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Qian W, Ma N, Zeng X, Shi M, Wang M, Yang Z, Tsui SKW. Identification of novel single nucleotide variants in the drug resistance mechanism of Mycobacterium tuberculosis isolates by whole-genome analysis. BMC Genomics 2024; 25:478. [PMID: 38745294 PMCID: PMC11094924 DOI: 10.1186/s12864-024-10390-3] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) represents a major global health challenge. Drug resistance in Mycobacterium tuberculosis (MTB) poses a substantial obstacle to effective TB treatment. Identifying genomic mutations in MTB isolates holds promise for unraveling the underlying mechanisms of drug resistance in this bacterium. METHODS In this study, we investigated the roles of single nucleotide variants (SNVs) in MTB isolates resistant to four antibiotics (moxifloxacin, ofloxacin, amikacin, and capreomycin) through whole-genome analysis. We identified the drug-resistance-associated SNVs by comparing the genomes of MTB isolates with reference genomes using the MuMmer4 tool. RESULTS We observed a strikingly high proportion (94.2%) of MTB isolates resistant to ofloxacin, underscoring the current prevalence of drug resistance in MTB. An average of 3529 SNVs were detected in a single ofloxacin-resistant isolate, indicating a mutation rate of approximately 0.08% under the selective pressure of ofloxacin exposure. We identified a set of 60 SNVs associated with extensively drug-resistant tuberculosis (XDR-TB), among which 42 SNVs were non-synonymous mutations located in the coding regions of nine key genes (ctpI, desA3, mce1R, moeB1, ndhA, PE_PGRS4, PPE18, rpsA, secF). Protein structure modeling revealed that SNVs of three genes (PE_PGRS4, desA3, secF) are close to the critical catalytic active sites in the three-dimensional structure of the coding proteins. CONCLUSION This comprehensive study elucidates novel resistance mechanisms in MTB against antibiotics, paving the way for future design and development of anti-tuberculosis drugs.
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Affiliation(s)
- Weiye Qian
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Nan Ma
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Xi Zeng
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mai Shi
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Mingqiang Wang
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Zhiyuan Yang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, 310018, China.
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China.
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2
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Huang M, Zhang Q, Jiao J, Shi J, Xu Y, Zhang C, Zhou R, Liu W, Liang Y, Chen H, Wang Y, Xu Z, Hu P. Comprehensive genetic analysis of facioscapulohumeral muscular dystrophy by Nanopore long-read whole-genome sequencing. J Transl Med 2024; 22:451. [PMID: 38741136 DOI: 10.1186/s12967-024-05259-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Facioscapulohumeral muscular dystrophy (FSHD) is a high-prevalence autosomal dominant neuromuscular disease characterized by significant clinical and genetic heterogeneity. Genetic diagnosis of FSHD remains a challenge because it cannot be detected by standard sequencing methods and requires a complex diagnosis workflow. METHODS We developed a comprehensive genetic FSHD detection method based on Oxford Nanopore Technologies (ONT) whole-genome sequencing. Using a case-control design, we applied this procedure to 29 samples and compared the results with those from optical genome mapping (OGM), bisulfite sequencing (BSS), and whole-exome sequencing (WES). RESULTS Using our ONT-based method, we identified 59 haplotypes (35 4qA and 24 4qB) among the 29 samples (including a mosaic sample), as well as the number of D4Z4 repeat units (RUs). The pathogenetic D4Z4 RU contraction identified by our ONT-based method showed 100% concordance with OGM results. The methylation levels of the most distal D4Z4 RU and the double homeobox 4 gene (DUX4) detected by ONT sequencing are highly consistent with the BSS results and showed excellent diagnostic efficiency. Additionally, our ONT-based method provided an independent methylation profile analysis of two permissive 4qA alleles, reflecting a more accurate scenario than traditional BSS. The ONT-based method detected 17 variations in three FSHD2-related genes from nine samples, showing 100% concordance with WES. CONCLUSIONS Our ONT-based FSHD detection method is a comprehensive method for identifying pathogenetic D4Z4 RU contractions, methylation level alterations, allele-specific methylation of two 4qA haplotypes, and variations in FSHD2-related genes, which will all greatly improve genetic testing for FSHD.
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Affiliation(s)
- Mingtao Huang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China
| | - Qinxin Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China
| | - Jiao Jiao
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China
| | - Jianquan Shi
- Department of Neurology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, 210006, People's Republic of China
| | - Yiyun Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China
| | - Cuiping Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China
| | - Ran Zhou
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China
| | - Wenwen Liu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China
| | - Yixuan Liang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China
| | - Hao Chen
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China
| | - Yan Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China.
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China.
| | - Ping Hu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, Jiangsu, 210004, People's Republic of China.
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Cheng X, Jiang G, Zhou X, Wang J, Zhao Z, Zhang J, Ni T. The landscape and clinical relevance of intronic polyadenylation in human cancers. J Genet Genomics 2024:S1673-8527(24)00099-7. [PMID: 38740258 DOI: 10.1016/j.jgg.2024.04.014] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/07/2024] [Accepted: 04/25/2024] [Indexed: 05/16/2024]
Abstract
Intronic polyadenylation (IPA) is an RNA 3' end processing event which has been reported to play important roles in cancer development. However, the comprehensive landscape of IPA events across various cancer types is lacking. Here, we apply IPAFinder to identify and quantify IPA events in 10,383 samples covering all 33 cancer types from The Cancer Genome Atlas (TCGA) project. We totally identify 21,835 IPA events, almost half of which are ubiquitously expressed. We identify 2,761 unique dynamically changed IPA events across cancer types. Furthermore, we observe 8,855 non-redundant clinically relevant IPA events, which could potentially be used as prognostic indicators. Our analysis also reveals that dynamic IPA usage within cancer signaling pathways may affect drug response. Finally, we develop a user-friendly data portal, IPACancer Atlas (http://www.tingni-lab.com/Pancan_IPA/), to search and explore IPAs in cancer.
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Affiliation(s)
- Xiaomeng Cheng
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Guanghui Jiang
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaolan Zhou
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jing Wang
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhaozhao Zhao
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China; MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jiayu Zhang
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, National Clinical Research Center for Aging and Medicine, Huashan Hospital, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Center for Evolutionary Biology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia 010070, China.
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Cebeci YE, Erturk RA, Ergun MA, Baysan M. Improving somatic exome sequencing performance by biological replicates. BMC Bioinformatics 2024; 25:124. [PMID: 38519906 PMCID: PMC10958848 DOI: 10.1186/s12859-024-05742-5] [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] [Received: 09/26/2023] [Accepted: 03/13/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) technologies offer fast and inexpensive identification of DNA sequences. Somatic sequencing is among the primary applications of NGS, where acquired (non-inherited) variants are based on comparing diseased and healthy tissues from the same individual. Somatic mutations in genetic diseases such as cancer are tightly associated with genomic instability. Genomic instability increases heterogenity, complicating sequencing efforts further, a task already challenged by the presence of short reads and repetitions in human DNA. This leads to low concordance among studies and limits reproducibility. This limitation is a significant problem since identified mutations in somatic sequencing are major biomarkers for diagnosis and the primary input of targeted therapies. Benchmarking studies were conducted to assess the error rates and increase reproducibility. Unfortunately, the number of somatic benchmarking sets is very limited due to difficulties in validating true somatic variants. Moreover, most NGS benchmarking studies are based on relatively simpler germline (inherited) sequencing. Recently, a comprehensive somatic sequencing benchmarking set was published by Sequencing Quality Control Phase 2 (SEQC2). We chose this dataset for our experiments because it is a well-validated, cancer-focused dataset that includes many tumor/normal biological replicates. Our study has two primary goals. First goal is to determine how replicate-based consensus approaches can improve the accuracy of somatic variant detection systems. Second goal is to develop highly predictive machine learning (ML) models by employing replicate-based consensus variants as labels during the training phase. RESULTS Ensemble approaches that combine alternative algorithms are relatively common; here, as an alternative, we study the performance enhancement potential of biological replicates. We first developed replicate-based consensus approaches that utilize the biological replicates available in this study to improve variant calling performance. Subsequently, we trained ML models using these biological replicates and achieved performance comparable to optimal ML models, those trained using high-confidence variants identified in advance. CONCLUSIONS Our replicate-based consensus approach can be used to improve variant calling performance and develop efficient ML models. Given the relative ease of obtaining biological replicates, this strategy allows for the development of efficient ML models tailored to specific datasets or scenarios.
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Affiliation(s)
- Yunus Emre Cebeci
- Department of Computer Engineering, Istanbul Technical University, 34469, Istanbul, Turkey
| | - Rumeysa Aslihan Erturk
- Department of Computer Engineering, Istanbul Technical University, 34469, Istanbul, Turkey
| | - Mehmet Arif Ergun
- Department of Computer Engineering, Istanbul Technical University, 34469, Istanbul, Turkey
| | - Mehmet Baysan
- Department of Computer Engineering, Istanbul Technical University, 34469, Istanbul, Turkey.
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Montúfar-Robles I, Barbosa-Cobos RE, Romero-Díaz J, Valencia-Pacheco G, Cabello-Gutiérrez C, Ramírez-Bello J. The functional TNFAIP3 rs2230926T/G (Phe127Cys) variant confers risk to systemic lupus erythematosus in a Latin American population. Hum Immunol 2024; 85:110736. [PMID: 38042682 DOI: 10.1016/j.humimm.2023.110736] [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] [Received: 05/22/2023] [Revised: 11/03/2023] [Accepted: 11/27/2023] [Indexed: 12/04/2023]
Abstract
TNFAIP3 is a classical systemic lupus erythematosus (SLE)-associated risk locus identified by genome-wide association studies (GWASs) and replicated by candidate gene association studies primarily in Caucasians and Asians. However, in Latin American populations, its role on SLE susceptibility is not known. We conducted a case-control study to evaluate whether the TNFAIP3 rs2230926T/G (Phe127Cys) variant is associated with risk of developing SLE in a cohort of Mexican patients. The TNFAIP3 rs2230926T/G variant was analyzed in 561 patients with SLE and 499 control subjects, using TaqMan probes. We found that the G allele was associated with susceptibility to SLE under the allelic (OR 2.09, p = 0.005) and genotypic (OR 2.14, p = 0.004) models. In conclusion, our results show that TNFAIP3 rs2230926T/G is a risk factor for the development of SLE in the Mexican population.
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Affiliation(s)
| | | | - Juanita Romero-Díaz
- Departamento de Inmunología y Reumatología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Guillermo Valencia-Pacheco
- Laboratorio de Hematología Centro de Investigaciones Regionales "Dr. Hideyo Noguchi", Universidad Autónoma de Yucatán, Yucatán, Mexico
| | - Carlos Cabello-Gutiérrez
- Departamento de Investigación en Virología y Micología, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Julian Ramírez-Bello
- Subdirección de Investigación Clínica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico.
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Łaźniak S, Sowińska A, Roszak A, Lianeri M, Pławski A, Mostowska A, Jagodziński PP. Role of rs2366152 single-nucleotide variant located in the long noncoding RNA HOTAIR gene in the cervical cancer susceptibility in a Polish population. J Appl Genet 2023:10.1007/s13353-023-00822-3. [PMID: 38157198 DOI: 10.1007/s13353-023-00822-3] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024]
Abstract
Previous studies have demonstrated an association of the NC_000012.12:g.53962605A > G, (rs2366152) single-nucleotide variant (SNV) situated in the long noncoding homeobox transcript antisense intergenic RNA (HOTAIR) gene with HPV16-related cervical cancer pathogenesis. However, little is known about the role of rs2366152 in cervical cancer progression and how oral birth control pills use, parity, menopausal status, and cigarette smoking influence the role of rs2366152 in cervical carcinogenesis. HRM analysis was used to determine the rs2366152 SNV prevalence in patients with cervical squamous cell carcinoma (SCC) (n = 470) and control group (n = 499) in a Polish Caucasian population. Logistic regression analyses were adjusted for age, using birth control pills, parity, menopausal status, and cigarette smoking. Our genetic studies revealed that the G/A vs. A/A (p = 0.031, p = 0.002) and G/A + G/G vs. A/A (p = 0.035, p = 0.003) genotypes of rs2366152 SNV were significantly related to the grade of differentiation G3 and tumor stage III, respectively. Moreover, cervical cancer risk increased among patients with rs2366152 SNV who smoked cigarettes and used birth control pills. We conclude that rs2366152 may promote the invasion and rapid growth of cervical SCC. Moreover, rs2366152 with cigarette smoking and using birth control pills can also be a risk factor for cervical cancerogenesis.
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Affiliation(s)
- Sebastian Łaźniak
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, 6 Święcickiego St., 60-781, Poznań, Poland
| | - Anna Sowińska
- Department of Computer Science and Statistics, Poznań University of Medical Sciences Poznań, Poznań, Poland
| | - Andrzej Roszak
- Department of Radiotherapy and Gynecological Oncology, Greater Poland Cancer Center, Poznań, Poland
- Department of Electroradiology, Poznań University of Medical Sciences, Poznań, Poland
| | - Margarita Lianeri
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, 6 Święcickiego St., 60-781, Poznań, Poland
| | - Andrzej Pławski
- Institute of Human Genetics, Polish Academy of Sciences, 60-479, Poznan, Poland
| | - Adrianna Mostowska
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, 6 Święcickiego St., 60-781, Poznań, Poland
| | - Paweł Piotr Jagodziński
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, 6 Święcickiego St., 60-781, Poznań, Poland.
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Long J, Chen M, Yu Y, Wu Q, Yang X. Triple-recognition strategy for one-pot detection of single nucleotide variants by aligner-mediated cleavage-triggered exponential amplification. Anal Chim Acta 2023; 1276:341617. [PMID: 37573107 DOI: 10.1016/j.aca.2023.341617] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 08/14/2023]
Abstract
The detection of single nucleotide variants (SNVs) is important for the diagnosis and treatment of cancer. To date, researchers have devised several methods to detect SNVs, but most of them are complex and time-consuming. To improve SNVs detection specificity and sensitivity, we developed a triple-recognition strategy, which facilitates aligner-mediated cleavage-triggered exponential amplification (Trec-AMC-EXPAR) for the rapid, specific, and one-pot detection of SNV. Under optimized conditions, Trec-AMC-EXPAR detected two clinically significant SNVs, PIK3CAH1047R and EGFR L858R within 80 min, with a reliable detection of 0.1% SNV in the wide type, which is lower than that of allele-specific PCR (AS-PCR) for detecting SNV. Finally, by spiking into normal human serum samples, mutants mixed with the wild-type targets in different ratios were analyzed, resulting in the relative standard deviation (RSD) of recovery ratios <3%. The findings suggested the potential application of Trec-AMC-EXPAR in clinical disease diagnosis. In summary, the proposed Trec-AMC-EXPAR technique provides a novel fast and convenient method for one-pot detection of SNV with high sensitivity and specificity.
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Affiliation(s)
- Jinyan Long
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Mengqi Chen
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Yang Yu
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Qiaomin Wu
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Xiaolan Yang
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China.
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Suominen L, Sjöstedt N, Vellonen KS, Gynther M, Auriola S, Kidron H. In vitro identification of decreased function phenotype ABCG2 variants. Eur J Pharm Sci 2023; 188:106527. [PMID: 37451410 DOI: 10.1016/j.ejps.2023.106527] [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] [Received: 03/27/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Reduced activity of efflux transporter ABCG2, caused e.g., by inhibition or decreased function genetic variants, can increase drug absorption and plasma levels. ABCG2 has one clinically significant single nucleotide variant Q141K (c.421C>A), which leads to decreased protein levels and transport activity. In addition to Q141K, ABCG2 has over 500 rare (<1% minor allele frequency) nonsynonymous variants, but their functionality remains unknown. We studied the transport activity and abundance of 30 rare ABCG2 variants. The variants were transiently expressed in HEK293 cells. Transport activity and protein abundance were measured from inside-out crude membrane vesicles. Results were normalised to the reference ABCG2, while Q141K was used to categorise variants into decreased and normal function phenotypes based on their apparent transport activity. Fourteen variants (G80E, D128V, T434M, Q437R, C438R, C438W, C438Y, L479S, P480L, S486N, T512N, S519P, G553D and K647E) had similar or lower apparent transport activity than Q141K and thus were categorised as having a decreased function phenotype. Protein abundance could not explain all of the observed changes in transport activity: Only six variants (D128V, Q437R, C438R, S519P, G553D, and K647E) had similar or lower abundance compared to Q141K. The decreased function variants may increase systemic drug exposure and therefore cause interindividual variability in pharmacokinetics. In the future, in vitro phenotype classification may help to design personalised drug treatments.
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Affiliation(s)
- Laura Suominen
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki FI-00014, Finland
| | - Noora Sjöstedt
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki FI-00014, Finland
| | | | - Mikko Gynther
- School of Pharmacy, University of Eastern Finland, Kuopio FI-70210, Finland
| | - Seppo Auriola
- School of Pharmacy, University of Eastern Finland, Kuopio FI-70210, Finland
| | - Heidi Kidron
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki FI-00014, Finland.
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Luo JQ, Mao SS, Chen JY, Ke XY, Zhu YF, Huang W, Sun HM, Liu ZJ. Antithrombin III deficiency in a patient with recurrent venous thromboembolism: A case report. World J Clin Cases 2023; 11:4956-4960. [PMID: 37583989 PMCID: PMC10424044 DOI: 10.12998/wjcc.v11.i20.4956] [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] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/19/2023] [Accepted: 06/26/2023] [Indexed: 07/06/2023] Open
Abstract
BACKGROUND Antithrombin III (AT3) deficiency, an autosomal dominant disease, increases the likelihood of an individual developing venous thromboembolism (VTE). Long-term anticoagulation treatment is required for those suffering from AT3 deficiency. CASE SUMMARY A man aged 23, who had a history of deep venous thrombosis (DVT), experienced recurrent pain and swelling in his right lower extremity for three days following withdrawal of Rivaroxaban. He was diagnosed with DVT and antithrombin III deficiency as genetic testing revealed a single nucleotide variant in SERPINC1 (c.667T>C, p.S223P). The patient was advised to accept long-term anticoagulant therapy. CONCLUSION Inherited AT3 deficiency due to SERPINC1 mutations results in recurrent VTE. Patients may benefit from long-term anticoagulant therapy.
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Affiliation(s)
- Jia-Qing Luo
- Department of Vascular Surgery, Changxing People's Hospital, Changxing 313100, Zhejiang Province, China
| | - Shuai-Shuai Mao
- Department of Endocrinology, Changxing People's Hospital, Changxing 313100, Zhejiang Province, China
| | - Jin-Yi Chen
- Department of Vascular Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310000, Zhejiang Province, China
| | - Xue-Ying Ke
- Department of Vascular Surgery, Sir Runrun Shaw Hospital of Zhejiang University School of Medicine, Hangzhou 310000, Zhejiang Province, China
| | - Yue-Feng Zhu
- Department of Vascular Surgery, Sir Runrun Shaw Hospital of Zhejiang University School of Medicine, Hangzhou 310000, Zhejiang Province, China
| | - Wei Huang
- Department of General Surgery, Changxing People's Hospital, Changxing 313100, Zhejiang Province, China
| | - Hai-Ming Sun
- Department of Vascular Surgery, Changxing People's Hospital, Changxing 313100, Zhejiang Province, China
| | - Zhen-Jie Liu
- Department of Vascular Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310000, Zhejiang Province, China
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Wrønding T, Vomstein K, Bosma EF, Mortensen B, Westh H, Heintz JE, Mollerup S, Petersen AM, Ensign LM, DeLong K, van Hylckama Vlieg JE, Thomsen AB, Nielsen HS. Antibiotic-free vaginal microbiota transplant with donor engraftment, dysbiosis resolution and live birth after recurrent pregnancy loss: a proof of concept case study. EClinicalMedicine 2023; 61:102070. [PMID: 37528843 PMCID: PMC10388571 DOI: 10.1016/j.eclinm.2023.102070] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 08/03/2023] Open
Abstract
Background Vaginal dysbiosis covers imbalances in the vaginal microbiota, defined by altered composition of bacteria, viruses, and fungi and is associated with euploid pregnancy losses, premature birth, infertility, or bacterial vaginosis. A large proportion of women who have vaginal dysbiosis do not experience any symptoms. Antibiotics are the traditional treatment, recently combined with local probiotics in some cases. Vaginal Microbiota Transplantation (VMT) with eubiotic vaginal bacterial microbiota after antibiotic eradication of pathogens has successfully been performed in a case study with five patients, but no VMT has been performed without the use of antibiotics. Methods This is a proof of concept case study. The patient was found to have vaginal dysbiosis at the RPL clinic at Copenhagen University Hospital Hvidovre, Denmark on the 23rd of June 2021. She was offered and accepted to receive experimental treatment in the form of a VMT as a compassionate use case. VMT is the transfer of cervicovaginal secretions (CVS) from a healthy donor with a Lactobacillus-dominant vaginal microbiome to a recipient with a dysbiotic vaginal microbiome. CVS is a mixture of e.g., mucus, bacteria, metabolites present in the vaginal canal. Potential donors were thoroughly screened for the absence of STIs, and the most suitable donor sample for the specific patient in this study was determined via an in vitro microbiome competition assay. Findings A 30-year-old patient with one livebirth and a complicated pregnancy history of two stillbirths and 1 s trimester pregnancy loss in gestational weeks 27 (2019), 17 (2020) and 23 (2020) respectively with complaints of vaginal irritation and discharge that had aggravated in all her pregnancies. Her vaginal microbiome composition showed a 90% dominance of Gardnerella spp. After one VMT there was a complete shift in microbiome composition to 81.2% L. crispatus and 9% L. jensenii with a concurrent resolvement of vaginal symptoms. Single nucleotide polymorphism-analysis confirmed her microbiome to be of donor origin and it remain stable now 1.5 years after the VMT. Five months after the VMT she became pregnant and has successfully delivered a healthy baby at term. Interpretation Here we report a successful VMT with confirmed donor strain engraftment followed by a successful pregnancy and delivery after a series of late pregnancy losses/stillbirths. Findings suggest that VMT is a potential treatment for severe vaginal dysbiosis. Further, larger studies are required. Funding The study was partially funded (i.e., analysis costs) by Freya Biosciences Aps, Fruebjergvej, 2100 Copenhagen, Denmark.
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Affiliation(s)
- Tine Wrønding
- Department of Obstetrics and Gynecology, The Fertility Clinic, Hvidovre University Hospital, Copenhagen, Denmark
| | - Kilian Vomstein
- Department of Obstetrics and Gynecology, The Fertility Clinic, Hvidovre University Hospital, Copenhagen, Denmark
| | | | | | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Julie Elm Heintz
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark
| | - Sarah Mollerup
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark
| | - Andreas Munk Petersen
- Department of Clinical Microbiology, Hvidovre University Hospital, Copenhagen, Denmark
- Department of Gastroenterology, Hvidovre University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Laura M. Ensign
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Departments of Gynecology and Obstetrics, Infectious Diseases, and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | | | | | | | - Henriette Svarre Nielsen
- Department of Obstetrics and Gynecology, The Fertility Clinic, Hvidovre University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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11
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Bassani Borges J, Fernandes Oliveira V, Dagli-Hernandez C, Monteiro Ferreira G, Kristini Almendros Afonso Barbosa T, da Silva Rodrigues Marçal E, Los B, Barbosa Malaquias V, Hernandes Bortolin R, Caroline Costa Freitas R, Akira Mori A, Medeiros Bastos G, Marques Gonçalves R, Branco Araújo D, Zatz H, Bertolami A, Arpad Faludi A, Chiara Bertolami M, Guerra de Moraes Rego Souza A, Ítalo Dias França J, Strelow Thurow H, Dominguez Crespo Hirata T, Takashi Imoto Nakaya H, Elim Jannes C, da Costa Pereira A, Nogueira Silbiger V, Ducati Luchessi A, Nayara Góes Araújo J, Arruda Nakazone M, Silva Carmo T, Rossi Silva Souza D, Moriel P, Yu Ting Wang J, Satya Naslavsky M, Gorjão R, Cristina Pithon-Curi T, Curi R, Moreno Fajardo C, Lin Wang HT, Regina Garófalo A, Cerda A, Ferraz Sampaio M, Dominguez Crespo Hirata R, Hiroyuki Hirata M. Identification of pathogenic variants in the Brazilian cohort with Familial Hypercholesterolemia using exon-targeted gene sequencing. Gene 2023; 875:147501. [PMID: 37217153 DOI: 10.1016/j.gene.2023.147501] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 05/24/2023]
Abstract
Familial hypercholesterolemia (FH) is a monogenic disease characterized by high plasma low-density lipoprotein cholesterol (LDL-c) levels and increased risk of premature atherosclerotic cardiovascular disease. Mutations in FH-related genes account for 40% of FH cases worldwide. In this study, we aimed to assess the pathogenic variants in FH-related genes in the Brazilian FH cohort FHBGEP using exon-targeted gene sequencing (ETGS) strategy. FH patients (n=210) were enrolled at five clinical sites and peripheral blood samples were obtained for laboratory testing and genomic DNA extraction. ETGS was performed using MiSeq platform (Illumina). To identify deleterious variants in LDLR, APOB, PCSK9, and LDLRAP1, the long-reads were subjected to Burrows-Wheeler Aligner (BWA) for alignment and mapping, followed by variant calling using Genome Analysis Toolkit (GATK) and ANNOVAR for variant annotation. The variants were further filtered using in-house custom scripts and classified according to the American College Medical Genetics and Genomics (ACMG) guidelines. A total of 174 variants were identified including 85 missense, 3 stop-gain, 9 splice-site, 6 InDel, and 71 in regulatory regions (3'UTR and 5'UTR). Fifty-two patients (24.7%) had 30 known pathogenic or likely pathogenic variants in FH-related genes according to the American College Medical and Genetics and Genomics guidelines. Fifty-three known variants were classified as benign, or likely benign and 87 known variants have shown uncertain significance. Four novel variants were discovered and classified as such due to their absence in existing databases. In conclusion, ETGS and in silico prediction studies are useful tools for screening deleterious variants and identification of novel variants in FH-related genes, they also contribute to the molecular diagnosis in the FHBGEP cohort.
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Affiliation(s)
- Jéssica Bassani Borges
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000 SP, Brazil; Laboratory of Molecular Research in Cardiology, Institute of Cardiology Dante Pazzanese, Sao Paulo 04012-909, Brazil; Department of Teaching and Research, Real and Benemerita Associação Portuguesa de Beneficiencia, Sao Paulo 01323-001, Brazil
| | - Victor Fernandes Oliveira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000 SP, Brazil
| | - Carolina Dagli-Hernandez
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000 SP, Brazil
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000 SP, Brazil; Laboratory of Molecular Research in Cardiology, Institute of Cardiology Dante Pazzanese, Sao Paulo 04012-909, Brazil
| | | | - Elisangela da Silva Rodrigues Marçal
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000 SP, Brazil; Laboratory of Molecular Research in Cardiology, Institute of Cardiology Dante Pazzanese, Sao Paulo 04012-909, Brazil
| | - Bruna Los
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000 SP, Brazil
| | - Vanessa Barbosa Malaquias
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000 SP, Brazil
| | - Raul Hernandes Bortolin
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000 SP, Brazil; Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, United States
| | - Renata Caroline Costa Freitas
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000 SP, Brazil; Department of Cardiac Surgery, Boston Children's Hospital, Boston, MA 02115, United States
| | - Augusto Akira Mori
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000 SP, Brazil
| | - Gisele Medeiros Bastos
- Laboratory of Molecular Research in Cardiology, Institute of Cardiology Dante Pazzanese, Sao Paulo 04012-909, Brazil; Department of Teaching and Research, Real and Benemerita Associação Portuguesa de Beneficiencia, Sao Paulo 01323-001, Brazil
| | | | - Daniel Branco Araújo
- Medical Clinic Division, Institute of Cardiology Dante Pazzanese, Sao Paulo 04012-909, Brazil
| | - Henry Zatz
- Medical Clinic Division, Institute of Cardiology Dante Pazzanese, Sao Paulo 04012-909, Brazil
| | - Adriana Bertolami
- Medical Clinic Division, Institute of Cardiology Dante Pazzanese, Sao Paulo 04012-909, Brazil
| | - André Arpad Faludi
- Medical Clinic Division, Institute of Cardiology Dante Pazzanese, Sao Paulo 04012-909, Brazil
| | | | | | - João Ítalo Dias França
- Laboratory of Epidemiology and Statistics, Institute of Cardiology Dante Pazzanese, Sao Paulo 04012-909, Brazil
| | - Helena Strelow Thurow
- Department of Teaching and Research, Real and Benemerita Associação Portuguesa de Beneficiencia, Sao Paulo 01323-001, Brazil
| | - Thiago Dominguez Crespo Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000 SP, Brazil
| | - Helder Takashi Imoto Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000 SP, Brazil
| | - Cinthia Elim Jannes
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of Sao Paulo, Sao Paulo 05403-900, Brazil
| | - Alexandre da Costa Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of Sao Paulo, Sao Paulo 05403-900, Brazil
| | - Vivian Nogueira Silbiger
- Department of Clinical and Toxicological Analysis, Federal University of Rio Grande do Norte, Natal 59078-900 Brazil; Northeast Biotechnology Network (RENORBIO), Graduate Program in Biotechnology, Federal University of Rio Grande do Norte, Natal 59078-900, Brazil
| | - André Ducati Luchessi
- Department of Clinical and Toxicological Analysis, Federal University of Rio Grande do Norte, Natal 59078-900 Brazil; Northeast Biotechnology Network (RENORBIO), Graduate Program in Biotechnology, Federal University of Rio Grande do Norte, Natal 59078-900, Brazil
| | - Jéssica Nayara Góes Araújo
- Northeast Biotechnology Network (RENORBIO), Graduate Program in Biotechnology, Federal University of Rio Grande do Norte, Natal 59078-900, Brazil
| | - Marcelo Arruda Nakazone
- Department of Cardiology and Cardiovascular Surgery, Faculdade de Medicina de São José do Rio Preto, Sao Jose do Rio Preto 15090-000, Brazil
| | - Tayanne Silva Carmo
- Department of Cardiology and Cardiovascular Surgery, Faculdade de Medicina de São José do Rio Preto, Sao Jose do Rio Preto 15090-000, Brazil
| | - Dorotéia Rossi Silva Souza
- Department of Biochemistry and Molecular Biology, Sao Jose do Rio Preto Medical School, Sao Jose do Rio Preto 15090-000, Brazil
| | - Patricia Moriel
- Department of Clinical Pathology, Faculty of Pharmaceutical Sciences, State University of Campinas-UNICAMP, Campinas 13083-871, Brazil
| | - Jaqueline Yu Ting Wang
- Human Genome and Stem-Cell Research Center, Biosciences Institute, University of Sao Paulo, Sao Paulo 05508-090, Brazil
| | - Michel Satya Naslavsky
- Human Genome and Stem-Cell Research Center, Biosciences Institute, University of Sao Paulo, Sao Paulo 05508-090, Brazil
| | - Renata Gorjão
- Interdisciplinary Post-graduate Program in Health Sciences, Cruzeiro do Sul University, Sao Paulo 01311-925, Brazil
| | - Tania Cristina Pithon-Curi
- Interdisciplinary Post-graduate Program in Health Sciences, Cruzeiro do Sul University, Sao Paulo 01311-925, Brazil
| | - Rui Curi
- Interdisciplinary Post-graduate Program in Health Sciences, Cruzeiro do Sul University, Sao Paulo 01311-925, Brazil
| | - Cristina Moreno Fajardo
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000 SP, Brazil
| | - Hui-Tzu Lin Wang
- Laboratory of Molecular Research in Cardiology, Institute of Cardiology Dante Pazzanese, Sao Paulo 04012-909, Brazil
| | - Adriana Regina Garófalo
- Laboratory of Molecular Research in Cardiology, Institute of Cardiology Dante Pazzanese, Sao Paulo 04012-909, Brazil
| | - Alvaro Cerda
- Department of Basic Sciences, Center of Excellence in Translational Medicine, BIOREN, Universidad de La Frontera, Temuco 4810296, Chile
| | - Marcelo Ferraz Sampaio
- Department of Cardiology, Real and Benemerita Associação Portuguesa de Beneficiencia, Sao Paulo 01323-001, Brazil
| | - Rosario Dominguez Crespo Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000 SP, Brazil
| | - Mario Hiroyuki Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo 05508-000 SP, Brazil.
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12
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Izquierdo-Lara RW, Heijnen L, Oude Munnink BB, Schapendonk CME, Elsinga G, Langeveld J, Post J, Prasad DK, Carrizosa C, Been F, van Beek J, Schilperoort R, Vriend R, Fanoy E, de Schepper EIT, Sikkema RS, Molenkamp R, Aarestrup FM, Medema G, Koopmans MPG, de Graaf M. Rise and fall of SARS-CoV-2 variants in Rotterdam: Comparison of wastewater and clinical surveillance. Sci Total Environ 2023; 873:162209. [PMID: 36796689 PMCID: PMC9927792 DOI: 10.1016/j.scitotenv.2023.162209] [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] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 06/04/2023]
Abstract
Monitoring of SARS-CoV-2 in wastewater (WW) is a promising tool for epidemiological surveillance, correlating not only viral RNA levels with the infection dynamics within the population, but also to viral diversity. However, the complex mixture of viral lineages in WW samples makes tracking of specific variants or lineages circulating in the population a challenging task. We sequenced sewage samples of 9 WW-catchment areas within the city of Rotterdam, used specific signature mutations from individual SARS-CoV-2 lineages to estimate their relative abundances in WW and compared them against those observed in clinical genomic surveillance of infected individuals between September 2020 and December 2021. We showed that especially for dominant lineages, the median of the frequencies of signature mutations coincides with the occurrence of those lineages in Rotterdam's clinical genomic surveillance. This, along with digital droplet RT-PCR targeting signature mutations of specific variants of concern (VOCs), showed that several VOCs emerged, became dominant and were replaced by the next VOC in Rotterdam at different time points during the study. In addition, single nucleotide variant (SNV) analysis provided evidence that spatio-temporal clusters can also be discerned from WW samples. We were able to detect specific SNVs in sewage, including one resulting in the Q183H amino acid change in the Spike gene, that was not captured by clinical genomic surveillance. Our results highlight the potential use of WW samples for genomic surveillance, increasing the set of epidemiological tools to monitor SARS-CoV-2 diversity.
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Affiliation(s)
- Ray W Izquierdo-Lara
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Leo Heijnen
- KWR Water Research Institute, Nieuwegein, the Netherlands
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Goffe Elsinga
- KWR Water Research Institute, Nieuwegein, the Netherlands
| | - Jeroen Langeveld
- Partners4urbanwater, Nijmegen, the Netherlands; Delft University of Technology, Stevinweg 1, 2628 CN Delft, the Netherlands
| | - Johan Post
- Partners4urbanwater, Nijmegen, the Netherlands
| | - Divyae K Prasad
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Christian Carrizosa
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Frederic Been
- KWR Water Research Institute, Nieuwegein, the Netherlands
| | - Janko van Beek
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Rianne Vriend
- Regional Public Health Service Rotterdam-Rijnmond, Rotterdam, the Netherlands
| | - Ewout Fanoy
- Regional Public Health Service Rotterdam-Rijnmond, Rotterdam, the Netherlands
| | - Evelien I T de Schepper
- Department of General Practice, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Reina S Sikkema
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Gertjan Medema
- KWR Water Research Institute, Nieuwegein, the Netherlands; Delft University of Technology, Stevinweg 1, 2628 CN Delft, the Netherlands; Pandemic and Disaster Preparedness Centre Rotterdam and Delft, the Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands; Pandemic and Disaster Preparedness Centre Rotterdam and Delft, the Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands; Pandemic and Disaster Preparedness Centre Rotterdam and Delft, the Netherlands.
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13
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Shirai R, Osumi T, Keino D, Nakabayashi K, Uchiyama T, Sekiguchi M, Hiwatari M, Yoshida M, Yoshida K, Yamada Y, Tomizawa D, Takae S, Kiyokawa N, Matsumoto K, Yoshioka T, Hata K, Hori T, Suzuki N, Kato M. Minimal residual disease detection by mutation-specific droplet digital PCR for leukemia/lymphoma. Int J Hematol 2023; 117:910-918. [PMID: 36867356 DOI: 10.1007/s12185-023-03566-2] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 03/04/2023]
Abstract
Minimal residual disease (MRD) is usually defined as the small number of cancer cells that remain in the body after treatment. The clinical significance of MRD kinetics is well recognized in treatment of hematologic malignancies, particularly acute lymphoblastic leukemia (ALL). Real time quantitative PCR targeting immunoglobulin (Ig) or T-cell receptor (TCR) rearrangement (PCR-MRD), as well as multiparametric flow cytometric analysis targeting antigen expression, are widely used in MRD detection. In this study, we devised an alternative method to detect MRD using droplet digital PCR (ddPCR), targeting somatic single nucleotide variants (SNVs). This ddPCR-based method (ddPCR-MRD) had sensitivity up to 1E-4. We assessed ddPCR-MRD at 26 time points from eight T-ALL patients, and compared it to the results of PCR-MRD. Almost all results were concordant between the two methods, but ddPCR-MRD detected micro-residual disease that was missed by PCR-MRD in one patient. We also measured MRD in stored ovarian tissue of four pediatric cancer patients, and detected 1E-2 of submicroscopic infiltration. Considering the universality of ddPCR-MRD, the methods can be used as a complement for not only ALL, but also other malignant diseases regardless of tumor-specific Ig/TCR or surface antigen patterns.
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Affiliation(s)
- Ryota Shirai
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | - Tomoo Osumi
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan.,Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Dai Keino
- Department of Pediatrics, St. Marianna University School of Medicine Hospital, Kawasaki, Japan.,Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Toru Uchiyama
- Department of Human Genetics, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Masahiro Sekiguchi
- Department of Pediatrics, the University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Mitsuteru Hiwatari
- Department of Pediatrics, the University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan.,Department of Pediatrics, School of Medicine, Teikyo University, Tokyo, Japan
| | - Masanori Yoshida
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | - Kaoru Yoshida
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yuji Yamada
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Daisuke Tomizawa
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Seido Takae
- Department of Obstetrics and Gynecology, St. Marianna University School of Medicine, Kanagawa, Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kimikazu Matsumoto
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Takako Yoshioka
- Department of Pathology, National Center for Child Health and Development, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan.,Department of Human Molecular Genetics, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Toshinori Hori
- Department of Pediatrics, Aichi Medical University, Nagakute, Japan
| | - Nao Suzuki
- Department of Obstetrics and Gynecology, St. Marianna University School of Medicine, Kanagawa, Japan
| | - Motohiro Kato
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan. .,Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan. .,Department of Pediatrics, the University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan.
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14
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Friedman JM, van Essen P, van Karnebeek CDM. Cerebral palsy and related neuromotor disorders: Overview of genetic and genomic studies. Mol Genet Metab 2022; 137:399-419. [PMID: 34872807 DOI: 10.1016/j.ymgme.2021.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 10/31/2021] [Accepted: 11/02/2021] [Indexed: 12/14/2022]
Abstract
Cerebral palsy (CP) is a debilitating condition characterized by abnormal movement or posture, beginning early in development. Early family and twin studies and more recent genomic investigations clearly demonstrate that genetic factors of major effect contribute to the etiology of CP. Most copy number variants and small alterations of nucleotide sequence that cause CP arise as a result of de novo mutations, so studies that estimate heritability on basis of recurrence frequency within families substantially underestimate genetic contributions to the etiology. At least 4% of patients with typical CP have disease-causing CNVs, and at least 14% have disease-causing single nucleotide variants or indels. The rate of pathogenic genomic lesions is probably more than twice as high among patients who have atypical CP, i.e., neuromotor dysfunction with additional neurodevelopmental abnormalities or malformations, or with MRI findings and medical history that are not characteristic of a perinatal insult. Mutations of many different genetic loci can produce a CP-like phenotype. The importance of genetic variants of minor effect and of epigenetic modifications in producing a multifactorial predisposition to CP is less clear. Recognizing the specific cause of CP in an affected individual is essential to providing optimal clinical management. An etiological diagnosis provides families an "enhanced compass" that improves overall well-being, facilitates access to educational and social services, permits accurate genetic counseling, and, for a subset of patients such as those with underlying inherited metabolic disorders, may make precision therapy that targets the pathophysiology available. Trio exome sequencing with assessment of copy number or trio genome sequencing with bioinformatics analysis for single nucleotide variants, indels, and copy number variants is clinically indicated in the initial workup of CP patients, especially those with additional malformations or neurodevelopmental abnormalities.
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Affiliation(s)
- Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Peter van Essen
- Department of Pediatrics, Amalia Children's Hospital, Radboud Centre for Mitochondrial Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Clara D M van Karnebeek
- Department of Pediatrics, Amalia Children's Hospital, Radboud Centre for Mitochondrial Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Departments of Human Genetics and Pediatrics, Emma Children's Hospital, Amsterdam University Medical Centres, Amsterdam, the Netherlands; Department of Pediatrics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada.
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15
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Li C, Zhi D, Wang K, Liu X. MetaRNN: differentiating rare pathogenic and rare benign missense SNVs and InDels using deep learning. Genome Med 2022; 14:115. [PMID: 36209109 PMCID: PMC9548151 DOI: 10.1186/s13073-022-01120-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [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: 11/24/2021] [Accepted: 09/22/2022] [Indexed: 11/22/2022] Open
Abstract
Multiple computational approaches have been developed to improve our understanding of genetic variants. However, their ability to identify rare pathogenic variants from rare benign ones is still lacking. Using context annotations and deep learning methods, we present pathogenicity prediction models, MetaRNN and MetaRNN-indel, to help identify and prioritize rare nonsynonymous single nucleotide variants (nsSNVs) and non-frameshift insertion/deletions (nfINDELs). We use independent test sets to demonstrate that these new models outperform state-of-the-art competitors and achieve a more interpretable score distribution. Importantly, prediction scores from both models are comparable, enabling easy adoption of integrated genotype-phenotype association analysis methods. All pre-computed nsSNV scores are available at http://www.liulab.science/MetaRNN. The stand-alone program is also available at https://github.com/Chang-Li2019/MetaRNN.
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Affiliation(s)
- Chang Li
- USF Genomics & College of Public Health, University of South Florida, 3720 Spectrum Boulevard, Suite 304, Tampa, FL, 33612, USA
| | - Degui Zhi
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kai Wang
- Children's Hospital of Philadelphia & Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiaoming Liu
- USF Genomics & College of Public Health, University of South Florida, 3720 Spectrum Boulevard, Suite 304, Tampa, FL, 33612, USA.
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16
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Hardy J, Pollock N, Gingrich T, Sweet P, Ramesh A, Kuong J, Basar A, Jiang H, Hwang K, Vukina J, Jaffe T, Olszewska M, Kurpisz M, Yatsenko AN. Genomic testing for copy number and single nucleotide variants in spermatogenic failure. J Assist Reprod Genet 2022; 39:2103-2114. [PMID: 35849255 PMCID: PMC9474750 DOI: 10.1007/s10815-022-02538-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/06/2022] [Indexed: 10/17/2022] Open
Abstract
PURPOSE To identify clinically significant genomic copy number (CNV) and single nucleotide variants (SNV) in males with unexplained spermatogenic failure (SPGF). MATERIALS AND METHODS Peripheral blood DNA from 97/102 study participants diagnosed with oligozoospermia, severe oligozoospermia, or non-obstructive azoospermia (NOA) was analyzed for CNVs via array comparative genomic hybridization (aCGH) and SNVs using whole-exome sequencing (WES). RESULTS Of the 2544 CNVs identified in individuals with SPGF, > 90% were small, ranging from 0.6 to 75 kb. Thirty, clinically relevant genomic aberrations, were detected in 28 patients (~ 29%). These included likely diagnostic CNVs in 3/41 NOA patients (~ 7%): 1 hemizygous, intragenic TEX11 deletion, 1 hemizygous DDX53 full gene deletion, and 1 homozygous, intragenic STK11 deletion. High-level mosaicism for X chromosome disomy (~ 10% 46,XY and ~ 90% 47,XXY) was also identified in 3 of 41 NOA patients who previously tested normal with conventional karyotyping. The remaining 24 CNVs detected were heterozygous, autosomal recessive carrier variants. Follow-up WES analysis confirmed 8 of 27 (30%) CNVs (X chromosome disomy excluded). WES analysis additionally identified 13 significant SNVs and/or indels in 9 patients (~ 9%) including X-linked AR, KAL1, and NR0B1 variants. CONCLUSION Using a combined genome-wide aCGH/WES approach, we identified pathogenic and likely pathogenic SNVs and CNVs in 15 patients (15%) with unexplained SPGF. This value equals the detection rate of conventional testing for aneuploidies and is considerably higher than the prevalence of Y chromosome microdeletions. Our results underscore the importance of comprehensive genomic analysis in emerging diagnostic testing of complex conditions like male infertility.
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Affiliation(s)
- J Hardy
- Department of OBGYN and Reproductive Sciences, Magee-Womens Research Institute, School of Medicine, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - N Pollock
- Department of OBGYN and Reproductive Sciences, Magee-Womens Research Institute, School of Medicine, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - T Gingrich
- Department of OBGYN and Reproductive Sciences, Magee-Womens Research Institute, School of Medicine, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - P Sweet
- Department of OBGYN and Reproductive Sciences, Magee-Womens Research Institute, School of Medicine, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - A Ramesh
- Department of OBGYN and Reproductive Sciences, Magee-Womens Research Institute, School of Medicine, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - J Kuong
- Department of OBGYN and Reproductive Sciences, Magee-Womens Research Institute, School of Medicine, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - A Basar
- Department of OBGYN and Reproductive Sciences, Magee-Womens Research Institute, School of Medicine, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - H Jiang
- Department of OBGYN and Reproductive Sciences, Magee-Womens Research Institute, School of Medicine, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA
| | - K Hwang
- Department of Urology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - J Vukina
- Department of Urology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - T Jaffe
- Department of Urology, School of Medicine, West Virginia University, Morgantown, WV, USA
| | - M Olszewska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - M Kurpisz
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - A N Yatsenko
- Department of OBGYN and Reproductive Sciences, Magee-Womens Research Institute, School of Medicine, University of Pittsburgh, 204 Craft Avenue, Pittsburgh, PA, 15213, USA.
- Department of Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States.
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.
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17
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Akiyama Y, Kondou R, Iizuka A, Miyata H, Maeda C, Kanematsu A, Ashizawa T, Nagashima T, Urakami K, Shimoda Y, Ohshima K, Shiomi A, Ohde Y, Terashima M, Uesaka K, Hirashima Y, Kiyohara Y, Katagiri H, Sugino T, Notsu A, Mori K, Takahashi M, Kenmotsu H, Yamaguchi K. Characterization of the Immunological Status of Hypermutated Solid Tumors in the Cancer Genome Analysis Project HOPE. Anticancer Res 2022; 42:3537-3549. [PMID: 35790264 DOI: 10.21873/anticanres.15840] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 03/31/2022] [Accepted: 06/02/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Many reports demonstrate that a high tumor mutation burden (TMB-H) is closely associated with good prognosis of cancer. However, specific studies investigating the association of various TMB statuses with overall survival in patients with solid tumors are scarce. PATIENTS AND METHODS In the present study, we investigated the association of TMB status with overall survival in 5,072 patients with cancer from the HOPE project and clarified the specific mechanism responsible for the good prognosis of the TMB-H group. All tumors were classified into one of four groups based on TMB: ultralow (UL), low (L), intermediate (I) and high (H). RESULTS The TMB-H group had a better prognosis than the TMB-I and TMB-L groups, but not than the TMB-UL group. Analyzing the expression of 293 immune response-associated genes, 17 genes were up-regulated in the TMB-H group compared to the TMB-I and TNB-L groups, and two genes [CD274 and interferon-γ (IFNG)] were identified as good prognostic factors. Analysis of immune cell populations inside tumors demonstrated that the frequencies of exhausted CD8+ T-cells, activated effector CD8+ T-cells and natural killer cells were significantly higher in the TMB-H group. The T-cell receptor repertoire numbers and the diversity evenness score (DE50) were lower in the TMB-H group than in TMB-UL group; however, no association of the DE50 value with the binding or elution affinity of epitope peptides from neoantigens was found. CONCLUSION One possible mechanism for the good prognosis of the TMB-UL group compared to the TMB-H group might be that the TMB-UL group features a balance between immunosuppression and immunostimulation.
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Affiliation(s)
- Yasuto Akiyama
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan;
| | - Ryota Kondou
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Akira Iizuka
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Haruo Miyata
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Chie Maeda
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Akari Kanematsu
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Tadashi Ashizawa
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan.,SRL, Tokyo, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Yuji Shimoda
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan.,SRL, Tokyo, Japan
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Akio Shiomi
- Division of Colon and Rectal Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Yasuhisa Ohde
- Division of Thoracic Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Masanori Terashima
- Division of Gastric Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Katsuhiko Uesaka
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Yasuyuki Hirashima
- Division of Gynecology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Yoshio Kiyohara
- Division of Dermatology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Hirohisa Katagiri
- Division of Orthopedic Oncology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Takashi Sugino
- Division of Pathology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Akifumi Notsu
- Clinical Research Center, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Keita Mori
- Clinical Research Center, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Mitsuru Takahashi
- Division of Orthopedic Oncology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Hirotsugu Kenmotsu
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
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18
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Wasilewska K, Gambin T, Rydzanicz M, Szczałuba K, Płoski R. Postzygotic mutations and where to find them - Recent advances and future implications in the field of non-neoplastic somatic mosaicism. Mutat Res Rev Mutat Res 2022; 790:108426. [PMID: 35690331 DOI: 10.1016/j.mrrev.2022.108426] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/05/2022] [Accepted: 06/03/2022] [Indexed: 01/01/2023]
Abstract
The technological progress of massively parallel sequencing (MPS) has triggered a remarkable development in the research on postzygotic mutations. Although the overwhelming majority of studies in the field focus on oncogenesis, non-neoplastic diseases are attracting more and more attention. The aim of this review was to summarize some of the most recent findings in the field of somatic mosaicism in diseases other than neoplastic events. We discuss the abundance and role of postzygotic mutations, with a special emphasis on disorders which occur only in a mosaic form (obligatory mosaic diseases; OMDs). Based on the list of OMDs compiled from the published literature and three databases (OMIM, Orphanet and MosaicBase), we demonstrate the prevalence of cancer-related genes across OMDs and suggest other sources to further explore OMDs and OMD-related genes. Additionally, we comment on some practical aspects related to mosaic diseases, such as approaches to tissue sampling, the MPS coverage required to detect variants at a very low frequency, as well as on bioinformatic and molecular tools dedicated to detect somatic mutations in MPS data.
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Affiliation(s)
- Krystyna Wasilewska
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Nowowiejska 15/19, 00-665 Warsaw, Poland
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Krzysztof Szczałuba
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland.
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19
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Zhu M, Zeng Q, Saputro BIL, Chew SP, Chew I, Frendy H, Tan JW, Li L. Tracking the molecular evolution and transmission patterns of SARS-CoV-2 lineage B.1.466.2 in Indonesia based on genomic surveillance data. Virol J 2022; 19:103. [PMID: 35710544 PMCID: PMC9202327 DOI: 10.1186/s12985-022-01830-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 04/19/2022] [Accepted: 06/02/2022] [Indexed: 12/22/2022] Open
Abstract
Background As a new epi-center of COVID-19 in Asia and a densely populated developing country, Indonesia is facing unprecedented challenges in public health. SARS-CoV-2 lineage B.1.466.2 was reported to be an indigenous dominant strain in Indonesia (once second only to the Delta variant). However, it remains unclear how this variant evolved and spread within such an archipelagic nation. Methods For statistical description, the spatiotemporal distributions of the B.1.466.2 variant were plotted using the publicly accessible metadata in GISAID. A total of 1302 complete genome sequences of Indonesian B.1.466.2 strains with high coverage were downloaded from the GISAID’s EpiCoV database on 28 August 2021. To determine the molecular evolutionary characteristics, we performed a time-scaled phylogenetic analysis using the maximum likelihood algorithm and called the single nucleotide variants taking the Wuhan-Hu-1 sequence as reference. To investigate the spatiotemporal transmission patterns, we estimated two dynamic parameters (effective population size and effective reproduction number) and reconstructed the phylogeography among different islands. Results As of the end of August 2021, nearly 85% of the global SARS-CoV-2 lineage B.1.466.2 sequences (including the first one) were obtained from Indonesia. This variant was estimated to account for over 50% of Indonesia’s daily infections during the period of March–May 2021. The time-scaled phylogeny suggested that SARS-CoV-2 lineage B.1.466.2 circulating in Indonesia might have originated from Java Island in mid-June 2020 and had evolved into two disproportional and distinct sub-lineages. High-frequency non-synonymous mutations were mostly found in the spike and NSP3; the S-D614G/N439K/P681R co-mutations were identified in its larger sub-lineage. The demographic history was inferred to have experienced four phases, with an exponential growth from October 2020 to February 2021. The effective reproduction number was estimated to have reached its peak (11.18) in late December 2020 and dropped to be less than one after early May 2021. The relevant phylogeography showed that Java and Sumatra might successively act as epi-centers and form a stable transmission loop. Additionally, several long-distance transmission links across seas were revealed. Conclusions SARS-CoV-2 variants circulating in the tropical archipelago may follow unique patterns of evolution and transmission. Continuous, extensive and targeted genomic surveillance is essential. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-022-01830-1.
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Affiliation(s)
- Mingjian Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qianli Zeng
- Shanghai Institute of Biological Products, Shanghai, China
| | | | - Sien Ping Chew
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ian Chew
- Zhejiang University School of Medicine, Hangzhou, China
| | - Holie Frendy
- Faculty of Medicine and Health Sciences, Krida Wacana Christian University, Jakarta, Indonesia
| | - Joanna Weihui Tan
- Faculty of Arts and Social Sciences, National University of Singapore, Singapore, Singapore
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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20
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Li B, Li Z, Yang J, Hong N, Jin L, Xu Y, Fu Q, Sun K, Yu Y, Lu Y, Chen S. Predisposition to atrioventricular septal defects may be caused by SOX7 variants that impair interaction with GATA4. Mol Genet Genomics 2022. [PMID: 35260939 DOI: 10.1007/s00438-022-01859-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 01/12/2022] [Indexed: 10/18/2022]
Abstract
Atrioventricular septal defects (AVSD) are a complicated subtype of congenital heart defects for which the genetic basis is poorly understood. Many studies have demonstrated that the transcription factor SOX7 plays a pivotal role in cardiovascular development. However, whether SOX7 single nucleotide variants are involved in AVSD pathogenesis is unclear. To explore the potential pathogenic role of SOX7 variants, we recruited a total of 100 sporadic non-syndromic AVSD Chinese Han patients and screened SOX7 variants in the patient cohort by targeted sequencing. Functional assays were performed to evaluate pathogenicity of nonsynonymous variants of SOX7. We identified three rare SOX7 variants, c.40C > G, c.542G > A, and c.743C > T, in the patient cohort, all of which were found to be highly conserved in mammals. Compared to the wild type, these SOX7 variants had increased mRNA expression and decreased protein expression. In developing hearts, SOX7 and GATA4 were highly expressed in the region of atrioventricular cushions. Moreover, SOX7 overexpression promoted the expression of GATA4 in human umbilical vein endothelial cells. A chromatin immunoprecipitation assay revealed that SOX7 could directly bind to the GATA4 promoter and luciferase assays demonstrated that SOX7 activated the GATA4 promoter. The SOX7 variants had impaired transcriptional activity relative to wild-type SOX7. Furthermore, the SOX7 variants altered the ability of GATA4 to regulate its target genes. In conclusion, our findings showed that deleterious SOX7 variants potentially contribute to human AVSD by impairing its interaction with GATA4. This study provides novel insights into the etiology of AVSD and contributes new strategies to the prenatal diagnosis of AVSD.
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21
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Li S, Liu L, Sun W, Zhou X, Zhou H. A large-scale genome and transcriptome sequencing analysis reveals the mutation landscapes induced by high-activity adenine base editors in plants. Genome Biol 2022; 23:51. [PMID: 35139891 PMCID: PMC8826654 DOI: 10.1186/s13059-022-02618-w] [Citation(s) in RCA: 4] [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: 11/03/2021] [Accepted: 01/18/2022] [Indexed: 12/30/2022] Open
Abstract
Background The high-activity adenine base editors (ABEs), engineered with the recently-developed tRNA adenosine deaminases (TadA8e and TadA9), show robust base editing activity but raise concerns about off-target effects. Results In this study, we perform a comprehensive evaluation of ABE8e- and ABE9-induced DNA and RNA mutations in Oryza sativa. Whole-genome sequencing analysis of plants transformed with four ABEs, including SpCas9n-TadA8e, SpCas9n-TadA9, SpCas9n-NG-TadA8e, and SpCas9n-NG-TadA9, reveal that ABEs harboring TadA9 lead to a higher number of off-target A-to-G (A>G) single-nucleotide variants (SNVs), and that those harboring CRISPR/SpCas9n-NG lead to a higher total number of off-target SNVs in the rice genome. An analysis of the T-DNAs carrying the ABEs indicates that the on-target mutations could be introduced before and/or after T-DNA integration into plant genomes, with more off-target A>G SNVs forming after the ABEs had integrated into the genome. Furthermore, we detect off-target A>G RNA mutations in plants with high expression of ABEs but not in plants with low expression of ABEs. The off-target A>G RNA mutations tend to cluster, while off-target A>G DNA mutations rarely clustered. Conclusion Our findings that Cas proteins, TadA variants, temporal expression of ABEs, and expression levels of ABEs contribute to ABE specificity in rice provide insight into the specificity of ABEs and suggest alternative ways to increase ABE specificity besides engineering TadA variants. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02618-w.
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Affiliation(s)
- Shaofang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Lang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, 541399, China.,Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Wenxian Sun
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Zhejiang, Hangzhou, China
| | - Huanbin Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. .,Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, 541399, China.
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22
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Hong KH, In JW, Lee J, Kim SY, Lee KA, Kim S, An Y, Lee D, Sung H, Kim JS, Lee H. Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay. Ann Lab Med 2022; 42:96-99. [PMID: 34374354 PMCID: PMC8368233 DOI: 10.3343/alm.2022.42.1.96] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 04/02/2021] [Revised: 04/20/2021] [Accepted: 07/16/2021] [Indexed: 12/31/2022] Open
Abstract
The sensitivity of molecular diagnostics could be affected by nucleotide variants in pathogen genes, and the sites affected by such variants should be monitored. We report a single-nucleotide variant (SNV) in the nucleocapsid (N) gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), i.e., G29179T, which impairs the diagnostic sensitivity of the Xpert Xpress SARS-CoV-2 assay (Cepheid, Sunnyvale, CA, USA). We observed significant differences between the threshold cycle (Ct) values for envelope (E) and N genes and confirmed the SNV as the cause of the differences using Sanger sequencing. This SNV, G29179T, is the most prevalent in Korea and is associated with the B.1.497 virus lineage, which is dominant in Korea. Clinical laboratories should be aware of the various SNVs in the SARS-CoV-2 genome and consider their potential effects on the diagnosis of coronavirus disease 2019.
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Affiliation(s)
- Ki Ho Hong
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Ji Won In
- Department of Laboratory Medicine, Seoul Medical Center, Seoul, Korea
| | - Jaehyeon Lee
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, Korea
| | - So Yeon Kim
- Department of Laboratory Medicine, National Medical Center, Seoul, Korea
| | - Kyoung Ah Lee
- Department of Laboratory Medicine, Seoul Medical Center, Seoul, Korea
| | - Seunghyun Kim
- Department of Laboratory Medicine, Seoul Medical Center, Seoul, Korea
| | - Yeoungim An
- Department of Laboratory Medicine, Seoul Medical Center, Seoul, Korea
| | - Donggeun Lee
- Department of Laboratory Medicine, Seoul Medical Center, Seoul, Korea
| | - Heungsup Sung
- University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea
| | - Jae-Seok Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Hyukmin Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
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23
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Xu YJ, He MK, Liu S, Huang LC, Bu XY, Kan A, Shi M. Construction of a single nucleotide variant score-related gene-based prognostic model in hepatocellular carcinoma: analysis of multi-independent databases and validation in vitro. Cancer Cell Int 2021; 21:610. [PMID: 34794449 PMCID: PMC8600893 DOI: 10.1186/s12935-021-02321-z] [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: 08/20/2021] [Accepted: 11/05/2021] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND The accumulation of single nucleotide variants (SNVs) and the emergence of neoantigens can affect tumour proliferation and the immune microenvironment. However, the SNV-related immune microenvironment characteristics and key genes involved in hepatocellular carcinoma (HCC) are still unclear. We aimed to evaluate differences in the SNV-related immune microenvironment, construct a prognostic model and validate the key genes in vitro. METHODS The categories of samples were defined by the expression of SNV score-related genes to evaluate the differences in mutational features, immune environment and prognosis. The survival model was constructed with survival-associated genes and verified in two independent test datasets. RCAN2, the key gene screened out for biofunction, was validated in vitro. RESULTS IC2, among the three integrated clusters (IC1, IC2, IC3) classified by the 82 SNV score-related genes, was distinct from the rest in SNV score and immune cell infiltration, showing a better prognosis. Seven prognostic markers, HTRA3, GGT5, RCAN2, LGALS3, CXCL1, CLEC3B, and CTHRC1, were screened to construct a prognostic model. The survival model distinguished high-risk patients with poor prognoses in three independent datasets (log-rank P < 0.0001, 0.011, and 0.0068, respectively) with acceptable sensitivity and specificity. RCAN2 was inversely correlated with NK cell infiltration, and knockdown of RCAN2 promoted proliferation in HCC. CONCLUSIONS This study revealed the characteristics of the HCC SNV-associated subgroup and screened seven latent markers for their accuracy of prognosis. Additionally, RCAN2 was preliminarily proven to influence proliferation in HCC and it had a close relationship with NK cell infiltration in vitro. With the capability to predict HCC outcomes, the model constructed with seven key differentially expressed genes offers new insights into individual therapy.
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Affiliation(s)
- Yu-Jie Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.,Department of Hepatic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Min-Ke He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.,Department of Hepatic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Shuang Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.,Department of Hepatic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Li-Chang Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.,Department of Hepatic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Xiao-Yun Bu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.,Department of Hepatic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Anna Kan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.,Department of Hepatic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Ming Shi
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China. .,Department of Hepatic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
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Mahjani B, De Rubeis S, Gustavsson Mahjani C, Mulhern M, Xu X, Klei L, Satterstrom FK, Fu J, Talkowski ME, Reichenberg A, Sandin S, Hultman CM, Grice DE, Roeder K, Devlin B, Buxbaum JD. Prevalence and phenotypic impact of rare potentially damaging variants in autism spectrum disorder. Mol Autism 2021; 12:65. [PMID: 34615535 PMCID: PMC8495954 DOI: 10.1186/s13229-021-00465-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 09/02/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Autism Sequencing Consortium identified 102 high-confidence autism spectrum disorder (ASD) genes, showing that individuals with ASD and with potentially damaging single nucleotide variation (pdSNV) in these genes had lower cognitive levels and delayed age at walking, when compared to ASD participants without pdSNV. Here, we made use of a Swedish sample of individuals with ASD (called PAGES, for Population-Based Autism Genetics & Environment Study) to evaluate the frequency of pdSNV and their impact on medical and psychiatric phenotypes, using an epidemiological frame and universal health reporting. We then combine findings with those for potentially damaging copy number variation (pdCNV). METHODS SNV and CNV calls were generated from whole-exome sequencing and chromosome microarray data, respectively. Birth and medical register data were used to collect phenotypes. RESULTS Of 808 individuals assessed by sequencing, 69 (9%) had pdSNV in the 102 ASC genes, and 144 (18%) had pdSNV in the 102 ASC genes or in a larger set of curated neurodevelopmental genes (from the Deciphering Developmental Disorders study, the gene2phenotype database, and the Radboud University gene lists). Three or more individuals had pdSNV in GRIN2B, POGZ, SATB1, DYNC1H1, SCN8A, or CREBBP. In comparison, out of the 996 individuals from whom CNV were called, 105 (11%) carried one or more pdCNV, including four or more individuals with CNV in the recurrent 15q11q13, 22q11.2, and 16p11.2 loci. Carriers of pdSNV were more likely to have intellectual disability (ID) and epilepsy, while carriers of pdCNV showed increased rates of congenital anomalies and scholastic skill disorders. Carriers of either pdSNV or pdCNV were more likely to have ID, scholastic skill disorders, and epilepsy. LIMITATIONS The cohort only included individuals with autistic disorder, the more severe form of ASD, and phenotypes are defined from medical registers. Not all genes studied are definitively ASD genes, and we did not have de novo information to aid in classification. CONCLUSIONS In this epidemiological sample, rare pdSNV were more common than pdCNV and the combined yield of potentially damaging variation was substantial at 27%. The results provide compelling rationale for the use of high-throughout sequencing as part of routine clinical workup for ASD and support the development of precision medicine in ASD.
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Affiliation(s)
- Behrang Mahjani
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Christina Gustavsson Mahjani
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maureen Mulhern
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xinyi Xu
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - F Kyle Satterstrom
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jack Fu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael E Talkowski
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Abraham Reichenberg
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sven Sandin
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Dorothy E Grice
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Kathryn Roeder
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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25
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Zago VHS, Scherrer DZ, Parra ES, Vieira IC, Marson FAL, de Faria EC. Effects of SNVs in ABCA1, ABCG1, ABCG5, ABCG8, and SCARB1 Genes on Plasma Lipids, Lipoproteins, and Adiposity Markers in a Brazilian Population. Biochem Genet 2021; 60:822-841. [PMID: 34505223 DOI: 10.1007/s10528-021-10131-1] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 08/25/2021] [Indexed: 10/20/2022]
Abstract
Several proteins are involved in cholesterol homeostasis, as scavenger receptor class B type I and ATP-binding cassette (ABC) transporters including ABCA1, ABCG1, ABCG5, and ABCG8. This study aimed to determine the effects of single nucleotide variants (SNVs) rs2275543 (ABCA1), rs1893590 (ABCG1), rs6720173 (ABCG5), rs6544718 (ABCG8), and rs5888 (SCARB1) on plasma lipids, lipoproteins, and adiposity markers in an asymptomatic population and its sex-specific effects. Volunteers (n = 590) were selected and plasma lipids, lipoproteins, and adiposity markers (waist-to-hip and waist-to-height ratios, lipid accumulation product and body adiposity index) were measured. Genomic DNA was isolated from peripheral blood cells according to the method adapted from Gross-Bellard. SNVs were detected in the TaqMan® OpenArray® Real-Time polymerase chain reaction platform and data analyses were performed using the TaqMan® Genotyper Software. The rs2275543*C point to an increase of high-density lipoprotein size in females while in males very-low-density lipoprotein, cholesterol, and triglycerides were statistically lower (P value < 0.05). The rs1893590*C was statistically associated with lower apolipoprotein A-I levels and higher activities of paraoxonase-1 and cholesteryl ester transfer protein (P value < 0.05). The rs6720173 was statistically associated with an increase in cholesterol and low-density lipoprotein cholesterol in males; moreover, rs6544718*T reduced adiposity markers in females (P value < 0.05). Regarding the rs5888, a decreased adiposity marker in the total population and in females occurred (P value < 0.05). Multivariate analysis of variance showed that SNVs could influence components of high-density lipoprotein metabolism, mainly through ABCG1 (P value < 0.05). The ABCA1 and ABCG5 variants showed sex-specific effects on lipids and lipoproteins, while SCARB1 and ABCG8 variants might influence adiposity markers in females. Our data indicate a possible role of ABCG1 on HDL metabolism.
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Affiliation(s)
- Vanessa Helena Souza Zago
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil
| | - Daniel Zanetti Scherrer
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil
| | - Eliane Soler Parra
- Department of Cardiology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil
| | - Isabela Calanca Vieira
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil
| | - Fernando Augusto Lima Marson
- Department of Pediatrics, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil. .,Department of Medical Genetics and Genomic Medicine, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil. .,Laboratory of Human and Medical Genetics and Laboratory of Cell and Molecular Tumor Biology and Bioactive Compounds, Post Graduate Program in Health Science, São Francisco University, Avenida São Francisco de Assis, 218, Jardim São José, Bragança Paulista, São Paulo, 12916-900, Brazil.
| | - Eliana Cotta de Faria
- Department of Clinical Pathology, Faculty of Medical Sciences, State University of Campinas, Tessália Vieira de Camargo St, 126, Campinas, São Paulo, 13084-971, Brazil.
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26
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Li X, Kumar S, Harmanci A, Li S, Kitchen RR, Zhang Y, Wali VB, Reddy SM, Woodward WA, Reuben JM, Rozowsky J, Hatzis C, Ueno NT, Krishnamurthy S, Pusztai L, Gerstein M. Whole-genome sequencing of phenotypically distinct inflammatory breast cancers reveals similar genomic alterations to non-inflammatory breast cancers. Genome Med 2021; 13:70. [PMID: 33902690 PMCID: PMC8077918 DOI: 10.1186/s13073-021-00879-x] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 03/25/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Inflammatory breast cancer (IBC) has a highly invasive and metastatic phenotype. However, little is known about its genetic drivers. To address this, we report the largest cohort of whole-genome sequencing (WGS) of IBC cases. METHODS We performed WGS of 20 IBC samples and paired normal blood DNA to identify genomic alterations. For comparison, we used 23 matched non-IBC samples from the Cancer Genome Atlas Program (TCGA). We also validated our findings using WGS data from the International Cancer Genome Consortium (ICGC) and the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We examined a wide selection of genomic features to search for differences between IBC and conventional breast cancer. These include (i) somatic and germline single-nucleotide variants (SNVs), in both coding and non-coding regions; (ii) the mutational signature and the clonal architecture derived from these SNVs; (iii) copy number and structural variants (CNVs and SVs); and (iv) non-human sequence in the tumors (i.e., exogenous sequences of bacterial origin). RESULTS Overall, IBC has similar genomic characteristics to non-IBC, including specific alterations, overall mutational load and signature, and tumor heterogeneity. In particular, we observed similar mutation frequencies between IBC and non-IBC, for each gene and most cancer-related pathways. Moreover, we found no exogenous sequences of infectious agents specific to IBC samples. Even though we could not find any strongly statistically distinguishing genomic features between the two groups, we did find some suggestive differences in IBC: (i) The MAST2 gene was more frequently mutated (20% IBC vs. 0% non-IBC). (ii) The TGF β pathway was more frequently disrupted by germline SNVs (50% vs. 13%). (iii) Different copy number profiles were observed in several genomic regions harboring cancer genes. (iv) Complex SVs were more frequent. (v) The clonal architecture was simpler, suggesting more homogenous tumor-evolutionary lineages. CONCLUSIONS Whole-genome sequencing of IBC manifests a similar genomic architecture to non-IBC. We found no unique genomic alterations shared in just IBCs; however, subtle genomic differences were observed including germline alterations in TGFβ pathway genes and somatic mutations in the MAST2 kinase that could represent potential therapeutic targets.
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Affiliation(s)
- Xiaotong Li
- Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Yale Cancer Center, Breast Medical Oncology, Yale School of Medicine, 300 George Street, Suite 120, Rm133, New Haven, CT 06511 USA
| | - Sushant Kumar
- Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
| | - Arif Harmanci
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center Houston, Houston, TX USA
| | - Shantao Li
- Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
| | - Robert R. Kitchen
- Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Yan Zhang
- Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH USA
- The Ohio State University Comprehensive Cancer Center (OSUCCC – James), Columbus, OH USA
| | - Vikram B. Wali
- Yale Cancer Center, Breast Medical Oncology, Yale School of Medicine, 300 George Street, Suite 120, Rm133, New Haven, CT 06511 USA
| | - Sangeetha M. Reddy
- Division of Hematology/Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX USA
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Wendy A. Woodward
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - James M. Reuben
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Joel Rozowsky
- Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
| | - Christos Hatzis
- Yale Cancer Center, Breast Medical Oncology, Yale School of Medicine, 300 George Street, Suite 120, Rm133, New Haven, CT 06511 USA
| | - Naoto T. Ueno
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Savitri Krishnamurthy
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Lajos Pusztai
- Yale Cancer Center, Breast Medical Oncology, Yale School of Medicine, 300 George Street, Suite 120, Rm133, New Haven, CT 06511 USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Computer Science, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Statistics and Data Science, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
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27
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Stranneheim H, Lagerstedt-Robinson K, Magnusson M, Kvarnung M, Nilsson D, Lesko N, Engvall M, Anderlid BM, Arnell H, Johansson CB, Barbaro M, Björck E, Bruhn H, Eisfeldt J, Freyer C, Grigelioniene G, Gustavsson P, Hammarsjö A, Hellström-Pigg M, Iwarsson E, Jemt A, Laaksonen M, Enoksson SL, Malmgren H, Naess K, Nordenskjöld M, Oscarson M, Pettersson M, Rasi C, Rosenbaum A, Sahlin E, Sardh E, Stödberg T, Tesi B, Tham E, Thonberg H, Töhönen V, von Döbeln U, Vassiliou D, Vonlanthen S, Wikström AC, Wincent J, Winqvist O, Wredenberg A, Ygberg S, Zetterström RH, Marits P, Soller MJ, Nordgren A, Wirta V, Lindstrand A, Wedell A. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. Genome Med 2021; 13:40. [PMID: 33726816 PMCID: PMC7968334 DOI: 10.1186/s13073-021-00855-5] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [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: 06/29/2020] [Accepted: 02/11/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND We report the findings from 4437 individuals (3219 patients and 1218 relatives) who have been analyzed by whole genome sequencing (WGS) at the Genomic Medicine Center Karolinska-Rare Diseases (GMCK-RD) since mid-2015. GMCK-RD represents a long-term collaborative initiative between Karolinska University Hospital and Science for Life Laboratory to establish advanced, genomics-based diagnostics in the Stockholm healthcare setting. METHODS Our analysis covers detection and interpretation of SNVs, INDELs, uniparental disomy, CNVs, balanced structural variants, and short tandem repeat expansions. Visualization of results for clinical interpretation is carried out in Scout-a custom-developed decision support system. Results from both singleton (84%) and trio/family (16%) analyses are reported. Variant interpretation is done by 15 expert teams at the hospital involving staff from three clinics. For patients with complex phenotypes, data is shared between the teams. RESULTS Overall, 40% of the patients received a molecular diagnosis ranging from 19 to 54% for specific disease groups. There was heterogeneity regarding causative genes (n = 754) with some of the most common ones being COL2A1 (n = 12; skeletal dysplasia), SCN1A (n = 8; epilepsy), and TNFRSF13B (n = 4; inborn errors of immunity). Some causative variants were recurrent, including previously known founder mutations, some novel mutations, and recurrent de novo mutations. Overall, GMCK-RD has resulted in a large number of patients receiving specific molecular diagnoses. Furthermore, negative cases have been included in research studies that have resulted in the discovery of 17 published, novel disease-causing genes. To facilitate the discovery of new disease genes, GMCK-RD has joined international data sharing initiatives, including ClinVar, UDNI, Beacon, and MatchMaker Exchange. CONCLUSIONS Clinical WGS at GMCK-RD has provided molecular diagnoses to over 1200 individuals with a broad range of rare diseases. Consolidation and spread of this clinical-academic partnership will enable large-scale national collaboration.
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Affiliation(s)
- Henrik Stranneheim
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kristina Lagerstedt-Robinson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Måns Magnusson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Malin Kvarnung
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Nicole Lesko
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Martin Engvall
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Henrik Arnell
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | | | - Michela Barbaro
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Erik Björck
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Helene Bruhn
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Christoph Freyer
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Giedre Grigelioniene
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Peter Gustavsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Hammarsjö
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Maritta Hellström-Pigg
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Erik Iwarsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anders Jemt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Mikael Laaksonen
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institutet of Technology, Stockholm, Sweden
| | - Sara Lind Enoksson
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Helena Malmgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Karin Naess
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Mikael Oscarson
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Chiara Rasi
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Adam Rosenbaum
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institutet of Technology, Stockholm, Sweden
| | - Ellika Sahlin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Eliane Sardh
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Tommy Stödberg
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Bianca Tesi
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Håkan Thonberg
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Virpi Töhönen
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ulrika von Döbeln
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Daphne Vassiliou
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Sofie Vonlanthen
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Ann-Charlotte Wikström
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Josephine Wincent
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ola Winqvist
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Wredenberg
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Sofia Ygberg
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Rolf H Zetterström
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Per Marits
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Johansson Soller
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institutet of Technology, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.
| | - Anna Wedell
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden.
- Science for Life Laboratory, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
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28
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Higuchi T, Oka S, Furukawa H, Tohma S, Yatsuhashi H, Migita K. Genetic risk factors for autoimmune hepatitis: implications for phenotypic heterogeneity and biomarkers for drug response. Hum Genomics 2021; 15:6. [PMID: 33509297 PMCID: PMC7841991 DOI: 10.1186/s40246-020-00301-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/15/2020] [Indexed: 01/10/2023] Open
Abstract
Autoimmune hepatitis (AIH) is a rare chronic progressive liver disease with autoimmune features. It mainly affects middle-aged women. AIH is occasionally complicated with liver cirrhosis that worsens the prognosis. Genetic and environmental factors are involved in the pathogenesis of AIH. Genetic studies of other diseases have been revealing of pathogenesis and drug efficacy. In this review, we summarize the genetic risk factors for AIH, including human leukocyte antigen (HLA) and non-HLA genes. A genome-wide association study (GWAS) on European AIH revealed the strongest associations to be with single nucleotide variants (SNVs) in HLA. Predisposing alleles for AIH were DRB1*03:01 and DRB1*04:01 in Europeans; DRB1*04:04, DRB1*04:05, and DRB1*13:01 in Latin Americans; and DRB1*04:01 and DRB1*04:05 in Japanese. Other risk SNVs in non-HLA genes for AIH were found by a candidate gene approach, but several SNVs were confirmed in replication studies. Some genetic factors of AIH overlapped with those of other autoimmune diseases. Larger-scale GWASs of other ethnic groups are required. The results of genetic studies might provide an explanation for the phenotypic heterogeneity of AIH and biomarkers for drug responses.
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Affiliation(s)
- Takashi Higuchi
- Molecular and Genetic Epidemiology Laboratory, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan.,Department of Nephrology, Ushiku Aiwa General Hospital, 896 Shishiko-cho, Ushiku, 300-1296, Japan.,Department of Rheumatology, National Hospital Organization Tokyo National Hospital, 3-1-1 Takeoka, Kiyose, 204-8585, Japan
| | - Shomi Oka
- Molecular and Genetic Epidemiology Laboratory, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan.,Department of Rheumatology, National Hospital Organization Tokyo National Hospital, 3-1-1 Takeoka, Kiyose, 204-8585, Japan.,Clinical Research Center for Allergy and Rheumatology, National Hospital Organization Sagamihara National Hospital, 18-1 Sakuradai, Minami-ku, Sagamihara, 252-0392, Japan
| | - Hiroshi Furukawa
- Molecular and Genetic Epidemiology Laboratory, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan. .,Department of Rheumatology, National Hospital Organization Tokyo National Hospital, 3-1-1 Takeoka, Kiyose, 204-8585, Japan. .,Clinical Research Center for Allergy and Rheumatology, National Hospital Organization Sagamihara National Hospital, 18-1 Sakuradai, Minami-ku, Sagamihara, 252-0392, Japan.
| | - Shigeto Tohma
- Department of Rheumatology, National Hospital Organization Tokyo National Hospital, 3-1-1 Takeoka, Kiyose, 204-8585, Japan.,Clinical Research Center for Allergy and Rheumatology, National Hospital Organization Sagamihara National Hospital, 18-1 Sakuradai, Minami-ku, Sagamihara, 252-0392, Japan
| | - Hiroshi Yatsuhashi
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, 2-1001-1 Kubara, Omura, 856-8562, Japan
| | - Kiyoshi Migita
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, 2-1001-1 Kubara, Omura, 856-8562, Japan.,Department of Rheumatology, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, 960-1295, Japan
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29
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Qaiser F, Yin Y, Mervis CB, Morris CA, Klein-Tasman BP, Tam E, Osborne LR, Yuen RKC. Rare and low frequency genomic variants impacting neuronal functions modify the Dup7q11.23 phenotype. Orphanet J Rare Dis 2021; 16:6. [PMID: 33407644 PMCID: PMC7788915 DOI: 10.1186/s13023-020-01648-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 06/23/2020] [Accepted: 12/14/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND 7q11.23 duplication (Dup7) is one of the most frequent recurrent copy number variants (CNVs) in individuals with autism spectrum disorder (ASD), but based on gold-standard assessments, only 19% of Dup7 carriers have ASD, suggesting that additional genetic factors are necessary to manifest the ASD phenotype. To assess the contribution of additional genetic variants to the Dup7 phenotype, we conducted whole-genome sequencing analysis of 20 Dup7 carriers: nine with ASD (Dup7-ASD) and 11 without ASD (Dup7-non-ASD). RESULTS We identified three rare variants of potential clinical relevance for ASD: a 1q21.1 microdeletion (Dup7-non-ASD) and two deletions which disrupted IMMP2L (one Dup7-ASD, one Dup7-non-ASD). There were no significant differences in gene-set or pathway variant burden between the Dup7-ASD and Dup7-non-ASD groups. However, overall intellectual ability negatively correlated with the number of rare loss-of-function variants present in nervous system development and membrane component pathways, and adaptive behaviour standard scores negatively correlated with the number of low-frequency likely-damaging missense variants found in genes expressed in the prenatal human brain. ASD severity positively correlated with the number of low frequency loss-of-function variants impacting genes expressed at low levels in the brain, and genes with a low level of intolerance. CONCLUSIONS Our study suggests that in the presence of the same pathogenic Dup7 variant, rare and low frequency genetic variants act additively to contribute to components of the overall Dup7 phenotype.
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Affiliation(s)
- Farah Qaiser
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
- Genetics & Genome Biology Program, The Hospital for Sick Children, 686 Bay St., Toronto, ON M5G 0A4 Canada
| | - Yue Yin
- Genetics & Genome Biology Program, The Hospital for Sick Children, 686 Bay St., Toronto, ON M5G 0A4 Canada
| | - Carolyn B. Mervis
- Department of Psychological and Brain Sciences, University of Louisville, Louisville, KY USA
| | - Colleen A. Morris
- Department of Pediatrics, UNLV School of Medicine, Las Vegas, NV USA
| | | | - Elaine Tam
- Department of Medicine, University of Toronto, Toronto, ON Canada
| | - Lucy R. Osborne
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
- Department of Medicine, University of Toronto, Toronto, ON Canada
| | - Ryan K. C. Yuen
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
- Genetics & Genome Biology Program, The Hospital for Sick Children, 686 Bay St., Toronto, ON M5G 0A4 Canada
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30
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Kawasaki A, Namba N, Sada KE, Hirano F, Kobayashi S, Nagasaka K, Sugihara T, Ono N, Fujimoto T, Kusaoi M, Tamura N, Yamagata K, Sumida T, Hashimoto H, Ozaki S, Makino H, Arimura Y, Harigai M, Tsuchiya N. Association of TERT and DSP variants with microscopic polyangiitis and myeloperoxidase-ANCA positive vasculitis in a Japanese population: a genetic association study. Arthritis Res Ther 2020; 22:246. [PMID: 33076992 PMCID: PMC7574242 DOI: 10.1186/s13075-020-02347-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/06/2020] [Indexed: 12/01/2022] Open
Abstract
Background Interstitial lung disease (ILD) is a severe complication with poor prognosis in anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV). Prevalence of AAV-associated ILD (AAV-ILD) in Japan is considerably higher than that in Europe. Recently, we reported that a MUC5B variant rs35705950, the strongest susceptibility variant to idiopathic pulmonary fibrosis (IPF), was strikingly increased in AAV-ILD patients but not in AAV patients without ILD; however, due to the low allele frequency in the Japanese population, the MUC5B variant alone cannot account for the high prevalence of AAV-ILD in Japan. In this study, we examined whether other IPF susceptibility alleles in TERT and DSP genes are associated with susceptibility to AAV subsets and AAV-ILD. Methods Five hundred and forty-four Japanese patients with AAV and 5558 controls were analyzed. Among the AAV patients, 432 were positive for myeloperoxidase (MPO)-ANCA (MPO-AAV). A total of 176 MPO-AAV patients were positive and 216 were negative for ILD based on CT or high-resolution CT. Genotypes of TERT and DSP variants were determined by TaqMan SNP Genotyping Assay, and their association was tested by chi-square test. Results When the frequencies of the IPF risk alleles TERT rs2736100A and DSP rs2076295G were compared between AAV subsets and healthy controls, both alleles were significantly increased in microscopic polyangiitis (MPA) (TERT P = 2.3 × 10−4, Pc = 0.0023, odds ratio [OR] 1.38; DSP P = 6.9 × 10−4, Pc = 0.0069, OR 1.32) and MPO-AAV (TERT P = 1.5 × 10−4, Pc = 0.0015, OR 1.33; DSP P = 0.0011, Pc = 0.011, OR 1.26). On the other hand, no significant association was detected when the allele frequencies were compared between MPO-AAV patients with and without ILD. Conclusions Unexpectedly, TERT and DSP IPF risk alleles were found to be associated with MPA and MPO-AAV, regardless of the presence of ILD. These findings suggest that TERT and DSP may be novel susceptibility genes to MPA/MPO-AAV and also that some susceptibility genes may be shared between IPF and MPA/MPO-AAV.
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Affiliation(s)
- Aya Kawasaki
- Molecular and Genetic Epidemiology Laboratory, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan. .,School of Medical Sciences, University of Tsukuba, Tsukuba, Japan.
| | - Natsumi Namba
- Molecular and Genetic Epidemiology Laboratory, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan.,School of Medical Sciences, University of Tsukuba, Tsukuba, Japan
| | - Ken-Ei Sada
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.,Department of Clinical Epidemiology, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Fumio Hirano
- Department of Rheumatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Lifetime Clinical Immunology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shigeto Kobayashi
- Department of Internal Medicine, Juntendo University Koshigaya Hospital, Koshigaya, Japan
| | - Kenji Nagasaka
- Department of Rheumatology, Ome Municipal General Hospital, Ome, Japan
| | - Takahiko Sugihara
- Department of Rheumatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Lifetime Clinical Immunology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Nobuyuki Ono
- Department of Rheumatology, Saga University, Saga, Japan
| | - Takashi Fujimoto
- The Center for Rheumatic Diseases, Nara Medical University, Kashihara, Japan
| | - Makio Kusaoi
- Department of Internal Medicine and Rheumatology, School of Medicine, Juntendo University, Tokyo, Japan
| | - Naoto Tamura
- Department of Internal Medicine and Rheumatology, School of Medicine, Juntendo University, Tokyo, Japan
| | - Kunihiro Yamagata
- Department of Nephrology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Takayuki Sumida
- Department of Internal Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | | | - Shoichi Ozaki
- Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | | | - Yoshihiro Arimura
- Department of Nephrology and Rheumatology, Kyorin University School of Medicine, Mitaka, Japan.,Department of Internal Medicine, Kichijoji Asahi Hospital, Musashino, Japan
| | - Masayoshi Harigai
- Department of Rheumatology, School of Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Naoyuki Tsuchiya
- Molecular and Genetic Epidemiology Laboratory, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan. .,School of Medical Sciences, University of Tsukuba, Tsukuba, Japan.
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31
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Magnusson M, Eisfeldt J, Nilsson D, Rosenbaum A, Wirta V, Lindstrand A, Wedell A, Stranneheim H. Loqusdb: added value of an observations database of local genomic variation. BMC Bioinformatics 2020; 21:273. [PMID: 32611382 PMCID: PMC7329469 DOI: 10.1186/s12859-020-03609-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 01/17/2020] [Accepted: 06/17/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Exome and genome sequencing is becoming the method of choice for rare disease diagnostics. One of the key challenges remaining is distinguishing the disease causing variants from the benign background variation. After analysis and annotation of the sequencing data there are typically thousands of candidate variants requiring further investigation. One of the most effective and least biased ways to reduce this number is to assess the rarity of a variant in any population. Currently, there are a number of reliable sources of information for major population frequencies when considering single nucleotide variants (SNVs) and small insertion and deletions (INDELs), with gnomAD as the most prominent public resource available. However, local variation or frequencies in sub-populations may be underrepresented in these public resources. In contrast, for structural variation (SV), the background frequency in the general population is more or less unknown mostly due to challenges in calling SVs in a consistent way. Keeping track of local variation is one way to overcome these problems and significantly reduce the number of potential disease causing variants retained for manual inspection, both for SNVs and SVs. RESULTS Here, we present loqusdb, a tool to solve the challenge of keeping track of any type of variant observations from genome sequencing data. Loqusdb was designed to handle a large flow of samples and unlike other solutions, samples can be added continuously to the database without rebuilding it, facilitating improvements and additions. We assessed the added value of a local observations database using 98 samples annotated with information from a background of 888 unrelated individuals. CONCLUSIONS We show both how powerful SV analysis can be when filtering for population frequencies and how the number of apparently rare SNVs/INDELs can be reduced by adding local population information even after annotating the data with other large frequency databases, such as gnomAD. In conclusion, we show that a local frequency database is an attractive, and a necessary addition to the publicly available databases that facilitate the analysis of exome and genome data in a clinical setting.
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Affiliation(s)
- Måns Magnusson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm, Sweden. .,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden. .,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden.
| | - Jesper Eisfeldt
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Adam Rosenbaum
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Wedell
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Henrik Stranneheim
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
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32
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Abstract
BACKGROUND Deep mutational scanning (DMS) studies exploit the mutational landscape of sequence variation by systematically and comprehensively assaying the effect of single amino acid variants (SAVs; also referred to as missense mutations, or non-synonymous Single Nucleotide Variants - missense SNVs or nsSNVs) for particular proteins. We assembled SAV annotations from 22 different DMS experiments and normalized the effect scores to evaluate variant effect prediction methods. Three trained on traditional variant effect data (PolyPhen-2, SIFT, SNAP2), a regression method optimized on DMS data (Envision), and a naïve prediction using conservation information from homologs. RESULTS On a set of 32,981 SAVs, all methods captured some aspects of the experimental effect scores, albeit not the same. Traditional methods such as SNAP2 correlated slightly more with measurements and better classified binary states (effect or neutral). Envision appeared to better estimate the precise degree of effect. Most surprising was that the simple naïve conservation approach using PSI-BLAST in many cases outperformed other methods. All methods captured beneficial effects (gain-of-function) significantly worse than deleterious (loss-of-function). For the few proteins with multiple independent experimental measurements, experiments differed substantially, but agreed more with each other than with predictions. CONCLUSIONS DMS provides a new powerful experimental means of understanding the dynamics of the protein sequence space. As always, promising new beginnings have to overcome challenges. While our results demonstrated that DMS will be crucial to improve variant effect prediction methods, data diversity hindered simplification and generalization.
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Affiliation(s)
- Jonas Reeb
- Department of Informatics, Bioinformatics & Computational Biology - i12, TUM (Technical University of Munich), Boltzmannstr 3, 85748, Garching/Munich, Germany.
| | - Theresa Wirth
- Department of Informatics, Bioinformatics & Computational Biology - i12, TUM (Technical University of Munich), Boltzmannstr 3, 85748, Garching/Munich, Germany
| | - Burkhard Rost
- Department of Informatics, Bioinformatics & Computational Biology - i12, TUM (Technical University of Munich), Boltzmannstr 3, 85748, Garching/Munich, Germany
- Institute for Advanced Study (TUM-IAS), Lichtenbergstr 2a, 85748, Garching/Munich, Germany
- TUM School of Life Sciences Weihenstephan (WZW), Alte Akademie 8, Freising, Germany
- Department of Biochemistry and Molecular Biophysics, Columbia University, 701 West, 168th Street, New York, NY, 10032, USA
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Venkatasubramani JP, Subramanyam P, Pal R, Reddy BK, Srinivasan DJ, Chattarji S, Iossifov I, Klann E, Bhattacharya A. N-terminal variant Asp14Asn of the human p70 S6 Kinase 1 enhances translational signaling causing different effects in developing and mature neuronal cells. Neurobiol Learn Mem 2020; 171:107203. [PMID: 32147585 DOI: 10.1016/j.nlm.2020.107203] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 01/23/2020] [Accepted: 02/29/2020] [Indexed: 01/02/2023]
Abstract
The ribosomal p70 S6 Kinase 1 (S6K1) has been implicated in the etiology of complex neurological diseases including autism, depression and dementia. Though no major gene disruption has been reported in humans in RPS6KB1, single nucleotide variants (SNVs) causing missense mutations have been identified, which have not been assessed for their impact on protein function. These S6K1 mutations have the potential to influence disease progression and treatment response. We mined the Simon Simplex Collection (SSC) and SPARK autism database to find inherited SNVs in S6K1 and characterized the effect of two missense SNVs, Asp14Asn (allele frequency = 0.03282%) and Glu44Gln (allele frequency = 0.0008244%), on S6K1 function in HEK293, human ES cells and primary neurons. Expressing Asp14Asn in HEK293 cells resulted in increased basal phosphorylation of downstream targets of S6K1 and increased de novo translation. This variant also showed blunted response to the specific S6K1 inhibitor, FS-115. In human embryonic cell line Shef4, Asp14Asn enhanced spontaneous neural fate specification in the absence of differentiating growth factors. In addition to enhanced translation, neurons expressing Asp14Asn exhibited impaired dendritic arborization and increased levels of phosphorylated ERK 1/2. Finally, in the SSC families tracked, Asp14Asn segregated with lower IQ scores when found in the autistic individual rather than the unaffected sibling. The Glu44Gln mutation showed a milder, but opposite phenotype in HEK cells as compared to Asp14Asn. Although the Glu44Gln mutation displayed increased neuronal translation, it had no impact on neuronal morphology. Our results provide the first characterization of naturally occurring human S6K1 variants on cognitive phenotype, neuronal morphology and maturation, underscoring again the importance of translation control in neural development and plasticity.
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Affiliation(s)
- Janani Priya Venkatasubramani
- Centre for Brain Development and Repair, Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bellary Road, Bangalore, India
| | - Prakash Subramanyam
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY, USA
| | - Rakhi Pal
- Centre for Brain Development and Repair, Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bellary Road, Bangalore, India
| | - Bharath K Reddy
- Centre for Brain Development and Repair, Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bellary Road, Bangalore, India
| | - Durga Jeyalakshmi Srinivasan
- Centre for Brain Development and Repair, Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bellary Road, Bangalore, India; University of Trans-Disciplinary Health Sciences and Technology, Bangalore, India
| | - Sumantra Chattarji
- Centre for Brain Development and Repair, Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bellary Road, Bangalore, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Post, Bellary Road, Bangalore, India
| | - Ivan Iossifov
- Cold Spring Harbor Laboratory, 1 Bungtown Rd., Cold Spring Harbor, New York, NY, USA
| | - Eric Klann
- Center for Neural Science, New York University, 4 Washington Place New York, NY, USA
| | - Aditi Bhattacharya
- Centre for Brain Development and Repair, Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bellary Road, Bangalore, India.
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Domínguez-Cruz MG, Muñoz MDL, Totomoch-Serra A, García-Escalante MG, Burgueño J, Valadez-González N, Pinto-Escalante D, Díaz-Badillo A. Maya gene variants related to the risk of type 2 diabetes in a family-based association study. Gene 2020; 730:144259. [PMID: 31759989 DOI: 10.1016/j.gene.2019.144259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 12/01/2022]
Abstract
Mexican Maya populations have a notably high prevalence of type 2 diabetes (T2D) as a consequence of the interaction between environmental factors and a genetic component. To assess the impact of 24 single nucleotide variants (SNVs) located in 18 T2D risk genes, we conducted a family-based association evaluation in samples from Maya communities with a high incidence of the disease. A total of four hundred individuals were recruited from three Maya communities with a high T2D incidence. Family pedigrees (100) and 49 nuclear families were included. Genotyping was performed by allelic discrimination with TaqMan probes. This study also included the family-based association test (FBAT) statistic U to assess the genetic associations with T2D, and the multivariate statistical and haplotype analyses. A positive association with TD2 risk was found for WFS1 rs6446482 (p = 0.046, Z = 1.994) under an additive model, and SIRT1 rs7896005 (p = 0.038, Z = 2.073) under the dominant model. Multivariate model analysis, including T2D status, age, and body mass index (BMI), displayed significant covariance in PPARGC-1α rs8192678; SIRT1 rs7896005; TCF7L2 rs7903146 and rs122243326; UCP3 rs3781907; and HHEX rs1111875 with a P < 0.05. This study revealed an association of SIRT1 and WFS1 with T2D risk.
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Affiliation(s)
- Miriam G Domínguez-Cruz
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - María de Lourdes Muñoz
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico.
| | - Armando Totomoch-Serra
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico; PhD Program in Medical Sciences, Universidad de La Frontera, Chile
| | - María G García-Escalante
- Laboratorios de Genética y Hematología, Centro de Investigaciones Regionales "Dr. Hideyo Noguchi", Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Juan Burgueño
- Centro Internacional de Mejoramiento de Maíz y Trigo, El Batán, Texcoco, State of Mexico, Mexico
| | - Nina Valadez-González
- Laboratorios de Genética y Hematología, Centro de Investigaciones Regionales "Dr. Hideyo Noguchi", Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Doris Pinto-Escalante
- Laboratorios de Genética y Hematología, Centro de Investigaciones Regionales "Dr. Hideyo Noguchi", Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Alvaro Díaz-Badillo
- Maestría en Salud Publica, Universidad México Americana del Norte, Reynosa, Tamaulipas, Mexico; Department of Epidemiology, Human Genetics & Environmental Sciences, The University of Texas Health Science Center at Houston, Brownville, TX, USA
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35
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Amiri Ghanatsaman Z, Wang GD, Asadollahpour Nanaei H, Asadi Fozi M, Peng MS, Esmailizadeh A, Zhang YP. Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication. BMC Genomics 2020; 21:207. [PMID: 32131720 PMCID: PMC7057629 DOI: 10.1186/s12864-020-6619-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 08/25/2019] [Accepted: 02/25/2020] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and three dogs from Iran which covers the eastern part of the Fertile Crescent located in Southwest Asia where the independent domestication of most of the plants and animals has been documented and also high haplotype sharing between wolves and dog breeds has been reported. RESULTS Higher diversity was found within the wolf genome compared with the dog genome. A total number of 12.45 million SNPs were detected in all individuals (10.45 and 7.82 million SNPs were identified for all the studied wolves and dogs, respectively) and a total number of 3.49 million small Indels were detected in all individuals (3.11 and 2.24 million small Indels were identified for all the studied wolves and dogs, respectively). A total of 10,571 copy number variation regions (CNVRs) were detected across the 6 individual genomes, covering 154.65 Mb, or 6.41%, of the reference genome (canFam3.1). Further analysis showed that the distribution of deleterious variants in the dog genome is higher than the wolf genome. Also, genomic annotation results from intron and intergenic regions showed that the proportion of variations in the wolf genome is higher than that in the dog genome, while the proportion of the coding sequences and 3'-UTR in the dog genome is higher than that in the wolf genome. The genes related to the olfactory and immune systems were enriched in the set of the structural variants (SVs) identified in this work. CONCLUSIONS Our results showed more deleterious mutations and coding sequence variants in the domestic dog genome than those in wolf genome. By providing the first Iranian dog and wolf variome map, our findings contribute to understanding the genetic architecture of the dog domestication.
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Affiliation(s)
- Zeinab Amiri Ghanatsaman
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
- Yong Researchers Society, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China
| | - Hojjat Asadollahpour Nanaei
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
- Yong Researchers Society, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Masood Asadi Fozi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China.
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China.
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Lindstrand A, Eisfeldt J, Pettersson M, Carvalho CMB, Kvarnung M, Grigelioniene G, Anderlid BM, Bjerin O, Gustavsson P, Hammarsjö A, Georgii-Hemming P, Iwarsson E, Johansson-Soller M, Lagerstedt-Robinson K, Lieden A, Magnusson M, Martin M, Malmgren H, Nordenskjöld M, Norling A, Sahlin E, Stranneheim H, Tham E, Wincent J, Ygberg S, Wedell A, Wirta V, Nordgren A, Lundin J, Nilsson D. From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability. Genome Med 2019; 11:68. [PMID: 31694722 PMCID: PMC6836550 DOI: 10.1186/s13073-019-0675-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [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: 05/07/2019] [Accepted: 10/09/2019] [Indexed: 12/30/2022] Open
Abstract
Background Since different types of genetic variants, from single nucleotide variants (SNVs) to large chromosomal rearrangements, underlie intellectual disability, we evaluated the use of whole-genome sequencing (WGS) rather than chromosomal microarray analysis (CMA) as a first-line genetic diagnostic test. Methods We analyzed three cohorts with short-read WGS: (i) a retrospective cohort with validated copy number variants (CNVs) (cohort 1, n = 68), (ii) individuals referred for monogenic multi-gene panels (cohort 2, n = 156), and (iii) 100 prospective, consecutive cases referred to our center for CMA (cohort 3). Bioinformatic tools developed include FindSV, SVDB, Rhocall, Rhoviz, and vcf2cytosure. Results First, we validated our structural variant (SV)-calling pipeline on cohort 1, consisting of three trisomies and 79 deletions and duplications with a median size of 850 kb (min 500 bp, max 155 Mb). All variants were detected. Second, we utilized the same pipeline in cohort 2 and analyzed with monogenic WGS panels, increasing the diagnostic yield to 8%. Next, cohort 3 was analyzed by both CMA and WGS. The WGS data was processed for large (> 10 kb) SVs genome-wide and for exonic SVs and SNVs in a panel of 887 genes linked to intellectual disability as well as genes matched to patient-specific Human Phenotype Ontology (HPO) phenotypes. This yielded a total of 25 pathogenic variants (SNVs or SVs), of which 12 were detected by CMA as well. We also applied short tandem repeat (STR) expansion detection and discovered one pathologic expansion in ATXN7. Finally, a case of Prader-Willi syndrome with uniparental disomy (UPD) was validated in the WGS data. Important positional information was obtained in all cohorts. Remarkably, 7% of the analyzed cases harbored complex structural variants, as exemplified by a ring chromosome and two duplications found to be an insertional translocation and part of a cryptic unbalanced translocation, respectively. Conclusion The overall diagnostic rate of 27% was more than doubled compared to clinical microarray (12%). Using WGS, we detected a wide range of SVs with high accuracy. Since the WGS data also allowed for analysis of SNVs, UPD, and STRs, it represents a powerful comprehensive genetic test in a clinical diagnostic laboratory setting.
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Affiliation(s)
- Anna Lindstrand
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden. .,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden. .,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Jesper Eisfeldt
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Maria Pettersson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Malin Kvarnung
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Giedre Grigelioniene
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Britt-Marie Anderlid
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Olof Bjerin
- The Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Peter Gustavsson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Hammarsjö
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Erik Iwarsson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maria Johansson-Soller
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kristina Lagerstedt-Robinson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Agne Lieden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Måns Magnusson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Marcel Martin
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Helena Malmgren
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ameli Norling
- The Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Ellika Sahlin
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Stranneheim
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Emma Tham
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Josephine Wincent
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sofia Ygberg
- The Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Wedell
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.,Science for Life Laboratory, Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Stockholm, Sweden
| | - Ann Nordgren
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Johanna Lundin
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Daniel Nilsson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
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Field MA, Burgio G, Chuah A, Al Shekaili J, Hassan B, Al Sukaiti N, Foote SJ, Cook MC, Andrews TD. Recurrent miscalling of missense variation from short-read genome sequence data. BMC Genomics 2019; 20:546. [PMID: 31307400 PMCID: PMC6631443 DOI: 10.1186/s12864-019-5863-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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] [Indexed: 12/30/2022] Open
Abstract
Background Short-read resequencing of genomes produces abundant information of the genetic variation of individuals. Due to their numerous nature, these variants are rarely exhaustively validated. Furthermore, low levels of undetected variant miscalling will have a systematic and disproportionate impact on the interpretation of individual genome sequence information, especially should these also be carried through into in reference databases of genomic variation. Results We find that sequence variation from short-read sequence data is subject to recurrent-yet-intermittent miscalling that occurs in a sequence intrinsic manner and is very sensitive to sequence read length. The miscalls arise from difficulties aligning short reads to redundant genomic regions, where the rate of sequencing error approaches the sequence diversity between redundant regions. We find the resultant miscalled variants to be sensitive to small sequence variations between genomes, and thereby are often intrinsic to an individual, pedigree, strain or human ethnic group. In human exome sequences, we identify 2–300 recurrent false positive variants per individual, almost all of which are present in public databases of human genomic variation. From the exomes of non-reference strains of inbred mice, we identify 3–5000 recurrent false positive variants per mouse – the number of which increasing with greater distance between an individual mouse strain and the reference C57BL6 mouse genome. We show that recurrently miscalled variants may be reproduced for a given genome from repeated simulation rounds of read resampling, realignment and recalling. As such, it is possible to identify more than two-thirds of false positive variation from only ten rounds of simulation. Conclusion Identification and removal of recurrent false positive variants from specific individual variant sets will improve overall data quality. Variant miscalls arising are highly sequence intrinsic and are often specific to an individual, pedigree or ethnicity. Further, read length is a strong determinant of whether given false variants will be called for any given genome – which has profound significance for cohort studies that pool datasets collected and sequenced at different points in time. Electronic supplementary material The online version of this article (10.1186/s12864-019-5863-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew A Field
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia.,Australian Institute of Tropical Health and Medicine, Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, Queensland, Australia
| | - Gaetan Burgio
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Aaron Chuah
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jalila Al Shekaili
- Department of Microbiology and Immunology, Sultan Qaboos University Hospital, Seeb, Oman
| | - Batool Hassan
- Department of Medicine, Sultan Qaboos University Hospital, Muscat, Oman
| | - Nashat Al Sukaiti
- Department of Paediatrics, Allergy, and Clinical Immunology Unit, Royal Hospital, Muscat, Oman
| | - Simon J Foote
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Matthew C Cook
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia.,Department of Immunology, Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - T Daniel Andrews
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia.
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Amano Y, Akazawa Y, Yasuda J, Yoshino K, Kojima K, Kobayashi N, Matsuzaki S, Nagasaki M, Kawai Y, Minegishi N, Ishida N, Motoki N, Hachiya A, Nakazawa Y, Yamamoto M, Koike K, Takeshita T. A low-frequency IL4R locus variant in Japanese patients with intravenous immunoglobulin therapy-unresponsive Kawasaki disease. Pediatr Rheumatol Online J 2019; 17:34. [PMID: 31269967 PMCID: PMC6610867 DOI: 10.1186/s12969-019-0337-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/07/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Kawasaki disease (KD) is a systemic vasculitis which may be associated with coronary artery aneurysms. A notable risk factor for the development of coronary artery aneurysms is resistance to intravenous immunoglobulin (IVIG) therapy, which comprises standard treatment for the acute phase of KD. The cause of IVIG resistance in KD is largely unknown; however, the contribution of genetic factors, especially variants in immune-related genes, has been suspected. METHODS To explore genetic variants related to IVIG-unresponsiveness, we designated KD patients who did not respond to both first and second courses of IVIG therapy as IVIG-unresponsive patients. Using genomic DNA from 30 IVIG-unresponsive KD patients, we performed pooled genome sequencing targeting 39 immune-related cytokine receptor genes. RESULTS The single nucleotide variant (SNV), rs563535954 (located in the IL4R locus), was concentrated in IVIG-unresponsive KD patients. Individual genotyping showed that the minor allele of rs563535954 was present in 4/33 patients with IVIG-unresponsive KD, compared with 20/1063 individuals in the Japanese genome variation database (odds ratio = 7.19, 95% confidence interval 2.43-21.47). Furthermore, the minor allele of rs563535954 was absent in 42 KD patients who responded to IVIG treatment (P = 0.0337), indicating that a low-frequency variant, rs563535954, is associated with IVIG-unresponsiveness in KD patients. Although rs563535954 is located in the 3'-untranslated region of IL4R, there was no alternation in IL4R expression associated with the mior allele of rs563535954. However, IVIG-unresponsive patients that exhibited the minor allele of rs563535954 tended to be classified into the low-risk group (based on previously reported risk scores) for prediction of IVIG-resistance. Therefore, IVIG-unresponsiveness associated with the minor allele of rs563535954 might differ from IVIG-unresponsiveness associated with previous risk factors used to evaluate IVIG-unresponsiveness in KD. CONCLUSION These findings suggest that the SNV rs563535954 could serve as a predictive indicator of IVIG-unresponsiveness, thereby improving the sensitivity of risk scoring systems, and may aid in prevention of coronary artery lesions in KD patients.
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Affiliation(s)
- Yuji Amano
- 0000 0001 1507 4692grid.263518.bDepartment of Microbiology and Immunology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621 Japan
| | - Yohei Akazawa
- 0000 0001 1507 4692grid.263518.bDepartment of Pediatrics, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621 Japan
| | - Jun Yasuda
- 0000 0001 2248 6943grid.69566.3aTohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan ,0000 0001 2248 6943grid.69566.3aGraduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Kazuhisa Yoshino
- 0000 0001 1507 4692grid.263518.bDepartment of Microbiology and Immunology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621 Japan
| | - Katsuhiko Kojima
- 0000 0001 1507 4692grid.263518.bDepartment of Microbiology and Immunology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621 Japan
| | - Norimoto Kobayashi
- 0000 0001 1507 4692grid.263518.bDepartment of Pediatrics, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621 Japan
| | - Satoshi Matsuzaki
- 0000 0001 1507 4692grid.263518.bDepartment of Pediatrics, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621 Japan
| | - Masao Nagasaki
- 0000 0001 2248 6943grid.69566.3aTohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan ,0000 0001 2248 6943grid.69566.3aGraduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan ,0000 0001 2248 6943grid.69566.3aGraduate School of Information Science, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8579 Japan
| | - Yosuke Kawai
- 0000 0001 2248 6943grid.69566.3aTohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan ,0000 0001 2248 6943grid.69566.3aGraduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Naoko Minegishi
- 0000 0001 2248 6943grid.69566.3aTohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan ,0000 0001 2248 6943grid.69566.3aGraduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Noriko Ishida
- 0000 0001 2248 6943grid.69566.3aTohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan ,0000 0001 2248 6943grid.69566.3aGraduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Noriko Motoki
- 0000 0001 1507 4692grid.263518.bDepartment of Pediatrics, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621 Japan
| | - Akira Hachiya
- 0000 0001 1507 4692grid.263518.bDepartment of Pediatrics, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621 Japan
| | - Yozo Nakazawa
- 0000 0001 1507 4692grid.263518.bDepartment of Pediatrics, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621 Japan
| | - Masayuki Yamamoto
- 0000 0001 2248 6943grid.69566.3aTohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan ,0000 0001 2248 6943grid.69566.3aGraduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Kenichi Koike
- 0000 0001 1507 4692grid.263518.bDepartment of Pediatrics, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621 Japan ,Shinonoi General Hospital, Minami Nagano Center, 666-1 Shinonoi, Nagano City, Nagano 388-8004 Japan
| | - Toshikazu Takeshita
- Department of Microbiology and Immunology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan.
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Abstract
Background Severe equine asthma is a chronic inflammatory disease of the lung in horses similar to low-Th2 late-onset asthma in humans. This study aimed to determine the utility of RNA-Seq to call gene sequence variants, and to identify sequence variants of potential relevance to the pathogenesis of asthma. Methods RNA-Seq data were generated from endobronchial biopsies collected from six asthmatic and seven non-asthmatic horses before and after challenge (26 samples total). Sequences were aligned to the equine genome with Spliced Transcripts Alignment to Reference software. Read preparation for sequence variant calling was performed with Picard tools and Genome Analysis Toolkit (GATK). Sequence variants were called and filtered using GATK and Ensembl Variant Effect Predictor (VEP) tools, and two RNA-Seq predicted sequence variants were investigated with both PCR and Sanger sequencing. Supplementary analysis of novel sequence variant selection with VEP was based on a score of <0.01 predicted with Sorting Intolerant from Tolerant software, missense nature, location within the protein coding sequence and presence in all asthmatic individuals. For select variants, effect on protein function was assessed with Polymorphism Phenotyping 2 and screening for non-acceptable polymorphism 2 software. Sequences were aligned and 3D protein structures predicted with Geneious software. Difference in allele frequency between the groups was assessed using a Pearson’s Chi-squared test with Yates’ continuity correction, and difference in genotype frequency was calculated using the Fisher’s exact test for count data. Results RNA-Seq variant calling and filtering correctly identified substitution variants in PACRG and RTTN. Sanger sequencing confirmed that the PACRG substitution was appropriately identified in all 26 samples while the RTTN substitution was identified correctly in 24 of 26 samples. These variants of uncertain significance had substitutions that were predicted to result in loss of function and to be non-neutral. Amino acid substitutions projected no change of hydrophobicity and isoelectric point in PACRG, and a change in both for RTTN. For PACRG, no difference in allele frequency between the two groups was detected but a higher proportion of asthmatic horses had the altered RTTN allele compared to non-asthmatic animals. Discussion RNA-Seq was sensitive and specific for calling gene sequence variants in this disease model. Even moderate coverage (<10–20 counts per million) yielded correct identification in 92% of samples, suggesting RNA-Seq may be suitable to detect sequence variants in low coverage samples. The impact of amino acid alterations in PACRG and RTTN proteins, and possible association of the sequence variants with asthma, is of uncertain significance, but their role in ciliary function may be of future interest.
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Affiliation(s)
- Laurence Tessier
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada.,BenchSci, Toronto, ON, Canada
| | - Olivier Côté
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada.,BioAssay Works, Ijamsville, MD, USA
| | - Dorothee Bienzle
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
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Totomoch-Serra A, Muñoz MDL, Burgueño J, Revilla-Monsalve MC, Perez-Muñoz A, Diaz-Badillo Á. The ADRA2A rs553668 variant is associated with type 2 diabetes and five variants were associated at nominal significance levels in a population-based case-control study from Mexico City. Gene 2018; 669:28-34. [PMID: 29800730 DOI: 10.1016/j.gene.2018.05.078] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 05/11/2018] [Accepted: 05/21/2018] [Indexed: 02/07/2023]
Abstract
Type 2 diabetes (T2D) is a disease with a prevalence of 9.4% in Mexicans. Its etiology is complex involving environmental and genetic factors. The aim of this study was to analyse the association between PPARG rs1801282, PPARGC1A rs8192678, VEGFA rs2010963, ADRA2A rs553668, KCNQ1 rs2237892, SIRT1 rs7896005, IGF2BP2 rs4402960, and UCP3 rs3781907 single nucleotide variants (SNVs) with T2D and metabolic traits in a case-control study of a population from Mexico City. A total of 831 blood samples of non-diabetic, with healthy control participants (416) and individuals with T2D (415) were collected over a five-year period. After DNA extraction, genotyping was performed with TaqMan probes using real-time PCR. The genotypes were analysed for association with T2D in linear and logistic regressions adjusting for age, sex, and body mass index using the dominant, recessive, and additive models with a Bonferroni correction for multiple comparisons p < 0.001 and for association with related T2D traits fixed with a p < 2.3 × 10-4. The univariate analysis gives a significant (p < 1 × 10-4) for sex, triglycerides, and HOMA-IR. Significant association with T2D was found for ADRA2A rs553668 under the recessive model (OR = 3.640 and 95% CI of 2.330-5.690 (p < 1 × 10-4); statistical power 0.999) and under the additive model (OR = 1.640 and 95% CI of 1.340-2.000 (p < 1 × 10-4); statistical power 0.997). Variants PPARG rs1801282, PPARGC1A rs8192678, SIRT1 rs7896005, IGF2BP2 rs4402960 and UCP3 rs3781907 were nominally associated (p > 0.001 and <0.050). Results describe association of ADRA2A rs553668 with T2D in a Mexican population. Variants with nominal association with T2D require to be replicated in additional Mexican populations.
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Affiliation(s)
- Armando Totomoch-Serra
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Mexico City, Mexico
| | - María de Lourdes Muñoz
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Mexico City, Mexico.
| | - Juan Burgueño
- Centro Internacional de Mejoramiento de Maíz y Trigo, Texcoco, State of Mexico, Mexico
| | | | - Ashael Perez-Muñoz
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Mexico City, Mexico
| | - Álvaro Diaz-Badillo
- Coordinación Académica, Colegio de Ciencias y Humanidades, Academia de Biología Humana, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico; South Texas Diabetes and Obesity Institute (STDOI), School of Medicine, University of Texas Rio Grande Valley (UTRGV), Edinburg City, TX, USA
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Ainslie-Garcia MH, Farzan A, Jafarikia M, Lillie BN. Single nucleotide variants in innate immune genes associated with Salmonella shedding and colonization in swine on commercial farms. Vet Microbiol 2018; 219:171-177. [PMID: 29778193 DOI: 10.1016/j.vetmic.2018.04.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 04/10/2018] [Accepted: 04/11/2018] [Indexed: 01/05/2023]
Abstract
Foodborne human salmonellosis is an important food safety concern worldwide. Food-producing animals are one of the major sources of human salmonellosis, and thus control of Salmonella at the farm level could reduce Salmonella spread in the food supply system. Genetic selection of pigs with resistance to Salmonella infection may be one way to control Salmonella on swine farms. The objective of this study was to investigate the association between genetic variants in the porcine innate immune system with on-farm Salmonella shedding and Salmonella colonization tested at slaughter. Fourteen groups of pigs (total 809) were followed from birth to slaughter. Fecal samples collected five times at different stages of production and tissue samples obtained from tonsil and lymph nodes at slaughter were cultured for Salmonella. Genomic DNA was extracted and analyzed for 40 single nucleotide variants and two indels within porcine innate immune genes that were previously associated with Salmonella infection or other infectious diseases. A survey was used to collect information on farm management practices. A multilevel mixed-effects logistic regression modelling method was used to identify SNVs that are associated with Salmonella shedding and/or Salmonella colonization. One single nucleotide variant in the C-type lectin MBL1 and one single nucleotide variant in the cytosolic pattern recognition receptor NOD1 was associated with increased risk of on-farm shedding (p = 0.010) and internal colonization tested at slaughter (p = 0.018), respectively. These findings indicate the potential of these variants for genetic selection programs aimed at controlling Salmonella shedding and colonization in pigs.
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Affiliation(s)
| | - Abdolvahab Farzan
- Department of Pathobiology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada; Department of Population Medicine, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
| | - Mohsen Jafarikia
- Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada; Canadian Center for Swine Improvement, Inc. 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada.
| | - Brandon N Lillie
- Department of Pathobiology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
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Sendorek DH, Caloian C, Ellrott K, Bare JC, Yamaguchi TN, Ewing AD, Houlahan KE, Norman TC, Margolin AA, Stuart JM, Boutros PC. Germline contamination and leakage in whole genome somatic single nucleotide variant detection. BMC Bioinformatics 2018; 19:28. [PMID: 29385983 PMCID: PMC5793408 DOI: 10.1186/s12859-018-2046-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 10/16/2017] [Accepted: 01/24/2018] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The clinical sequencing of cancer genomes to personalize therapy is becoming routine across the world. However, concerns over patient re-identification from these data lead to questions about how tightly access should be controlled. It is not thought to be possible to re-identify patients from somatic variant data. However, somatic variant detection pipelines can mistakenly identify germline variants as somatic ones, a process called "germline leakage". The rate of germline leakage across different somatic variant detection pipelines is not well-understood, and it is uncertain whether or not somatic variant calls should be considered re-identifiable. To fill this gap, we quantified germline leakage across 259 sets of whole-genome somatic single nucleotide variant (SNVs) predictions made by 21 teams as part of the ICGC-TCGA DREAM Somatic Mutation Calling Challenge. RESULTS The median somatic SNV prediction set contained 4325 somatic SNVs and leaked one germline polymorphism. The level of germline leakage was inversely correlated with somatic SNV prediction accuracy and positively correlated with the amount of infiltrating normal cells. The specific germline variants leaked differed by tumour and algorithm. To aid in quantitation and correction of leakage, we created a tool, called GermlineFilter, for use in public-facing somatic SNV databases. CONCLUSIONS The potential for patient re-identification from leaked germline variants in somatic SNV predictions has led to divergent open data access policies, based on different assessments of the risks. Indeed, a single, well-publicized re-identification event could reshape public perceptions of the values of genomic data sharing. We find that modern somatic SNV prediction pipelines have low germline-leakage rates, which can be further reduced, especially for cloud-sharing, using pre-filtering software.
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Affiliation(s)
- Dorota H. Sendorek
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario M5G 0A3 Canada
| | - Cristian Caloian
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario M5G 0A3 Canada
| | - Kyle Ellrott
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA USA
- Computational Biology Program, Oregon Health & Science University, Portland, OR USA
| | | | - Takafumi N. Yamaguchi
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario M5G 0A3 Canada
| | - Adam D. Ewing
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA USA
- Mater Research Institute, University of Queensland, Woolloongabba, Queensland Australia
| | - Kathleen E. Houlahan
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario M5G 0A3 Canada
| | | | - Adam A. Margolin
- Sage Bionetworks, Seattle, WA USA
- Computational Biology Program, Oregon Health & Science University, Portland, OR USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR USA
| | - Joshua M. Stuart
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA USA
| | - Paul C. Boutros
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario M5G 0A3 Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario Canada
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Strouhal M, Oppelt J, Mikalová L, Arora N, Nieselt K, González-Candelas F, Šmajs D. Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes. BMC Res Notes 2018; 11:16. [PMID: 29325576 PMCID: PMC5765698 DOI: 10.1186/s13104-017-3106-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 08/22/2017] [Accepted: 12/19/2017] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Treponema pallidum subsp. pallidum (TPA) is the causative agent of syphilis. Genetic analyses of TPA reference strains and human clinical isolates have revealed two genetically distinct groups of syphilis-causing treponemes, called Nichols-like and SS14-like groups. So far, no genetic intermediates, i.e. strains containing a mixed pattern of Nichols-like and SS14-like genomic sequences, have been identified. Recently, Sun et al. (Oncotarget 2016. https://doi.org/10.18632/oncotarget.10154 ) described a new "phylogenetic group" (called Lineage 2) among Chinese TPA strains. This lineage exhibited a "mosaic genomic structure" of Nichols-like and SS14-like lineages. RESULTS We reanalyzed the primary sequencing data (Project Number PRJNA305961) from the Sun et al. publication with respect to the molecular basis of Lineage 2. While Sun et al. based the analysis on several selected genomic single nucleotide variants (SNVs) and a subset of highly variable but phylogenetically poorly informative genes, which may confound the phylogenetic analysis, our reanalysis primarily focused on a complete set of whole genomic SNVs. Based on our reanalysis, only two separate TPA clusters were identified: one consisted of Nichols-like TPA strains, the other was formed by the SS14-like TPA strains, including all Chinese strains.
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Affiliation(s)
- Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic
| | - Jan Oppelt
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Lenka Mikalová
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic
| | - Natasha Arora
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Kay Nieselt
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
| | - Fernando González-Candelas
- Unidad Mixta Infección y Salud Pública FISABIO, Universidad de Valencia, Valencia, Spain.,Institute for Integrative Systems Biology (I2SysBio), Universidad de Valencia-CSIC, Valencia, Spain.,CIBER Epidemiologia y Salud Pública (CIBERESP), Valencia, Spain
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic.
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Abstract
Background High throughput sequencing technology enables the both the human genome and transcriptome to be screened at the single nucleotide resolution. Tools have been developed to infer single nucleotide variants (SNVs) from both DNA and RNA sequencing data. To evaluate how much difference can be expected between DNA and RNA sequencing data, and among tissue sources, we designed a study to examine the single nucleotide difference among five sources of high throughput sequencing data generated from the same individual, including exome sequencing from blood, tumor and adjacent normal tissue, and RNAseq from tumor and adjacent normal tissue. Results Through careful quality control and analysis of the SNVs, we found little difference between DNA-DNA pairs (1%–2%). However, between DNA-RNA pairs, SNV differences ranged anywhere from 10% to 20%. Conclusions Only a small portion of these differences can be explained by RNA editing. Instead, the majority of the DNA-RNA differences should be attributed to technical errors from sequencing and post-processing of RNAseq data. Our analysis results suggest that SNV detection using RNAseq is subject to high false positive rates. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4022-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yan Guo
- Department of Biomedical Informatics, Vanderbilt University, 2220 Pierce Ave, 571 PRB, Nashville, TN, 37027, USA.
| | - Shilin Zhao
- Department of Biomedical Informatics, Vanderbilt University, 2220 Pierce Ave, 571 PRB, Nashville, TN, 37027, USA
| | - Quanhu Sheng
- Department of Biomedical Informatics, Vanderbilt University, 2220 Pierce Ave, 571 PRB, Nashville, TN, 37027, USA
| | - David C Samuels
- Vanderbilt Genetics Institute, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TN, USA
| | - Yu Shyr
- Department of Biostatistics, Vanderbilt University, 2220 Pierce Ave, 571 PRB, Nashville, TN, 37027, USA.
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Rustagi N, Zhou A, Watkins WS, Gedvilaite E, Wang S, Ramesh N, Muzny D, Gibbs RA, Jorde LB, Yu F, Xing J. Extremely low-coverage whole genome sequencing in South Asians captures population genomics information. BMC Genomics 2017; 18:396. [PMID: 28532386 PMCID: PMC5440948 DOI: 10.1186/s12864-017-3767-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 09/14/2016] [Accepted: 05/07/2017] [Indexed: 11/18/2022] Open
Abstract
Background The cost of Whole Genome Sequencing (WGS) has decreased tremendously in recent years due to advances in next-generation sequencing technologies. Nevertheless, the cost of carrying out large-scale cohort studies using WGS is still daunting. Past simulation studies with coverage at ~2x have shown promise for using low coverage WGS in studies focused on variant discovery, association study replications, and population genomics characterization. However, the performance of low coverage WGS in populations with a complex history and no reference panel remains to be determined. Results South Indian populations are known to have a complex population structure and are an example of a major population group that lacks adequate reference panels. To test the performance of extremely low-coverage WGS (EXL-WGS) in populations with a complex history and to provide a reference resource for South Indian populations, we performed EXL-WGS on 185 South Indian individuals from eight populations to ~1.6x coverage. Using two variant discovery pipelines, SNPTools and GATK, we generated a consensus call set that has ~90% sensitivity for identifying common variants (minor allele frequency ≥ 10%). Imputation further improves the sensitivity of our call set. In addition, we obtained high-coverage for the whole mitochondrial genome to infer the maternal lineage evolutionary history of the Indian samples. Conclusions Overall, we demonstrate that EXL-WGS with imputation can be a valuable study design for variant discovery with a dramatically lower cost than standard WGS, even in populations with a complex history and without available reference data. In addition, the South Indian EXL-WGS data generated in this study will provide a valuable resource for future Indian genomic studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3767-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Navin Rustagi
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Anbo Zhou
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - W Scott Watkins
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA
| | - Erika Gedvilaite
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Shuoguo Wang
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Naveen Ramesh
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna Muzny
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lynn B Jorde
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA.
| | - Fuli Yu
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Jinchuan Xing
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
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Abstract
In silico prediction methods have increasingly been valuable and popular in molecular biology, especially in human genetics, for deleteriousness prediction to filter and prioritize huge amounts of DNA variation identified by sequencing human genomes. There is a rich collection of available methods developed upon different levels/aspects of knowledge about how DNA variations affect gene expression. Given the fact that their predictions are not always consistent or even opposite of what was expected, using consensus prediction or majority vote among these methods is preferred to trusting any single one. Because querying different databases for different methods is both tedious and time-consuming for such big data sets, one database integrating predictions from multiple databases can facilitate the process. In this chapter, we describe the general steps of obtaining comprehensive predictions and annotations for large numbers of variants from dbNSFP, the first and probably the most widely used database of its kind.
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Affiliation(s)
- Xueqiu Jian
- Center for Human Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Xiaoming Liu
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, 1200 Pressler St, E529, Houston, TX, 77030, USA.
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Fleming DS, Koltes JE, Fritz-Waters ER, Rothschild MF, Schmidt CJ, Ashwell CM, Persia ME, Reecy JM, Lamont SJ. Single nucleotide variant discovery of highly inbred Leghorn and Fayoumi chicken breeds using pooled whole genome resequencing data reveals insights into phenotype differences. BMC Genomics 2016; 17:812. [PMID: 27760519 PMCID: PMC5070165 DOI: 10.1186/s12864-016-3147-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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: 12/31/2015] [Accepted: 10/05/2016] [Indexed: 11/22/2022] Open
Abstract
Background Analyses of sequence variants of two distinct and highly inbred chicken lines allowed characterization of genomic variation that may be associated with phenotypic differences between breeds. These lines were the Leghorn, the major contributing breed to commercial white-egg production lines, and the Fayoumi, representative of an outbred indigenous and robust breed. Unique within- and between-line genetic diversity was used to define the genetic differences of the two breeds through the use of variant discovery and functional annotation. Results Downstream fixation test (FST) analysis and subsequent gene ontology (GO) enrichment analysis elucidated major differences between the two lines. The genes with high FST values for both breeds were used to identify enriched gene ontology terms. Over-enriched GO annotations were uncovered for functions indicative of breed-related traits of pathogen resistance and reproductive ability for Fayoumi and Leghorn, respectively. Conclusions Variant analysis elucidated GO functions indicative of breed-predominant phenotypes related to genomic variation in the lines, showing a possible link between the genetic variants and breed traits. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3147-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - J E Koltes
- Iowa State University, Ames, IA, USA.,Department of Animal Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | | | | | | | - C M Ashwell
- North Carolina State University, Raleigh, NC, USA
| | - M E Persia
- Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - J M Reecy
- Iowa State University, Ames, IA, USA
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González-Peñas J, Amigo J, Santomé L, Sobrino B, Brenlla J, Agra S, Paz E, Páramo M, Carracedo Á, Arrojo M, Costas J. Targeted resequencing of regulatory regions at schizophrenia risk loci: Role of rare functional variants at chromatin repressive states. Schizophr Res 2016; 174:10-16. [PMID: 27066855 DOI: 10.1016/j.schres.2016.03.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 03/24/2016] [Indexed: 12/30/2022]
Abstract
There is mounting evidence that regulatory variation plays an important role in genetic risk for schizophrenia. Here, we specifically search for regulatory variants at risk by sequencing promoter regions of twenty-three genes implied in schizophrenia by copy number variant or genome-wide association studies. After strict quality control, a total of 55,206bp per sample were analyzed in 526 schizophrenia cases and 516 controls from Galicia, NW Spain, using the Applied Biosystems SOLiD System. Variants were filtered based on frequency from public databases, chromatin states from the RoadMap Epigenomics Consortium at tissues relevant for schizophrenia, such as fetal brain, mid-frontal lobe, and angular gyrus, and prediction of functionality from RegulomeDB. The proportion of rare variants at polycomb repressive chromatin state at relevant tissues was higher in cases than in controls. The proportion of rare variants with predicted regulatory role was significantly higher in cases than in controls (P=0.0028, OR=1.93, 95% C.I.=1.23-3.04). Combination of information from both sources led to the identification of an excess of carriers of rare variants with predicted regulatory role located at polycomb repressive chromatin state at relevant tissues in cases versus controls (P=0.0016, OR=19.34, 95% C.I.=2.45-2495.26). The variants are located at two genes affected by the 17q12 copy number variant, LHX1 and HNF1B. These data strongly suggest that a specific epigenetic mechanism, chromatin remodeling by histone modification during early development, may be impaired in a subset of schizophrenia patients, in agreement with previous data.
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Affiliation(s)
- Javier González-Peñas
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Jorge Amigo
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain; Grupo de Medicina Xenómica, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Fundación Pública Galega de Medicina Xenómica, Complexo Hospitalario Universitario de Santiago (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Luis Santomé
- Fundación Pública Galega de Medicina Xenómica, Complexo Hospitalario Universitario de Santiago (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Beatriz Sobrino
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain; Grupo de Medicina Xenómica, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Fundación Pública Galega de Medicina Xenómica, Complexo Hospitalario Universitario de Santiago (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Julio Brenlla
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain; Servizo de Psiquiatría, Complexo Hospitalario Universitario de Santiago de Compostela, Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Santiago Agra
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain; Servizo de Psiquiatría, Complexo Hospitalario Universitario de Santiago de Compostela, Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Eduardo Paz
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain; Servizo de Psiquiatría, Complexo Hospitalario Universitario de Santiago de Compostela, Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Mario Páramo
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain; Servizo de Psiquiatría, Complexo Hospitalario Universitario de Santiago de Compostela, Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Ángel Carracedo
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain; Grupo de Medicina Xenómica, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Fundación Pública Galega de Medicina Xenómica, Complexo Hospitalario Universitario de Santiago (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Manuel Arrojo
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain; Servizo de Psiquiatría, Complexo Hospitalario Universitario de Santiago de Compostela, Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Javier Costas
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain.
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Yu Y, Wu T, Johnson-Buck A, Li L, Su X. A two-layer assay for single-nucleotide variants utilizing strand displacement and selective digestion. Biosens Bioelectron 2016; 82:248-54. [PMID: 27100949 DOI: 10.1016/j.bios.2016.03.070] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/21/2016] [Accepted: 03/28/2016] [Indexed: 11/17/2022]
Abstract
Point mutations have emerged as prominent biomarkers for disease diagnosis, particularly in the case of cancer. Discovering single-nucleotide variants (SNVs) is also of great importance for the identification of single-nucleotide polymorphisms within the population. The competing requirements of thermodynamic stability and specificity in conventional nucleic acid hybridization probes make it challenging to achieve highly precise detection of point mutants. Here, we present a fluorescence-based assay for low-abundance mutation detection based on toehold-mediated strand displacement and nuclease-mediated strand digestion that enables highly precise detection of point mutations. We demonstrate that this combined assay provides 50-1000-fold discrimination (mean value: 255) between all possible single-nucleotide mutations and their corresponding wild-type sequence for a model DNA target. Using experiments and kinetic modeling, we investigate probe properties that obtain additive benefits from both strand displacement and nucleolytic digestion, thus providing guidance for the design of enzyme-mediated nucleic acid assays in the future.
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Affiliation(s)
- Yingjie Yu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Materials Science and Engineering, Stony Brook University, Stony Brook, NY 11790, USA
| | - Tongbo Wu
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | | | - Lidan Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
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Yang S, Hemarajata P, Hindler J, Ward K, Adisetiyo H, Li F, Aldrovandi GM, Green NM, Russell D, Rubin Z, Humphries RM. Investigation of a suspected nosocomial transmission of blaKPC3-mediated carbapenem-resistant Klebsiella pneumoniae by whole genome sequencing. Diagn Microbiol Infect Dis 2015; 84:337-42. [PMID: 26867964 DOI: 10.1016/j.diagmicrobio.2015.12.019] [Citation(s) in RCA: 11] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 11/25/2015] [Accepted: 12/24/2015] [Indexed: 10/22/2022]
Abstract
Whole genome sequencing (WGS) was compared to pulse-field gel electrophoresis (PFGE) of XbaI-digested genomic DNA, as methods by which to evaluate a potential transmission of carbapenem-resistant Klebsiella pneumoniae between 2 hospital inpatients. PFGE result demonstrated only 1-band difference between the isolates, suggesting probable relatedness. In contrast, while WGS data demonstrated the same sequence type and very similar chromosomal sequences, over 20 single nucleotide variants were identified between the isolates, bringing into question whether there was a transmission event. WGS also identified an additional plasmid, with an XbaI restriction site in the isolates of the second patient that was not identified by PFGE. While WGS provided additional information that was not available by PFGE, in this study, neither method could definitively conclude the relatedness between the isolates.
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Affiliation(s)
- Shangxin Yang
- Pathology & Laboratory Medicine, UCLA, Los Angeles, CA, USA
| | | | - Janet Hindler
- Pathology & Laboratory Medicine, UCLA, Los Angeles, CA, USA
| | - Kevin Ward
- Pathology & Laboratory Medicine, UCLA, Los Angeles, CA, USA
| | - Helty Adisetiyo
- Mi Next Generation Science (MiNGS) Core Laboratory, Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Fan Li
- Mi Next Generation Science (MiNGS) Core Laboratory, Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Grace M Aldrovandi
- Mi Next Generation Science (MiNGS) Core Laboratory, Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Nicole M Green
- Los Angeles County Public Health Laboratory, Downey, CA, USA
| | - Dana Russell
- Division of Infectious Diseases, UCLA, Los Angeles, CA, USA
| | - Zachary Rubin
- Division of Infectious Diseases, UCLA, Los Angeles, CA, USA
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