Evaluation of second-generation sequencing of 19 dilated cardiomyopathy genes for clinical applications.
Medical sequencing for diseases with locus and allelic heterogeneities has been limited by the high cost and low throughput of traditional sequencing technologies. "Second-generation" sequencing (SGS) technologies allow the parallel processing of a large number of genes and, therefore, offer great promise for medical sequencing; however, their use in clinical laboratories is still in its infancy. Our laboratory offers clinical resequencing for dilated cardiomyopathy (DCM) using an array-based platform that interrogates 19 of more than 30 genes known to cause DCM. We explored both the feasibility and cost effectiveness of using PCR amplification followed by SGS technology for sequencing these 19 genes in a set of five samples enriched for known sequence alterations (109 unique substitutions and 27 insertions and deletions). While the analytical sensitivity for substitutions was comparable to that of the DCM array (98%), SGS technology performed better than the DCM array for insertions and deletions (90.6% versus 58%). Overall, SGS performed substantially better than did the current array-based testing platform; however, the operational cost and projected turnaround time do not meet our current standards. Therefore, efficient capture methods and/or sample pooling strategies that shorten the turnaround time and decrease reagent and labor costs are needed before implementing this platform into routine clinical applications.
Gowrisankar
Sivakumar
S
Laboratory for Molecular Medicine, Partners HealthCare Center for Personalized Genetic Medicine, 65 Landsdowne St., Cambridge, MA 02139, USA.
Lerner-Ellis
Jordan P
JP
Cox
Stephanie
S
White
Emily T
ET
Manion
Megan
M
LeVan
Kevin
K
Liu
Jonathan
J
Farwell
Lisa M
LM
Iartchouk
Oleg
O
Rehm
Heidi L
HL
Funke
Birgit H
BH
D002311:Cardiomyopathy, Dilated / Q000235:genetics*; D005820:Genetic Testing / Q000191:economics / Q000379:methods; D006801:Humans; D008969:Molecular Sequence Data; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis / Q000191:economics / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000191:economics / Q000379:methods*; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000191:economics / Q000379:methods*; D012984:Software