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Heron EA, Valle G, Bernasconi A. Editorial: Identification of phenotypically important genomic variants. Front Bioinform 2023; 3:1328945. [PMID: 38025396 PMCID: PMC10668015 DOI: 10.3389/fbinf.2023.1328945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023] Open
Affiliation(s)
| | - Giorgio Valle
- Department of Biology, Università di Padova, Padova, Italy
| | - Anna Bernasconi
- Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Milan, Italy
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Mottaz A, Pasche E, Michel PA, Mottin L, Teodoro D, Ruch P. Designing an Optimal Expansion Method to Improve the Recall of a Genomic Variant Curation-Support Service. Stud Health Technol Inform 2022; 294:839-843. [PMID: 35612222 DOI: 10.3233/shti220603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The importance of genomic data for health is rapidly growing but accessing and gathering information about variants from different sources is hindered by highly heterogeneous representations of variants, as outlined by clinical associations (AMP/ASCO/CAP) in their recommendations. To enable a smooth and effective retrieval of variant-containing documents from different resources, we developed a tool (https://goldorak.hesge.ch/synvar/) that generates for any given SNP - including variant not present in existing databases - its corresponding description at the genome, transcript and protein levels. It provides variant descriptions in the HGVS format as well as in many non-standard formats found in the literature along with database identifiers. We present the SynVar service and evaluate its impact on the recall of a genomic variant curation-support service. Using SynVar to search variants in the literature enables to increase the recall by +133.8% without a strong impact on precision (i.e. 93%).
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Affiliation(s)
- Anaïs Mottaz
- HES-SO / HEG Geneva, Information Sciences, Geneva, Switzerland
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Emilie Pasche
- HES-SO / HEG Geneva, Information Sciences, Geneva, Switzerland
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Pierre-André Michel
- HES-SO / HEG Geneva, Information Sciences, Geneva, Switzerland
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Luc Mottin
- HES-SO / HEG Geneva, Information Sciences, Geneva, Switzerland
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Douglas Teodoro
- HES-SO / HEG Geneva, Information Sciences, Geneva, Switzerland
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
- Department of Radiology and Medical Informatics, University of Geneva, Geneva, Switzerland
| | - Patrick Ruch
- HES-SO / HEG Geneva, Information Sciences, Geneva, Switzerland
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
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Shu HY, Zhang W, Zheng CC, Gao MY, Li YC, Wang YG. Identification and Functional Characterization of a Low-Density Lipoprotein Receptor Gene Pathogenic Variant in Familial Hypercholesterolemia. Front Genet 2021; 12:650077. [PMID: 34497632 PMCID: PMC8419346 DOI: 10.3389/fgene.2021.650077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 06/01/2021] [Indexed: 11/13/2022] Open
Abstract
We report a single-point variant of low-density lipoprotein receptor (LDLR) in a Chinese proband with a clinical diagnosis of familial hypercholesterolemia (FH) with a comprehensive functional analysis. Target exome capture-based next-generation sequencing was used for sequencing and identification of genomic variants in the LDLR gene. The expression, cellular location, and function of the mutant LDLR were analyzed. Sequencing of LDLR in FH patients indicated a point variant of single-base substitution (G < A) at a position of 2389 in the 16th exon, which led to a loss of the 16th exon in the LDLR messenger RNA. This genomic variant was found to cause exon 16 deletion in the mutant LDLR protein. Subsequent functional analyses showed that the mutant LDLR was retained in the Golgi apparatus and rarely expressed in the cellular membranes of HepG2 cells. Accordingly, the intake ability of HepG2 cells with the mutant LDLR was significantly reduced (P < 0.05). In conclusion, our results suggest that a mutant with a single-base substitution (c. 2389G > A) in the 16th exon of the LDLR gene was associated with miscleavage of messenger RNA and the retention of mutant LDLR in the Golgi apparatus, which revealed a pathogenic variant in LDLR underlying the pathogenesis of FH.
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Affiliation(s)
- Hong-Yan Shu
- Department of Endocrinology and Metabolic Diseases, Zibo Municipal Hospital, Zibo, China
| | - Wei Zhang
- Department of Endocrinology and Metabolic Diseases, Zibo Municipal Hospital, Zibo, China
| | - Cong-Cong Zheng
- Department of Endocrinology and Metabolic Diseases, Zibo Municipal Hospital, Zibo, China
| | - Man-Yun Gao
- Department of Endocrinology and Metabolic Diseases, Zibo Municipal Hospital, Zibo, China
| | - Yong-Cun Li
- Department of Endocrinology and Metabolic Diseases, Zibo Municipal Hospital, Zibo, China
| | - Yan-Gang Wang
- Department of Endocrinology and Metabolic Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
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Antohi C, Haba D, Caba L, Ciofu ML, Drug VL, Bărboi OB, Dobrovăț BI, Pânzaru MC, Gorduza NC, Lupu VV, Dimofte D, Gug C, Gorduza EV. Novel Mutation in APC Gene Associated with Multiple Osteomas in a Family and Review of Genotype-Phenotype Correlations of Extracolonic Manifestations in Gardner Syndrome. Diagnostics (Basel) 2021; 11:1560. [PMID: 34573902 PMCID: PMC8466590 DOI: 10.3390/diagnostics11091560] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 12/24/2022] Open
Abstract
Gardner syndrome is a neoplasic disease that associates intestinal polyposis and colorectal adenocarcinoma with osteomas and soft tissue tumors determined by germline mutations in the APC gene. The early diagnosis and identification of high-risk individuals are important because patients have a 100% risk of colon cancer. We present the case of a family with Gardner syndrome. Cephalometric, panoramic X-rays and CBCT of the proband and her brother showed multiple osteomas affecting the skull bones, mandible and paranasal sinuses. The detailed family history showed an autosomal dominant transmission with the presence of the disease in the mother and maternal grandfather of the proband. Both had the typical signs of disease and died in the fourth decade of life. Based on these aspects the clinical diagnosis was Gardner syndrome. By gene sequencing, a novel pathogenic variant c.4609dup (p.Thr1537Asnfs*7) in heterozygous status was identified in the APC gene in both siblings. We reviewed literature data concerning the correlation between the localization of mutations in the APC gene and the extracolonic manifestations of familial adenomatous polyposis as well as their importance in early diagnosis and adequate oncological survey of patients and families based on abnormal genomic variants.
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Affiliation(s)
- Cristina Antohi
- Odontology-Periodontology-Fixed Prosthetics Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania;
| | - Danisia Haba
- Oral and Maxillofacial Surgery Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iaşi, Romania; (D.H.); (B.I.D.)
| | - Lavinia Caba
- Medicine of Mother and Child Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (M.-C.P.); (V.V.L.); (E.V.G.)
| | - Mihai Liviu Ciofu
- Oral and Maxillofacial Surgery Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iaşi, Romania; (D.H.); (B.I.D.)
| | - Vasile-Liviu Drug
- Medical I Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (V.-L.D.); (O.-B.B.)
| | - Oana-Bogdana Bărboi
- Medical I Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (V.-L.D.); (O.-B.B.)
| | - Bogdan Ionuț Dobrovăț
- Oral and Maxillofacial Surgery Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iaşi, Romania; (D.H.); (B.I.D.)
| | - Monica-Cristina Pânzaru
- Medicine of Mother and Child Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (M.-C.P.); (V.V.L.); (E.V.G.)
| | | | - Vasile Valeriu Lupu
- Medicine of Mother and Child Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (M.-C.P.); (V.V.L.); (E.V.G.)
| | | | - Cristina Gug
- Microscopic Morphology Department, “Victor Babes” University of Medicine and Pharmacy, 300041 Timișoara, Romania;
| | - Eusebiu Vlad Gorduza
- Medicine of Mother and Child Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (M.-C.P.); (V.V.L.); (E.V.G.)
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Lee K, Wei CH, Lu Z. Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature. Brief Bioinform 2021; 22:bbaa142. [PMID: 32770181 PMCID: PMC8138883 DOI: 10.1093/bib/bbaa142] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/07/2020] [Accepted: 06/25/2020] [Indexed: 12/28/2022] Open
Abstract
MOTIVATION To obtain key information for personalized medicine and cancer research, clinicians and researchers in the biomedical field are in great need of searching genomic variant information from the biomedical literature now than ever before. Due to the various written forms of genomic variants, however, it is difficult to locate the right information from the literature when using a general literature search system. To address the difficulty of locating genomic variant information from the literature, researchers have suggested various solutions based on automated literature-mining techniques. There is, however, no study for summarizing and comparing existing tools for genomic variant literature mining in terms of how to search easily for information in the literature on genomic variants. RESULTS In this article, we systematically compared currently available genomic variant recognition and normalization tools as well as the literature search engines that adopted these literature-mining techniques. First, we explain the problems that are caused by the use of non-standard formats of genomic variants in the PubMed literature by considering examples from the literature and show the prevalence of the problem. Second, we review literature-mining tools that address the problem by recognizing and normalizing the various forms of genomic variants in the literature and systematically compare them. Third, we present and compare existing literature search engines that are designed for a genomic variant search by using the literature-mining techniques. We expect this work to be helpful for researchers who seek information about genomic variants from the literature, developers who integrate genomic variant information from the literature and beyond.
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Affiliation(s)
- Kyubum Lee
- National Center for Biotechnology Information
| | | | - Zhiyong Lu
- National Center for Biotechnology Information
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Chang X, Zhong D, Wang X, Bonizzoni M, Li Y, Zhou G, Cui L, Wei X, Yan G. Genomic Variant Analyses in Pyrethroid Resistant and Susceptible Malaria Vector, Anopheles sinensis. G3 (Bethesda) 2020; 10:2185-93. [PMID: 32423920 DOI: 10.1534/g3.120.401279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Anopheles sinensis is a major malaria vector in Southeast Asia. Resistance to pyrethroid insecticides in this species has impeded malaria control in the region. Previous studies found that An. sinensis populations from Yunnan Province, China were highly resistant to deltamethrin and did not carry mutations in the voltage-gated sodium channel gene that cause knockdown resistance. In this study, we tested the hypothesis that other genomic variants are associated with the resistance phenotype. Using paired-end whole genome sequencing (DNA-seq), we generated 108 Gb of DNA sequence from deltamethrin -resistant and -susceptible mosquito pools with an average coverage of 83.3× depth. Using a stringent filtering method, we identified a total of 916,926 single nucleotide variants (SNVs), including 32,240 non-synonymous mutations. A total of 958 SNVs differed significantly in allele frequency between deltamethrin -resistant and -susceptible mosquitoes. Of these, 43 SNVs were present within 37 genes that code for immunity, detoxification, cuticular, and odorant proteins. A subset of 12 SNVs were randomly selected for genotyping of individual mosquitoes by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and showed consistent allele frequencies with the pooled DNA-seq derived allele frequencies. In addition, copy number variations (CNVs) were detected in 56 genes, including 33 that contained amplification alleles and 23 that contained deletion alleles in resistant mosquitoes compared to susceptible mosquitoes. The genomic variants described here provide a useful resource for future studies on the genetic mechanism of insecticide resistance in this important malaria vector species.
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Lee SY, Hwang H, Kang YM, Kim H, Kim DG, Jeong JE, Kim JY, Yoo JS. SAAVpedia: Identification, Functional Annotation, and Retrieval of Single Amino Acid Variants for Proteogenomic Interpretation. J Proteome Res 2019; 18:4133-4142. [PMID: 31612721 DOI: 10.1021/acs.jproteome.9b00366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Next-generation genome sequencing has enabled the discovery of numerous disease- or drug-response-associated nonsynonymous single nucleotide variants (nsSNVs) that alter the amino acid sequences of a protein. Although several studies have attempted to characterize pathogenic nsSNVs, few have been confirmed as single amino acid variants (SAAVs) at the protein level. Here we developed the SAAVpedia platform to identify, annotate, and retrieve pathogenic SAAV candidates from proteomic and genomic data. The platform consists of four modules: SAAVidentifier, SAAVannotator, SNV/SAAVretriever, and SAAVvisualizer. The SAAVidentifier provides a reference database containing 18 206 090 SAAVs and performs the identification and quality assessment of SAAVs. The SAAVannotator provides functional annotation with biological, clinical, and pharmacological information for the interpretation of condition-specific SAAVs. The SNV/SAAVretriever module enables bidirectional navigation between relevant SAAVs and nsSNVs with diverse genomic and proteomic data. SAAVvisualizer provides various statistical plots based on functional annotations of detected SAAVs. To demonstrate the utility of SAAVpedia, the proteogenomic pipeline with protein-protein interaction network analysis was applied to proteomic data from breast cancer and glioblastoma patients. We identified 1326 and 12 breast-cancer- and glioblastoma-related genes that contained one or more SAAVs, including BRCA2 and FAM49B, respectively. SAAVpedia is a suitable platform for confirming whether a genomic variant is maintained in an amino acid sequence. Furthermore, as a result of the SAAV discovery of these positive controls, the SAAVpedia could play a key role in the protein functional study for the Human Proteome Project (HPP).
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Affiliation(s)
- Soo Youn Lee
- Research Center for Bioconvergence Analysis , Korea Basic Science Institute , 162 Yeongudaji-ro , Cheongju 28119 , Korea
| | - Heeyoun Hwang
- Research Center for Bioconvergence Analysis , Korea Basic Science Institute , 162 Yeongudaji-ro , Cheongju 28119 , Korea
| | - Young-Mook Kang
- Drug Information Platform Center , Korea Research Institute of Chemical Technology , 141 Gajeong-ro , Daejeon 34114 , Korea
| | - Hyejin Kim
- Research Center for Bioconvergence Analysis , Korea Basic Science Institute , 162 Yeongudaji-ro , Cheongju 28119 , Korea.,Graduate School of Analytical Science and Technology , Chungnam National University , 99 Daehak-ro , Daejeon 34134 , Korea
| | - Dong Geun Kim
- Research Center for Bioconvergence Analysis , Korea Basic Science Institute , 162 Yeongudaji-ro , Cheongju 28119 , Korea.,Graduate School of Analytical Science and Technology , Chungnam National University , 99 Daehak-ro , Daejeon 34134 , Korea
| | - Ji Eun Jeong
- Research Center for Bioconvergence Analysis , Korea Basic Science Institute , 162 Yeongudaji-ro , Cheongju 28119 , Korea.,Graduate School of Analytical Science and Technology , Chungnam National University , 99 Daehak-ro , Daejeon 34134 , Korea
| | - Jin Young Kim
- Research Center for Bioconvergence Analysis , Korea Basic Science Institute , 162 Yeongudaji-ro , Cheongju 28119 , Korea
| | - Jong Shin Yoo
- Research Center for Bioconvergence Analysis , Korea Basic Science Institute , 162 Yeongudaji-ro , Cheongju 28119 , Korea.,Graduate School of Analytical Science and Technology , Chungnam National University , 99 Daehak-ro , Daejeon 34134 , Korea
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Yang C, Song Y, Chen Z, Yuan X, Chen X, Ding G, Guan Y, McGrath M, Song C, Tong Y, Wang H. A Nonsense Mutation in COL4A4 Gene Causing Isolated Hematuria in Either Heterozygous or Homozygous State. Front Genet 2019; 10:628. [PMID: 31312213 PMCID: PMC6614519 DOI: 10.3389/fgene.2019.00628] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/17/2019] [Indexed: 01/15/2023] Open
Abstract
Alport syndrome (AS) is a hereditary nephropathy characterized by glomerular basement membrane lesions. AS shows a relatively rare entity with autosomal dominant gene mutation (accounts for less than 5% of AS cases) and is widely believed to be a consequence of heterozygous variants in the COL4A3 and COL4A4 genes. Until now, there have been no reports of homozygous variants in genes in AS patients, and it is scarce to detect both homozygous and heterozygous variants in a single AS pedigree. We performed genetic analysis by exome sequencing (exome-seq) in a Chinese family with AS and found four individuals harboring the COL4A4 c.4599T > G variant, a novel COL4A4 nonsense mutation that gains stop codon and results in a truncated protein. The proband and her two siblings were determined to be heterozygous, whereas their mother was homozygous. The proband satisfied the criteria for the diagnosis of AS, which included clinical manifestations of microscopic hematuria and proteinuria, and pathological features of the glomerular basement membrane (GBM), including irregular thickening and splitting. However, the other three individuals who were homozygous or heterozygous for the variant exhibited mild clinical features with isolated microscopic hematuria. In summary, we identified a novel pathogenic variant in either the heterozygous or homozygous state of the COL4A4 gene in a Chinese family with AS. Our results also suggest that the severity of clinical manifestations may not be entirely attributed to by the COL4A4 genetic variant itself in patients.
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Affiliation(s)
- Cheng Yang
- Renal Department, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuan Song
- Renal Department, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhaowei Chen
- Renal Department, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiaohan Yuan
- Renal Department, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xinhua Chen
- Renal Department, Renmin Hospital of Wuhan University, Wuhan, China
| | - Guohua Ding
- Renal Department, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yang Guan
- Ultrastructure Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Mary McGrath
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Chunhua Song
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Yongqing Tong
- Department of Laboratory Science, Renmin Hospital of Wuhan University, Wuhan, China
| | - Huiming Wang
- Renal Department, Renmin Hospital of Wuhan University, Wuhan, China
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