Effective application of next-generation sequencing (NGS) approaches in systematics and population genetics: case studies in Eucalyptus and Acacia

2016 ◽  
Vol 29 (3) ◽  
pp. 235 ◽  
Author(s):  
Hugh Cross ◽  
Ed Biffin ◽  
Kor-jent van Dijk ◽  
Andrew Lowe ◽  
Michelle Waycott
Keyword(s):  
Next Generation Sequencing ◽  
Case Studies ◽  
Research Question ◽  
Cost Effective ◽  
Next Generation ◽  
Variable Regions ◽  
Cost Effective Approach ◽  
Next Generation Sequencing Ngs ◽  
Multiple Samples ◽  
Generation Sequencing

Next-generation sequencing (NGS) provides numerous tools for population and systematic studies. These tools are a boon to researchers working with non-model and poorly characterised organisms where little or no genomic resources exist. Several techniques have been developed to subsample the genomes of multiple individuals from related populations and species, so as to discover variable regions. We describe here the use of a modified AFLPseq method that provides a rapid and cost-effective approach to screening variable gene regions (SNPs) for multiple samples. Our method provides an adaptable toolkit for multiple downstream applications, which can be scaled up or down depending on the needs of the research question and budget. Using minor modifications to the protocol, we successfully recovered variable and useful markers that were applied to three case studies examining different scales of biological organisation, namely, from within populations to phylogenetic questions at the genus level and above. The case studies on Acacia and Eucalyptus generated genomic data across multiple taxonomic hierarchies, including demonstrating the detection of Acacia pinguifolia J.M.Black individuals used in restoration and their population origins, regional phylogeography of Acacia pycnantha Benth., and SNP-marker conservatism across some 70million years of divergence among the Myrtaceae.

scholarly journals Applying Next-Generation Sequencing Platforms for Pharmacogenomic Testing in Clinical Practice

2021 ◽  
Vol 12 ◽  
Author(s):  
Alireza Tafazoli ◽  
Henk-Jan Guchelaar ◽  
Wojciech Miltyk ◽  
Adam J. Kretowski ◽  
Jesse J. Swen
Keyword(s):  
Clinical Practice ◽  
Drug Therapy ◽  
Next Generation Sequencing ◽  
Cost Effective ◽  
Genetic Data ◽  
Next Generation ◽  
Cost Effective Approach ◽  
Sequencing Platforms ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Pharmacogenomics (PGx) studies the use of genetic data to optimize drug therapy. Numerous clinical centers have commenced implementing pharmacogenetic tests in clinical routines. Next-generation sequencing (NGS) technologies are emerging as a more comprehensive and time- and cost-effective approach in PGx. This review presents the main considerations for applying NGS in guiding drug treatment in clinical practice. It discusses both the advantages and the challenges of implementing NGS-based tests in PGx. Moreover, the limitations of each NGS platform are revealed, and the solutions for setting up and management of these technologies in clinical practice are addressed.

scholarly journals Combined use of gap-PCR and next-generation sequencing improves thalassaemia carrier screening among premarital adults in China

2020 ◽  
Vol 73 (8) ◽  
pp. 488-492 ◽  
Author(s):  
Jianghong Zhao ◽  
Jia Li ◽  
Qiaohong Lai ◽  
Yanping Yu
Keyword(s):  
Next Generation Sequencing ◽  
Southern China ◽  
Cost Effective ◽  
Carrier Screening ◽  
Lower Sensitivity ◽  
Carrier Rate ◽  
Next Generation ◽  
Cost Effective Method ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AimsThalassaemia is one of the most common genetics disorders in the world, especially in southern China. The aim of the present study was to investigate the feasibility of combining the gap-PCR and next-generation sequencing (NGS) for thalassaemia carrier screening in the Chinese population.MethodsBlood samples were obtained from 944 prepregnancy couples; thalassaemia carrier screening was performed by using a routine haematological method and a combination of gap-PCR and NGS method.ResultsWe found that the α thalassaemia carrier rate was 11% (207/1888); the β thalassaemia carrier rate was 3.7% (70/1888); the composite α thalassaemia and β thalassaemia carrier rate was 0.4% (8/1888). We also identified seven novel mutations, including HBA1: c.412A>G, −50 (G>A), HBB: c.*+129T>A, HBB: c.-64G>C, HBB: c.-180G>C, HBB: c.*+5G>A and HBB: c.-113A>G. By comparing the combined gap-PCR and NGS method, the MCV+MCH and HbA2 detection strategy showed a lower sensitivity of 61.05% (105/172) and a higher missed diagnosis ratio of 38.95% (67/172) for α thalassaemia mutations. The sensitivity was improved with the MCV+MCH and HbA2 detection screen when compared with MCV+MCH detection for β thalassaemia (98.51% vs 85.90%).ConclusionsOur study suggests the combined gap-PCR and NGS method is a cost-effective method for the thalassaemia carrier screening, particularly for the α thalassaemia mutation carriers.

scholarly journals Review of Clinical Next-Generation Sequencing

2017 ◽  
Vol 141 (11) ◽  
pp. 1544-1557 ◽  
Author(s):  
Sophia Yohe ◽  
Bharat Thyagarajan
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Care ◽  
Cost Effective ◽  
Next Generation ◽  
Inherited Disorders ◽  
Academic Center ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

Context.— Next-generation sequencing (NGS) is a technology being used by many laboratories to test for inherited disorders and tumor mutations. This technology is new for many practicing pathologists, who may not be familiar with the uses, methodology, and limitations of NGS. Objective.— To familiarize pathologists with several aspects of NGS, including current and expanding uses; methodology including wet bench aspects, bioinformatics, and interpretation; validation and proficiency; limitations; and issues related to the integration of NGS data into patient care. Data Sources.— The review is based on peer-reviewed literature and personal experience using NGS in a clinical setting at a major academic center. Conclusions.— The clinical applications of NGS will increase as the technology, bioinformatics, and resources evolve to address the limitations and improve quality of results. The challenge for clinical laboratories is to ensure testing is clinically relevant, cost-effective, and can be integrated into clinical care.

scholarly journals Identification and phylogenetic analysis of voltage-gated sodium channel haplotypes in the malaria vector Anopheles sinensis using a high-throughput amplicon sequencing approach

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Ruoyao Ni ◽  
Nian Liu ◽  
Mei Li ◽  
Weiping Qian ◽  
Xinghui Qiu
Keyword(s):  
Next Generation Sequencing ◽  
Sodium Channel ◽  
Phylogenetic Analyses ◽  
Cost Effective ◽  
Amplicon Sequencing ◽  
Anopheles Sinensis ◽  
Next Generation ◽  
Voltage Gated ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Background Anopheles sinensis is a dominant vector for malaria transmission in Asian countries. Voltage-gated sodium channel (VGSC) mutation-mediated knock-down resistance (kdr) has developed in many A. sinensis populations because of intensive and long-term use of pyrethroids. Our previous study showed that multiple mutations at position 1014 of the VGSC were heterogeneously distributed in A. sinensis populations across Sichuan, China. Methods To understand resistance genotypes at the haplotype level and reconstruct the phylogenetic relationship of VGSC haplotypes, a cost-effective next-generation sequencing (NGS)-based amplicon sequencing approach was established to clarify haplotypes containing codon 1014 of the VGSC gene from a total of 446 adults collected in 12 locations of Sichuan, China. Results Nineteen (19) haplotypes were identified, including 11 wild 1014L, 6 resistance 1014F, and 2 resistance 1014C haplotypes. We found that resistance haplotypes of A. sinensis VGSC were widely distributed at frequencies ranging from 3.67 to 92.61%. The frequencies of the 1014C haplotype in the southeast of Sichuan (Luzhou, Guangan, and Suining) were relatively higher than those in other sampling locations. Phylogenetic analyses support that kdr-type mutation at position 1014 is not singly originated and resistance 1014C haplotypes evolve from TTT-encoding 1014F. Conclusions A cost-effective next-generation sequencing (NGS)-based amplicon sequencing approach has been established in this study. The data revealed the patchy distribution of VGSC resistance haplotypes with overall high frequencies in Sichuan, China. Phylogenetic analyses support multiple origins and sequential evolution (1014L → 1014F → 1014C) for kdr-type mutations in A. sinensis. Graphical abstract

scholarly journals Problems of unknown significance: Counseling in the era of next generation sequencing

2018 ◽  
Vol 21 (1) ◽  
pp. 73-76 ◽  
Author(s):  
U Fahrioğlu
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Disorders ◽  
New Technology ◽  
Cost Effective ◽  
Next Generation ◽  
Effective Manner ◽  
Unknown Significance ◽  
Technical Issues ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Dear Editor Next generation sequencing (NGS) has changed the way we approach the diagnosis, prognosis and treatment of genetic disorders. It gave us base pair (bp) precision, multi-gene approach that can be executed in a timely and cost-effective manner. Despite some minor technical issues in NGS, it comes with great advantages. However, the clinical, and especially, genetic counseling profession will need to rise to the challenge to face some of the new issues, dilemmas and problems this new technology is bringing to the table. Some of the counseling guidelines predate the NGS era and will urgently need to be brought up to par with the technology.

scholarly journals Development of a potent and protective germline-like antibody lineage against Zika virus in a convalescent human

2019 ◽  
Author(s):  
Fei Gao ◽  
Xiaohe Lin ◽  
Linling He ◽  
Ruoke Wang ◽  
Han Wang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Zika Virus ◽  
Neutralizing Antibodies ◽  
Great Promise ◽  
Human Antibody ◽  
Next Generation ◽  
Zikv Infection ◽  
Variable Regions ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AbstractZika virus (ZIKV) specific neutralizing antibodies hold a great promise for antibody-based interventions and vaccine design against ZIKV infection. However, their development in infected patients remain unknown. Here, we report on the dynamic development of a potent and protective ZIKV-specific human antibody ZK2B10 initially isolated from a ZIKV convalescent individual using next-generation sequencing (NGS). The unbiased repertoire analysis showed dramatic changes in many families of heavy and light chain variable regions. However, lineage tracing of ZK2B10 revealed limited somatic hypermutation throughout the 12 months since the onset of symptom. In particular, NGS-derived germline-like somatic variants neutralized and protected mice from lethal challenge of ZIKV without detectable cross-reactivity with Dengue virus (DENV). Site-directed mutagenesis identified two residues within λ chain, N31 and S91 that are essential to the functional maturation. The dynamic features unveiled here will assist us to better understand the pathogenesis of ZIKV infection and inform rational design of vaccines.Author summaryRecently emerged ZIKV is associated with severe neurological complications such as Guillain–Barré syndrome in adults and congenital microcephaly in newborns. No ZIKV-specific therapeutics or vaccines are currently available. We and others have identified a number of neutralizing antibodies capable of protecting experimental animals from ZIKV infection. However, the development of these potent antibodies during ZIKV natural infection remains unknown. Here, we report on the longitudinal analysis of one such antibody ZK2B10 using next-generation sequencing (NGS), bioinformatics and functional analysis. We found that the ZK2B10 germline-like antibodies possess strong neutralizing activity in vitro and impressive protectivity against lethal ZIKV infection in vivo. These findings suggest that the potent and protective antibody response against ZIKV can be generated within relative short term with high germline identity which provide great hope and promise for successful vaccine development against ZIKV.

scholarly journals An interlaboratory study of complex variant detection

2017 ◽  
Author(s):  
Stephen E Lincoln ◽  
Justin M Zook ◽  
Shimul Chowdhury ◽  
Shazia Mahamdallie ◽  
Andrew Fellowes ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Validation Studies ◽  
Cost Effective ◽  
Interlaboratory Study ◽  
Next Generation ◽  
Variant Detection ◽  
Synthetic Controls ◽  
Next Generation Sequencing Ngs ◽  
Uniform Assessment ◽  
Generation Sequencing

ABSTRACTNext-generation sequencing (NGS) is widely used and cost-effective. Depending on the specific methods, NGS can have limitations detecting certain technically challenging variant types even though they are both prevalent in patients and medically important. These types are underrepresented in validation studies, hindering the uniform assessment of test methodologies by laboratory directors and clinicians. Specimens containing such variants can be difficult to obtain; thus, we evaluated a novel solution to this problem in which a diverse set of technically challenging variants was synthesized and introduced into a known genomic background. This specimen was sequenced by 7 laboratories using 10 different NGS workflows. The specimen was compatible with all 10 workflows and presented biochemical and bioinformatic challenges similar to those of patient specimens. Only 10 of 22 challenging variants were correctly identified by all 10 workflows, and only 3 workflows detected all 22. Many, but not all, of the sensitivity limitations were bioinformatic in nature. We conclude that Synthetic controls can provide an efficient and informative mechanism to augment studies with technically challenging variants that are difficult to obtain otherwise. Data from such specimens can facilitate inter-laboratory methodologic comparisons and can help establish standards that improve communication between clinicians and laboratories.

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