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Clinical Chemistry 45: 982-986, 1999;
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(Clinical Chemistry. 1999;45:982-986.)
© 1999 American Association for Clinical Chemistry, Inc.


Articles

TaqMan PCR-based Gene Dosage Assay for Predictive Testing in Individuals from a Cancer Family with INK4 Locus Haploinsufficiency

Ingrid Laurendeau, Michel Bahuau, Nicolas Vodovar, Claire Larramendy, Martine Olivi, Ivan Bieche, Michel Vidaud and Dominique Vidauda

Laboratoire de Génétique Moléculaire, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris V, 4 Avenue de l'Observatoire, 75006 Paris, France.
a Author for correspondence. Fax 33 1 44 07 17 54; e-mail dvidaud{at}teaser.fr


   Abstract
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Abstract
Introduction
Patients and Methods
Results
Discussion
References
 
Background: A genetic syndrome of cutaneous malignant melanoma and nervous system tumors recently has been characterized and shown to be linked to the INK4 locus in the 9p21 region. Hemizygosity at adjacent physically mapped microsatellite markers indicated deletion of p16, p19, and p15 clustered tumor suppressors. Because individuals from this family could benefit from predictive testing in terms of cancer prevention, we developed a direct test without need to analyze parental DNAs to comply with the rules of individual consent and secrecy.

Methods: We developed an assay using TaqManTM real-time quantitative PCR, with p15 as the test sequence and albumin (ALB) as the reference gene. The normalized ratio of p15/ALB is expected to yield a value of ~1 in individuals without the deletion, whereas a ratio of ~0.5, indicating p15 haploinsufficiency, is expected in predisposed individuals.

Results: All patients harboring the previously defined at-risk haplotype were correctly identified using this approach. In six individuals with deletions, the p15/ALB ratios were 0.472–0.556 (SD, 0.013–0.078). In the five individuals without deletions, the ratios were 0.919–1.019 (SD, 0.006–0.075).

Conclusions: This is the first report of a high-throughput, automatable gene dosage assay successfully applied to the identification of a germ-line deletion. This approach, not limited by marker informativeness or the need for harvesting live cells, can be applied to any condition with haploinsufficiency and extended to the characterization of most abnormalities of the ploidy.© 1999 American Association for Clinical Chemistry


   Introduction
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Abstract
Introduction
Patients and Methods
Results
Discussion
References
 
A genetic syndrome consisting of cutaneous malignant melanoma (CMM)1 and nervous system tumors (NSTs) recently has been defined on the basis of a five-generation family with a predisposing allele to CMM/dysplastic nevi, astrocytoma/glioblastoma, neurofibroma, schwannoma, and meningioma (1). This CMM-NST syndrome recently has been shown to be linked to the INK4 locus, with all patients sharing a common haplotype as defined by genetic markers of the 9p21 region, and has been demonstrated to result from a large germ-line deletion that ablates the whole cluster containing the p16, p19, and p15 tumor suppressor genes (2). Such a large DNA lesion was characterized by hemizygosity mapping based on the segregation of adjacent physically mapped microsatellite markers. We are now addressing the question of direct genetic testing aimed at identification of subjects with individual risk among the 100 initially surveyed. Indeed, a direct test that did not require the analysis of parental DNAs, as opposed to indirect microsatellite-based diagnosis, was a prerequisite for complying with the rules of individual consent and secrecy.

The recent development of real-time quantitative PCR based on the 5'-3' exonuclease activity of the Taq polymerase (3), referred as TaqManTM, has offered the opportunity to set up an original gene dosage assay using the ABI PRISM 7700 Sequence Detection System (Perkin-Elmer Biosystems), in which p15 was selected as the test sequence and albumin (ALB) as the reference disomic gene used to normalize the amounts of input genomic DNAs. Briefly, during the PCR process, a dual-labeled TaqMan probe annealed to the target sequence is cleaved by the 5'-3' exonuclease activity of the Taq polymerase, releasing the reporter dye (FAM) from the quencher dye (TAMRA). Upon excitation of by an argon laser, the release of the FAM produces an increase in the fluorescent emission, which is captured at 518 nm by a charged-couple device camera and analyzed through the algorithms of the ABI PRISM 7700 Sequence Detection System computer software (4)(5).

To develop a direct automatable predictive test in the family with INK4 locus haploinsufficiency, this p15 gene dosage assay was applied to a panel of 11 test, haplotype-positive or -negative, individuals from this large kindred.


   Patients and Methods
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Abstract
Introduction
Patients and Methods
Results
Discussion
References
 
patients, nucleic acids, and reference dna
High-molecular weight DNAs were prepared using standard proteinase K digestions followed by phenol-chloroform extractions (6) from whole-blood leukocytes or lymphoblastoid cell lines from 11 individuals, including 3 clinically affected and 3 healthy, all haplotype-sharing, relatives, as well as in 5 healthy haplotype-negative relatives, including 1 spouse (Fig. 1 ). The haplotypes have been defined elsewhere (1). High-quality human genomic DNA (Boehringer Mannheim) served as reference DNA.



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Figure 1. Test individuals from the CMM-NST family.

Squares refer to males, and circles refer to females. Hatched symbols denote the development of CMM or NST. The haplotype status of each test relative is indicated beneath his or her individual symbol, INK4 refers to the at-risk haplotype, and wt refers to any other wild-type haplotype, as previously defined and according to an individual numbering system based on a pedigree published elsewhere (2).

real-time pcr
In the TaqMan approach, one of the main variables, referred as Ct, is defined as the fractional cycle number at which the fluorescence generated by cleavage of the probe ({Delta}Rn) crosses a fixed threshold. The target gene copy number in unknown samples is inferred by plotting the Ct value against a calibration curve. To correctly determine the starting copy number regardless of the precise amounts and qualities of input genomic DNAs, we also quantified an internal control gene (ALB) in each single reaction. The normalized gene dose, N, is given by the following ratio:

The 7700 Sequence Detection System software automatically determines the Ct value and infers the starting copy number in each sample. The real-time PCR and the calibration curve are presented in Fig. 2 for ALB. Normalized gene doses N were then determined for each sample in three independent assays, and the corresponding means were calculated. In this method, a nondeleted test sequence is expected to yield a ratio of N = 1, as opposed to N = 0.5 when it is heterozygously deleted.



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Figure 2. Albumin (ALB) gene dosage by real-time PCR.

Top, amplification plots for reactions with starting ALB gene copy number of 33 000 (A1, 100 ng), 8250 (A4, 25 ng), 2062 (A7, 6.25 ng), or 515 (A10, 1.56 ng). The cycle number is plotted vs the change in normalized reporter signal ({Delta}Rn). For each reaction tube, the fluorescence signal of the reporter dye (FAM) is divided by the fluorescence signal of the passive reference dye (ROX) to obtain a ratio defined as the normalized reporter signal (Rn). {Delta}Rn represents the normalized reporter signal (Rn) minus the baseline signal established in the first 15 PCR cycles. {Delta}Rn increases during PCR as ALB PCR product copy number increases until the reaction reaches a plateau. Ct represents the fractional cycle number at which a significant increase in Rn above a baseline signal (horizontal black line) can first be detected. Three replicates were performed for each reference DNA sample, but the data for only one are shown here. Bottom, calibration curve plotting log starting copy number vs Ct. The black symbols represent the triplicate PCR amplification of the reference DNA samples and red symbols the triplicate PCR amplification of unknown genomic DNA, all included inside the calibration curve. The copy number of ALB (x) can be calculated as follows: y = -3.374x + 40.593, where the Ct value is substituted as y.

primers and probes
Primers and probes were chosen with assistance of the computer programs OligoTM, Ver. 4.0 (National Biosciences) and Primer ExpressTM, Ver. 1.0 (PE Biosystems). Their nucleotide sequences are shown in Table 1 . Primers were purchased from Life Technologies, and probes were purchased from PE Biosystems. The TaqMan PCR Core Reagent Kit, MicroAmp Optical TubesTM, and MicroAmp Optical CapsTM were from PE Biosystems.


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Table 1. Primers and probes.

pcr amplification
TaqMan amplification reactions were carried out in reaction volumes of 50 µL, using the components as supplied in the TaqMan PCR Core Reagent Kit. Each reaction contained 1x TaqMan buffer; 200 nmol/L each primer; 100 nmol/L each corresponding fluorogenic probe; 5 mmol/L MgCl2, 200 µmol/L each dATP, dCTP, and dGTP; 400 µmol/L dUTP; 1.25 U of AmpliTaqTM Gold, and 0.5 U of AmpEraseTM uracil N-glycosylase. Each sample was analyzed in triplicate, using 20 ng of DNA in each reaction. The reference DNA was serially diluted and run in parallel to establish the calibration curve and to infer copy numbers from the cycle thresholds (Cts), assuming a conversion factor of 6.6 pg of DNA per diploid genome. Thermal cycling was initiated with a 2-min incubation at 50 °C, followed by a first denaturation step of 10 min at 95 °C, and then 40 cycles of 95 °C for 15 s and 65 °C for 1 min.


   Results
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Abstract
Introduction
Patients and Methods
Results
Discussion
References
 
The results are presented in Table 2 as p15 gene dosage performed in triplicate and in three independent assays. Although the ALB and p15 genes were quantified on the same plate, the low interassay variability, which the use of a calibration curve helped reduce, allowed us to ascertain these genes in different plates. In addition, accurate results can be obtained with duplicate amplification.


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Table 2. Predictive testing based on a p15 TaqMan assay.1

The six haplotype-sharing affected or healthy individuals showed INK4 haploinsufficiency, i.e., were heterozygotes for the INK4 locus deletion [N {approx} 0.5 (0.472–0.556; SD, 0.013–0.078)]. This is in contrast to healthy, haplotype-negative individuals who were shown to contain two copies of the p15 gene per cell [N {approx} 1 (0.919–1.019; SD, 0.006–0.075)]. Therefore, all results were clear-cut with relatively small SDs, rendering the deletional status unambiguous.


   Discussion
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Abstract
Introduction
Patients and Methods
Results
Discussion
References
 
Since 1985, the identification of point mutations has been greatly facilitated by the development of PCR-based assays, but diagnosis of large gene rearrangements still awaited rapid and efficient technology. Recently, analysis of the loss of heterozygosity at a given locus by the use of highly polymorphic microsatellite markers allowed the characterization of a large number of gene deletions, especially in DNAs derived from tumor tissues. Nevertheless, this technology is limited by the presence of polymorphic markers and by their informativeness. In 1998, Cairns et al. (7) published a comparative study between microsatellite and quantitative PCR analyses to detect p16 copy number in primary bladder tumors and concluded that quantitative PCR, which is rapid, accurate, and sensitive, was certainly the most efficient method to identify genetic changes leading to tumorigenesis.

In the aim to identify subjects with individual risk in a large French family diagnosed with a CMM-NST syndrome associated with a whole INK4 locus germ-line deletion, a combination of microsatellite markers of the 9p21 region, flanking the deletion and defining the at-risk haplotype was initially studied. However, this indirect test, which was limited by marker informativeness and required the analysis of nuclear families, possibly including both deceased parents and minor children, was not compatible with the present rules of individual consent and secrecy. Thus, a TaqMan PCR-based gene dosage assay based on the quantification of the p15 gene was developed. This direct and accurate test allowed us to rapidly analyze all the family members willing to benefit from predictive testing and to identify those at risk.

After an initial optimization step for adequate primer pairs and probes, the TaqMan gene dosage method can be used efficiently to assay any chromosome, gene, or exon and thus has a wide variety of applications in both clinical and research settings. This is especially the case with autosomal dominant conditions with haploinsufficiency, such as familial breast and ovarian cancer (8), neurofibromatosis type 1 (9), or in carrier detection in X-linked disorders such as Duchenne muscular dystrophy (10). We believe this high-throughput, fast-turnaround time (up to 96 samples/2 h, which corresponds to 12 individuals tested using our approach), and simple method is clearly a cost-effective alternative to fluorescence in situ hybridization in clinical applications. In this respect, TaqMan lends itself particularly well to routine diagnosis of common microdeletion syndromes. Because of its accuracy, this novel approach, more reliable than end-point PCR gene dosage (11) and not limited by short tandem repeat marker informativeness (12), also strengthens the potentialities of DNA diagnosis in the field of human aneuploidies.


   Acknowledgments
 
This work was supported by the Association pour la Recherche sur le Cancer and the French Ministère de L'Enseignement Supérieur et de la Recherche.


   Footnotes
 
1 Nonstandard abbreviations: CMM, cutaneous malignant melanoma; NST, nervous system tumor; and Ct, threshold cycle.


   References
Top
Abstract
Introduction
Patients and Methods
Results
Discussion
References
 

  1. Bahuau M, Vidaud D, Kujas M, Palangié A, Assouline B, Chaignaud-Lebreton M, et al. Familial aggregation of malignant melanoma/dysplastic naevi and tumours of the nervous system: an original syndrome of tumour proneness. Ann Genet 1997;40:78-91. [Web of Science][Medline] [Order article via Infotrieve]
  2. Bahuau M, Vidaud D, Jenkins RB, Bièche I, Kimmel DW, Assouline B, et al. Germ-line deletion involving the INK4 locus in familial proneness to melanoma and nervous system tumors. Cancer Res 1998;58:2298-2303. [Abstract/Free Full Text]
  3. Holland PM, Abramson RD, Watson R, Gelfand DH. Detection of specific polymerase chain reaction product by utilizing the 5' to 3' exonuclease activity of Thermus aquaticus DNA polymerase. Proc Natl Acad Sci U S A 1991;88:7276-7280. [Abstract/Free Full Text]
  4. Lie YS, Petropoulos CJ. Advances in quantitative PCR technology: 5' nuclease assays. Curr Opin Biotechnol 1998;9:43-48. [Web of Science][Medline] [Order article via Infotrieve]
  5. Lo YMD, Tein MSC, Lau TK, Haines CJ, Leung TN, Poon PMK, et al. Quantitative analysis of fetal DNA in maternal plasma and serum: implications for noninvasive prenatal diagnosis. Am J Hum Genet 1998;62:768-775. [Web of Science][Medline] [Order article via Infotrieve]
  6. Sambrook J Fritsch EF Maniatis T eds. Molecular cloning: a laboratory manual 1989 Cold Spring Harbor Laboratory Cold Spring Harbor, NY. .
  7. Cairns JP, Chiang PW, Ramamoorthy S, Kurnit DM, Sidransky D. A comparison between microsatellite and quantitative PCR analyses to detect frequent p16 copy number changes in primary bladder tumors. Clin Cancer Res 1998;4:441-444. [Abstract/Free Full Text]
  8. Petrij-Bosch A, Peelen T, van Vliet M, van Eijk R, Olmer R, Drusedeau M, et al. BRCA1 genomic deletions are major founder mutations in Dutch breast cancer patients. Nat Genet 1997;17:341-345. [Web of Science][Medline] [Order article via Infotrieve]
  9. Shen MH, Harper PS, Upadhyaya M. Molecular genetics of neurofibromatosis type 1 (NF1). J Med Genet 1996;33:2-17. [Abstract/Free Full Text]
  10. van Essen AJ, Kneppers AL, van der Hout AH, Scheffer H, Ginjaar IB, ten Kate LP, et al. The clinical and molecular genetic approach to Duchenne and Becker muscular dystrophy: an updated protocol. J Med Genet 1997;34:805-812. [Abstract/Free Full Text]
  11. Celi FS, Cohen MM, Antonarakis SE, Wertheimer E, Roth J, Shuldiner AR. Determination of gene dosage by a quantitative adaptation of the polymerase chain reaction (gd-PCR): rapid detection of deletions and duplications of gene sequences. Genomics 1994;21:304-310. [Web of Science][Medline] [Order article via Infotrieve]
  12. Verma L, Macdonald F, Leedham P, McConachie M, Dhanjal S, Hultén M. Rapid and simple prenatal DNA diagnosis of Down's syndrome. Lancet 1998;352:9-12. [Web of Science][Medline] [Order article via Infotrieve]



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