Methods of detecting genetic deletions and mutations...

Details Methods of detecting genetic deletions and mutations... Methods of detecting genetic deletions and mutations...

1995-06-07

2001-10-16

Campbell, Eggerton A. (Department: 1656)

Chemistry: molecular biology and microbiology

Measuring or testing process involving enzymes or...

Involving nucleic acid

C536S023100

Reexamination Certificate

active

06303294

ABSTRACT:

FIELD OF THE INVENTION
The present invention relates to the field of human diagnostics. More particularly, the invention relates to the detection of genetic deletions and mutations associated with DiGeorge Syndrome (DGS) and related syndromes of Velocardiofacial (Shprintzen) syndrome, CHARGE association, conotruncal cardiac defect, and cleft palate in humans using probes within the common region of overlap for substantially all deletions and mutations associated with these diseases.
BACKGROUND OF THE INVENTION
DiGeorge syndrome (DGS) is a developmental field defect of the third and fourth pharyngeal pouches characterized by thymic aplasia or hypoplasia, absent or hypoplastic parathyroid glands and conotruncal cardiac malformations. The etiology is presumed to be heterogenous with reported cases demonstrating autosomal dominant, autosomal recessive, X-linked and chromosomal modes of inheritance (Lammer and Opitz, (1986)
Am J. Med. Genet.
2:113-127). Approximately 15-20% of patients with DGS have detectable chromosomal abnormalities (Greenberg, et al. (1988)
Am. J. Hum. Genet.
43: 605-611). There are several examples of specific associations between chromosomal deletions and diseases, including Prader-Willi syndrome (Ledbetter et al. (1982)
Am. J. Hum. Genet.
34: 278-285), Langer-Gideon syndrome (Langer et al. (1984),
Am. J. Med. Genet.
19: 81-111), Miller-Dieker syndrome (Dobyns et al., (1983),
J. Pediatr
102: 552-558; Stratton et al.,(1984),
Human Genet
67: 193-200) the aniridia-Wilms tumor association (Riccardi et al, (1978),
Pediatrics
61: 604-610), and retinoblastoma (Lele et al. (1963),
Ann. Hum Genet
27: 171-174). DiGeorge syndrome has been linked to chromosomal deletion of chromosome 22. All of these syndromes have been analyzed using molecular techniques (reviewed by Schinzel (1988),
J. Med. Genet,
5: 454-462). DGS has many of the characteristics associated with this group of deletions syndromes, which have been referred to by Schmickel (1986),
J. Pediatr.
109: 231-241, as “contiguous gene syndromes”. These syndromes tend to be relatively rare, are often sporadic, and have few examples where the disorder is familial. Patients show variation in the severity of their associated symptoms and often manifest additional phenotypic features, possible reflective of the number of genes involved. The majority of cytogenetically abnormal cases of DGS reported involved chromosome 22 and result from malsegregation of a familial balanced translocation leading to monosomy 22pter→22q11 (Back et al. (1980),
Ann. Genet.
23: 244-288; de la Chapelle et al. (1981),
Hum Genet.
57: 253-256; Kelley, et al. (1982)
J. Pediatr.
101: 197-200 (1982); Greenberg et al., (1984),
Human Genet.
65: 317-319; Greenberg et al. (1988)
Am. J. Hum. Genet.
43: 605-611; Augusseau, et al. (1986)
Hum. Genet
74: 206; Bowen et al., (1986),
Clin. Genet.
29: 174-177; Faed, et al. (1987),
J. Med/Genet
24: 225-234 (1987). Two patients have been reported with interstitial deletions, del(22)(q11.21→q11.23) (Greenberg et al. (1988),
Am. J. Human Genet
43: 605-611; Mascarello et al. (1989),
Am. J. Med. Genet
32: 112-114; El-Fouley et al. (1991),
Am J. Med. Genet
38: 569-578 and Driscoll, et al. (1992),
Am. J. Hum Genet.
50: 924-933. Based on cytogenetic studies, it has been hypothesized that the deletion of contiguous genes located on chromosome 22 results in DGS and that the region critical to DGS (DGCR) lies in 22q11. (de la Chapelle et al.,(1981),
Hum. Genet
57:253-256; Kelley et al., (1982),
J. Pediatr.
101: 197-200; Schmickel, (1986),
J. Pediatr.
109: 231-241). The description of a DGS-associated region within 22q11 which invariably involves codeletion of loci D22S75, D22S66 and D22S259 has begun to delineate the DiGeorge syndrome chromosome region (DGCR), hereinafter referred to as the DiGeorge Critical Region (Driscoll et al (1992),
Am J. Human Genet.
50: 924-933.
Velo-cardio-facial syndrome (VCF) is an autosomal dominant disorder characterized by cleft palate, cardiac defects, learning disabilities and a typical facial dysmorphism (Shprintzen et al. (1978),
Cleft Palate J.
15: 56; Spprintzen et al. (1981),
Pediatr.
67: 167-172 and Williams et al. (1985),
J. Craniofacial Genet
5: 175-180). Additional features have been described including microcephaly, short stature, inguinal and umbilical hernias, Robin sequence, scoliosis, platybasia, ophthalmologic abnormalities, neonatal hypocalcemia and decreased lymphoid tissue (Shprintzen et al. (1985),
Am J. Human Genet
37: A77; Williams et al, (1985)
J. Craniofacial Genet.
5: 175-180). The presence of neonatal hypocalcemia, absent or hypoplastic lymphoid tissue and T-cell dysfunction, which are features of DiGeorge syndrome (DGS), suggests that DGS and VCF may share a common pathogenesis (Goldberg et al. (1985),
Am. J. Hum. Genet.
37: A54). Review of previously reported DGS cases with autosomal dominant transmission suggests that these families actually have clinical features more consistent with the diagnosis of VCF (Lammer and Opitz, (1986),
Am. J. Med. Genet.
29: 113-127; Stevens et al. (1990),
Pediatrics
85: 526-530. Based on the phenotypic overlap between DGS and VCF, it is believed that VCF could be caused by deletion of genes from within the DGCR or from a partially overlapping region.
CHARGE association is a condition in which the abnormalities which constitute DGS also play a significant role. Conotruncal cardiac defects are a spearate condition in which deletions of 22q11 have been shown to play a significant role.
Even high resolution cytogenetic studies are not always adequate to detect genetic deletions associated with conditions such as DGS, VCF and related conditions such as CHARGE association, conotruncal defect, cleft palate. In many cases deletions within chromosome 22 are molecular deletions which may only be detected by means of molecular studies. Large molecular deletions can be detected for example, by restriction fragment length polymorphism (RFLP) analysis using several anonymous DNA markers located within the DGCR. However, RFLP studies are not always fully informative. In the past, studies of uninformative patients involved segregation of maternal and paternal homologs of chromosome 22 into different somatic cell hybrids. However, the construction of somatic cell hybrids is labor intensive and is not practical as a routine diagnostic tool. A fast and efficient method for detecting conditions associated with deletions, mutations, and translocations involving chromosome 22 such as are seen in DGS, VCF, CHARGE association, conotruncal defect, and cleft palate is greatly needed.
Probes to deletion and translocation regions have been used diagnostically. For example, fluorescence in situ hybridization (FISH) utilizing cosmid probes from the 17p13.3 region has been used to identify submicroscopic deletions and to define cryptic translocations in patients with Miller-Dieker syndrome (Kuwano et al. (1991),
Am J. Human Genetics,
49: 707-714).
Therefore, probes directed to the DiGeorge syndrome critical region are greatly desired to enhance the detection of genetic deletions and mutations associated with DiGeorge syndrome and the related conditions of Velocardiofacial syndrome, CHARGE association, conotruncal cardiac defect and cleft palate. Diagnosis of a deletion or mutation will permit the clinician to provide the proband as well as the family with an accurate assessment of the recurrence risk and to offer prenatal monitoring for the detection of a deletion in subsequent pregnancies. In addition to the use of ultrasonography and fetal echocardiography for the detection of cleft palate and congenital heart defects, amniocentesis or chorionic villus sampling can be utilized for the cytogenetic, fluorescence in situ hybridization (FISH) and molecular evaluation of the fetus for 22q11 deletions and mutations (Driscoll et al (1991)
Lancet
338: 1390-1391).
SUMMARY OF THE INVENTION
There is provided by this invention novel methods of detecting genetic deletions, translocations, and

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