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Zhang Y, Wymant C, Laeyendecker O, Grabowski MK, Hall M, Hudelson S, Piwowar-Manning E, McCauley M, Gamble T, Hosseinipour MC, Kumarasamy N, Hakim JG, Kumwenda J, Mills LA, Santos BR, Grinsztejn B, Pilotto JH, Chariyalertsak S, Makhema J, Chen YQ, Cohen MS, Fraser C, Eshleman SH. Evaluation of Phylogenetic Methods for Inferring the Direction of Human Immunodeficiency Virus (HIV) Transmission: HIV Prevention Trials Network (HPTN) 052. Clin Infect Dis 2021; 72:30-37. [PMID: 31922537 PMCID: PMC7823077 DOI: 10.1093/cid/ciz1247] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/07/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Phylogenetic analysis can be used to assess human immunodeficiency virus (HIV) transmission in populations. We inferred the direction of HIV transmission using whole-genome HIV sequences from couples with known linked infection and known transmission direction. METHODS Complete next-generation sequencing (NGS) data were obtained for 105 unique index-partner sample pairs from 32 couples enrolled in the HIV Prevention Trials Network (HPTN) 052 study (up to 2 samples/person). Index samples were obtained up to 5.5 years before partner infection; partner samples were obtained near the time of seroconversion. The bioinformatics method, phyloscanner, was used to infer transmission direction. Analyses were performed using samples from individual sample pairs, samples from all couples (1 sample/person; group analysis), and all available samples (multisample group analysis). Analysis was also performed using NGS data from defined regions of the HIV genome (gag, pol, env). RESULTS Using whole-genome NGS data, transmission direction was inferred correctly (index to partner) for 98 of 105 (93.3%) of the individual sample pairs, 99 of 105 (94.3%) sample pairs using group analysis, and 31 of the 32 couples (96.9%) using multisample group analysis. There were no cases where the incorrect transmission direction (partner to index) was inferred. The accuracy of the method was higher with greater time between index and partner sample collection. Pol region sequences performed better than env or gag sequences for inferring transmission direction. CONCLUSIONS We demonstrate the potential of a phylogenetic method to infer the direction of HIV transmission between 2 individuals using whole-genome and pol NGS data.
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Affiliation(s)
- Yinfeng Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chris Wymant
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Oliver Laeyendecker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - M Kathryn Grabowski
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Sarah Hudelson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Estelle Piwowar-Manning
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Marybeth McCauley
- HIV Prevention Trials Network Leadership and Operations Center, FHI, Washington, District of Columbia, USA
| | - Theresa Gamble
- HIV Prevention Trials Network Leadership and Operations Center, FHI, Durham, North Carolina, USA
| | - Mina C Hosseinipour
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- University of North Carolina Project–Malawi, Institute for Global Health and Infectious Diseases, Lilongwe, Malawi
| | - Nagalingeswaran Kumarasamy
- Chennai Antiviral Research and Treatment Clinical Research Site, Infectious Diseases Medical Centre, Voluntary Health Services, Chennai, India
| | - James G Hakim
- Department of Medicine, University of Zimbabwe, Harare, Zimbabwe
| | | | - Lisa A Mills
- US Centers for Disease Control and Prevention, HIV Research Branch, Kisumu, Kenya
| | - Breno R Santos
- Department of Infectious Diseases, Hospital Nossa Senhora da Conceição, Porto Alegre, Brazil
| | - Beatriz Grinsztejn
- Instituto Nacional de Infectologia Evandro Chagas-Fiocruz, Rio de Janeiro, Brazil
| | - Jose H Pilotto
- Hospital Geral de Nova Iguacu and Laboratorio de AIDS e Imunologia Molecular–Instituto Oswaldo Cruz/Fiocruz, Rio de Janeiro, Brazil
| | - Suwat Chariyalertsak
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Joseph Makhema
- Botswana-Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Ying Q Chen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Myron S Cohen
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Susan H Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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2
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Zhan Y, Zhang J, Yao S, Luo G. High-Throughput Two-Dimensional Polymerase Chain Reaction Technology. Anal Chem 2020; 92:674-682. [PMID: 31820952 DOI: 10.1021/acs.analchem.9b02030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polymerase chain reaction (PCR) is a very powerful tool for clinical gene detection. Multiplex PCR especially improves the throughput of this technology. However, it is often necessary to employ techniques such as electrophoresis, mass spectrometry, or sequencing after multiplex PCR amplification for product identification, which requires additional equipment and has high risks of contamination. In this work, we developed a high-throughput two-dimensional (2D) PCR technology that can identify multiple target genes simultaneously in just one closed tube and within a relatively short time by using both fluorescence and the melting temperature (Tm). As an example, a method detecting 9 human papillomavirus (HPV) subtypes and reference genes in a single tube was successfully established using 2D PCR. If designed properly, 2D PCR is believed to have the capability to identify more than 30 genes in one closed tube at a time. This method is particularly suitable for distinguishing microorganisms, single-nucleotide polymorphisms, and the methylation of genes and will be of great help to clinical work.
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Affiliation(s)
- Yuxia Zhan
- Comprehensive Laboratory , The Third Affiliated Hospital of Soochow University , Changzhou , Jiangsu 213003 , China.,Changzhou Key Lab of Individualized Diagnosis and Treatment Associated with High Technology Research , Changzhou , Jiangsu 213003 , China
| | - Jun Zhang
- Comprehensive Laboratory , The Third Affiliated Hospital of Soochow University , Changzhou , Jiangsu 213003 , China.,Changzhou Key Lab of Individualized Diagnosis and Treatment Associated with High Technology Research , Changzhou , Jiangsu 213003 , China
| | - Shuang Yao
- Comprehensive Laboratory , The Third Affiliated Hospital of Soochow University , Changzhou , Jiangsu 213003 , China.,Changzhou Key Lab of Individualized Diagnosis and Treatment Associated with High Technology Research , Changzhou , Jiangsu 213003 , China
| | - Guanghua Luo
- Comprehensive Laboratory , The Third Affiliated Hospital of Soochow University , Changzhou , Jiangsu 213003 , China.,Changzhou Key Lab of Individualized Diagnosis and Treatment Associated with High Technology Research , Changzhou , Jiangsu 213003 , China
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3
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Landi L, Murolo S, Romanazzi G. Detection of 'Candidatus Phytoplasma solani' in roots from Bois noir symptomatic and recovered grapevines. Sci Rep 2019; 9:2013. [PMID: 30765733 PMCID: PMC6375969 DOI: 10.1038/s41598-018-38135-9] [Citation(s) in RCA: 9] [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: 02/23/2018] [Accepted: 12/17/2018] [Indexed: 12/12/2022] Open
Abstract
'Candidatus Phytoplasma solani' is the causal agent of Bois noir (BN) in grapevine (Vitis vinifera). It is usually detected in leaves, where typical disease symptoms are seen. However, little information is available on the presence of this phytoplasma in grapevine roots. Here, we investigated 'Ca. P. solani' in roots collected from 28 symptomatic, 27 recovered and eight asymptomatic grapevine plants. Protocols based on high-resolution melting (HRM) combined with real-time quantitative PCR (qPCR-HRM) and nested-qPCR-HRM were developed to identify 'Ca. P. solani' tuf-type variants with single nucleotide polymorphisms. In all, 21.4% of roots from symptomatic plants were positive to 'Ca. P. solani' using qPCR-HRM, and 60.7% with nested-qPCR HRM. Also, 7.4% of roots from recovered plants were positive using qPCR-HRM, which reached 44.4% using nested-qPCR HRM. These analyses identified tuf-type b1 on 88.2% of the positive samples from symptomatic grapevines, and 66.6% from recovered grapevines, with all other samples identified as tuf-type a. This study reports the presence of 'Ca. P. solani' in the roots of both symptomatic and recovered grapevines. These qPCR-HRM and nested-qPCR-HRM protocols can be applied to increase the sensitivity of detection of, and to simplify and speed up the screening for, 'Ca. P. solani' tuf-types.
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Affiliation(s)
- Lucia Landi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche, I-60131, Ancona, Italy
| | - Sergio Murolo
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche, I-60131, Ancona, Italy
| | - Gianfranco Romanazzi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche, I-60131, Ancona, Italy.
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4
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Li S, Liu SM, Fu HW, Huang JZ, Shu QY. High-resolution melting-based TILLING of γ ray-induced mutations in rice. J Zhejiang Univ Sci B 2018; 19:620-629. [PMID: 30070085 DOI: 10.1631/jzus.b1700414] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Targeting Induced Local Lesions IN Genomes (TILLING) is a reverse genetics strategy for the high-throughput screening of induced mutations. γ radiation, which often induces both insertion/deletion (Indel) and point mutations, has been widely used in mutation induction and crop breeding. The present study aimed to develop a simple, high-throughput TILLING system for screening γ ray-induced mutations using high-resolution melting (HRM) analysis. Pooled rice (Oryza sativa) samples mixed at a 1:7 ratio of Indel mutant to wild-type DNA could be distinguished from the wild-type controls by HRM analysis. Thus, an HRM-TILLING system that analyzes pooled samples of four M2 plants is recommended for screening γ ray-induced mutants in rice. For demonstration, a γ ray-mutagenized M2 rice population (n=4560) was screened for mutations in two genes, OsLCT1 and SPDT, using this HRM-TILLING system. Mutations including one single nucleotide substitution (G→A) and one single nucleotide insertion (A) were identified in OsLCT1, and one trinucleotide (TTC) deletion was identified in SPDT. These mutants can be used in rice breeding and genetic studies, and the findings are of importance for the application of γ ray mutagenesis to the breeding of rice and other seed crops.
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Affiliation(s)
- Shan Li
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China.,Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Song-Mei Liu
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hao-Wei Fu
- Jiaxing Academy of Agricultural Sciences, Jiaxing 314016, China
| | - Jian-Zhong Huang
- Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou 310029, China
| | - Qing-Yao Shu
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou 310058, China.,Hubei Collaborative Innovation Center for Grain Industry, Jingzhou 434025, China
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5
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Słomka M, Sobalska-Kwapis M, Wachulec M, Bartosz G, Strapagiel D. High Resolution Melting (HRM) for High-Throughput Genotyping-Limitations and Caveats in Practical Case Studies. Int J Mol Sci 2017; 18:ijms18112316. [PMID: 29099791 PMCID: PMC5713285 DOI: 10.3390/ijms18112316] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/06/2017] [Accepted: 10/31/2017] [Indexed: 01/02/2023] Open
Abstract
High resolution melting (HRM) is a convenient method for gene scanning as well as genotyping of individual and multiple single nucleotide polymorphisms (SNPs). This rapid, simple, closed-tube, homogenous, and cost-efficient approach has the capacity for high specificity and sensitivity, while allowing easy transition to high-throughput scale. In this paper, we provide examples from our laboratory practice of some problematic issues which can affect the performance and data analysis of HRM results, especially with regard to reference curve-based targeted genotyping. We present those examples in order of the typical experimental workflow, and discuss the crucial significance of the respective experimental errors and limitations for the quality and analysis of results. The experimental details which have a decisive impact on correct execution of a HRM genotyping experiment include type and quality of DNA source material, reproducibility of isolation method and template DNA preparation, primer and amplicon design, automation-derived preparation and pipetting inconsistencies, as well as physical limitations in melting curve distinction for alternative variants and careful selection of samples for validation by sequencing. We provide a case-by-case analysis and discussion of actual problems we encountered and solutions that should be taken into account by researchers newly attempting HRM genotyping, especially in a high-throughput setup.
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Affiliation(s)
- Marcin Słomka
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pilarskiego 14/16, 90-231 Łódź, Poland.
- BBMRI.pl Consortium, 54-066 Wrocław, Poland.
| | - Marta Sobalska-Kwapis
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pilarskiego 14/16, 90-231 Łódź, Poland.
- BBMRI.pl Consortium, 54-066 Wrocław, Poland.
| | - Monika Wachulec
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236 Łódź, Poland.
| | - Grzegorz Bartosz
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236 Łódź, Poland.
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pilarskiego 14/16, 90-231 Łódź, Poland.
- BBMRI.pl Consortium, 54-066 Wrocław, Poland.
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6
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Palumbo PJ, Wilson EA, Piwowar-Manning E, McCauley M, Gamble T, Kumwenda N, Makhema J, Kumarasamy N, Chariyalertsak S, Hakim JG, Hosseinipour MC, Melo MG, Godbole SV, Pilotto JH, Grinsztejn B, Panchia R, Chen YQ, Cohen MS, Eshleman SH, Fogel JM. Association of HIV diversity and virologic outcomes in early antiretroviral treatment: HPTN 052. PLoS One 2017; 12:e0177281. [PMID: 28481902 PMCID: PMC5421787 DOI: 10.1371/journal.pone.0177281] [Citation(s) in RCA: 2] [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: 12/08/2016] [Accepted: 04/24/2017] [Indexed: 11/19/2022] Open
Abstract
Higher HIV diversity has been associated with virologic outcomes in children on antiretroviral treatment (ART). We examined the association of HIV diversity with virologic outcomes in adults from the HPTN 052 trial who initiated ART at CD4 cell counts of 350-550 cells/mm3. A high resolution melting (HRM) assay was used to analyze baseline (pre-treatment) HIV diversity in six regions in the HIV genome (two in gag, one in pol, and three in env) from 95 participants who failed ART. We analyzed the association of HIV diversity in each genomic region with baseline (pre-treatment) factors and three clinical outcomes: time to virologic suppression after ART initiation, time to ART failure, and emergence of HIV drug resistance at ART failure. After correcting for multiple comparisons, we did not find any association of baseline HIV diversity with demographic, laboratory, or clinical characteristics. For the 18 analyses performed for clinical outcomes evaluated, there was only one significant association: higher baseline HIV diversity in one of the three HIV env regions was associated with longer time to ART failure (p = 0.008). The HRM diversity assay may be useful in future studies exploring the relationship between HIV diversity and clinical outcomes in individuals with HIV infection.
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Affiliation(s)
- Philip J Palumbo
- Dept. of Pathology, Johns Hopkins Univ. School of Medicine, Baltimore, Maryland, United States of America
| | - Ethan A Wilson
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Estelle Piwowar-Manning
- Dept. of Pathology, Johns Hopkins Univ. School of Medicine, Baltimore, Maryland, United States of America
| | - Marybeth McCauley
- Science Facilitation Department, FHI 360, Washington DC, United States of America
| | - Theresa Gamble
- Science Facilitation Department, FHI 360, Durham, North Carolina, United States of America
| | | | - Joseph Makhema
- Botswana-Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | - Suwat Chariyalertsak
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - James G Hakim
- Dept. of Medicine, Univ. of Zimbabwe, Harare, Zimbabwe
| | - Mina C Hosseinipour
- Division of Infectious Diseases, Univ. of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC Project-Malawi, Institute for Global Health and Infectious Diseases, Lilongwe, Malawi
| | - Marineide G Melo
- Hospital Nossa Senhora da Conceição, Serviço de Infectologia, Porto Alegre, Brazil
| | | | - Jose H Pilotto
- Hospital Geral de Nova Iguacu and Laboratorio de AIDS e Imunologia Molecular-IOC/Fiocruz, Rio de Janeiro, Brazil
| | - Beatriz Grinsztejn
- Instituto Nacional de Infectologia Evandro Chagas-INI-Fiocruz, Rio de Janeiro, Brazil
| | - Ravindre Panchia
- Univ. of the Witwatersrand, Perinatal HIV Research Unit, Soweto HPTN CRS, Soweto, South Africa
| | - Ying Q Chen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Myron S Cohen
- Dept. of Medicine, Univ. of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Susan H Eshleman
- Dept. of Pathology, Johns Hopkins Univ. School of Medicine, Baltimore, Maryland, United States of America
| | - Jessica M Fogel
- Dept. of Pathology, Johns Hopkins Univ. School of Medicine, Baltimore, Maryland, United States of America
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7
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Analysis of HIV Diversity in HIV-Infected Black Men Who Have Sex with Men (HPTN 061). PLoS One 2016; 11:e0167629. [PMID: 27936098 PMCID: PMC5147928 DOI: 10.1371/journal.pone.0167629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/17/2016] [Indexed: 01/01/2023] Open
Abstract
Background HIV populations often diversify in response to selective pressures, such as the immune response and antiretroviral drug use. We analyzed HIV diversity in Black men who have sex with men who were enrolled in the HIV Prevention Trials Network 061 study. Methods A high resolution melting (HRM) diversity assay was used to measure diversity in six regions of the HIV genome: two in gag, one in pol, and three in env. HIV diversity was analyzed for 146 men who were HIV infected at study enrollment, including three with acute infection and 13 with recent infection (identified using a multi-assay algorithm), and for 21 men who seroconverted during the study. HIV diversification was analyzed in a paired analysis for 62 HIV-infected men using plasma samples from the enrollment and 12-month (end of study) visits. Results Men with acute or recent infection at enrollment and seroconverters had lower median HRM scores (lower HIV diversity) than men with non-recent infection in all six regions analyzed. In univariate analyses, younger age, higher CD4 cell count, and HIV drug resistance were associated with lower median HRM scores in multiple regions; ARV drug detection was marginally associated with lower diversity in the pol region. In multivariate analysis, acute or recent infection (all six regions) and HIV drug resistance (both gag regions) were associated with lower median HRM scores. Diversification in the pol region over 12 months was greater for men with acute or recent infection, higher CD4 cell count, and lower HIV viral load at study enrollment. Conclusions HIV diversity was significantly associated with duration of HIV infection, and lower gag diversity was observed in men who had HIV drug resistance. HIV pol diversification was more pronounced in men with acute or recent infection, higher CD4 cell count, and lower HIV viral load.
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8
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High-resolution melting (HRM) re-analysis of a polyposis patients cohort reveals previously undetected heterozygous and mosaic APC gene mutations. Fam Cancer 2016; 14:247-57. [PMID: 25604157 PMCID: PMC4430602 DOI: 10.1007/s10689-015-9780-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Familial adenomatous polyposis is most frequently caused by pathogenic variants in either the APC gene or the MUTYH gene. The detection rate of pathogenic variants depends on the severity of the phenotype and sensitivity of the screening method, including sensitivity for mosaic variants. For 171 patients with multiple colorectal polyps without previously detectable pathogenic variant, APC was reanalyzed in leukocyte DNA by one uniform technique: high-resolution melting (HRM) analysis. Serial dilution of heterozygous DNA resulted in a lowest detectable allelic fraction of 6 % for the majority of variants. HRM analysis and subsequent sequencing detected pathogenic fully heterozygous APC variants in 10 (6 %) of the patients and pathogenic mosaic variants in 2 (1 %). All these variants were previously missed by various conventional scanning methods. In parallel, HRM APC scanning was applied to DNA isolated from polyp tissue of two additional patients with apparently sporadic polyposis and without detectable pathogenic APC variant in leukocyte DNA. In both patients a pathogenic mosaic APC variant was present in multiple polyps. The detection of pathogenic APC variants in 7 % of the patients, including mosaics, illustrates the usefulness of a complete APC gene reanalysis of previously tested patients, by a supplementary scanning method. HRM is a sensitive and fast pre-screening method for reliable detection of heterozygous and mosaic variants, which can be applied to leukocyte and polyp derived DNA.
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9
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Fraley SI, Athamanolap P, Masek BJ, Hardick J, Carroll KC, Hsieh YH, Rothman RE, Gaydos CA, Wang TH, Yang S. Nested Machine Learning Facilitates Increased Sequence Content for Large-Scale Automated High Resolution Melt Genotyping. Sci Rep 2016; 6:19218. [PMID: 26778280 PMCID: PMC4726007 DOI: 10.1038/srep19218] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 12/08/2015] [Indexed: 12/31/2022] Open
Abstract
High Resolution Melt (HRM) is a versatile and rapid post-PCR DNA analysis technique primarily used to differentiate sequence variants among only a few short amplicons. We recently developed a one-vs-one support vector machine algorithm (OVO SVM) that enables the use of HRM for identifying numerous short amplicon sequences automatically and reliably. Herein, we set out to maximize the discriminating power of HRM + SVM for a single genetic locus by testing longer amplicons harboring significantly more sequence information. Using universal primers that amplify the hypervariable bacterial 16 S rRNA gene as a model system, we found that long amplicons yield more complex HRM curve shapes. We developed a novel nested OVO SVM approach to take advantage of this feature and achieved 100% accuracy in the identification of 37 clinically relevant bacteria in Leave-One-Out-Cross-Validation. A subset of organisms were independently tested. Those from pure culture were identified with high accuracy, while those tested directly from clinical blood bottles displayed more technical variability and reduced accuracy. Our findings demonstrate that long sequences can be accurately and automatically profiled by HRM with a novel nested SVM approach and suggest that clinical sample testing is feasible with further optimization.
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Affiliation(s)
- Stephanie I Fraley
- Bioengineering, The University of California San Diego, La Jolla, California, 92093, USA.,Emergency Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Pornpat Athamanolap
- Biomedical Engineering, The Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Billie J Masek
- Emergency Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA.,Infectious Disease, Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Justin Hardick
- Emergency Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA.,Infectious Disease, Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Karen C Carroll
- Medical Microbiology, Pathology, The Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Yu-Hsiang Hsieh
- Emergency Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Richard E Rothman
- Emergency Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Charlotte A Gaydos
- Infectious Disease, Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Tza-Huei Wang
- Biomedical Engineering, The Johns Hopkins University, Baltimore, Maryland, 21218, USA.,Mechanical Engineering, The Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Samuel Yang
- Emergency Medicine, Stanford University, Stanford, California, 94305, USA.,Emergency Medicine, The Johns Hopkins University, Baltimore, Maryland, 21218, USA
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10
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Identifying Recent HIV Infections: From Serological Assays to Genomics. Viruses 2015; 7:5508-24. [PMID: 26512688 PMCID: PMC4632395 DOI: 10.3390/v7102887] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 10/12/2015] [Accepted: 10/13/2015] [Indexed: 01/07/2023] Open
Abstract
In this paper, we review serological and molecular based methods to identify HIV infection recency. The accurate identification of recent HIV infection continues to be an important research area and has implications for HIV prevention and treatment interventions. Longitudinal cohorts that follow HIV negative individuals over time are the current gold standard approach, but they are logistically challenging, time consuming and an expensive enterprise. Methods that utilize cross-sectional testing and biomarker information have become an affordable alternative to the longitudinal approach. These methods use well-characterized biological makers to differentiate between recent and established HIV infections. However, recent results have identified a number of limitations in serological based assays that are sensitive to the variability in immune responses modulated by HIV subtypes, viral load and antiretroviral therapy. Molecular methods that explore the dynamics between the timing of infection and viral evolution are now emerging as a promising approach. The combination of serological and molecular methods may provide a good solution to identify recent HIV infection in cross-sectional data. As part of this review, we present the advantages and limitations of serological and molecular based methods and their potential complementary role for the identification of HIV infection recency.
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11
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Mourah S, Denis MG, Narducci FE, Solassol J, Merlin JL, Sabourin JC, Scoazec JY, Ouafik L, Emile JF, Heller R, Souvignet C, Bergougnoux L, Merlio JP. Detection of BRAF V600 mutations in melanoma: evaluation of concordance between the Cobas® 4800 BRAF V600 mutation test and the methods used in French National Cancer Institute (INCa) platforms in a real-life setting. PLoS One 2015; 10:e0120232. [PMID: 25789737 PMCID: PMC4366252 DOI: 10.1371/journal.pone.0120232] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 01/20/2015] [Indexed: 01/01/2023] Open
Abstract
Vemurafenib is approved for the treatment of metastatic melanoma in patients with BRAF V600 mutation. In pivotal clinical trials, BRAF testing has always been done with the approved cobas 4800 BRAF test. In routine practice, several methods are available and are used according to the laboratories usual procedures. A national, multicenter, non-interventional study was conducted with prospective and consecutive collection of tumor samples. A parallel evaluation was performed in routine practice between the cobas 4800 BRAF V600 mutation test and home brew methods (HBMs) of 12 national laboratories, labelled and funded by the French National Cancer Institute (INCa). For 420 melanoma samples tested, the cobas method versus HBM showed a high concordance (93.3%; kappa = 0.86) in BRAF V600 genotyping with similar mutation rates (34.0% versus 35.7%, respectively). Overall, 97.4% and 98.6% of samples gave valid results using the cobas and HBM, respectively. Of the 185 samples strictly fulfilling the cobas guidelines, the concordance rate was even higher (95.7%; kappa = 0.91; 95%CI [0.85; 0.97]). Out of the 420 samples tested, 28 (6.7%) showed discordance between HBM and cobas. This prospective study shows a high concordance rate between the cobas 4800 BRAF V600 test and home brew methods in the routine detection of BRAF V600E mutations.
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Affiliation(s)
- Samia Mourah
- Department of Pharmacology-Genetics, AP-HP, Saint-Louis Hospital, Paris, France
- INSERM UMRS 976 Paris, F-75010, France
- * E-mail:
| | - Marc G. Denis
- Department of Biochemistry, Nantes University Hospital, Nantes, France
| | | | - Jérôme Solassol
- Department of Biology—Pathology, Montpellier University Hospital, Montpellier, France
| | - Jean-Louis Merlin
- Department of Tumor Biology, Alexis Vautrin Center, Vandoeuvre les Nancy, France
| | | | - Jean-Yves Scoazec
- Laboratory of Pathology and Cytopathology, Edouard Herriot Hospital, Lyon, France
- Department of Biology and Pathology, Gustave Roussy Hospital, Villejuif, France
| | - L’Houcine Ouafik
- Department of Cancer Biology, Marseille Nord University Hospital, Marseille, France
| | - Jean-François Emile
- Department of Pathology, Ambroise Paré Hospital, Boulogne-Billancourt, France
| | - Remy Heller
- Department of Microbiology and Molecular Biology, Colmar hospital, Colmar, France
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Discrimination of tiger using a novel high resolution melting (HRM) and multiplex SNP-specific HRM (MSS-HRM) technique. Forensic Sci Int Genet 2014; 13:30-3. [PMID: 25064274 DOI: 10.1016/j.fsigen.2014.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 06/26/2014] [Accepted: 07/01/2014] [Indexed: 11/22/2022]
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13
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Cousins MM, Konikoff J, Sabin D, Khaki L, Longosz AF, Laeyendecker O, Celum C, Buchbinder SP, Seage GR, Kirk GD, Moore RD, Mehta SH, Margolick JB, Brown J, Mayer KH, Kobin BA, Wheeler D, Justman JE, Hodder SL, Quinn TC, Brookmeyer R, Eshleman SH. A comparison of two measures of HIV diversity in multi-assay algorithms for HIV incidence estimation. PLoS One 2014; 9:e101043. [PMID: 24968135 PMCID: PMC4072769 DOI: 10.1371/journal.pone.0101043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 06/03/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Multi-assay algorithms (MAAs) can be used to estimate HIV incidence in cross-sectional surveys. We compared the performance of two MAAs that use HIV diversity as one of four biomarkers for analysis of HIV incidence. METHODS Both MAAs included two serologic assays (LAg-Avidity assay and BioRad-Avidity assay), HIV viral load, and an HIV diversity assay. HIV diversity was quantified using either a high resolution melting (HRM) diversity assay that does not require HIV sequencing (HRM score for a 239 base pair env region) or sequence ambiguity (the percentage of ambiguous bases in a 1,302 base pair pol region). Samples were classified as MAA positive (likely from individuals with recent HIV infection) if they met the criteria for all of the assays in the MAA. The following performance characteristics were assessed: (1) the proportion of samples classified as MAA positive as a function of duration of infection, (2) the mean window period, (3) the shadow (the time period before sample collection that is being assessed by the MAA), and (4) the accuracy of cross-sectional incidence estimates for three cohort studies. RESULTS The proportion of samples classified as MAA positive as a function of duration of infection was nearly identical for the two MAAs. The mean window period was 141 days for the HRM-based MAA and 131 days for the sequence ambiguity-based MAA. The shadows for both MAAs were <1 year. Both MAAs provided cross-sectional HIV incidence estimates that were very similar to longitudinal incidence estimates based on HIV seroconversion. CONCLUSIONS MAAs that include the LAg-Avidity assay, the BioRad-Avidity assay, HIV viral load, and HIV diversity can provide accurate HIV incidence estimates. Sequence ambiguity measures obtained using a commercially-available HIV genotyping system can be used as an alternative to HRM scores in MAAs for cross-sectional HIV incidence estimation.
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Affiliation(s)
- Matthew M. Cousins
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jacob Konikoff
- Department of Biostatistics, School of Public Health, University of California Los Angeles, Los Angeles, California, United States of America
| | - Devin Sabin
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Leila Khaki
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Andrew F. Longosz
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Oliver Laeyendecker
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Connie Celum
- Departments of Global Health and Medicine, University of Washington, Seattle, Washington, United States of America
| | - Susan P. Buchbinder
- Bridge HIV, San Francisco Department of Health, San Francisco, California, United States of America
- Departments of Epidemiology and Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - George R. Seage
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Gregory D. Kirk
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Richard D. Moore
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Shruti H. Mehta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Joseph B. Margolick
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Joelle Brown
- Department of Epidemiology, School of Public Health, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Kenneth H. Mayer
- The Fenway Institute/Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, Massachusetts, United States of America
| | - Beryl A. Kobin
- Laboratory of Infectious Disease Prevention, New York Blood Center, New York, New York, United States of America
| | - Darrell Wheeler
- Graduate School of Social Work, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Jessica E. Justman
- Departments of Epidemiology and Medicine, Columbia University, New York, New York, United States of America
| | - Sally L. Hodder
- Department of Medicine, Division of Infectious Diseases, New Jersey Medical School, Newark, New Jersey, United States of America
| | - Thomas C. Quinn
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Ron Brookmeyer
- Department of Biostatistics, School of Public Health, University of California Los Angeles, Los Angeles, California, United States of America
| | - Susan H. Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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HIV diversity as a biomarker for HIV incidence estimation: including a high-resolution melting diversity assay in a multiassay algorithm. J Clin Microbiol 2013; 52:115-21. [PMID: 24153134 DOI: 10.1128/jcm.02040-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multiassay algorithms (MAAs) can be used to estimate cross-sectional HIV incidence. We previously identified a robust MAA that includes the BED capture enzyme immunoassay (BED-CEIA), the Bio-Rad Avidity assay, viral load, and CD4 cell count. In this report, we evaluated MAAs that include a high-resolution melting (HRM) diversity assay that does not require sequencing. HRM scores were determined for eight regions of the HIV genome (2 in gag, 1 in pol, and 5 in env). The MAAs that were evaluated included the BED-CEIA, the Bio-Rad Avidity assay, viral load, and the HRM diversity assay, using HRM scores from different regions and a range of region-specific HRM diversity assay cutoffs. The performance characteristics based on the proportion of samples that were classified as MAA positive by duration of infection were determined for each MAA, including the mean window period. The cross-sectional incidence estimates obtained using optimized MAAs were compared to longitudinal incidence estimates for three cohorts in the United States. The performance of the HRM-based MAA was nearly identical to that of the MAA that included CD4 cell count. The HRM-based MAA had a mean window period of 154 days and provided cross-sectional incidence estimates that were similar to those based on cohort follow-up. HIV diversity is a useful biomarker for estimating HIV incidence. MAAs that include the HRM diversity assay can provide accurate HIV incidence estimates using stored blood plasma or serum samples without a requirement for CD4 cell count data.
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15
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Boursault L, Haddad V, Vergier B, Cappellen D, Verdon S, Bellocq JP, Jouary T, Merlio JP. Tumor homogeneity between primary and metastatic sites for BRAF status in metastatic melanoma determined by immunohistochemical and molecular testing. PLoS One 2013; 8:e70826. [PMID: 23976959 PMCID: PMC3748080 DOI: 10.1371/journal.pone.0070826] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 06/23/2013] [Indexed: 02/07/2023] Open
Abstract
BRAF inhibitors have demonstrated improvement of overall survival in patients with metastatic melanoma and BRAFV600 mutations. In order to evaluate BRAF tumor heterogeneity between primary and metastatic site, we have evaluated the performance of immunohistochemistry (IHC) with an anti-BRAFV600E antibody in both localization by comparison with high resolution melting analysis followed by Sanger sequencing in a parallel blinded study. A total of 230 samples distributed as primary melanoma (n = 88) and different types of metastatic samples (n = 142) were studied in 99 patients with advanced or metastatic melanoma (stage III or IV). The prevalence of each BRAF mutation was c.1799T>A, BRAFV600E (45.2%), c.1799_1800TG>AA, BRAFV600E2 (3.0%), c.1798_1799GT>AA, BRAFV600K (3.0%), c.1801 A>G, BRAFK601E (1.3%), c.1789_1790CT>TC, BRAFL597S (0.4%), c.1780G>A, BRAFD594N (0.9%) respectively. IHC was positive in 109/112 samples harboring BRAFV600E/E2 mutations and negative in other cases. The cytoplasmic staining was either strongly positive in tumor cells of BRAFV600E mutated cases. It appeared strong brown, different from the vesicular grey cytoplasmic pigmentation of melanophages. Concordance between the two techniques was 96.4%. Sensitivity of IHC for detecting the BRAFV600E/E2 mutations was 97.3%, while specificity was 100%. Both our IHC and molecular study demonstrated homogeneity between primary and metastatic sites for BRAF status in melanoma. This study also provides evidence that IHC may be a cost-effective first-line method for BRAFV600E detection. Thereafter, molecular techniques should be used in negative, ambiguous or non-contributive cases.
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Affiliation(s)
| | - Véronique Haddad
- Tumor Bank and Tumor Biology Laboratory, CHU Bordeaux, Pessac, France
| | | | - David Cappellen
- Tumor Bank and Tumor Biology Laboratory, CHU Bordeaux, Pessac, France
| | - Severine Verdon
- Tumor Bank and Tumor Biology Laboratory, CHU Bordeaux, Pessac, France
| | | | - Thomas Jouary
- Department of Dermatology, CHU Bordeaux, Bordeaux, France
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16
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Cousins MM, Swan D, Magaret CA, Hoover DR, Eshleman SH. Analysis of HIV using a high resolution melting (HRM) diversity assay: automation of HRM data analysis enhances the utility of the assay for analysis of HIV incidence. PLoS One 2012; 7:e51359. [PMID: 23240016 PMCID: PMC3519891 DOI: 10.1371/journal.pone.0051359] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 11/01/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND HIV diversity may be a useful biomarker for discriminating between recent and non-recent HIV infection. The high resolution melting (HRM) diversity assay was developed to quantify HIV diversity in viral populations without sequencing. In this assay, HIV diversity is expressed as a single numeric HRM score that represents the width of a melting peak. HRM scores are highly associated with diversity measures obtained with next generation sequencing. In this report, a software package, the HRM Diversity Assay Analysis Tool (DivMelt), was developed to automate calculation of HRM scores from melting curve data. METHODS DivMelt uses computational algorithms to calculate HRM scores by identifying the start (T1) and end (T2) melting temperatures for a DNA sample and subtracting them (T2 - T1 = HRM score). DivMelt contains many user-supplied analysis parameters to allow analyses to be tailored to different contexts. DivMelt analysis options were optimized to discriminate between recent and non-recent HIV infection and to maximize HRM score reproducibility. HRM scores calculated using DivMelt were compared to HRM scores obtained using a manual method that is based on visual inspection of DNA melting curves. RESULTS HRM scores generated with DivMelt agreed with manually generated HRM scores obtained from the same DNA melting data. Optimal parameters for discriminating between recent and non-recent HIV infection were identified. DivMelt provided greater discrimination between recent and non-recent HIV infection than the manual method. CONCLUSION DivMelt provides a rapid, accurate method of determining HRM scores from melting curve data, facilitating use of the HRM diversity assay for large-scale studies.
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Affiliation(s)
- Matthew M. Cousins
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - David Swan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Craig A. Magaret
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Donald R. Hoover
- Department of Statistics and Biostatistics and Institute for Health, Health Care Policy and Aging Research, Rutgers University, Piscataway, New Jersey, United States of America
| | - Susan H. Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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Abstract
BACKGROUND We used a novel high resolution melting (HRM) diversity assay to analyze HIV diversity in Ugandan children (age 0.6-12.4 years) who were enrolled in an observational study of antiretroviral treatment (ART). Children were maintained on ART if they were clinically and immunologically stable. METHODS HIV diversity was measured before ART (baseline) in 76 children and after 48 or 96 weeks of ART in 14 children who were not virally suppressed. HIV diversity (expressed as HRM scores) was measured in 6 regions of the HIV genome (2 in gag, 1 in pol, 3 in env). RESULTS Higher baseline HRM scores were significantly associated with older age (≥2 years, P ≤ 0.001 for all 6 regions). HRM scores from different regions were weakly correlated. Higher baseline HRM scores in 3 regions (1 in gag, 2 in env) were associated with ART failure. HIV diversity was lower in 4 regions (2 in gag, 1 in pol, 1 in env) after 48-96 weeks of nonsuppressive ART compared with baseline. CONCLUSIONS Higher levels of HIV diversity were observed in older children before ART, and higher levels of diversity in some regions of the HIV genome were associated with ART failure. Prolonged exposure to nonsuppressive ART was associated with a significant decrease in viral diversity in selected regions of the HIV genome.
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