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Lanjouw L, Bart J, Mourits MJE, Willems SM, van der Hout AH, ter Elst A, de Bock GH. BRCA1/2 Testing Landscape in Ovarian Cancer: A Nationwide, Real-World Data Study. Cancers (Basel) 2024; 16:1682. [PMID: 38730634 PMCID: PMC11083399 DOI: 10.3390/cancers16091682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Analyzing BRCA1/2 tumor pathogenic variants (TPVs) in epithelial tubal/ovarian cancers (EOCs) has become an essential part of the diagnostic workflow in many centers to guide treatment options and genetic cascade testing. However, there is no standardization of testing procedures, including techniques, gene assays, or sequencers used, and data on the execution of tumor tests remains scarce. Therefore, we evaluated characteristics of BRCA1/2 tumor testing in advanced-stage EOC with real-world national data. Pathology reports of patients diagnosed with EOC in 2019 in the Netherlands were obtained from the Dutch Pathology Registry (PALGA), and data regarding histological subtype and BRCA1/2 tumor tests were extracted. A total of 999 patients with advanced-stage EOC were included. Tumor tests were performed for 502 patients (50.2%) and BRCA1/2 TPVs were detected in 14.7%. Of all tests, 48.6% used hybrid capture techniques and 26.5% used PCR-based techniques. More than half of the tests (55.0%) analyzed other genes in addition to BRCA1/2. Overall, this study highlights the heterogeneity in the execution of BRCA1/2 tumor tests. Despite a lack of evidence of quality differences, we emphasize that adequate reporting and internal and external quality monitors are essential for the high-quality implementation and execution of reliable BRCA1/2 tumor testing, which is crucial for identifying all patients with BRCA1/2 TPVs.
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Affiliation(s)
- Lieke Lanjouw
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Joost Bart
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Marian J. E. Mourits
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Stefan M. Willems
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Annemieke H. van der Hout
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Arja ter Elst
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Geertruida H. de Bock
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
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Blanchet G, Bellinger MR, Kearns AM, Cortes-Rodriguez N, Masuda B, Campana MG, Rutz C, Fleischer RC, Sutton JT. Reduction of genetic diversity in 'Alalā (Hawaiian crow; Corvus hawaiiensis) between the late 1800s and the late 1900s. J Hered 2024; 115:32-44. [PMID: 37846510 DOI: 10.1093/jhered/esad063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/26/2023] [Accepted: 10/12/2023] [Indexed: 10/18/2023] Open
Abstract
Genetic and genomic data are increasingly used to aid conservation management of endangered species by providing insights into evolutionary histories, factors associated with extinction risks, and potential for future adaptation. For the 'Alalā, or Hawaiian crow (Corvus hawaiiensis), genetic concerns include negative correlations between inbreeding and hatching success. However, it is unclear if low genetic diversity and inbreeding depression are consequences of a historical population bottleneck, or if 'Alalā had historically low genetic diversity that predated human influence, perhaps as a result of earlier declines or founding events. In this study, we applied a hybridization-based sequence capture to generate a genome-wide single nucleotide polymorphism (SNP) dataset for comparing historical specimens collected in the 1890s, when 'Alalā were more numerous, to samples taken between 1973 and 1998, when 'Alalā population densities were near the lowest documented levels in the wild, prior to all individuals being collected for captive rearing. We found low genome-wide diversity in both sample groups, however, the modern sample group (1973 to 1998 cohort) exhibited relatively fewer polymorphic alleles, a lower proportion of polymorphic loci, and lower observed heterozygosity, consistent with a population decline and potential bottleneck effects. These results combined with a current low population size highlight the importance of continued efforts by conservation managers to mitigate inbreeding and maintain founder representation to preserve what genetic diversity remains.
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Affiliation(s)
- Geneviève Blanchet
- Department of Biology, University of Hawai'i at Hilo, 200 W Kāwili St, Hilo, Hawai'i 96720, United States
| | - M Renee Bellinger
- Department of Biology, University of Hawai'i at Hilo, 200 W Kāwili St, Hilo, Hawai'i 96720, United States
- U.S. Geological Survey, Pacific Island Ecosystems Research Center, PO Box 44, Hawai'i National Park, Hawai'i 96718, United States
| | - Anna M Kearns
- Center for Conservation Genomics, National Zoo and Conservation Biology Institute, Smithsonian Institution, Washington DC 20008, United States
| | - Nandadevi Cortes-Rodriguez
- Center for Conservation Genomics, National Zoo and Conservation Biology Institute, Smithsonian Institution, Washington DC 20008, United States
| | - Bryce Masuda
- San Diego Zoo Wildlife Alliance, P.O. Box 39, Volcano, HI 96785, United States
| | - Michael G Campana
- Center for Conservation Genomics, National Zoo and Conservation Biology Institute, Smithsonian Institution, Washington DC 20008, United States
| | - Christian Rutz
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews KY16 9TH, United Kingdom
| | - Robert C Fleischer
- Center for Conservation Genomics, National Zoo and Conservation Biology Institute, Smithsonian Institution, Washington DC 20008, United States
| | - Jolene T Sutton
- Department of Biology, University of Hawai'i at Hilo, 200 W Kāwili St, Hilo, Hawai'i 96720, United States
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Liu X, Xu Z, Feng B, Zhou Q, Guo S, Liao S, Ou Y, Fan X, Wang T. Dissection of a novel major stable QTL on chromosome 7D for grain hardness and its breeding value estimation in bread wheat. FRONTIERS IN PLANT SCIENCE 2024; 15:1356687. [PMID: 38362452 PMCID: PMC10867189 DOI: 10.3389/fpls.2024.1356687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 01/18/2024] [Indexed: 02/17/2024]
Abstract
Grain hardness (Gh) is important for wheat processing and end-product quality. Puroindolines polymorphism explains over 60% of Gh variation and the novel genetic factors remain to be exploited. In this study, a total of 153 quantitative trait loci (QTLs), clustered into 12 genomic intervals (C1-C12), for 13 quality-related traits were identified using a recombinant inbred line population derived from the cross of Zhongkemai138 (ZKM138) and Chuanmai44 (CM44). Among them, C7 (harboring eight QTLs for different quality-related traits) and C8 (mainly harboring QGh.cib-5D.1 for Gh) were attributed to the famous genes, Rht-D1 and Pina, respectively, indicating that the correlation of involved traits was supported by the pleotropic or linked genes. Notably, a novel major stable QTL for Gh was detected in the C12, QGh.cib-7D, with ZKM138-derived allele increasing grain hardness, which was simultaneously mapped by the BSE-Seq method. The geographic pattern and transmissibility of this locus revealed that the increasing-Gh allele is highly frequently present in 85.79% of 373 worldwide wheat varieties and presented 99.31% transmissibility in 144 ZKM138-derivatives, indicating the non-negative effect on yield performance and that its indirect passive selection has happened during the actual breeding process. Thus, the contribution of this new Gh-related locus was highlighted in consideration of improving the efficiency and accuracy of the soft/hard material selection in the molecular marker-assisted process. Further, TraesCS7D02G099400, TraesCS7D02G098000, and TraesCS7D02G099500 were initially deduced to be the most potential candidate genes of QGh.cib-7D. Collectively, this study provided valuable information of elucidating the genetic architecture of Gh for wheat quality improvement.
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Affiliation(s)
- Xiaofeng Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Insitute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu, China
| | - Zhibin Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Qiang Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Shaodan Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Simin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuhao Ou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
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Cai Y, Lv J, Li R, Huang X, Wang S, Bao Z, Zeng Q. Deqformer: high-definition and scalable deep learning probe design method. Brief Bioinform 2024; 25:bbae007. [PMID: 38305453 PMCID: PMC10835675 DOI: 10.1093/bib/bbae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/22/2023] [Accepted: 01/01/2024] [Indexed: 02/03/2024] Open
Abstract
Target enrichment sequencing techniques are gaining widespread use in the field of genomics, prized for their economic efficiency and swift processing times. However, their success depends on the performance of probes and the evenness of sequencing depth among each probe. To accurately predict probe coverage depth, a model called Deqformer is proposed in this study. Deqformer utilizes the oligonucleotides sequence of each probe, drawing inspiration from Watson-Crick base pairing and incorporating two BERT encoders to capture the underlying information from the forward and reverse probe strands, respectively. The encoded data are combined with a feed-forward network to make precise predictions of sequencing depth. The performance of Deqformer is evaluated on four different datasets: SNP panel with 38 200 probes, lncRNA panel with 2000 probes, synthetic panel with 5899 probes and HD-Marker panel for Yesso scallop with 11 000 probes. The SNP and synthetic panels achieve impressive factor 3 of accuracy (F3acc) of 96.24% and 99.66% in 5-fold cross-validation. F3acc rates of over 87.33% and 72.56% are obtained when training on the SNP panel and evaluating performance on the lncRNA and HD-Marker datasets, respectively. Our analysis reveals that Deqformer effectively captures hybridization patterns, making it robust for accurate predictions in various scenarios. Deqformer leads to a novel perspective for probe design pipeline, aiming to enhance efficiency and effectiveness in probe design tasks.
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Affiliation(s)
- Yantong Cai
- MOE Key Laboratory of Marine Genetics and Breeding & Fang Zongxi Center for Marine Evo-Devo, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jia Lv
- MOE Key Laboratory of Marine Genetics and Breeding & Fang Zongxi Center for Marine Evo-Devo, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Rui Li
- MOE Key Laboratory of Marine Genetics and Breeding & Fang Zongxi Center for Marine Evo-Devo, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Xiaowen Huang
- MOE Key Laboratory of Marine Genetics and Breeding & Fang Zongxi Center for Marine Evo-Devo, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding & Fang Zongxi Center for Marine Evo-Devo, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
- Southern Marine Science and Engineer Guangdong Laboratory, Guangzhou, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Zhenmin Bao
- Southern Marine Science and Engineer Guangdong Laboratory, Guangzhou, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Qifan Zeng
- MOE Key Laboratory of Marine Genetics and Breeding & Fang Zongxi Center for Marine Evo-Devo, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
- Southern Marine Science and Engineer Guangdong Laboratory, Guangzhou, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
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Liu M, Yu B, Tian Y, Li F. Regulatory function and mechanism research for m6A modification WTAP via SUCLG2-AS1- miR-17-5p-JAK1 axis in AML. BMC Cancer 2024; 24:98. [PMID: 38233760 PMCID: PMC10795285 DOI: 10.1186/s12885-023-11687-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/28/2023] [Indexed: 01/19/2024] Open
Abstract
Acute myeloid leukemia (AML), characterized by the abnormal accumulation of immature marrow cells in the bone marrow, is a malignant tumor of the blood system. Currently, the pathogenesis of AML is not yet clear. Therefore, this study aims to explore the mechanisms underlying the development of AML. Firstly, we identified a competing endogenous RNA (ceRNA) SUCLG2-AS1-miR-17-5p-JAK1 axis through bioinformatics analysis. Overexpression of SUCLG2-AS1 inhibits proliferation, migration and invasion and promotes apoptosis of AML cells. Secondly, luciferase reporter assay and RIP assay validated that SUCLG2-AS1 functioned as ceRNA for sponging miR-17-5p, further leading to JAK1 underexpression. Additionally, the results of MeRIP-qPCR and m6A RNA methylation quantification indicted that SUCLG2-AS1(lncRNA) had higher levels of m6A RNA methylation compared with controls, and SUCLG2-AS1 is regulated by m6A modification of WTAP in AML cells. WTAP, one of the main regulatory components of m6A methyltransferase complexes, proved to be highly expressed in AML and elevated WTAP is associated with poor prognosis of AML patients. Taken together, the WTAP-SUCLG2-AS1-miR-17-5p-JAK1 axis played essential roles in the process of AML development, which provided a novel therapeutic target for AML.
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Affiliation(s)
- Miaomiao Liu
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, No.126 Xinmin Street, Changchun, Jilin, 130021, P.R. China
| | - Bingxin Yu
- Department of Ultrasonography, The Third Hospital of Jilin University, Changchun, Jilin, 130033, P.R. China
| | - Yong Tian
- Department of Human Anatomy, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, Jilin, 130021, P.R. China
| | - Fan Li
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, No.126 Xinmin Street, Changchun, Jilin, 130021, P.R. China.
- The Key Laboratory for Bionics Engineering, Ministry of Education, Jilin University, Changchun, 130021, P.R. China.
- Engineering Research Center for Medical Biomaterials of Jilin Province, Jilin University, Changchun, 130021, P.R. China.
- Key Laboratory for Health Biomedical Materials of Jilin Province, Jilin University, Changchun, 130021, P.R. China.
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, Xinjiang, 830017, P.R. China.
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Zhao Y, Deng W, Wang Z, Wang Y, Zheng H, Zhou K, Xu Q, Bai L, Liu H, Ren Z, Jiang Z. Genetics of congenital heart disease. Clin Chim Acta 2024; 552:117683. [PMID: 38030030 DOI: 10.1016/j.cca.2023.117683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/01/2023]
Abstract
During embryonic development, the cardiovascular system and the central nervous system exhibit a coordinated developmental process through intricate interactions. Congenital heart disease (CHD) refers to structural or functional abnormalities that occur during embryonic or prenatal heart development and is the most common congenital disorder. One of the most common complications in CHD patients is neurodevelopmental disorders (NDD). However, the specific mechanisms, connections, and precise ways in which CHD co-occurs with NDD remain unclear. According to relevant research, both genetic and non-genetic factors are significant contributors to the co-occurrence of sporadic CHD and NDD. Genetic variations, such as chromosomal abnormalities and gene mutations, play a role in the susceptibility to both CHD and NDD. Further research should aim to identify common molecular mechanisms that underlie the co-occurrence of CHD and NDD, possibly originating from shared genetic mutations or shared gene regulation. Therefore, this review article summarizes the current advances in the genetics of CHD co-occurring with NDD, elucidating the application of relevant gene detection techniques. This is done with the aim of exploring the genetic regulatory mechanisms of CHD co-occurring with NDD at the gene level and promoting research and treatment of developmental disorders related to the cardiovascular and central nervous systems.
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Affiliation(s)
- Yuanqin Zhao
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
| | - Wei Deng
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
| | - Zhaoyue Wang
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
| | - Yanxia Wang
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
| | - Hongyu Zheng
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
| | - Kun Zhou
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
| | - Qian Xu
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
| | - Le Bai
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
| | - Huiting Liu
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
| | - Zhong Ren
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
| | - Zhisheng Jiang
- Institute of Cardiovascular Disease, Key Lab for Arteriosclerology of Hunan Province, International Joint Laboratory for Arteriosclerotic Disease Research of Hunan Province, University of South China, Hengyang 421001, China.
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Chen S, Zhou Z, Li Y, Du Y, Chen G. Application of single-cell sequencing to the research of tumor microenvironment. Front Immunol 2023; 14:1285540. [PMID: 37965341 PMCID: PMC10641410 DOI: 10.3389/fimmu.2023.1285540] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023] Open
Abstract
Single-cell sequencing is a technique for detecting and analyzing genomes, transcriptomes, and epigenomes at the single-cell level, which can detect cellular heterogeneity lost in conventional sequencing hybrid samples, and it has revolutionized our understanding of the genetic heterogeneity and complexity of tumor progression. Moreover, the tumor microenvironment (TME) plays a crucial role in the formation, development and response to treatment of tumors. The application of single-cell sequencing has ushered in a new age for the TME analysis, revealing not only the blueprint of the pan-cancer immune microenvironment, but also the heterogeneity and differentiation routes of immune cells, as well as predicting tumor prognosis. Thus, the combination of single-cell sequencing and the TME analysis provides a unique opportunity to unravel the molecular mechanisms underlying tumor development and progression. In this review, we summarize the recent advances in single-cell sequencing and the TME analysis, highlighting their potential applications in cancer research and clinical translation.
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Affiliation(s)
| | | | | | | | - Guoan Chen
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, China
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Blanchet S, Fargeot L, Raffard A. Phylogenetically-conserved candidate genes unify biodiversity-ecosystem function relationships and eco-evolutionary dynamics across biological scales. Mol Ecol 2023; 32:4467-4481. [PMID: 37296539 DOI: 10.1111/mec.17043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023]
Abstract
The intra- and interspecific facets of biodiversity have traditionally been analysed separately, limiting our understanding of how evolution has shaped biodiversity, how biodiversity (as a whole) alters ecological dynamics and hence eco-evolutionary feedbacks at the community scale. Here, we propose using candidate genes phylogenetically-conserved across species and sustaining functional traits as an inclusive biodiversity unit transcending the intra- and interspecific boundaries. This framework merges knowledge from functional genomics and functional ecology, and we first provide guidelines and a concrete example for identifying phylogenetically-conserved candidate genes (PCCGs) within communities and for measuring biodiversity from PCCGs. We then explain how biodiversity measured at PCCGs can be linked to ecosystem functions, which unifies recent observations that both intra- and interspecific biodiversity are important for ecosystem functions. We then highlight the eco-evolutionary processes shaping PCCG diversity patterns and argue that their respective role can be inferred from concepts derived from population genetics. Finally, we explain how PCCGs may shift the field of eco-evolutionary dynamics from a focal-species approach to a more realistic focal-community approach. This framework provides a novel perspective to investigate the global ecosystem consequences of diversity loss across biological scales, and how these ecological changes further alter biodiversity evolution.
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Affiliation(s)
- Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS), Station d'Écologie Théorique et Expérimentale du CNRS à Moulis, UAR2029, Moulis, France
| | - Laura Fargeot
- Centre National de la Recherche Scientifique (CNRS), Station d'Écologie Théorique et Expérimentale du CNRS à Moulis, UAR2029, Moulis, France
| | - Allan Raffard
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, Thonon-les-Bains, France
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9
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Huang C, Huang Y, Wang Z, Lin Y, Li Y, Chen Y, Chen X, Zhang C, Li W, Zhang W, Fang X, Huang Z. Multiplex PCR-based next generation sequencing as a novel, targeted and accurate molecular approach for periprosthetic joint infection diagnosis. Front Microbiol 2023; 14:1181348. [PMID: 37275128 PMCID: PMC10232910 DOI: 10.3389/fmicb.2023.1181348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/27/2023] [Indexed: 06/07/2023] Open
Abstract
Objectives Periprosthetic joint infection (PJI) diagnosis remains challenging, and the identification of the causative microorganism is, by far, the most important aspect. Here, we use multiple PCR-based targeted next-generation sequencing (tNGS) to detect pathogens in PJI. To explore 1. the ability of targeted next-generation sequencing (tNGS) to detect pathogens in PJI; 2. the consistency of tNGS, metagenomic NGS (mNGS), and culture results; and 3. the ability of tNGS to detect drug resistance genes in PJI. Methods PJI was diagnosed according to the Musculoskeletal Infection Society (MSIS) criteria. The microorganisms were detected by culture, mNGS and tNGS to compare the diagnostic effectiveness of the three methods for PJI and to compare their consistency in detecting microorganisms. Drug resistance genes were detected using tNGS. The costs and turnaround times of mNGS and tNGS were compared. Results Forty-three patients with PJI, 21 patients without PJI and 10 negative control cases were included. The culture, tNGS, and mNGS sensitivities for PJI diagnosis were 74.41%, 88.37%, and 93.02%, respectively, with no significant differences. The specificities were 90.48%, 95.24%, and 95.24%, respectively, with no significant differences. tNGS detected drug resistance genes in 37.5% of culture-positive PJIs. tNGS was superior to mNGS for turnaround time (14.5 h vs. 28 h) and cost ($150 vs. $260). Conclusions tNGS can effectively identify PJI pathogens and may provide drug resistance information, while tNGS is superior to mNGS regarding cost and turnaround time. A multidisciplinary, multi-technology based algorithm to diagnose PJI is appropriate. Highlights 298 microorganisms and 86 drug resistance genes were included in the tNGS panel.Diagnostic efficacy of tNGS is not inferior to that of commonly used indicators.tNGS is superior to mNGS in cost and turnaround time.
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Affiliation(s)
- Changyu Huang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ying Huang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ziwen Wang
- Fujian Medical University, Fuzhou, China
| | - Yiming Lin
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yongbin Li
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yang Chen
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xiaoqing Chen
- Department of Orthopedic Surgery, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Chaofan Zhang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenbo Li
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenming Zhang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xinyu Fang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zida Huang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
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10
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Geier CB, Voll RE, Warnatz K. [Principles of the diagnostics of inborn errors of immunity]. Z Rheumatol 2023; 82:285-297. [PMID: 37079035 DOI: 10.1007/s00393-023-01351-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2023] [Indexed: 04/21/2023]
Abstract
Inborn errors of immunity (IEI) are a heterogeneous group of nearly 500 diseases characterized by a congenital dysfunction of the immune system. The vast majority of IEIs are rare diseases but all IEIs share a cumulative prevalence of 1:1200-1:2000. In addition to a pathological susceptibility to infections, IEIs can also present with lymphoproliferative, autoimmune or autoinflammatory manifestations. There is often an overlap with classical rheumatic and inflammatory disease patterns. Therefore, a basic knowledge of the clinical presentation and the diagnostics of IEIs is also relevant for the practicing rheumatologist.
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Affiliation(s)
- Christoph B Geier
- Klinik für Rheumatologie und Klinische Immunologie, Medizinische Universitätsklinik - Medizinische Fakultät, Universität Freiburg, Freiburg, Deutschland
- Centrum für Chronische Immundefizienz (CCI), Medizinische Universitätsklinik - Medizinische Fakultät, Universität Freiburg, Freiburg, Deutschland
| | - Reinhard E Voll
- Klinik für Rheumatologie und Klinische Immunologie, Medizinische Universitätsklinik - Medizinische Fakultät, Universität Freiburg, Freiburg, Deutschland
- Centrum für Chronische Immundefizienz (CCI), Medizinische Universitätsklinik - Medizinische Fakultät, Universität Freiburg, Freiburg, Deutschland
| | - Klaus Warnatz
- Klinik für Rheumatologie und Klinische Immunologie, Medizinische Universitätsklinik - Medizinische Fakultät, Universität Freiburg, Freiburg, Deutschland.
- Centrum für Chronische Immundefizienz (CCI), Medizinische Universitätsklinik - Medizinische Fakultät, Universität Freiburg, Freiburg, Deutschland.
- Klinik für Klinische Immunologie, Universitätsspital Zürich, Zürich, Schweiz.
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11
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Arizmendi A, Rudd Garces G, Crespi JA, Olivera LH, Barrientos LS, Peral García P, Giovambattista G. Analysis of Doberman Pinscher and Toy Poodle samples with targeted next-generation sequencing. Gene 2023; 853:147069. [PMID: 36427679 DOI: 10.1016/j.gene.2022.147069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/04/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022]
Abstract
Next-generation sequencing (NGS) technologies have enabled the identification of many causal variants of genetic disorders, the development of parentage tests and the analysis of multiple traits in domestic animals. In this study, we evaluated the performance of a Canine Targeted Genotyping-by-Sequencing (GBS) custom panel (Thermo Fisher Scientific, Waltham, Ma, USA) in a cohort of 95 dog DNA samples, comprising 76 Doberman Pinschers and 19 Toy Poodles from Argentina. The used panel included 383 targets (228 parentage SNVs, 137 genetic disorder markers and 18 trait markers). While paternity analysis showed correct duo (97.4%; LOD > 2.98E+13) and trio (100%; LOD > 2.20E+15) parentage assignment, the panel resulted still insufficient for excluding close relatives in inbred populations. In this sense, close relatives were wrongly assigned as parents in 12.6% of duos and 0.3% of trios. We detected 17 polymorphic markers (genetic disorders, n = 4; hair type, n = 3; coat color, n = 10) and estimated their allele frequencies in the studied breeds. The accuracy of targeted GBS results were evaluated for three markers that were associated with Progressive rod-cone degeneration, von Willebrand disease type 1 and dilated cardiomyopathy by pyrosequencing and Sanger sequencing genotyping, showing 94-100% concordance among assays. The targeted GBS custom panel resulted cost-effective strategy to study the prevalence of genetic disorders and traits in a large number of samples and to analyze genetic interactions between previously reported variants. Once assays based on AgriSeq technology were standardized, their uses are a good strategy for large-scale routine genetic evaluation of animal populations.
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Affiliation(s)
- A Arizmendi
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando N. Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 S/N, 1900 La Plata, Buenos Aires, Argentina; Servicio de Cardiología, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 S/N, 1900 La Plata, Buenos Aires, Argentina
| | - G Rudd Garces
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando N. Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 S/N, 1900 La Plata, Buenos Aires, Argentina
| | - J A Crespi
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando N. Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 S/N, 1900 La Plata, Buenos Aires, Argentina
| | - L H Olivera
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando N. Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 S/N, 1900 La Plata, Buenos Aires, Argentina
| | - L S Barrientos
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando N. Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 S/N, 1900 La Plata, Buenos Aires, Argentina
| | - P Peral García
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando N. Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 S/N, 1900 La Plata, Buenos Aires, Argentina
| | - G Giovambattista
- IGEVET - Instituto de Genética Veterinaria "Ing. Fernando N. Dulout" (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, Calle 60 y 118 S/N, 1900 La Plata, Buenos Aires, Argentina.
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12
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Liu Z, Simayijiang H, Wang Q, Yang J, Sun H, Wu R, Yan J. DNA and protein analyses of hair in forensic genetics. Int J Legal Med 2023; 137:613-633. [PMID: 36732435 DOI: 10.1007/s00414-023-02955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023]
Abstract
Hair is one of the most common pieces of biological evidence found at a crime scene and plays an essential role in forensic investigation. Hairs, especially non-follicular hairs, are usually found at various crime scenes, either by natural shedding or by forcible shedding. However, the genetic material in hairs is usually highly degraded, which makes forensic analysis difficult. As a result, the value of hair has not been fully exploited in forensic investigations and trials. In recent years, with advances in molecular biology, forensic analysis of hair has achieved remarkable strides and provided crucial clues in numerous cases. This article reviews recent developments in DNA and protein analysis of hair and attempts to provide a comprehensive solution to improve forensic hair analysis.
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Affiliation(s)
- Zhiyong Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Halimureti Simayijiang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, People's Republic of China
| | - Qiangwei Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Jingyi Yang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China. .,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, People's Republic of China.
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13
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Pei XM, Yeung MHY, Wong ANN, Tsang HF, Yu ACS, Yim AKY, Wong SCC. Targeted Sequencing Approach and Its Clinical Applications for the Molecular Diagnosis of Human Diseases. Cells 2023; 12:493. [PMID: 36766834 PMCID: PMC9913990 DOI: 10.3390/cells12030493] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/19/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The outbreak of COVID-19 has positively impacted the NGS market recently. Targeted sequencing (TS) has become an important routine technique in both clinical and research settings, with advantages including high confidence and accuracy, a reasonable turnaround time, relatively low cost, and fewer data burdens with the level of bioinformatics or computational demand. Since there are no clear consensus guidelines on the wide range of next-generation sequencing (NGS) platforms and techniques, there is a vital need for researchers and clinicians to develop efficient approaches, especially for the molecular diagnosis of diseases in the emergency of the disease and the global pandemic outbreak of COVID-19. In this review, we aim to summarize different methods of TS, demonstrate parameters for TS assay designs, illustrate different TS panels, discuss their limitations, and present the challenges of TS concerning their clinical application for the molecular diagnosis of human diseases.
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Affiliation(s)
- Xiao Meng Pei
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Martin Ho Yin Yeung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Alex Ngai Nick Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Hin Fung Tsang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
- Department of Clinical Laboratory and Pathology, Hong Kong Adventist Hospital, Hong Kong, China
| | - Allen Chi Shing Yu
- Codex Genetics Limited, Unit 212, 2/F., Building 16W, No. 16 Science Park West Avenue, The Hong Kong Science Park, Hong Kong 852, China
| | - Aldrin Kay Yuen Yim
- Codex Genetics Limited, Unit 212, 2/F., Building 16W, No. 16 Science Park West Avenue, The Hong Kong Science Park, Hong Kong 852, China
| | - Sze Chuen Cesar Wong
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
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14
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Dai Y, Sheng K, Hu L. Diagnostic efficacy of targeted high-throughput sequencing for lower respiratory infection in preterm infants. Am J Transl Res 2022; 14:8204-8214. [PMID: 36505277 PMCID: PMC9730095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/26/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVE To examine the pathogen diagnostic performance of targeted high-throughput next-gen sequencing (tNGS) in respiratory infectious diseases in preterm infants using dynamic follow-up. METHODS Clinical samples of respiratory secretions were consecutively collected from 20 preterm infants weekly for 5 weeks, during which 10 developed bronchopulmonary dysplasia. Pathogen identification from these collected specimens was performed by both conventional cultivation and tNGS. RESULTS We found that targeted next-generation sequencing shared a 90.9% full or partial consistency for lower respiratory pathogen detection with the traditional culture-based approach, and increased the detection rate by 105.9%. Moreover, most of the pathogens identified by tNGS were diminished in patients after treatment. CONCLUSION This study reveals the high sensitivity and performance of targeted high-throughput sequencing for respiratory infectious disease diagnosis and pathogen identification. The trial registry number is NCT03850457, and the trial URL is https://clinicaltrials.gov/ct2/show/NCT03850457.
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Affiliation(s)
- Yi Dai
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical CenterShanghai, China
| | - Kai Sheng
- Geriatrics Department, Tong Ren Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Lan Hu
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical CenterShanghai, China
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15
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Murad Leite Andrade MH, Acharya JP, Benevenuto J, de Bem Oliveira I, Lopez Y, Munoz P, Resende MFR, Rios EF. Genomic prediction for canopy height and dry matter yield in alfalfa using family bulks. THE PLANT GENOME 2022; 15:e20235. [PMID: 35818699 DOI: 10.1002/tpg2.20235] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/30/2022] [Indexed: 06/15/2023]
Abstract
Genomic selection (GS) has proven to be an effective method to increase genetic gain rates and accelerate breeding cycles in many crop species. However, its implementation requires large investments to phenotype of the training population and for routine genotyping. Alfalfa (Medicago sativa L.) is one of the major cultivated forage legumes, showing high-quality nutritional value. Alfalfa breeding is usually carried out by phenotypic recurrent selection and is commonly done at the family level. The application of GS in alfalfa could be simplified and less costly by genotyping and phenotyping families in bulks. For this study, an alfalfa reference population composed of 142 full-sib and 35 half-sib families was bulk-genotyped using target enrichment sequencing and phenotyped for dry matter yield (DMY) and canopy height (CH) in Florida, USA. Genotyping of the family bulks with 17,707 targeted probes resulted in 114,945 single-nucleotide polymorphisms. The markers revealed a population structure that matched the mating design, and the linkage disequilibrium slowly decayed in this breeding population. After exploring multiple prediction scenarios, a strategy was proposed including data from multiple harvests and accounting for the G×E in the training population, which led to a higher predictive ability of up to 38 and 24% for DMY and CH, respectively. Although this study focused on the implementation of GS in alfalfa families, the bulk methodology and the prediction schemes used herein could guide future studies in alfalfa and other crops bred in bulks.
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Affiliation(s)
| | - Janam P Acharya
- Agronomy Dep., Univ. of Florida, Gainesville, FL, 32611, USA
| | - Juliana Benevenuto
- Horticultural Sciences Dep., Univ. of Florida, Gainesville, FL, 32611, USA
| | | | - Yolanda Lopez
- Agronomy Dep., Univ. of Florida, Gainesville, FL, 32611, USA
| | - Patricio Munoz
- Horticultural Sciences Dep., Univ. of Florida, Gainesville, FL, 32611, USA
| | - Marcio F R Resende
- Horticultural Sciences Dep., Univ. of Florida, Gainesville, FL, 32611, USA
| | - Esteban F Rios
- Agronomy Dep., Univ. of Florida, Gainesville, FL, 32611, USA
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16
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Steiert TA, Fuß J, Juzenas S, Wittig M, Hoeppner M, Vollstedt M, Varkalaite G, ElAbd H, Brockmann C, Görg S, Gassner C, Forster M, Franke A. High-throughput method for the hybridisation-based targeted enrichment of long genomic fragments for PacBio third-generation sequencing. NAR Genom Bioinform 2022; 4:lqac051. [PMID: 35855323 PMCID: PMC9278042 DOI: 10.1093/nargab/lqac051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/08/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022] Open
Abstract
Hybridisation-based targeted enrichment is a widely used and well-established technique in high-throughput second-generation short-read sequencing. Despite the high potential to genetically resolve highly repetitive and variable genomic sequences by, for example PacBio third-generation sequencing, targeted enrichment for long fragments has not yet established the same high-throughput due to currently existing complex workflows and technological dependencies. We here describe a scalable targeted enrichment protocol for fragment sizes of >7 kb. For demonstration purposes we developed a custom blood group panel of challenging loci. Test results achieved > 65% on-target rate, good coverage (142.7×) and sufficient coverage evenness for both non-paralogous and paralogous targets, and sufficient non-duplicate read counts (83.5%) per sample for a highly multiplexed enrichment pool of 16 samples. We genotyped the blood groups of nine patients employing highly accurate phased assemblies at an allelic resolution that match reference blood group allele calls determined by SNP array and NGS genotyping. Seven Genome-in-a-Bottle reference samples achieved high recall (96%) and precision (99%) rates. Mendelian error rates were 0.04% and 0.13% for the included Ashkenazim and Han Chinese trios, respectively. In summary, we provide a protocol and first example for accurate targeted long-read sequencing that can be used in a high-throughput fashion.
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Affiliation(s)
- Tim Alexander Steiert
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Janina Fuß
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Simonas Juzenas
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
- Institute of Biotechnology, Life Science Centre, Vilnius University, Vilnius 02241, Lithuania
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Marc Patrick Hoeppner
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Melanie Vollstedt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Greta Varkalaite
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas 44307, Lithuania
| | - Hesham ElAbd
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Christian Brockmann
- Institute of Transfusion Medicine, University Hospital of Schleswig-Holstein, Kiel 24105, Germany
| | - Siegfried Görg
- Institute of Transfusion Medicine, University Hospital of Schleswig-Holstein, Kiel 24105, Germany
| | - Christoph Gassner
- Institute of Translational Medicine, Private University in the Principality of Liechtenstein, Triesen 9495, Liechtenstein
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
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17
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Panda G, Ray A. Decrypting the mechanistic basis of CRISPR/Cas9 protein. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 172:60-76. [PMID: 35577099 DOI: 10.1016/j.pbiomolbio.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/14/2022] [Accepted: 05/10/2022] [Indexed: 12/25/2022]
Abstract
CRISPR/Cas system, a newly but extensively investigated genome-editing method, harbors practical solutions for various genetic problems. It relies on short guide RNAs (gRNAs) to recruit the Cas9 protein, a DNA cleaving enzyme, to its genomic target DNAs. The Cas9 enzyme exhibits some unique properties, like the ability to differentiate self vs. non-self - DNA strands using the base-pairing potential of crRNA, i.e., only CRISPR DNA is entirely complementary to the CRISPR repeat sequences at the crRNA whereas the presence of mismatches in the upstream region of the spacer permit CRISPR interference which is inhibited in case of CRISPR-DNA, allosteric regulation in its domains, and domain reorientation on sgRNA binding. Several groups have contributed their efforts in understanding the functioning of the CRISPR/Cas system, but even then, there is a lot more to explore in this area. The structural and sequence-based understanding of the whole CRISPR-associated bacterial ortholog family landscape is still ambiguous. A better understanding of the underlying energetics of the CRISPR/Cas9 system should reveal critical parameters to design better CRISPR/Cas9s.
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Affiliation(s)
- Gayatri Panda
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Arjun Ray
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.
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18
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Danilevsky A, Polsky AL, Shomron N. Adaptive sequencing using nanopores and deep learning of mitochondrial DNA. Brief Bioinform 2022; 23:6634223. [PMID: 35804265 DOI: 10.1093/bib/bbac251] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 05/13/2022] [Accepted: 05/30/2022] [Indexed: 12/24/2022] Open
Abstract
Nanopore sequencing is an emerging technology that reads DNA by utilizing a unique method of detecting nucleic acid sequences and identifies the various chemical modifications they carry. Deep learning has increased in popularity as a useful technique to solve many complex computational tasks. 'Adaptive sequencing' is an implementation of selective sequencing, intended for use on the nanopore sequencing platform. In this study, we demonstrated an alternative method of software-based selective sequencing that is performed in real time by combining nanopore sequencing and deep learning. Our results showed the feasibility of using deep learning for classifying signals from only the first 200 nucleotides in a raw nanopore sequencing signal format. This was further demonstrated by comparing the accuracy of our deep learning classification model across data from several human cell lines and other eukaryotic organisms. We used custom deep learning models and a script that utilizes a 'Read Until' framework to target mitochondrial molecules in real time from a human cell line sample. This achieved a significant separation and enrichment ability of 2.3-fold. In a series of very short sequencing experiments (10, 30 and 120 min), we identified genomic and mitochondrial reads with accuracy above 90%, although mitochondrial DNA comprised only 0.1% of the total input material. The uniqueness of our method is the ability to distinguish two groups of DNA even without a labeled reference. This contrasts with studies that required a well-defined reference, whether of a DNA sequence or of another type of representation. Additionally, our method showed higher correlation to the theoretically possible enrichment factor, compared with other published methods. We believe that our results will lay the foundation for rapid and selective sequencing using nanopore technology and will pave the approach for clinical applications that use nanopore sequencing data.
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Affiliation(s)
- Artem Danilevsky
- Faculty of Medicine and Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Avital Luba Polsky
- Faculty of Medicine and Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noam Shomron
- Faculty of Medicine and Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 69978, Israel
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19
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Target Enrichment Approaches for Next-Generation Sequencing Applications in Oncology. Diagnostics (Basel) 2022; 12:diagnostics12071539. [PMID: 35885445 PMCID: PMC9318977 DOI: 10.3390/diagnostics12071539] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/29/2022] Open
Abstract
Screening for genomic sequence variants in genes of predictive and prognostic significance is an integral part of precision medicine. Next-generation sequencing (NGS) technologies are progressively becoming platforms of choice to facilitate this, owing to their massively parallel sequencing capability, which can be used to simultaneously screen multiple markers in multiple samples for a variety of variants (single nucleotide and multi nucleotide variants, insertions and deletions, gene copy number variations, and fusions). A crucial step in the workflow of targeted NGS is the enrichment of the genomic regions of interest to be sequenced, against the whole genomic background. This ensures that the NGS effort is focused to predominantly screen target regions of interest with minimal off-target sequencing, making it more accurate and economical. Polymerase chain reaction-based (PCR, or amplicon-based) and hybridization capture-based methodologies are the two prominent approaches employed for target enrichment. This review summarizes the basic principles of target enrichment utilized by these methods, their multiple variations that have evolved over time, automation approaches, overall comparison of their advantages and drawbacks, and commercially available choices for these methodologies.
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20
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Improving genetic diagnosis of Mendelian disease with RNA sequencing: a narrative review. JOURNAL OF BIO-X RESEARCH 2022. [DOI: 10.1097/jbr.0000000000000100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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21
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Veldman A, Kiewiet MBG, Heiner-Fokkema MR, Nelen MR, Sinke RJ, Sikkema-Raddatz B, Voorhoeve E, Westra D, Dollé MET, Schielen PCJI, van Spronsen FJ. Towards Next-Generation Sequencing (NGS)-Based Newborn Screening: A Technical Study to Prepare for the Challenges Ahead. Int J Neonatal Screen 2022; 8:ijns8010017. [PMID: 35323196 PMCID: PMC8949100 DOI: 10.3390/ijns8010017] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/28/2022] [Accepted: 02/08/2022] [Indexed: 01/27/2023] Open
Abstract
Newborn screening (NBS) aims to identify neonates with severe conditions for whom immediate treatment is required. Currently, a biochemistry-first approach is used to identify these disorders, which are predominantly inherited meta1bolic disorders (IMD). Next-generation sequencing (NGS) is expected to have some advantages over the current approach, for example the ability to detect IMDs that meet all screening criteria but lack an identifiable biochemical footprint. We have now designed a technical study to explore the use of NGS techniques as a first-tier approach in NBS. Here, we describe the aim and set-up of the NGS-first for the NBS (NGSf4NBS) project, which will proceed in three steps. In Step 1, we will identify IMDs eligible for NGS-first testing, based on treatability. In Step 2, we will investigate the feasibility, limitations and comparability of different technical NGS approaches and analysis workflows for NBS, eventually aiming to develop a rapid NGS-based workflow. Finally, in Step 3, we will prepare for the incorporation of this workflow into the existing Dutch NBS program and propose a protocol for referral of a child after a positive NGS test result. The results of this study will be the basis for an additional analytical route within NBS that will be further studied for its applicability within the NBS program, e.g., regarding the ethical, legal, financial and social implications.
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Affiliation(s)
- Abigail Veldman
- Division of Metabolic Diseases, Beatrix Children’s Hospital, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
- Correspondence: (A.V.); (M.B.G.K.)
| | - Mensiena B. G. Kiewiet
- Division of Metabolic Diseases, Beatrix Children’s Hospital, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (R.J.S.); (B.S.-R.)
- Correspondence: (A.V.); (M.B.G.K.)
| | - Margaretha Rebecca Heiner-Fokkema
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
| | - Marcel R. Nelen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (M.R.N.); (D.W.)
| | - Richard J. Sinke
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (R.J.S.); (B.S.-R.)
| | - Birgit Sikkema-Raddatz
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (R.J.S.); (B.S.-R.)
| | - Els Voorhoeve
- Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands; (E.V.); (M.E.T.D.)
| | - Dineke Westra
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (M.R.N.); (D.W.)
| | - Martijn E. T. Dollé
- Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands; (E.V.); (M.E.T.D.)
| | - Peter C. J. I. Schielen
- Centre for Population Screening, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands;
| | - Francjan J. van Spronsen
- Division of Metabolic Diseases, Beatrix Children’s Hospital, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
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22
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Unveiling forensically relevant biogeographic, phenotype and Y-chromosome SNP variation in Pakistani ethnic groups using a customized hybridisation enrichment forensic intelligence panel. PLoS One 2022; 17:e0264125. [PMID: 35176104 PMCID: PMC8853543 DOI: 10.1371/journal.pone.0264125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 02/03/2022] [Indexed: 11/19/2022] Open
Abstract
Massively parallel sequencing following hybridisation enrichment provides new opportunities to obtain genetic data for various types of forensic testing and has proven successful on modern as well as degraded and ancient DNA. A customisable forensic intelligence panel that targeted 124 SNP markers (67 ancestry informative markers, 23 phenotype markers from the HIrisplex panel, and 35 Y-chromosome SNPs) was used to examine biogeographic ancestry, phenotype and sex and Y-lineage in samples from different ethnic populations of Pakistan including Pothwari, Gilgit, Baloach, Pathan, Kashmiri and Siraiki. Targeted sequencing and computational data analysis pipeline allowed filtering of variants across the targeted loci. Study samples showed an admixture between East Asian and European ancestry. Eye colour was predicted accurately based on the highest p-value giving overall prediction accuracy of 92.8%. Predictions were consistent with reported hair colour for all samples, using the combined highest p-value approach and step-wise model incorporating probability thresholds for light or dark shade. Y-SNPs were successfully recovered only from male samples which indicates the ability of this method to identify biological sex and allow inference of Y-haplogroup. Our results demonstrate practicality of using hybridisation enrichment and MPS to aid in human intelligence gathering and will open many insights into forensic research in South Asia.
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23
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Cuevas-Córdoba B, Fresno C, Haase-Hernández JI, Barbosa-Amezcua M, Mata-Rocha M, Muñoz-Torrico M, Salazar-Lezama MA, Martínez-Orozco JA, Narváez-Díaz LA, Salas-Hernández J, González-Covarrubias V, Soberón X. A bioinformatics pipeline for Mycobacterium tuberculosis sequencing that cleans contaminant reads from sputum samples. PLoS One 2021; 16:e0258774. [PMID: 34699523 PMCID: PMC8547644 DOI: 10.1371/journal.pone.0258774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 10/06/2021] [Indexed: 12/30/2022] Open
Abstract
Next-Generation Sequencing (NGS) is widely used to investigate genomic variation. In several studies, the genetic variation of Mycobacterium tuberculosis has been analyzed in sputum samples without previous culture, using target enrichment methodologies for NGS. Alignments obtained by different programs generally map the sequences under default parameters, and from these results, it is assumed that only Mycobacterium reads will be obtained. However, variants of interest microorganism in clinical samples can be confused with a vast collection of reads from other bacteria, viruses, and human DNA. Currently, there are no standardized pipelines, and the cleaning success is never verified since there is a lack of rigorous controls to identify and remove reads from other sputum-microorganisms genetically similar to M. tuberculosis. Therefore, we designed a bioinformatic pipeline to process NGS data from sputum samples, including several filters and quality control points to identify and eliminate non-M. tuberculosis reads to obtain a reliable genetic variant report. Our proposal uses the SURPI software as a taxonomic classifier to filter input sequences and perform a mapping that provides the highest percentage of Mycobacterium reads, minimizing the reads from other microorganisms. We then use the filtered sequences to perform variant calling with the GATK software, ensuring the mapping quality, realignment, recalibration, hard-filtering, and post-filter to increase the reliability of the reported variants. Using default mapping parameters, we identified reads of contaminant bacteria, such as Streptococcus, Rhotia, Actinomyces, and Veillonella. Our final mapping strategy allowed a sequence identity of 97.8% between the input reads and the whole M. tuberculosis reference genome H37Rv using a genomic edit distance of three, thus removing 98.8% of the off-target sequences with a Mycobacterium reads loss of 1.7%. Finally, more than 200 unreliable genetic variants were removed during the variant calling, increasing the report’s reliability.
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Affiliation(s)
- Betzaida Cuevas-Córdoba
- Laboratorio de Farmacogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
- Instituto de Investigaciones Biológicas, Universidad Veracruzana, Xalapa, Veracruz, México
| | - Cristóbal Fresno
- Departamento de Desarrollo Tecnológico, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Joshua I. Haase-Hernández
- Departamento de Desarrollo Tecnológico, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Martín Barbosa-Amezcua
- Laboratorio de Farmacogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Minerva Mata-Rocha
- Laboratorio de Farmacogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Marcela Muñoz-Torrico
- Clínica de Tuberculosis y Enfermedades Pleurales, Instituto Nacional de Enfermedades Respiratorias (INER), Ciudad de México, México
| | - Miguel A. Salazar-Lezama
- Clínica de Tuberculosis y Enfermedades Pleurales, Instituto Nacional de Enfermedades Respiratorias (INER), Ciudad de México, México
| | - José A. Martínez-Orozco
- Clínica de Tuberculosis y Enfermedades Pleurales, Instituto Nacional de Enfermedades Respiratorias (INER), Ciudad de México, México
| | - Luis A. Narváez-Díaz
- Clínica de Tuberculosis y Enfermedades Pleurales, Instituto Nacional de Enfermedades Respiratorias (INER), Ciudad de México, México
| | - Jorge Salas-Hernández
- Clínica de Tuberculosis y Enfermedades Pleurales, Instituto Nacional de Enfermedades Respiratorias (INER), Ciudad de México, México
| | - Vanessa González-Covarrubias
- Laboratorio de Farmacogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
- * E-mail: (XS); (VGC)
| | - Xavier Soberón
- Laboratorio de Farmacogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
- * E-mail: (XS); (VGC)
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24
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Dickson ZW, Hackenberger D, Kuch M, Marzok A, Banerjee A, Rossi L, Klowak JA, Fox-Robichaud A, Mossmann K, Miller MS, Surette MG, Golding GB, Poinar H. Probe design for simultaneous, targeted capture of diverse metagenomic targets. CELL REPORTS METHODS 2021; 1:100069. [PMID: 35474894 PMCID: PMC9017208 DOI: 10.1016/j.crmeth.2021.100069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 06/10/2021] [Accepted: 08/05/2021] [Indexed: 11/20/2022]
Abstract
The compounding challenges of low signal, high background, and uncertain targets plague many metagenomic sequencing efforts. One solution has been DNA capture, wherein probes are designed to hybridize with target sequences, enriching them in relation to their background. However, balancing probe depth with breadth of capture is challenging for diverse targets. To find this balance, we have developed the HUBDesign pipeline, which makes use of sequence homology to design probes at multiple taxonomic levels. This creates an efficient probe set capable of simultaneously and specifically capturing known and related sequences. We validated HUBDesign by generating probe sets targeting the breadth of coronavirus diversity, as well as a suite of bacterial pathogens often underlying sepsis. In separate experiments demonstrating significant, simultaneous enrichment, we captured SARS-CoV-2 and HCoV-NL63 in a human RNA background and seven bacterial strains in human blood. HUBDesign (https://github.com/zacherydickson/HUBDesign) has broad applicability wherever there are multiple organisms of interest.
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Affiliation(s)
- Zachery W. Dickson
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Dirk Hackenberger
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Melanie Kuch
- McMaster aDNA Center, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada
| | - Art Marzok
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster Immunology Research Center, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Arinjay Banerjee
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster Immunology Research Center, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
- Vaccine and Infectious Disease Organization, Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Laura Rossi
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
| | | | | | - Karen Mossmann
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster Immunology Research Center, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Matthew S. Miller
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster Immunology Research Center, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Michael G. Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | | | - Hendrik Poinar
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada
- McMaster aDNA Center, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L9, Canada
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25
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Luka MM, Kamau E, de Laurent ZR, Morobe JM, Alii LK, Nokes DJ, Agoti CN. Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018. Wellcome Open Res 2021; 6:178. [PMID: 34522789 PMCID: PMC8408540 DOI: 10.12688/wellcomeopenres.16911.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Virus genome sequencing is increasingly utilized in epidemiological surveillance. Genomic data allows comprehensive evaluation of underlying viral diversity and epidemiology to inform control. For human rhinovirus (HRV), genomic amplification and sequencing is challenging due to numerous types, high genetic diversity and inadequate reference sequences. Methods: We developed a tiled amplicon type-specific protocol for genome amplification and sequencing on the Illumina MiSeq platform of two HRV types, A15 and A101. We then assessed added value in analyzing whole genomes relative to the VP4/2 region only in the investigation of HRV molecular epidemiology within the community in Kilifi, coastal Kenya. Results: We processed 73 nasopharyngeal swabs collected between 2016-2018, and 48 yielded at least 70% HRV genome coverage. These included all A101 samples (n=10) and 38 (60.3%) A15 samples. Phylogenetic analysis revealed that the Kilifi A101 sequences interspersed with global A101 genomes available in GenBank collected between 1999-2016. On the other hand, our A15 sequences formed a monophyletic group separate from the global genomes collected in 2008 and 2019. An improved phylogenetic resolution was observed with the genome phylogenies compared to the VP4/2 phylogenies. Conclusions: We present a type-specific full genome sequencing approach for obtaining HRV genomic data and characterizing infections.
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Affiliation(s)
- Martha M Luka
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Everlyn Kamau
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Zaydah R de Laurent
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - John Mwita Morobe
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Leonard K Alii
- Department of Mathematics and Computer Science, Pwani University, Kilifi, Kenya
| | - D James Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Charles N Agoti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,Department of Public Health, Pwani University, Kilifi, Kenya
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26
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Baas FS, Rishi G, Swinkels DW, Subramaniam VN. Genetic Diagnosis in Hereditary Hemochromatosis: Discovering and Understanding the Biological Relevance of Variants. Clin Chem 2021; 67:1324-1341. [PMID: 34402502 DOI: 10.1093/clinchem/hvab130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/23/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND Hereditary hemochromatosis (HH) is a genetic disease, leading to iron accumulation and possible organ damage. Patients are usually homozygous for p. Cys282Tyr in the homeostatic iron regulator gene but may have mutations in other genes involved in the regulation of iron. Next-generation sequencing is increasingly being utilized for the diagnosis of patients, leading to the discovery of novel genetic variants. The clinical significance of these variants is often unknown. CONTENT Determining the pathogenicity of such variants of unknown significance is important for diagnostics and genetic counseling. Predictions can be made using in silico computational tools and population data, but additional evidence is required for a conclusive pathogenicity classification. Genetic disease models, such as in vitro models using cellular overexpression, induced pluripotent stem cells or organoids, and in vivo models using mice or zebrafish all have their own challenges and opportunities when used to model HH and other iron disorders. Recent developments in gene-editing technologies are transforming the field of genetic disease modeling. SUMMARY In summary, this review addresses methods and developments regarding the discovery and classification of genetic variants, from in silico tools to in vitro and in vivo models, and presents them in the context of HH. It also explores recent gene-editing developments and how they can be applied to the discussed models of genetic disease.
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Affiliation(s)
- Floor S Baas
- Translational Metabolic Laboratory (TML 831), Radboudumc, Nijmegen, the Netherlands.,Hepatogenomics Research Group, School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Gautam Rishi
- Hepatogenomics Research Group, School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Dorine W Swinkels
- Translational Metabolic Laboratory (TML 831), Radboudumc, Nijmegen, the Netherlands
| | - V Nathan Subramaniam
- Hepatogenomics Research Group, School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD, Australia
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27
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Günther B, Marre S, Defois C, Merzi T, Blanc P, Peyret P, Arnaud-Haond S. Capture by hybridization for full-length barcode-based eukaryotic and prokaryotic biodiversity inventories of deep sea ecosystems. Mol Ecol Resour 2021; 22:623-637. [PMID: 34486815 DOI: 10.1111/1755-0998.13500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/04/2021] [Accepted: 09/01/2021] [Indexed: 01/04/2023]
Abstract
Biodiversity inventory of marine systems remains limited due to unbalanced access to the three ocean dimensions. The use of environmental DNA (eDNA) for metabarcoding allows fast and effective biodiversity inventory and is forecast as a future biodiversity research and biomonitoring tool. However, in poorly understood ecosystems, eDNA results remain difficult to interpret due to large gaps in reference databases and PCR bias limiting the detection of some major phyla. Here, we aimed to circumvent these limitations by avoiding PCR and recollecting larger DNA fragments to improve assignment of detected taxa through phylogenetic reconstruction. We applied capture by hybridization (CBH) to enrich DNA from deep-sea sediment samples and compared the results with those obtained through an up-to-date metabarcoding PCR-based approach (MTB). Originally developed for bacterial communities and targeting 16S rDNA, the CBH approach was applied to 18S rDNA to improve the detection of species forming benthic communities of eukaryotes, with a particular focus on metazoans. The results confirmed the possibility of extending CBH to metazoans with two major advantages: (i) CBH revealed a broader spectrum of prokaryotic, eukaryotic, and particularly metazoan diversity, and (ii) CBH allowed much more robust phylogenetic reconstructions of full-length barcodes with up to 1900 base pairs. This is particularly important for taxa whose assignment is hampered by gaps in reference databases. This study provides a database and probes to apply 18S CBH to diverse marine systems, confirming this promising new tool to improve biodiversity assessments in data-poor ecosystems such as those in the deep sea.
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Affiliation(s)
- Babett Günther
- MARBEC, Universite of Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Sophie Marre
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - Clémence Defois
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
| | - Thomas Merzi
- Total SE, Centre Scientifique et Technique Jean Feger, Pau, France
| | - Philippe Blanc
- Total SE, Centre Scientifique et Technique Jean Feger, Pau, France
| | - Pierre Peyret
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, Clermont-Ferrand, France
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28
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Luka MM, Kamau E, de Laurent ZR, Morobe JM, Alii LK, Nokes DJ, Agoti CN. Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018. Wellcome Open Res 2021; 6:178. [DOI: 10.12688/wellcomeopenres.16911.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2021] [Indexed: 01/10/2023] Open
Abstract
Background: Virus genome sequencing is increasingly utilized in epidemiological surveillance. Genomic data allows comprehensive evaluation of underlying viral diversity and epidemiology to inform control. For human rhinovirus (HRV), genomic amplification and sequencing is challenging due to numerous types, high genetic diversity and inadequate reference sequences. Methods: We developed a tiled amplicon type-specific protocol for genome amplification and sequencing on the Illumina MiSeq platform of two HRV types, A15 and A101. We then assessed added value in analyzing whole genomes relative to the VP4/2 region only in the investigation of HRV molecular epidemiology within the community in Kilifi, coastal Kenya. Results: We processed 73 samples collected between 2016-2018, and 48 yielded at least 70% HRV genome coverage. These included all A101 samples (n=10) and 38 (60.3%) A15 samples. Phylogenetic analysis revealed that the Kilifi A101 sequences interspersed with global A101 genomes available in GenBank collected between 1999-2016. On the other hand, our A15 sequences formed a monophyletic group separate from the global genomes collected in 2008 and 2019. Improved phylogenetic resolution was observed with the genome phylogenies compared to the VP4/2 phylogenies. Conclusions: We present a type-specific full genome sequencing approach for obtaining HRV genomic data and characterizing infections.
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29
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Claes KBM, Rosseel T, De Leeneer K. Dealing with Pseudogenes in Molecular Diagnostics in the Next Generation Sequencing Era. Methods Mol Biol 2021; 2324:363-381. [PMID: 34165726 DOI: 10.1007/978-1-0716-1503-4_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Presence of pseudogenes is a dreadful issue in next generation sequencing (NGS), because their contamination can interfere with the detection of variants in the genuine gene and generate false positive and false negative variants.In this chapter we focus on issues related to the application of NGS strategies for analysis of genes with pseudogenes in a clinical setting. The degree to which a pseudogene impacts the ability to accurately detect and map variants in its parent gene depends on the degree of similarity (homology) with the parent gene itself. Hereby, target enrichment and mapping strategies are crucial factors to avoid "contaminating" pseudogene sequences. For target enrichment, we describe advantages and disadvantages of PCR- and capture-based strategies. For mapping strategies, we discuss crucial parameters that need to be considered to accurately distinguish sequences of functional genes from pseudogenic sequences. Finally, we discuss some examples of genes associated with Mendelian disorders, for which interesting NGS approaches are described to avoid interference with pseudogene sequences.
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Affiliation(s)
| | - Toon Rosseel
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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30
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Collet A, Tarabeux J, Girard E, D’Enghien CD, Golmard L, Deshaies V, Lermine A, Laugé A, Moncoutier V, Lefol C, Copigny F, Dehainault C, Tenreiro H, Guy C, Abidallah K, Barbaroux C, Rouleau E, Servant N, Pauw AD, Stoppa-Lyonnet D, Houdayer C. Pros and cons of HaloPlex enrichment in cancer predisposition genetic diagnosis. AIMS GENETICS 2021. [DOI: 10.3934/genet.2015.4.263] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
AbstractPanel sequencing is a practical option in genetic diagnosis. Enrichment and library preparation steps are critical in the diagnostic setting. In order to test the value of HaloPlex technology in diagnosis, we designed a custom oncogenetic panel including 62 genes. The procedure was tested on a training set of 71 controls and then blindly validated on 48 consecutive hereditary breast/ovarian cancer (HBOC) patients tested negative for BRCA1/2 mutation. Libraries were sequenced on HiSeq2500 and data were analysed with our academic bioinformatics pipeline. Point mutations were detected using Varscan2, median size indels were detected using Pindel and large genomic rearrangements (LGR) were detected by DESeq. Proper coverage was obtained. However, highly variable read depth was observed within genes. Excluding pseudogene analysis, all point mutations were detected on the training set. All indels were also detected using Pindel. On the other hand, DESeq allowed LGR detection but with poor specificity, preventing its use in diagnostics. Mutations were detected in 8% of BRCA1/2-negative HBOC cases. HaloPlex technology appears to be an efficient and promising solution for gene panel diagnostics. Data analysis remains a major challenge and geneticists should enhance their bioinformatics knowledge in order to ensure good quality diagnostic results.
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Affiliation(s)
- Agnès Collet
- Institut Curie, Département de Biopathologie, Paris, France
| | | | - Elodie Girard
- Institut Curie, Paris, France
- Inserm U900, Paris, France
- Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France
| | | | - Lisa Golmard
- Institut Curie, Département de Biopathologie, Paris, France
- Institut Curie, Inserm U830, Paris, France
| | - Vivien Deshaies
- Institut Curie, Paris, France
- Inserm U900, Paris, France
- Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France
| | - Alban Lermine
- Institut Curie, Paris, France
- Inserm U900, Paris, France
- Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France
| | - Anthony Laugé
- Institut Curie, Département de Biopathologie, Paris, France
| | | | - Cédrick Lefol
- Institut Curie, Département de Biopathologie, Paris, France
| | | | | | | | - Christophe Guy
- Institut Curie, Département de Biopathologie, Paris, France
| | | | | | | | - Nicolas Servant
- Institut Curie, Paris, France
- Inserm U900, Paris, France
- Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France
| | | | - Dominique Stoppa-Lyonnet
- Institut Curie, Département de Biopathologie, Paris, France
- Institut Curie, Inserm U830, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Claude Houdayer
- Institut Curie, Département de Biopathologie, Paris, France
- Institut Curie, Inserm U830, Paris, France
- Faculté des Sciences pharmaceutiques et biologiques, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
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31
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Abstract
![]()
Targeted
sequencing enables sensitive and cost-effective analysis
by focusing resources on molecules of interest. Existing methods,
however, are limited in enrichment power and target capture length.
Here, we present a novel method that uses compound nucleic acid cytometry
to achieve million-fold enrichments of molecules >10 kbp in length
using minimal prior target information. We demonstrate the approach
by sequencing HIV proviruses in infected individuals. Our method is
useful for rare target sequencing in research and clinical applications,
including for identifying cancer-associated mutations or sequencing
viruses infecting cells.
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Affiliation(s)
- Chen Sun
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States
| | - Kai-Chun Chang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States.,California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California 94158, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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Lee H, Lee B, Kim DG, Cho YA, Kim JS, Suh YL. Detection of TERT Promoter Mutations Using Targeted Next-Generation Sequencing: Overcoming GC Bias through Trial and Error. Cancer Res Treat 2021; 54:75-83. [PMID: 33940787 PMCID: PMC8756133 DOI: 10.4143/crt.2021.107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/30/2021] [Indexed: 11/21/2022] Open
Abstract
Purpose Detection of telomerase reverse transcriptase (TERT) promoter mutations is a crucial process in the integrated diagnosis of glioblastomas. However, the TERT promoter region is difficult to amplify because of its high guanine-cytosine (GC) content (> 80%). This study aimed to analyze the capturing of TERT mutations by targeted next-generation sequencing (NGS) using formalin-fixed paraffin-embedded tissues. Materials and Methods We compared the detection rate of TERT mutations between targeted NGS and Sanger sequencing in 25 cases of isocitrate dehydrgenase (IDH)-wildtype glioblastomas and 10 cases of non-neoplastic gastric tissues. Our customized panel consisted of 232 essential glioma-associated genes. Results Sanger sequencing detected TERT mutations in 17 out of 25 glioblastomas, but all TERT mutations were missed by targeted NGS. After the manual visualization of the NGS data using an integrative genomics viewer, 16 cases showed a TERT mutation with a very low read depth (mean, 21.59; median, 25), which revealed false-negative results using auto-filtering. We optimized our customized panel by extending the length of oligonucleotide baits and increasing the number of baits spanning the coverage of the TERT promoter, which did not amplify well due to the high GC content. Conclusion Our study confirmed that it is crucial to consider the recognition of molecular bias and to carefully interpret NGS data.
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Affiliation(s)
- Hyunwoo Lee
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Boram Lee
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Digital Health, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Deok Geun Kim
- Department of Digital Health, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Clinical Genomic Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yoon Ah Cho
- Department of Pathology, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang, Korea
| | - Jung-Sun Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Digital Health, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yeon-Lim Suh
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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33
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Elliott I, Thangnimitchok N, de Cesare M, Linsuwanon P, Paris DH, Day NPJ, Newton PN, Bowden R, Batty EM. Targeted capture and sequencing of Orientia tsutsugamushi genomes from chiggers and humans. INFECTION GENETICS AND EVOLUTION 2021; 91:104818. [PMID: 33771726 PMCID: PMC8164161 DOI: 10.1016/j.meegid.2021.104818] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/12/2022]
Abstract
Scrub typhus is a febrile disease caused by Orientia tsutsugamushi, transmitted by larval stage Trombiculid mites (chiggers), whose primary hosts are small mammals. The phylogenomics of O. tsutsugamushi in chiggers, small mammals and humans remains poorly understood. To combat the limitations imposed by the low relative quantities of pathogen DNA in typical O. tsutsugamushi clinical and ecological samples, along with the technical, safety and cost limitations of cell culture, a novel probe-based target enrichment sequencing protocol was developed. The method was designed to capture variation among conserved genes and facilitate phylogenomic analysis at the scale of population samples. A whole-genome amplification step was incorporated to enhance the efficiency of sequencing by reducing duplication rates. This resulted in on-target capture rates of up to 93% for a diverse set of human, chigger, and rodent samples, with the greatest success rate in samples with real-time PCR Ct values below 35. Analysis of the best-performing samples revealed phylogeographic clustering at local, provincial and international scales. Applying the methodology to a comprehensive set of samples could yield a more complete understanding of the ecology, genomic evolution and population structure of O. tsutsugamushi and other similarly challenging organisms, with potential benefits in the development of diagnostic tests and vaccines.
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Affiliation(s)
- Ivo Elliott
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
| | - Neeranuch Thangnimitchok
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | | | - Piyada Linsuwanon
- Department of Entomology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Daniel H Paris
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland; Department of Clinical Research, University of Basel, Basel, Switzerland
| | - Nicholas P J Day
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom; Division of Advanced Technology and Biology, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Elizabeth M Batty
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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34
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Scheiper-Welling S, Körber S, Geisen C, Verhoff MA, Kauferstein S. Genetic analysis of sudden unexpected death cases: Evaluation of library preparation methods to handle heterogeneous sample material. Forensic Sci Int 2021; 322:110768. [PMID: 33774385 DOI: 10.1016/j.forsciint.2021.110768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/04/2021] [Accepted: 03/16/2021] [Indexed: 10/21/2022]
Abstract
Over the past years, next-generation sequencing (NGS) technologies revolutionized the possibilities in a broad range of application areas. Also in the field of forensic genetics, NGS continuously gained in importance and attentiveness. A significant number of sudden cardiac deaths (SCD) in the young is due to heritable arrhythmia syndromes emphasizing the need of examining the genetic basis in these cases also with regard to the identification of relatives and/or patients being at risk. As a result, high-throughput methods became of increasing value in molecular autopsy investigations enabling the analysis of a broad spectrum of genes. Most standard protocols are optimized for high-quality samples and frequently not directly applicable to challenging forensic sample material. In the present study, we intended to examine a comprehensive gene panel associated with SCD and inherited arrhythmogenic disorders. We compared three different hybridization-based library preparation technologies in order to implement a suitable NGS workflow for heterogeneous, forensic as well as diagnostic sample material. The results obtained indicated, that the Illumina technologies Nextera DNA Flex and TruSeq were compatible with samples exhibiting varying levels of degradation. In comparison, the TruSight method also resulted in good sequencing data, but seemed to be more dependent on DNA integrity. The preparation protocols evaluated in our study are not restricted to molecular autopsy investigations and might be helpful for and transferrable to further forensic research applications.
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Affiliation(s)
- Stefanie Scheiper-Welling
- Institute of Legal Medicine, Goethe University, University Hospital Frankfurt, Frankfurt, Germany; German Red Cross Blood Center, Institute of Transfusion Medicine and Immunohaematology, University Hospital Frankfurt, Frankfurt, Germany.
| | - Stephanie Körber
- German Red Cross Blood Center, Institute of Transfusion Medicine and Immunohaematology, University Hospital Frankfurt, Frankfurt, Germany
| | - Christof Geisen
- German Red Cross Blood Center, Institute of Transfusion Medicine and Immunohaematology, University Hospital Frankfurt, Frankfurt, Germany
| | - Marcel A Verhoff
- Institute of Legal Medicine, Goethe University, University Hospital Frankfurt, Frankfurt, Germany
| | - Silke Kauferstein
- Institute of Legal Medicine, Goethe University, University Hospital Frankfurt, Frankfurt, Germany
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35
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New challenges, new opportunities: Next generation sequencing and its place in the advancement of HLA typing. Hum Immunol 2021; 82:478-487. [PMID: 33551127 DOI: 10.1016/j.humimm.2021.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 12/29/2020] [Accepted: 01/18/2021] [Indexed: 02/07/2023]
Abstract
The Human Leukocyte Antigen (HLA) system has a critical role in immunorecognition, transplantation, and disease association. Early typing techniques provided the foundation for genotyping methods that revealed HLA as one of the most complex, polymorphic regions of the human genome. Next Generation Sequencing (NGS), the latest molecular technology introduced in clinical tissue typing laboratories, has demonstrated advantages over other established methods. NGS offers high-resolution sequencing of entire genes in time frames and price points considered unthinkable just a few years ago, contributing a wealth of data informing histocompatibility assessment and standards of clinical care. Although the NGS platforms share a high-throughput massively parallel processing model, differing chemistries provide specific strengths and weaknesses. Research-oriented Third Generation Sequencing and related advances in bioengineering continue to broaden the future of NGS in clinical settings. These diverse applications have demanded equally innovative strategies for data management and computational bioinformatics to support and analyze the unprecedented volume and complexity of data generated by NGS. We discuss some of the challenges and opportunities associated with NGS technologies, providing a comprehensive picture of the historical developments that paved the way for the NGS revolution, its current state and future possibilities for HLA typing.
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36
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Steele JL, Stevens RC, Cabrera OA, Bassill GJ, Cramer SM, Guzman F, Shuber AP. Novel CRISPR-based sequence specific enrichment methods for target loci and single base mutations. PLoS One 2020; 15:e0243781. [PMID: 33362267 PMCID: PMC7757808 DOI: 10.1371/journal.pone.0243781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/25/2020] [Indexed: 01/10/2023] Open
Abstract
The programmable sequence specificity of CRISPR has found uses in gene editing and diagnostics. This manuscript describes an additional application of CRISPR through a family of novel DNA enrichment technologies. CAMP (CRISPR Associated Multiplexed PCR) and cCAMP (chimeric CRISPR Associated Multiplexed PCR) utilize the sequence specificity of the Cas9/sgRNA complex to target loci for the ligation of a universal adapter that is used for subsequent amplification. cTRACE (chimeric Targeting Rare Alleles with CRISPR-based Enrichment) also applies this method to use Cas9/sgRNA to target loci for the addition of universal adapters, however it has an additional selection for specific mutations through the use of an allele-specific primer. These three methods can produce multiplex PCR that significantly reduces the optimization required for every target. The methods are also not specific to any downstream analytical platform. We additionally will present a mutation specific enrichment technology that is non-amplification based and leaves the DNA in its native state: TRACE (Targeting Rare Alleles with CRISPR-based Enrichment). TRACE utilizes the Cas9/sgRNA complex to sterically protect the ends of targeted sequences from exonuclease activity which digests both the normal variant as well as any off-target sequences.
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Affiliation(s)
| | | | - Oscar A. Cabrera
- Genetics Research LLC, Waltham, Massachusetts, United States of America
| | - Gary J. Bassill
- Genetics Research LLC, Waltham, Massachusetts, United States of America
| | - Sabrina M. Cramer
- Genetics Research LLC, Waltham, Massachusetts, United States of America
| | - Felipe Guzman
- Genetics Research LLC, Waltham, Massachusetts, United States of America
| | - Anthony P. Shuber
- Genetics Research LLC, Waltham, Massachusetts, United States of America
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37
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Novel target capture DNA library preparation method using CircLigase-mediated hook ligation. N Biotechnol 2020; 59:44-50. [PMID: 32688061 DOI: 10.1016/j.nbt.2020.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 11/22/2022]
Abstract
Target capture DNA library preparation methods primarily use the biotin-streptavidin interaction to enrich target DNA, requiring complex operations and a time-consuming workflow with a series of wash steps at regulated temperatures. Here, a new method is presented termed 'hook ligation' for target DNA library preparation, using CircLigase to capture target DNA. The concept was validated by library preparation, sequencing, and acquisition of target DNA fragment information through bioinformatics analysis. An efficient reference point for single-strand DNA ligation to a hook sequence using CircLigase is also provided and it is shown that the efficiency can be influenced by the length and the position of the complementary area on the target DNA.
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38
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Xiao H, Zhou WH. [Application of RNA sequencing in clinical diagnosis of Mendelian disease]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2020; 22:1138-1142. [PMID: 33059815 PMCID: PMC7568994 DOI: 10.7499/j.issn.1008-8830.2005004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Gene panel and whole exome sequencing are now commonly used to detect Mendelian disease, but the current molecular diagnostic rate of DNA sequencing is only 35%-50%. In recent years, RNA sequencing emerges as a promising diagnostic method. It can detect new pathogenic mutations, and analyze allele-specific expression. This will be helpful to understand the relationship between disease genotype and phenotype, and can complement genome sequencing in order to expand the traditional genomic diagnostic methods of Mendelian disease. RNA sequencing is expected to become a routine tool for diagnosing Mendelian diseases. This article reviews the application of RNA sequencing in the clinical diagnosis of Mendelian disease.
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Affiliation(s)
- Hui Xiao
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai 201102, China.
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Almomani R, Marchi M, Sopacua M, Lindsey P, Salvi E, de Koning B, Santoro S, Magri S, Smeets HJM, Martinelli Boneschi F, Malik RR, Ziegler D, Hoeijmakers JGJ, Bönhof G, Dib-Hajj S, Waxman SG, Merkies ISJ, Lauria G, Faber CG, Gerrits MM. Evaluation of molecular inversion probe versus TruSeq® custom methods for targeted next-generation sequencing. PLoS One 2020; 15:e0238467. [PMID: 32877464 PMCID: PMC7467307 DOI: 10.1371/journal.pone.0238467] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/16/2020] [Indexed: 11/18/2022] Open
Abstract
Resolving the genetic architecture of painful neuropathy will lead to better disease management strategies. We aimed to develop a reliable method to re-sequence multiple genes in a large cohort of painful neuropathy patients at low cost. In this study, we compared sensitivity, specificity, targeting efficiency, performance and cost effectiveness of Molecular Inversion Probes-Next generation sequencing (MIPs-NGS) and TruSeq® Custom Amplicon-Next generation sequencing (TSCA-NGS). Capture probes were designed to target nine sodium channel genes (SCN3A, SCN8A-SCN11A, and SCN1B-SCN4B). One hundred sixty-six patients with diabetic and idiopathic neuropathy were tested by both methods, 70 patients were validated by Sanger sequencing. Sensitivity, specificity and performance of both techniques were comparable, and in agreement with Sanger sequencing. The average targeted regions coverage for MIPs-NGS was 97.3% versus 93.9% for TSCA-NGS. MIPs-NGS has a more versatile assay design and is more flexible than TSCA-NGS. The cost of MIPs-NGS is >5 times cheaper than TSCA-NGS when 500 or more samples are tested. In conclusion, MIPs-NGS is a reliable, flexible, and relatively inexpensive method to detect genetic variations in a large cohort of patients. In our centers, MIPs-NGS is currently implemented as a routine diagnostic tool for screening of sodium channel genes in painful neuropathy patients.
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Affiliation(s)
- Rowida Almomani
- Department of Genetics and Cell Biology, Clinical Genomics Unit, Maastricht University, Maastricht, The Netherlands
- MHeNs school of Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Margherita Marchi
- Neuroalgology Units, Fondazione IRCCS Istituto Neurologico “Carlo Besta” Milan, Milan, Italy
| | - Maurice Sopacua
- MHeNs school of Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
- Department of Neurology, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Patrick Lindsey
- Department of Genetics and Cell Biology, Clinical Genomics Unit, Maastricht University, Maastricht, The Netherlands
| | - Erika Salvi
- Neuroalgology Units, Fondazione IRCCS Istituto Neurologico “Carlo Besta” Milan, Milan, Italy
| | - Bart de Koning
- Department of Clinical Genetics, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Silvia Santoro
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Stefania Magri
- Neuroalgology Units, Fondazione IRCCS Istituto Neurologico “Carlo Besta” Milan, Milan, Italy
| | - Hubert J. M. Smeets
- Department of Genetics and Cell Biology, Clinical Genomics Unit, Maastricht University, Maastricht, The Netherlands
- MHeNs school of Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Filippo Martinelli Boneschi
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Rayaz R. Malik
- Institute of Human Development, Centre for Endocrinology and Diabetes, University of Manchester and Central Manchester NHS Foundation Trust, Manchester Academic Health Science Center, Manchester, United Kingdom
- Department of Medicine, Weill Cornell Medicine, Doha, Qatar
| | - Dan Ziegler
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research, Düsseldorf, Germany
- Department of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Janneke G. J. Hoeijmakers
- MHeNs school of Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
- Department of Neurology, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Gidon Bönhof
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research, Düsseldorf, Germany
| | - Sulayman Dib-Hajj
- Department of Neurology, Yale University School of Medicine, Yale, New Haven, United States of America
- Center for Neuroscience and Regeneration Research, Yale University School of Medicine, Yale, New Haven, United States of America
- Center for Neuroscience and Regeneration Research, Veterans Affairs Medical Center, West Haven, Connecticut, United States of America
| | - Stephen G. Waxman
- Department of Neurology, Yale University School of Medicine, Yale, New Haven, United States of America
- Center for Neuroscience and Regeneration Research, Yale University School of Medicine, Yale, New Haven, United States of America
- Center for Neuroscience and Regeneration Research, Veterans Affairs Medical Center, West Haven, Connecticut, United States of America
| | - Ingemar S. J. Merkies
- Department of Neurology, Maastricht University Medical Center+, Maastricht, the Netherlands
- Department of Neurology, St Elisabeth Hospital, Willemstad, Curaçao
| | - Giuseppe Lauria
- Neuroalgology Units, Fondazione IRCCS Istituto Neurologico “Carlo Besta” Milan, Milan, Italy
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy
| | - Catharina G. Faber
- MHeNs school of Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
- Department of Neurology, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Monique M. Gerrits
- Department of Clinical Genetics, Maastricht University Medical Center+, Maastricht, the Netherlands
- * E-mail:
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The Potential of HTS Approaches for Accurate Genotyping in Grapevine ( Vitis vinifera L.). Genes (Basel) 2020; 11:genes11080917. [PMID: 32785184 PMCID: PMC7464945 DOI: 10.3390/genes11080917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/03/2020] [Accepted: 08/06/2020] [Indexed: 11/16/2022] Open
Abstract
The main challenge associated with genotyping based on conventional length polymorphisms is the cross-laboratory standardization of allele sizes. This step requires the inclusion of standards and manual sizing to avoid false results. Capillary electrophoresis (CE) approaches limit the information to the length polymorphism and do not allow the determination of a complete marker sequence. As an alternative, high-throughput sequencing (HTS) offers complete information regarding marker sequences and their flanking regions. In this work, we investigated the suitability of a semi-quantitative sequencing approach for microsatellite genotyping using Illumina paired-end technology. Twelve microsatellite loci that are well established for grapevine CE typing were analysed on 96 grapevine samples from six different countries. We redesigned primers to the length of the amplicon for short sequencing (~100 bp). The primer pair was flanked with a 10 bp overhang for the introduction of barcodes on both sides of the amplicon to enable high multiplexing. The highest data peaks were determined as simple sequence repeat (SSR) alleles and compared with the CE dataset based on 12 reference samples. The comparison showed that HTS SSR genotyping can successfully replace the CE system in further experiments. We believe that, with next-generation sequencing, genotyping can be improved in terms of its speed, accuracy, and price.
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Jayaraman P, Mosbruger T, Hu T, Tairis NG, Wu C, Clark PM, D’Arcy M, Ferriola D, Mackiewicz K, Gai X, Monos D, Sarmady M. AnthOligo: automating the design of oligonucleotides for capture/enrichment technologies. Bioinformatics 2020; 36:4353-4356. [PMID: 32484858 PMCID: PMC7520035 DOI: 10.1093/bioinformatics/btaa552] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/22/2020] [Accepted: 05/28/2020] [Indexed: 11/13/2022] Open
Abstract
SUMMARY A number of methods have been devised to address the need for targeted genomic resequencing. One of these methods, region-specific extraction (RSE) is characterized by the capture of long DNA fragments (15-20 kb) by magnetic beads, after enzymatic extension of oligonucleotides hybridized to selected genomic regions. Facilitating the selection of the most appropriate capture oligos for targeting a region of interest, satisfying the properties of temperature (Tm) and entropy (ΔG), while minimizing the formation of primer-dimers in a pooled experiment, is therefore necessary. Manual design and selection of oligos becomes very challenging, complicated by factors such as length of the target region and number of targeted regions. Here we describe, AnthOligo, a web-based application developed to optimally automate the process of generation of oligo sequences used to target and capture the continuum of large and complex genomic regions. Apart from generating oligos for RSE, this program may have wider applications in the design of customizable internal oligos to be used as baits for gene panel analysis or even probes for large-scale comparative genomic hybridization array processes. AnthOligo was tested by capturing the Major Histocompatibility Complex (MHC) of a random sample.The application provides users with a simple interface to upload an input file in BED format and customize parameters for each task. The task of probe design in AnthOligo commences when a user uploads an input file and concludes with the generation of a result-set containing an optimal set of region-specific oligos. AnthOligo is currently available as a public web application with URL: http://antholigo.chop.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Taishan Hu
- Department of Pathology and Laboratory Medicine
| | | | - Chao Wu
- Department of Biomedical Health & Informatics, The Children's Hospitals of Philadelphia, Philadelphia, PA, USA
| | - Peter M Clark
- Department of Research & Development, The Janssen Pharmaceutical Companies of Johnson & Johnson, Raritan, NJ, USA
| | - Monica D’Arcy
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | | | - Katarzyna Mackiewicz
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Xiaowu Gai
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, Center for Personalized Medicine, Children’s Hospital of Los Angeles, Los Angeles, CA, USA
| | - Dimitrios Monos
- Department of Pathology and Laboratory Medicine
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mahdi Sarmady
- Department of Pathology and Laboratory Medicine
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Giebner H, Langen K, Bourlat SJ, Kukowka S, Mayer C, Astrin JJ, Misof B, Fonseca VG. Comparing diversity levels in environmental samples: DNA sequence capture and metabarcoding approaches using 18S and COI genes. Mol Ecol Resour 2020; 20:1333-1345. [PMID: 32462738 DOI: 10.1111/1755-0998.13201] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/20/2020] [Accepted: 05/15/2020] [Indexed: 12/25/2022]
Abstract
Environmental DNA studies targeting multiple taxa using metabarcoding provide remarkable insights into levels of species diversity in any habitat. The main drawbacks are the presence of primer bias and difficulty in identifying rare species. We tested a DNA sequence-capture method in parallel with the metabarcoding approach to reveal possible advantages of one method over the other. Both approaches were performed using the same eDNA samples and the same 18S and COI regions, followed by high throughput sequencing. Metabarcoded eDNA libraries were PCR amplified with one primer pair from 18S and COI genes. DNA sequence-capture libraries were enriched with 3,639 baits targeting the same gene regions. We tested amplicon sequence variants (ASVs) and operational taxonomic units (OTUs) in silico approaches for both markers and methods, using for this purpose the metabarcoding data set. ASVs methods uncovered more species for the COI gene, whereas the opposite occurred for the 18S gene, suggesting that clustering reads into OTUs could bias diversity richness especially using 18S with relaxed thresholds. Additionally, metabarcoding and DNA sequence-capture recovered 80%-90% of the control sample species. DNA sequence-capture was 8x more expensive, nonetheless it identified 1.5x more species for COI and 13x more genera for 18S than metabarcoding. Both approaches offer reliable results, sharing ca. 40% species and 72% families and retrieve more taxa when nuclear and mitochondrial markers are combined. eDNA metabarcoding is quite well established and low-cost, whereas DNA-sequence capture for biodiversity assessment is still in its infancy, is more time-consuming but provides more taxonomic assignments.
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Affiliation(s)
- Hendrik Giebner
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Kathrin Langen
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Sarah J Bourlat
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Sandra Kukowka
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Christoph Mayer
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Jonas J Astrin
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Vera G Fonseca
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany.,Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
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43
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Shedding light on dark genes: enhanced targeted resequencing by optimizing the combination of enrichment technology and DNA fragment length. Sci Rep 2020; 10:9424. [PMID: 32523024 PMCID: PMC7287100 DOI: 10.1038/s41598-020-66331-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/23/2020] [Indexed: 12/16/2022] Open
Abstract
The exome contains many obscure regions difficult to explore with current short-read sequencing methods. Repetitious genomic regions prevent the unique alignment of reads, which is essential for the identification of clinically-relevant genetic variants. Long-read technologies attempt to resolve multiple-mapping regions, but they still produce many sequencing errors. Thus, a new approach is required to enlighten the obscure regions of the genome and rescue variants that would be otherwise neglected. This work aims to improve the alignment of multiple-mapping reads through the extension of the standard DNA fragment size. As Illumina can sequence fragments up to 550 bp, we tested different DNA fragment lengths using four major commercial WES platforms and found that longer DNA fragments achieved a higher genotypability. This metric, which indicates base calling calculated by combining depth of coverage with the confidence of read alignment, increased from hundreds to thousands of genes, including several associated with clinical phenotypes. While depth of coverage has been considered crucial for the assessment of WES performance, we demonstrated that genotypability has a greater impact in revealing obscure regions, with ~1% increase in variant calling in respect to shorter DNA fragments. Results confirmed that this approach enlightened many regions previously not explored.
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44
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Xu P, Modavi C, Demaree B, Twigg F, Liang B, Sun C, Zhang W, Abate AR. Microfluidic automated plasmid library enrichment for biosynthetic gene cluster discovery. Nucleic Acids Res 2020; 48:e48. [PMID: 32095820 PMCID: PMC7192590 DOI: 10.1093/nar/gkaa131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/22/2020] [Accepted: 02/19/2020] [Indexed: 12/13/2022] Open
Abstract
Microbial biosynthetic gene clusters are a valuable source of bioactive molecules. However, because they typically represent a small fraction of genomic material in most metagenomic samples, it remains challenging to deeply sequence them. We present an approach to isolate and sequence gene clusters in metagenomic samples using microfluidic automated plasmid library enrichment. Our approach provides deep coverage of the target gene cluster, facilitating reassembly. We demonstrate the approach by isolating and sequencing type I polyketide synthase gene clusters from an Antarctic soil metagenome. Our method promotes the discovery of functional-related genes and biosynthetic pathways.
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Affiliation(s)
- Peng Xu
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Cyrus Modavi
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Benjamin Demaree
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA, USA
| | - Frederick Twigg
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Benjamin Liang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Chen Sun
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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45
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McNulty SN, Mann PR, Robinson JA, Duncavage EJ, Pfeifer JD. Impact of Reducing DNA Input on Next-Generation Sequencing Library Complexity and Variant Detection. J Mol Diagn 2020; 22:720-727. [PMID: 32142899 DOI: 10.1016/j.jmoldx.2020.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/07/2020] [Accepted: 02/20/2020] [Indexed: 12/23/2022] Open
Abstract
PCR amplification, a key step in next-generation sequencing (NGS) library construction, can generate an unlimited amount of product from limited input; however, it cannot create more information than was present in the original template. Thus, NGS libraries can be made from very little DNA, but reducing the input may compromise assay sensitivity in ways that are difficult to ascertain unless library complexity (ie, the number of unique DNA molecules represented in the library) and depth of coverage with unique sequence reads (those derived from input DNA molecules) versus duplicate sequence reads (those resulting from overamplification of particular molecules) are discretely measured. A series of experiments was performed to explore the impact of low DNA input on an amplicon-based NGS assay using unique molecular identifiers to track unique versus duplicate reads. At high sequencing depths, unique and total (unique plus duplicate) read coverage are not well correlated, so increasing the number of sequenced reads does not necessarily improve sensitivity. Unique coverage depth tends to improve with more input, but improvements are not consistent. Fluctuations in library complexity complicated variant detection using both standardized and clinical specimens, often resulting in technical replicates with vastly different estimates of variant allelic fraction. In conclusion, depth of coverage with unique reads must be tracked in clinical NGS to ensure that sensitivity and accuracy are maintained.
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Affiliation(s)
- Samantha N McNulty
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri.
| | - Patrick R Mann
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Joshua A Robinson
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Eric J Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - John D Pfeifer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
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46
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Leong KW, Yu F, Adalsteinsson VA, Reed S, Gydush G, Ladas I, Li J, Tantisira KG, Makrigiorgos GM. A nuclease-polymerase chain reaction enables amplification of probes used for capture-based DNA target enrichment. Nucleic Acids Res 2019; 47:e147. [PMID: 31598677 PMCID: PMC6902007 DOI: 10.1093/nar/gkz870] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 09/06/2019] [Accepted: 10/01/2019] [Indexed: 11/13/2022] Open
Abstract
DNA target enrichment via hybridization capture is a commonly adopted approach which remains expensive due in-part to using biotinylated-probe panels. Here we provide a novel isothermal amplification reaction to amplify rapidly existing probe panels without knowledge of the sequences involved, thereby decreasing a major portion of the overall sample preparation cost. The reaction employs two thermostable enzymes, BST-polymerase and duplex-specific nuclease DSN. DSN initiates random ‘nicks’ on double-stranded-DNA which enable BST to polymerize DNA by displacing the nicked-strand. Displaced strands re-hybridize and the process leads to an exponential chain-reaction generating biotinylated DNA fragments within minutes. When starting from single-stranded-DNA, DNA is first converted to double-stranded-DNA via terminal-deoxynucleotidyl-transferase (TdT) prior to initiation of BST–DSN reaction. Biotinylated probes generated by TdT–BST–DSN (TBD) reactions using panels of 33, 190 or 7186 DNA targets are used for hybrid-capture-based target enrichment from amplified circulating-DNA, followed by targeted re-sequencing. Polymerase-nuclease isothermal-chain-reactions generate random amplified probes with no apparent sequence dependence. One round of target-capture using TBD probes generates a modest on-target sequencing ratio, while two successive rounds of capture generate >80% on-target reads with good sequencing uniformity. TBD-reactions generate enough capture-probes to increase by approximately two to three orders-of-magnitude the target-enrichment experiments possible from an initial set of probes.
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Affiliation(s)
- Ka Wai Leong
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Fangyan Yu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Sarah Reed
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gregory Gydush
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ioannis Ladas
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jiang Li
- The Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medicine School, Boston, MA 02142, USA
| | - Kelan G Tantisira
- The Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medicine School, Boston, MA 02142, USA
| | - Gerassimos Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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47
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Bewicke-Copley F, Arjun Kumar E, Palladino G, Korfi K, Wang J. Applications and analysis of targeted genomic sequencing in cancer studies. Comput Struct Biotechnol J 2019; 17:1348-1359. [PMID: 31762958 PMCID: PMC6861594 DOI: 10.1016/j.csbj.2019.10.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 10/18/2019] [Accepted: 10/22/2019] [Indexed: 12/31/2022] Open
Abstract
Next Generation Sequencing (NGS) has dramatically improved the flexibility and outcomes of cancer research and clinical trials, providing highly sensitive and accurate high-throughput platforms for large-scale genomic testing. In contrast to whole-genome (WGS) or whole-exome sequencing (WES), targeted genomic sequencing (TS) focuses on a panel of genes or targets known to have strong associations with pathogenesis of disease and/or clinical relevance, offering greater sequencing depth with reduced costs and data burden. This allows targeted sequencing to identify low frequency variants in targeted regions with high confidence, thus suitable for profiling low-quality and fragmented clinical DNA samples. As a result, TS has been widely used in clinical research and trials for patient stratification and the development of targeted therapeutics. However, its transition to routine clinical use has been slow. Many technical and analytical obstacles still remain and need to be discussed and addressed before large-scale and cross-centre implementation. Gold-standard and state-of-the-art procedures and pipelines are urgently needed to accelerate this transition. In this review we first present how TS is conducted in cancer research, including various target enrichment platforms, the construction of target panels, and selected research and clinical studies utilising TS to profile clinical samples. We then present a generalised analytical workflow for TS data discussing important parameters and filters in detail, aiming to provide the best practices of TS usage and analyses.
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Key Words
- BAM, Binary Alignment Map
- BWA, Burrows-Wheeler Aligner
- Background error
- CLL, Chronic Lymphocytic Leukaemia
- COSMIC, Catalogue of Somatic Mutations in Cancer
- Cancer genomics
- Clinical samples
- ESP, Exome Sequencing Project
- FF, Fresh Frozen
- FFPE, Formalin Fixed Paraffin Embedded
- FL, Follicular Lymphoma
- GATK, Genome Analysis Toolkit
- ICGC, International Cancer Genome Consortium
- MBC, Molecular Barcode
- NCCN, the National Comprehensive Cancer Network®
- NGS, Next Generation Sequencing
- NHL, Non-Hodgkin Lymphoma
- NSCLC, Non-Small Cell Lung Carcinoma
- PCR duplicates
- QC, Quality Control
- SAM, Sequence Alignment Map
- TCGA, The Cancer Genome Atlas
- TS, Targeted Sequencing
- Targeted sequencing
- UMI, Unique Molecular Identifiers
- VAF, Variant Allele Frequency
- Variant calling
- WES, Whole Exome Sequencing
- WGS, Whole Genome Sequencing
- tFL, Transformed Follicular Lymphoma
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Affiliation(s)
- Findlay Bewicke-Copley
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Emil Arjun Kumar
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Giuseppe Palladino
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Koorosh Korfi
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Jun Wang
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
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48
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Raz O, Biezuner T, Spiro A, Amir S, Milo L, Titelman A, Onn A, Chapal-Ilani N, Tao L, Marx T, Feige U, Shapiro E. Short tandem repeat stutter model inferred from direct measurement of in vitro stutter noise. Nucleic Acids Res 2019; 47:2436-2445. [PMID: 30698816 PMCID: PMC6412005 DOI: 10.1093/nar/gky1318] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 12/19/2018] [Accepted: 01/02/2019] [Indexed: 11/14/2022] Open
Abstract
Short tandem repeats (STRs) are polymorphic genomic loci valuable for various applications such as research, diagnostics and forensics. However, their polymorphic nature also introduces noise during in vitro amplification, making them difficult to analyze. Although it is possible to overcome stutter noise by using amplification-free library preparation, such protocols are presently incompatible with single cell analysis and with targeted-enrichment protocols. To address this challenge, we have designed a method for direct measurement of in vitro noise. Using a synthetic STR sequencing library, we have calibrated a Markov model for the prediction of stutter patterns at any amplification cycle. By employing this model, we have managed to genotype accurately cases of severe amplification bias, and biallelic STR signals, and validated our model for several high-fidelity PCR enzymes. Finally, we compared this model in the context of a naïve STR genotyping strategy against the state-of-the-art on a benchmark of single cells, demonstrating superior accuracy.
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Affiliation(s)
- Ofir Raz
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Tamir Biezuner
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Adam Spiro
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Shiran Amir
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Lilach Milo
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Alon Titelman
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Amos Onn
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Noa Chapal-Ilani
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Liming Tao
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Tzipy Marx
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Uriel Feige
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Ehud Shapiro
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 761001, Israel
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49
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Identifying genetic markers for a range of phylogenetic utility-From species to family level. PLoS One 2019; 14:e0218995. [PMID: 31369563 PMCID: PMC6675087 DOI: 10.1371/journal.pone.0218995] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/13/2019] [Indexed: 12/03/2022] Open
Abstract
Resolving the phylogenetic relationships of closely related species using a small set of loci is challenging as sufficient information may not be captured from a limited sample of the genome. Relying on few loci can also be problematic when conflict between gene-trees arises from incomplete lineage sorting and/or ongoing hybridization, problems especially likely in recently diverged lineages. Here, we developed a method using limited genomic resources that allows identification of many low copy candidate loci from across the nuclear and chloroplast genomes, design probes for target capture and sequence the captured loci. To validate our method we present data from Eucalyptus and Melaleuca, two large and phylogenetically problematic genera within the Myrtaceae family. With one annotated genome, one transcriptome and two whole-genome shotgun sequences of one Eucalyptus and four Melaleuca species, respectively, we identified 212 loci representing 263 kbp for targeted sequence capture and sequencing. Of these, 209 were successfully tested from 47 samples across five related genera of Myrtaceae. The average percentage of reads mapped back to the reference was 57.6% with coverage of more than 20 reads per position across 83.5% of the data. The methods developed here should be applicable across a large range of taxa across all kingdoms. The core methods are very flexible, providing a platform for various genomic resource availabilities and are useful from shallow to deep phylogenies.
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50
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Sun K, Jiang P, Cheng SH, Cheng THT, Wong J, Wong VWS, Ng SSM, Ma BBY, Leung TY, Chan SL, Mok TSK, Lai PBS, Chan HLY, Sun H, Chan KCA, Chiu RWK, Lo YMD. Orientation-aware plasma cell-free DNA fragmentation analysis in open chromatin regions informs tissue of origin. Genome Res 2019; 29:418-427. [PMID: 30808726 PMCID: PMC6396422 DOI: 10.1101/gr.242719.118] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/25/2019] [Indexed: 12/14/2022]
Abstract
Cell-free DNA (cfDNA) in human plasma is a class of biomarkers with many current and potential future diagnostic applications. Recent studies have shown that cfDNA molecules are not randomly fragmented and possess information related to their tissues of origin. Pathologies causing death of cells from particular tissues result in perturbations in the relative distribution of DNA from the affected tissues. Such tissue-of-origin analysis is particularly useful in the development of liquid biopsies for cancer. It is therefore of value to accurately determine the relative contributions of the tissues to the plasma DNA pool in a simultaneous manner. In this work, we report that in open chromatin regions, cfDNA molecules show characteristic fragmentation patterns reflected by sequencing coverage imbalance and differentially phased fragment end signals. The latter refers to differences in the read densities of sequences corresponding to the orientation of the upstream and downstream ends of cfDNA molecules in relation to the reference genome. Such cfDNA fragmentation patterns preferentially occur in tissue-specific open chromatin regions where the corresponding tissues contributed DNA into the plasma. Quantitative analyses of such signals allow measurement of the relative contributions of various tissues toward the plasma DNA pool. These findings were validated by plasma DNA sequencing data obtained from pregnant women, organ transplantation recipients, and cancer patients. Orientation-aware plasma DNA fragmentation analysis therefore has potential diagnostic applications in noninvasive prenatal testing, organ transplantation monitoring, and cancer liquid biopsy.
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Affiliation(s)
- Kun Sun
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - Peiyong Jiang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - Suk Hang Cheng
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - Timothy H T Cheng
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - John Wong
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - Vincent W S Wong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - Simon S M Ng
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - Brigette B Y Ma
- Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - Tak Y Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - Stephen L Chan
- Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - Tony S K Mok
- Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - Paul B S Lai
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - Henry L Y Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - Hao Sun
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - K C Allen Chan
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - Rossa W K Chiu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
| | - Y M Dennis Lo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, 999077, China
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