Whole genome amplification from a single cell: implications for genetic analysis

Update in preimplantation genetic diagnosis. Age, genetics, and infertility

PGD has been successfully used for several years. Over 40 babies have been born worldwide by use of these techniques. Unfortunately, a number of misdiagnoses have been made, a distressing consequence of a new frontier. Significant advances have been made to improve the efficiency and accuracy of PCR and FISH. The widespread use of this technology awaits further documentation of safety and accuracy. Other issues must also be addressed. First, the cost-effectiveness of the techniques relative to the traditional alternatives must be evaluated. A number of ethical issues regarding embryo screening must be addressed including what diseases are serious enough to warrant the procedure. Another concern is the use of this technology for nongenetic disorders such as gender selection. Finally, the experimental nature of these procedures must continually be discussed with patients, and long-term follow-up studies must be undertaken. Development of more accurate and less expensive assays coupled with improved IVF success rates may make PGD a more widely used clinical tool. The future awaits these developments.

Mapping of bovine FcgammaR (FCGR) genes by sperm typing allows extended use of human map information

Polymorphic sites within the bovine FcgammaRI (FCGR1), FcgammaRII (FCGR2), and FcgammaRIII (FCGR3) genes were used for proximal mapping of these genes to bovine Chromosome (Chr) 3 (BTA3) with paternal half-sib families from Norwegian Cattle. A fine-structure genetic map of the region was obtained by the analysis of 288 sperm cells from three bulls that were heterozygous for the loci included in the study. No recombinants were observed between FCGR2 and FCGR3 (242 sperm cells). Considering FCGR2 and FCGR3 as a single locus, a three-point linkage analysis for [FCGR2/FCGR3], FCGR1, and INRA003 was carried out. The best-supported order of the loci was found to be INRA003-FCGR1-[FCGR2/FCGR3]. Map distances in a two-point linkage analysis were 10.3 cM between [FCGR2/FCGR3] and FCGR1, and 25.5 cM between FCGR1 and INRA003, respectively. This linkage mapping of the bovine FCGR gene family resembles the human situation where all FCGR genes are located at Chr 1 (HSA1), at position q21-q24. Moreover, the results locate the evolutionary breakpoint between HSA1q and BTA3 within the human 1q24 region.

Early complete hydatidiform moles contain inner cell mass derivatives

In four cases of early complete hydatidiform moles, confirmed to be androgenetic in origin by DNA studies, we have identified nonchorionic inner cell mass derived structures which are not commonly observed in specimens of later gestational age. These structures include nucleated red blood cells, endothelial cells, stromal macrophages, amnion and yolk sac. The latter four structures were confirmed by specific immunocytochemical stains. Recognition that such structures can accompany complete hydatidiform moles has both theoretical and practical significance. From a theoretical perspective, it demonstrates that the maternal genome is not required for the initiation of amniogenesis, development of the yolk sac, vasculogenesis, or hematopoiesis. From a practical perspective it emphasizes that complete hydatidiform moles, with their markedly increased risk of subsequent choriocarcinoma, cannot be excluded based on the finding of "fetal structures."

Consistent allelic loss on mouse chromosome 7 distal to tyrosinase in 4-nitroquinoline-1-oxide-induced oral cavity tumors with loss of heterozygosity at Ha-ras-1

We have previously shown that all CBA/J mice exposed to 4-nitroquinoline-1-oxide (4NQO) eventually develop oral cavity squamous cell carcinomas, and two-thirds of these tumors have Ha-ras-1 (Hras1) point mutations at codon 12. Half of the tumors with Hras1 mutations have loss of heterozygosity (LOH) at Hras1. In the study reported here, seven tumors with LOH at Hras1, six heterozygous for Hras1, and six without Hras1 mutations were analyzed to define the extent of LOH on chromosome (Chr) 7. Microsatellite polymorphisms present in CBA/J mice were used as informative allelic markers. Tumors with LOH at Hras1 showed consistent allelic loss at the distal portion of Chr 7. The boundary of allelic loss lay between the tyrosinase and hemoglobin beta chain loci, which are 6 cM apart. None of the tumors that remained heterozygous for Hras1 or had no Hras1 mutations had evidence of chromosomal loss involving Chr 7. Because LOH was only detected in advanced lesions long after exposure to 4NQO had ceased, we presume that the chromosomal alterations by which LOH occurred were independent of the carcinogen exposure. The development of LOH in only half of the tumors with Hras1 point mutations suggests that LOH was not caused by the initial Hras1 point mutation but was a highly selected event during tumorigenesis.

Spermatozoa lacking acrosin protein show delayed fertilization

Acrosin (ACR), a serine proteinase located in the acrosome of the sperm, has been presumed to be involved in the recognition and binding of the sperm to the zona pellucida of the ovum and the sperm penetration through the zona pellucida. To examine the function of acrosin in vivo, we have generated mice carrying a mutation at the acrosin locus (Acr) through targeted disruption in embryonic stem (ES) cells. One chimeric male and female transmitted the targeted gene through their germ line. Homozygous Acr-/- mice are fertile and yield litters comparable in number and size to those of Acr+/+ mice. These data show that sperm of the homozygous Acr-/- mice are able to penetrate the zona pellucida, fertilize the ovum, and produce viable offspring. However, spermatozoa lacking acrosin protein show a delayed fertilization. One chimeric male which contained the targeted gene in 20% of its sperm transmitted only the Acr+ allele to its progeny. Furthermore, in vitro fertilization with equally mixed sperm cells of Acr+/+ and Acr-/- mice resulted in fertilization only with the Acr+ sperm cells. Incubation of oocytes with Acr+ or Acr- sperm show that the Acr+ sperm are faster to fertilize the oocytes than the Acr- sperm cells. These results suggest that Acr- sperm have a selective disadvantage when they are in competition with Acr+ sperm.

The natural somatic mutation frequency and human carcinogenesis

Much recent attention has been paid to the important role of the DNA mismatch repair system in controlling the accumulation of somatic mutations in human tissues and the association of mismatch repair deficiency with carcinogenesis. In the absence of an intact mismatch repair system, cells accumulate mutations at a rate some 1000 times faster than normal cells, and this mutator phenotype is easily measured by the detection of the formation of new variant alleles at microsatellite loci. However, the mismatch repair system is not 100% efficient, even when intact, and the pattern of microsatellite alterations in a wide variety of tumors is consistent with these being due to clonal amplification from tissues that are genetically heterogeneous at microsatellite loci rather than mismatch repair deficiency in the tumor itself. On this basis, it can be estimated that the mutation frequency of microsatellites in normal human tissues is approximately 10(-2) per locus per cell. Similarly, a frequency of mutation at minisatellite loci in normal tissues of around 10(-1) per locus per cell can be estimated. Such elevated levels of mutation are consistent with a recent study of the frequency of HPRT mutation in human kidneys that demonstrated these to be frequent (average 2.5 x 10(-4) in individuals of 70 years or more) and exponentially related to age. Taken as a whole, the data suggest that somatic mutation in human epithelial cells may be some 10-fold higher than in peripheral blood lymphocytes and that the underlying rate of spontaneous mutation is sufficient to account for a large proportion of human carcinogenesis without the need to evoke either stepwise alteration to a mutator phenotype of clonal expansion at all the mutation steps in carcinogenesis. The exponential increase in mutation frequency with age is predictable on the basis that the mutation rate is controlled at the level of repair and that mutation in genes that affect the efficiency of these processes will gradually increase the underlying rate. In addition, the age relatedness of mutation frequency strongly supports the concept that mutation is cell division dependent and that cellular proliferation per se is an important risk factor for cancer. Comparison of somatic mutations with those in the human germline mutation suggests common mechanistic origins and that the high levels of somatic mutation that occur are a direct reflection of the germline mutation rate selected over evolutionary time. Thus, the somatic accumulation of mutations can be seen as a natural process within the human body and cancer a normal part of the human life cycle. This point of view may explain why it has been so difficult to significantly reduce cancer incidence and suggests that, for this to be achieved, the means of altering the natural somatic mutation rate needs to be identified.

Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed on less than one nanogram of genomic DNA

Genetic analysis of limiting quantities of genomic DNA play an important role in DNA forensics, paleoarcheology, genetic disease diagnosis, genetic linkage analysis, and genetic diversity studies. We have tested the ability of degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR) to amplify picogram quantities of human genomic DNA for the purpose of increasing the amount of template for genotyping with microsatellite repeat markers. DNA was uniformly amplified at a large number of typable loci throughout the human genome with starting template DNAs from as little as 15 pg to as much as 400 ng. A much greater-fold enrichment was seen for the smaller genomic DOP-PCRs. All markers tested were amplified from starting genomic DNAs in the range of 0.6-40 ng with amplifications of 200- to 600-fold. The DOP-PCR-amplified genomic DNA was an excellent and reliable template for genotyping with microsatellites, which give distinct bands with no increase in stutter artifact on di-, tri-, and tetranucleotide repeats. There appears to be equal amplification of genomic DNA from 55 of 55 tested discrete microsatellites implying near complete coverage of the human genome. Thus, DOP-PCR appears to allow unbiased, hundreds-fold whole genome amplification of human genomic DNA for genotypic analysis.

Prenatal diagnosis of Duchenne and Becker muscular dystrophy

Prenatal diagnosis of Duchenne and Becker muscular dystrophy is performed as a routine procedure in many laboratories around the world, using numerous molecular genetic techniques. Rather than discussing methods that are commonly in use, this review concentrates on some of the methods that are less widely available. This includes techniques than can be applied to routine diagnosis, to difficult cases where DNA analysis is unhelpful, and alternatives to standard methods of prenatal diagnosis.

Individual variation in recombination among human males

Studies of recombination between the markers D6S291 and D6S109 in individuals by sperm typing provide direct evidence for significant variation in recombination among humans. A statistically significant difference in the recombination fraction (range 5.1%-11.2%) was detected among five donors. This variation could reflect polymorphisms in genes affecting recombination or in chromosome structure. Ignoring this variability in studies designed to examine the relationship between physical and genetic distances could lead to incorrect inferences. Individual variation in recombination makes it difficult to predict the recombination fraction for an interval in any particular individual. This could be important in certain genetic counseling situations.

Frequent clones of p53-mutated keratinocytes in normal human skin

The multiple genetic hit model of cancer predicts that normal individuals should have stable populations of cancer-prone, but noncancerous, mutant cells awaiting further genetic hits. We report that whole-mount preparations of human skin contain clonal patches of p53-mutated keratinocytes, arising from the dermal-epidermal junction and from hair follicles. These clones, 60-3000 cells in size, are present at frequencies exceeding 40 cells per cm2 and together involve as much as 4% of the epidermis. In sun-exposed skin, clones are both more frequent and larger than in sun-shielded skin. We conclude that, in addition to being a tumorigenic mutagen, sunlight acts as a tumor promoter by favoring the clonal expansion of p53-mutated cells. These combined actions of sunlight result in normal individuals carrying a substantial burden of keratinocytes predisposed to cancer.

Use of tagged random hexamer amplification (TRHA) to clone and sequence minute quantities of DNA--application to a 180 kb plasmid isolated from Sphingomonas F199

We have developed a novel method to clone and sequence minute quantities of DNA. The method was applied to sequence a 180 kb plasmid pNL1. The first step was the production of a size distributed population of DNA molecules that were derived from the 180 kb plasmid pNL1. The first step was accomplished by a random synthesis reaction using Klenow fragment and random hexamers tagged with a T7 primer at the primer 5'-end (T7-dN6, 5'-GTAATACGACTCACTATAGGGCNNNNNN-3'. In the second step, Klenow-synthesized molecules were amplified by PCR using T7 primer (5'-GTAATACGACTCACTATAGGGC-3'). With a hundred nanograms starting plasmid DNA from pNL1, we were able to generate Klenow-synthesized molecules with sizes ranging from 28 bp to >23 kb which were detectable on an agarose gel. The Klenow-synthesized molecules were then used as templates for standard PCR with T7 primer. PCR products of sizes ranging from 0.3 to 1.3 kb were obtained for cloning and sequencing. From the same Klenow-synthesized molecules, we were also able to generate PCR products with sizes up to 23 kb by long range PCR. A total 232.5 kb sequences were obtained from 593 plasmid clones and over twenty putative genes were identified. Sequences from these 593 clones were assembled into 62 contigs and 99 individual sequence fragments with a total unique sequence of 86.3 kb.

New advances in sex preselection

OBJECTIVE

To review the current developments in the field of preconceptual sex selection and to discuss the moral dilemmas that accompany the scientific progress.

DESIGN

A survey of the major publications on sex preselection.

RESULTS

Examination of current methods of preconceptual gender selection revealed that in vivo methods such as timing of intercourse, the use of ovulation induction medications, and artificial insemination do not appear to affect the sex ratio to a clinically significant degree. In vitro separation of X- and Y-bearing spermatozoa by gradient techniques have been reported to alter significantly the sex ratio at birth. However, these trials were noncontrolled, and molecular biological techniques could not validate that these methods indeed change the Y- to X-bearing spermatozoa ratio sufficiently for clinical use. Nevertheless recent scientific advances have made highly reliable preconceptual sex selection possible by using preimplantation diagnosis or sperm separation by flow cytometry combined with IVF. At present, these methods have been used to avoid sex-linked disorders. Both involve the invasive procedure of IVF and thus are held by most as inappropriate for nonmedical indications. However, improvement in flow cytometry output of sexed spermatozoa might provide in the near future sufficient sorted gametes for artificial insemination. This technique then will provide an available noninvasive method of sexing for social purposes.

CONCLUSIONS

Reliable preconceptual sex selection is currently possible only by preimplantation diagnosis, or sperm separation by flow cytometry combined with IVF. Both methods involve invasive procedures and are at present exclusively used for medical indications. It may be that in the near future, an improvement in flow cytometry output of sexed spermatozoa will provide sufficient sorted gametes for artificial insemination. In such a case, the medical community will be forced to take a stand, whether this reliable noninvasive method of sexing will be allowed for social purposes.

17p (p53) allelic losses, 4N (G2/tetraploid) populations, and progression to aneuploidy in Barrett's esophagus

Increased 4N (G2/tetraploid) cell populations have been postulated to be genetically unstable intermediates in the progression to many cancers, but the mechanism by which they develop and their relationship to instability have been difficult to investigate in humans in vivo. Barrett's esophagus is an excellent model system in which to investigate the order in which genetic and cell cycle abnormalities develop relative to each other during human neoplastic progression. Neoplastic progression in Barrett's esophagus is characterized by inactivation of the p53 gene, the development of increased 4N (G2/tetraploid) cell fractions, and the appearance of aneuploid cell populations. We investigated the hypothesis that patients whose biopsies have increased 4N (G2/tetraploid) cell fractions are predisposed to progression to aneuploidy and determined the relationship between inactivation of p53 and the development of 4N abnormalities in Barrett's epithelium. Our results indicate that increased 4N (G2/tetraploid) populations predict progression to aneuploidy and that the development of 4N abnormalities is interdependent with inactivation of the p53 gene in Barrett's esophagus in vivo.

Theoretical uncertainty of measurements using quantitative polymerase chain reaction

Current quantitative polymerase chain reaction (PCR) protocols are only indicative of the quantity of a target sequence relative to a standard, because no means of estimating the amplification rate is yet available. The variability of PCR performed on isolated cells has already been reported by several authors, but it could not be extensively studied, because of lack of a system for doing kinetic data acquisition and of statistical methods suitable for analyzing this type of data. We used the branching process theory to simulate and analyze quantitative kinetic PCR data. We computed the probability distribution of the offspring of a single molecule. We demonstrated that the rate of amplication has a severe influence on the shape of this distribution. For high values of the amplification rate, the distribution has several maxima of probability. A single amplification trajectory is used to estimate the initial copy number of the target sequence as well as its confidence interval, provided that the amplification is done over more than 20 cycles. The consequence of possible molecular fluctuations in the early stage of amplification is that small copy numbers result in relatively larger intervals than large initial copy numbers. The confidence interval amplitude is the theoretical uncertainty of measurements using quantitative PCR. We expect these results to be applicable to the data produced by the next generation of thermocyclers for quantitative applications.

Practical histological microdissection for PCR analysis

Recovery of cells by histological microdissection is increasingly used for analysis by polymerase chain reaction (PCR) or microchemical techniques. This paper describes techniques of histological microdissection. Sections of archival formalin-fixed, paraffin-embedded tissue up to 15 years old were mounted on plain glass slides. Sections 6-7 microns in thickness stained with toluidine blue were dissected under proteinase K buffer solution, using an electrolytically sharpened tungsten needle in a bacteriological loop-holder and a Leitz mechanical micromanipulator (model M). Detached cell groups were recovered in a silicone-coated pipette tip for PCR analysis after digestion in 25-50 microliters of proteinase K (500/ml) in TRIS-HCl buffer (pH 8.3). Consistent amplification and analysis of microsatellite loci were obtained from 2 microliters of crude lysate using 28-30 cycles of PCR incorporating a 32P 5'-end-labelled primer, electrophoresis under denaturing conditions on 6 per cent polyacrylamide gels, and autoradiographic detection.

The use of embryo genotyping in the propagation of genes involved in the immune response

Multiple ovulation and embryo transfer (MOET) now enables researchers to produce identical twin animals, to obtain progeny from pre-pubertal females and to obtain more offspring from valuable animals. MOET and sexed semen have produced genetic progress of up to 60% of milk production. The oestrous cycles of animals are synchronized with progestagens before superovulation with gonadal hormones, pregnant mare serum gonadotrophin and follicle stimulating hormone. Surgical, non-surgical and laparoscopic methods are applied to recover and transfer embryos. Sexing and genotyping of the pre-implantation embryos is a key step in improving the management and breeding programmes for livestock, as well as in the human for the prenatal diagnosis of genetic disorders. Several serological and physiological methods have been used to determine the sex of the pre-implantation embryos; none has had satisfactory results in terms of time and accuracy. Sexing by polymerase chain reaction (PCR) using male-specific chromosome sequences alone or with female-specific chromosomal DNA probes simultaneously has been sufficient to identify the sex of the embryos with 100% accuracy. However, caution should be taken against sources of the contamination. The MHC class I, class II and background genes have been implicated in resistance to internal parasites in animals. Biotechnological methods such as screening of embryos prior to transfer using PCR and primer extension pre-amplification have already made it possible to detect transgenic or genetically disordered embryos and could be applied to select those embryos bearing immunological genotypes of interest, such as resistance to internal parasites. Ultimately, cloning and nuclear transplantation would provide the possibility of isolating these resistance genes and to transfer them to livestock pre-implantation embryos to propagate these desirable traits.

Preimplantation genetic diagnosis of cystic fibrosis (delta F508)

Cystic fibrosis is a common autosomal recessive condition caused by mutations in the cystic fibrosis transmembrane regulator gene. The major mutation is a three base pair deletion (delta F508). If both partners carry this deletion, the chance of having an affected child is 1 in 4. In vitro fertilization (IVF) with preimplantation genetic diagnosis allows the selection of the unaffected embryos only to be returned to the uterus. Preimplantation genetic diagnosis was attempted in 14 couples in which both partners carry the delta F508 deletion. A total of 22 cycles resulted in 170 normally fertilized embryos of which, 145 embryos were successfully biopsied and in 18 cycles, one or two unaffected embryos were transferred. A total of five clinical pregnancies established and at birth all five singletons have been confirmed as homozygous for the normal allele. From our experience, cleavage stage biopsy after in vitro fertilization provides sufficient embryos diagnosed as unaffected for transfer in this autosomal recessive disease. Also, pregnancy rates after the preimplantation diagnosis are similar to those with infertile couples. Prospects for applying preimplantation genetic diagnosis to autosomal dominant conditions, where incidences of having affected embryos would be higher, therefore, appear good.

Direct detection of expanded trinucleotide repeats using PCR and DNA hybridization techniques

Recently, unstable trinucleotide repeats have been shown to be the etiologic factor in seven neuropsychiatric diseases, and they may play a similar role in other genetic disorders which exhibit genetic anticipation. We have tested one polymerase chain reaction (PCR)-based and two hybridization-based methods for direct detection of unstable DNA expansion in genomic DNA. This technique employs a single primer (asymmetric) PCR using total genomic DNA as a template to efficiently screen for the presence of large trinucleotide repeat expansions. High-stringency Southern blot hybridization with a PCR-generated trinucleotide repeat probe allowed detection of the DNA fragment containing the expansion. Analysis of myotonic dystrophy patients containing different degrees of (CTG)n expansion demonstrated the identification of the site of trinucleotide instability in some affected individuals without any prior information regarding genetic map location. The same probe was used for fluorescent in situ hybridization and several regions of (CTG)n/(CAG)n repeats in the human genome were detected, including the myotonic dystrophy locus on chromosome 19q. Although limited at present to large trinucleotide repeat expansions, these strategies can be applied to directly clone genes involved in disorders caused by large expansions of unstable DNA.

Polymerase chain reaction amplification specificity: incidence of allele dropout using different DNA preparation methods for heterozygous single cells

PURPOSE

The purpose was to evaluate methods of DNA preparation in a single cell to determine the ability to amplify and correctly diagnose a targeted gene.

METHODS

One- or two-cell lymphoblasts (n = 100/group), heterozygous for the normal and 4-base pair insertion on exon 11 of the beta-hexosaminidase A gene, were collected and prepared under the following conditions: (1) freeze-thaw liquid nitrogen, then boiling (LN2); (2) potassium hydroxide/dithiothreitol, heated to 65 degrees C, followed by acid neutralization (KOH); (3) boiling only (Bl); and (4) water only (H2O). Cells were analyzed by polymerase chain reaction using nested primers.

RESULTS

The total number of cells amplifying [in brackets] and the cells with amplification for both alleles (heterozygous), the normal allele, or the mutant allele were as follows, respectively: LN2 [38], 11, 16, 11; KOH [97], 91, 5, 1; Bl [41], 17, 13, 11; and H2O [85], 41, 16, 28. With two cells per reaction tube the results were as follows: LN2 [85], 53, 14, 18; and KOH [97], 96, 1, 0.

CONCLUSIONS

KOH lysis was significantly greater than with all other methods (P < 0.006) and should be used for single cells. This study also demonstrates the importance of using heterozygous cells to determine the ability to amplify both alleles as a method of quality control for single-cell analysis.

Preimplantation diagnosis of inherited disease by embryo biopsy: an update of the world figures

PURPOSE

Cleavage stage embryo biopsy and preimplantation diagnosis was first reported five years ago. The annual collation of the world figures for centres offering this procedure is important to continually assess the efficiency and success of the biopsy, diagnosis and pregnancies obtained.

MATERIALS AND METHODS

Data was collected from 14 centres worldwide. The largest series of diagnosis has been performed for those patients carrying X-linked disease where the embryos have been sexed either by PCR or FISH. PCR has also been used for the specific diagnosis of a number of single gene defects, mainly for cystic fibrosis but also for the diagnosis of Lesch Nyhan syndrome, Fragile X, Duchenne muscular dystrophy, Tay Sachs, haemophilia and RhD blood typing.

RESULTS

For PCR sexing, a total of 62 cycles have been performed with 14 pregnancies, 8 deliveries and 11 babies born. For FISH sexing, 70 cycles have resulted in 15 pregnancies, 8 deliveries and 11 babies born. For the specific diagnosis of single genes defects, a total of 65 cycles resulted in 21 pregnancies, 12 deliveries and 12 babies born. Overall, 197 cycles were performed, with 171 embryo transfers (86%), 50 pregnancies (25% per cycle, 29% per transfer), 28 deliveries and 34 babies born.

CONCLUSIONS

New methods are being developed to increase the scope of preimplantation diagnoses that can be offered. From next year, the biochemical and miscarriage rates will also be recorded.

Review: preimplantation diagnosis of inherited disease

Preimplantation diagnosis of inherited diseases has become possible with the techniques of in vitro fertilization, blastomere biopsy of the 6- to 10-cell embryo and DNA analysis of the single blastomeres. Disease-free embryos are selected for transfer to the uterus, thereby avoiding the need for termination of a fetus diagnosed as affected in prenatal diagnosis in the first or early-second trimester of pregnancy. The genetic indications for preimplantation diagnosis are theoretically the same as for prenatal diagnosis, but the defects must be detectable by the polymerase chain reaction. For X-linked recessive diseases, fluorescence in situ hybridization can be used as an alternative for the selection of female embryos. So far almost 40 healthy children have been born worldwide after preimplantation diagnosis for genetic disease. The possibilities and limitations of preimplantation diagnosis, especially in prevention of inherited disease, are discussed in this review.

Prenatal diagnosis by analysis of fetal cells in maternal blood

The data accumulated thus far indicate that fetal NRBCs are the target cell type of choice in maternal blood for most investigators, although some groups continue to work with the trophoblast. Reports of persistent circulation of hematopoietic stem cells, lymphoid/myeloid progenitors, and lymphocytes mandate that removal of these cell types must occur before clinical diagnosis of the current pregnancy can be made. In selected cases, accurate detection of fetal aneuploidy has been made from fetal cells in maternal blood; the clinical evaluation sponsored by the National Institute of Child Health and Human Development will determine the sensitivity and specificity of cytogenetic diagnosis in a larger group of pregnant women, but this information will not be available for several years. At present, detection of uniquely fetal, paternally inherited gene polymorphisms or mutations such as the Rh(D) antigen is possible only because the mother lacks these genes; hence, maternal cell contamination does not hinder diagnosis. Currently the presence of large numbers of maternal cells in enriched samples precludes single-gene diagnosis for conditions in which the mother carries a mutant gene, because her cells are preferentially amplified and difficult to distinguish from those of the fetus. It is likely, however, that as techniques of individual fetal cell isolation are perfected, maternal cell contamination will no longer be an issue, and the entire fetal genome will become available for diagnosis and therapy. Pediatricians need to be aware of the progress of research in this field, because fetal cell isolation from maternal blood not only could change prenatal diagnosis but would change the amount of genetic information that arrives with a newborn infant at birth. The ultimate goal of this work is to diagnose noninvasively, in the first trimester, the common fetal aneuploidies and single-gene disorders, to permit in utero treatment, or to allow low-risk pregnant women carrying an abnormal fetus an opportunity for reproductive choice.

Duplication and loss of chromosome 21 in two children with Down syndrome and acute leukemia

Acute leukemia in Down syndrome (DS) is often associated with additional changes in the number or structure of chromosome 21. We present two DS patients whose leukemic karyotypes were associated with changes in chromosome 21 ploidy. Patient 1 developed acute lymphocytic leukemia (type L1); disomy for chromosome 21 was evident in all blast cells examined. Loss of the paternal chromosome in the leukemic clone produced maternal uniparental disomy with isodisomy over a 25-cM interval. The second patient had acute monoblastic leukemia (type M5) with tetrasomy 21 in all leukemic cells. DNA polymorphism analysis showed duplicate paternal chromosomes in the constitutional genotype. The maternal chromosome was subsequently duplicated in the leukemic clone. The distinct inheritance patterns of chromosome 21 in the blast cells of these patients would appear to indicate that leukemogenesis occurred by different genetic mechanisms in each individual.

A microdissection approach to detect molecular markers during progression of prostate cancer

To investigate the underlying mechanisms of carcinogenesis, we have developed a technique to determine the frequency of genetic changes in prostatic carcinoma tissue. We have demonstrated that at a ratio of between 1:4 and 1:9 mutant-normal alleles, the signal from a mutant TP53 allele is not apparent after polymerase chain reaction (PCR) amplification and further direct sequencing or single-strand conformation polymorphism (SSCP) analysis. To bypass this problem, which is inherent in the heterogeneity of the prostate tissue and of the tumour, we selected areas of graded prostate tumours (Gleason score) from cryosectioned preparations and microdissected these cells (20-100 cells). After anionic resin removal of proteins, PCR amplification of TP53 gene exons 5/6 and SSCP analysis, an abnormal SSCP band shift was observed in suspected tumour cells, compared with microdissected stromal cells used as an internal control, while (1) a crude preparation of tissue DNA carrying the tumour did not show any abnormality and (2) immunostaining by a set of monoclonal antibodies against TP53 protein remained negative. Nucleotide sequence analysis of the different bands confirmed the presence of a mutation in the TP53 gene exon 6 position 13,336 in an abnormal band for one specimen, while no mutation was detected in the normal SSCP band. By targeting recognised tumour cells we can find DNA mutations which are undetectable using the standard technique of whole-tissue DNA extraction, particularly in a heterogeneous tumour such as carcinoma of the prostate.

Genotypic analysis of multiple loci in somatic cells by whole genome amplification

To screen multiple loci in small purified samples of diploid and aneuploid cells a PCR-based technique of whole genome amplification was adapted to the study of somatic lesions. DNA samples from different numbers of flow-sorted diploid and aneuploid cells from biopsies were amplified with a degenerate 15mer primer. Aliquots of these reactions were then used in locus-specific reactions using a single round of PCR cycles with individual sets of primers representing polymorphic markers for different regions. As a result, polymorphic markers for different chromosomal regions, including VNTRs and dinucleotide repeats, can be used to perform up to 30 locus-specific PCR assays with a single sample obtained from fewer than 1000 cells.

Recent advances in reproductive genetic technologies

New possibilities for the diagnosis and treatment of reproductive and genetic disorders are becoming available as a result of a series of recent technical advances. Intracytoplasmic sperm injection (ICSI) allows treatment of numerous infertile men whose sperm cannot penetrate the egg to initiate fertilization. Molecular genetic testing provides clients of reproductive age with additional information that permits prevention of genetic diseases such as fragile X syndrome, the leading cause of inherited mental retardation. Preimplantation genetic testing (PGT) offers couples who carry genetic disorders the prospect of having children with a greatly decreased risk of initiating a pregnancy involving an affected individual. Flow-cytometric sperm separation offers a new, effective approach for prevention of X-linked genetic disorders. Two major causes of recurrent pregnancy loss (RPL) involve recurrent trisomies and immunological disorders. Of the latter, 70% of studied populations of patients can attain live births with simple treatment protocols. Maternal serum assays involving multiple markers reduce both false positives and false negatives in detection of trisomies. Despite these advances in research, many safe and effective methods of diagnosis and treatment remain under-utilized in the clinical arena.

Whole genome amplification of single cells: mathematical analysis of PEP and tagged PCR

We construct a mathematical model for two whole genome amplification strategies, primer extension preamplification (PEP) and tagged polymerase chain reaction (tagged PCR). An explicit formula for the expected target yield of PEP is obtained. The distribution of the target yield and the coverage properties of these two strategies are studied by simulations. From our studies we find that polymerase with high processivity may increase the efficiency of PEP and tagged PCR.

Marfan syndrome as a paradigm for transcript-targeted preimplantation diagnosis of heterozygous mutations

Among the many clinical applications of the polymerase chain reaction (PCR) is its potential use in preimplantation diagnosis of genetic disorders. Performing PCR on single blastomeres from early cleavage stage (six- to eight-cell) human embryos should, in principle, enable reliable determination of disease status for certain inherited conditions. However, reports of misdiagnoses using this technique have diminished enthusiasm for its widespread clinical use. One principal source of error is the propensity for genome-targeted PCR to exclusively amplify one allele in reactions assaying a single heterozygous diploid cell. Complete reaction failure is also common. Employing the Marfan syndrome (MFS) as a paradigm, we have developed a reliable, reverse transcription-PCR-based method of genotyping single cells that overcomes these obstacles. The technique should facilitate accurate preimplantation diagnosis of MFS and other selected genetic diseases caused by heterozygous or compound-heterozygous mutations.

Enzymatic amplification of specific deoxyribonucleic acid sequences from single cells: evaluation of a simplified and rapid method for use in preimplantation genetic diagnosis

OBJECTIVE

To develop a simplified polymerase chain reaction (PCR) protocol on single cells for the purpose of preimplantation genetic diagnosis. Also to evaluate a new thermal cycler, RoboCycler 40 (Stratagene, La Jolla, CA), for reducing the time to complete PCR amplification.

DESIGN

PCR amplification without DNA purification or reamplification of a 149 base pair (bp) segment of the human Y chromosome was used as a model. The assay was tested in human fetal cells, single lymphocytes and single human blastomeres.

RESULTS

Amplification of the 149 bp segment using fetal cells was 100% correct. Results on single lymphocytes were concordant in all but one of the 15 male cases. However, 2 of the 25 female cases were identified as male suggesting the occurrence of DNA contamination. Analysis of 61 blastomeres were concordant in 57 cases (93%); results for male blastomeres showed 12% of false negatives. No false positives were detected for female cells. Amplification using the simplified PCR protocol in combination with the RoboCycler was completed in 2 hours.

CONCLUSION

These data show that this PCR assay performed directly, without DNA extraction or purification and without re-amplification is a practical and effective approach for amplification of specific DNA sequences in single cells. Furthermore, the simplified PCR protocol significantly reduced the time to complete DNA amplification. The reduced time is expected to facilitate the management of a routine program for preimplantation genetic diagnosis.

Gametic and somatic tissue-specific heterogeneity of the expanded SCA1 CAG repeat in spinocerebellar ataxia type 1

Spinocerebellar ataxia type 1 is associated with expansion of an unstable CAG repeat within the SCA1 gene. Male gametic heterogeneity of the expanded repeat is demonstrated using single sperm and low-copy genome analysis. Low-copy genome analysis of peripheral blood also reveals somatic heterogeneity of the expanded SCA1 allele, thus establishing mitotic instability at this locus. Comparative analysis of a large normal allele and a small affected allele suggests a role of midstream CAT interspersions in stabilizing long (CAG)n stretches. Within the brain, tissue-specific mosaicism of the expanded allele is also observed. The differences in SCA1 allele heterogeneity between sperm and blood and within the brain parallels the findings in Huntington disease, suggesting that both disorders share a common mechanism for tissue-specific instability.

Molecular biology and physiology at the single-cell level

The functional characterization of the many complex proteins expressed in the CNS is a daunting task. The development of nucleic acid amplification techniques has provided a powerful tool to tackle this challenging enterprise. Recently, these techniques have been successfully used to correlate the functional properties of various CNS proteins with their specific mRNA expression patterns in the brain.

Cytogenetic and molecular studies of Down syndrome individuals with leukemia

There is an increased risk of leukemia in Down syndrome (DS) patients, with estimates ranging from 14 to 30 times the incidence rate observed for chromosomally normal children. Furthermore, one type of leukemia, called "transient leukemia" (TL), occurs almost exclusively in DS infants. The basis of the association between DS and leukemia is unknown, but we and others have hypothesized that it may be influenced by the mechanism of origin of the extra chromosome. Therefore, we initiated a cytogenetic and molecular study of nondisjunction in leukemia DS individuals. To date, we have obtained blood and/or tissue samples from 55 individuals consisting of 17 cases with TL, 7 cases of acute nonlymphocytic leukemia subtype M7 (ANLL-M7, or acute megakaryoblastic leukemia, postulated to be related to TL), and 31 cases of other forms of leukemia. Analysis of these cases suggests differences between DS children with TL and those with other types of leukemia or DS individuals with no history of leukemia. Specifically, the TL and ANLL-M7 cases have a highly significant increase in the frequency of "atypical" constitutional karyotypes (i.e., mosaic trisomies, rings, and/or isochromosomes) and are almost always male. Additionally, genetic mapping studies suggest an increase in the frequency of disomic homozygosity, especially in proximal 21q, in DS individuals with TL and ANLL-M7.

Normal pregnancy after preimplantation DNA diagnosis of a dystrophin gene deletion

To perform preimplantation DNA diagnosis for Duchenne muscular dystrophy (DMD) in a female carrier of a dystrophin gene deletion of exons 3-18, we developed a polymerase chain reaction (PCR)-based assay of exon 17 sequences. Exon 17 was efficiently amplified in all 50 single blastomeres of normal control embryos and in five blastomeres of one male embryo of the DMD carrier obtained after a first preimplantation diagnosis (PID) for gender determination. In ten blastomeres of another two male embryos of the DMD carrier, no PCR signals were observed, probably as a result of the deletion. After intracytoplasmic sperm injection, embryos were analysed for exon 17 and three of the four embryos showing normal PCR signals were replaced, resulting in a singleton pregnancy. Prenatal diagnosis showed a female karyotype and DNA analysis indicated that the fetus was not a DMD carrier.

The 18q- syndrome: analysis of chromosomes by bivariate flow karyotyping and the PCR reveals a successive set of deletion breakpoints within 18q21.2-q22.2

The 18q- syndrome is one of several terminal deletion disorders that occur in humans. Previous G-banding studies suggest that the loss of a critical band, 18q21.3, results in mental retardation, craniofacial anomalies, and metabolic defects. However, it is difficult to reconcile the consistent loss of a single region with the large variability in clinical phenotype. The purpose of this study was to reassess the extent of chromosomal loss in a cohort of 17 18q- syndrome patients by using fluorescent-activated chromosome sorting, PCR, and FISH. Bivariate flow karyotypes revealed heterogeneity among the deletions; they ranged in size from 9 to 26 Mb. To confirm this heterogeneity at a molecular level, deleted and normal chromosomes 18 of six patients were collected by flow sorting, preamplified by random priming, and assayed for marker content by the PCR. This analysis defined five unique breakpoints among the six patients. We conclude that the terminal deletions in the 18q- syndrome occur over a broad region spanning the interval from 18q21.2 to 18q22.2. Our results suggest that the variability in clinical phenotype may be more representative of a contiguous-gene syndrome with a baseline deficit of 18q22.2-qter than of the loss of a single critical region within 18q21.3.

Analysis of randomly amplified flow-sorted chromosomes using the polymerase chain reaction

Bivariate fluorescence-activated sorting is a method for obtaining relatively pure fractions of chromosomal DNA. Unfortunately, the yields (< 0.25 microgram/day) frequently limit the types of molecular analysis that can be performed. The polymerase chain reaction (PCR) is capable of amplifying unique sequences from scant amounts of template DNA. The purpose of this study was to determine whether the sensitivity of the PCR could be used to detect sequences specific to chromosomes discriminated and purified by flow cytometry. Flow-sorted chromosomal DNA was prepared by collecting approximately 10(5) chromosomes onto a nitrocellulose filter and eluting the DNA by boiling. Amplification products were not detected when different amounts of chromosomal DNA were used in a single 30 to 40-cycle PCR assay. However, when the eluted DNA was primed with degenerate 15-bp oligonucleotides and randomly amplified prior to performing the PCR assay, sequence-tagged sites (STSs) were detected after gel electrophoresis and ethidium bromide staining. This random amplification step eliminated the need for both reamplification with nested primers and detection by DNA hybridization. Furthermore, the random amplification scheme provided enough template DNA from a single sort (10(5) chromosomes) to perform > 1000 PCR assays. Representational analysis of one chromosome type revealed that > 74% of 70 STSs were detected. Moreover, the technology could be used to identify and delineate the breakpoint region of a marker chromosome. This amplification scheme should simplify greatly the molecular analysis of normal and aberrant chromosomes.

The polymerase chain reaction in histopathology

Thanks to the advent of the polymerase chain reaction (PCR) molecular genetic study of histological samples is now a relatively straightforward task and the vast histopathology archives are now open to molecular analysis. In this review we outline technical aspects of PCR analysis of histological material and evaluate its application to the diagnosis and study of genetic, infectious and neoplastic disease. In addition, we describe a number of newly developed methods for the correlation of PCR analysis with histology, which will aid the understanding of the molecular basis of pathological processes.

Perspectives on molecular assays for measuring mutation in humans and rodents

The original idea for this article was to examine the new molecular techniques for detection of mutation directly at the DNA level in exposed individuals or their offspring and to assess their relative advantages and disadvantages for mutation monitoring in humans and rodents. However, an examination of the articles and a comparison of the technology indicated that our constant quests for methods improvement were leading to some loss of insight into the important health-related questions that should be guiding these endeavors. As a result, individual methods are not covered here in great technical detail. Instead, a few molecular methods are presented in a general overview, along with some of the biological issues related to the detection of induced mutations within individuals and populations. Some hypothetical scenarios are also presented because molecular approaches will continue to change rapidly, and we must continually adjust our thinking to combine the useful attributes of each current and future technical approach with the most appropriate biological questions.

Preimplantation diagnosis

Research towards preimplantation diagnosis of genetic disease was initiated in the UK in the mid 1980s with the aim of helping those couples who would prefer selection to occur at this stage rather than during pregnancy. Following in vitro fertilisation, (IVF), biopsy and removal of 1 or 2 of the totipotent cells from the cleavage stage 3 day old embryo provides the material for molecular genetic diagnosis without interfering with development. Earliest applications were in the avoidance of X-linked disease by sexing embryos and selecting females for transfer to the mother. Initially, polymerase chain reaction (PCR) amplification of DNA from the biopsied blastomeres was performed using primers specific for sequences derived from the Y chromosome and this led to the birth of several normal girls. To reduce the risk of misdiagnosis due to amplification failure, PCR based methods for sexing the embryo now employ both X and Y specific sequences, but the preferred method is currently considered to be fluorescent in situ hybridisation (FISH) with fluorochrome labelled DNA probes to the embryonic nuclei that have been fixed and spread on slides. Dual FISH with probes from X and Y chromosomes allows unequivocal diagnosis of sex and determination of chromosome copy number, avoiding transfer of embryos with abnormal numbers of sex chromosomes, including those with only the maternal X that would be at 50% risk for the X-linked disease. The application of FISH for preimplantation diagnosis has also led to the realisation that chromosomal mosaicism is common at the cleavage stage of development, a finding that has important implications for diagnosis of both dominant single gene disorders and trisomies, as well as for our understanding of early human development. Cloning and sequencing of the relevant genes has enabled the development of methods for the diagnosis of certain recessive single gene disorders in cleavage stage embryos. PCR based methods have to be developed for each condition, sometimes for each family if there is heterogeneity. Preimplantation diagnosis has been successful so far for cystic fibrosis, Tay Sachs disease, and Lesch-Nyhan syndrome. Worldwide, 32 pregnancies have been established following all types of preimplantation diagnosis and with 29 babies born, there is no evidence for any adverse effect on development.

Enrichment of fetal cells from maternal blood by high gradient magnetic cell sorting (double MACS) for PCR-based genetic analysis

For simple and effective isolation of fetal cells from peripheral maternal blood, we combined depletion of maternal cells and enrichment of fetal cells by high-gradient magnetic cell separation (MACS). First CD45+ and CD14+ cells were depleted from maternal peripheral blood mononuclear cells by MACS. From the depleted fraction, CD71+ erythroid cells were enriched up to 80 per cent by MACS. This double-MACS' procedure yielded an average depletion rate of 780-fold and an average enrichment rate of 500-fold, with approximate recovery rates of 40-55 per cent. For paternity testing, cells from unseparated blood and the various fractions were analysed for polymorphism of the HLA-DQ-A1 locus and D1S80 locus by the polymerase chain reaction (PCR). In CD45-/CD71+ sorted cells from maternal blood, but not in unfractionated cells from maternal blood or CD45-/CD14- cells, paternal alleles could be detected. In the CD45-/CD71+ fraction, the relative frequency of paternal alleles compared with maternal alleles ranged from 1 in 20 to 1 in 200 (determined by titration and depending on the quality of separation and biological variation). In 7 out of 11 cases, between weeks 12 and 25 of gestation, we could identify paternal alleles by PCR, either HLA-DQ-A1 or D1S80. This double-MACS procedure is simple, fast, efficient, and reliable for non-invasive prenatal diagnosis.

Multipoint mapping calculations for sperm-typing data

This paper explains how multipoint likelihoods can be computed for sperm-typing data. Experimental errors such as multiple sperm per tube, inadequate amplification, and contamination by exogenous DNA are explicitly taken into account. By limiting the number of sperm theoretically possible per tube to a predetermined maximum and by assuming no chiasma interference, maximum-likelihood estimation can be carried out rapidly using the theory of hidden Markov chains.