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Li W, Li W, Song Z, Gao Z, Xie K, Wang Y, Wang B, Hu J, Zhang Q, Ning C, Wang D, Fan X. Marker Density and Models to Improve the Accuracy of Genomic Selection for Growth and Slaughter Traits in Meat Rabbits. Genes (Basel) 2024; 15:454. [PMID: 38674388 PMCID: PMC11050255 DOI: 10.3390/genes15040454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
The selection and breeding of good meat rabbit breeds are fundamental to their industrial development, and genomic selection (GS) can employ genomic information to make up for the shortcomings of traditional phenotype-based breeding methods. For the practical implementation of GS in meat rabbit breeding, it is necessary to assess different marker densities and GS models. Here, we obtained low-coverage whole-genome sequencing (lcWGS) data from 1515 meat rabbits (including parent herd and half-sibling offspring). The specific objectives were (1) to derive a baseline for heritability estimates and genomic predictions based on randomly selected marker densities and (2) to assess the accuracy of genomic predictions for single- and multiple-trait linear mixed models. We found that a marker density of 50 K can be used as a baseline for heritability estimation and genomic prediction. For GS, the multi-trait genomic best linear unbiased prediction (GBLUP) model results in more accurate predictions for virtually all traits compared to the single-trait model, with improvements greater than 15% for all of them, which may be attributed to the use of information on genetically related traits. In addition, we discovered a positive correlation between the performance of the multi-trait GBLUP and the genetic correlation between the traits. We anticipate that this approach will provide solutions for GS, as well as optimize breeding programs, in meat rabbits.
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Affiliation(s)
- Wenjie Li
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
- Department of Animal Genetics and Breeding, University of Anhui Agricultural, Hefei 230031, China
| | - Wenqiang Li
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
| | - Zichen Song
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
| | - Zihao Gao
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
| | - Kerui Xie
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
| | - Yubing Wang
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
| | - Bo Wang
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
| | - Jiaqing Hu
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
| | - Qin Zhang
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
| | - Chao Ning
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
| | - Dan Wang
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Ministry of Agriculture and Rural Affairs, Taian 271000, China
| | - Xinzhong Fan
- Department of Animal Genetics and Breeding, Shandong Agricultural University, Taian 271000, China; (W.L.); (W.L.); (Z.S.); (K.X.); (B.W.); (J.H.); (Q.Z.); (C.N.)
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Thia JA, Endersby-Harshman N, Collier S, Nassar MS, Tawfik EA, Alfageeh MB, Elfekih S, Hoffmann AA. Mitochondrial DNA variation in Aedes aegypti (Diptera: Culicidae) mosquitoes from Jeddah, Saudi Arabia. J Med Entomol 2024; 61:250-256. [PMID: 37738428 PMCID: PMC10784777 DOI: 10.1093/jme/tjad131] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/24/2023] [Accepted: 09/04/2023] [Indexed: 09/24/2023]
Abstract
Wolbachia (Hertig 1936) (Rickettsiales: Ehrlichiaceae) has emerged as a valuable biocontrol tool in the fight against dengue by suppressing the transmission of the virus through mosquitoes. Monitoring the dynamics of Wolbachia is crucial for evaluating the effectiveness of release programs. Mitochondrial (mtDNA) markers serve as important tools for molecular tracking of infected mitochondrial backgrounds over time but require an understanding of the variation in release sites. In this study, we investigated the mitochondrial lineages of Aedes aegypti (Linnaeus 1762) in Jeddah, Saudi Arabia, which is a prospective release site for the "wAlbBQ" Wolbachia-infected strain of this mosquito species. We employed a combination of comprehensive mitogenomic analysis (including all protein-coding genes) and mtDNA marker analysis (cox1 and nad5) using data collected from Jeddah. We combined our mitogenome and mtDNA marker data with those from previous studies to place mitochondrial variation in Saudi Arabia into a broader global context. Our findings revealed the presence of 4 subclades that can be broadly categorized into 2 major mitochondrial lineages. Ae. aegypti mosquitoes from Jeddah belonged to both major lineages. Whilst mitogenomic data offered a higher resolution for distinguishing Jeddah mosquitoes from the wAlbBQ strain, the combination of cox1 and nad5 mtDNA markers alone proved to be sufficient. This study provides the first important characterization of Ae. aegypti mitochondrial lineages in Saudi Arabia and offers essential baseline information for planning future molecular monitoring efforts during the release of Wolbachia-infected mosquitoes.
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Affiliation(s)
- Joshua A Thia
- Pest and Environmental Adaptation Research Group, Bio21 Institute and The School of Biosciences, University of Melbourne, Parkville, VIC, Australia
| | - Nancy Endersby-Harshman
- Pest and Environmental Adaptation Research Group, Bio21 Institute and The School of Biosciences, University of Melbourne, Parkville, VIC, Australia
| | - Sophie Collier
- Pest and Environmental Adaptation Research Group, Bio21 Institute and The School of Biosciences, University of Melbourne, Parkville, VIC, Australia
| | - Majed S Nassar
- Advanced Diagnostics and Therapeutics Institute, Health Sector, King Abdulaziz City for Science and Technology, P.O. Box 6086, Riyadh 11442, Saudi Arabia
| | - Essam A Tawfik
- Advanced Diagnostics and Therapeutics Institute, Health Sector, King Abdulaziz City for Science and Technology, P.O. Box 6086, Riyadh 11442, Saudi Arabia
| | - Mohamed B Alfageeh
- Advanced Diagnostics and Therapeutics Institute, Health Sector, King Abdulaziz City for Science and Technology, P.O. Box 6086, Riyadh 11442, Saudi Arabia
| | - Samia Elfekih
- Pest and Environmental Adaptation Research Group, Bio21 Institute and The School of Biosciences, University of Melbourne, Parkville, VIC, Australia
- CSIRO Health and Biosecurity, Australian Centre for Disease Preparedness (ACDP), Geelong, VIC, Australia
| | - Ary A Hoffmann
- Pest and Environmental Adaptation Research Group, Bio21 Institute and The School of Biosciences, University of Melbourne, Parkville, VIC, Australia
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Chen L, Ma R, Luo C, Xie Q, Ning X, Sun K, Meng F, Zhou M, Sun J. Noninvasive early differential diagnosis and progression monitoring of ovarian cancer using the copy number alterations of plasma cell-free DNA. Transl Res 2023; 262:12-24. [PMID: 37499745 DOI: 10.1016/j.trsl.2023.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/20/2023] [Accepted: 07/23/2023] [Indexed: 07/29/2023]
Abstract
Ovarian cancer (OV) is the most lethal gynecological malignancy and requires improved early detection methods and more effective intervention to achieve a better prognosis. The lack of sensitive and noninvasive biomarkers with clinical utility remains a challenge. Here, we conducted a genome-wide copy number variation (CNV) profiling analysis using low-coverage whole genome sequencing (LC-WGS) of plasma cfDNA in patients with nonmalignant and malignant ovarian tumors and identified 10 malignancy-specific and 12 late-stage-specific CNV markers from plasma cfDNA LC-WGS data. Concordance analysis indicated a significant correlation of identified CNV markers between CNV profiles of plasma cfDNA and tissue DNA (Pearson's r = 0.64, P = 0.006 for the TCGA cohort and r = 0.51, P = 0.04 for the Dariush cohort). By leveraging these specific CNV markers and machine learning algorithms, we developed robust predictive models showing excellent performance in distinguishing between malignant and nonmalignant ovarian tumors with F1-scores of 0.90 and ranging from 0.75 to 0.99, and prediction accuracy of 0.89 and ranging from 0.66 to 0.98, respectively, as well as between early- and late-stage ovarian tumors with F1-scores of 0.84 and ranging from 0.61 to 1.00, and prediction accuracy of 0.82 and ranging from 0.63 to 0.96 in our institute cohort and other external validation cohorts. Furthermore, we also discovered and validated certain CNV features associated with survival outcomes and platinum-based chemotherapy response in multicenter cohorts. In conclusion, our study demonstrated the clinical utility of CNV profiling in plasma cfDNA using LC-WGS as a cost-effective and accessible liquid biopsy for OV.
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Affiliation(s)
- Lu Chen
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, P. R. China; School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou P. R. China
| | - Rong Ma
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, P. R. China
| | - Chang Luo
- Department of Birth Control, Red Cross Central Hospital of Harbin, Harbin, P. R. China
| | - Qin Xie
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, P. R. China
| | - Xin Ning
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, P. R. China
| | - Kaidi Sun
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, P. R. China
| | - Fanling Meng
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, P. R. China.
| | - Meng Zhou
- School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou P. R. China.
| | - Jie Sun
- School of Biomedical Engineering, Eye Hospital, Wenzhou Medical University, Wenzhou P. R. China.
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Hyblova M, Gnip A, Kucharik M, Budis J, Sekelska M, Minarik G. Maternal Copy Number Imbalances in Non-Invasive Prenatal Testing: Do They Matter? Diagnostics (Basel) 2022; 12:diagnostics12123056. [PMID: 36553064 PMCID: PMC9777446 DOI: 10.3390/diagnostics12123056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Non-invasive prenatal testing (NIPT) has become a routine practice in screening for common aneuploidies of chromosomes 21, 18, and 13 and gonosomes X and Y in fetuses worldwide since 2015 and has even expanded to include smaller subchromosomal events. In fact, the fetal fraction represents only a small proportion of cell-free DNA on a predominant background of maternal DNA. Unlike fetal findings that have to be confirmed using invasive testing, it has been well documented that NIPT provides information on maternal mosaicism, occult malignancies, and hidden health conditions due to copy number variations (CNVs) with diagnostic resolution. Although large duplications or deletions associated with certain medical conditions or syndromes are usually well recognized and easy to interpret, very little is known about small, relatively common copy number variations on the order of a few hundred kilobases and their potential impact on human health. We analyzed data from 6422 NIPT patient samples with a CNV detection resolution of 200 kb for the maternal genome and identified 942 distinct CNVs; 328 occurred repeatedly. We defined them as multiple occurring variants (MOVs). We scrutinized the most common ones, compared them with frequencies in the gnomAD SVs v2.1, dbVar, and DGV population databases, and analyzed them with an emphasis on genomic content and potential association with specific phenotypes.
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Affiliation(s)
- Michaela Hyblova
- Medirex Group Academy n.o., Novozamocka 67, 949 05 Nitra, Slovakia
- Trisomy Test s.r.o., Novozamocka 67, 949 05 Nitra, Slovakia
- Correspondence:
| | - Andrej Gnip
- Medirex a.s., Galvaniho 17/C, 820 16 Bratislava, Slovakia
| | | | - Jaroslav Budis
- Geneton s.r.o., Ilkovicova 8, 841 04 Bratislava, Slovakia
| | - Martina Sekelska
- Medirex Group Academy n.o., Novozamocka 67, 949 05 Nitra, Slovakia
- Trisomy Test s.r.o., Novozamocka 67, 949 05 Nitra, Slovakia
| | - Gabriel Minarik
- Medirex Group Academy n.o., Novozamocka 67, 949 05 Nitra, Slovakia
- Trisomy Test s.r.o., Novozamocka 67, 949 05 Nitra, Slovakia
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Li Q, Zhu X, Wang C, Meng J, Chen D, Kong X. Identification of a Rare Case With Nagashima-Type Palmoplantar Keratoderma and 18q Deletion Syndrome via Exome Sequencing and Low-Coverage Whole-Genome Sequencing. Front Genet 2021; 12:707411. [PMID: 34616427 PMCID: PMC8488357 DOI: 10.3389/fgene.2021.707411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/16/2021] [Indexed: 11/13/2022] Open
Abstract
Nagashima-type palmoplantar keratoderma (NPPK) is characterized by non-progressive, diffuse, and cross-gradient hyperkeratosis caused by mutations in the SERPINB7 gene on chromosome 18q21.33. Chromosome 18q deletion syndrome (18q- syndrome) is a terminal deletion or microdeletion syndrome characterized by intellectual disability and congenital malformations. This paper describes an 18-year-old man with palmoplantar keratoderma and diffuse white matter abnormalities in the brain. Trio-based exome sequencing (ES) revealed a suspected mosaic compound heterozygous mutation for c.796C>T (p.Arg266∗) in exon 8 inherited from the mother and a de novo exons 4–6 deletion of SERPINB7. Additional copy number variant (CNV) analysis of the ES data indicated a heterozygous gross deletion of 18q22.3-q23. The two SERPINB7 gene variants were verified by Sanger sequencing and quantitative real-time polymerase chain reaction (qRT-PCR). Finally, low-coverage whole-genome sequencing (WGS) confirmed the 18q22.3-q23 deletion and additionally detected a mosaic 18q21.33-q22.3 deletion, together explaining NPPK and the neurological phenotypes of the proband. The gross deletion of all exons of SERPINB7 was revealed for the first time. More rarely, c.796C>T (p.Arg266∗) was likely to be mosaic, while the exon deletion was mosaic. In conclusion, the combination of multiple molecular genetic testing methods provides comprehensive informative molecular findings and promotes the diagnosis of complex diseases, as in this case.
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Affiliation(s)
- Qianqian Li
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaofan Zhu
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Conghui Wang
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jingjing Meng
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Duo Chen
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangdong Kong
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Yang Z, Slone J, Wang X, Zhan J, Huang Y, Namjou B, Kaufman KM, Pauciulo M, Harley JB, Muglia LJ, Chepelev I, Huang T. Validation of low-coverage whole-genome sequencing for mitochondrial DNA variants suggests mitochondrial DNA as a genetic cause of preterm birth. Hum Mutat 2021; 42:1602-1614. [PMID: 34467602 PMCID: PMC9290920 DOI: 10.1002/humu.24279] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/17/2021] [Accepted: 08/29/2021] [Indexed: 01/06/2023]
Abstract
Preterm birth (PTB), or birth that occurs earlier than 37 weeks of gestational age, is a major contributor to infant mortality and neonatal hospitalization. Mutations in the mitochondrial genome (mtDNA) have been linked to various rare mitochondrial disorders and may be a contributing factor in PTB given that maternal genetic factors have been strongly linked to PTB. However, to date, no study has found a conclusive connection between a particular mtDNA variant and PTB. Given the high mtDNA copy number per cell, an automated pipeline was developed for detecting mtDNA variants using low‐coverage whole‐genome sequencing (lcWGS) data. The pipeline was first validated against samples of known heteroplasmy, and then applied to 929 samples from a PTB cohort from diverse ethnic backgrounds with an average gestational age of 27.18 weeks (range: 21–30). Our new pipeline successfully identified haplogroups and a large number of mtDNA variants in this large PTB cohort, including 8 samples carrying known pathogenic variants and 47 samples carrying rare mtDNA variants. These results confirm that lcWGS can be utilized to reliably identify mtDNA variants. These mtDNA variants may make a contribution toward preterm birth in a small proportion of live births.
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Affiliation(s)
- Zeyu Yang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Jesse Slone
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Xinjian Wang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Jack Zhan
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Yongbo Huang
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Kenneth M Kaufman
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Michael Pauciulo
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Louis J Muglia
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Burroughs Wellcome Fund, Research Triangle Park, North Carolina, USA
| | - Iouri Chepelev
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Taosheng Huang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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Maass KK, Schad PS, Finster AME, Puranachot P, Rosing F, Wedig T, Schwarz N, Stumpf N, Pfister SM, Pajtler KW. From Sampling to Sequencing: A Liquid Biopsy Pre-Analytic Workflow to Maximize Multi-Layer Genomic Information from a Single Tube. Cancers (Basel) 2021; 13:3002. [PMID: 34203921 DOI: 10.3390/cancers13123002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/03/2021] [Accepted: 06/09/2021] [Indexed: 01/09/2023] Open
Abstract
Simple Summary Liquid biopsies seek to isolate tumor derived genetic material that circulates in blood plasma or cerebrospinal fluid. The less-invasive character of liquid biopsies combined with the option for serial analyses bears enormous potential for treatment monitoring or surveillance. We aimed to establish robust sampling protocols and pre-analytical workflows to allow for site independent multi-layer liquid biopsy testing. For an optimal usage of precious material, we explored sample stabilization in various conservation tubes and describe a protocol for the parallel isolation of cell-free DNA and RNA. Quantification and quality control steps were optimized for minimal sample use with both high sensitivity and reproducibility. We provide detailed step-by-step information on how to i) choose the best-suited protocol and ii) implement this in the liquid biopsy workflow. We believe that our study has potential to increase comparability of liquid biopsy approaches to bring these one step closer to routine clinical application. Abstract Liquid biopsies hold great promise for the management of cancer. Reliable liquid biopsy data depend on stable and reproducible pre-analytical protocols that comply with quality measures, irrespective of the sampling and processing site. We established a workflow for plasma preservation, followed by processing, cell-free nucleic acid isolation, quantification, and enrichment of potentially tumor-derived cell-free DNA and RNA. Employing the same input material for a direct comparison of different kits and protocols allowed us to formulate unbiased recommendations for sample collection, storage, and processing. The presented workflow integrates the stabilization in Norgen, PAX, or Streck tubes and subsequent parallel isolation of cell-free DNA and RNA with NucleoSnap and NucleoSpin. Qubit, Bioanalyzer, and TapeStation quantification and quality control steps were optimized for minimal sample use and high sensitivity and reproducibility. We show the efficiency of the proposed workflow by successful droplet digital PCR amplification of both cell-free DNA and RNA and by detection of tumor-specific alterations in low-coverage whole-genome sequencing and DNA methylation profiling of plasma-derived cell-free DNA. For the first time, we demonstrated successful parallel extraction of cell-free DNA and RNA from plasma samples. This workflow paves the road towards multi-layer genomic analysis from one single liquid biopsy sample.
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Abstract
Eusociality is a highly conspicuous and ecologically impactful behavioral syndrome that has evolved independently across multiple animal lineages. So far, comparative genomic analyses of advanced sociality have been mostly limited to insects. Here, we study the only clade of animals known to exhibit eusociality in the marine realm-lineages of socially diverse snapping shrimps in the genus Synalpheus. To investigate the molecular impact of sociality, we assembled the mitochondrial genomes of eight Synalpheus species that represent three independent origins of eusociality and analyzed patterns of molecular evolution in protein-coding genes. Synonymous substitution rates are lower and potential signals of relaxed purifying selection are higher in eusocial relative to noneusocial taxa. Our results suggest that mitochondrial genome evolution was shaped by eusociality-linked traits-extended generation times and reduced effective population sizes that are hallmarks of advanced animal societies. This is the first direct evidence of eusociality impacting genome evolution in marine taxa. Our results also strongly support the idea that eusociality can shape genome evolution through profound changes in life history and demography.
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Affiliation(s)
- Solomon T C Chak
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ
- Department of Biological Sciences, SUNY College at Old Westbury, Old Westbury, NY
| | - Juan Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC
- Smithsonian Institution, Smithsonian Marine Station at Fort Pierce, Fort Pierce, FL
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
| | - Phillip Barden
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY
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Xu C, Guo Z, Zhang J, Lu Q, Tian Q, Liu S, Li K, Wang K, Tao Z, Li C, Lv Z, Zhang Z, Yang X, Yang F. Non-invasive prediction of fetal growth restriction by whole-genome promoter profiling of maternal plasma DNA: a nested case-control study. BJOG 2020; 128:458-466. [PMID: 32364311 PMCID: PMC7818264 DOI: 10.1111/1471-0528.16292] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2020] [Indexed: 11/28/2022]
Abstract
Objective To predict fetal growth restriction (FGR) by whole‐genome promoter profiling of maternal plasma. Design Nested case–control study. Setting Hospital‐based. Population or Sample 810 pregnancies: 162 FGR cases and 648 controls. Methods We identified gene promoters with a nucleosome footprint that differed between FGR cases and controls based on maternal plasma cell‐free DNA (cfDNA) nucleosome profiling. Optimal classifiers were developed using support vector machine (SVM) and logistic regression (LR) models. Main outcome measures Genes with differential coverages in promoter regions through the low‐coverage whole‐genome sequencing data analysis among FGR cases and controls. Receiver operating characteristic (ROC) analysis (area under the curve [AUC], accuracy, sensitivity and specificity) was used to evaluate the performance of classifiers. Results Through the low‐coverage whole‐genome sequencing data analysis of FGR cases and controls, genes with significantly differential DNA coverage at promoter regions (−1000 to +1000 bp of transcription start sites) were identified. The non‐invasive ‘FGR classifier 1’ (CFGR1) had the highest classification performance (AUC, 0.803; 95% CI 0.767–0.839; accuracy, 83.2%) was developed based on 14 genes with differential promoter coverage using a support vector machine. Conclusions A promising FGR prediction method was successfully developed for assessing the risk of FGR at an early gestational age based on maternal plasma cfDNA nucleosome profiling. Tweetable abstract A promising FGR prediction method was successfully developed, based on maternal plasma cfDNA nucleosome profiling. A promising FGR prediction method was successfully developed, based on maternal plasma cfDNA nucleosome profiling.
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Affiliation(s)
- C Xu
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.,Department of Obstetrics and Gynaecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Z Guo
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - J Zhang
- Department of Obstetrics and Gynaecology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Q Lu
- Department of Obstetrics and Gynaecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Q Tian
- Department of Obstetrics and Gynaecology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - S Liu
- Department of Obstetrics and Gynaecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - K Li
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - K Wang
- Department of Obstetrics and Gynaecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Z Tao
- Department of Obstetrics and Gynaecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - C Li
- Department of Obstetrics and Gynaecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Z Lv
- Department of Pathology, Cangzhou People's Hospital, Cangzhou, China.,Department of Pharmacy, Cangzhou People's Hospital, Cangzhou, China
| | - Z Zhang
- Department of Pathology, Cangzhou People's Hospital, Cangzhou, China.,Department of Pharmacy, Cangzhou People's Hospital, Cangzhou, China
| | - X Yang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - F Yang
- Department of Obstetrics and Gynaecology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Zhujiang Hospital, Southern Medical University, Guangzhou, China
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10
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Sekelska M, Izsakova A, Kubosova K, Tilandyova P, Csekes E, Kuchova Z, Hyblova M, Harsanyova M, Kucharik M, Budis J, Szemes T, Minarik G. Result of Prospective Validation of the Trisomy Test ® for the Detection of Chromosomal Trisomies. Diagnostics (Basel) 2019; 9:E138. [PMID: 31581694 PMCID: PMC6963324 DOI: 10.3390/diagnostics9040138] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 01/28/2023] Open
Abstract
Noninvasive prenatal testing (NIPT) is one of the most common prenatal screening tests used worldwide. Trisomy Test® belongs to NIPT tests based on low-coverage whole-genome sequencing. In our prospective study, 7279 samples of pregnant women collected during approximately two years were analyzed. In this cohort, 117 positive cases for trisomies 21, 18, and 13 were reported. An in-house designed bioinformatic pipeline and proprietary biostatistical approach was used for the detection of trisomies. The pooled sensitivity and specificity of our test reached 99.12% and 99.94%, respectively. The proportion of repeatedly uninformative results after repeated blood draws was 1.11%. Based on the presented results, we can confirm that the Trisomy Test® is fully comparable with other commercial NIPT tests available worldwide.
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Affiliation(s)
- Martina Sekelska
- Trisomy Test Ltd., Ilkovičova 8, 841 04 Bratislava, Slovakia; (A.I.); (K.K.); (P.T.); (E.C.); (Z.K.); (M.H.); (G.M.)
- Medirex Inc., Galvaniho 17/C, 821 06 Bratislava, Slovakia
| | - Anita Izsakova
- Trisomy Test Ltd., Ilkovičova 8, 841 04 Bratislava, Slovakia; (A.I.); (K.K.); (P.T.); (E.C.); (Z.K.); (M.H.); (G.M.)
- Medirex Inc., Galvaniho 17/C, 821 06 Bratislava, Slovakia
| | - Katarina Kubosova
- Trisomy Test Ltd., Ilkovičova 8, 841 04 Bratislava, Slovakia; (A.I.); (K.K.); (P.T.); (E.C.); (Z.K.); (M.H.); (G.M.)
- Medirex Inc., Galvaniho 17/C, 821 06 Bratislava, Slovakia
| | - Petra Tilandyova
- Trisomy Test Ltd., Ilkovičova 8, 841 04 Bratislava, Slovakia; (A.I.); (K.K.); (P.T.); (E.C.); (Z.K.); (M.H.); (G.M.)
- Medirex Inc., Galvaniho 17/C, 821 06 Bratislava, Slovakia
| | - Erika Csekes
- Trisomy Test Ltd., Ilkovičova 8, 841 04 Bratislava, Slovakia; (A.I.); (K.K.); (P.T.); (E.C.); (Z.K.); (M.H.); (G.M.)
- Medirex Inc., Galvaniho 17/C, 821 06 Bratislava, Slovakia
| | - Zaneta Kuchova
- Trisomy Test Ltd., Ilkovičova 8, 841 04 Bratislava, Slovakia; (A.I.); (K.K.); (P.T.); (E.C.); (Z.K.); (M.H.); (G.M.)
- Medirex Inc., Galvaniho 17/C, 821 06 Bratislava, Slovakia
| | - Michaela Hyblova
- Trisomy Test Ltd., Ilkovičova 8, 841 04 Bratislava, Slovakia; (A.I.); (K.K.); (P.T.); (E.C.); (Z.K.); (M.H.); (G.M.)
- Medirex Inc., Galvaniho 17/C, 821 06 Bratislava, Slovakia
| | - Maria Harsanyova
- Geneton Ltd., Galvaniho 7, 821 06 Bratislava, Slovakia; (M.H.); (M.K.); (J.B.); (T.S.)
| | - Marcel Kucharik
- Geneton Ltd., Galvaniho 7, 821 06 Bratislava, Slovakia; (M.H.); (M.K.); (J.B.); (T.S.)
| | - Jaroslav Budis
- Geneton Ltd., Galvaniho 7, 821 06 Bratislava, Slovakia; (M.H.); (M.K.); (J.B.); (T.S.)
| | - Tomas Szemes
- Geneton Ltd., Galvaniho 7, 821 06 Bratislava, Slovakia; (M.H.); (M.K.); (J.B.); (T.S.)
| | - Gabriel Minarik
- Trisomy Test Ltd., Ilkovičova 8, 841 04 Bratislava, Slovakia; (A.I.); (K.K.); (P.T.); (E.C.); (Z.K.); (M.H.); (G.M.)
- Medirex Inc., Galvaniho 17/C, 821 06 Bratislava, Slovakia
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11
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Zhang X, Mizukoshi M, Zhang H, Tan E, Igarashi Y, Suzuki Y, Mitsuyama S, Kinoshita S, Saito K, Watabe S, Asakawa S. Ultrahigh-Density Linkage Map Construction Using Low-Coverage Whole-Genome Sequencing of a Doubled Haploid Population: Case Study of Torafugu (Takifugu rubripes). Genes (Basel) 2018; 9:genes9030120. [PMID: 29495372 PMCID: PMC5867841 DOI: 10.3390/genes9030120] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/15/2018] [Accepted: 02/20/2018] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing enables genome-wide genotyping of a large population and further facilitates the construction of a genetic linkage map. Low-coverage whole-genome sequencing has been employed for genetic linkage map construction in several species. However, this strategy generally requires available high-quality reference genomes and/or designed inbred pedigree lines, which restrict the scope of application for non-model and unsequenced species. Here, using torafugu (Takifugu rubripes) as a test model, we propose a new strategy for ultrahigh-density genetic linkage map construction using low-coverage whole-genome sequencing of a haploid/doubled haploid (H/DH) population without above requirements. Low-coverage (≈1×) whole-genome sequencing data of 165 DH individuals were used for de novo assembly and further performed single nucleotide polymorphisms (SNPs) calling, resulting in the identification of 1,070,601 SNPs. Based on SNP genotypes and de novo assembly, genotypes were associated with short DNA segments and an ultrahigh-density linkage map was constructed containing information of 802,277 SNPs in 3090 unique positions. Comparative analyses showed near-perfect concordance between the present linkage map and the latest published torafugu genome (FUGU5). This strategy would facilitate ultrahigh-density linkage map construction in various sexually reproducing organisms for which H/DH populations can be generated.
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Affiliation(s)
- Xiang Zhang
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
| | - Misaki Mizukoshi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
| | - Hong Zhang
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
| | - Engkong Tan
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
| | - Yoji Igarashi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.
| | - Susumu Mitsuyama
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
| | - Shigeharu Kinoshita
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
| | - Kazuyoshi Saito
- Akita Prefectural Fisheries Promotion Center, Oga, Akita 010-0531, Japan.
| | - Shugo Watabe
- School of Marine Bioscience, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan.
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
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