Semi-automated unidirectional sequence analysis for mutation detection in a clinical diagnostic setting.
BACKGROUND
The past 10 years have seen an improvement in sequence data quality due to the introduction of capillary sequencers and new sequencing chemistries. In parallel, new software programs for automated mutation detection have been developed. We evaluated the sensitivity of semiautomated unidirectional sequence analysis for the detection of heterozygous base substitutions using the Mutation Surveyor software package.


METHODS
Detection rates for heterozygous base substitutions in 29 genes by automated and visual inspection were compared. Examples of heterozygous bases not detected in one direction during bidirectional analysis were also sought through a national survey of United Kingdom (UK) genetics laboratories. Sequence quality was assessed in a consecutive cohort of 50 patients for whom the 39 exons of the ABCC8 gene had been sequenced in one direction.


RESULTS
A total of 701 different heterozygous base substitutions were detected by the software with no false negatives (sensitivity >or=99.57%). Four examples of heterozygous bases missed in one direction during bidirectional analysis were reported. Two were detected using unidirectional analysis settings, and the other two bases had low-quality scores. Of the 1950 amplicons examined, 97.2% had a quality score >or=30 and an average PHRED-like score >or=50 for the defined region of interest, and 98.1% of the 323,650 bases had a PHRED score >40.


CONCLUSIONS
We found no evidence to support a requirement for bidirectional sequencing. Semiautomated analysis of good quality unidirectional sequence data has high sensitivity and is suitable for heterozygote mutation scanning in clinical diagnostic laboratories. Further work is required to determine minimum quality parameters for semiautomated analysis.
Ellard
Sian
S
Department of Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom. sian.ellard@rdeft.nhs.uk
Shields
Beverley
B
Tysoe
Carolyn
C
Treacy
Rebecca
R
Yau
Shu
S
Mattocks
Christopher
C
Wallace
Andrew
A
D018528:ATP-Binding Cassette Transporters / Q000235:genetics; D001483:Base Sequence; D019411:Clinical Laboratory Techniques; D015331:Cohort Studies; D004252:DNA Mutational Analysis / Q000379:methods*; D005091:Exons; D016368:Frameshift Mutation; D006580:Genetic Carrier Screening; D006801:Humans; D007753:Laboratories / Q000145:classification*; D008969:Molecular Sequence Data; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D024661:Potassium Channels, Inwardly Rectifying / Q000235:genetics; D011955:Receptors, Drug / Q000235:genetics; D012680:Sensitivity and Specificity; D012984:Software; D064233:Sulfonylurea Receptors
D018528:ATP-Binding Cassette Transporters; D024661:Potassium Channels, Inwardly Rectifying; D011955:Receptors, Drug; D064233:Sulfonylurea Receptors