Detection and characterization of NF1 microdeletions by custom high resolution array CGH.
In 5% to 10% of cases, neurofibromatosis type 1 is caused by microdeletions scattered across the entire NF1 gene and various neighboring genes. The phenotype appears to be more severe in patients with NF1 microdeletions than in patients with NF1 single point mutations. We have developed a new method for detecting and characterizing NF1 microdeletions based on a custom high-resolution oligonucleotide array comparative genomic hybridization by using the custom 8x15K Agilent array format. The array comprised a total of 14,207 oligonucleotide probes spanning the whole of chromosome 17, including 12,314 probes spanning an approximately 8 Mb interval surrounding the NF1 locus. We validated this approach by testing NF1 microdeleted DNA samples previously characterized by means of microsatellites and real-time PCR methods. Our array comparative genomic hybridization provided enough information for subsequent long-range PCR and nucleotide sequencing of the microdeletion endpoints. Unlike previously described methods, our array comparative genomic hybridization was able to unambiguously differentiate between the three types of microdeletions (type I, type II, and atypical) and to characterize atypical microdeletions. Further comparative studies of patients with well-characterized genotypes and phenotypes and different microdeletions sizes and breakpoints will help determine whether haploinsufficiency of deleted genes and/or genes rearrangements influence clinical outcomes.
Pasmant
Eric
E
UMR745 INSERM, Université Paris Descartes, Faculté des Sciences Pharmaceutiques et Biologiques, 4 avenue de l'Observatoire, 75006 Paris, France. eric.pasmant@etu.univ-paris5.fr
Sabbagh
Audrey
A
Masliah-Planchon
Julien
J
Haddad
Véronique
V
Hamel
Marie-José
MJ
Laurendeau
Ingrid
I
Soulier
Jean
J
Parfait
Béatrice
B
Wolkenstein
Pierre
P
Bièche
Ivan
I
Vidaud
Michel
M
Vidaud
Dominique
D
D055028:Comparative Genomic Hybridization / Q000379:methods*; D006801:Humans; D018895:Microsatellite Repeats / Q000235:genetics; D009154:Mutation / Q000235:genetics; D009456:Neurofibromatosis 1 / Q000235:genetics; D025542:Neurofibromin 1 / Q000235:genetics*; D016133:Polymerase Chain Reaction
D025542:Neurofibromin 1