Literature DB >> 19948190

Optimization of allele-specific PCR using patient-specific HIV consensus sequences for primer design.

Valerie F Boltz1, Frank Maldarelli, Neil Martinson, Lynn Morris, James A McIntyre, Glenda Gray, Mark J Hopley, Toshio Kimura, Douglas L Mayers, Patrick Robinson, John W Mellors, John M Coffin, Sarah E Palmer.   

Abstract

Allele-specific PCR based on subtype consensus sequences is a powerful technique for detecting low frequency drug resistant mutants in HIV-1 infected patients. However, this approach can be limited by genetic variation in the region complementary to the primers, leading to variability in allele detection. The goals of this study were to quantify this effect and then to improve assay performance. Copyright (c) 2009 Elsevier B.V. All rights reserved.

Entities:  

Mesh：

Substances：

Year:  2009        PMID： 19948190      PMCID： PMC4734888          DOI： 10.1016/j.jviromet.2009.11.025

Source DB:  PubMed          Journal:  J Virol Methods        ISSN： 0166-0934            Impact factor:   2.014


  18 in total

Review 1.  HIV resistance to nevirapine and other non-nucleoside reverse transcriptase inhibitors.

Authors:  Mark A Wainberg
Journal:  J Acquir Immune Defic Syndr       Date:  2003-09       Impact factor: 3.731

2.  Blinded, multicenter comparison of methods to detect a drug-resistant mutant of human immunodeficiency virus type 1 at low frequency.

Authors:  Elias K Halvas; Grace M Aldrovandi; Peter Balfe; Ingrid A Beck; Valerie F Boltz; John M Coffin; Lisa M Frenkel; J Darren Hazelwood; Victoria A Johnson; Mary Kearney; Andrea Kovacs; Daniel R Kuritzkes; Karin J Metzner; Dwight V Nissley; Marek Nowicki; Sarah Palmer; Rainer Ziermann; Richard Y Zhao; Cheryl L Jennings; James Bremer; Don Brambilla; John W Mellors
Journal:  J Clin Microbiol       Date:  2006-07       Impact factor: 5.948

3.  Selection and persistence of non-nucleoside reverse transcriptase inhibitor-resistant HIV-1 in patients starting and stopping non-nucleoside therapy.

Authors:  Sarah Palmer; Valerie Boltz; Frank Maldarelli; Mary Kearney; Elias K Halvas; Diane Rock; Judith Falloon; Richard T Davey; Robin L Dewar; Julia A Metcalf; John W Mellors; John M Coffin
Journal:  AIDS       Date:  2006-03-21       Impact factor: 4.177

4.  Improvement in allele-specific PCR assay with the use of polymorphism-specific primers for the analysis of minor variant drug resistance in HIV-1 subtype C.

Authors:  Christopher F Rowley; Christian L Boutwell; Shahin Lockman; M Essex
Journal:  J Virol Methods       Date:  2008-03-04       Impact factor: 2.014

5.  Persistence of nevirapine-resistant HIV-1 in women after single-dose nevirapine therapy for prevention of maternal-to-fetal HIV-1 transmission.

Authors:  S Palmer; V Boltz; N Martinson; F Maldarelli; G Gray; J McIntyre; J Mellors; L Morris; J Coffin
Journal:  Proc Natl Acad Sci U S A       Date:  2006-04-25       Impact factor: 11.205

6.  Changes in human immunodeficiency virus type 1 populations after treatment interruption in patients failing antiretroviral therapy.

Authors:  A J Hance; V Lemiale; J Izopet; D Lecossier; V Joly; P Massip; F Mammano; D Descamps; F Brun-Vézinet; F Clavel
Journal:  J Virol       Date:  2001-07       Impact factor: 5.103

7.  HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy.

Authors:  J M Coffin
Journal:  Science       Date:  1995-01-27       Impact factor: 47.728

8.  Rare mutations at codon 103 of HIV-1 reverse transcriptase can confer resistance to non-nucleoside reverse transcriptase inhibitors.

Authors:  P Richard Harrigan; Theresa Mo; Brian Wynhoven; Jennifer Hirsch; Zabrina Brumme; Paula McKenna; Theresa Pattery; Johan Vingerhoets; Lee T Bacheler
Journal:  AIDS       Date:  2005-03-24       Impact factor: 4.177

9.  Decay of K103N mutants in cellular DNA and plasma RNA after single-dose nevirapine to reduce mother-to-child HIV transmission.

Authors:  Shayne Loubser; Peter Balfe; Gayle Sherman; Scott Hammer; Louise Kuhn; Lynn Morris
Journal:  AIDS       Date:  2006-04-24       Impact factor: 4.177

Review 10.  HIV-1 reverse transcriptase inhibitor resistance mutations and fitness: a view from the clinic and ex vivo.

Authors:  Javier Martinez-Picado; Miguel Angel Martínez
Journal:  Virus Res       Date:  2008-03-04       Impact factor: 3.303
View more
  12 in total

1.  PAPNC, a novel method to calculate nucleotide diversity from large scale next generation sequencing data.

Authors:  Wei Shao; Mary F Kearney; Valerie F Boltz; Jonathan E Spindler; John W Mellors; Frank Maldarelli; John M Coffin
Journal:  J Virol Methods       Date:  2014-03-26       Impact factor: 2.014

2.  Simultaneous detection of major drug resistance mutations in the protease and reverse transcriptase genes for HIV-1 subtype C by use of a multiplex allele-specific assay.

Authors:  Guoqing Zhang; Fangping Cai; Zhiyong Zhou; Joshua DeVos; Nick Wagar; Karidia Diallo; Isaac Zulu; Nellie Wadonda-Kabondo; Jeffrey S A Stringer; Paul J Weidle; Clement B Ndongmo; Izukanji Sikazwe; Abdoulaye Sarr; Matthew Kagoli; John Nkengasong; Feng Gao; Chunfu Yang
Journal:  J Clin Microbiol       Date:  2013-08-28       Impact factor: 5.948

3.  Low-frequency nevirapine (NVP)-resistant HIV-1 variants are not associated with failure of antiretroviral therapy in women without prior exposure to single-dose NVP.

Authors:  Valerie F Boltz; Yajing Bao; Shahin Lockman; Elias K Halvas; Mary F Kearney; James A McIntyre; Robert T Schooley; Michael D Hughes; John M Coffin; John W Mellors
Journal:  J Infect Dis       Date:  2014-01-16       Impact factor: 5.226

4.  Role of low-frequency HIV-1 variants in failure of nevirapine-containing antiviral therapy in women previously exposed to single-dose nevirapine.

Authors:  Valerie F Boltz; Yu Zheng; Shahin Lockman; Feiyu Hong; Elias K Halvas; James McIntyre; Judith S Currier; Margret C Chibowa; Cecelia Kanyama; Apsara Nair; Willis Owino-Ong'or; Michael Hughes; John M Coffin; John W Mellors
Journal:  Proc Natl Acad Sci U S A       Date:  2011-05-16       Impact factor: 11.205

5.  Ultrasensitive allele-specific PCR reveals rare preexisting drug-resistant variants and a large replicating virus population in macaques infected with a simian immunodeficiency virus containing human immunodeficiency virus reverse transcriptase.

Authors:  Valerie F Boltz; Zandrea Ambrose; Mary F Kearney; Wei Shao; Vineet N Kewalramani; Frank Maldarelli; John W Mellors; John M Coffin
Journal:  J Virol       Date:  2012-08-29       Impact factor: 5.103

6.  Basis for early and preferential selection of the E138K mutation in HIV-1 reverse transcriptase.

Authors:  Matthew McCallum; Maureen Oliveira; Ruxandra-Ilinca Ibanescu; Victor G Kramer; Daniela Moisi; Eugene L Asahchop; Bluma G Brenner; P Richard Harrigan; Hongtao Xu; Mark A Wainberg
Journal:  Antimicrob Agents Chemother       Date:  2013-07-15       Impact factor: 5.191

7.  Clinical implications of HIV-1 minority variants.

Authors:  Jonathan Z Li; Daniel R Kuritzkes
Journal:  Clin Infect Dis       Date:  2013-02-27       Impact factor: 9.079

8.  Concordance between allele-specific PCR and ultra-deep pyrosequencing for the detection of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations.

Authors:  Gillian M Hunt; Lynn Morris; Anitha Moorthy; Ashraf Coovadia; Elaine J Abrams; Renate Strehlau; Louise Kuhn; Deborah Persaud
Journal:  J Virol Methods       Date:  2014-07-14       Impact factor: 2.014

9.  Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data.

Authors:  Alexander R Macalalad; Michael C Zody; Patrick Charlebois; Niall J Lennon; Ruchi M Newman; Christine M Malboeuf; Elizabeth M Ryan; Christian L Boutwell; Karen A Power; Doug E Brackney; Kendra N Pesko; Joshua Z Levin; Gregory D Ebel; Todd M Allen; Bruce W Birren; Matthew R Henn
Journal:  PLoS Comput Biol       Date:  2012-03-15       Impact factor: 4.475

10.  Longitudinal Detection and Persistence of Minority Drug-Resistant Populations and Their Effect on Salvage Therapy.

Authors:  Masako Nishizawa; Masakazu Matsuda; Junko Hattori; Teiichiro Shiino; Tetsuro Matano; Walid Heneine; Jeffrey A Johnson; Wataru Sugiura
Journal:  PLoS One       Date:  2015-09-11       Impact factor: 3.240
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.