A novel, single nucleotide polymorphism-based assay to detect 22q11 deletions.
Velocardiofacial syndrome, DiGeorge syndrome, and conotruncal anomaly face syndrome, now collectively referred to as 22q11deletion syndrome (22q11DS) are caused by microdeletions on chromosome 22q11. The great majority ( approximately 90%) of these deletions are 3 Mb in size. The remaining deleted patients have nested break-points resulting in overlapping regions of hemizygosity. Diagnostic testing for the disorder is traditionally done by fluorescent in situ hybridization (FISH) using probes located in the proximal half of the region common to all deletions. We developed a novel, high-resolution single-nucleotide polymorphism (SNP) genotyping assay to detect 22q11 deletions. We validated this assay using DNA from 110 nondeleted controls and 77 patients with 22q11DS that had previously been tested by FISH. The assay was 100% sensitive (all deletions were correctly identified). Our assay was also able to detect a case of segmental uniparental disomy at 22q11 that was not detected by the FISH assay. We used Bayesian networks to identify a set of 17 SNPs that are sufficient to ascertain unambiguously the deletion status of 22q11DS patients. Our SNP based assay is a highly accurate, sensitive, and specific method for the diagnosis of 22q11 deletion syndrome.
Funke
Birgit H
BH
Harvard Medical School-Partners Healthcare Center for Genetics and Genomics, Cambridge, MA 02139, USA. bfunke@partners.org
Brown
Alison C
AC
Ramoni
Marco F
MF
Regan
Maura E
ME
Baglieri
Chris
C
Finn
Christine T
CT
Babcock
Melanie
M
Shprintzen
Robert J
RJ
Morrow
Bernice E
BE
Kucherlapati
Raju
R
D001483:Base Sequence; D001499:Bayes Theorem; D002872:Chromosome Deletion; D002892:Chromosomes, Human, Pair 22; D004247:DNA; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity
D004247:DNA