Abstract：
BACKGROUND:Targeted resequencing offers a cost-effective alternative to whole-genome and whole-exome sequencing when investigating regions known to be associated with a trait or disease. There are a number of approaches to targeted resequencing, including microfluidic PCR amplification, which may be enhanced by multiplex PCR. Currently, there is no open-source software that can design next-generation multiplex PCR experiments that ensures primers are unique at a genome-level and efficiently pools compatible primers. RESULTS:We present MPD, a software package that automates the design of multiplex PCR primers for next-generation sequencing. The core of MPD is implemented in C for speed and uses a hashed genome to ensure primer uniqueness, avoids placing primers over sites of known variation, and efficiently pools compatible primers. A JavaScript web application ( http://multiplexprimer.io ) utilizing the MPD Perl package provides a convenient platform for users to make designs. Using a realistic set of genes identified by genome-wide association studies (GWAS), we achieve 90% coverage of all exonic regions using stringent design criteria. Using the first 47 primer pools for wet-lab validation, we sequenced ~25Kb at 99.7% completeness with a mean coverage of 300X among 313 samples simultaneously and identified 224 variants. The number and nature of variants we observe are consistent with high quality sequencing. CONCLUSIONS:MPD can successfully design multiplex PCR experiments suitable for next-generation sequencing, and simplifies retooling targeted resequencing pipelines to focus on new targets as new genetic evidence emerges.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Wingo TS,Kotlar A,Cutler DJdoi
10.1186/s12859-016-1453-3subject
Has Abstractpub_date
2017-01-05 00:00:00pages
14issue
1issn
1471-2105pii
10.1186/s12859-016-1453-3journal_volume
18pub_type
杂志文章abstract：BACKGROUND:DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations. RESULTS:Here, we describe a method to detect copy number varia...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-10-80
更新日期：2009-03-06 00:00:00
abstract：BACKGROUND:The identification of protein coding regions (exons) in DNA sequences using signal processing techniques is an important component of bioinformatics and biological signal processing. In this paper, a new method is presented for the identification of exonic regions in DNA sequences. This method is based on th...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-12-430
更新日期：2011-11-03 00:00:00
abstract：BACKGROUND:Protein-protein interactions (PPIs) play key roles in various cellular functions. In addition, some critical inter-species interactions such as host-pathogen interactions and pathogenicity occur through PPIs. Phytopathogenic bacteria infect hosts through attachment to host tissue, enzyme secretion, exopolysa...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-9-41
更新日期：2008-01-24 00:00:00
abstract：BACKGROUND:The MAQC project demonstrated that microarrays with comparable content show inter- and intra-platform reproducibility. However, since the content of gene databases still increases, the development of new generations of microarrays covering new content is mandatory. To better understand the potential challeng...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-10-186
更新日期：2009-06-18 00:00:00
abstract：BACKGROUND:Data are the evidentiary basis for scientific hypotheses, analyses and publication, for policy formation and for decision-making. They are essential to the evaluation and testing of results by peer scientists both present and future. There is broad consensus in the scientific and conservation communities tha...
journal_title：BMC bioinformatics
pub_type： 指南,杂志文章
doi：10.1186/1471-2105-12-S15-S1
更新日期：2011-01-01 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-7-84
更新日期：2006-02-22 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-018-2103-8
更新日期：2018-03-09 00:00:00
abstract：BACKGROUND:A range of rare and common genetic variants have been discovered to be potentially associated with mental diseases, but many more have not been uncovered. Powerful integrative methods are needed to systematically prioritize both variants and genes that confer susceptibility to mental diseases in personal gen...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-018-2469-7
更新日期：2018-12-28 00:00:00
abstract：BACKGROUND:The specific recognition of genomic cis-regulatory elements by transcription factors (TFs) plays an essential role in the regulation of coordinated gene expression. Studying the mechanisms determining binding specificity in protein-DNA interactions is thus an important goal. Most current approaches for model...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-9-436
更新日期：2008-10-16 00:00:00
abstract：BACKGROUND:Various computer-based methods exist for the detection and quantification of protein spots in two dimensional gel electrophoresis images. Area-based methods are commonly used for spot quantification: an area is assigned to each spot and the sum of the pixel intensities in that area, the so-called volume, is ...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-15-181
更新日期：2014-06-11 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-11-93
更新日期：2010-02-18 00:00:00
abstract：BACKGROUND:Interpretation of gene expression microarray data in the light of external information on both columns and rows (experimental variables and gene annotations) facilitates the extraction of pertinent information hidden in these complex data. Biologists classically interpret genes of interest after retrieving f...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-14-178
更新日期：2013-06-06 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-016-1183-6
更新日期：2016-08-30 00:00:00
abstract：BACKGROUND:In this study, we extended the replica exchange Monte Carlo (REMC) sampling method to protein-small molecule docking conformational prediction using RosettaLigand. In contrast to the traditional Monte Carlo (MC) and REMC sampling methods, these methods use multi-objective optimization Pareto front informatio...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-017-1733-6
更新日期：2017-07-10 00:00:00
abstract：BACKGROUND:In microarray experiments the numbers of replicates are often limited due to factors such as cost, availability of sample or poor hybridization. There are currently few choices for the analysis of a pair of microarrays where N = 1 in each condition. In this paper, we demonstrate the effectiveness of a new al...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-9-489
更新日期：2008-11-21 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-9-S12-S7
更新日期：2008-12-12 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-5-101
更新日期：2004-07-26 00:00:00
abstract：BACKGROUND:The cost of DNA sequencing has undergone a dramatical reduction in the past decade. As a result, sequencing technologies have been increasingly applied to genomic research. RNA-Seq is becoming a common technique for surveying gene expression based on DNA sequencing. As it is not clear how increased sequencin...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-13-S13-S5
更新日期：2012-01-01 00:00:00
abstract：BACKGROUND:During the past decade, many software packages have been developed for analysis and visualization of various types of microarrays. We have developed and maintained the widely used dChip as a microarray analysis software package accessible to both biologist and data analysts. However, challenges arise when dC...
journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-9-231
更新日期：2008-05-08 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-15-S2-S5
更新日期：2014-01-01 00:00:00
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pub_type： 杂志文章
doi：10.1186/s12859-018-2580-9
更新日期：2019-01-07 00:00:00
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pub_type： 杂志文章
doi：10.1186/s12859-017-1585-0
更新日期：2017-03-16 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-6-S1-S18
更新日期：2005-01-01 00:00:00
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pub_type： 杂志文章
doi：10.1186/s12859-016-1387-9
更新日期：2016-12-13 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
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更新日期：2012-08-07 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-7-53
更新日期：2006-02-06 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-10-S15-S11
更新日期：2009-12-03 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
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更新日期：2020-05-29 00:00:00
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pub_type： 杂志文章
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更新日期：2006-05-15 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
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更新日期：2009-01-20 00:00:00
