conditions.
Article
Medical Laboratory Technology
Chunyu Gu, Hong Wang, Jianbo Shu, Jie Zheng, Dong Li, Chunquan Cai, Peiyuan Zhang
Summary: This study described atypical symptoms of A-T in a 5-year-old girl and proposed a dual-omics diagnostic approach combining RNA-seq with WES. The study also discussed phenotypic heterogeneity of A-T among family members and individuals.
CLINICA CHIMICA ACTA
(2021)
Article
Biochemical Research Methods
Daudi Jjingo, Gerald Mboowa, Ivan Sserwadda, Robert Kakaire, Davis Kiberu, Marion Amujal, Ronald Galiwango, David Kateete, Moses Joloba, Christopher C. Whalen
Summary: In resource-limited settings, one-year in-person bioinformatics training and mentorship is a viable and effective approach for developing bioinformatics skills, suitable for those with limited resources.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Moses Ocan, Fred Katabazi Ashaba, Savannah Mwesigwa, Kigozi Edgar, Moses R. Kamya, Sam L. Nsobya
Summary: This study investigated the mutations associated with artemisinin resistance in Plasmodium falciparum parasites in Uganda. The results showed a significant increase in the prevalence of pfmdr-2 gene mutations in samples collected from 2005 to 2013, while the prevalence of K13 and arps10 gene mutations did not change significantly. The findings suggest the need for continuous surveillance of molecular markers of artemisinin resistance in malaria-affected regions.
Article
Infectious Diseases
Nametso Kelentse, Sikhulile Moyo, Wonderful T. Choga, Kwana Lechiile, Tshepo B. Leeme, David S. Lawrence, Ishmael Kasvosve, Rosemary Musonda, Mosepele Mosepele, Thomas S. Harrison, Joseph N. Jarvis, Simani Gaseitsiwe
Summary: This study compared the patterns of HIV-1 drug resistance mutations between the cerebrospinal fluid (CSF) and plasma of individuals with HIV-associated cryptococcal meningitis. The results showed high concordance in HIV-1 drug resistance mutations between the CSF and plasma, suggesting intercompartmental mixing and possibly a lack of compartmentalization. Some individuals also harbored minority HIV-1 drug resistance mutations.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Pharmacology & Pharmacy
Blessing R. Sitabule, Houcemeddine Othman, Ananyo Choudhury, David Twesigomwe, Neil A. Hanchard
Summary: African populations have high genetic variation and are burdened by both infectious and noninfectious diseases, necessitating the understanding of pharmacogenomic variation. Using specific genes, this article emphasizes the importance of pharmacogenomics in Africa and discusses future challenges and opportunities.
CLINICAL PHARMACOLOGY & THERAPEUTICS
(2023)
Article
Biotechnology & Applied Microbiology
Sheila Nabweyambo, Stephen Kanyerezi, John H. -O. Petterson, Fred Ashaba Katabazi, Alfred Ssekagiri, Savannah Mwesigwa, Gerald Mboowa, Faith Nakazzi, Annette Keesiga, Moses Adroma, Freddie Bwanga, Naomi McGovern, Obondo James Sande, Annettee Nakimuli
Summary: This study investigated the +936C/T polymorphism in the 3' UTR of the VEGFA gene and found no significant association with increased susceptibility to pre-eclampsia among pregnant women in Uganda. Further studies with a larger sample size are recommended.
Review
Genetics & Heredity
Stephen Tukwasibwe, Gerald Mboowa, Ivan Sserwadda, Joaniter I. Nankabirwa, Emmanuel Arinaitwe, Isaac Ssewanyana, Yoweri Taremwa, Gerald Tumusiime, Moses R. Kamya, Prasanna Jagannathan, Annettee Nakimuli
Summary: Vaccination is a highly effective public health strategy in preventing infectious diseases and has saved millions of lives. However, the efficacy of the RTS,S/AS01 malaria vaccine is challenged by genetic variation in humans and malaria parasites, leading to variable responses. This review focuses on human genetic factors that determine variable responses to vaccination and how immune system gene variation affects the immunogenicity and efficacy of the RTS,S/AS01 vaccine.
Editorial Material
Biochemistry & Molecular Biology
Alan Christoffels, Gerald Mboowa, Peter van Heusden, Sello Makhubela, George Githinji, Sarah Mwangi, Harris Onywera, Ndodo Nnaemeka, Daniel Gyamfi Amoako, Idowu Olawoye, Amadou Diallo, Placide Mbala-Kingebeni, Samuel O. Oyola, Bright Adu, Christopher Mvelase, Pascale Ondoa, Fred Athanasius Dratibi, Abdourahmane Sow, Nicksy Gumede, Sofonias K. Tessema, Ahmed Ogwell Ouma, Yenew Kebede Tebeje
Summary: Wealthy countries have abundant genomics expertise that can be quickly utilized to address disease threats. African countries should invest in a federated data-management system for genomics epidemiology to better deal with such threats.
Article
Multidisciplinary Sciences
Richard Mayanja, Adrian Muwonge, Dickson Aruhomukama, Fred Ashaba Katabazi, Mudarshiru Bbuye, Edgar Kigozi, Annettee Nakimuli, Musa Sekikubo, Christine Florence Najjuka, David Patrick Kateete
Summary: This study aimed to investigate the source of EKE organisms for neonates in a maternity ward in Uganda. The results showed evidence of transmission of drug-resistant EKE bacteria in the ward and highlighted the high prevalence of drug resistance genes. This calls for more effective infection prevention/control measures and antimicrobial stewardship programs in hospitals to reduce the spread of drug-resistant bacteria and improve patient outcomes.
Article
Virology
Brian Nyiro, Sharon Bright Amanya, Alice Bayiyana, Francis Wasswa, Eva Nabulime, Alex Kayongo, Immaculate Nankya, Gerald Mboowa, David Patrick Kateete, Obondo James Sande
Summary: The reduced expression of CCR5 plays a role in HIV control among Ugandan HIV controllers.
Article
Microbiology
Eric G. Kariuki, Caleb Kibet, Juan C. Paredes, Gerald Mboowa, Oscar Mwaura, John Njogu, Daniel Masiga, Timothy D. H. Bugg, Chrysantus M. Tanga
Summary: The gut microbiome of black soldier fly larvae plays a positive role in waste bioconversion, particularly in lignocellulosic diets. This study found significant changes in the gut microbiomes and enzyme activities of black soldier fly larvae reared on lignocellulosic diets such as chicken manure and brewers' spent grain. These findings provide valuable insights into the potential applications of black soldier fly larvae in the bioconversion of waste materials.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Microbiology
Francis Kakooza, Reuben Kiggundu, Gerald Mboowa, Patrick David Kateete, Olga Tendo Nsangi, Jupiter Marina Kabahita, Bernard Ssentalo Bagaya, Daniel Golparian, Magnus Unemo
Summary: A recent study found that there is very limited data on antimicrobial resistance (AMR) surveillance in Neisseria gonorrhoeae (NG) in Africa. There are significant variations in surveillance protocols, methods, and quality assurance among different studies, making comparisons of AMR data difficult. Therefore, establishing a strengthened, standardized, and quality-assured surveillance system in Africa is crucial for identifying AMR trends, detecting emerging resistance, and refining treatment guidelines. Achieving this goal requires leadership and financial commitments from national and international stakeholders.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Immunology
Megan E. Carey, Zoe A. Dyson, Silvia Argimon, Louise Cerdeira, Corin Yeats, David Aanensen, Gerald Mboowa, Stephen Baker, Sofonias K. Tessema, Anthony M. Smith, Iruka N. Okeke, Kathryn E. Holt
Summary: This article describes freely available platforms that support the generation, analysis, and visualization of Salmonella Typhi genomic data. It highlights opportunities to access training and tools, as well as outlines remaining challenges. The article also introduces various initiatives and consortiums that demonstrate the value of Salmonella Typhi genomic data and the utility of freely available platforms and services.
OPEN FORUM INFECTIOUS DISEASES
(2023)
Article
Infectious Diseases
Ivan Sserwadda, Benson R. Kidenya, Stephen Kanyerezi, Inyasi Lawrence Akaro, Baraka Mkinze, Stephen E. Mshana, Suhaila O. Hashim, Everlyne Isoe, Jeremiah Seni, Moses L. Joloba, Gerald Mboowa
Summary: This hospital-based longitudinal study using whole-genome sequencing (WGS) revealed the genetic resistance elements in ESBL E. coli isolates from Uganda and Tanzania, highlighting a concerning prevalence and diversity of multi-drug resistant E. coli in clinical settings in East Africa. Urgent measures are needed to strengthen infection-prevention controls and advocate for the routine use of WGS in national AMR surveillance programs.
BMC INFECTIOUS DISEASES
(2023)
Article
Public, Environmental & Occupational Health
B. R. Kidenya, G. Mboowa, I. Sserwadda, S. Kanyerezi, E. Nakafu, I. L. Akaro, B. Mkinze, M. L. Joloba, J. Seni
Summary: Acinetobacter baumannii is an important nosocomial pathogen with high resistance to drugs. A study found that orthopedic patients and the hospital environment act as a reservoir for multiple β-lactamase-producing A. baumannii with virulence genes.
JOURNAL OF HOSPITAL INFECTION
(2023)
Article
Dentistry, Oral Surgery & Medicine
Dunstan Kalanzi, Harriet Mayanja-Kizza, Damalie Nakanjako, Fred Semitala, Gerald Mboowa, Muhammad Mbabali, Edgar Kigozi, Fred Ashaba Katabazi, Ivan Sserwadda, David P. Kateete, Beatrice Achan, Nelson K. Sewankambo, Adrian Muwonge
Summary: This study aimed to improve early detection of dental caries in HIV patients by analyzing the characteristics of oral microbiota along the decayed, missing, filled teeth (DMFT) index. The analysis revealed differences in the abundance of core genera, changes in oral microbial biomass, and a correlation between the occurrence of dental caries and reduced oral microbial entropy. This study demonstrates the potential utility of microbiota dynamics in characterizing dental caries and proposes a microbial framework for understanding dental caries among HIV positive individuals in resource limited settings.
FRONTIERS IN ORAL HEALTH
(2022)