An analysis of exome sequencing for diagnostic testing of the genes associated with muscle disease and spastic paraplegia.
In this study, we assess exome sequencing (ES) as a diagnostic alternative for genetically heterogeneous disorders. Because ES readily identified a previously reported homozygous mutation in the CAPN3 gene for an individual with an undiagnosed limb girdle muscular dystrophy, we evaluated ES as a generalizable clinical diagnostic tool by assessing the targeting efficiency and sequencing coverage of 88 genes associated with muscle disease (MD) and spastic paraplegia (SPG). We used three exome-capture kits on 125 individuals. Exons constituting each gene were defined using the UCSC and CCDS databases. The three exome-capture kits targeted 47-92% of bases within the UCSC-defined exons and 97-99% of bases within the CCDS-defined exons. An average of 61.2-99.5% and 19.1-99.5% of targeted bases per gene were sequenced to 20X coverage within the CCDS-defined MD and SPG coding exons, respectively. Greater than 95-99% of targeted known mutation positions were sequenced to ≥1X coverage and 55-87% to ≥20X coverage in every exome. We conclude, therefore, that ES is a rapid and efficient first-tier method to screen for mutations, particularly within the CCDS annotated exons, although its application requires disclosure of the extent of coverage for each targeted gene and supplementation with second-tier Sanger sequencing for full coverage.
Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
Cristina
C
Dias
Murat
M
Sincan
Praveen F
PF
Cherukuri
Rosemarie
R
Rupps
Yan
Y
Huang
Hannah
H
Briemberg
Kathryn
K
Selby
James C
JC
Mullikin
Thomas C
TC
Markello
David R
DR
Adams
William A
WA
Gahl
Cornelius F
CF
Boerkoel
D002154:Calpain / Q000235:genetics; D059472:Exome; D005260:Female; D006801:Humans; D009124:Muscle Proteins / Q000235:genetics; D009135:Muscular Diseases / Q000235:genetics*; D049288:Muscular Dystrophies, Limb-Girdle / Q000235:genetics; D009154:Mutation; D010264:Paraplegia / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*; D055815:Young Adult
D009124:Muscle Proteins; C105884:CAPN3 protein, human; D002154:Calpain