New polymorphic short tandem repeats for PCR-based Charcot-Marie-Tooth disease type 1A duplication diagnosis.
BACKGROUND
Charcot-Marie-Tooth disease type 1A (CMT1A) accounts for 70-90% of cases of CMT1 and is most frequently caused by the tandem duplication of a 1.4-Mb genomic fragment on chromosome 17p12. Molecular diagnosis of CMT1A has been based primarily on pulsed-field electrophoresis, fluorescence in situ hybridization, polymorphic allele dosage analysis, and quantitative PCR. We sought to improve the fidelity and applicability of PCR-based diagnosis by developing a panel of novel, highly polymorphic short tandem repeats (STRs) from within the CMT1A duplicated region.


METHODS
We used a recently available genomic sequence to identify potentially polymorphic simple repeats. We then amplified these sequences in a multiethnic cohort of unaffected individuals and assessed the heterozygosity and number of alleles for each STR. Highly informative markers were then tested in a set of previously diagnosed CMT1A duplication patients, and the ability to identify the genomic duplication through the presence of three bands was assessed.


RESULTS
We identified 34 polymorphic markers, 15 of which were suitable for CMT1A diagnosis on the basis of high heterozygosity in different ethnic groups, peak uniformity, and a large number of alleles. On the basis of the fluorescent dye and allele range of each marker, we developed two panels, each of which could be analyzed concurrently. Panel 1, which comprised 10 markers, detected 37 of 39 duplications, whereas panel 2, which comprised the remaining 5 markers, identified 21 of 39 duplications. Through the combination of both panels, we identified 39 of 39 duplications in previously diagnosed CMT1A patients.


CONCLUSIONS
The newly developed 15-marker set has the capability of detecting > 99% of duplications and thus is a powerful and versatile diagnostic tool.
Badano
J L
JL
Departments of Molecular and Human Genetics and Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.
Inoue
K
K
Katsanis
N
N
Lupski
J R
JR
D044466:Asian People / Q000235:genetics; D044383:Black People / Q000235:genetics; D002607:Charcot-Marie-Tooth Disease / Q000175:diagnosis* / Q000208:ethnology / Q000235:genetics; D002886:Chromosomes, Human, Pair 17; D020440:Gene Duplication; D006630:Hispanic or Latino / Q000235:genetics; D006801:Humans; D009185:Myelin Proteins / Q000235:genetics*; D016133:Polymerase Chain Reaction; D020080:Tandem Repeat Sequences; D044465:White People / Q000235:genetics
D009185:Myelin Proteins; C073687:PMP22 protein, human