title: Practical tools to implement massive parallel pyrosequencing of PCR products in next generation molecular diagnostics.
abstract: Despite improvements in terms of sequence quality and price per basepair, Sanger sequencing remains restricted to screening of individual disease genes. The development of massively parallel sequencing (MPS) technologies heralded an era in which molecular diagnostics for multigenic disorders becomes reality. Here, we outline different PCR amplification based strategies for the screening of a multitude of genes in a patient cohort. We performed a thorough evaluation in terms of set-up, coverage and sequencing variants on the data of 10 GS-FLX experiments (over 200 patients). Crucially, we determined the actual coverage that is required for reliable diagnostic results using MPS, and provide a tool to calculate the number of patients that can be screened in a single run. Finally, we provide an overview of factors contributing to false negative or false positive mutation calls and suggest ways to maximize sensitivity and specificity, both important in a routine setting. By describing practical strategies for screening of multigenic disorders in a multitude of samples and providing answers to questions about minimum required coverage, the number of patients that can be screened in a single run and the factors that may affect sensitivity and specificity we hope to facilitate the implementation of MPS technology in molecular diagnostics.
authors: Center for Medical Genetics, Ghent University, Ghent, Belgium. Kim.deleeneer@UGent.be
authors: Kim
authors: K
authors: De Leeneer
authors: Joachim
authors: J
authors: De Schrijver
authors: Lieven
authors: L
authors: Clement
authors: Machteld
authors: M
authors: Baetens
authors: Steve
authors: S
authors: Lefever
authors: Sarah
authors: S
authors: De Keulenaer
authors: Wim
authors: W
authors: Van Criekinge
authors: Dieter
authors: D
authors: Deforce
authors: Filip
authors: F
authors: Van Nieuwerburgh
authors: Sofie
authors: S
authors: Bekaert
authors: Filip
authors: F
authors: Pattyn
authors: Bram
authors: B
authors: De Wilde
authors: Paul
authors: P
authors: Coucke
authors: Jo
authors: J
authors: Vandesompele
authors: Kathleen
authors: K
authors: Claes
authors: Jan
authors: J
authors: Hellemans
mesh_terms: D004252:DNA Mutational Analysis; D005188:False Negative Reactions; D005189:False Positive Reactions; D059014:High-Throughput Nucleotide Sequencing / Q000295:instrumentation / Q000379:methods*; D006801:Humans; D057089:Pathology, Molecular / Q000295:instrumentation / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000295:instrumentation / Q000379:methods*; D011786:Quality Control