Massively parallel pyrosequencing in HIV research.

نویسندگان

  • Frederic D Bushman
  • Christian Hoffmann
  • Keshet Ronen
  • Nirav Malani
  • Nana Minkah
  • Heather Marshall Rose
  • Pablo Tebas
  • Gary P Wang
چکیده

Several methods for massively parallel pyrosequencing have recently been commercialized. As an example, consider the use of the 454 Life Sciences pyrosequencing method for metagenomic analysis of woolly mammoth DNA [1,2]. DNA from a mammoth carcass was purified and fragmented, and DNA linkers were ligated to the free ends. DNAs were then denatured and strands annealed to beads conjugated with oligonucleotides complementary to the linker sequences. This step is carried out with very low DNA concentrations so that on average only one strand binds to each bead. Bead-bound DNA is then PCR amplified in an oil–water emulsion, where each water droplet in the emulsion contains on average a single bead. The amplified DNA strands anneal to the beads,

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Improved Detection of Rare HIV-1 Variants using 454 Pyrosequencing

454 pyrosequencing, a massively parallel sequencing (MPS) technology, is often used to study HIV genetic variation. However, the substantial mismatch error rate of the PCR required to prepare HIV-containing samples for pyrosequencing has limited the detection of rare variants within viral populations to those present above ~1%. To improve detection of rare variants, we varied PCR enzymes and co...

متن کامل

DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations

Treatment of HIV-infected individuals with antiretroviral agents selects for drug-resistant mutants, resulting in frequent treatment failures. Although the major antiretroviral resistance mutations are routinely characterized by DNA sequencing, treatment failures are still common, probably in part because undetected rare resistance mutations facilitate viral escape. Here we combined DNA bar cod...

متن کامل

HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications.

Integration of retroviral DNA into host cell DNA is a defining feature of retroviral replication. HIV integration is known to be favored in active transcription units, which promotes efficient transcription of the viral genes, but the molecular mechanisms responsible for targeting are not fully clarified. Here we used pyrosequencing to map 40,569 unique sites of HIV integration. Computational p...

متن کامل

A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes

BACKGROUND Massively parallel pyrosequencing of amplicons from the V6 hypervariable regions of small-subunit (SSU) ribosomal RNA (rRNA) genes is commonly used to assess diversity and richness in bacterial and archaeal populations. Recent advances in pyrosequencing technology provide read lengths of up to 240 nucleotides. Amplicon pyrosequencing can now be applied to longer variable regions of t...

متن کامل

Comparison of Major and Minor Viral SNPs Identified through Single Template Sequencing and Pyrosequencing in Acute HIV-1 Infection

Massively parallel sequencing (MPS) technologies, such as 454-pyrosequencing, allow for the identification of variants in sequence populations at lower levels than consensus sequencing and most single-template Sanger sequencing experiments. We sought to determine if the greater depth of population sampling attainable using MPS technology would allow detection of minor variants in HIV founder vi...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:
  • AIDS

دوره 22 12  شماره 

صفحات  -

تاریخ انتشار 2008