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Chen H, Wang B, Cai L, Yang X, Hu Y, Zhang Y, Leng X, Liu W, Fan D, Niu B, Zhou Q. A comprehensive performance evaluation, comparison, and integration of computational methods for detecting and estimating cross-contamination of human samples in cancer next-generation sequencing analysis. J Biomed Inform 2024; 152:104625. [PMID: 38479675 DOI: 10.1016/j.jbi.2024.104625] [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: 01/16/2024] [Revised: 02/25/2024] [Accepted: 03/10/2024] [Indexed: 03/17/2024]
Abstract
Cross-sample contamination is one of the major issues in next-generation sequencing (NGS)-based molecular assays. This type of contamination, even at very low levels, can significantly impact the results of an analysis, especially in the detection of somatic alterations in tumor samples. Several contamination identification tools have been developed and implemented as a crucial quality-control step in the routine NGS bioinformatic pipeline. However, no study has been published to comprehensively and systematically investigate, evaluate, and compare these computational methods in the cancer NGS analysis. In this study, we comprehensively investigated nine state-of-the-art computational methods for detecting cross-sample contamination. To explore their application in cancer NGS analysis, we further compared the performance of five representative tools by qualitative and quantitative analyses using in silico and simulated experimental NGS data. The results showed that Conpair achieved the best performance for identifying contamination and predicting the level of contamination in solid tumors NGS analysis. Moreover, based on Conpair, we developed a Python script, Contamination Source Predictor (ConSPr), to identify the source of contamination. We anticipate that this comprehensive survey and the proposed tool for predicting the source of contamination will assist researchers in selecting appropriate cross-contamination detection tools in cancer NGS analysis and inspire the development of computational methods for detecting sample cross-contamination and identifying its source in the future.
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Affiliation(s)
- Huijuan Chen
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing 100176, China; Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China; WillingMed Technology Beijing Co. Ltd., Beijing 100176, China
| | - Bing Wang
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing 100176, China
| | - Lili Cai
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing 100176, China
| | - Xiaotian Yang
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing 100176, China
| | - Yali Hu
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing 100176, China
| | - Yiran Zhang
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing 100176, China
| | - Xue Leng
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing 100176, China
| | - Wen Liu
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing 100176, China
| | - Dongjie Fan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Beifang Niu
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing 100176, China; Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China; ChosenMed Technology (Zhejiang) Co. Ltd., Zhejiang 311103, China.
| | - Qiming Zhou
- Beijing ChosenMed Clinical Laboratory Co. Ltd., Beijing 100176, China; ChosenMed Technology (Zhejiang) Co. Ltd., Zhejiang 311103, China.
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2
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Moss S, Pretorius E, Ceesay S, Hutchins H, da Silva ET, Ndiath MO, Jones RT, Vasileva H, Phelan J, Acford-Palmer H, Collins E, Rodrigues A, Krishna S, Clark TG, Last A, Campino S. Genomic surveillance of Anopheles mosquitoes on the Bijagós Archipelago using custom targeted amplicon sequencing identifies mutations associated with insecticide resistance. Parasit Vectors 2024; 17:10. [PMID: 38178249 PMCID: PMC10768400 DOI: 10.1186/s13071-023-06085-5] [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: 06/28/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Insecticide resistance is reducing the efficacy of vector control interventions, consequently threatening efforts to control vector-borne diseases, including malaria. Investigating the prevalence of molecular markers of resistance is a useful tool for monitoring the spread of insecticide resistance in disease vectors. The Bijagós Archipelago (Bijagós) in Guinea-Bissau is a region of stable malaria transmission where insecticide-treated nets are the mainstay for malaria control. However, the prevalence of molecular markers of insecticide resistance in malaria vectors is not well understood. METHODS A total of 214 Anopheles mosquitoes were analysed from 13 islands across the Bijagós. These mosquitoes were collected using CDC light traps in November 2019, during the peak malaria transmission season. High-throughput multiplex amplicon sequencing was used to investigate the prevalence of 17 different molecular markers associated with insecticide resistance in four genes: vgsc, rdl, ace1 and gste2. RESULTS Of the 17 screened mutations, four were identified in mosquitoes from the Bijagós: vgsc L995F (12.2%), N1570Y (6.2%) and A1746S (0.7%) and rdl A269G (1.1%). This study is the first to report the L995F knock-down resistance (kdr)-west allele in Anopheles melas on the Archipelago. An additional eight non-synonymous single-nucleotide polymorphisms were identified across the four genes which have not been described previously. The prevalences of the vgsc L995F and N1570Y mutations were higher on Bubaque Island than on the other islands in this study; Bubaque is the most populous island in the archipelago, with the greatest population mobility and connection to continental Guinea-Bissau. CONCLUSIONS This study provides the first surveillance data for genetic markers present in malaria vectors from islands across the Bijagós Archipelago. Overall prevalence of insecticide resistance mutations was found to be low. However, the identification of the vgsc L995F and N1570Y mutations associated with pyrethroid resistance warrants further monitoring. This is particularly important as the mainstay of malaria control on the islands is the use of pyrethroid insecticide-treated nets.
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Affiliation(s)
- Sophie Moss
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| | - Elizabeth Pretorius
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Sainey Ceesay
- Medical Research Council, The Gambia (MRCG), Fajara, Gambia
| | - Harry Hutchins
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Eunice Teixeira da Silva
- Ministério de Saúde Pública, Bissau, Guinea-Bissau
- Projecto de Saúde Bandim, Bissau, Guinea-Bissau
| | | | - Robert T Jones
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Hristina Vasileva
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Holly Acford-Palmer
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Emma Collins
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Sanjeev Krishna
- Clinical Academic Group, Institute for Infection and Immunity, St. George's University Hospitals NHS Foundation Trust-St. George's University of London, London, UK
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon
- Institut Für Tropenmedizin Universitätsklinikum Tübingen, Tübingen, Germany
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Anna Last
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
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3
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Phelan JE, Turkiewicz A, Manko E, Thorpe J, Vanheer LN, van de Vegte-Bolmer M, Ngoc NTH, Binh NTH, Thieu NQ, Gitaka J, Nolder D, Beshir KB, Dombrowski JG, Di Santi SM, Bousema T, Sutherland CJ, Campino S, Clark TG. Rapid profiling of Plasmodium parasites from genome sequences to assist malaria control. Genome Med 2023; 15:96. [PMID: 37950308 PMCID: PMC10636944 DOI: 10.1186/s13073-023-01247-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 10/13/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Malaria continues to be a major threat to global public health. Whole genome sequencing (WGS) of the underlying Plasmodium parasites has provided insights into the genomic epidemiology of malaria. Genome sequencing is rapidly gaining traction as a diagnostic and surveillance tool for clinical settings, where the profiling of co-infections, identification of imported malaria parasites, and detection of drug resistance are crucial for infection control and disease elimination. To support this informatically, we have developed the Malaria-Profiler tool, which rapidly (within minutes) predicts Plasmodium species, geographical source, and resistance to antimalarial drugs directly from WGS data. RESULTS The online and command line versions of Malaria-Profiler detect ~ 250 markers from genome sequences covering Plasmodium speciation, likely geographical source, and resistance to chloroquine, sulfadoxine-pyrimethamine (SP), and other anti-malarial drugs for P. falciparum, but also providing mutations for orthologous resistance genes in other species. The predictive performance of the mutation library was assessed using 9321 clinical isolates with WGS and geographical data, with most being single-species infections (P. falciparum 7152/7462, P. vivax 1502/1661, P. knowlesi 143/151, P. malariae 18/18, P. ovale ssp. 5/5), but co-infections were identified (456/9321; 4.8%). The accuracy of the predicted geographical profiles was high to both continental (96.1%) and regional levels (94.6%). For P. falciparum, markers were identified for resistance to chloroquine (49.2%; regional range: 24.5% to 100%), sulfadoxine (83.3%; 35.4- 90.5%), pyrimethamine (85.4%; 80.0-100%) and combined SP (77.4%). Markers associated with the partial resistance of artemisinin were found in WGS from isolates sourced from Southeast Asia (30.6%). CONCLUSIONS Malaria-Profiler is a user-friendly tool that can rapidly and accurately predict the geographical regional source and anti-malarial drug resistance profiles across large numbers of samples with WGS data. The software is flexible with modifiable bioinformatic pipelines. For example, it is possible to select the sequencing platform, display specific variants, and customise the format of outputs. With the increasing application of next-generation sequencing platforms on Plasmodium DNA, Malaria-Profiler has the potential to be integrated into point-of-care and surveillance settings, thereby assisting malaria control. Malaria-Profiler is available online (bioinformatics.lshtm.ac.uk/malaria-profiler) and as standalone software ( https://github.com/jodyphelan/malaria-profiler ).
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Affiliation(s)
- Jody E Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK.
| | - Anna Turkiewicz
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK
| | - Emilia Manko
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK
| | - Joseph Thorpe
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK
| | - Leen N Vanheer
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK
| | - Marga van de Vegte-Bolmer
- Department of Medical Microbiology and Radboud Center for Infectious Diseases, Radboud University Medical Center, University of Nijmegen, Nijmegen, The Netherlands
| | - Nguyen Thi Hong Ngoc
- Molecular Biology Department, Parasitology and Entomology, Vietnam National Institute of Malariology, Hanoi, Vietnam
| | - Nguyen Thi Huong Binh
- Molecular Biology Department, Parasitology and Entomology, Vietnam National Institute of Malariology, Hanoi, Vietnam
| | - Nguyen Quang Thieu
- Molecular Biology Department, Parasitology and Entomology, Vietnam National Institute of Malariology, Hanoi, Vietnam
| | - Jesse Gitaka
- Directorate of Research and Innovation, Mount Kenya University, Gen. Kago Rd, Thika, Kenya
| | - Debbie Nolder
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK
- UK Health Security Agency Malaria Reference Laboratory, LSHTM, London, WC1E 7HT, UK
| | - Khalid B Beshir
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK
| | - Jamille G Dombrowski
- Department of Parasitology, Institute of Biomedical Sciences, Univ. of São Paulo, São Paulo, Brazil
| | - Silvia Maria Di Santi
- School of Medicine, Instituto de Medicina Tropical, University of São Paulo, São Paulo, Brazil
| | - Teun Bousema
- Department of Medical Microbiology and Radboud Center for Infectious Diseases, Radboud University Medical Center, University of Nijmegen, Nijmegen, The Netherlands
| | - Colin J Sutherland
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK
- UK Health Security Agency Malaria Reference Laboratory, LSHTM, London, WC1E 7HT, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine (LSHTM), London, WC1E 7HT, UK.
- Faculty of Epidemiology and Population Health, LSHTM, London, WC1E 7HT, UK.
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4
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Acford-Palmer H, Campos M, Bandibabone J, N'Do S, Bantuzeko C, Zawadi B, Walker T, Phelan JE, Messenger LA, Clark TG, Campino S. Detection of insecticide resistance markers in Anopheles funestus from the Democratic Republic of the Congo using a targeted amplicon sequencing panel. Sci Rep 2023; 13:17363. [PMID: 37833354 PMCID: PMC10575962 DOI: 10.1038/s41598-023-44457-0] [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: 08/18/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023] Open
Abstract
Vector control strategies have been successful in reducing the number of malaria cases and deaths globally, but the spread of insecticide resistance represents a significant threat to disease control. Insecticide resistance has been reported across Anopheles (An.) vector populations, including species within the An. funestus group. These mosquitoes are responsible for intense malaria transmission across sub-Saharan Africa, including in the Democratic Republic of the Congo (DRC), a country contributing > 12% of global malaria infections and mortality events. To support the continuous efficacy of vector control strategies, it is essential to monitor insecticide resistance using molecular surveillance tools. In this study, we developed an amplicon sequencing ("Amp-seq") approach targeting An. funestus, and using multiplex PCR, dual index barcoding, and next-generation sequencing for high throughput and low-cost applications. Using our Amp-seq approach, we screened 80 An. funestus field isolates from the DRC across a panel of nine genes with mutations linked to insecticide resistance (ace-1, CYP6P4, CYP6P9a, GSTe2, vgsc, and rdl) and mosquito speciation (cox-1, mtND5, and ITS2). Amongst the 18 non-synonymous mutations detected, was N485I, in the ace-1 gene associated with carbamate resistance. Overall, our panel represents an extendable and much-needed method for the molecular surveillance of insecticide resistance in An. funestus populations.
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Affiliation(s)
- Holly Acford-Palmer
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Monica Campos
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Janvier Bandibabone
- Centre de Recherche en Sciences Naturelles de Lwiro, Sud-Kivu, Democratic Republic of the Congo
| | - Sévérin N'Do
- Médecins Sans Frontières (MSF) OCBA, Barcelona, Spain
- Institut de Recherche en Sciences de La Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Chimanuka Bantuzeko
- Centre de Recherche en Sciences Naturelles de Lwiro, Sud-Kivu, Democratic Republic of the Congo
- Université Officielle de Bukavu (UOB), Bukavu, Democratic Republic of the Congo
| | - Bertin Zawadi
- Centre de Recherche en Sciences Naturelles de Lwiro, Sud-Kivu, Democratic Republic of the Congo
| | - Thomas Walker
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - Jody E Phelan
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Louisa A Messenger
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Department of Environmental and Occupational Health, School of Public Health, University of Nevada, Las Vegas, Las Vegas, USA
| | - Taane G Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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5
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Kristan M, Acford-Palmer H, Campos MO, Collins EL, Phelan J, Portwood NM, Pelloquin B, Clarke S, Lines J, Clark TG, Walker T, Campino S, Messenger LA. Towards environmental detection, quantification, and molecular characterization of Anopheles stephensi and Aedes aegypti from experimental larval breeding sites. Sci Rep 2023; 13:2729. [PMID: 36792622 PMCID: PMC9932160 DOI: 10.1038/s41598-023-29657-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/08/2023] [Indexed: 02/17/2023] Open
Abstract
The invasion and establishment of An. stephensi mosquitoes in the Horn of Africa represents a significant regional threat, which may jeopardise malaria control, particularly in urban areas which were formally free from disease transmission. Novel vector surveillance methods are urgently needed, both agnostic to mosquito larval morphology, and simple to implement at the sampling stage. Using new multiplex TaqMan assays, specifically targeting An. stephensi and Ae. aegypti, we validated the use of environmental DNA (eDNA) for simultaneous vector detection in shared artificial breeding sites. Study findings demonstrated that An. stephensi and Ae. aegypti eDNA deposited by as few as one second instar larva in 1L of water was detectable. Characterization of molecular insecticide resistance mechanisms, using novel amplicon-sequencing panels for both vector species, was possible from eDNA shed by as few as 16-32 s instar larvae in 50 ml of water. An. stephensi eDNA, derived from emergent pupae for 24 h, was remarkably stable, and still detectable ~ 2 weeks later. eDNA surveillance has the potential to be implemented in local endemic communities and at points of country entry, to monitor the spread of invasive vector species. Further studies are required to validate the feasibility of this technique under field conditions.
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Affiliation(s)
- Mojca Kristan
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| | - Holly Acford-Palmer
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Monica Oliveira Campos
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Emma L Collins
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Jody Phelan
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Natalie M Portwood
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Bethanie Pelloquin
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Sian Clarke
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Jo Lines
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Taane G Clark
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Thomas Walker
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - Susana Campino
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Louisa A Messenger
- Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
- Department of Environmental and Occupational Health, School of Public Health, University of Nevada, Las Vegas, NV, USA.
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