Titre

Ultra high throughput sequencing in human DNA variation detection: a comparative study on the NDUFA3-PRPF31 region.

Type
article
Institution
UNIL/CHUV/Unisanté + institutions partenaires
Périodique
PLoS One
Auteur(s)
Benaglio, P.
Auteure/Auteur
Rivolta, C.
Auteure/Auteur
Liens vers les personnes
Liens vers les unités
ISSN
1932-6203[electronic], 1932-6203[linking]
Statut éditorial
Publié
Date de publication
2010
Volume
5
Numéro
9
Première page
e13071
Peer-reviewed
Oui
Langue
anglais
Résumé
BACKGROUND: Ultra high throughput sequencing (UHTS) technologies find an important application in targeted resequencing of candidate genes or of genomic intervals from genetic association studies. Despite the extraordinary power of these new methods, they are still rarely used in routine analysis of human genomic variants, in part because of the absence of specific standard procedures. The aim of this work is to provide human molecular geneticists with a tool to evaluate the best UHTS methodology for efficiently detecting DNA changes, from common SNPs to rare mutations. METHODOLOGY/PRINCIPAL FINDINGS: We tested the three most widespread UHTS platforms (Roche/454 GS FLX Titanium, Illumina/Solexa Genome Analyzer II and Applied Biosystems/SOLiD System 3) on a well-studied region of the human genome containing many polymorphisms and a very rare heterozygous mutation located within an intronic repetitive DNA element. We identify the qualities and the limitations of each platform and describe some peculiarities of UHTS in resequencing projects. CONCLUSIONS/SIGNIFICANCE: When appropriate filtering and mapping procedures are applied UHTS technology can be safely and efficiently used as a tool for targeted human DNA variations detection. Unless particular and platform-dependent characteristics are needed for specific projects, the most relevant parameter to consider in mainstream human genome resequencing procedures is the cost per sequenced base-pair associated to each machine.
PID Serval
serval:BIB_42A7D6B604D2
DOI
PMID
WOS
Permalien
Open Access
Oui
Date de création
2010-10-15T14:44:03.230Z
Date de création dans IRIS
2025-05-20T17:05:29Z
Fichier(s)
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Nom

BIB_42A7D6B604D2.P001.pdf

Version du manuscrit

preprint

Taille

917.4 KB

Format

Adobe PDF

PID Serval

serval:BIB_42A7D6B604D2.P001

URN

urn:nbn:ch:serval-BIB_42A7D6B604D23

Somme de contrôle

(MD5):c7673e9d8b513c57fb273ddbc86cad03