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Network assisted analysis of de novo variants using protein-protein interaction information identified 46 candidate genes for congenital heart disease. PLoS Genet 2022; 18:e1010252. [PMID: 35671298 PMCID: PMC9205499 DOI: 10.1371/journal.pgen.1010252] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 06/17/2022] [Accepted: 05/12/2022] [Indexed: 11/19/2022] Open
Abstract
De novo variants (DNVs) with deleterious effects have proved informative in identifying risk genes for early-onset diseases such as congenital heart disease (CHD). A number of statistical methods have been proposed for family-based studies or case/control studies to identify risk genes by screening genes with more DNVs than expected by chance in Whole Exome Sequencing (WES) studies. However, the statistical power is still limited for cohorts with thousands of subjects. Under the hypothesis that connected genes in protein-protein interaction (PPI) networks are more likely to share similar disease association status, we developed a Markov Random Field model that can leverage information from publicly available PPI databases to increase power in identifying risk genes. We identified 46 candidate genes with at least 1 DNV in the CHD study cohort, including 18 known human CHD genes and 35 highly expressed genes in mouse developing heart. Our results may shed new insight on the shared protein functionality among risk genes for CHD. The topologic information in a pathway may be informative to identify functionally interrelated genes and help improve statistical power in DNV studies. Under the hypothesis that connected genes in PPI networks are more likely to share similar disease association status, we developed a novel statistical model that can leverage information from publicly available PPI databases. Through simulation studies under multiple settings, we proved our method can increase statistical power in identifying additional risk genes compared to methods without using the PPI network information. We then applied our method to a real example for CHD DNV data, and then visualized the subnetwork of candidate genes to find potential functional gene clusters for CHD.
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52
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Sant' Ana I, Torrini R, Alves Coelho MC, Cantoni J, Madeira M, Ribeiro M. X-linked hypophosphatemic rickets: Description of seven new variants in patients followed up in reference hospitals in Rio de Janeiro. Mol Genet Genomic Med 2022; 10:e1941. [PMID: 35384411 PMCID: PMC9184672 DOI: 10.1002/mgg3.1941] [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: 08/05/2021] [Revised: 03/20/2022] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
Background X‐linked hypophosphatemic rickets (XLHR) is a rare genetic disease, often delayed in diagnosis due to the low degree of suspicion and limited access to sophisticated diagnostic tools that confirm the diagnosis, such as genetic testing. Methods Through a cross‐sectional and observational study, 26 patients with a previously presumptive diagnosis of X‐linked hypophosphatemic rickets (based on clinical history, laboratory findings, and physical examination), were followed for approximately 12 months. During 12 months of follow‐up, only 16 patients underwent genetic testing and enrolled in the study. Previous data were analyzed, such as clinical history (e.g., gender, current age, age of clinical diagnosis, age of admission to hospital, family history, and previous orthopedic surgery), physical exam, imaging tests (e.g., radiological changes) and laboratory tests (e.g., tubular maximum reabsorption rate of phosphate to glomerular filtration rate, alkaline phosphatase, and phosphate levels) at the time of the patient’s admission to IEDE and UFRJ, to corroborate and substantiate our research. These data were extracted from the medical records of the patients. Results Among the 16 patients analyzed by molecular biology techniques, the new generation sequencing (NGS), using DNA samples from oral swabs, we obtained seven variants never previously described, which were verified by Sanger sequencing. Among the seven variants never previously described, the most common coding impact was the nonsense mutation. We found two frameshift, one intronic splicing variant, three nonsense, and one deletion splice junction loss. Among patients with new mutations who presented data in the medical record, 100% showed a reduction in TmP/GFR (average of 1.98 mg/dl), the most sensitive laboratory parameter at the time of diagnosis, as well as serum phosphorus (100% had hypophosphatemia on arrival at the referral hospitals––average of 2.4 mg/dl and median 2.3 mg/dl). We also performed NGS on three mothers of the patients with identified mutations. Among these mothers, only one tested negative for the mutation and no family history was reported as well. This mother had serum phosphate of 3.5 mg/dl (normal range: 2.5–4.5 mg/dl) at the time of genetic test collection. The others had a positive test, low serum phosphorus at the time of the molecular test, in addition to a positive family history. Conclusion This study describes seven new variants in the PHEX gene and aims to increase the knowledge of the scientific community about the types of mutations involving this gene, increasing information on the genetic basis of this condition, enabling future considerations about genotype–phenotype correlation, in addition to diagnosis accurate and early.
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Affiliation(s)
- Iara Sant' Ana
- Instituto Estadual de Diabetes e Endocrinologia Luiz Capriglione (IEDE), Rio de Janeiro, Brazil.,Endocrinology Division, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Renato Torrini
- Instituto Estadual de Diabetes e Endocrinologia Luiz Capriglione (IEDE), Rio de Janeiro, Brazil
| | | | - Joyce Cantoni
- Instituto Estadual de Diabetes e Endocrinologia Luiz Capriglione (IEDE), Rio de Janeiro, Brazil
| | - Miguel Madeira
- Endocrinology Division, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Márcia Ribeiro
- Medical Genetic Service, Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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53
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Amaral MD. Precision medicine for rare diseases: The times they are A-Changin'. Curr Opin Pharmacol 2022; 63:102201. [DOI: 10.1016/j.coph.2022.102201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 12/30/2022]
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Qiuju H, Jianlong Z, Qi W, Zhifa L, Ding W, Xiaofang S, Yingjun X. Epilepsy Combined With Multiple Gene Heterozygous Mutation. Front Pediatr 2022; 10:763642. [PMID: 35299674 PMCID: PMC8921529 DOI: 10.3389/fped.2022.763642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 01/26/2022] [Indexed: 11/16/2022] Open
Abstract
The fast pace of gene discovery has resulted in groundbreaking advances in the field of epilepsy genetics. Clinical testing using comprehensive gene panels, exomes, or genomes is now increasingly available and has significantly increased the diagnostic yield for early-onset epilepsies and enabled precision medicine approaches. In this paper, we report a case of epilepsy in a pedigree. The proband had heterozygous mutations in KCNC1 (NM_001112741.1:c.959G>A, p. Arg320His), CAPN3 (NM_000070.2:c.526G>A, p. Val176Met), and NEFH (NM_021076.3:c. 2595 delC, p. Lys866Argfs*51). Sanger sequencing verification was consistent with the results of whole-exome sequencing. The KCNC1 mutation was a de novo mutation, and the CAPN3 and NEFH mutations were inherited from their father and mother, respectively. Based on the American College of Medical Genetics and Genomics (ACMG) guidelines, a heterozygous mutation was found for APOB (NM_000384.2: c.10579C > T, p. Arg3527Trp). The heterozygous mutation at this site was inherent in the pedigree. Coexpression analysis indicated that heterozygous mutations of KCNC1, CAPN3, NEFH, and APOB were closely related to the clinical phenotypes of the patient, and the clinical phenotypic heterogeneity of the disease may be the result of the interaction of multiple genes.
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Affiliation(s)
- He Qiuju
- Department of Obstetrics and Gynaecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Zhuang Jianlong
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, China
| | - Wen Qi
- Department of Obstetrics and Gynaecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Li Zhifa
- Gastrointestinal Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wang Ding
- Department of Obstetrics and Gynaecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Sun Xiaofang
- Department of Obstetrics and Gynaecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xie Yingjun
- Department of Obstetrics and Gynaecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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Anzar I, Sverchkova A, Samarakoon P, Ellingsen EB, Gaudernack G, Stratford R, Clancy T. Personalized
HLA
typing leads to the discovery of novel
HLA
alleles and tumor‐specific
HLA
variants. HLA 2022; 99:313-327. [PMID: 35073457 PMCID: PMC9546058 DOI: 10.1111/tan.14562] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/08/2022] [Accepted: 01/21/2022] [Indexed: 11/29/2022]
Abstract
Accurate and full‐length typing of the HLA region is important in many clinical and research settings. With the advent of next generation sequencing (NGS), several HLA typing algorithms have been developed, including many that are applicable to whole exome sequencing (WES). However, most of these solutions operate by providing the closest‐matched HLA allele among the known alleles in IPD‐IMGT/HLA Database. These database‐matching approaches have demonstrated very high performance when typing well characterized HLA alleles. However, as they rely on the completeness of the HLA database, they are not optimal for detecting novel or less well characterized alleles. Furthermore, the database‐matching approaches are also not adequate in the context of cancer, where a comprehensive characterization of somatic HLA variation and expression patterns of a tumor's HLA locus may guide therapy and clinical outcome, because of the pivotal role HLA alleles play in tumor antigen recognition and immune escape. Here, we describe a personalized HLA typing approach applied to WES data that leverages the strengths of database‐matching approaches while simultaneously allowing for the discovery of novel HLA alleles and tumor‐specific HLA variants, through the systematic integration of germline and somatic variant calling. We applied this approach on WES from 10 metastatic melanoma patients and validated the HLA typing results using HLA targeted NGS sequencing from patients where at least one HLA germline candidate was detected on Class I HLA. Targeted NGS sequencing confirmed 100% performance for the 1st and 2nd fields. In total, five out of the six detected HLA germline variants were because of Class I ambiguities at the third or fourth fields, and their detection recovered the correct HLA allele genotype. The sixth germline variant let to the formal discovery of a novel Class I allele. Finally, we demonstrated a substantially improved somatic variant detection accuracy in HLA alleles with a 91% of success rate in simulated experiments. The approach described here may allow the field to genotype more accurately using WES data, leading to the discovery of novel HLA alleles and help characterize the relationship between somatic variation in the HLA region and immunosurveillance.
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Affiliation(s)
- Irantzu Anzar
- NEC OncoImmunity AS, Oslo Cancer Cluster, Ullernchausseen 64/66, 0379 Oslo Norway
| | - Angelina Sverchkova
- NEC OncoImmunity AS, Oslo Cancer Cluster, Ullernchausseen 64/66, 0379 Oslo Norway
| | - Pubudu Samarakoon
- NEC OncoImmunity AS, Oslo Cancer Cluster, Ullernchausseen 64/66, 0379 Oslo Norway
| | | | - Gustav Gaudernack
- Ultimovacs ASA, Oslo Cancer Cluster, Ullernchausseen 64/66 Oslo Norway
| | - Richard Stratford
- NEC OncoImmunity AS, Oslo Cancer Cluster, Ullernchausseen 64/66, 0379 Oslo Norway
| | - Trevor Clancy
- NEC OncoImmunity AS, Oslo Cancer Cluster, Ullernchausseen 64/66, 0379 Oslo Norway
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Wang D, Li J, Wang Y, Wang E. A comparison on predicting functional impact of genomic variants. NAR Genom Bioinform 2022; 4:lqab122. [PMID: 35047814 PMCID: PMC8759571 DOI: 10.1093/nargab/lqab122] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/13/2021] [Accepted: 12/20/2021] [Indexed: 12/23/2022] Open
Abstract
Single-nucleotide polymorphism (SNPs) may cause the diverse functional impact on RNA or protein changing genotype and phenotype, which may lead to common or complex diseases like cancers. Accurate prediction of the functional impact of SNPs is crucial to discover the ‘influential’ (deleterious, pathogenic, disease-causing, and predisposing) variants from massive background polymorphisms in the human genome. Increasing computational methods have been developed to predict the functional impact of variants. However, predictive performances of these computational methods on massive genomic variants are still unclear. In this regard, we systematically evaluated 14 important computational methods including specific methods for one type of variant and general methods for multiple types of variants from several aspects; none of these methods achieved excellent (AUC ≥ 0.9) performance in both data sets. CADD and REVEL achieved excellent performance on multiple types of variants and missense variants, respectively. This comparison aims to assist researchers and clinicians to select appropriate methods or develop better predictive methods.
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Affiliation(s)
- Dong Wang
- School of Computer Science and Technology, Harbin Institute of Technology Harbin, Harbin, Heilongjiang, 150001,China
| | - Jie Li
- To whom correspondence should be addressed. Tel: +86 0451 86413309;
| | - Yadong Wang
- Correspondence may also be addressed to Yadong Wang. Tel: +86 0451 86413309;
| | - Edwin Wang
- Department of Medical Genetics, University of Calgary, Calgary, HSC 1185, Canada
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Analysis of 5-Azacytidine Resistance Models Reveals a Set of Targetable Pathways. Cells 2022; 11:cells11020223. [PMID: 35053339 PMCID: PMC8774143 DOI: 10.3390/cells11020223] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 01/27/2023] Open
Abstract
The mechanisms by which myelodysplastic syndrome (MDS) cells resist the effects of hypomethylating agents (HMA) are currently the subject of intensive research. A better understanding of mechanisms by which the MDS cell becomes to tolerate HMA and progresses to acute myeloid leukemia (AML) requires the development of new cellular models. From MDS/AML cell lines we developed a model of 5-azacytidine (AZA) resistance whose stability was validated by a transplantation approach into immunocompromised mice. When investigating mRNA expression and DNA variants of the AZA resistant phenotype we observed deregulation of several cancer-related pathways including the phosphatidylinosito-3 kinase signaling. We have further shown that these pathways can be modulated by specific inhibitors that, while blocking the proliferation of AZA resistant cells, are unable to increase their sensitivity to AZA. Our data reveal a set of molecular mechanisms that can be targeted to expand therapeutic options during progression on AZA therapy.
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58
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Hussen BM, Abdullah ST, Salihi A, Sabir DK, Sidiq KR, Rasul MF, Hidayat HJ, Ghafouri-Fard S, Taheri M, Jamali E. The emerging roles of NGS in clinical oncology and personalized medicine. Pathol Res Pract 2022; 230:153760. [PMID: 35033746 DOI: 10.1016/j.prp.2022.153760] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/29/2021] [Accepted: 01/06/2022] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) has been increasingly popular in genomics studies over the last decade, as new sequencing technology has been created and improved. Recently, NGS started to be used in clinical oncology to improve cancer therapy through diverse modalities ranging from finding novel and rare cancer mutations, discovering cancer mutation carriers to reaching specific therapeutic approaches known as personalized medicine (PM). PM has the potential to minimize medical expenses by shifting the current traditional medical approach of treating cancer and other diseases to an individualized preventive and predictive approach. Currently, NGS can speed up in the early diagnosis of diseases and discover pharmacogenetic markers that help in personalizing therapies. Despite the tremendous growth in our understanding of genetics, NGS holds the added advantage of providing more comprehensive picture of cancer landscape and uncovering cancer development pathways. In this review, we provided a complete overview of potential NGS applications in scientific and clinical oncology, with a particular emphasis on pharmacogenomics in the direction of precision medicine treatment options.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq; Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq
| | - Sara Tharwat Abdullah
- Department of Pharmacology and Toxicology, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | - Abbas Salihi
- Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq; Department of Biology, College of Science, Salahaddin University, Kurdistan Region, Erbil, Iraq
| | - Dana Khdr Sabir
- Department of Medical Laboratory Sciences, Charmo University, Kurdistan Region, Iraq
| | - Karzan R Sidiq
- Department of Biology, College of Education, University of Sulaimani, Sulaimani 334, Kurdistan, Iraq
| | - Mohammed Fatih Rasul
- Department of Medical Analysis, Faculty of Applied Science, Tishk International University, Kurdistan Region, Erbil, Iraq
| | - Hazha Jamal Hidayat
- Department of Biology, College of Education, Salahaddin University, Kurdistan Region, Erbil, Iraq
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Elena Jamali
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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59
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Identification of Copy Number Alterations from Next-Generation Sequencing Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1361:55-74. [DOI: 10.1007/978-3-030-91836-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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60
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Du X, DeForest N, Majithia AR. Human Genetics to Identify Therapeutic Targets for NAFLD: Challenges and Opportunities. Front Endocrinol (Lausanne) 2021; 12:777075. [PMID: 34950105 PMCID: PMC8688763 DOI: 10.3389/fendo.2021.777075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/23/2021] [Indexed: 12/15/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a continuous progression of pathophysiologic stages that is challenging to diagnose due to its inherent heterogeneity and poor standardization across a wide variety of diagnostic measures. NAFLD is heritable, and several loci have been robustly associated with various stages of disease. In the past few years, larger genetic association studies using new methodology have identified novel genes associated with NAFLD, some of which have shown therapeutic promise. This mini-review provides an overview of the heterogeneity in NAFLD phenotypes and diagnostic methods, discusses genetic associations in relation to the specific stages for which they were identified, and offers a perspective on the design of future genetic mapping studies to accelerate therapeutic target identification.
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Affiliation(s)
- Xiaomi Du
- Division of Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA, United States
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, United States
| | - Natalie DeForest
- Division of Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA, United States
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, United States
| | - Amit R. Majithia
- Division of Endocrinology, Department of Medicine, University of California San Diego, La Jolla, CA, United States
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61
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Morgan M, Kumar L, Li Y, Baptissart M. Post-transcriptional regulation in spermatogenesis: all RNA pathways lead to healthy sperm. Cell Mol Life Sci 2021; 78:8049-8071. [PMID: 34748024 DOI: 10.1007/s00018-021-04012-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/11/2021] [Accepted: 10/25/2021] [Indexed: 01/22/2023]
Abstract
Multiple RNA pathways are required to produce functional sperm. Here, we review RNA post-transcriptional regulation during spermatogenesis with particular emphasis on the role of 3' end modifications. From early studies in the 1970s, it became clear that spermiogenesis transcripts could be stored for days only to be translated at advanced stages of spermatid differentiation. The transition between the translationally repressed and active states was observed to correlate with the shortening of the transcripts' poly(A) tail, establishing a link between RNA 3' end metabolism and male germ cell differentiation. Since then, numerous RNA metabolic pathways have been implicated not only in the progression through spermatogenesis, but also in the maintenance of genomic integrity. Recent studies have characterized the elusive 3' biogenesis of Piwi-interacting RNAs (piRNAs), identified a critical role for messenger RNA (mRNA) 3' uridylation in meiotic progression, established the mechanisms that destabilize transcripts with long 3' untranslated regions (3'UTRs) in post-mitotic cells, and defined the physiological relevance of RNA exonucleases and deadenylases in male germ cells. In this review, we discuss RNA processing in the male germline in the light of the most recent findings. A brief recollection of different RNA-processing events will aid future studies exploring post-transcriptional regulation in spermatogenesis.
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Affiliation(s)
- Marcos Morgan
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA.
| | - Lokesh Kumar
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
| | - Yin Li
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
| | - Marine Baptissart
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
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62
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Xie Y, Li M, Dong W, Jiang W, Zhao H. M-DATA: A statistical approach to jointly analyzing de novo mutations for multiple traits. PLoS Genet 2021; 17:e1009849. [PMID: 34735430 PMCID: PMC8568192 DOI: 10.1371/journal.pgen.1009849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/29/2021] [Indexed: 11/22/2022] Open
Abstract
Recent studies have demonstrated that multiple early-onset diseases have shared risk genes, based on findings from de novo mutations (DNMs). Therefore, we may leverage information from one trait to improve statistical power to identify genes for another trait. However, there are few methods that can jointly analyze DNMs from multiple traits. In this study, we develop a framework called M-DATA (Multi-trait framework for De novo mutation Association Test with Annotations) to increase the statistical power of association analysis by integrating data from multiple correlated traits and their functional annotations. Using the number of DNMs from multiple diseases, we develop a method based on an Expectation-Maximization algorithm to both infer the degree of association between two diseases as well as to estimate the gene association probability for each disease. We apply our method to a case study of jointly analyzing data from congenital heart disease (CHD) and autism. Our method was able to identify 23 genes for CHD from joint analysis, including 12 novel genes, which is substantially more than single-trait analysis, leading to novel insights into CHD disease etiology.
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Affiliation(s)
- Yuhan Xie
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Mo Li
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Weilai Dong
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Wei Jiang
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
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63
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Yu S, Chen WX, Zhang YF, Ni Y, Lu P, Wang B, Wang Y, Wu B, Ni Q, Wang H, Xu ZM. Apparent homozygosity for a novel splicing variant in EPS8 causes congenital profound hearing loss. Eur J Med Genet 2021; 64:104362. [PMID: 34637946 DOI: 10.1016/j.ejmg.2021.104362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 08/17/2021] [Accepted: 10/08/2021] [Indexed: 12/27/2022]
Abstract
Autosomal recessive deafness-102 (DFNB102), a new profound prelingual non-syndromic hearing loss, is caused by mutations in the EPS8 gene. To date, only three such consanguineous families with three different homozygous variants in EPS8 have been reported. Here, we report the fourth case from a non-consanguineous Chinese family, an 11-month-old male infant presented with congenital profound non-syndromic hearing loss. Trio whole-exome sequencing initially identified the patient with a novel seemingly homozygous splicing variant NM_004447.5: c.1435-2A > T in intron 14 of the EPS8 gene and was inherited from his father; further CNVs analysis identified a novel 65.9 kb intragenic deletion and was inherited from his mother. The deletion is covering intron 14 that could account for the apparent homozygosity of the patient. In vitro splicing assay showed the variant c.1435-2A > T creates a new donor site at position c.1443, which is predicted to produce a stop codon after 14 additional amino acids (p.His479Cysfs*14). Furthermore, quantitative allele-specific expression assay showed that relative EPS8 gene expression in the patient significantly decreased (0-fold for the wild-type transcript and 0.25-0.27-fold for the mutant transcript) compared to the control (P < 0.05), indicating the pathogenicity of the identified variants. Overall, our study provides additional evidence that EPS8 is a causative gene for DFNB102 and highlights the clinical utility of simultaneous analysis of CNVs and SNVs to avoid potential errors in the diagnosis and interpretation of patients with apparent homozygosity.
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Affiliation(s)
- Sha Yu
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Wen-Xia Chen
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yun-Fei Zhang
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yihua Ni
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Ping Lu
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bin Wang
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yan Wang
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Qi Ni
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Huijun Wang
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.
| | - Zheng-Min Xu
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.
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Vorsteveld EE, Hoischen A, van der Made CI. Next-Generation Sequencing in the Field of Primary Immunodeficiencies: Current Yield, Challenges, and Future Perspectives. Clin Rev Allergy Immunol 2021; 61:212-225. [PMID: 33666867 PMCID: PMC7934351 DOI: 10.1007/s12016-021-08838-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2021] [Indexed: 12/18/2022]
Abstract
Primary immunodeficiencies comprise a group of inborn errors of immunity that display significant clinical and genetic heterogeneity. Next-generation sequencing techniques and predominantly whole exome sequencing have revolutionized the understanding of the genetic and molecular basis of genetic diseases, thereby also leading to a sharp increase in the discovery of new genes associated with primary immunodeficiencies. In this review, we discuss the current diagnostic yield of this generic diagnostic approach by evaluating the studies that have employed next-generation sequencing techniques in cohorts of patients with primary immunodeficiencies. The average diagnostic yield for primary immunodeficiencies is determined to be 29% (range 10-79%) and 38% specifically for whole-exome sequencing (range 15-70%). The significant variation between studies is mainly the result of differences in clinical characteristics of the studied cohorts but is also influenced by varying sequencing approaches and (in silico) gene panel selection. We further discuss other factors contributing to the relatively low yield, including the inherent limitations of whole-exome sequencing, challenges in the interpretation of novel candidate genetic variants, and promises of exploring the non-coding part of the genome. We propose strategies to improve the diagnostic yield leading the way towards expanded personalized treatment in PIDs.
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Affiliation(s)
- Emil E Vorsteveld
- Department of Human Genetics, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases (RCI), Radboudumc, Nijmegen, The Netherlands.
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Caspar I van der Made
- Department of Human Genetics, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases (RCI), Radboudumc, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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65
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Peng Y, Yang S, Huang X, Pang J, Liu J, Hu J, Shen X, Tang C, Wang H. Whole Exome Sequencing Analysis in Fetal Skeletal Dysplasia Detected by Ultrasonography: An Analysis of 38 Cases. Front Genet 2021; 12:728544. [PMID: 34567078 PMCID: PMC8461062 DOI: 10.3389/fgene.2021.728544] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/05/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Skeletal dysplasias (SDs) are a heterogeneous group of genetic disorders that primarily affect bone and cartilage. This study aims to identify the genetic causes for fetal SDs, and evaluates the diagnostic yield of prenatal whole-exome sequencing (WES) for this disorder. Methods: WES was performed on 38 fetuses with sonographically identified SDs and normal results of karyotype and single nucleotide polymorphism (SNP) analysis. Candidate variants were selected by bioinformatics analysis, and verified by Sanger sequencing. Results: WES revealed pathogenic or likely pathogenic variants associated with SDs in 65.79% (25/38) of fetuses, variants of uncertain significance (VUS) in SDs-related genes in 10.53% (4/38) cases, and incidental findings in 31.58% (12/38) fetuses. The SDs-associated variants identified in the present study affected 10 genes, and 35.71% (10/28) of the variants were novel. Conclusion: WES has a high diagnostic rate for prenatal SDs, which improves pregnancy management, prenatal counseling and recurrence risk assessment for future pregnancies. The newly identified variants expanded mutation spectrum of this disorder.
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Affiliation(s)
- Ying Peng
- Prenatal Diagnosis Center, National Health Commission Key Laboratory of Birth Defects Research, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Shuting Yang
- Prenatal Diagnosis Center, National Health Commission Key Laboratory of Birth Defects Research, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Xiaoliang Huang
- Prenatal Diagnosis Center, National Health Commission Key Laboratory of Birth Defects Research, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Jialun Pang
- Prenatal Diagnosis Center, National Health Commission Key Laboratory of Birth Defects Research, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Jing Liu
- Prenatal Diagnosis Center, National Health Commission Key Laboratory of Birth Defects Research, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Jiancheng Hu
- Prenatal Diagnosis Center, National Health Commission Key Laboratory of Birth Defects Research, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | | | - Chengyuan Tang
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Hua Wang
- Prenatal Diagnosis Center, National Health Commission Key Laboratory of Birth Defects Research, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
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66
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Pattan V, Kashyap R, Bansal V, Candula N, Koritala T, Surani S. Genomics in medicine: A new era in medicine. World J Methodol 2021; 11:231-242. [PMID: 34631481 PMCID: PMC8472545 DOI: 10.5662/wjm.v11.i5.231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 06/18/2021] [Accepted: 07/19/2021] [Indexed: 02/06/2023] Open
Abstract
The sequencing of complete human genome revolutionized the genomic medicine. However, the complex interplay of gene-environment-lifestyle and influence of non-coding genomic regions on human health remain largely unexplored. Genomic medicine has great potential for diagnoses or disease prediction, disease prevention and, targeted treatment. However, many of the promising tools of genomic medicine are still in their infancy and their application may be limited because of the limited knowledge we have that precludes its use in many clinical settings. In this review article, we have reviewed the evolution of genomic methodologies/tools, their limitations, and scope, for current and future clinical application.
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Affiliation(s)
- Vishwanath Pattan
- Division of Endocrinology, Wyoming Medical Center, Casper, WY 82601, United States
| | - Rahul Kashyap
- Department of Anesthesiology and Peri-operative Medicine, Mayo Clinic, Rochester, MN 55905, United States
| | - Vikas Bansal
- Department of Anesthesiology and Peri-operative Medicine, Mayo Clinic, Rochester, MN 55905, United States
| | - Narsimha Candula
- Hospital Medicine, University Florida Health, Jacksonville, FL 32209, United States
| | - Thoyaja Koritala
- Hospital Medicine, Mayo Clinic Health System, Mankato, MN 56001, United States
| | - Salim Surani
- Department of Internal Medicine, Texas A&M University, Corpus Christi, TX 78405, United States
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67
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Nair SV, Madhulaxmi, Thomas G, Ankathil R. Next-Generation Sequencing in Cancer. J Maxillofac Oral Surg 2021; 20:340-344. [PMID: 34408360 DOI: 10.1007/s12663-020-01462-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 09/28/2020] [Indexed: 11/28/2022] Open
Abstract
Objective In this article, we provide a gestalt idea about NGS technologies and their applications in cancer research and molecular diagnosis. Background Next-generation sequencing (NGS) advancements like DNA sequencing and RNA sequencing allow uncovering of genomic, transcriptomic, and epigenomic scenes of individual malignant growths. An assortment of genomic abnormalities can be screened at the same time, for example common and uncommon variations, auxiliary variations like insertions and deletions, copy-number variation, and fusion transcripts. Conclusion NGS innovations together with bioinformatics investigation, which extend our insight, are progressively used to analyze multiple genes in a cost-effective way and have been applied in examining clinical cancer samples and offering NGS-based molecular diagnosis. Application NGS is progressively significant as a device for the diagnosis of cancers.
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Affiliation(s)
- S Vinod Nair
- Department of Oral and Maxillofacial Surgery, P.M.S Dental College, Vattapara, Trivandrum, India
| | - Madhulaxmi
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College, Chennai, India
| | - Gigi Thomas
- Community Medicine, Regional Cancer Centre, Trivandrum, India
| | - Ravindran Ankathil
- Human Genome Centre, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, George Town, Malaysia
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68
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Gutman T, Goren G, Efroni O, Tuller T. Estimating the predictive power of silent mutations on cancer classification and prognosis. NPJ Genom Med 2021; 6:67. [PMID: 34385450 PMCID: PMC8361094 DOI: 10.1038/s41525-021-00229-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/24/2021] [Indexed: 02/07/2023] Open
Abstract
In recent years it has been shown that silent mutations, in and out of the coding region, can affect gene expression and may be related to tumorigenesis and cancer cell fitness. However, the predictive ability of these mutations for cancer type diagnosis and prognosis has not been evaluated yet. In the current study, based on the analysis of 9,915 cancer genomes and approximately three million mutations, we provide a comprehensive quantitative evaluation of the predictive power of various types of silent and non-silent mutations over cancer classification and prognosis. The results indicate that silent-mutation models outperform the equivalent null models in classifying all examined cancer types and in estimating the probability of survival 10 years after the initial diagnosis. Additionally, combining both non-silent and silent mutations achieved the best classification results for 68% of the cancer types and the best survival estimation results for up to nine years after the diagnosis. Thus, silent mutations hold considerable predictive power over both cancer classification and prognosis, most likely due to their effect on gene expression. It is highly advised that silent mutations are integrated in cancer research in order to unravel the full genomic landscape of cancer and its ramifications on cancer fitness.
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Affiliation(s)
- Tal Gutman
- Department of Biomedical Engineering, the Engineering Faculty, Tel Aviv University, Tel-Aviv, Israel
| | - Guy Goren
- Department of Electrical Engineering, the Engineering Faculty, Tel Aviv University, Tel-Aviv, Israel
| | - Omri Efroni
- Department of Electrical Engineering, the Engineering Faculty, Tel Aviv University, Tel-Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, the Engineering Faculty, Tel Aviv University, Tel-Aviv, Israel.
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AshaRani PV, Amron S, Zainuldin NAB, Tohari S, Ng AYJ, Song G, Venkatesh B, Mathuru AS. Whole-Exome Sequencing to Identify Potential Genetic Risk in Substance Use Disorders: A Pilot Feasibility Study. J Clin Med 2021; 10:jcm10132810. [PMID: 34202351 PMCID: PMC8269170 DOI: 10.3390/jcm10132810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/15/2021] [Accepted: 06/22/2021] [Indexed: 01/11/2023] Open
Abstract
Genetics intersects with environmental, cultural, and social factors in the development of addictive disorders. This study reports the feasibility of whole-exome sequencing of trios (subject and two family members) to discover potential genetic variants in the development of substance use disorders (SUD). Family trios were recruited from the National Addictions Management Service in Singapore during the 2016–2018 period. Recruited subjects had severe alcohol use disorder (AUD) or opioid use disorder (OUD), with nicotine dependence (ND) and a family history of addictive disorders. Demographic characteristics and severity of addiction were captured. Whole-exome sequencing (WES) and analysis were performed on salivary samples collected from the trios. WES revealed variants in several genes in each individual and disruptive protein mutations in most. Variants were identified in genes previously associated with SUDs, such as Pleckstrin homology domain-containing family M member 3 (PLEKHM3), coiled-coil serine-rich protein 1 (CCSER1), LIM and calponin homology domains-containing protein 1 (LIMCH1), dynein axonemal heavy chain 8 (DNAH8), and the taste receptor type 2 member 38 (TAS2R38) involved in the perception of bitterness. The feasibility study suggests that subjects with a severe addiction profile, polysubstance use, and family history of addiction may often harbor gene variants that may predispose them to SUDs. This study could serve as a model for future precision medicine-based personalized interventional strategies for behavioral addictions and SUDs and for the discovery of potentially pathogenic genetic variants.
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Affiliation(s)
- P. V. AshaRani
- Research Division, Institute of Mental Health, Singapore 539747, Singapore;
| | - Syidda Amron
- National Addictions Management Service, Institute of Mental Health, Singapore 539747, Singapore; (S.A.); (N.A.B.Z.); (G.S.)
| | - Noor Azizah Bte Zainuldin
- National Addictions Management Service, Institute of Mental Health, Singapore 539747, Singapore; (S.A.); (N.A.B.Z.); (G.S.)
| | - Sumanty Tohari
- Institute of Molecular and Cell Biology, Singapore 138673, Singapore; (S.T.); (A.Y.J.N.)
| | - Alvin Y. J. Ng
- Institute of Molecular and Cell Biology, Singapore 138673, Singapore; (S.T.); (A.Y.J.N.)
| | - Guo Song
- National Addictions Management Service, Institute of Mental Health, Singapore 539747, Singapore; (S.A.); (N.A.B.Z.); (G.S.)
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, Singapore 138673, Singapore; (S.T.); (A.Y.J.N.)
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Correspondence: (B.V.); (A.S.M.)
| | - Ajay S. Mathuru
- Institute of Molecular and Cell Biology, Singapore 138673, Singapore; (S.T.); (A.Y.J.N.)
- Yale-NUS College, Singapore 138610, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- Correspondence: (B.V.); (A.S.M.)
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Han Q, Yang Y, Wu S, Liao Y, Zhang S, Liang H, Cram DS, Zhang Y. Cruxome: a powerful tool for annotating, interpreting and reporting genetic variants. BMC Genomics 2021; 22:407. [PMID: 34082700 PMCID: PMC8173893 DOI: 10.1186/s12864-021-07728-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/20/2021] [Indexed: 01/23/2023] Open
Abstract
Background Next-generation sequencing (NGS) is an efficient tool used for identifying pathogenic variants that cause Mendelian disorders. However, the lack of bioinformatics training of researchers makes the interpretation of identified variants a challenge in terms of precision and efficiency. In addition, the non-standardized phenotypic description of human diseases also makes it difficult to establish an integrated analysis pathway for variant annotation and interpretation. Solutions to these bottlenecks are urgently needed. Results We develop a tool named “Cruxome” to automatically annotate and interpret single nucleotide variants (SNVs) and small insertions and deletions (InDels). Our approach greatly simplifies the current burdensome task of clinical geneticists and scientists to identify the causative pathogenic variants and build personal knowledge reference bases. The integrated architecture of Cruxome offers key advantages such as an interactive and user-friendly interface and the assimilation of electronic health records of the patient. By combining a natural language processing algorithm, Cruxome can efficiently process the clinical description of diseases to HPO standardized vocabularies. By using machine learning, in silico predictive algorithms, integrated multiple databases and supplementary tools, Cruxome can automatically process SNVs and InDels variants (trio-family or proband-only cases) and clinical diagnosis records, then annotate, score, identify and interpret pathogenic variants to finally generate a standardized clinical report following American College of Medical Genetics and Genomics/ Association for Molecular Pathology (ACMG/AMP) guidelines. Cruxome also provides supplementary tools to examine and visualize the genes or variations in historical cases, which can help to better understand the genetic basis of the disease. Conclusions Cruxome is an efficient tool for annotation and interpretation of variations and dramatically reduces the workload for clinical geneticists and researchers to interpret NGS results, simplifying their decision-making processes. We present an online version of Cruxome, which is freely available to academics and clinical researchers. The site is accessible at http://114.251.61.49:10024/cruxome/. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07728-6.
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Affiliation(s)
- Qingmei Han
- Berry Genomics Company Limited, Building 5, Courtyard 4, Shengmingyuan Road, ZGC Life Science Park, Changping District, 102200, Beijing, China
| | - Ying Yang
- Xian Children's Hospital, 710003, Xian, China
| | - Shengyang Wu
- Berry Genomics Company Limited, Building 5, Courtyard 4, Shengmingyuan Road, ZGC Life Science Park, Changping District, 102200, Beijing, China
| | - Yingchun Liao
- Berry Genomics Company Limited, Building 5, Courtyard 4, Shengmingyuan Road, ZGC Life Science Park, Changping District, 102200, Beijing, China
| | - Shuang Zhang
- Berry Genomics Company Limited, Building 5, Courtyard 4, Shengmingyuan Road, ZGC Life Science Park, Changping District, 102200, Beijing, China
| | - Hongbin Liang
- Berry Genomics Company Limited, Building 5, Courtyard 4, Shengmingyuan Road, ZGC Life Science Park, Changping District, 102200, Beijing, China
| | - David S Cram
- Berry Genomics Company Limited, Building 5, Courtyard 4, Shengmingyuan Road, ZGC Life Science Park, Changping District, 102200, Beijing, China.
| | - Yu Zhang
- Berry Genomics Company Limited, Building 5, Courtyard 4, Shengmingyuan Road, ZGC Life Science Park, Changping District, 102200, Beijing, China.
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Yu S, Chen WX, Zhang YF, Chen C, Ni Y, Duan B, Wang H, Xu ZM. Recessive LOXHD1 variants cause a prelingual down-sloping hearing loss: genotype-phenotype correlation and three additional children with novel variants. Int J Pediatr Otorhinolaryngol 2021; 145:110715. [PMID: 33892339 DOI: 10.1016/j.ijporl.2021.110715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/06/2021] [Accepted: 04/08/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Biallelic mutations in LOXHD1 have been identified as the cause of DFNB77 (deafness, autosomal recessive 77). It is a new progressive, severe-to-profound, and late-onset nonsyndromic sensorineural hearing loss (NSHL), and is highly heterogeneous genetically and phenotypically. This study aimed to provide an additional three cases of DFNB77. METHODS We presented three unrelated children diagnosed with prelingual mild-to-severe NSHL, and their audiograms showed mild hearing loss at 250 Hz before downsloping to a moderate-to-severe degree. Trio whole-exome sequencing (WES) was conducted to identify the pathogenic variants. Additionally, we reviewed the literature to further analyze the relationships between the genotype and audiology phenotype of LOXHD1. RESULTS Six novel possible pathogenic LOXHD1 variants were identified, including three missense, one nonsense, and two splicing variants. The literature review showed that 68.5% of patients with DFNB77 onset before five years old; Most variants (62%) were associated with a down-sloping audiogram of mild-to-moderate hearing loss at low frequencies (200Hz, 500Hz), particularly variants in the protein domain of PLAT 9. We found that compared with homozygous LOXHD1 variants, individuals with heterozygous compound variants had a significantly milder phenotype, especially individuals carrying one missense and one splicing or bi-allelic missense variants (P < 0.05). Audiometric analysis at different ages showed that the hearing loss degree was aggravated at all frequencies by increasing age. CONCLUSIONS We report three children with prelingual NSHL carrying six novel LOXHD1 variants. Furthermore, our work indicates that DFNB77 may be milder than previously reported and recommends considering the genotype combination and mutation location of LOXHD1 and race-specificity in DFNB77 molecular diagnoses and management.
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Affiliation(s)
- Sha Yu
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Wen-Xia Chen
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yun-Fei Zhang
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Chao Chen
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yihua Ni
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bo Duan
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Huijun Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.
| | - Zheng-Min Xu
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.
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Abstract
BACKGROUND Lupus B cells not only produce autoantibodies against nuclear antigens but also provide co-stimulation to T cells. However, there is still a lack of comprehensive understanding of the mechanism underlying lupus B cell hyperactivation. METHODS This study focuses on the detection of B cell activation status, analysis of early BCR signaling response, DNA sequencing, and quantity determination of BCR signaling regulators in murine lupus models. RESULTS Our result showed that there is a B cell hyperactivation with a significant elevation of B cell activation markers, and a BCR signaling hyperactivity with an abnormal increase of phosphorylated BCR signaling molecules and cytoplasmic calcium in the early response to BCR crosslinking in B6.Sle1/2/3 lupus mouse. Whole exome sequencing identified a multiple point mutation in the exon of many BCR signaling regulators in common murine lupus models, MRL/lpr, NZM2410, BXSB, NZB, and NZW strains. cNDA sequencing confirmed FcγR2b, Ly9, Pirb, Siglecg, and CD22 BCR signaling regulator variants in B6.Sle1/2/3 lupus mouse, but surface protein expression of these regulators on B cells showed an abnormal increase. CONCLUSION Our findings support that these BCR signaling regulator variants are potential causative genes of B cell hyperactivation in murine lupus models through their possible functional reduction.
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Affiliation(s)
- J Y Ju
- Department of Immunology, 372527Weifang Medical University, Weifang, China
| | - Z W Xu
- Department of Immunology, 372527Weifang Medical University, Weifang, China
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73
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Network-based analysis on genetic variants reveals the immunological mechanism underlying Alzheimer's disease. J Neural Transm (Vienna) 2021; 128:803-816. [PMID: 33909139 DOI: 10.1007/s00702-021-02337-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/11/2021] [Indexed: 12/14/2022]
Abstract
Alzheimer's Disease (AD) is a neurodegenerative disorder characterized by the impairment of cognitive function and loss of memory. Previous studies indicate an essential role of immune response in AD, but the detailed mechanisms remain unclear. In this study, we obtained 1664 credible risk variants (CRVs) based on the most significant SNP detected by International Genomics of Alzheimer's Project, from which 99 genes (CRVs-related genes) were identified. Function analysis revealed that these genes were mainly involved in immune response and amyloid-β and its precursor metabolisms, indicating a potential role of immune response in regulating neurobiological processes in the etiology of neurodegenerative disease. Pathway crosstalk analysis revealed the complicated connections between immune-related pathways. Further, we found that the CRVs-related genes showed temporal-specific expression in the thalamus in adolescence developmental period. Cell type-specific expression analysis found that CRVs-related genes might be specifically expressed in brain cells such as astrocytes and oligodendrocytes. Protein-protein interaction network analysis identified the highly interconnected 'hub' genes, all of which were susceptible loci of AD. These results indicated that the CRVs may exert a potential influence in AD by regulating immune response, thalamus development, astrocytes activities, and amyloid-β binding. Our results provided hints for further experimental verification of AD pathophysiology.
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Farjami M, Fathi M, Ghasemi MM, Rajati M, Eslahi A, Alimardani M, Mojarrad M. Investigation of MYO15A and MYO7A Mutations in Iranian Patients with Nonsyndromic Hearing Loss. Fetal Pediatr Pathol 2021; 40:121-130. [PMID: 31997689 DOI: 10.1080/15513815.2019.1686790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Hearing loss (HL) is the most common sensory disorder in humans, which affects individuals in both inherited and acquired forms. MYO15A and MYO7A gene mutations have a significant role in the development of deafness. In this study, we assessed the prevalence of MYO15A and MYO7A mutations in one hundred non-relative deaf Iranians. Materials and methods: The existence of MYO15A and MYO7A mutations were assessed using the tetra-primer ARMS-PCR method, High Resolution Melting (HRM) and sequencing method. Results: A heterozygote missense mutation, p.V2135L (c.6403G > T) in the MYO15A gene, was found in a patient using the sequencing method. Conclusion: These results explain the negligible prevalence of selected mutations among Iranian patients. Identifying common mutations in patients of an ethnic group can reduce the financial costs and time needed for identifying the causes of deafness.
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Affiliation(s)
- Mahsa Farjami
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mozhgan Fathi
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Mehdi Ghasemi
- Sinus and Surgical Endoscopic Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohsen Rajati
- Ear, Nose and Throat Research Center, Qaem Hospital, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Atieh Eslahi
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Malihe Alimardani
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Mojarrad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Medical Genetics Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Keller N, Paketci C, Altmueller J, Fuhrmann N, Wunderlich G, Schrank B, Unver O, Yilmaz S, Boostani R, Karimiani EG, Motameny S, Thiele H, Nürnberg P, Maroofian R, Yis U, Wirth B, Karakaya M. Genomic variants causing mitochondrial dysfunction are common in hereditary lower motor neuron disease. Hum Mutat 2021; 42:460-472. [PMID: 33600046 DOI: 10.1002/humu.24181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/29/2020] [Accepted: 02/10/2021] [Indexed: 11/08/2022]
Abstract
Hereditary lower motor neuron diseases (LMND) other than 5q-spinal muscular atrophy (5q-SMA) can be classified according to affected muscle groups. Proximal and distal forms of non-5q-SMA represent a clinically and genetically heterogeneous spectrum characterized by significant overlaps with axonal forms of Charcot-Marie-Tooth (CMT) disease. A consensus for the best approach to molecular diagnosis needs to be reached, especially in light of continuous novel gene discovery and falling costs of next-generation sequencing (NGS). We performed exome sequencing (ES) in 41 families presenting with non-5q-SMA or axonal CMT, 25 of which had undergone a previous negative neuromuscular disease (NMD) gene panel analysis. The total diagnostic yield of ES was 41%. Diagnostic success in the cohort with a previous NMD-panel analysis was significantly extended by ES, primarily due to novel gene associated-phenotypes and uncharacteristic phenotypic presentations. We recommend early ES for individuals with hereditary LMND presenting uncharacteristic or significantly overlapping features. As mitochondrial dysfunction was the underlying pathomechanism in 47% of the solved individuals, we highlight the sensitivity of the anterior horn cell and peripheral nerve to mitochondrial imbalance as well as the necessity to screen for mitochondrial disorders in individuals presenting predominant lower motor neuron symptoms.
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Affiliation(s)
- Natalie Keller
- Institute of Human Genetics and Institute of Genetics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Center for Rare Diseases Cologne, University Hospital Cologne, Cologne, Germany
| | - Cem Paketci
- Department of Pediatric Neurology, Dokuz Eylül University, Izmir, Turkey
| | - Janine Altmueller
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Nico Fuhrmann
- Institute of Human Genetics and Institute of Genetics, University of Cologne, Cologne, Germany
| | - Gilbert Wunderlich
- Center for Rare Diseases Cologne, University Hospital Cologne, Cologne, Germany
- Department of Neurology, University Hospital Cologne, Cologne, Germany
| | - Bertold Schrank
- Department of Neurology, DKD HELIOS Kliniken, Wiesbaden, Germany
| | - Olcay Unver
- Department of Pediatric Neurology, Marmara University, Istanbul, Turkey
| | - Sanem Yilmaz
- Department of Pediatric Neurology, Ege University, Izmir, Turkey
| | - Reza Boostani
- Department of Neurology, Ghaem Hospital, Medical School, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St. George's University of London, Cranmer Terrace, London, UK
| | - Susanne Motameny
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Reza Maroofian
- Molecular and Clinical Sciences Institute, St. George's University of London, Cranmer Terrace, London, UK
| | - Uluc Yis
- Department of Pediatric Neurology, Dokuz Eylül University, Izmir, Turkey
| | - Brunhilde Wirth
- Institute of Human Genetics and Institute of Genetics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Center for Rare Diseases Cologne, University Hospital Cologne, Cologne, Germany
| | - Mert Karakaya
- Institute of Human Genetics and Institute of Genetics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Center for Rare Diseases Cologne, University Hospital Cologne, Cologne, Germany
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Jiang H, Guo C, Xie J, Pan J, Huang Y, Li M, Guo Y. Case report: exome sequencing achieved a definite diagnosis in a Chinese family with muscle atrophy. BMC Neurol 2021; 21:96. [PMID: 33653295 PMCID: PMC7923504 DOI: 10.1186/s12883-021-02093-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/04/2021] [Indexed: 11/25/2022] Open
Abstract
Background Due to large genetic and phenotypic heterogeneity, the conventional workup for Charcot-Marie-Tooth (CMT) diagnosis is often underpowered, leading to diagnostic delay or even lack of diagnosis. In the present study, we explored how bioinformatics analysis on whole-exome sequencing (WES) data can be used to diagnose patients with CMT disease efficiently. Case presentation The proband is a 29-year-old female presented with a severe amyotrophy and distal skeletal deformity that plagued her family for over 20 years since she was 5-year-old. No other aberrant symptoms were detected in her speaking, hearing, vision, and intelligence. Similar symptoms manifested in her younger brother, while her parents and her older brother showed normal. To uncover the genetic causes of this disease, we performed exome sequencing for the proband and her parents. Subsequent bioinformatics analysis on the KGGSeq platform and further Sanger sequencing identified a novel homozygous GDAP1 nonsense mutation (c.218C > G, p.Ser73*) that responsible for the family. This genetic finding then led to a quick diagnosis of CMT type 4A (CMT4A), confirmed by nerve conduction velocity and electromyography examination of the patients. Conclusions The patients with severe muscle atrophy and distal skeletal deformity were caused by a novel homozygous nonsense mutation in GDAP1 (c.218C > G, p.Ser73*), and were diagnosed as CMT4A finally. This study expanded the mutation spectrum of CMT disease and demonstrated how affordable WES could be effectively employed for the clinical diagnosis of unexplained phenotypes. Supplementary Information The online version contains supplementary material available at 10.1186/s12883-021-02093-z.
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Affiliation(s)
- Hui Jiang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.,Key Laboratory of Tropical Diseases Control (SYSU), Sun Yat-sen University, Guangzhou, 510080, China.,Center for Precision Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Chunmiao Guo
- Department of Neurology, The Second Affiliated Hospital, Fujian University of Medical Science, Quanzhou, 362000, China
| | - Jie Xie
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.,Key Laboratory of Tropical Diseases Control (SYSU), Sun Yat-sen University, Guangzhou, 510080, China.,Center for Precision Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jingxin Pan
- Department of Hematology, The Second Affiliated Hospital, Fujian University of Medical Science, Quanzhou, 362000, China
| | - Ying Huang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.,Key Laboratory of Tropical Diseases Control (SYSU), Sun Yat-sen University, Guangzhou, 510080, China.,Center for Precision Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Miaoxin Li
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China. .,Key Laboratory of Tropical Diseases Control (SYSU), Sun Yat-sen University, Guangzhou, 510080, China. .,Center for Precision Medicine, Sun Yat-sen University, Guangzhou, 510080, China. .,The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong, China. .,State Key Laboratory for Cognitive and Brain Sciences, The University of Hong Kong, Hong Kong SAR, China.
| | - Yibin Guo
- Key Laboratory of Tropical Diseases Control (SYSU), Sun Yat-sen University, Guangzhou, 510080, China. .,Center for Precision Medicine, Sun Yat-sen University, Guangzhou, 510080, China. .,School of Medicine, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China.
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77
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Sakaguchi N, Suyama M. In silico identification of pseudo-exon activation events in personal genome and transcriptome data. RNA Biol 2021; 18:382-390. [PMID: 32865117 PMCID: PMC7951959 DOI: 10.1080/15476286.2020.1809195] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/03/2020] [Accepted: 08/08/2020] [Indexed: 12/25/2022] Open
Abstract
Causative mutations for human genetic disorders have mainly been identified in exonic regions that code for amino acid sequences. Recently, however, it has been reported that mutations in deep intronic regions can also cause certain human genetic disorders by creating novel splice sites, leading to pseudo-exon activation. To investigate how frequently pseudo-exon activation events occur in normal individuals, we conducted in silico identification of such events using personal genome data and corresponding high-quality transcriptome data. With rather stringent conditions, on average, 2.6 pseudo-exon activation events per individual were identified. More pseudo-exon activation events were found in 5' donor splice sites than in 3' acceptor splice sites. Although pseudo-exon activation events have sporadically been reported as causative mutations in genetic disorders, it is revealed in this study that such events can be observed in normal individuals at a certain frequency. We estimate that human genomes typically contain on average at least 10 pseudo-exon activation events. The actual number should be higher than this, because we used stringent criteria to identify pseudo-exon activation events. This suggests that it is worth considering the possibility of pseudo-exon activation when searching for causative mutations of genetic disorders if candidate mutations are not identified in coding regions or RNA splice sites.
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Affiliation(s)
- Narumi Sakaguchi
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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78
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Kausthubham N, Shukla A, Gupta N, Bhavani GS, Kulshrestha S, Das Bhowmik A, Moirangthem A, Bijarnia-Mahay S, Kabra M, Puri RD, Mandal K, Verma IC, Bielas SL, Phadke SR, Dalal A, Girisha KM. A data set of variants derived from 1455 clinical and research exomes is efficient in variant prioritization for early-onset monogenic disorders in Indians. Hum Mutat 2021; 42:e15-e61. [PMID: 33502066 PMCID: PMC10052794 DOI: 10.1002/humu.24172] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/05/2021] [Accepted: 01/24/2021] [Indexed: 12/16/2022]
Abstract
Given the genomic uniqueness, a local data set is most desired for Indians, who are underrepresented in existing public databases. We hypothesize patients with rare monogenic disorders and their family members can provide a reliable source of common variants in the population. Exome sequencing (ES) data from families with rare Mendelian disorders was aggregated from five centers in India. The dataset was refined by excluding related individuals and removing the disease-causing variants (refined cohort). The efficiency of these data sets was assessed in a new set of 50 exomes against gnomAD and GenomeAsia. Our original cohort comprised 1455 individuals from 1203 families. The refined cohort had 836 unrelated individuals that retained 1,251,064 variants with 181,125 population-specific and 489,618 common variants. The allele frequencies from our cohort helped to define 97,609 rare variants in gnomAD and 44,520 rare variants in GenomeAsia as common variants in our population. Our variant dataset provided an additional 1.7% and 0.1% efficiency for prioritizing heterozygous and homozygous variants respectively for rare monogenic disorders. We observed additional 19 genes/human knockouts. We list carrier frequency for 142 recessive disorders. This is a large and useful resource of exonic variants for Indians. Despite limitations, datasets from patients are efficient tools for variant prioritization in a resource-limited setting.
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Affiliation(s)
- Neethukrishna Kausthubham
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Gandham S Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Samarth Kulshrestha
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Aneek Das Bhowmik
- Division of Diagnostics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,ASPIRE (Diagnostics Facility), CSIR-Centre for Cellular & Molecular Biology, CCMB Annexe II, Hyderabad, India
| | - Amita Moirangthem
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Sunita Bijarnia-Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Madhulika Kabra
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Ratna D Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Kausik Mandal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Ishwar C Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Ashwin Dalal
- Division of Diagnostics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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79
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Beil A, Hornsby W, Uhlmann WR, Aatre R, Arscott P, Wolford B, Eagle KA, Yang B, McNamara J, Willer C, Roberts JS. Disclosure of clinically actionable genetic variants to thoracic aortic dissection biobank participants. BMC Med Genomics 2021; 14:66. [PMID: 33648514 PMCID: PMC7923508 DOI: 10.1186/s12920-021-00902-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 02/14/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Disclosure of pathogenic variants to thoracic aortic dissection biobank participants was implemented. The impact and costs, including confirmatory genetic testing in a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory, were evaluated. METHODS We exome sequenced 240 cases with thoracic aortic dissection and 258 controls, then examined 11 aortopathy genes. Pathogenic variants in 6 aortopathy genes (COL3A1, FBN1, LOX, PRKG1, SMAD3, and TGFBR2) were identified in 26 participants, representing 10.8% of the cohort (26/240). A second research sample was used to validate the initial findings. Mailed letters to participants disclosed that a potentially disease causing DNA alteration had been identified (neither the gene nor variant was disclosed). Participants were offered clinical genetic counseling and confirmatory genetic testing in a CLIA laboratory. RESULTS Excluding 6 participants who were deceased or lost to follow-up, 20 participants received the disclosure letter, 10 of whom proceeded with genetic counseling, confirmatory genetic testing, and enrolled in a survey study. Participants reported satisfaction with the letter (4.2 ± 0.7) and genetic counseling (4.4 ± 0.4; [out of 5, respectively]). The psychosocial impact was characterized by low decisional regret (11.5 ± 11.6) and distress (16.0 ± 4.2, [out of 100, respectively]). The average cost for 26 participants was $400, including validation and sending letters. The average cost for those who received genetic counseling and CLIA laboratory confirmation was $605. CONCLUSIONS Participants were satisfied with the return of clinically significant biobank genetic results and CLIA laboratory testing; however, the process required significant time and resources. These findings illustrate the trade-offs involved for researchers considering returning research genetic results.
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Affiliation(s)
- Adelyn Beil
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, 48109, USA
| | - Whitney Hornsby
- Department of Internal Medicine, Michigan Medicine, 5804 Medical Science II, 1241 E. Catherine Street, Ann Arbor, MI, 48109-5618, USA
| | - Wendy R Uhlmann
- Department of Internal Medicine, Michigan Medicine, 5804 Medical Science II, 1241 E. Catherine Street, Ann Arbor, MI, 48109-5618, USA
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Center for Bioethics and Social Sciences in Medicine, University of Michigan, Ann Arbor, MI, 48109-2029, USA
| | - Rajani Aatre
- Department of Internal Medicine, Michigan Medicine, 5804 Medical Science II, 1241 E. Catherine Street, Ann Arbor, MI, 48109-5618, USA
| | - Patricia Arscott
- Department of Internal Medicine, Michigan Medicine, 5804 Medical Science II, 1241 E. Catherine Street, Ann Arbor, MI, 48109-5618, USA
| | - Brooke Wolford
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Kim A Eagle
- Department of Internal Medicine, Michigan Medicine, 5804 Medical Science II, 1241 E. Catherine Street, Ann Arbor, MI, 48109-5618, USA
| | - Bo Yang
- Department of Cardiac Surgery, Michigan Medicine, Ann Arbor, MI, 48109, USA
| | - Jennifer McNamara
- Department of Internal Medicine, Michigan Medicine, 5804 Medical Science II, 1241 E. Catherine Street, Ann Arbor, MI, 48109-5618, USA
| | - Cristen Willer
- Department of Internal Medicine, Michigan Medicine, 5804 Medical Science II, 1241 E. Catherine Street, Ann Arbor, MI, 48109-5618, USA.
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - J Scott Roberts
- Center for Bioethics and Social Sciences in Medicine, University of Michigan, Ann Arbor, MI, 48109-2029, USA.
- Department of Health Behavior and Health Education, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA.
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80
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Chen T, Sun J, Liu G, Yin C, Liu H, Qu L, Fang S, Shifra A, Gilad G. A Homozygous Mutation in 5' Untranslated Region of TNFRSF11A Leading to Molecular Diagnosis of Osteopetrosis Coinheritance With Wiskott-Aldrich Syndrome. J Pediatr Hematol Oncol 2021; 43:e264-e267. [PMID: 32097281 PMCID: PMC7993917 DOI: 10.1097/mph.0000000000001760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 01/30/2020] [Indexed: 01/17/2023]
Abstract
Wiskott-Aldrich syndrome (WAS) and osteopetrosis are 2 different, rare hereditary diseases. Here we report clinical and molecular genetics investigations on an infant patient with persistent thrombocytopenia and prolonged fever. He was clinical diagnosed as osteopetrosis according to clinical presentation, radiologic skeletal features, and bone biopsy results. Gene sequencing demonstrated a de novo homozygous mutation in 5'-untranslated region of TNFRSF11A, c.-45A>G, which is relating to osteopetrosis. Meanwhile, a hemizygous transition mutation in WAS gene, c.400G>A diagnosed the infant with WAS. This is the first clinical report for the diagnosis of osteopetrosis coinheritance with WAS in a single patient.
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Affiliation(s)
- Tianping Chen
- Departments of Hematology
- Hematology Research Centre, Anhui Provincial Research Institute of Pediatrics
- Hematology Research Centre, Anhui Medical University, Hefei, People’s Republic of China
| | - Jun Sun
- Orthopedics
- Hematology Research Centre, Anhui Provincial Research Institute of Pediatrics
| | - Guanghui Liu
- Neonatal
- Hematology Research Centre, Anhui Provincial Research Institute of Pediatrics
| | - Chuangao Yin
- Radiology
- Hematology Research Centre, Anhui Provincial Research Institute of Pediatrics
| | - Haipeng Liu
- Hematology Research Centre, Anhui Provincial Research Institute of Pediatrics
| | - Lijun Qu
- Departments of Hematology
- Hematology Research Centre, Anhui Provincial Research Institute of Pediatrics
| | - Shijin Fang
- Respiratory, Anhui Provincial Children’s Hospital
| | - Ash Shifra
- The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider Children’s Medical Center, Petah Tikva, Israel
| | - Gil Gilad
- The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider Children’s Medical Center, Petah Tikva, Israel
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81
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Zamani M, Seifi T, Zeighami J, Mazaheri N, Jahangirnezhad E, Gholamzadeh M, Sedaghat A, Shariati G, Galehdari H. Identification of the rs797045105 in the SERAC1 Gene by Whole-exome Sequencing in a Patient Suspicious of MEGDEL Syndrome. Basic Clin Neurosci 2021; 11:549-556. [PMID: 33613893 PMCID: PMC7878045 DOI: 10.32598/bcn.9.10.455] [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: 10/13/2017] [Revised: 11/10/2017] [Accepted: 05/13/2019] [Indexed: 12/04/2022] Open
Abstract
Introduction: Whole Exome Sequencing (WES) has been increasingly utilized in genetic determinants of various inherited diseases. Methods: We applied WES for a patient presenting 3-Methylglutaconic Aciduria (MEG), Deafness (D), Encephalopathy (E), and Leigh-like (L) syndrome. Then Sanger sequencing was used for the detected variant validation. Results: We found an insertion, rs797045105 (chr6, 158571484, C>CCATG), in the SERAC1 gene with homozygous genotype in the patient and heterozygous genotype in her unaffected parents. Notably, bioinformatics analysis using mutation taster (prob>0.99) and DDIGin (prob=86.51) predicted this mutation as disease-causing. Also, the variant was not present in our database, including 700 exome files. Conclusion: These findings emphasize the pathogenicity of rs797045105 for MEGDEL syndrome. On the other hand, our data shed light on the significance of WES application as a genetic test to identify and characterize the comprehensive spectrum of genetic variation and classification for patients with neurometabolic disorders.
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Affiliation(s)
- Mina Zamani
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran.,Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Tahereh Seifi
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran.,Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Jawaher Zeighami
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran
| | - Neda Mazaheri
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran.,Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | | | - Minoo Gholamzadeh
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran
| | - Alireza Sedaghat
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran.,Diabetes Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Gholamreza Shariati
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran.,Department of Genetics, School of Medicine, Ahvaz Jundishapur University of medical Sciences, Ahvaz, Iran
| | - Hamid Galehdari
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran.,Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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82
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Roessler HI, Knoers NVAM, van Haelst MM, van Haaften G. Drug Repurposing for Rare Diseases. Trends Pharmacol Sci 2021; 42:255-267. [PMID: 33563480 DOI: 10.1016/j.tips.2021.01.003] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 12/17/2022]
Abstract
Currently, there are about 7000 identified rare diseases, together affecting 10% of the population. However, fewer than 6% of all rare diseases have an approved treatment option, highlighting their tremendous unmet needs in drug development. The process of repurposing drugs for new indications, compared with the development of novel orphan drugs, is a time-saving and cost-efficient method resulting in higher success rates, which can therefore drastically reduce the risk of drug development for rare diseases. Although drug repurposing is not novel, new strategies have been developed in recent years to do it in a systematic and rational way. Here, we review applied methodologies, recent accomplished progress, and the challenges associated in drug repurposing for rare diseases.
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Affiliation(s)
- Helen I Roessler
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Nine V A M Knoers
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands; Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Mieke M van Haelst
- Department of Clinical Genetics, Amsterdam University Medical Center, Location AMC, University of Amsterdam, Amsterdam, The Netherlands; Department of Clinical Genetics, Amsterdam University Medical Center, Location VUMC, VU University Amsterdam, Amsterdam, The Netherlands
| | - Gijs van Haaften
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
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83
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Eghbali M, Fatemi KS, Salehpour S, Abiri M, Saei H, Talebi S, Olyaei NA, Yassaee VR, Modarressi MH. Whole-Exome Sequencing Uncovers Novel Causative Variants and Additional Findings in Three Patients Affected by Glycogen Storage Disease Type VI and Fanconi-Bickel Syndrome. Front Genet 2021; 11:601566. [PMID: 33505429 PMCID: PMC7831547 DOI: 10.3389/fgene.2020.601566] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/07/2020] [Indexed: 01/08/2023] Open
Abstract
Glycogen storage diseases (GSDs) are the heterogeneous group of disorders caused by mutations in at least 30 different genes. Different types of GSDs, especially liver GSDs, take overlapping symptoms and can be clinically indistinguishable. This survey evaluated the use of whole-exome sequencing (WES) for the genetic analysis of the liver GSD-suspected patients in three unrelated families. An in-house filtering pipeline was used to assess rare pathogenic variants in GSD-associated genes, autosomal recessive/mendelian disorder genes (carrier status for genetic counseling subjects), and the ACMG's list of 59 actionable genes. For the interpretation of the causative variants and the incidental/secondary findings, ACMG guidelines were applied. Additionally, we have explored PharmGKB class IA/IB pharmacogenetic variants. The segregation analysis was performed using Sanger sequencing for the novel causative variants. Bioinformatics analysis of the exome data in three individuals revealed three novel homozygous causative variants in the GSD-associated genes. The first variant, c.298_307delATGATCAACC in PYGL gene has related to HERS disease (GSD VI). Both variants of c.1043dupT and c.613-1G > C in SLC2A2 gene have been associated with Fanconi-Bickel syndrome (GSDXI). Eight pathogenic/likely pathogenic medical actionable findings in Mendelian disease genes and 10 pharmacogenetic variants with underlying drug response phenotypes have been identified. No known/expected pathogenic variants were detected in the ACMG's list of 59 actionable genes. The logical filtering steps can help in finding other medical actionable secondary/incidental findings as well as effectively identifying the causative variants in heterogeneous conditions such as GSDs. Three novel variants related to GSD genes recognized in liver GSD-suspected patients with early infantile and childhood-age onset.
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Affiliation(s)
- Maryam Eghbali
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Kiyana Sadat Fatemi
- Dr. Zenali's Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Shadab Salehpour
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Pediatric Endocrinology and Metabolism, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Abiri
- Shahid Akbarabadi Clinical Research Development Unit, Iran University of Medical Sciences, Tehran, Iran.,Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hassan Saei
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Saeed Talebi
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Nasrin Alipour Olyaei
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Reza Yassaee
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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84
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Prasad A, Bhargava H, Gupta A, Shukla N, Rajagopal S, Gupta S, Sharma A, Valadi J, Nigam V, Suravajhala P. Next Generation Sequencing. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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85
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He J, Han J, Liu J, Yang R, Wang J, Wang X, Chen X. Genetic and Epigenetic Impact of Chronic Inflammation on Colon Mucosa Cells. Front Genet 2021; 12:722835. [PMID: 34764977 PMCID: PMC8576270 DOI: 10.3389/fgene.2021.722835] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 09/13/2021] [Indexed: 12/20/2022] Open
Abstract
Chronic inflammation increases cancer risk, and cancer development is characterized by stepwise accumulation of genetic and epigenetic alterations. During chronic inflammation, infectious agents and intrinsic mediators of inflammatory responses can induce genetic and epigenetic changes. This study tried to evaluate both the genetic and epigenetic influence of chronic inflammation on colon mucosa cells. Repetitive dextran sulfate sodium (DSS) treatment induced chronic colitis model. Whole-exome sequencing (WES) (200× coverage) was performed to detect somatic variations in colon mucosa cells. With the use of whole-genome bisulfite sequencing (BS) at 34-fold coverage (17-fold per strand), the methylome of both the colitis and control tissue was comparatively analyzed. Bioinformatics assay showed that there was no significant single-nucleotide polymorphism/insertion or deletion (SNP/InDel) mutation accumulation in colitis tissue, while it accumulated in aged mice. Forty-eight genes with SNP/InDel mutation were overlapped in the three colitis tissues, two (Wnt3a and Lama2) of which are in the cancer development-related signaling pathway. Differentially methylated region (DMR) assay showed that many genes in the colitis tissue are enriched in the cancer development-related signaling pathway, such as PI3K-AKT, Ras, Wnt, TGF-beta, and MAPK signaling pathway. Together, these data suggested that even though chronic inflammation did not obviously increase genetic mutation accumulation, it could both genetically and epigenetically alter some genes related to cancer development.
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Affiliation(s)
- Jia He
- Department of Burn Surgery, The First People’s Hospital of Foshan, Foshan, China
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Jimin Han
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Jia Liu
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Ronghua Yang
- Department of Burn Surgery, The First People’s Hospital of Foshan, Foshan, China
| | - Jingru Wang
- Department of Burn Surgery, The First People’s Hospital of Foshan, Foshan, China
| | - Xusheng Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, China
- *Correspondence: Xiaodong Chen, ; Xusheng Wang,
| | - Xiaodong Chen
- Department of Burn Surgery, The First People’s Hospital of Foshan, Foshan, China
- *Correspondence: Xiaodong Chen, ; Xusheng Wang,
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86
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Koriath CAM, Kenny J, Ryan NS, Rohrer JD, Schott JM, Houlden H, Fox NC, Tabrizi SJ, Mead S. Genetic testing in dementia - utility and clinical strategies. Nat Rev Neurol 2021; 17:23-36. [PMID: 33168964 DOI: 10.1038/s41582-020-00416-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2020] [Indexed: 02/07/2023]
Abstract
Techniques for clinical genetic testing in dementia disorders have advanced rapidly but remain to be more widely implemented in practice. A positive genetic test offers a precise molecular diagnosis, can help members of an affected family to determine personal risk, provides a basis for reproductive choices and can offer options for clinical trials. The likelihood of identifying a specific genetic cause of dementia depends on the clinical condition, the age at onset and family history. Attempts to match phenotypes to single genes are mostly inadvisable owing to clinical overlap between the dementias, genetic heterogeneity, pleiotropy and concurrent mutations. Currently, the appropriate genetic test in most cases of dementia is a next-generation sequencing gene panel, though some conditions necessitate specific types of test such as repeat expansion testing. Whole-exome and whole-genome sequencing are becoming financially feasible but raise or exacerbate complex issues such as variants of uncertain significance, secondary findings and the potential for re-analysis in light of new information. However, the capacity for data analysis and counselling is already restricting the provision of genetic testing. Patients and their relatives need to be given reliable information to enable them to make informed choices about tests, treatments and data sharing; the ability of patients with dementia to make decisions must be considered when providing this information.
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Affiliation(s)
| | - Joanna Kenny
- South West Thames Regional Genetics Service, London, UK
| | - Natalie S Ryan
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- UK Dementia Research Institute, UCL Queen Square Institute of Neurology, London, UK
| | - Jonathan D Rohrer
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Jonathan M Schott
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Henry Houlden
- Neurogenetics Laboratory, National Hospital for Neurology and Neurosurgery, London, UK
| | - Nick C Fox
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- UK Dementia Research Institute, UCL Queen Square Institute of Neurology, London, UK
| | - Sarah J Tabrizi
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Simon Mead
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, London, UK.
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87
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Du Q, Zhang D, Zhuang Y, Xia Q, Wen T, Jia H. The Molecular Genetics of Marfan Syndrome. Int J Med Sci 2021; 18:2752-2766. [PMID: 34220303 PMCID: PMC8241768 DOI: 10.7150/ijms.60685] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/18/2021] [Indexed: 12/27/2022] Open
Abstract
Marfan syndrome (MFS) is a complex connective tissue disease that is primarily characterized by cardiovascular, ocular and skeletal systems disorders. Despite its rarity, MFS severely impacts the quality of life of the patients. It has been shown that molecular genetic factors serve critical roles in the pathogenesis of MFS. FBN1 is associated with MFS and the other genes such as FBN2, transforming growth factor beta (TGF-β) receptors (TGFBR1 and TGFBR2), latent TGF-β-binding protein 2 (LTBP2) and SKI, amongst others also have their associated syndromes, however high overlap may exist between these syndromes and MFS. Abnormalities in the TGF-β signaling pathway also contribute to the development of aneurysms in patients with MFS, although the detailed molecular mechanism remains unclear. Mutant FBN1 protein may cause unstableness in elastic structures, thereby perturbing the TGF-β signaling pathway, which regulates several processes in cells. Additionally, DNA methylation of FBN1 and histone acetylation in an MFS mouse model demonstrated that epigenetic factors play a regulatory role in MFS. The purpose of the present review is to provide an up-to-date understanding of MFS-related genes and relevant assessment technologies, with the aim of laying a foundation for the early diagnosis, consultation and treatment of MFS.
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Affiliation(s)
- Qiu Du
- Marfan Research Group, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, Sichuan, China
| | - Dingding Zhang
- Marfan Research Group, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, Sichuan, China.,Sichuan Provincial Key Laboratory for Genetic Disease, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, Sichuan, China
| | - Yue Zhuang
- Department of Rheumatology and Immunology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 611731, Sichuan, China
| | - Qiongrong Xia
- Marfan Research Group, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, Sichuan, China
| | - Taishen Wen
- Sichuan Provincial Key Laboratory for Genetic Disease, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, Sichuan, China
| | - Haiping Jia
- Department of Immunology, North Sichuan Medical College, Nanchong, 637100, Sichuan, China
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88
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Swietlik EM, Prapa M, Martin JM, Pandya D, Auckland K, Morrell NW, Gräf S. 'There and Back Again'-Forward Genetics and Reverse Phenotyping in Pulmonary Arterial Hypertension. Genes (Basel) 2020; 11:E1408. [PMID: 33256119 PMCID: PMC7760524 DOI: 10.3390/genes11121408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/17/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
Although the invention of right heart catheterisation in the 1950s enabled accurate clinical diagnosis of pulmonary arterial hypertension (PAH), it was not until 2000 when the landmark discovery of the causative role of bone morphogenetic protein receptor type II (BMPR2) mutations shed new light on the pathogenesis of PAH. Since then several genes have been discovered, which now account for around 25% of cases with the clinical diagnosis of idiopathic PAH. Despite the ongoing efforts, in the majority of patients the cause of the disease remains elusive, a phenomenon often referred to as "missing heritability". In this review, we discuss research approaches to uncover the genetic architecture of PAH starting with forward phenotyping, which in a research setting should focus on stable intermediate phenotypes, forward and reverse genetics, and finally reverse phenotyping. We then discuss potential sources of "missing heritability" and how functional genomics and multi-omics methods are employed to tackle this problem.
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Affiliation(s)
- Emilia M. Swietlik
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- Royal Papworth Hospital NHS Foundation Trust, Cambridge CB2 0AY, UK
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Matina Prapa
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Jennifer M. Martin
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
| | - Divya Pandya
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
| | - Kathryn Auckland
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
| | - Nicholas W. Morrell
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- Royal Papworth Hospital NHS Foundation Trust, Cambridge CB2 0AY, UK
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge CB2 0QQ, UK
- NIHR BioResource for Translational Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Stefan Gräf
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- NIHR BioResource for Translational Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
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89
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Ryu CS, Bae J, Kim IJ, Kim J, Oh SH, Kim OJ, Kim NK. MPG and NPRL3 Polymorphisms are Associated with Ischemic Stroke Susceptibility and Post-Stroke Mortality. Diagnostics (Basel) 2020; 10:diagnostics10110947. [PMID: 33202874 PMCID: PMC7696846 DOI: 10.3390/diagnostics10110947] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/16/2020] [Accepted: 11/12/2020] [Indexed: 01/04/2023] Open
Abstract
Ischemic stroke is a complicated disease which is affected by environmental factors and genetic factors. In this field, various studies using whole-exome sequencing (WES) have focused on novel and linkage variants in diverse diseases. Thus, we have investigated the various novel variants, which focused on their linkages to each other, in ischemic stroke. Specifically, we analyzed the N-methylpurine DNA glycosylase (MPG) gene, which plays an initiating role in DNA repair, and the nitrogen permease regulator-like 3 (NPRL3) gene, which is involved in regulating the mammalian target of rapamycin pathway. We took blood samples of 519 ischemic stroke patients and 417 controls. Genetic polymorphisms were detected by polymerase chain reaction (PCR), real-time PCR, and restriction fragment length polymorphism (RFLP) analysis. We found that two NPRL3 polymorphisms (rs2541618 C>T and rs75187722 G>A), as well as the MPG rs2562162 C>T polymorphism, were significantly associated with ischemic stroke. In Cox proportional hazard regression models, the MPG rs2562162 was associated with the survival of small-vessel disease patients in ischemic stroke. Our study showed that NPRL3 and MPG polymorphisms are associated with ischemic stroke prevalence and ischemic stroke survival. Taken together, these findings suggest that NPRL3 and MPG genotypes may be useful clinical biomarkers for ischemic stroke development and prognosis.
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Affiliation(s)
- Chang Soo Ryu
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea;
| | - Jinkun Bae
- Department of Emergency Medicine, CHA Bundang Medical Center, School of Medicine, CHA University, Seongnam 13496, Korea;
| | - In Jai Kim
- Department of Internal Medicine, CHA Bundang Medical Center, School of Medicine, CHA University, Seongnam 13496, Korea;
| | - Jinkwon Kim
- Department of Neurology, CHA Bundang Medical Center, School of Medicine, CHA University, Seongnam 13496, Korea; (J.K.); (S.H.O.)
| | - Seung Hun Oh
- Department of Neurology, CHA Bundang Medical Center, School of Medicine, CHA University, Seongnam 13496, Korea; (J.K.); (S.H.O.)
| | - Ok Joon Kim
- Department of Neurology, CHA Bundang Medical Center, School of Medicine, CHA University, Seongnam 13496, Korea; (J.K.); (S.H.O.)
- Correspondence: (O.J.K.); (N.K.K.)
| | - Nam Keun Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea;
- Correspondence: (O.J.K.); (N.K.K.)
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90
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Rim J, Byler M, Soldatos A, Notarangelo L, Leibovitch E, Jacobson S, Gorman M, Lebel RR, Werner K. Opinion and Special Articles: Cerebellar Ataxia and Liver Failure Complicating IPEX Syndrome. Neurology 2020; 96:e956-e959. [PMID: 33168705 DOI: 10.1212/wnl.0000000000011195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Joshua Rim
- From the Cleveland Clinic Foundation (J.R.), Neurological Institute, OH; SUNY Upstate Medical University Genetics Section (M.B., R.R.L.), Syracuse, NY; National Institute of Neurological Disorders and Stroke (NINDS) (A.S., E.L., S.J.), Bethesda; National Institute of Allergy and Infectious Diseases (NIAID) (L.N.), Bethesda, MD; Boston Children's Hospital (M.G.), Pediatric MS and Related Disorders and Neuro-immunology, MA; and Duke University (K.W.), Department of Pediatrics, Durham, NC.
| | - Melissa Byler
- From the Cleveland Clinic Foundation (J.R.), Neurological Institute, OH; SUNY Upstate Medical University Genetics Section (M.B., R.R.L.), Syracuse, NY; National Institute of Neurological Disorders and Stroke (NINDS) (A.S., E.L., S.J.), Bethesda; National Institute of Allergy and Infectious Diseases (NIAID) (L.N.), Bethesda, MD; Boston Children's Hospital (M.G.), Pediatric MS and Related Disorders and Neuro-immunology, MA; and Duke University (K.W.), Department of Pediatrics, Durham, NC
| | - Ariane Soldatos
- From the Cleveland Clinic Foundation (J.R.), Neurological Institute, OH; SUNY Upstate Medical University Genetics Section (M.B., R.R.L.), Syracuse, NY; National Institute of Neurological Disorders and Stroke (NINDS) (A.S., E.L., S.J.), Bethesda; National Institute of Allergy and Infectious Diseases (NIAID) (L.N.), Bethesda, MD; Boston Children's Hospital (M.G.), Pediatric MS and Related Disorders and Neuro-immunology, MA; and Duke University (K.W.), Department of Pediatrics, Durham, NC
| | - Luigi Notarangelo
- From the Cleveland Clinic Foundation (J.R.), Neurological Institute, OH; SUNY Upstate Medical University Genetics Section (M.B., R.R.L.), Syracuse, NY; National Institute of Neurological Disorders and Stroke (NINDS) (A.S., E.L., S.J.), Bethesda; National Institute of Allergy and Infectious Diseases (NIAID) (L.N.), Bethesda, MD; Boston Children's Hospital (M.G.), Pediatric MS and Related Disorders and Neuro-immunology, MA; and Duke University (K.W.), Department of Pediatrics, Durham, NC
| | - Emily Leibovitch
- From the Cleveland Clinic Foundation (J.R.), Neurological Institute, OH; SUNY Upstate Medical University Genetics Section (M.B., R.R.L.), Syracuse, NY; National Institute of Neurological Disorders and Stroke (NINDS) (A.S., E.L., S.J.), Bethesda; National Institute of Allergy and Infectious Diseases (NIAID) (L.N.), Bethesda, MD; Boston Children's Hospital (M.G.), Pediatric MS and Related Disorders and Neuro-immunology, MA; and Duke University (K.W.), Department of Pediatrics, Durham, NC
| | - Steven Jacobson
- From the Cleveland Clinic Foundation (J.R.), Neurological Institute, OH; SUNY Upstate Medical University Genetics Section (M.B., R.R.L.), Syracuse, NY; National Institute of Neurological Disorders and Stroke (NINDS) (A.S., E.L., S.J.), Bethesda; National Institute of Allergy and Infectious Diseases (NIAID) (L.N.), Bethesda, MD; Boston Children's Hospital (M.G.), Pediatric MS and Related Disorders and Neuro-immunology, MA; and Duke University (K.W.), Department of Pediatrics, Durham, NC
| | - Mark Gorman
- From the Cleveland Clinic Foundation (J.R.), Neurological Institute, OH; SUNY Upstate Medical University Genetics Section (M.B., R.R.L.), Syracuse, NY; National Institute of Neurological Disorders and Stroke (NINDS) (A.S., E.L., S.J.), Bethesda; National Institute of Allergy and Infectious Diseases (NIAID) (L.N.), Bethesda, MD; Boston Children's Hospital (M.G.), Pediatric MS and Related Disorders and Neuro-immunology, MA; and Duke University (K.W.), Department of Pediatrics, Durham, NC
| | - Robert Roger Lebel
- From the Cleveland Clinic Foundation (J.R.), Neurological Institute, OH; SUNY Upstate Medical University Genetics Section (M.B., R.R.L.), Syracuse, NY; National Institute of Neurological Disorders and Stroke (NINDS) (A.S., E.L., S.J.), Bethesda; National Institute of Allergy and Infectious Diseases (NIAID) (L.N.), Bethesda, MD; Boston Children's Hospital (M.G.), Pediatric MS and Related Disorders and Neuro-immunology, MA; and Duke University (K.W.), Department of Pediatrics, Durham, NC
| | - Klaus Werner
- From the Cleveland Clinic Foundation (J.R.), Neurological Institute, OH; SUNY Upstate Medical University Genetics Section (M.B., R.R.L.), Syracuse, NY; National Institute of Neurological Disorders and Stroke (NINDS) (A.S., E.L., S.J.), Bethesda; National Institute of Allergy and Infectious Diseases (NIAID) (L.N.), Bethesda, MD; Boston Children's Hospital (M.G.), Pediatric MS and Related Disorders and Neuro-immunology, MA; and Duke University (K.W.), Department of Pediatrics, Durham, NC
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91
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Kumawat RL, Pathak B. Functionalized carbon nanotube electrodes for controlled DNA sequencing. NANOSCALE ADVANCES 2020; 2:4041-4050. [PMID: 36132799 PMCID: PMC9417824 DOI: 10.1039/d0na00241k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 07/14/2020] [Indexed: 06/14/2023]
Abstract
In the last decade, solid-state nanopores/nanogaps have attracted significant attention in the rapid detection of DNA nucleotides. However, reducing the noise through controlled translocation of the DNA nucleobases is a central issue for the development of nanogap/nanopore-based DNA sequencing to achieve single-nucleobase resolution. Furthermore, the high reactivity of the graphene pores/gaps causes clogging of the pore/gap, leading to the blockage of the pores/gaps, sticking, and irreversible pore closure. To address the prospective of functionalization of the carbon nanostructure and for accomplishing this objective, herein, we have studied the performance of functionalized closed-end cap armchair carbon nanotube (CNT) nanogap-embedded electrodes, which can improve the coupling through non-bonding electrons and may provide the possibility of N/O-H⋯π interactions with the nucleotides, as single-stranded DNA is transmigrated across the electrode. We have investigated the effect of functionalizing the closed-end cap CNT (6,6) electrodes with purine (adenine, guanine) and pyrimidine (thymine, cytosine) molecules. Weak hydrogen bonds formed between the probe molecule and the target DNA nucleobase enhance the electronic coupling and temporarily stabilize the translocating nucleobase against the orientational fluctuations, which may reduce noise in the current signal during experimental measurements. The findings of our density functional theory and non-equilibrium Green's function-based study indicate that this modeled setup could allow DNA nucleotide sequencing with a better and reliable yield, giving current traces that differ by at least 1 order of current magnitude for all the four target nucleotides. Thus, we feel that the functionalized armchair CNT (6,6) nanogap-embedded electrodes may be utilized for controlled DNA sequencing.
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Affiliation(s)
- Rameshwar L Kumawat
- Discipline of Metallurgy Engineering and Materials Science Indore Madhya Pradesh 453552 India
| | - Biswarup Pathak
- Discipline of Metallurgy Engineering and Materials Science Indore Madhya Pradesh 453552 India
- Discipline of Chemistry, School of Basic Sciences, Indian Institute of Technology (IIT) Indore Indore Madhya Pradesh 453552 India
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92
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Yao Z, You FM, N'Diaye A, Knox RE, McCartney C, Hiebert CW, Pozniak C, Xu W. Evaluation of variant calling tools for large plant genome re-sequencing. BMC Bioinformatics 2020; 21:360. [PMID: 32807073 PMCID: PMC7430858 DOI: 10.1186/s12859-020-03704-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/28/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Discovering single nucleotide polymorphisms (SNPs) from agriculture crop genome sequences has been a widely used strategy for developing genetic markers for several applications including marker-assisted breeding, population diversity studies for eco-geographical adaption, genotyping crop germplasm collections, and others. Accurately detecting SNPs from large polyploid crop genomes such as wheat is crucial and challenging. A few variant calling methods have been previously developed but they show a low concordance between their variant calls. A gold standard of variant sets generated from one human individual sample was established for variant calling tool evaluations, however hitherto no gold standard of crop variant set is available for wheat use. The intent of this study was to evaluate seven SNP variant calling tools (FreeBayes, GATK, Platypus, Samtools/mpileup, SNVer, VarScan, VarDict) with the two most popular mapping tools (BWA-mem and Bowtie2) on wheat whole exome capture (WEC) re-sequencing data from allohexaploid wheat. RESULTS We found the BWA-mem mapping tool had both a higher mapping rate and a higher accuracy rate than Bowtie2. With the same mapping quality (MQ) cutoff, BWA-mem detected more variant bases in mapping reads than Bowtie2. The reads preprocessed with quality trimming or duplicate removal did not significantly affect the final mapping performance in terms of mapped reads. Based on the concordance and receiver operating characteristic (ROC), the Samtools/mpileup variant calling tool with BWA-mem mapping of raw sequence reads outperformed other tests followed by FreeBayes and GATK in terms of specificity and sensitivity. VarDict and VarScan were the poorest performing variant calling tools with the wheat WEC sequence data. CONCLUSION The BWA-mem and Samtools/mpileup pipeline, with no need to preprocess the raw read data before mapping onto the reference genome, was ascertained the optimum for SNP calling for the complex wheat genome re-sequencing. These results also provide useful guidelines for reliable variant identification from deep sequencing of other large polyploid crop genomes.
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Affiliation(s)
- Zhen Yao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, Manitoba, R6M 1Y5, Canada
| | - Frank M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
| | - Amidou N'Diaye
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5A8, Canada
| | - Ron E Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Box 1030, Swift Current, Saskatchewan, S9H 3X2, Canada
| | - Curt McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, Manitoba, R6M 1Y5, Canada
| | - Colin W Hiebert
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, Manitoba, R6M 1Y5, Canada
| | - Curtis Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5A8, Canada
| | - Wayne Xu
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, Manitoba, R6M 1Y5, Canada.
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93
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Tubeuf H, Charbonnier C, Soukarieh O, Blavier A, Lefebvre A, Dauchel H, Frebourg T, Gaildrat P, Martins A. Large-scale comparative evaluation of user-friendly tools for predicting variant-induced alterations of splicing regulatory elements. Hum Mutat 2020; 41:1811-1829. [PMID: 32741062 DOI: 10.1002/humu.24091] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 07/11/2020] [Accepted: 07/26/2020] [Indexed: 12/20/2022]
Abstract
Discriminating which nucleotide variants cause disease or contribute to phenotypic traits remains a major challenge in human genetics. In theory, any intragenic variant can potentially affect RNA splicing by altering splicing regulatory elements (SREs). However, these alterations are often ignored mainly because pioneer SRE predictors have proved inefficient. Here, we report the first large-scale comparative evaluation of four user-friendly SRE-dedicated algorithms (QUEPASA, HEXplorer, SPANR, and HAL) tested both as standalone tools and in multiple combined ways based on two independent benchmark datasets adding up to >1,300 exonic variants studied at the messenger RNA level and mapping to 89 different disease-causing genes. These methods display good predictive power, based on decision thresholds derived from the receiver operating characteristics curve analyses, with QUEPASA and HAL having the best accuracies either as standalone or in combination. Still, overall there was a tight race between the four predictors, suggesting that all methods may be of use. Additionally, QUEPASA and HEXplorer may be beneficial as well for predicting variant-induced creation of pseudoexons deep within introns. Our study highlights the potential of SRE predictors as filtering tools for identifying disease-causing candidates among the plethora of variants detected by high-throughput DNA sequencing and provides guidance for their use in genomic medicine settings.
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Affiliation(s)
- Hélène Tubeuf
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Camille Charbonnier
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Omar Soukarieh
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Arnaud Lefebvre
- Computer Science, Information Processing and Systems Laboratory, UNIROUEN, Normandie University, Mont-Saint-Aignan, France
| | - Hélène Dauchel
- Computer Science, Information Processing and Systems Laboratory, UNIROUEN, Normandie University, Mont-Saint-Aignan, France
| | - Thierry Frebourg
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Pascaline Gaildrat
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Alexandra Martins
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
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94
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Bis JC, Jian X, Kunkle BW, Chen Y, Hamilton-Nelson KL, Bush WS, Salerno WJ, Lancour D, Ma Y, Renton AE, Marcora E, Farrell JJ, Zhao Y, Qu L, Ahmad S, Amin N, Amouyel P, Beecham GW, Below JE, Campion D, Cantwell L, Charbonnier C, Chung J, Crane PK, Cruchaga C, Cupples LA, Dartigues JF, Debette S, Deleuze JF, Fulton L, Gabriel SB, Genin E, Gibbs RA, Goate A, Grenier-Boley B, Gupta N, Haines JL, Havulinna AS, Helisalmi S, Hiltunen M, Howrigan DP, Ikram MA, Kaprio J, Konrad J, Kuzma A, Lander ES, Lathrop M, Lehtimäki T, Lin H, Mattila K, Mayeux R, Muzny DM, Nasser W, Neale B, Nho K, Nicolas G, Patel D, Pericak-Vance MA, Perola M, Psaty BM, Quenez O, Rajabli F, Redon R, Reitz C, Remes AM, Salomaa V, Sarnowski C, Schmidt H, Schmidt M, Schmidt R, Soininen H, Thornton TA, Tosto G, Tzourio C, van der Lee SJ, van Duijn CM, Valladares O, Vardarajan B, Wang LS, Wang W, Wijsman E, Wilson RK, Witten D, Worley KC, Zhang X, Bellenguez C, Lambert JC, Kurki MI, Palotie A, Daly M, Boerwinkle E, Lunetta KL, Destefano AL, Dupuis J, Martin ER, Schellenberg GD, Seshadri S, Naj AC, Fornage M, Farrer LA. Whole exome sequencing study identifies novel rare and common Alzheimer's-Associated variants involved in immune response and transcriptional regulation. Mol Psychiatry 2020; 25:1859-1875. [PMID: 30108311 PMCID: PMC6375806 DOI: 10.1038/s41380-018-0112-7] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 05/01/2018] [Accepted: 05/14/2018] [Indexed: 12/21/2022]
Abstract
The Alzheimer's Disease Sequencing Project (ADSP) undertook whole exome sequencing in 5,740 late-onset Alzheimer disease (AD) cases and 5,096 cognitively normal controls primarily of European ancestry (EA), among whom 218 cases and 177 controls were Caribbean Hispanic (CH). An age-, sex- and APOE based risk score and family history were used to select cases most likely to harbor novel AD risk variants and controls least likely to develop AD by age 85 years. We tested ~1.5 million single nucleotide variants (SNVs) and 50,000 insertion-deletion polymorphisms (indels) for association to AD, using multiple models considering individual variants as well as gene-based tests aggregating rare, predicted functional, and loss of function variants. Sixteen single variants and 19 genes that met criteria for significant or suggestive associations after multiple-testing correction were evaluated for replication in four independent samples; three with whole exome sequencing (2,778 cases, 7,262 controls) and one with genome-wide genotyping imputed to the Haplotype Reference Consortium panel (9,343 cases, 11,527 controls). The top findings in the discovery sample were also followed-up in the ADSP whole-genome sequenced family-based dataset (197 members of 42 EA families and 501 members of 157 CH families). We identified novel and predicted functional genetic variants in genes previously associated with AD. We also detected associations in three novel genes: IGHG3 (p = 9.8 × 10-7), an immunoglobulin gene whose antibodies interact with β-amyloid, a long non-coding RNA AC099552.4 (p = 1.2 × 10-7), and a zinc-finger protein ZNF655 (gene-based p = 5.0 × 10-6). The latter two suggest an important role for transcriptional regulation in AD pathogenesis.
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Affiliation(s)
- Joshua C Bis
- Department of Medicine (General Internal Medicine), University of Washington, Seattle, WA, USA
| | - Xueqiu Jian
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Brian W Kunkle
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Yuning Chen
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Kara L Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - William S Bush
- Case Western Reserve University, Cleveland Heights, OH, USA
| | - William J Salerno
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Daniel Lancour
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Yiyi Ma
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Alan E Renton
- Department of Neuroscience and Ronald M Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edoardo Marcora
- Department of Neuroscience and Ronald M Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John J Farrell
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Yi Zhao
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Liming Qu
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Shahzad Ahmad
- Erasmus University Medical Center, Rotterdam, Netherlands
| | - Najaf Amin
- Inserm, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Philippe Amouyel
- Inserm, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- Institut Pasteur de Lille, Lille, France
- University Lille, U1167-Excellence Laboratory LabEx DISTALZ, Lille, France
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Jennifer E Below
- Department of Medical Genetics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dominique Campion
- Department of Genetics and CNR-MAJ, Normandie Université, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
- Department of Research, Centre Hospitalier du Rouvray, Sotteville-lès-, Rouen, France
| | - Laura Cantwell
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Camille Charbonnier
- Department of Genetics and CNR-MAJ, Normandie Université, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Jaeyoon Chung
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Paul K Crane
- Department of Medicine (General Internal Medicine), University of Washington, Seattle, WA, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - L Adrienne Cupples
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, USA
| | - Jean-François Dartigues
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, F-33000, Bordeaux, France
| | - Stéphanie Debette
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, F-33000, Bordeaux, France
- Department of Neurology and Institute for Neurodegenerative Diseases, Bordeaux University Hospital, Memory Clinic, F-33000, Bordeaux, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut François Jacob, Direction de le Recherche Fondamentale, CEA, Evry, France
| | - Lucinda Fulton
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA
| | | | | | - Richard A Gibbs
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Alison Goate
- Department of Neuroscience and Ronald M Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin Grenier-Boley
- Inserm, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
| | - Seppo Helisalmi
- Institute of Clinical Medicine - Neurology and Department of Neurology, University of Eastern Finland, Kuopio, Finland
| | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Daniel P Howrigan
- Program in Medical and Population Genetics and Genetic Analysis Platform, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - M Arfan Ikram
- Erasmus University Medical Center, Rotterdam, Netherlands
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Jan Konrad
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Amanda Kuzma
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mark Lathrop
- McGill University and Génome Québec Innovation Centre, Montréal, Canada
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Honghuang Lin
- Department of Medicine (Computational Biomedicine), Boston University School of Medicine, Boston, MA, USA
| | - Kari Mattila
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | | | - Donna M Muzny
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Waleed Nasser
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Benjamin Neale
- Program in Medical and Population Genetics and Genetic Analysis Platform, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Kwangsik Nho
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Gaël Nicolas
- Department of Genetics and CNR-MAJ, Normandie Université, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Devanshi Patel
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Markus Perola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
- University of Tartu, Estonian Genome Center, Tartu, Estonia
| | - Bruce M Psaty
- Department of Medicine (General Internal Medicine), University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Services, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Olivier Quenez
- Department of Genetics and CNR-MAJ, Normandie Université, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Richard Redon
- Inserm, CNRS, Univ. Nantes, CHU Nantes, l'institut du thorax, Nantes, France
| | | | - Anne M Remes
- Institute of Clinical Medicine - Neurology and Department of Neurology, University of Eastern Finland, Kuopio, Finland
- Unit of Clinical Neuroscience, Neurology, University of Oulu and Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - Chloe Sarnowski
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Helena Schmidt
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University of Graz, Graz, Austria
| | - Michael Schmidt
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Reinhold Schmidt
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University of Graz, Graz, Austria
| | - Hilkka Soininen
- Institute of Clinical Medicine - Neurology and Department of Neurology, University of Eastern Finland, Kuopio, Finland
- Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | | | | | - Christophe Tzourio
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, team VINTAGE, UMR 1219, F-33000, Bordeaux, France
| | | | | | - Otto Valladares
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Li-San Wang
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Weixin Wang
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ellen Wijsman
- Department of Medicine (Medical Genetics), University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA
| | - Daniela Witten
- Department of Statistics, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Kim C Worley
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xiaoling Zhang
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Celine Bellenguez
- Inserm, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Jean-Charles Lambert
- Inserm, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Mitja I Kurki
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics and Genetic Analysis Platform, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics and Genetic Analysis Platform, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Mark Daly
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kathryn L Lunetta
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Anita L Destefano
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Departments of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Josée Dupuis
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | | | - Sudha Seshadri
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, USA
- Departments of Neurology, Boston University School of Medicine, Boston, MA, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
| | - Adam C Naj
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Myriam Fornage
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Lindsay A Farrer
- Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA.
- Departments of Neurology, Boston University School of Medicine, Boston, MA, USA.
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA.
- Department of Ophthalmology, Boston University School of Medicine, Boston, MA, USA.
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95
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Curi RA, Pereira GL, Alvarez MVN, Baldassini WA, Machado Neto OR, Chardulo LAL. Exome analysis and functional classification of identified variants in racing Quarter Horses. Anim Genet 2020; 51:716-721. [PMID: 32696541 DOI: 10.1111/age.12976] [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: 03/25/2020] [Revised: 04/27/2020] [Accepted: 06/15/2020] [Indexed: 11/26/2022]
Abstract
The main objectives of this study were to identify and functionally classify SNPs and indels by exome sequencing of animals of the racing line of Quarter Horses. Based on the individual genomic estimated breeding values (GEBVs) for maximum speed index (SImax) obtained for 349 animals, two groups of 20 extreme animals were formed. Of these individuals, 20 animals with high GEBVs for SImax and 19 with low GEBVs for SImax had their exons and 5' and 3' UTRs sequenced. Considering SNPs and indels, 105 182 variants were identified in the expressed regions of the Quarter Horse genome. Of these, 72 166 variants were already known and 33 016 are new variants and were deposited in a database. The analysis of the set of gene variants significantly related (Padjusted < 0.05) to extreme animals in conjunction with the predicted impact of the changes and the physiological role of protein product pointed to two candidate genes potentially related to racing performance: SLC3A1 on ECA15 and CCN6 on ECA10.
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Affiliation(s)
- R A Curi
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
| | - G L Pereira
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
| | - M V N Alvarez
- Department of Parasitology, Institute of Biosciences, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
| | - W A Baldassini
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
| | - O R Machado Neto
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
| | - L A L Chardulo
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
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96
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Marcou CA, Baudhuin LM. All Clinical Exomes Are Not Alike: Coverage Matters. Clin Chem 2020; 66:9-11. [PMID: 32609853 DOI: 10.1093/clinchem.2019.310615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 10/10/2019] [Indexed: 11/13/2022]
Affiliation(s)
- Cherisse A Marcou
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Linnea M Baudhuin
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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97
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Strianese O, Rizzo F, Ciccarelli M, Galasso G, D’Agostino Y, Salvati A, Del Giudice C, Tesorio P, Rusciano MR. Precision and Personalized Medicine: How Genomic Approach Improves the Management of Cardiovascular and Neurodegenerative Disease. Genes (Basel) 2020; 11:E747. [PMID: 32640513 PMCID: PMC7397223 DOI: 10.3390/genes11070747] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022] Open
Abstract
Life expectancy has gradually grown over the last century. This has deeply affected healthcare costs, since the growth of an aging population is correlated to the increasing burden of chronic diseases. This represents the interesting challenge of how to manage patients with chronic diseases in order to improve health care budgets. Effective primary prevention could represent a promising route. To this end, precision, together with personalized medicine, are useful instruments in order to investigate pathological processes before the appearance of clinical symptoms and to guide physicians to choose a targeted therapy to manage the patient. Cardiovascular and neurodegenerative diseases represent suitable models for taking full advantage of precision medicine technologies applied to all stages of disease development. The availability of high technology incorporating artificial intelligence and advancement progress made in the field of biomedical research have been substantial to understand how genes, epigenetic modifications, aging, nutrition, drugs, microbiome and other environmental factors can impact health and chronic disorders. The aim of the present review is to address how precision and personalized medicine can bring greater clarity to the clinical and biological complexity of these types of disorders associated with high mortality, involving tremendous health care costs, by describing in detail the methods that can be applied. This might offer precious tools for preventive strategies and possible clues on the evolution of the disease and could help in predicting morbidity, mortality and detecting chronic disease indicators much earlier in the disease course. This, of course, will have a major effect on both improving the quality of care and quality of life of the patients and reducing time efforts and healthcare costs.
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Affiliation(s)
- Oriana Strianese
- Clinical Research and Innovation, Clinica Montevergine S.p.A., 83013 Mercogliano, Italy; (O.S.); (C.D.G.)
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Baronissi, Italy; (F.R.); (Y.D.); (A.S.)
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Baronissi, Italy; (F.R.); (Y.D.); (A.S.)
| | - Michele Ciccarelli
- Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Baronissi, Italy; (M.C.); (G.G.)
| | - Gennaro Galasso
- Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Baronissi, Italy; (M.C.); (G.G.)
| | - Ylenia D’Agostino
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Baronissi, Italy; (F.R.); (Y.D.); (A.S.)
| | - Annamaria Salvati
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Baronissi, Italy; (F.R.); (Y.D.); (A.S.)
| | - Carmine Del Giudice
- Clinical Research and Innovation, Clinica Montevergine S.p.A., 83013 Mercogliano, Italy; (O.S.); (C.D.G.)
| | - Paola Tesorio
- Unit of Cardiology, Clinica Montevergine S.p.A., 83013 Mercogliano, Italy;
| | - Maria Rosaria Rusciano
- Clinical Research and Innovation, Clinica Montevergine S.p.A., 83013 Mercogliano, Italy; (O.S.); (C.D.G.)
- Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, 84084 Baronissi, Italy; (M.C.); (G.G.)
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98
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Shedding light on dark genes: enhanced targeted resequencing by optimizing the combination of enrichment technology and DNA fragment length. Sci Rep 2020; 10:9424. [PMID: 32523024 PMCID: PMC7287100 DOI: 10.1038/s41598-020-66331-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/23/2020] [Indexed: 12/16/2022] Open
Abstract
The exome contains many obscure regions difficult to explore with current short-read sequencing methods. Repetitious genomic regions prevent the unique alignment of reads, which is essential for the identification of clinically-relevant genetic variants. Long-read technologies attempt to resolve multiple-mapping regions, but they still produce many sequencing errors. Thus, a new approach is required to enlighten the obscure regions of the genome and rescue variants that would be otherwise neglected. This work aims to improve the alignment of multiple-mapping reads through the extension of the standard DNA fragment size. As Illumina can sequence fragments up to 550 bp, we tested different DNA fragment lengths using four major commercial WES platforms and found that longer DNA fragments achieved a higher genotypability. This metric, which indicates base calling calculated by combining depth of coverage with the confidence of read alignment, increased from hundreds to thousands of genes, including several associated with clinical phenotypes. While depth of coverage has been considered crucial for the assessment of WES performance, we demonstrated that genotypability has a greater impact in revealing obscure regions, with ~1% increase in variant calling in respect to shorter DNA fragments. Results confirmed that this approach enlightened many regions previously not explored.
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He X, Chen S, Li R, Han X, He Z, Yuan D, Zhang S, Duan X, Niu B. Comprehensive fundamental somatic variant calling and quality management strategies for human cancer genomes. Brief Bioinform 2020; 22:5854402. [PMID: 32510555 DOI: 10.1093/bib/bbaa083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 12/21/2022] Open
Abstract
Next-generation sequencing (NGS) technology has revolutionised human cancer research, particularly via detection of genomic variants with its ultra-high-throughput sequencing and increasing affordability. However, the inundation of rich cancer genomics data has resulted in significant challenges in its exploration and translation into biological insights. One of the difficulties in cancer genome sequencing is software selection. Currently, multiple tools are widely used to process NGS data in four stages: raw sequence data pre-processing and quality control (QC), sequence alignment, variant calling and annotation and visualisation. However, the differences between these NGS tools, including their installation, merits, drawbacks and application, have not been fully appreciated. Therefore, a systematic review of the functionality and performance of NGS tools is required to provide cancer researchers with guidance on software and strategy selection. Another challenge is the multidimensional QC of sequencing data because QC can not only report varied sequence data characteristics but also reveal deviations in diverse features and is essential for a meaningful and successful study. However, monitoring of QC metrics in specific steps including alignment and variant calling is neglected in certain pipelines such as the 'Best Practices Workflows' in GATK. In this review, we investigated the most widely used software for the fundamental analysis and QC of cancer genome sequencing data and provided instructions for selecting the most appropriate software and pipelines to ensure precise and efficient conclusions. We further discussed the prospects and new research directions for cancer genomics.
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Raspa M, Moultrie R, Wagner L, Edwards A, Andrews S, Frisch MK, Turner-Brown L, Wheeler A. Ethical, Legal, and Social Issues Related to the Inclusion of Individuals With Intellectual Disabilities in Electronic Health Record Research: Scoping Review. J Med Internet Res 2020; 22:e16734. [PMID: 32436848 PMCID: PMC7273235 DOI: 10.2196/16734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/17/2020] [Accepted: 02/22/2020] [Indexed: 01/31/2023] Open
Abstract
Background Data from electronic health records (EHRs) are increasingly used in the field of genetic research to further precision medicine initiatives. However, many of these efforts exclude individuals with intellectual disabilities, which often stem from genetic conditions. To include this important subpopulation in EHR research, important ethical, legal, and social issues should be considered. Objective The goal of this study was to review prior research to better understand what ethical, legal, and social issues may need further investigation when considering the research use of EHRs for individuals with genetic conditions that may result in intellectual disability. This information will be valuable in developing methods and best practices for involving this group in research given they are considered a vulnerable population that may need special research protections. Methods We conducted a scoping review to examine issues related to the use of EHRs for research purposes and those more broadly associated with genetic research. The initial search yielded a total of 460 unique citations. We used an evaluative coding process to determine relevancy for inclusion. Results This approach resulted in 59 articles in the following areas: informed consent, privacy and security, return of results, and vulnerable populations. The review included several models of garnering informed consent in EHR or genetic research, including tiered or categorical, blanket or general, open, and opt-out models. Second, studies reported on patients’ concerns regarding the privacy and security of EHR or genetic data, such as who has access, type of data use in research, identifiability, and risks associated with privacy breach. The literature on return of research results using biospecimens examined the dissension in the field, particularly when sharing individualized genetic results. Finally, work involving vulnerable populations highlighted special considerations when conducting EHR or genetic research. Conclusions The results frame important questions for researchers to consider when designing EHR studies, which include individuals with intellectual disabilities, including appropriate safeguards and protections.
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Affiliation(s)
- Melissa Raspa
- RTI International, Research Triangle Park, NC, United States
| | | | - Laura Wagner
- RTI International, Research Triangle Park, NC, United States
| | - Anne Edwards
- RTI International, Research Triangle Park, NC, United States
| | - Sara Andrews
- RTI International, Research Triangle Park, NC, United States
| | - Mary Katherine Frisch
- The University of North Carolina at Chapel Hill, TEACCH Autism Program, Chapel Hill, NC, United States
| | - Lauren Turner-Brown
- The University of North Carolina at Chapel Hill, TEACCH Autism Program, Chapel Hill, NC, United States
| | - Anne Wheeler
- RTI International, Research Triangle Park, NC, United States
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