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Ganatra H, Tan JK, Simmons A, Bigogno CM, Khurana V, Ghose A, Ghosh A, Mahajan I, Boussios S, Maniam A, Ayodele O. Applying whole-genome and whole-exome sequencing in breast cancer: a review of the landscape. Breast Cancer 2024:10.1007/s12282-024-01628-9. [PMID: 39190283 DOI: 10.1007/s12282-024-01628-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 08/19/2024] [Indexed: 08/28/2024]
Abstract
Whole-genome sequencing (WGS) and whole-exome sequencing (WES) are crucial within the context of breast cancer (BC) research. They play a role in the detection of predisposed genes, risk stratification, and identification of rare single nucleotide polymorphisms (SNPs). These technologies aid in the discovery of associations between various syndromes and BC, understanding the tumour microenvironment (TME), and even identifying unknown mutations that could be useful in future for personalised treatments. Genetic analysis can find the associated risk of BC and can be used in early screening, diagnosis, specific treatment plans, and prevention in patients who are at high risk of tumour formation. This article focuses on the application of WES and WGS, and how uncovering novel candidate genes associated with BC can aid in treating and preventing BC.
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Affiliation(s)
- Hetvi Ganatra
- Barts Cancer Institute, Cancer Research UK City of London, Queen Mary University of London, London, UK
| | - Joecelyn Kirani Tan
- School of Medicine, University of St. Andrews, Fife, Scotland, UK
- Andrews Oncology Society, Scotland, UK
| | - Ana Simmons
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Carola Maria Bigogno
- Department of Medical Oncology, Barts Cancer Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK
- British Oncology Network for Undergraduate Societies (BONUS), London, UK
| | - Vatsala Khurana
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Aruni Ghose
- Department of Medical Oncology, Barts Cancer Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK
- Department of Medical Oncology, Medway NHS Foundation Trust, Gillingham, Kent, UK
- Department of Medical Oncology, Mount Vernon Cancer Centre, Mount Vernon and Watford NHS Trust, Watford, UK
| | - Adheesh Ghosh
- UCL Cancer Institute, University College London, London, UK
| | - Ishika Mahajan
- Department of Oncology, Lincoln Oncology Centre, Lincoln County Hospital, United Lincolnshire Hospitals NHS Trust, Lincoln, UK
| | - Stergios Boussios
- Department of Medical Oncology, Medway NHS Foundation Trust, Gillingham, Kent, UK.
- Faculty of Life Sciences & Medicine, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK.
- Kent and Medway Medical School, University of Kent, Canterbury, Kent, UK.
- Faculty of Medicine, Health, and Social Care, Canterbury Christ Church University, Canterbury, UK.
- AELIA Organization, 9th Km Thessaloniki-hermi, 57001, Thessaloniki, Greece.
| | - Akash Maniam
- Department of Medical Oncology, Portsmouth Hospitals University NHS Trust, Portsmouth, UK
- Faculty of Science and Health, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
- Caribbean Cancer Research Institute, Port of Spain, Trinidad and Tobago
| | - Olubukola Ayodele
- Department of Medical Oncology, University Hospitals of Leicester NHS Trust, Leicester, UK
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
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Kassem PH, Montasser IF, Mahmoud RM, Ghorab RA, AbdelHakam DA, Fathi MESA, Wahed MAA, Mohey K, Ibrahim M, Hadidi ME, Masssoud YM, Salah M, Abugable A, Bahaa M, Khamisy SE, Meteini ME. Genomic landscape of hepatocellular carcinoma in Egyptian patients by whole exome sequencing. BMC Med Genomics 2024; 17:202. [PMID: 39123171 PMCID: PMC11311965 DOI: 10.1186/s12920-024-01965-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 07/17/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the most common primary liver cancer. Chronic hepatitis and liver cirrhosis lead to accumulation of genetic alterations driving HCC pathogenesis. This study is designed to explore genomic landscape of HCC in Egyptian patients by whole exome sequencing. METHODS Whole exome sequencing using Ion Torrent was done on 13 HCC patients, who underwent surgical intervention (7 patients underwent living donor liver transplantation (LDLT) and 6 patients had surgical resection}. RESULTS Mutational signature was mostly S1, S5, S6, and S12 in HCC. Analysis of highly mutated genes in both HCC and Non-HCC revealed the presence of highly mutated genes in HCC (AHNAK2, MUC6, MUC16, TTN, ZNF17, FLG, MUC12, OBSCN, PDE4DIP, MUC5b, and HYDIN). Among the 26 significantly mutated HCC genes-identified across 10 genome sequencing studies-in addition to TCGA, APOB and RP1L1 showed the highest number of mutations in both HCC and Non-HCC tissues. Tier 1, Tier 2 variants in TCGA SMGs in HCC and Non-HCC (TP53, PIK3CA, CDKN2A, and BAP1). Cancer Genome Landscape analysis revealed Tier 1 and Tier 2 variants in HCC (MSH2) and in Non-HCC (KMT2D and ATM). For KEGG analysis, the significantly annotated clusters in HCC were Notch signaling, Wnt signaling, PI3K-AKT pathway, Hippo signaling, Apelin signaling, Hedgehog (Hh) signaling, and MAPK signaling, in addition to ECM-receptor interaction, focal adhesion, and calcium signaling. Tier 1 and Tier 2 variants KIT, KMT2D, NOTCH1, KMT2C, PIK3CA, KIT, SMARCA4, ATM, PTEN, MSH2, and PTCH1 were low frequency variants in both HCC and Non-HCC. CONCLUSION Our results are in accordance with previous studies in HCC regarding highly mutated genes, TCGA and specifically enriched pathways in HCC. Analysis for clinical interpretation of variants revealed the presence of Tier 1 and Tier 2 variants that represent potential clinically actionable targets. The use of sequencing techniques to detect structural variants and novel techniques as single cell sequencing together with multiomics transcriptomics, metagenomics will integrate the molecular pathogenesis of HCC in Egyptian patients.
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Affiliation(s)
- Perihan Hamdy Kassem
- Clinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Iman Fawzy Montasser
- Tropical Medicine Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
| | - Ramy Mohamed Mahmoud
- Clinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Rasha Ahmed Ghorab
- Clinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Dina A AbdelHakam
- Clinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | | | - Marwa A Abdel Wahed
- Clinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Khaled Mohey
- Clinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Mariam Ibrahim
- Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Mohamed El Hadidi
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham Dubai Campus, Dubai, United Arab Emirates
- Bioinformatics Group, Center for Informatics Science(CIS), School of Information Technology and Computer Science(ITCS), Nile University, Giza, Egypt
| | - Yasmine M Masssoud
- Tropical Medicine Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Manar Salah
- Tropical Medicine Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Arwa Abugable
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Mohamad Bahaa
- Hepato-Pancreatico-Biliary Surgery Department and liver Transplantation, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | | | - Mahmoud El Meteini
- Hepato-Pancreatico-Biliary Surgery Department and liver Transplantation, Faculty of Medicine, Ain Shams University, Cairo, Egypt
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Ji Y, Zhao J, Gong J, Sedlazeck FJ, Fan S. Unveiling novel genetic variants in 370 challenging medically relevant genes using the long read sequencing data of 41 samples from 19 global populations. Mol Genet Genomics 2024; 299:65. [PMID: 38972030 DOI: 10.1007/s00438-024-02158-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 06/16/2024] [Indexed: 07/08/2024]
Abstract
BACKGROUND A large number of challenging medically relevant genes (CMRGs) are situated in complex or highly repetitive regions of the human genome, hindering comprehensive characterization of genetic variants using next-generation sequencing technologies. In this study, we employed long-read sequencing technology, extensively utilized in studying complex genomic regions, to characterize genetic alterations, including short variants (single nucleotide variants and short insertions and deletions) and copy number variations, in 370 CMRGs across 41 individuals from 19 global populations. RESULTS Our analysis revealed high levels of genetic variants in CMRGs, with 68.73% exhibiting copy number variations and 65.20% containing short variants that may disrupt protein function across individuals. Such variants can influence pharmacogenomics, genetic disease susceptibility, and other clinical outcomes. We observed significant differences in CMRG variation across populations, with individuals of African ancestry harboring the highest number of copy number variants and short variants compared to samples from other continents. Notably, 15.79% to 33.96% of short variants were exclusively detectable through long-read sequencing. While the T2T-CHM13 reference genome significantly improved the assembly of CMRG regions, thereby facilitating variant detection in these regions, some regions still lacked resolution. CONCLUSION Our results provide an important reference for future clinical and pharmacogenetic studies, highlighting the need for a comprehensive representation of global genetic diversity in the reference genome and improved variant calling techniques to fully resolve medically relevant genes.
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Affiliation(s)
- Yanfeng Ji
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, 200438, China
| | - Junfan Zhao
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, 200438, China
| | - Jiao Gong
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, 200438, China
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, 77005, USA.
| | - Shaohua Fan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, 200438, China.
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Mohd Nippah NF, Abu N, Ab Mutalib NS, Alias H. Advances in next-generation sequencing for relapsed pediatric acute lymphoblastic leukemia: current insights and future directions. Front Genet 2024; 15:1394523. [PMID: 38894724 PMCID: PMC11183504 DOI: 10.3389/fgene.2024.1394523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
Leukemia is one of the most common cancers in children; and its genetic diversity in the landscape of acute lymphoblastic leukemia (ALL) is important for diagnosis, risk assessment, and therapeutic approaches. Relapsed ALL remains the leading cause of cancer deaths among children. Almost 20% of children who are treated for ALL and achieve complete remission experience disease recurrence. Relapsed ALL has a poor prognosis, and relapses are more likely to have mutations that affect signaling pathways, chromatin patterning, tumor suppression, and nucleoside metabolism. The identification of ALL subtypes has been based on genomic alterations for several decades, using the molecular landscape at relapse and its clinical significance. Next-generation sequencing (NGS), also known as massive parallel sequencing, is a high-throughput, quick, accurate, and sensitive method to examine the molecular landscape of cancer. This has undoubtedly transformed the study of relapsed ALL. The implementation of NGS has improved ALL genomic analysis, resulting in the recent identification of various novel molecular entities and a deeper understanding of existing ones. Thus, this review aimed to consolidate and critically evaluate the most current information on relapsed pediatric ALL provided by NGS technology. In this phase of targeted therapy and personalized medicine, identifying the capabilities, benefits, and drawbacks of NGS will be essential for healthcare professionals and researchers offering genome-driven care. This would contribute to precision medicine to treat these patients and help improve their overall survival and quality of life.
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Affiliation(s)
- Nur Farhana Mohd Nippah
- Department of Pediatrics, Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
| | - Nadiah Abu
- UKM Medical Molecular Biology Institute (UMBI), National University of Malaysia, Kuala Lumpur, Malaysia
| | - Nurul Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), National University of Malaysia, Kuala Lumpur, Malaysia
| | - Hamidah Alias
- Department of Pediatrics, Faculty of Medicine, National University of Malaysia, Kuala Lumpur, Malaysia
- UKM Medical Molecular Biology Institute (UMBI), National University of Malaysia, Kuala Lumpur, Malaysia
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Mio C, Zucco J, Fabbro D, Bregant E, Baldan F, Allegri L, D'Elia AV, Collini V, Imazio M, Damante G, Faletra F. The impact of the European Society of Cardiology guidelines and whole exome sequencing on genetic testing in hereditary cardiac diseases. Clin Genet 2024. [PMID: 38837338 DOI: 10.1111/cge.14569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/14/2024] [Accepted: 05/26/2024] [Indexed: 06/07/2024]
Abstract
In the last decade, an incredible improvement has been made in elucidating the genetic bases of cardiomyopathies. Here we report the impact of either the European Society of Cardiology (ESC) guidelines or the use of whole exome sequencing (WES) in terms of a number of variants of uncertain significance (VUS) and missed diagnoses in a series of 260 patients affected by inherited cardiac disorders. Samples were analyzed using a targeted gene panel of 128 cardiac-related genes and/or WES in a subset of patients, with a three-tier approach. Analyzing (i) only a subset of genes related to the clinical presentation, strictly following the ESC guidelines, 20.77% positive test were assessed. The incremental diagnostic rate for (ii) the whole gene panel, and (iii) the WES was 4.71% and 11.67%, respectively. The diverse analytical approaches increased the number of VUSs and incidental findings. Indeed, the use of WES highlights that there is a small percentage of syndromic conditions that standard analysis would not have detected. Moreover, the use of targeted sequencing coupled with "narrow" analytical approach prevents the detection of variants in actionable genes that could allow for preventive treatment. Our data suggest that genetic testing might aid clinicians in the diagnosis of inheritable cardiac disorders.
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Affiliation(s)
- Catia Mio
- Department of Medicine (DMED), University of Udine, Udine, Italy
| | - Jessica Zucco
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Dora Fabbro
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Elisa Bregant
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Federica Baldan
- Department of Medicine (DMED), University of Udine, Udine, Italy
| | - Lorenzo Allegri
- Department of Medicine (DMED), University of Udine, Udine, Italy
| | - Angela Valentina D'Elia
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Valentino Collini
- Cardiology, Cardiothoracic Department, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Massimo Imazio
- Department of Medicine (DMED), University of Udine, Udine, Italy
- Cardiology, Cardiothoracic Department, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Giuseppe Damante
- Department of Medicine (DMED), University of Udine, Udine, Italy
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
| | - Flavio Faletra
- Institute of Medical Genetics, Azienda Sanitaria Universitaria Friuli Centrale (ASUFC), Udine, Italy
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Holm LL, Doktor TK, Flugt KK, Petersen US, Petersen R, Andresen B. All exons are not created equal-exon vulnerability determines the effect of exonic mutations on splicing. Nucleic Acids Res 2024; 52:4588-4603. [PMID: 38324470 PMCID: PMC11077056 DOI: 10.1093/nar/gkae077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 01/05/2024] [Accepted: 01/26/2024] [Indexed: 02/09/2024] Open
Abstract
It is now widely accepted that aberrant splicing of constitutive exons is often caused by mutations affecting cis-acting splicing regulatory elements (SREs), but there is a misconception that all exons have an equal dependency on SREs and thus a similar vulnerability to aberrant splicing. We demonstrate that some exons are more likely to be affected by exonic splicing mutations (ESMs) due to an inherent vulnerability, which is context dependent and influenced by the strength of exon definition. We have developed VulExMap, a tool which is based on empirical data that can designate whether a constitutive exon is vulnerable. Using VulExMap, we find that only 25% of all exons can be categorized as vulnerable, whereas two-thirds of 359 previously reported ESMs in 75 disease genes are located in vulnerable exons. Because VulExMap analysis is based on empirical data on splicing of exons in their endogenous context, it includes all features important in determining the vulnerability. We believe that VulExMap will be an important tool when assessing the effect of exonic mutations by pinpointing whether they are located in exons vulnerable to ESMs.
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Affiliation(s)
- Lise L Holm
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
- Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Thomas K Doktor
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
- Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Katharina K Flugt
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
- Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Ulrika S S Petersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
- Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Rikke Petersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
- Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Brage S Andresen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
- Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
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Godown J, Kim EH, Everitt MD, Chung WK, Lytrivi ID, Kirmani S, Kantor PF, Ware SM, Ballweg JA, Lal AK, Bansal N, Towbin J, Lipshultz SE, Lee TM. Genetic Testing Resources and Practice Patterns Among Pediatric Cardiomyopathy Programs. Pediatr Cardiol 2024:10.1007/s00246-024-03498-6. [PMID: 38714589 DOI: 10.1007/s00246-024-03498-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/11/2024] [Indexed: 05/10/2024]
Abstract
The use of genetic testing has enhanced the diagnostic accuracy of heritable genetic cardiomyopathies. However, it remains unclear how genetic information is interpreted and incorporated into clinical practice for children with cardiomyopathy. The primary aim of this study was to understand how clinical practice differs regarding sequence variant classifications amongst pediatric cardiologists who treat children with cardiomyopathy. A secondary aim was to understand the availability of genetic testing and counseling resources across participating pediatric cardiomyopathy programs. An electronic survey was distributed to pediatric heart failure, cardiomyopathy, or heart transplantation physicians between August and September 2022. A total of 106 individual providers from 68 unique centers responded to the survey. Resources for genetic testing and genetic counseling vary among large pediatric cardiomyopathy programs. A minority of centers reported having a geneticist (N = 16, 23.5%) or a genetic counselor (N = 21, 31%) on faculty within the division of pediatric cardiology. A total of 9 centers reported having both (13%). Few centers (N = 13, 19%) have a formal process in place to re-engage patients who were previously discharged from cardiology follow-up if variant reclassification would alter clinical management. Clinical practice patterns were uniform in response to pathogenic or likely pathogenic variants but were more variable for variants of uncertain significance. Efforts to better incorporate genetic expertise and resources into the clinical practice of pediatric cardiomyopathy may help to standardize the interpretation of genetic information and better inform clinical decision-making surrounding heritable cardiomyopathies.
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Affiliation(s)
- Justin Godown
- Division of Pediatric Cardiology, Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, TN, USA
- BioMarin Pharmaceutical Inc, Novato, CA, USA
| | - Emily H Kim
- Division of Pediatric Cardiology, Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, TN, USA
| | - Melanie D Everitt
- Department of Pediatrics, University of Colorado, Children's Hospital Colorado, Aurora, CO, USA
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Irene D Lytrivi
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Sonya Kirmani
- Department of Pediatrics, University of Wisconsin School of Medicine, Madison, WI, USA
| | - Paul F Kantor
- Department of Pediatrics, Keck School of Medicine of USC, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Stephanie M Ware
- Department of Pediatrics and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jean A Ballweg
- Department of Pediatrics, Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Ashwin K Lal
- Division of Pediatric Cardiology, University of Utah, Primary Children's Hospital, Salt Lake City, Utah, USA
| | - Neha Bansal
- Division of Pediatric Cardiology, Mount Sinai Kravis Children's Hospital, New York, NY, USA
| | - Jeffrey Towbin
- Heart Institute, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Steven E Lipshultz
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, Clinical and Translational Research Center, University at Buffalo, 875 Ellicott Street, Suite 5018, Buffalo, NY, 14203, USA.
| | - Teresa M Lee
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
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Jerschow E, Dubin R, Chen CC, iAkushev A, Sehanobish E, Asad M, Chiarella SE, Porcelli SA, Greally J. Aspirin-exacerbated respiratory disease is associated with variants in filaggrin, epithelial integrity, and cellular interactions. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2024; 3:100205. [PMID: 38317805 PMCID: PMC10838899 DOI: 10.1016/j.jacig.2024.100205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 11/15/2023] [Accepted: 12/01/2023] [Indexed: 02/07/2024]
Abstract
Background Previous studies have determined that up to 6% of patients with aspirin-exacerbated respiratory disease (AERD) have family history of AERD, indicating a possible link with genetic polymorphisms. However, whole exome sequencing (WES) studies of such associations are currently lacking. Objectives We sought to examine whether WES can identify pathogenic variants associated with AERD. Methods Diagnoses of AERD were confirmed in patients with nasal polyps and asthma. WES was performed using an Illumina sequencing platform. Human Phenotype Ontology terms were used to define the patients' phenotypes. Exomiser was used to annotate, filter, and prioritize possible disease-causing genetic variants. Results Of 39 patients with AERD, 41% reported a family history of asthma and 5% reported a family history of AERD. Pathogenic exome variants in the filaggrin gene (FLG) were found in 2 patients (5%). Other variants not known to be pathogenic were detected in an additional 16 patients (41%) in genes related to epithelial integrity and cellular interactions, including genes encoding desmoglein 3 (DSG3), dynein axonemal heavy chain 9 (DNAH9), collagen type VII alpha 1 chain (COL7A1), collagen type XVII alpha 1 chain (COL17A1), chromodomain helicase DNA binding protein-7 (CHD7), TSC complex subunit 2/tuberous sclerosis-2 protein (TSC2), P-selectin (SELP), and platelet-derived growth factor receptor-alpha (PDGFRA). Conclusion WES identified a monogenic susceptibility to AERD in 5% of patients with FLG pathogenic variants. Other variants not previously identified as pathogenic were found in genes relevant to epithelial integrity and cellular interactions and may further reveal genetic factors that contribute to this condition.
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Affiliation(s)
- Elina Jerschow
- Mayo Clinic, Rochester, Minn
- Albert Einstein College of Medicine, Bronx, NY
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9
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Park SY, Park SY, Seo S, Kwon HS, Kim SH, Kim SH, Park HK, Chang YS, Kim CW, Lee BJ, Park HS, Cho YS, Oh HB, Ostrov DA, Won S, Kim TB. HLA-DRB1 is associated with cefaclor-induced immediate hypersensitivity. World Allergy Organ J 2024; 17:100901. [PMID: 38638799 PMCID: PMC11021981 DOI: 10.1016/j.waojou.2024.100901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/13/2024] [Accepted: 03/22/2024] [Indexed: 04/20/2024] Open
Abstract
Background Drug-induced hypersensitivity such as anaphylaxis is an important cause of drug-related morbidity and mortality. Cefaclor is a leading cause of drug induced type I hypersensitivity in Korea, but little is yet known about genetic biomarkers to predict this hypersensitivity reaction. We aimed to evaluate the possible involvement of genes in cefaclor induced type I hypersensitivity. Methods Whole exome sequencing (WES) and HLA genotyping were performed in 43 patients with cefaclor induced type I hypersensitivity. In addition, homology modeling was performed to identify the binding forms of cefaclor to HLA site. Results Anaphylaxis was the most common phenotype of cefaclor hypersensitivity (90.69%). WES results show that rs62242177 and rs62242178 located in LIMD1 region were genome-wide significant at the 5 × 10-8 significance level. Cefaclor induced type I hypersensitivity was significantly associated with HLA-DRB1∗04:03 (OR 4.61 [95% CI 1.51-14.09], P < 0.002) and HLA-DRB1∗14:54 (OR 3.86 [95% CI 1.09-13.67], P < 0.002). Conclusion LIMD1, HLA-DRB1∗04:03 and HLA-DRB1∗14:54 may affect susceptibility to cefaclor induced type I hypersensitivity. Further confirmative studies with a larger patient population should be performed to ascertain the role of HLA-DRB1 and LIMD1 in the development of cefaclor induced hypersensitivity.
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Affiliation(s)
- So-Young Park
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
- Division of Pulmonary, Allergy and Critical Care Medicine, Chung-Ang University Gwangmyeong Hospital, Gwangmyeong, South Korea
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, South Korea
| | - So Young Park
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Sujin Seo
- Department of Public Health Science, Seoul National University, Seoul, South Korea
| | - Hyouk-Soo Kwon
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Seung-Hyun Kim
- Department of Allergy and Clinical Immunology, Ajou University School of Medicine, Suwon, South Korea
| | - Sae-Hoon Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Hye-Kyung Park
- Department of Internal Medicine, School of Medicine, Busan National University, Busan, South Korea
| | - Yoon-Seok Chang
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Cheol-Woo Kim
- Department of Internal Medicine, Inha University College of Medicine, Incheon, South Korea
| | - Byung Jae Lee
- Division of Allergy, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hae-Sim Park
- Department of Allergy and Clinical Immunology, Ajou University School of Medicine, Suwon, South Korea
| | - You Sook Cho
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Heung-Bum Oh
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - David A. Ostrov
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, USA
| | - Sungho Won
- Department of Public Health Science, Seoul National University, Seoul, South Korea
| | - Tae Bum Kim
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
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10
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Alganmi N, Bashanfar A, Alotaibi R, Banjar H, Karim S, Mirza Z, Abusamra H, Al-Attas M, Turkistany S, Abuzenadah A. Uncovering hidden genetic risk factors for breast and ovarian cancers in BRCA-negative women: a machine learning approach in the Saudi population. PeerJ Comput Sci 2024; 10:e1942. [PMID: 38660159 PMCID: PMC11042021 DOI: 10.7717/peerj-cs.1942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/26/2024] [Indexed: 04/26/2024]
Abstract
Breast and ovarian cancers are prevalent worldwide, with genetic factors such as BRCA1 and BRCA2 mutations playing a significant role. However, not all patients carry these mutations, making it challenging to identify risk factors. Researchers have turned to whole exome sequencing (WES) as a tool to identify genetic risk factors in BRCA-negative women. WES allows the sequencing of all protein-coding regions of an individual's genome, providing a comprehensive analysis that surpasses traditional gene-by-gene sequencing methods. This technology offers efficiency, cost-effectiveness and the potential to identify new genetic variants contributing to the susceptibility to the diseases. Interpreting WES data for disease-causing variants is challenging due to its complex nature. Machine learning techniques can uncover hidden genetic-variant patterns associated with cancer susceptibility. In this study, we used the extreme gradient boosting (XGBoost) and random forest (RF) algorithms to identify BRCA-related cancer high-risk genes specifically in the Saudi population. The experimental results exposed that the RF method scored superior performance with an accuracy of 88.16% and an area under the receiver-operator characteristic curve of 0.95. Using bioinformatics analysis tools, we explored the top features of the high-accuracy machine learning model that we built to enhance our knowledge of genetic interactions and find complex genetic patterns connected to the development of BRCA-related cancers. We were able to identify the significance of HLA gene variations in these WES datasets for BRCA-related patients. We find that immune response mechanisms play a major role in the development of BRCA-related cancer. It specifically highlights genes associated with antigen processing and presentation, such as HLA-B, HLA-A and HLA-DRB1 and their possible effects on tumour progression and immune evasion. In summary, by utilizing machine learning approaches, we have the potential to aid in the development of precision medicine approaches for early detection and personalized treatment strategies.
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Affiliation(s)
- Nofe Alganmi
- Computer Science, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Arwa Bashanfar
- Information Technology, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Reem Alotaibi
- Information Technology, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Haneen Banjar
- Computer Science, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sajjad Karim
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Lab Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Zeenat Mirza
- Department of Medical Lab Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- King Fahd Medical Research Center, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Heba Abusamra
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Manal Al-Attas
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shereen Turkistany
- Center of Innovation Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Adel Abuzenadah
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Lab Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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11
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Shadab M, Abbasi AA, Ejaz A, Ben-Mahmoud A, Gupta V, Kim HG, Vona B. Autosomal recessive non-syndromic hearing loss genes in Pakistan during the previous three decades. J Cell Mol Med 2024; 28:e18119. [PMID: 38534090 DOI: 10.1111/jcmm.18119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 11/29/2023] [Accepted: 01/02/2024] [Indexed: 03/28/2024] Open
Abstract
Hearing loss is a clinically and genetically heterogeneous disorder, with over 148 genes and 170 loci associated with its pathogenesis. The spectrum and frequency of causal variants vary across different genetic ancestries and are more prevalent in populations that practice consanguineous marriages. Pakistan has a rich history of autosomal recessive gene discovery related to non-syndromic hearing loss. Since the first linkage analysis with a Pakistani family that led to the mapping of the DFNB1 locus on chromosome 13, 51 genes associated with this disorder have been identified in this population. Among these, 13 of the most prevalent genes, namely CDH23, CIB2, CLDN14, GJB2, HGF, MARVELD2, MYO7A, MYO15A, MSRB3, OTOF, SLC26A4, TMC1 and TMPRSS3, account for more than half of all cases of profound hearing loss, while the prevalence of other genes is less than 2% individually. In this review, we discuss the most common autosomal recessive non-syndromic hearing loss genes in Pakistani individuals as well as the genetic mapping and sequencing approaches used to discover them. Furthermore, we identified enriched gene ontology terms and common pathways involved in these 51 autosomal recessive non-syndromic hearing loss genes to gain a better understanding of the underlying mechanisms. Establishing a molecular understanding of the disorder may aid in reducing its future prevalence by enabling timely diagnostics and genetic counselling, leading to more effective clinical management and treatments of hearing loss.
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Affiliation(s)
- Madiha Shadab
- Department of Zoology, Mirpur University of Science and Technology, Mirpur, Pakistan
| | - Ansar Ahmed Abbasi
- Department of Zoology, Mirpur University of Science and Technology, Mirpur, Pakistan
| | - Ahsan Ejaz
- Department of Physics, University of Kotli Azad Jammu and Kashmir, Kotli, Pakistan
- School of Nuclear Science and Technology, Lanzhou University, Lanzhou, China
| | - Afif Ben-Mahmoud
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Vijay Gupta
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
- College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Institute for Auditory Neuroscience and Inner Ear Lab, University Medical Center Göttingen, Göttingen, Germany
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12
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Zhang L, Lou H, Huang Y, Dong L, Gong X, Zhang X, Bao W, Xiao R. Identification of Synonymous Pathogenic Variants in Monogenic Disorders by Integrating Exome with Transcriptome Sequencing. J Mol Diagn 2024; 26:267-277. [PMID: 38280421 DOI: 10.1016/j.jmoldx.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 11/23/2023] [Accepted: 12/20/2023] [Indexed: 01/29/2024] Open
Abstract
Exome sequencing is becoming a first-tier clinical diagnostic test for Mendelian diseases, drastically reducing the time and cost of diagnostic odyssey and improving the diagnosis rate. Despite its success, exome sequencing faces practical challenges in assessing the pathogenicity of numerous intronic and synonymous variants, leaving a significant proportion of patients undiagnosed. In this study, a whole-blood transcriptome database was constructed that showed the expression profile of 2981 Online Mendelian Inheritance in Man disease genes in blood samples. Meanwhile, a workflow integrating exome sequencing, blood transcriptome sequencing, and in silico prediction tools to identify and validate splicing-altering intronic or synonymous variants was proposed. Following this pipeline, seven synonymous variants in eight patients were discovered. Of these, the functional evidence of c.981G>A (PIGN), c.1161A>G (ALPL), c.858G>A (ATP6AP2), and c.1011G>T (MTHFR) have not been reported previously. RNA sequencing validation confirmed that these variants induced aberrant splicing, expanding the disease-causing variant spectrum of these genes. Overall, this study shows the feasibility of combining multi-omics data to identify splicing-altering variants, especially the power of RNA sequencing. It also reveals that synonymous variants, which often are overlooked in standard diagnostic approaches, comprise an important portion of unresolved genetic diseases.
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Affiliation(s)
- Lin Zhang
- Prenatal Diagnosis Center, Peking University People's Hospital, Beijing, China.
| | | | - Yanhong Huang
- Prenatal Diagnosis Center, Liaocheng Maternal and Child Health Care Hospital, Liaocheng, China
| | - Liping Dong
- Newborn Screening Center, Zibo Maternal and Child Health Care Hospital, Zibo, China
| | - Xueye Gong
- Department of Medical Genetics and Prenatal Diagnosis, Binzhou Maternal and Child Health Care Hospital, Binzhou, China
| | - Xiaoning Zhang
- Department of the Clinical Laboratory, Binzhou Maternal and Child Health Care Hospital, Binzhou, China
| | - Wenqi Bao
- Becreative Lab Co., Ltd., Beijing, China
| | - Rui Xiao
- National Engineering Laboratory for Key Technology of Birth Defect Control and Prevention, Screening and Diagnostic R&D Center, Hangzhou, China
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13
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Abugable AA, Antar S, El-Khamisy SF. Chromosomal single-strand break repair and neurological disease: Implications on transcription and emerging genomic tools. DNA Repair (Amst) 2024; 135:103629. [PMID: 38266593 DOI: 10.1016/j.dnarep.2024.103629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024]
Abstract
Cells are constantly exposed to various sources of DNA damage that pose a threat to their genomic integrity. One of the most common types of DNA breaks are single-strand breaks (SSBs). Mutations in the repair proteins that are important for repairing SSBs have been reported in several neurological disorders. While several tools have been utilised to investigate SSBs in cells, it was only through recent advances in genomics that we are now beginning to understand the architecture of the non-random distribution of SSBs and their impact on key cellular processes such as transcription and epigenetic remodelling. Here, we discuss our current understanding of the genome-wide distribution of SSBs, their link to neurological disorders and summarise recent technologies to investigate SSBs at the genomic level.
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Affiliation(s)
- Arwa A Abugable
- School of Biosciences, Firth Court, University of Sheffield, Sheffield, UK; The healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Sarah Antar
- School of Biosciences, Firth Court, University of Sheffield, Sheffield, UK; The healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK; Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Mansoura University, Egypt
| | - Sherif F El-Khamisy
- School of Biosciences, Firth Court, University of Sheffield, Sheffield, UK; The healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK; Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, Bradford, UK.
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14
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Choon YW, Choon YF, Nasarudin NA, Al Jasmi F, Remli MA, Alkayali MH, Mohamad MS. Artificial intelligence and database for NGS-based diagnosis in rare disease. Front Genet 2024; 14:1258083. [PMID: 38371307 PMCID: PMC10870236 DOI: 10.3389/fgene.2023.1258083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/24/2023] [Indexed: 02/20/2024] Open
Abstract
Rare diseases (RDs) are rare complex genetic diseases affecting a conservative estimate of 300 million people worldwide. Recent Next-Generation Sequencing (NGS) studies are unraveling the underlying genetic heterogeneity of this group of diseases. NGS-based methods used in RDs studies have improved the diagnosis and management of RDs. Concomitantly, a suite of bioinformatics tools has been developed to sort through big data generated by NGS to understand RDs better. However, there are concerns regarding the lack of consistency among different methods, primarily linked to factors such as the lack of uniformity in input and output formats, the absence of a standardized measure for predictive accuracy, and the regularity of updates to the annotation database. Today, artificial intelligence (AI), particularly deep learning, is widely used in a variety of biological contexts, changing the healthcare system. AI has demonstrated promising capabilities in boosting variant calling precision, refining variant prediction, and enhancing the user-friendliness of electronic health record (EHR) systems in NGS-based diagnostics. This paper reviews the state of the art of AI in NGS-based genetics, and its future directions and challenges. It also compare several rare disease databases.
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Affiliation(s)
- Yee Wen Choon
- Institute for Artificial Intelligence and Big Data, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, Malaysia
- Faculty of Data Science and Informatics, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, Malaysia
| | - Yee Fan Choon
- Faculty of Dentistry, Lincoln University College, Petaling Jaya, Selangor, Malaysia
| | - Nurul Athirah Nasarudin
- Health Data Science Lab, Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Fatma Al Jasmi
- Health Data Science Lab, Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Muhamad Akmal Remli
- Institute for Artificial Intelligence and Big Data, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, Malaysia
- Faculty of Data Science and Informatics, Universiti Malaysia Kelantan, Kota Bharu, Kelantan, Malaysia
| | | | - Mohd Saberi Mohamad
- Health Data Science Lab, Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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15
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Sears T, Pagadala M, Castro A, Lee KH, Kong J, Tanaka K, Lippman S, Zanetti M, Carter H. Integrated germline and somatic features reveal divergent immune pathways driving ICB response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.12.575430. [PMID: 38293085 PMCID: PMC10827124 DOI: 10.1101/2024.01.12.575430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Immune Checkpoint Blockade (ICB) has revolutionized cancer treatment, however mechanisms determining patient response remain poorly understood. Here we used machine learning to predict ICB response from germline and somatic biomarkers and interpreted the learned model to uncover putative mechanisms driving superior outcomes. Patients with higher T follicular helper infiltrates were robust to defects in the class-I Major Histocompatibility Complex (MHC-I). Further investigation uncovered different ICB responses in MHC-I versus MHC-II neoantigen reliant tumors across patients. Despite similar response rates, MHC-II reliant responses were associated with significantly longer durable clinical benefit (Discovery: Median OS=63.6 vs. 34.5 months P=0.0074; Validation: Median OS=37.5 vs. 33.1 months, P=0.040). Characteristics of the tumor immune microenvironment reflected MHC neoantigen reliance, and analysis of immune checkpoints revealed LAG3 as a potential target in MHC-II but not MHC-I reliant responses. This study highlights the value of interpretable machine learning models in elucidating the biological basis of therapy responses.
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Affiliation(s)
- Timothy Sears
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA USA
| | - Meghana Pagadala
- Biomedical Sciences Program, University of California San Diego, La Jolla, CA,, USA
| | - Andrea Castro
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Ko-Han Lee
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA USA
| | - JungHo Kong
- Division of Genomics and Precision Medicine, Department of Medicine, University of California San Diego, La Jolla, CA USA
| | - Kairi Tanaka
- School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Scott Lippman
- Moores Cancer Center, University of California San Diego, La Jolla, CA USA
| | - Maurizio Zanetti
- Moores Cancer Center, University of California San Diego, La Jolla, CA USA
- The Laboratory of Immunology, Moores Cancer Center and Department of Medicine, University of California San Diego, La Jolla, CA USA
| | - Hannah Carter
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA USA
- The Laboratory of Immunology, Moores Cancer Center and Department of Medicine, University of California San Diego, La Jolla, CA USA
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16
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He J, Mahmoudi A, Gu Y, Fu J, Yuan Q, Liu W. Case report: A novel mutation in the EYA1 gene in a child with branchiootic syndrome with secretory otitis media and bilateral vestibular hypofunction. Front Genet 2024; 14:1292085. [PMID: 38259619 PMCID: PMC10801012 DOI: 10.3389/fgene.2023.1292085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024] Open
Abstract
Branchiootic syndrome (BOS) is a rare, autosomal dominant syndrome characterized by malformations of the ear associated with hearing loss, second branchial arch anomalies, and the absence of renal anomalies. Herein, we report the case of an 8-year-old male patient with BOS. The proband also experiences mixed conductive and sensorineural hearing loss in the right ear, and severe-to-profound sensorineural hearing loss in the left ear. Preauricular pits, branchial fistulae, and cochlear hypoplasia were present bilaterally. Type III cup-shaped ear, and external auditory canal stenosis were detected in the right ear. Lateral semicircular canal-vestibule dysplasia was detected in the left ear. Moreover, the patient had unilateral secretory otitis media (SOM) in the right ear and bilateral vestibular hypofunction (VH), which has not been reported in previous studies. The patient's hearing on the right side was restored to nearly normal after myringotomy. Whole exome sequencing identified a novel frameshift mutation in EYA1 (NM_000503.6): c.1697_1698delinT [p.(Lys566IlefsTer73)] in the proband, which was defined a "pathogenic" mutation according to American College of Medical Genetics and Genomics guidelines. This is the first report of a child presenting with BOS, SOM and VH, which expands the known clinical manifestations of this syndrome. We also observed a novel EYA1 gene mutation in this patient with BOS, which enriches the mutation map and provides a reference for genetic diagnosis of this syndrome.
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Affiliation(s)
- Jun He
- Department of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ahmad Mahmoudi
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, United States
| | - Yu Gu
- Department of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jinfeng Fu
- Department of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qiulin Yuan
- Department of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wei Liu
- Department of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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17
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Nurchis MC, Radio FC, Salmasi L, Heidar Alizadeh A, Raspolini GM, Altamura G, Tartaglia M, Dallapiccola B, Pizzo E, Gianino MM, Damiani G. Cost-Effectiveness of Whole-Genome vs Whole-Exome Sequencing Among Children With Suspected Genetic Disorders. JAMA Netw Open 2024; 7:e2353514. [PMID: 38277144 PMCID: PMC10818217 DOI: 10.1001/jamanetworkopen.2023.53514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/05/2023] [Indexed: 01/27/2024] Open
Abstract
Importance The diagnosis of rare diseases and other genetic conditions can be daunting due to vague or poorly defined clinical features that are not recognized even by experienced clinicians. Next-generation sequencing technologies, such as whole-genome sequencing (WGS) and whole-exome sequencing (WES), have greatly enhanced the diagnosis of genetic diseases by expanding the ability to sequence a large part of the genome, rendering a cost-effectiveness comparison between them necessary. Objective To assess the cost-effectiveness of WGS compared with WES and conventional testing in children with suspected genetic disorders. Design, Setting, and Participants In this economic evaluation, a bayesian Markov model was implemented from January 1 to June 30, 2023. The model was developed using data from a cohort of 870 pediatric patients with suspected genetic disorders who were enrolled and underwent testing in the Ospedale Pediatrico Bambino Gesù, Rome, Italy, from January 1, 2015, to December 31, 2022. The robustness of the model was assessed through probabilistic sensitivity analysis and value of information analysis. Main Outcomes and Measures Overall costs, number of definitive diagnoses, and incremental cost-effectiveness ratios per diagnosis were measured. The cost-effectiveness analyses involved 4 comparisons: first-tier WGS with standard of care; first-tier WGS with first-tier WES; first-tier WGS with second-tier WES; and first-tier WGS with second-tier WGS. Results The ages of the 870 participants ranged from 0 to 18 years (539 [62%] girls). The results of the analysis suggested that adopting WGS as a first-tier strategy would be cost-effective compared with all other explored options. For all threshold levels above €29 800 (US $32 408) per diagnosis that were tested up to €50 000 (US $54 375) per diagnosis, first-line WGS vs second-line WES strategy (ie, 54.6%) had the highest probability of being cost-effective, followed by first-line vs second-line WGS (ie, 54.3%), first-line WGS vs the standard of care alternative (ie, 53.2%), and first-line WGS vs first-line WES (ie, 51.1%). Based on sensitivity analyses, these estimates remained robust to assumptions and parameter uncertainty. Conclusions and Relevance The findings of this economic evaluation encourage the development of policy changes at various levels (ie, macro, meso, and micro) of international health systems to ensure an efficient adoption of WGS in clinical practice and its equitable access.
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Affiliation(s)
- Mario Cesare Nurchis
- School of Economics, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | | | - Luca Salmasi
- Department of Economics and Finance, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Aurora Heidar Alizadeh
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gian Marco Raspolini
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gerardo Altamura
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Bruno Dallapiccola
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Elena Pizzo
- Department of Applied Health Research, University College London, London, United Kingdom
| | - Maria Michela Gianino
- Department of Public Health Sciences and Paediatrics, Università di Torino, Turin, Italy
| | - Gianfranco Damiani
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Rome, Italy
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18
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Di Girolamo R, Rizzo G, Khalil A, Alameddine S, Lisi G, Liberati M, Novelli A, D'Antonio F. Whole exome sequencing in fetuses with isolated increased nuchal translucency: a systematic review and meta-analysis. J Matern Fetal Neonatal Med 2023; 36:2193285. [PMID: 37019452 DOI: 10.1080/14767058.2023.2193285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
OBJECTIVE To estimate the incremental yield of detecting pathogenic or likely pathogenic diagnostic genetic variants (DGV) by whole exome sequencing (WES) over standard karyotype and chromosomal microarray (CMA) analyses in fetuses with isolated increased nuchal translucency (NT) and normal fetal anatomy at the time of 11-14 weeks scan. MATERIALS AND METHODS Medline and Embase databases were searched. Inclusion criteria were fetuses with NT >95th percentile, normal karyotype and CMA and no associated structural anomalies at the time of the 11-14 weeks scan. The primary outcome was to estimate the incremental yield of detecting pathogenic or likely pathogenic genetic variants by WES over standard karyotype and CMA analyses in fetuses with isolated increased nuchal translucency. The secondary outcomes were the detection of a genetic variant of unknown significance. Sub-analysis according to different NT cutoffs (between 3.0 and 5.5 mm and > 5.5 mm) and considering fetuses with isolated NT in which fetal anatomy was confirmed to be normal at the anomaly scan were also performed. Random effects model meta-analyses of proportion were used to analyze the data. RESULTS Eight articles (324 fetuses) were included in the systematic review. Of the fetuses with negative standard karyotype and CMA analysis, the 8.07% (95% CI 5.4-11.3) had pathogenic or likely pathogenic genetic variants detected exclusively by WES. When stratifying the analysis according to NT cutoffs, genetic anomalies detected exclusively at WES analysis were found in 44.70% (95% CI 26.8-63.4) of fetuses with NT between 3.0 mm and 5.5 mm and 55.3% (95% CI 36.6-73.2) in those fetuses with NT >5.5 mm and positive WES results. The 7.84% (95% CI 1.6-18.2) had variants of unknown significance identified by WES. When considering fetuses with isolated increased NT and normal fetal anatomy at the anomaly scan, the rate of pathogenic or likely pathogenic genetic variants detected by WES was 3.87% (95% CI 1.6-7.1), while variants of unknown significance were detected in 4.27% (95% CI 2.2-7.0) of cases. CONCLUSIONS Pathogenic and likely pathogenic genetic variants detected by WES are present in a significant proportion of fetuses with increased NT but normal standard karyotype and CMA analysis, also when no anomalies are detected at the anomaly scan. Further large studies sharing objective protocols of imaging assessment are needed to confirm these findings and to elucidate which gene panels should be assessed in fetuses with isolated increased NT to rule out associated genetic anomalies, which may potentially impact post-natal outcomes.
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Affiliation(s)
- Raffaella Di Girolamo
- Centre for High-Risk Pregnancy and Fetal Care, Department of Obstetrics and Gynaecology, University of Chieti, Chieti, Italy
| | - Giuseppe Rizzo
- Department of Obstetrics and Gynaecology Fondazione Policlinico Tor Vergata, Università Roma Tor Vergata
| | - Asma Khalil
- Fetal Medicine Unit, Saint George's Hospital, London, United Kingdom
| | - Sara Alameddine
- Centre for High-Risk Pregnancy and Fetal Care, Department of Obstetrics and Gynaecology, University of Chieti, Chieti, Italy
| | - Gabriele Lisi
- Pediatric Surgery Unit, Department of Medicine and Aging Science, University Gabriele D'Annunzio of Chieti-Pescara, Chieti, Italy
| | - Marco Liberati
- Centre for High-Risk Pregnancy and Fetal Care, Department of Obstetrics and Gynaecology, University of Chieti, Chieti, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Francesco D'Antonio
- Centre for High-Risk Pregnancy and Fetal Care, Department of Obstetrics and Gynaecology, University of Chieti, Chieti, Italy
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19
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Garg A, Warrier S A, Subadra K. A Diagnostic Challenge of Oral Psoriasis in a Pediatric Patient: A Case Report and Review of the Literature. Cureus 2023; 15:e49572. [PMID: 38156126 PMCID: PMC10754223 DOI: 10.7759/cureus.49572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2023] [Indexed: 12/30/2023] Open
Abstract
Congenital psoriasis is a rare skin disease that can clinically manifest in the oral cavity in many ways. Although manifestations over the skin are frequent, oral manifestations are rare, especially in pediatric patients. A clear family history, proper examination, and investigations are essential to diagnose this condition. This case report aims to highlight the oral and systemic manifestations of a case of psoriasis in a male pediatric patient.
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Affiliation(s)
- Arnesh Garg
- Sri Ramachandra Dental College and Hospital, Sri Ramachandra Institute of Higher Education and Research, Chennai, IND
| | - Aravind Warrier S
- Oral Medicine and Radiology, Sri Ramachandra Institute of Higher Education and Research, Chennai, IND
| | - K Subadra
- Oral Medicine and Radiology, Sri Ramachandra Institute of Higher Education and Research, Chennai, IND
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20
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Islam MS, Gopalan V, Lam AK, Shiddiky MJA. Current advances in detecting genetic and epigenetic biomarkers of colorectal cancer. Biosens Bioelectron 2023; 239:115611. [PMID: 37619478 DOI: 10.1016/j.bios.2023.115611] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023]
Abstract
Colorectal carcinoma (CRC) is the third most common cancer in terms of diagnosis and the second in terms of mortality. Recent studies have shown that various proteins, extracellular vesicles (i.e., exosomes), specific genetic variants, gene transcripts, cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and altered epigenetic patterns, can be used to detect, and assess the prognosis of CRC. Over the last decade, a plethora of conventional methodologies (e.g., polymerase chain reaction [PCR], direct sequencing, enzyme-linked immunosorbent assay [ELISA], microarray, in situ hybridization) as well as advanced analytical methodologies (e.g., microfluidics, electrochemical biosensors, surface-enhanced Raman spectroscopy [SERS]) have been developed for analyzing genetic and epigenetic biomarkers using both optical and non-optical tools. Despite these methodologies, no gold standard detection method has yet been implemented that can analyze CRC with high specificity and sensitivity in an inexpensive, simple, and time-efficient manner. Moreover, until now, no study has critically reviewed the advantages and limitations of these methodologies. Here, an overview of the most used genetic and epigenetic biomarkers for CRC and their detection methods are discussed. Furthermore, a summary of the major biological, technical, and clinical challenges and advantages/limitations of existing techniques is also presented.
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Affiliation(s)
- Md Sajedul Islam
- Cancer Molecular Pathology, School of Medicine & Dentistry, Griffith University, Gold Coast Campus, Southport, QLD, 4222, Australia; Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia
| | - Vinod Gopalan
- Cancer Molecular Pathology, School of Medicine & Dentistry, Griffith University, Gold Coast Campus, Southport, QLD, 4222, Australia; Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia.
| | - Alfred K Lam
- Cancer Molecular Pathology, School of Medicine & Dentistry, Griffith University, Gold Coast Campus, Southport, QLD, 4222, Australia; Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, 4222, Australia; Pathology Queensland, Gold Coast University Hospital, Southport, QLD, 4215, Australia
| | - Muhammad J A Shiddiky
- Rural Health Research Institute, Charles Sturt University, Orange, NSW, 2800, Australia.
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21
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Wang XQ, Yuan F, Yu BR. Whole-Exome Sequencing Reveals Mutational Signature of Hypertrophic Cardiomyopathy. Int J Gen Med 2023; 16:4617-4628. [PMID: 37850193 PMCID: PMC10577257 DOI: 10.2147/ijgm.s422598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/21/2023] [Indexed: 10/19/2023] Open
Abstract
Background Hypertrophic cardiomyopathy (HCM) is an extremely insidious and lethal disease caused by genetic variation. It has been studied for nearly 70 years since its discovery, but its cause of the disease remains a mystery. This study is aimed to explore the genetic pathogenesis of HCM in order to provide new insight for the diagnosis and treatment of HCM. Methods Patients with HCM at 4 hospitals from January 1, 2020, to December 31, 2021, were collected. Peripheral blood of these patients was collected for whole exome sequencing. Moreover, data on the HCM transcriptome were analyzed in the GEO database. Results Totally, 14 patients were enrolled, and 6 single-nucleotide variation (SNV) mutant genes represented by MUC12 were observed. Most of the gene mutations in HCM patients were synonymous and non-synonymous, and the types of base mutations were mainly C > T and G > A. Copy number variants (CNVs) predominantly occurred on chromosome 1 in HCM patients. Furthermore, we found that the only ATP2A2 gene was differentially expressed in 3 groups of transcriptome data in GEO database, and the presence of ATP2A2 mutation in 10 samples was observed in this study. Conclusion In summary, 7 mutated genes represented by MUC12 and ATP2A2 were found in this study, which may provide novel insights into the pathogenic mechanism of HCM.
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Affiliation(s)
- Xi-Qin Wang
- Department of Internal Medicine, Yuhua Yunfang Integrated Traditional Chinese and Western Medicine Clinic, Shijiazhuang, Hebei, 050023, People’s Republic of China
| | - Fang Yuan
- Department of Cardiovascular Medicine, Fuwai Central China Cardiovascular Hospital, Zhengzhou, Henan, 450000, People’s Republic of China
| | - Bao-Rui Yu
- Department of Cardiovascular Medicine, Fuwai Central China Cardiovascular Hospital, Zhengzhou, Henan, 450000, People’s Republic of China
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22
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Pu T, Peddle A, Zhu J, Tejpar S, Verbandt S. Neoantigen identification: Technological advances and challenges. Methods Cell Biol 2023; 183:265-302. [PMID: 38548414 DOI: 10.1016/bs.mcb.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Neoantigens have emerged as promising targets for cutting-edge immunotherapies, such as cancer vaccines and adoptive cell therapy. These neoantigens are unique to tumors and arise exclusively from somatic mutations or non-genomic aberrations in tumor proteins. They encompass a wide range of alterations, including genomic mutations, post-transcriptomic variants, and viral oncoproteins. With the advancements in technology, the identification of immunogenic neoantigens has seen rapid progress, raising new opportunities for enhancing their clinical significance. Prediction of neoantigens necessitates the acquisition of high-quality samples and sequencing data, followed by mutation calling. Subsequently, the pipeline involves integrating various tools that can predict the expression, processing, binding, and recognition potential of neoantigens. However, the continuous improvement of computational tools is constrained by the availability of datasets which contain validated immunogenic neoantigens. This review article aims to provide a comprehensive summary of the current knowledge as well as limitations in neoantigen prediction and validation. Additionally, it delves into the origin and biological role of neoantigens, offering a deeper understanding of their significance in the field of cancer immunotherapy. This article thus seeks to contribute to the ongoing efforts to harness neoantigens as powerful weapons in the fight against cancer.
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Affiliation(s)
- Ting Pu
- Digestive Oncology Unit, KULeuven, Leuven, Belgium
| | | | - Jingjing Zhu
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
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23
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Kaur J, Chandrashekar DS, Varga Z, Sobottka B, Janssen E, Gandhi K, Kowalski J, Kiraz U, Varambally S, Aneja R. Whole-Exome Sequencing Reveals High Mutational Concordance between Primary and Matched Recurrent Triple-Negative Breast Cancers. Genes (Basel) 2023; 14:1690. [PMID: 37761830 PMCID: PMC10531222 DOI: 10.3390/genes14091690] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
PURPOSE Triple-negative breast cancer (TNBC) is a molecularly complex and heterogeneous breast cancer subtype with distinct biological features and clinical behavior. Although TNBC is associated with an increased risk of metastasis and recurrence, the molecular mechanisms underlying TNBC metastasis remain unclear. We performed whole-exome sequencing (WES) analysis of primary TNBC and paired recurrent tumors to investigate the genetic profile of TNBC. METHODS Genomic DNA extracted from 35 formalin-fixed paraffin-embedded tissue samples from 26 TNBC patients was subjected to WES. Of these, 15 were primary tumors that did not have recurrence, and 11 were primary tumors that had recurrence (nine paired primary and recurrent tumors). Tumors were analyzed for single-nucleotide variants and insertions/deletions. RESULTS The tumor mutational burden (TMB) was 7.6 variants/megabase in primary tumors that recurred (n = 9); 8.2 variants/megabase in corresponding recurrent tumors (n = 9); and 7.3 variants/megabase in primary tumors that did not recur (n = 15). MUC3A was the most frequently mutated gene in all groups. Mutations in MAP3K1 and MUC16 were more common in our dataset. No alterations in PI3KCA were detected in our dataset. CONCLUSIONS We found similar mutational profiles between primary and paired recurrent tumors, suggesting that genomic features may be retained during local recurrence.
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Affiliation(s)
- Jaspreet Kaur
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA;
| | - Darshan S. Chandrashekar
- Department of Pathology—Molecular and Cellular, University of Alabama at Birmingham, Birmingham, AL 35233, USA; (D.S.C.); (S.V.)
| | - Zsuzsanna Varga
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091 Zurich, Switzerland; (Z.V.); (B.S.)
| | - Bettina Sobottka
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091 Zurich, Switzerland; (Z.V.); (B.S.)
| | - Emiel Janssen
- Department of Pathology, Stavanger University Hospital, Health Stavanger HF, 4068 Stavanger, Norway; (E.J.); (U.K.)
| | - Khanjan Gandhi
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA;
| | - Jeanne Kowalski
- Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA;
| | - Umay Kiraz
- Department of Pathology, Stavanger University Hospital, Health Stavanger HF, 4068 Stavanger, Norway; (E.J.); (U.K.)
| | - Sooryanarayana Varambally
- Department of Pathology—Molecular and Cellular, University of Alabama at Birmingham, Birmingham, AL 35233, USA; (D.S.C.); (S.V.)
| | - Ritu Aneja
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA;
- Department of Clinical and Diagnostic Sciences, School of Health Professions, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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24
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Zeber-Lubecka N, Suchta K, Kulecka M, Kluska A, Piątkowska M, Dabrowski MJ, Jankowska K, Grymowicz M, Smolarczyk R, Hennig EE. Exome sequencing to explore the possibility of predicting genetic susceptibility to the joint occurrence of polycystic ovary syndrome and Hashimoto's thyroiditis. Front Immunol 2023; 14:1193293. [PMID: 37545519 PMCID: PMC10397507 DOI: 10.3389/fimmu.2023.1193293] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/26/2023] [Indexed: 08/08/2023] Open
Abstract
A large body of evidence indicates that women with polycystic ovary syndrome (PCOS) have a higher risk of developing Hashimoto's thyroiditis (HT) than healthy individuals. Given the strong genetic impact on both diseases, common predisposing genetic factors are possibly involved but are not fully understood. Here, we performed whole-exome sequencing (WES) for 250 women with sporadic PCOS, HT, combined PCOS and HT (PCOS+HT), and healthy controls to explore the genetic background of the joint occurrence of PCOS and HT. Based on relevant comparative analyses, multivariate logistic regression prediction modeling, and the most informative feature selection using the Monte Carlo feature selection and interdependency discovery algorithm, 77 variants were selected for further validation by TaqMan genotyping in a group of 533 patients. In the allele frequency test, variants in RAB6A, GBP3, and FNDC7 genes were found to significantly (padjusted < 0.05) differentiated the PCOS+HT and PCOS groups, variant in HIF3A differentiated the PCOS+HT and HT groups, whereas variants in CDK20 and CCDC71 differentiated the PCOS+HT and both single disorder groups. TaqMan genotyping data were used to create final prediction models, which differentiated between PCOS+HT and PCOS or HT with a prediction accuracy of AUC = 0.78. Using a 70% cutoff of the prediction score improved the model parameters, increasing the AUC value to 0.87. In summary, we demonstrated the polygenic burden of both PCOS and HT, and many common and intersecting signaling pathways and biological processes whose disorders mutually predispose patients to the development of both diseases.
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Affiliation(s)
- Natalia Zeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Katarzyna Suchta
- Department of Gynaecological Endocrinology, Medical University of Warsaw, Warsaw, Poland
| | - Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Magdalena Piątkowska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | | | - Katarzyna Jankowska
- Department of Endocrinology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Monika Grymowicz
- Department of Gynaecological Endocrinology, Medical University of Warsaw, Warsaw, Poland
| | - Roman Smolarczyk
- Department of Gynaecological Endocrinology, Medical University of Warsaw, Warsaw, Poland
| | - Ewa E. Hennig
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
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25
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Satam H, Joshi K, Mangrolia U, Waghoo S, Zaidi G, Rawool S, Thakare RP, Banday S, Mishra AK, Das G, Malonia SK. Next-Generation Sequencing Technology: Current Trends and Advancements. BIOLOGY 2023; 12:997. [PMID: 37508427 PMCID: PMC10376292 DOI: 10.3390/biology12070997] [Citation(s) in RCA: 82] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
The advent of next-generation sequencing (NGS) has brought about a paradigm shift in genomics research, offering unparalleled capabilities for analyzing DNA and RNA molecules in a high-throughput and cost-effective manner. This transformative technology has swiftly propelled genomics advancements across diverse domains. NGS allows for the rapid sequencing of millions of DNA fragments simultaneously, providing comprehensive insights into genome structure, genetic variations, gene expression profiles, and epigenetic modifications. The versatility of NGS platforms has expanded the scope of genomics research, facilitating studies on rare genetic diseases, cancer genomics, microbiome analysis, infectious diseases, and population genetics. Moreover, NGS has enabled the development of targeted therapies, precision medicine approaches, and improved diagnostic methods. This review provides an insightful overview of the current trends and recent advancements in NGS technology, highlighting its potential impact on diverse areas of genomic research. Moreover, the review delves into the challenges encountered and future directions of NGS technology, including endeavors to enhance the accuracy and sensitivity of sequencing data, the development of novel algorithms for data analysis, and the pursuit of more efficient, scalable, and cost-effective solutions that lie ahead.
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Affiliation(s)
- Heena Satam
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Kandarp Joshi
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Upasana Mangrolia
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Sanober Waghoo
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Gulnaz Zaidi
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Shravani Rawool
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Ritesh P. Thakare
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Shahid Banday
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Alok K. Mishra
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Gautam Das
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Sunil K. Malonia
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
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26
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Xie J, Friedman R. Editorial: Evolution in Neurogenomics. Front Genet 2023; 14:1220750. [PMID: 37333499 PMCID: PMC10272802 DOI: 10.3389/fgene.2023.1220750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 05/23/2023] [Indexed: 06/20/2023] Open
Affiliation(s)
- Jiuyong Xie
- Department of Physiology and Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Robert Friedman
- Department of Biological Sciences (Retired), University of South Carolina, Columbia, SC, United States
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27
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Zheng J, Zhang X, Yang Y, Cui J, Fang L, Zhou M, Chen Q. Highly Sensitive and Selective DNA Sequencing Device Using Metal Adatom Adsorption on 2D Phosphorene. ACS OMEGA 2023; 8:17768-17778. [PMID: 37251187 PMCID: PMC10210229 DOI: 10.1021/acsomega.3c00540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/26/2023] [Indexed: 05/31/2023]
Abstract
Two-dimensional (2D) material revolutionarily extends the technique capability of traditional nanopore/nanogap-based DNA sequencing devices. However, challenges associated with DNA sequencing on nanopores still remained in improving the sensitivity and specificity. Herein, by first-principles calculation, we theoretically studied the potential of transition-metal elements (Cr, Fe, Co, Ni, and Au) anchored on monolayer black phosphorene (BP) to act as all-electronic DNA sequencing devices. The spin-polarized band structures appeared in Cr-, Fe-, Co-, and Au-doped BP. Remarkably, the adsorption energy of nucleobases can be significantly enhanced on BP with Co, Fe, and Cr doping, which contribute to the enlarged current signal and lower noise levels. Furthermore, the order of nucleobases in terms of their adsorption energies onto the Cr@BP is C > A > G > T, which exhibits more distinct adsorption energies than Fe@BP or Co@BP. Therefore, Cr-doped BP is more effective to avoid ambiguity in recognizing various bases. We thus envisaged a possibility of a highly sensitive and selective DNA sequencing device based on phosphorene.
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Affiliation(s)
- Junfeng Zheng
- Biomedical
Analysis Center, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, P. R. China
| | - Xuan Zhang
- Department
of Pharmacology, College of Pharmacy and Laboratory Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, P. R. China
| | - Youhao Yang
- Biomedical
Analysis Center, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, P. R. China
| | - Jin Cui
- United
Microelectronics Center Co., Ltd. (CUMEC), Chongqing 401332, P. R. China
| | - Liang Fang
- Key
Laboratory of Optoelectronic Technology & Systems (Ministry of
Education), College of Optoelectronic Engineering, Chongqing University, Chongqing 400044, P. R. China
| | - Miao Zhou
- College
of Physics, Chongqing University, Chongqing 400044, P. R. China
| | - Qian Chen
- Biomedical
Analysis Center, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, P. R. China
- Key Laboratory
of Electromagnetic Radiation Protection, Ministry of Education, Army Medical University (Third Military Medical University), Chongqing 400038, China
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28
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Yaldiz B, Kucuk E, Hampstead J, Hofste T, Pfundt R, Corominas Galbany J, Rinne T, Yntema HG, Hoischen A, Nelen M, Gilissen C. Twist exome capture allows for lower average sequence coverage in clinical exome sequencing. Hum Genomics 2023; 17:39. [PMID: 37138343 PMCID: PMC10155375 DOI: 10.1186/s40246-023-00485-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/20/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. RESULTS We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. CONCLUSION We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques.
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Affiliation(s)
- Burcu Yaldiz
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Erdi Kucuk
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Juliet Hampstead
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Tom Hofste
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Jordi Corominas Galbany
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Tuula Rinne
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Marcel Nelen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
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29
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Cai M, Guo C, Wang X, Lin M, Xu S, Huang H, Lin N, Xu L. Classifying and evaluating fetuses with multicystic dysplastic kidney in etiologic studies. Exp Biol Med (Maywood) 2023; 248:858-865. [PMID: 37208928 PMCID: PMC10484196 DOI: 10.1177/15353702231164933] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/18/2023] [Indexed: 05/21/2023] Open
Abstract
Multicystic dysplastic kidney (MCDK) is one of the most common fetal malformations, but its etiology remains unclear. Identification of the molecular etiology could provide a basis for prenatal diagnosis, consultation, and prognosis evaluation for MCDK fetuses. We used chromosome microarray analysis (CMA) and whole-exome sequencing (WES) to conduct genetic tests on MCDK fetuses and explore their genetic etiology. A total of 108 MCDK fetuses with or without other extrarenal abnormalities were selected. Karyotype analysis of 108 MCDK fetuses showed an abnormal karyotype in 4 (3.7%, 4/108) of the fetuses. However, CMA detected 15 abnormal copy number variations (CNVs) (14 pathogenic CNVs, and one variant of unknown significance [VUS] CNVs), in addition to four cases that were consistent with the results of karyotype analysis. Out of the 14 pathogenic CNVs cases, three were of 17q12 microdeletion, two of 22q11.21 microdeletion, 22q11.21 microduplication uniparental disomy (UPD), and one case of 4q31.3q32.2 microdeletion, 7q11.23 microduplication, 15q11.2 microdeletion, 16p11.2 microdeletion, and 17p12 microdeletion. Of the 89 MCDK fetuses with normal karyotype analysis and CMA, 15 were tested by WES. Two (13.3%, 2/15) fetuses were identified by WES as Bardet-Biedl syndrome (BBS) 1 and BBS2. Combined application of CMA-WES to detect MCDK fetuses can significantly improve the detection rate of genetic etiology, providing a basis for consultation, and prognosis evaluation.
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Affiliation(s)
- Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou 350001, China
| | - Chong Guo
- Child Healthcare Department, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou 350001, China
| | - Xinrui Wang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou 350001, China
| | - Min Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou 350001, China
| | - Shiyi Xu
- Guangxi Medical University, Guangxi 541000, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou 350001, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou 350001, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou 350001, China
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Trilla-Fuertes L, Gámez-Pozo A, Nogué M, Busquier I, Arias F, López-Campos F, Fernández-Montes A, Ruiz A, Velázquez C, Martín-Bravo C, Pérez-Ruiz E, Asensio E, Hernández-Yagüe X, Rodrigues A, Ghanem I, López-Vacas R, Hafez A, Arias P, Dapía I, Solís M, Dittmann A, Ramos R, Llorens C, Maurel J, Campos-Barros Á, Fresno Vara JÁ, Feliu J. Utility of CYP2D6 copy number variants as prognostic biomarker in localized anal squamous cell carcinoma. Cancer 2023. [PMID: 37096763 DOI: 10.1002/cncr.34797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 04/26/2023]
Abstract
BACKGROUND Anal squamous cell carcinoma (ASCC) is an infrequent tumor whose treatment has not changed since the 1970s. The aim of this study is the identification of biomarkers allowing personalized treatments and improvement of therapeutic outcomes. METHODS Forty-six paraffin tumor samples from ASCC patients were analyzed by whole-exome sequencing. Copy number variants (CNVs) were identified and their relation to disease-free survival (DFS) was studied and validated in an independent retrospective cohort of 101 ASCC patients from the Multidisciplinary Spanish Digestive Cancer Group (GEMCAD). GEMCAD cohort proteomics allowed assessing the biological features of these tumors. RESULTS On the discovery cohort, the median age was 61 years old, 50% were males, stages I/II/III: 3 (7%)/16 (35%)/27 (58%), respectively, median DFS was 33 months, and overall survival was 45 months. Twenty-nine genes whose duplication was related to DFS were identified. The most representative was duplications of the CYP2D locus, including CYP2D6, CYP2D7P, and CYP2D8P genes. Patients with CYP2D6 CNV had worse DFS at 5 years than those with two CYP2D6 copies (21% vs. 84%; p < .0002, hazard ratio [HR], 5.8; 95% confidence interval [CI], 2.7-24.9). In the GEMCAD validation cohort, patients with CYP2D6 CNV also had worse DFS at 5 years (56% vs. 87%; p = .02, HR = 3.6; 95% CI, 1.1-5.7). Mitochondria and mitochondrial cell-cycle proteins were overexpressed in patients with CYP2D6 CNV. CONCLUSIONS Tumor CYP2D6 CNV identified patients with a significantly worse DFS at 5 years among localized ASCC patients treated with 5-fluorouracil, mitomycin C, and radiotherapy. Proteomics pointed out mitochondria and mitochondrial cell-cycle genes as possible therapeutic targets for these high-risk patients. PLAIN LANGUAGE SUMMARY Anal squamous cell carcinoma is an infrequent tumor whose treatment has not been changed since the 1970s. However, disease-free survival in late staged tumors is between 40% and 70%. The presence of an alteration in the number of copies of CYP2D6 gene is a biomarker of worse disease-free survival. The analysis of the proteins in these high-risk patients pointed out mitochondria and mitochondrial cell-cycle genes as possible therapeutic targets. Therefore, the determination of the number of copies of CYP2D6 allows the identification of anal squamous carcinoma patients with a high-risk of relapse that could be redirected to a clinical trial. Additionally, this study may be useful to suggest new treatment strategies to increase current therapy efficacy.
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Affiliation(s)
| | - Angelo Gámez-Pozo
- Molecular Oncology Lab, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
- Biomedica Molecular Medicine SL, Madrid, Spain
| | - Miguel Nogué
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital de Granollers, Barcelona, Spain
| | - Isabel Busquier
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Provincial de Castellón, Castellón, Spain
| | - Fernando Arias
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Radiotherapy Oncology Service, Complejo Hospitalario de Navarra, Navarra, Spain
| | - Fernando López-Campos
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Radiotherapy Oncology Service, Hospital Ramón y Cajal, Madrid, Spain
| | - Ana Fernández-Montes
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Complejo Hospitalario Universitario de Ourense, Ourense, Spain
| | - Ana Ruiz
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Universitario Puerta de Hierro Majadahonda, IDIPHISA, Madrid, Spain
| | - Concepción Velázquez
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Miguel Servet, Zaragoza, Spain
| | | | - Elisabeth Pérez-Ruiz
- Unidad de Gestión Clínica Intercentros de Oncología Médica, Hospitales Universitarios Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga, Hospitales Universitarios Regional y Virgen de la Victoria, Málaga, Spain
| | - Elena Asensio
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital General Universitario de Elche, Elche, Spain
| | - Xavier Hernández-Yagüe
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Instituto Catalán de Oncología-Girona, Girona, Spain
| | - Aline Rodrigues
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Ismael Ghanem
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Universitario La Paz, Madrid, Spain
| | - Rocío López-Vacas
- Molecular Oncology Lab, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
| | - Ahmed Hafez
- Biotechvana SL, Parque Científico de Madrid, Madrid, Spain
| | - Pedro Arias
- Pharmacogenetics Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Autonomous University of Madrid, Madrid, Spain
| | - Irene Dapía
- Pharmacogenetics Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Autonomous University of Madrid, Madrid, Spain
| | - Mario Solís
- Bioinformatics Unit, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain
| | - Antje Dittmann
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Ricardo Ramos
- Genomics Unit, Parque Científico de Madrid, Madrid, Spain
| | - Carlos Llorens
- Biotechvana SL, Parque Científico de Madrid, Madrid, Spain
| | - Joan Maurel
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Department, Hospital Clínic of Barcelona, Translational Genomics and Targeted Therapeutics in Solid Tumors Group, IDIBAPS, University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
| | - Ángel Campos-Barros
- Institute of Medical and Molecular Genetics, IdiPAZ, Hospital Universitario La Paz/CIBERER Unit 753, ISCIII, Madrid, Spain
| | - Juan Ángel Fresno Vara
- Molecular Oncology Lab, Hospital Universitario La Paz-IdiPAZ, Madrid, Spain
- Biomedica Molecular Medicine SL, Madrid, Spain
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
| | - Jaime Feliu
- Spanish Multidisciplinary Group of Digestive Cancer, Barcelona, Spain
- Medical Oncology Service, Hospital Universitario La Paz, Madrid, Spain
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
- Cátedra UAM-Amgen, Universidad Autónoma de Madrid, Madrid, Spain
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Soilly AL, Robert-Viard C, Besse C, Bruel AL, Gerard B, Boland A, Piton A, Duffourd Y, Muller J, Poë C, Jouan T, El Doueiri S, Faivre L, Bacq-Daian D, Isidor B, Genevieve D, Odent S, Philip N, Doco-Fenzy M, Lacombe D, Asensio ML, Deleuze JF, Binquet C, Thauvin-Robinet C, Lejeune C. Cost of exome analysis in patients with intellectual disability: a micro-costing study in a French setting. BMC Health Serv Res 2023; 23:386. [PMID: 37085862 PMCID: PMC10120135 DOI: 10.1186/s12913-023-09373-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 04/04/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND With the development of next generation sequencing technologies in France, exome sequencing (ES) has recently emerged as an opportunity to improve the diagnosis rate of patients presenting an intellectual disability (ID). To help French policy makers determine an adequate tariff for ES, we aimed to assess the unit cost per ES diagnostic test for ID from the preparation of the pre-analytical step until the report writing step and to identify its main cost drivers. METHODS A micro-costing bottom-up approach was conducted for the year 2018 in a French setting as part of the DISSEQ study, a cost-effectiveness study funded by the Ministry of Health and performed in collaboration with the GAD (Génétique des Anomalies du Développement), a genetic team from the Dijon University Hospital, and a public sequencing platform, the Centre National de Recherche en Génomique Humaine (CNRGH). The analysis was conducted from the point of view of these two ES stakeholders. All of the resources (labor, equipment, disposables and reagents, reusable material) required to analyze blood samples were identified, collected and valued. Several sensitivity analyses were performed. RESULTS The unit nominal cost per ES diagnostic test for ID was estimated to be €2,019.39. Labor represented 50.7% of the total cost. The analytical step (from the preparation of libraries to the analysis of sequences) represented 88% of the total cost. Sensitivity analyses suggested that a simultaneous price decrease of 20% for the capture kit and 50% for the sequencing support kit led to an estimation of €1,769 per ES diagnostic test for ID. CONCLUSION This is the first estimation of ES cost to be done in the French setting of ID diagnosis. The estimation is especially influenced by the price of equipment kits, but more generally by the organization of the centers involved in the different steps of the analysis and the time period in which the study was conducted. This information can now be used to define an adequate tariff and assess the efficiency of ES. TRIAL REGISTRATION ClinicalTrials.gov identifier NCT03287206 on September 19, 2017.
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Affiliation(s)
- A L Soilly
- CHU Dijon Bourgogne, Délégation à la Recherche Clinique et à l'Innovation, USMR, F-21000, Dijon, France
- CHU Dijon Bourgogne, Délégation à la Recherche Clinique et à l'Innovation, Unité Innovation, F-21000, Dijon, France
| | - C Robert-Viard
- CHU Dijon Bourgogne, Délégation à la Recherche Clinique et à l'Innovation, Unité Innovation, F-21000, Dijon, France
- CHU Dijon Bourgogne, Inserm, Université de Bourgogne, CIC 1432, Module Épidémiologie Clinique, F21000, Dijon, France
| | - C Besse
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - A L Bruel
- Inserm, Université Bourgogne-Franche-Comté, UMR1231, équipe GAD, Dijon, France
| | - B Gerard
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace (IGMA), 67000, Strasbourg, France
| | - A Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - A Piton
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace (IGMA), 67000, Strasbourg, France
| | - Y Duffourd
- Inserm, Université Bourgogne-Franche-Comté, UMR1231, équipe GAD, Dijon, France
| | - J Muller
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace (IGMA), 67000, Strasbourg, France
- Unité Fonctionnelle de Bioinformatique Médicale appliquée au diagnostic (UF7363), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Inserm UMRS_1112, Institut de Génétique Médicale d'Alsace, Université de Strasbourg, France et CHRU, Strasbourg, France
| | - C Poë
- Inserm, Université Bourgogne-Franche-Comté, UMR1231, équipe GAD, Dijon, France
| | - T Jouan
- Inserm, Université Bourgogne-Franche-Comté, UMR1231, équipe GAD, Dijon, France
| | - S El Doueiri
- CHU Dijon Bourgogne, Service financier, 21000, Dijon, France
| | - L Faivre
- Inserm, Université Bourgogne-Franche-Comté, UMR1231, équipe GAD, Dijon, France
- CHU Dijon-Bourgogne, Centres de Référence Maladies Rares « Anomalies du Développement et syndromes malformatif de l'Est » et « Déficiences intellectuelles de causes rares », Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Dijon, France
| | - D Bacq-Daian
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - B Isidor
- Service de Génétique Médicale, CHU de Nantes, Nantes, France
| | - D Genevieve
- Département de Génétique Médicale, Centre de Référence Maladies Rares, Anomalies du Développement et Syndromes Malformatifs Sud-Languedoc Roussillon, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - S Odent
- Service de Génétique Clinique, Centre Hospitalier Universitaire Rennes, F-35203, Rennes, France
- Centre National de la Recherche Scientifique Unité Mixte de Recherche 6290, Institut Génétique et Développement de Rennes, Université de Rennes 1, F-35203, Rennes, France
| | - N Philip
- Département de Génétique Médicale, Hôpital d'Enfants de La Timone, Marseille, France
| | - M Doco-Fenzy
- Service de Génétique, CHU de Reims, EA3801, Reims, France
- CRMR Anddi-Rares constitutif, CLAD-EST, CHU Reims, Reims, France
| | - D Lacombe
- CHU de Bordeaux, Génétique Médicale, INSERM U1211, Laboratoire MRGM, Université de Bordeaux, Bordeaux, France
| | - M L Asensio
- CHU Dijon Bourgogne, Inserm, Université de Bourgogne, CIC 1432, Module Épidémiologie Clinique, F21000, Dijon, France
| | - J F Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - C Binquet
- CHU Dijon Bourgogne, Inserm, Université de Bourgogne, CIC 1432, Module Épidémiologie Clinique, F21000, Dijon, France
| | - C Thauvin-Robinet
- Inserm, Université Bourgogne-Franche-Comté, UMR1231, équipe GAD, Dijon, France
- CHU Dijon-Bourgogne, Centres de Référence Maladies Rares « Anomalies du Développement et syndromes malformatif de l'Est » et « Déficiences intellectuelles de causes rares », Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Dijon, France
| | - C Lejeune
- CHU Dijon Bourgogne, Inserm, Université de Bourgogne, CIC 1432, Module Épidémiologie Clinique, F21000, Dijon, France.
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Nguyen XTA, Moekotte L, Plomp AS, Bergen AA, van Genderen MM, Boon CJF. Retinitis Pigmentosa: Current Clinical Management and Emerging Therapies. Int J Mol Sci 2023; 24:ijms24087481. [PMID: 37108642 PMCID: PMC10139437 DOI: 10.3390/ijms24087481] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/01/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Retinitis pigmentosa (RP) comprises a group of inherited retinal dystrophies characterized by the degeneration of rod photoreceptors, followed by the degeneration of cone photoreceptors. As a result of photoreceptor degeneration, affected individuals experience gradual loss of visual function, with primary symptoms of progressive nyctalopia, constricted visual fields and, ultimately, central vision loss. The onset, severity and clinical course of RP shows great variability and unpredictability, with most patients already experiencing some degree of visual disability in childhood. While RP is currently untreatable for the majority of patients, significant efforts have been made in the development of genetic therapies, which offer new hope for treatment for patients affected by inherited retinal dystrophies. In this exciting era of emerging gene therapies, it remains imperative to continue supporting patients with RP using all available options to manage their condition. Patients with RP experience a wide variety of physical, mental and social-emotional difficulties during their lifetime, of which some require timely intervention. This review aims to familiarize readers with clinical management options that are currently available for patients with RP.
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Affiliation(s)
- Xuan-Thanh-An Nguyen
- Department of Ophthalmology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Lude Moekotte
- Department of Ophthalmology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Astrid S Plomp
- Department of Clinical Genetics, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Arthur A Bergen
- Department of Clinical Genetics, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Maria M van Genderen
- Department of Ophthalmology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
- Bartiméus, Diagnostic Center for Complex Visual Disorders, 3703 AJ Zeist, The Netherlands
| | - Camiel J F Boon
- Department of Ophthalmology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Department of Ophthalmology, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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Avershina E, Khezri A, Ahmad R. Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics-Current State and Whole Genome Sequencing Implementation Perspectives. Antibiotics (Basel) 2023; 12:antibiotics12040781. [PMID: 37107143 PMCID: PMC10135054 DOI: 10.3390/antibiotics12040781] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/19/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Antimicrobial resistance (AMR), defined as the ability of microorganisms to withstand antimicrobial treatment, is responsible for millions of deaths annually. The rapid spread of AMR across continents warrants systematic changes in healthcare routines and protocols. One of the fundamental issues with AMR spread is the lack of rapid diagnostic tools for pathogen identification and AMR detection. Resistance profile identification often depends on pathogen culturing and thus may last up to several days. This contributes to the misuse of antibiotics for viral infection, the use of inappropriate antibiotics, the overuse of broad-spectrum antibiotics, or delayed infection treatment. Current DNA sequencing technologies offer the potential to develop rapid infection and AMR diagnostic tools that can provide information in a few hours rather than days. However, these techniques commonly require advanced bioinformatics knowledge and, at present, are not suited for routine lab use. In this review, we give an overview of the AMR burden on healthcare, describe current pathogen identification and AMR screening methods, and provide perspectives on how DNA sequencing may be used for rapid diagnostics. Additionally, we discuss the common steps used for DNA data analysis, currently available pipelines, and tools for analysis. Direct, culture-independent sequencing has the potential to complement current culture-based methods in routine clinical settings. However, there is a need for a minimum set of standards in terms of evaluating the results generated. Additionally, we discuss the use of machine learning algorithms regarding pathogen phenotype detection (resistance/susceptibility to an antibiotic).
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Affiliation(s)
- Ekaterina Avershina
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
| | - Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
- Institute of Clinical Medicine, Faculty of Health Science, UiT The Arctic University of Norway, Hansine Hansens veg, 189019 Tromsø, Norway
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Yadav RK, Tripathi MK, Tiwari S, Tripathi N, Asati R, Patel V, Sikarwar RS, Payasi DK. Breeding and Genomic Approaches towards Development of Fusarium Wilt Resistance in Chickpea. Life (Basel) 2023; 13:life13040988. [PMID: 37109518 PMCID: PMC10144025 DOI: 10.3390/life13040988] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/29/2023] Open
Abstract
Chickpea is an important leguminous crop with potential to provide dietary proteins to both humans and animals. It also ameliorates soil nitrogen through biological nitrogen fixation. The crop is affected by an array of biotic and abiotic factors. Among different biotic stresses, a major fungal disease called Fusarium wilt, caused by Fusarium oxysporum f. sp. ciceris (FOC), is responsible for low productivity in chickpea. To date, eight pathogenic races of FOC (race 0, 1A, and 1B/C, 2-6) have been reported worldwide. The development of resistant cultivars using different conventional breeding methods is very time consuming and depends upon the environment. Modern technologies can improve conventional methods to solve these major constraints. Understanding the molecular response of chickpea to Fusarium wilt can help to provide effective management strategies. The identification of molecular markers closely linked to genes/QTLs has provided great potential for chickpea improvement programs. Moreover, omics approaches, including transcriptomics, metabolomics, and proteomics give scientists a vast viewpoint of functional genomics. In this review, we will discuss the integration of all available strategies and provide comprehensive knowledge about chickpea plant defense against Fusarium wilt.
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Affiliation(s)
- Rakesh Kumar Yadav
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Manoj Kumar Tripathi
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Sushma Tiwari
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Niraj Tripathi
- Directorate of Research Services, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur 482004, India
| | - Ruchi Asati
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Vinod Patel
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - R S Sikarwar
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
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Senarathne UD, Indika NLR, Jezela-Stanek A, Ciara E, Frye RE, Chen C, Stepien KM. Biochemical, Genetic and Clinical Diagnostic Approaches to Autism-Associated Inherited Metabolic Disorders. Genes (Basel) 2023; 14:genes14040803. [PMID: 37107561 PMCID: PMC10138025 DOI: 10.3390/genes14040803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Autism spectrum disorders (ASD) are a heterogeneous group of neurodevelopmental disorders characterized by impaired social interaction, limited communication skills, and restrictive and repetitive behaviours. The pathophysiology of ASD is multifactorial and includes genetic, epigenetic, and environmental factors, whereas a causal relationship has been described between ASD and inherited metabolic disorders (IMDs). This review describes biochemical, genetic, and clinical approaches to investigating IMDs associated with ASD. The biochemical work-up includes body fluid analysis to confirm general metabolic and/or lysosomal storage diseases, while the advances and applications of genomic testing technology would assist with identifying molecular defects. An IMD is considered likely underlying pathophysiology in ASD patients with suggestive clinical symptoms and multiorgan involvement, of which early recognition and treatment increase their likelihood of achieving optimal care and a better quality of life.
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Affiliation(s)
- Udara D. Senarathne
- Department of Biochemistry, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka
- Department of Chemical Pathology, Monash Health Pathology, Monash Health, Melbourne, VIC 3168, Australia
| | - Neluwa-Liyanage R. Indika
- Department of Biochemistry, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka
| | - Aleksandra Jezela-Stanek
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland
| | - Elżbieta Ciara
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland
| | - Richard E. Frye
- Autism Discovery and Treatment Foundation, Phoenix, AZ 85050, USA
| | - Cliff Chen
- Clinical Neuropsychology Department, Manchester Centre for Clinical Neurosciences, Salford Royal NHS Foundation Trust, Salford M6 8HD, UK
| | - Karolina M. Stepien
- Adult Inherited Metabolic Diseases, Mark Holland Unit, Salford Royal NHS Foundation Trust, Salford M6 8HD, UK
- Division of Diabetes, Endocrinology and Gastroenterology, University of Manchester, Manchester M13 9PL, UK
- Correspondence:
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Ao X, Parisien M, Zidan M, Grant AV, Martinsen AE, Winsvold BS, Diatchenko L. Rare variant analyses in large-scale cohorts identified SLC13A1 associated with chronic pain. Pain 2023:00006396-990000000-00273. [PMID: 36943258 DOI: 10.1097/j.pain.0000000000002882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 12/16/2022] [Indexed: 03/23/2023]
Abstract
ABSTRACT Chronic pain is a prevalent disease with increasing clinical challenges. Genome-wide association studies in chronic pain patients have identified hundreds of common pathogenic variants, yet they only explained a portion of individual variance of chronic pain. With the advances in next-generation sequencing technologies, it is now feasible to conduct rarer variants studies in large-scale databases. Here, we performed gene-based rare variant analyses in 200,000 human subjects in the UK biobank whole-exome sequencing database for investigating 9 different chronic pain states and validated our findings in 3 other large-scale databases. Our analyses identified the SLC13A1 gene coding for sodium/sulfate symporter associated with chronic back pain and multisite pain at the genome-wide level and with chronic headache, knee, and neck and shoulder pain at the nominal level. Seven loss-of-function rare variants were identified within the gene locus potentially contributing to the development of chronic pain, with 2 of them individually associated with back pain and multisite pain. These 2 rare variants were then tested for replication in 3 other biobanks, and the strongest evidence was found for rs28364172 as an individual contributor. Transcriptional analyses of Slc13a1 in rodents showed substantial regulation of its expression in the dorsal root ganglia and the sciatic nerve in neuropathic pain assays. Our results stress the importance of the SLC13A1 gene in sulfate homeostasis in the nervous system and its critical role in preventing pain states, thus suggesting new therapeutic approaches for treating chronic pain in a personalized manner, especially in people with mutations in the SLC13A1 gene.
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Affiliation(s)
- Xiang Ao
- Faculty of Dental Medicine and Oral Health Sciences, Department of Anesthesia, Faculty of Medicine and Health Sciences, Alan Edwards Centre for Research on Pain, McGill University, Montreal, QC, Canada
| | - Marc Parisien
- Faculty of Dental Medicine and Oral Health Sciences, Department of Anesthesia, Faculty of Medicine and Health Sciences, Alan Edwards Centre for Research on Pain, McGill University, Montreal, QC, Canada
| | - Maha Zidan
- Faculty of Dental Medicine and Oral Health Sciences, Department of Anesthesia, Faculty of Medicine and Health Sciences, Alan Edwards Centre for Research on Pain, McGill University, Montreal, QC, Canada
| | - Audrey V Grant
- Faculty of Dental Medicine and Oral Health Sciences, Department of Anesthesia, Faculty of Medicine and Health Sciences, Alan Edwards Centre for Research on Pain, McGill University, Montreal, QC, Canada
| | - Amy E Martinsen
- Department of Research, Innovation and Education, Oslo University Hospital, Oslo, Norway
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Bendik S Winsvold
- Department of Research, Innovation and Education, Oslo University Hospital, Oslo, Norway
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Neurology and Department of Research, Innovation and Education, Oslo University Hospital, Oslo, Norway
| | - Luda Diatchenko
- Faculty of Dental Medicine and Oral Health Sciences, Department of Anesthesia, Faculty of Medicine and Health Sciences, Alan Edwards Centre for Research on Pain, McGill University, Montreal, QC, Canada
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Kim YR, Kim HM, Lee B, Baek JI, Lee KY, Park HJ, Kim UK. Identification of novel missense mutation related with non-syndromic sensorineural deafness, DFNA11 in korean family by NGS. Genes Genomics 2023; 45:225-230. [PMID: 36630074 DOI: 10.1007/s13258-022-01357-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 12/17/2022] [Indexed: 01/12/2023]
Abstract
BACKGOUND Hereditary hearing loss is one of the most common genetically heterogeneous defects in human. About 70% of hereditary hearing loss is defined as non-syndromic hearing loss showing loss of hearing ability without any other symptoms. Up to date, the identified genes associated with non-syndromic hearing loss are 128, including 52 genes for DFNA and 76 genes for DFNB. Because of high levels of heterogeneity, it is difficult to identify the causative factors for hearing loss using Sanger sequencing. OBJECTIVE Our aim was to detect causative factors and investigate pathogenic mutations, which co-segregates within the candidate family. METHODS We used Next Generation Sequencing technique to investigate whole-exome sequences of a Korean family with non-syndromic hereditary hearing loss. The family showed autosomal dominant inheritance pattern. RESULTS We identified a novel missense variation, c.1978G > A in MYO7A gene, in the family with the autosomal dominant inheritance pattern. c.1978G > A produced Gly660Arg in the motor head domain of Myosin VIIA disrupt the ATP- and actin-binding motif function. CONCLUSION This study is the first to report pathogenic mutations within MYO7A gene in Korean family and our data would facilitate diagnosing the primary cause of hereditary hearing loss in Korean.
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Affiliation(s)
- Ye-Ri Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea
- Advanced Bio-Resource Research Center, Kyungpook National University, Daegu, Republic of Korea
| | - Hye-Min Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea
| | - Byeonghyeon Lee
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Republic of Korea
| | - Jeong-In Baek
- Department of Companion Animal Health, College of Rehabilitation and Health, Deagu Haany University, Gyeongsan, Republic of Korea
| | - Kyu-Yup Lee
- Department of Internal Medicine, Research Institute of Aging and Metabolism, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | | | - Un-Kyung Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea.
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea.
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Singh M, Agarwal V, Jindal D, Pancham P, Agarwal S, Mani S, Tiwari RK, Das K, Alghamdi BS, Abujamel TS, Ashraf GM, Jha SK. Recent Updates on Corticosteroid-Induced Neuropsychiatric Disorders and Theranostic Advancements through Gene Editing Tools. Diagnostics (Basel) 2023; 13:diagnostics13030337. [PMID: 36766442 PMCID: PMC9914305 DOI: 10.3390/diagnostics13030337] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/28/2022] [Accepted: 10/16/2022] [Indexed: 01/19/2023] Open
Abstract
The vast use of corticosteroids (CCSs) globally has led to an increase in CCS-induced neuropsychiatric disorders (NPDs), a very common manifestation in patients after CCS consumption. These neuropsychiatric disorders range from depression, insomnia, and bipolar disorders to panic attacks, overt psychosis, and many other cognitive changes in such subjects. Though their therapeutic importance in treating and improving many clinical symptoms overrides the complications that arise after their consumption, still, there has been an alarming rise in NPD cases in recent years, and they are seen as the greatest public health challenge globally; therefore, these potential side effects cannot be ignored. It has also been observed that many of the neuronal functional activities are regulated and controlled by genomic variants with epigenetic factors (DNA methylation, non-coding RNA, and histone modeling, etc.), and any alterations in these regulatory mechanisms affect normal cerebral development and functioning. This study explores a general overview of emerging concerns of CCS-induced NPDs, the effective molecular biology approaches that can revitalize NPD therapy in an extremely specialized, reliable, and effective manner, and the possible gene-editing-based therapeutic strategies to either prevent or cure NPDs in the future.
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Affiliation(s)
- Manisha Singh
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT), Noida 201309, India
- Correspondence: (M.S.); (S.K.J.)
| | - Vinayak Agarwal
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT), Noida 201309, India
| | - Divya Jindal
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT), Noida 201309, India
| | - Pranav Pancham
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT), Noida 201309, India
| | - Shriya Agarwal
- Department of Molecular Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Shalini Mani
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT), Noida 201309, India
| | - Raj Kumar Tiwari
- School of Health Sciences, Pharmaceutical Sciences, UPES, Dehradun 248007, India
| | - Koushik Das
- School of Health Sciences, Pharmaceutical Sciences, UPES, Dehradun 248007, India
| | - Badrah S. Alghamdi
- Department of Physiology, Neuroscience Unit, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Pre-Clinical Research Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Tukri S. Abujamel
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ghulam Md. Ashraf
- Pre-Clinical Research Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, University City, Sharjah 27272, United Arab Emirates
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering & Technology, Sharda University, Greater Noida 201310, India
- Department of Biotechnology, School of Applied & Life Sciences (SALS), Uttaranchal University, Dehradun 248007, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali 140413, India
- Correspondence: (M.S.); (S.K.J.)
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Mittal S, Pathak B. Towards a graphene semi/hybrid-nanogap: a new architecture for ultrafast DNA sequencing. NANOSCALE 2023; 15:757-767. [PMID: 36525055 DOI: 10.1039/d2nr05200h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The tremendous upsurge in the research of next-generation sequencing (NGS) methods has broadly been driven by the rise of the wonder material graphene and continues to dominate the futuristic approaches for fast and accurate DNA sequencing. The success of graphene has also triggered the search for many new potential NGS methods capable of ultrafast, reliable, and controlled DNA sequencing. The present study delves into the potential of a new NGS architecture utilizing graphene, namely, a 'semi/hybrid-nanogap' for the identification of DNA nucleobases with single-base resolution. In the framework of first-principles density functional theory methods, we have calculated the transmission function and current-voltage (I-V) characteristics which are of particular significance for DNA sequencing applications. It is noted that the interaction energy values are significantly reduced compared to the previously reported graphene nanodevices, which can lead to a controlled translocation during experimental measurements. Based on the transmission function, each nucleobase can be identified with pertinent sensitivity. It is noticed that the use of highly conductive nucleobase analogs can facilitate improved single nucleobase sensing by increasing the transmission sensitivity. Therefore, we believe that the present study opens up promising frontiers for sequencing applications.
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Affiliation(s)
- Sneha Mittal
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India.
| | - Biswarup Pathak
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India.
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40
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Musa NH, Thilakavathy K, Mohamad NA, Kennerson ML, Inche Mat LN, Loh WC, Abdul Rashid AM, Baharin J, Ibrahim A, Wan Sulaiman WA, Hoo FK, Basri H, Yusof Khan AHK. Case report: Incomplete penetrance of autosomal dominant myotonia congenita caused by a rare CLCN1 variant c.1667T>A (p.I556N) in a Malaysian family. Front Genet 2023; 13:972007. [PMID: 36659963 PMCID: PMC9842662 DOI: 10.3389/fgene.2022.972007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/23/2022] [Indexed: 01/04/2023] Open
Abstract
Myotonia congenita (MC) is a rare neuromuscular disease caused by mutations within the CLCN1 gene encoding skeletal muscle chloride channels. MC is characterized by delayed muscle relaxation during contraction, resulting in muscle stiffness. There is a lack of MC case reports and data on the prevalence among Malaysians. We report a clinical case of a 50-year-old woman presents with muscle stiffness and cramp episodes that started in early childhood. She had difficulty initiating muscle movement and presented with transient muscle weakness after rest, which usually improved after repeated contraction (warm-up phenomenon). She was diagnosed with MC after myotonic discharge on electromyography (EMG). Her brother had similar symptoms; however, no additional family members showed MC symptoms. Serum creatine kinase levels were elevated in both the proband and her brother with 447 U/L and 228 U/L recorded, respectively. Genetic analysis by whole-exome sequencing (WES) revealed a previously reported pathogenic CLCN1 gene variant c.1667T>A (p.I556N). Genetic screening of all family members revealed that the same variant was observed in the children of both the proband and her brother; however, the children did not present with either clinical or electrophysiological MC symptoms. The multiplex ligation-dependent probe amplification (MLPA) analysis conducted identified neither exon deletion nor duplication in CLCN1. In conclusion, this report describes the first case of MC in Malaysia in which incomplete penetrance observed in this family is caused by a known pathogenic CLCN1 variant.
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Affiliation(s)
- Nurul Huda Musa
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia,Centre of Foundation Studies, Universiti Teknologi MARA, Cawangan Selangor, Kampus Dengkil, Dengkil, Selangor, Malaysia
| | - Karuppiah Thilakavathy
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia,Genetics and Regenerative Research Group, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia,*Correspondence: Abdul Hanif Khan Yusof Khan, ; Karuppiah Thilakavathy,
| | - Nur Afiqah Mohamad
- Department of Neurology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia,Center for Foundation Studies, Foundation in Science, Lincoln University College, Petaling Jaya, Malaysia
| | - Marina L. Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney Local Health District, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia,Molecular Medicine Laboratory, Concord Hospital, Concord, NSW, Australia
| | - Liyana Najwa Inche Mat
- Department of Neurology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Wei Chao Loh
- Department of Neurology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Anna Misyail Abdul Rashid
- Department of Neurology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Janudin Baharin
- Department of Neurology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Azliza Ibrahim
- Department of Neurology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Wan Aliaa Wan Sulaiman
- Department of Neurology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Fan Kee Hoo
- Department of Neurology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Hamidon Basri
- Department of Neurology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Abdul Hanif Khan Yusof Khan
- Department of Neurology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia,*Correspondence: Abdul Hanif Khan Yusof Khan, ; Karuppiah Thilakavathy,
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41
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Yao J, Ding Y, Liu X, Huang J, Zhang M, Zhang Y, Lv Y, Xie Z, Zuo J. Application value of whole exome sequencing in screening and identifying novel mutations of hypopharyngeal cancer. Sci Rep 2023; 13:107. [PMID: 36596842 PMCID: PMC9810646 DOI: 10.1038/s41598-022-27273-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 12/29/2022] [Indexed: 01/05/2023] Open
Abstract
The research on targeted therapy of hypopharyngeal cancer is very scarce. The discovery of new targeted driver genes will promote the progress of hypopharyngeal cancer therapy to a great extent. In our research, whole-exome sequencing in 10 patients with hypopharyngeal cancer was performed to identify single nucleotide variations (SNVs) and insertions and deletions (INDELs). American College of Medical Genetics and Genomics (ACMG) guidelines were used to evaluate the pathogenicity of the selected variants. 8113 mutation sites in 5326 genes were identified after strict screening. We identified 72 pathogenic mutations in 53 genes according to the ACMG guidelines. Gene Ontology (GO) annotation and KEGG enrichment analysis show the effect of these genes on cancer. Protein-protein interaction (PPI) was analyzed by string online software. The validation results of the ualcan database showed that 22 of the 53 genes may be related to the poor prognosis of patients with hypopharyngeal cancer. RBM20 has the most significant correlation with hypopharyngeal cancer, and it is likely to be the driver gene of hypopharyngeal cancer. In conclusion, we found possible therapeutic targets for hypopharyngeal cancer, especially RBM20 and KMT2C. Our study provides a basis for the pathogenesis and targeted therapy of hypopharyngeal cancer.
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Affiliation(s)
- Jingwei Yao
- grid.412017.10000 0001 0266 8918Gastroenterology Department, The Affiliated Nanhua Hospital of University of South China, Hengyang, 421001 Hunan People’s Republic of China ,grid.12955.3a0000 0001 2264 7233Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003 People’s Republic of China ,grid.412017.10000 0001 0266 8918Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan People’s Republic of China ,grid.412017.10000 0001 0266 8918Clinical Laboratory, The Third Affiliated Hospital of University of South China, Hengyang, 421000 Hunan People’s Republic of China
| | - Yubo Ding
- grid.412017.10000 0001 0266 8918Gastroenterology Department, The Affiliated Nanhua Hospital of University of South China, Hengyang, 421001 Hunan People’s Republic of China ,grid.412017.10000 0001 0266 8918Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan People’s Republic of China
| | - Xiong Liu
- grid.284723.80000 0000 8877 7471Department of Otolaryngology-Head and Neck Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 People’s Republic of China
| | - Jialu Huang
- grid.412017.10000 0001 0266 8918Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan People’s Republic of China
| | - Minghui Zhang
- grid.412017.10000 0001 0266 8918Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan People’s Republic of China
| | - Yu Zhang
- grid.412017.10000 0001 0266 8918Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan People’s Republic of China
| | - Yufan Lv
- grid.412017.10000 0001 0266 8918Gastroenterology Department, The Affiliated Nanhua Hospital of University of South China, Hengyang, 421001 Hunan People’s Republic of China ,grid.412017.10000 0001 0266 8918Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan People’s Republic of China
| | - Zhuoyi Xie
- grid.412017.10000 0001 0266 8918Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan People’s Republic of China
| | - Jianhong Zuo
- grid.412017.10000 0001 0266 8918Gastroenterology Department, The Affiliated Nanhua Hospital of University of South China, Hengyang, 421001 Hunan People’s Republic of China ,grid.412017.10000 0001 0266 8918Transformation Research Lab, Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan People’s Republic of China ,grid.412017.10000 0001 0266 8918Clinical Laboratory, The Third Affiliated Hospital of University of South China, Hengyang, 421000 Hunan People’s Republic of China
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Chen Y, Wu Z, Sutlive J, Wu K, Mao L, Nie J, Zhao XZ, Guo F, Chen Z, Huang Q. Noninvasive prenatal diagnosis targeting fetal nucleated red blood cells. J Nanobiotechnology 2022; 20:546. [PMID: 36585678 PMCID: PMC9805221 DOI: 10.1186/s12951-022-01749-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/15/2022] [Indexed: 12/31/2022] Open
Abstract
Noninvasive prenatal diagnosis (NIPD) aims to detect fetal-related genetic disorders before birth by detecting markers in the peripheral blood of pregnant women, holding the potential in reducing the risk of fetal birth defects. Fetal-nucleated red blood cells (fNRBCs) can be used as biomarkers for NIPD, given their remarkable nature of carrying the entire genetic information of the fetus. Here, we review recent advances in NIPD technologies based on the isolation and analysis of fNRBCs. Conventional cell separation methods rely primarily on physical properties and surface antigens of fNRBCs, such as density gradient centrifugation, fluorescence-activated cell sorting, and magnetic-activated cell sorting. Due to the limitations of sensitivity and purity in Conventional methods, separation techniques based on micro-/nanomaterials have been developed as novel methods for isolating and enriching fNRBCs. We also discuss emerging methods based on microfluidic chips and nanostructured substrates for static and dynamic isolation of fNRBCs. Additionally, we introduce the identification techniques of fNRBCs and address the potential clinical diagnostic values of fNRBCs. Finally, we highlight the challenges and the future directions of fNRBCs as treatment guidelines in NIPD.
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Affiliation(s)
- Yanyu Chen
- grid.207374.50000 0001 2189 3846Academy of Medical Sciences, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China ,grid.49470.3e0000 0001 2331 6153School of Physics and Technology, Wuhan University, Wuhan, 430072 China
| | - Zhuhao Wu
- grid.411377.70000 0001 0790 959XDepartment of Intelligent Systems Engineering, Indiana University, Bloomington, IN 47405 USA
| | - Joseph Sutlive
- grid.38142.3c000000041936754XDivision of Thoracic and Cardiac Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115 USA
| | - Ke Wu
- grid.49470.3e0000 0001 2331 6153School of Physics and Technology, Wuhan University, Wuhan, 430072 China
| | - Lu Mao
- grid.207374.50000 0001 2189 3846Academy of Medical Sciences, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052 China
| | - Jiabao Nie
- grid.38142.3c000000041936754XDivision of Thoracic and Cardiac Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115 USA ,grid.261112.70000 0001 2173 3359Department of Biological Sciences, Northeastern University, Boston, MA 02115 USA
| | - Xing-Zhong Zhao
- grid.49470.3e0000 0001 2331 6153School of Physics and Technology, Wuhan University, Wuhan, 430072 China
| | - Feng Guo
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, 47405, United States.
| | - Zi Chen
- Division of Thoracic and Cardiac Surgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Qinqin Huang
- The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450052, China.
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Chang LH, Chi NF, Chen CY, Lin YS, Hsu SL, Tsai JY, Huang HC, Lin CJ, Chung CP, Tung CY, Jeng CJ, Lee YC, Liu YT, Lee IH. Monogenic Causes in Familial Stroke Across Intracerebral Hemorrhage and Ischemic Stroke Subtypes Identified by Whole-Exome Sequencing. Cell Mol Neurobiol 2022:10.1007/s10571-022-01315-3. [PMID: 36580209 DOI: 10.1007/s10571-022-01315-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/20/2022] [Indexed: 12/30/2022]
Abstract
Whole exome sequencing (WES) has been used to detect rare causative variants in neurological diseases. However, the efficacy of WES in genetic diagnosis of clinically heterogeneous familial stroke remains inconclusive. We prospectively searched for disease-causing variants in unrelated probands with defined familial stroke by candidate gene/hotspot screening and/or WES, depending on stroke subtypes and neuroimaging features at a referral center. The clinical significance of each variant was determined according to the American College of Medical Genetics guidelines. Among 161 probands (mean age at onset 53.2 ± 13.7 years; male 63.4%), 33 participants (20.5%) had been identified with 19 pathogenic/likely pathogenic variants (PVs; WES applied 152/161 = 94.4%). Across subtypes, the highest hit rate (HR) was intracerebral hemorrhage (ICH, 7/18 = 38.9%), particularly with the etiological subtype of structural vasculopathy (4/4 = 100%, PVs in ENG, KRIT1, PKD1, RNF213); followed by ischemic small vessel disease (SVD, 15/48 = 31.3%; PVs in NOTCH3, HTRA1, HBB). In contrast, large artery atherosclerosis (LAA, 4/44 = 9.1%) and cardioembolism (0/11 = 0%) had the lowest HR. NOTCH3 was the most common causative gene (16/161 = 9.9%), presenting with multiple subtypes of SVD (n = 13), ICH (n = 2), or LAA (n = 1). Importantly, we disclosed two previously unreported PVs, KRIT1 p.E379* in a familial cerebral cavernous malformation, and F2 p.F382L in a familial cerebral venous sinus thrombosis. The contribution of monogenic etiologies was particularly high in familial ICH and SVD subtypes in our Taiwanese cohort. Utilizing subtype-guided hotspot screening and/or subsequent WES, we unraveled monogenic causes in 20.5% familial stroke probands, including 1.2% novel PVs. Genetic diagnosis may enable early diagnosis, management and lifestyle modification. Among 161 familial stroke probands, 33 (20.5%) had been identified pathogenic or likely pathogenic monogenic variants related to stroke. The positive hit rate among all subtypes was high in intracerebral hemorrhage (ICH) and ischemic small vessel disease (SVD). Notably, two previously unreported variants, KRIT1 p.E379* in a familial cerebral cavernous malformation and F2 p.F382L in familial cerebral venous sinus thrombosis, were disclosed. CVT cerebral venous thrombosis; HTN Hypertensive subtype; LAA large artery atherosclerosis; SV structural vasculopathy; U Undetermined.
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Affiliation(s)
- Li-Hsin Chang
- Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Nai-Fang Chi
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chun-Yu Chen
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan
| | - Yung-Shuan Lin
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan
| | - Shao-Lun Hsu
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan
| | - Jui-Yao Tsai
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan
| | - Hui-Chi Huang
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan
| | - Chun-Jen Lin
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chih-Ping Chung
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chien-Yi Tung
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chung-Jiuan Jeng
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Anatomy and Cell Biology, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Chung Lee
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yo-Tsen Liu
- Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei, Taiwan. .,Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan. .,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan. .,Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - I-Hui Lee
- Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei, Taiwan. .,Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan. .,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan. .,Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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Athanasopoulou K, Daneva GN, Boti MA, Dimitroulis G, Adamopoulos PG, Scorilas A. The Transition from Cancer "omics" to "epi-omics" through Next- and Third-Generation Sequencing. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122010. [PMID: 36556377 PMCID: PMC9785810 DOI: 10.3390/life12122010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
Deciphering cancer etiopathogenesis has proven to be an especially challenging task since the mechanisms that drive tumor development and progression are far from simple. An astonishing amount of research has revealed a wide spectrum of defects, including genomic abnormalities, epigenomic alterations, disturbance of gene transcription, as well as post-translational protein modifications, which cooperatively promote carcinogenesis. These findings suggest that the adoption of a multidimensional approach can provide a much more precise and comprehensive picture of the tumor landscape, hence serving as a powerful tool in cancer research and precision oncology. The introduction of next- and third-generation sequencing technologies paved the way for the decoding of genetic information and the elucidation of cancer-related cellular compounds and mechanisms. In the present review, we discuss the current and emerging applications of both generations of sequencing technologies, also referred to as massive parallel sequencing (MPS), in the fields of cancer genomics, transcriptomics and proteomics, as well as in the progressing realms of epi-omics. Finally, we provide a brief insight into the expanding scope of sequencing applications in personalized cancer medicine and pharmacogenomics.
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Pitfalls of whole exome sequencing in undefined clinical conditions with a suspected genetic etiology. Genes Genomics 2022; 45:637-655. [PMID: 36454368 DOI: 10.1007/s13258-022-01341-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/26/2022] [Indexed: 12/03/2022]
Abstract
BACKGROUND Whole-Exome Sequencing (WES) is a valuable tool for the molecular diagnosis of patients with a suspected genetic condition. In complex and heterogeneous diseases, the interpretation of WES variants is more challenging given the absence of diagnostic handles and other reported cases with overlapping clinical presentations. OBJECTIVE To describe candidate variants emerging from trio-WES and possibly associated with the clinical phenotype in clinically heterogeneous conditions. METHODS We performed WES in ten patients from eight families, selected because of the lack of a clear clinical diagnosis or suspicion, the presence of multiple clinical signs, and the negative results of traditional genetic tests. RESULTS Although we identified ten candidate variants, reaching the diagnosis of these cases is challenging, given the complexity and the rarity of these syndromes and because affected genes are already associated with known genetic diseases only partially recapitulating patients' phenotypes. However, the identification of these variants could shed light into the definition of new genotype-phenotype correlations. Here, we describe the clinical and molecular data of these cases with the aim of favoring the match with other similar cases and, hopefully, confirm our diagnostic hypotheses. CONCLUSION This study emphasizes the major limitations associated with WES data interpretation, but also highlights its clinical utility in unraveling novel genotype-phenotype correlations in complex and heterogeneous undefined clinical conditions with a suspected genetic etiology.
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Huang M, Xu H. Genetic susceptibility to autoimmunity-Current status and challenges. Adv Immunol 2022; 156:25-54. [PMID: 36410874 DOI: 10.1016/bs.ai.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Autoimmune diseases (ADs) often arise from a combination of genetic and environmental triggers that disrupt the immune system's capability to properly tolerate body self-antigens. Familial studies provided the earliest insights into the risk loci of such diseases, while genome-wide association studies (GWAS) significantly broadened the horizons. A drug targeting a prominent pathological pathway can be applied to multiple indications sharing overlapping mechanisms. Advances in genomic technologies used in genetic studies provide critical insights into future research on gene-environment interactions in autoimmunity. This Review summarizes the history and recent advances in the understanding of genetic susceptibility to ADs and related immune disorders, including coronavirus disease 2019 (COVID-19), and their indications for the development of diagnostic or prognostic markers for translational applications.
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Affiliation(s)
| | - Huji Xu
- School of Medicine, Tsinghua University, Beijing, China; Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, The Navel Medical University, Shanghai, China; Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing, China.
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47
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Downey J, Lam JC, Li VO, Gozes I. Somatic Mutations and Alzheimer’s Disease. J Alzheimers Dis 2022; 90:475-493. [DOI: 10.3233/jad-220643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Alzheimer’s disease (AD) represents a global health challenge, with an estimated 55 million people suffering from the non-curable disease across the world. While amyloid-β plaques and tau neurofibrillary tangles in the brain define AD proteinopathy, it has become evident that diverse coding and non-coding regions of the genome may significantly contribute to AD neurodegeneration. The diversity of factors associated with AD pathogenesis, coupled with age-associated damage, suggests that a series of triggering events may be required to initiate AD. Since somatic mutations accumulate with aging, and aging is a major risk factor for AD, there is a great potential for somatic mutational events to drive disease. Indeed, recent data from the Gozes team/laboratories as well as other leading laboratories correlated the accumulation of somatic brain mutations with the progression of tauopathy. In this review, we lay the current perspectives on the principal genetic factors associated with AD and the potential causes, highlighting the contribution of somatic mutations to the pathogenesis of late onset Alzheimer’s disease. The roles that artificial intelligence and big data can play in accelerating the progress of causal somatic mutation markers/biomarkers identification, and the associated drug discovery/repurposing, have been highlighted for future AD and other neurodegenerative studies, with the aim to bring hope for the vulnerable aging population.
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Affiliation(s)
- Jocelyn Downey
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
| | - Jacqueline C.K. Lam
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
- Department of Computer Science and Technology, University of Cambridge, UK
| | - Victor O.K. Li
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
| | - Illana Gozes
- The Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Adams Super Center for Brain Studies and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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48
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Khoruddin NA, Lim WF, Teh LK, Noorizhab MNF, Mohd Yusof FZ, Salleh MZ. Toward precision nutrition: A cross‐sectional study on the genetic risks of nutrients deficiencies and eating behaviors among the Orang Asli and Malays. PRECISION MEDICAL SCIENCES 2022. [DOI: 10.1002/prm2.12081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Nurul Ain Khoruddin
- Integrative Pharmacogenomics Institute (iPROMISE) Universiti Teknologi MARA (UiTM) Selangor Bandar Puncak Alam Malaysia
- Faculty of Applied Sciences Universiti Teknologi MARA (UiTM) Selangor Shah Alam Malaysia
| | - Wai Feng Lim
- Integrative Pharmacogenomics Institute (iPROMISE) Universiti Teknologi MARA (UiTM) Selangor Bandar Puncak Alam Malaysia
| | - Lay Kek Teh
- Integrative Pharmacogenomics Institute (iPROMISE) Universiti Teknologi MARA (UiTM) Selangor Bandar Puncak Alam Malaysia
- Faculty of Pharmacy Universiti Teknologi MARA (UiTM) Selangor Bandar Puncak Alam Malaysia
| | - Mohd Nur Fakhruzzaman Noorizhab
- Integrative Pharmacogenomics Institute (iPROMISE) Universiti Teknologi MARA (UiTM) Selangor Bandar Puncak Alam Malaysia
- Faculty of Pharmacy Universiti Teknologi MARA (UiTM) Selangor Bandar Puncak Alam Malaysia
| | - Farida Zuraina Mohd Yusof
- Integrative Pharmacogenomics Institute (iPROMISE) Universiti Teknologi MARA (UiTM) Selangor Bandar Puncak Alam Malaysia
- Faculty of Applied Sciences Universiti Teknologi MARA (UiTM) Selangor Shah Alam Malaysia
| | - Mohd Zaki Salleh
- Integrative Pharmacogenomics Institute (iPROMISE) Universiti Teknologi MARA (UiTM) Selangor Bandar Puncak Alam Malaysia
- Faculty of Pharmacy Universiti Teknologi MARA (UiTM) Selangor Bandar Puncak Alam Malaysia
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Willcox MC, Burgueño JA, Jeffers D, Rodriguez-Chanona E, Guadarrama-Espinoza A, Kehel Z, Chepetla D, Shrestha R, Swarts K, Buckler ES, Hearne S, Chen C. Mining alleles for tar spot complex resistance from CIMMYT's maize Germplasm Bank. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.937200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The tar spot complex (TSC) is a devastating disease of maize (Zea mays L.), occurring in 17 countries throughout Central, South, and North America and the Caribbean, and can cause grain yield losses of up to 80%. As yield losses from the disease continue to intensify in Central America, Phyllachora maydis, one of the causal pathogens of TSC, was first detected in the United States in 2015, and in 2020 in Ontario, Canada. Both the distribution and yield losses due to TSC are increasing, and there is a critical need to identify the genetic resources for TSC resistance. The Seeds of Discovery Initiative at CIMMYT has sought to combine next-generation sequencing technologies and phenotypic characterization to identify valuable alleles held in the CIMMYT Germplasm Bank for use in germplasm improvement programs. Individual landrace accessions of the “Breeders' Core Collection” were crossed to CIMMYT hybrids to form 918 unique accessions topcrosses (F1 families) which were evaluated during 2011 and 2012 for TSC disease reaction. A total of 16 associated SNP variants were identified for TSC foliar leaf damage resistance and increased grain yield. These variants were confirmed by evaluating the TSC reaction of previously untested selections of the larger F1 testcross population (4,471 accessions) based on the presence of identified favorable SNPs. We demonstrated the usefulness of mining for donor alleles in Germplasm Bank accessions for newly emerging diseases using genomic variation in landraces.
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Panikker P, Roy S, Ghosh A, Poornachandra B, Ghosh A. Advancing precision medicines for ocular disorders: Diagnostic genomics to tailored therapies. Front Med (Lausanne) 2022; 9:906482. [PMID: 35911417 PMCID: PMC9334564 DOI: 10.3389/fmed.2022.906482] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/29/2022] [Indexed: 11/20/2022] Open
Abstract
Successful sequencing of the human genome and evolving functional knowledge of gene products has taken genomic medicine to the forefront, soon combining broadly with traditional diagnostics, therapeutics, and prognostics in patients. Recent years have witnessed an extraordinary leap in our understanding of ocular diseases and their respective genetic underpinnings. As we are entering the age of genomic medicine, rapid advances in genome sequencing, gene delivery, genome surgery, and computational genomics enable an ever-increasing capacity to provide a precise and robust diagnosis of diseases and the development of targeted treatment strategies. Inherited retinal diseases are a major source of blindness around the world where a large number of causative genes have been identified, paving the way for personalized diagnostics in the clinic. Developments in functional genetics and gene transfer techniques has also led to the first FDA approval of gene therapy for LCA, a childhood blindness. Many such retinal diseases are the focus of various clinical trials, making clinical diagnoses of retinal diseases, their underlying genetics and the studies of natural history important. Here, we review methodologies for identifying new genes and variants associated with various ocular disorders and the complexities associated with them. Thereafter we discuss briefly, various retinal diseases and the application of genomic technologies in their diagnosis. We also discuss the strategies, challenges, and potential of gene therapy for the treatment of inherited and acquired retinal diseases. Additionally, we discuss the translational aspects of gene therapy, the important vector types and considerations for human trials that may help advance personalized therapeutics in ophthalmology. Retinal disease research has led the application of precision diagnostics and precision therapies; therefore, this review provides a general understanding of the current status of precision medicine in ophthalmology.
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Affiliation(s)
| | - Shomereeta Roy
- Grow Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
| | - Anuprita Ghosh
- Grow Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
| | | | - Arkasubhra Ghosh
- Grow Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
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