Cytogenetics in reproductive medicine: the contribution of comparative genomic hybridization (CGH)

Which assisted reproductive technology (ART) treatment strategy is the most clinically and cost-effective for women of advanced maternal age: a Markov model

Objective

To evaluate the clinical and cost-effectiveness of preimplantation genetic testing for aneuploidy, social freezing, donor and autologous assisted reproductive technology (ART) treatment strategies for women aged 35–45 following 6–12 months of infertility.

Methods

Four Markov decision-analytic models comprising: (i) Preimplantation genetic testing for aneuploidy (PGT-A); (ii) autologous ART from age 40 using oocytes cryopreserved at age 32 (social freezing); (iii) ART using donated oocytes (donor ART); (iv) standard autologous ART treatment (standard care) were developed for a hypothetical cohort of 35 to 45 years old ART naïve women with 6–12 months of infertility. Input probabilities for key parameters including live birth rates were obtained from the available literature. Deterministic and probabilistic sensitivity analyses were conducted to address uncertainty in estimating the parameters and around the model’s assumptions. Cost effectiveness was assessed from both societal and patient perspectives .

Result(s)

For infertile women at age 40 and above, social freezing is the most cost-saving strategy with the highest chance of a cumulative live birth at a lowest cost from a societal perspective. PGT-A and donor ART were associated with higher treatment costs and cumulative live-birth rates compared with the autologous ART. Among the four ART strategies, standard autologous ART has the lowest cumulative live birth rate of 45% at age 35 and decreasing to 1.6% by age 45 years. At a willingness-to-pay threshold of Australian dollars (A$)50,000, our model shows all alternative treatment strategies –PGT-A, social freezing and donor ART have a higher probability of being cost-effective compared to the standard autologous ART treatment. However, higher out-of-pocket expenditure may impede their access to these alternate strategies.

Conclusion

Given current evidence, all alternate strategies have a higher probability of being cost-effective compared to the standard autologous ART treatment. Whether this represents value for money depends on societal and individual’s willingness-to-pay for children conceived with ART treatment.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12913-022-08485-2.

Guidelines for the design, analysis and interpretation of 'omics' data: focus on human endometrium

BACKGROUND

'Omics' high-throughput analyses, including genomics, epigenomics, transcriptomics, proteomics and metabolomics, are widely applied in human endometrial studies. Analysis of endometrial transcriptome patterns in physiological and pathophysiological conditions has been to date the most commonly applied 'omics' technique in human endometrium. As the technologies improve, proteomics holds the next big promise for this field. The 'omics' technologies have undoubtedly advanced our knowledge of human endometrium in relation to fertility and different diseases. Nevertheless, the challenges arising from the vast amount of data generated and the broad variation of 'omics' profiling according to different environments and stimuli make it difficult to assess the validity, reproducibility and interpretation of such 'omics' data. With the expansion of 'omics' analyses in the study of the endometrium, there is a growing need to develop guidelines for the design of studies, and the analysis and interpretation of 'omics' data.

METHODS

Systematic review of the literature in PubMed, and references from relevant articles were investigated up to March 2013.

RESULTS

The current review aims to provide guidelines for future 'omics' studies on human endometrium, together with a summary of the status and trends, promise and shortcomings in the high-throughput technologies. In addition, the approaches presented here can be adapted to other areas of high-throughput 'omics' studies.

CONCLUSION

A highly rigorous approach to future studies, based on the guidelines provided here, is a prerequisite for obtaining data on biological systems which can be shared among researchers worldwide and will ultimately be of clinical benefit.

Preimplantation genetic diagnosis (PGD) influences adrenal development and response to cold stress in resulting mice

Preimplantation genetic diagnosis (PGD) has gained widespread application in clinical medicine and hence the health of PGD offspring needs to be systematically assessed. Given the critical role of the stress response in growth and health, assessments of the development and function of the stress system might help to clarify the health outcomes of PGD. In this study, we constructed a PGD-conceived mouse model and used naturally conceived mice as controls; we used this model to evaluate the potential effect of PGD procedures on the stress system of the offspring. Serum and tissues of stress organs, namely the hypothalamus, locus coeruleus and adrenal gland, were collected from 5-week-old mice in the basal state or after cold stress. The serum levels of stress-related hormones and the structural and functional indices of the stress organs were then examined. In the basal state, ultrastructural abnormalities and low expression of genes involved in steroid hormone synthesis were found in the adrenals of the PGD mice, which had low corticosterone and high epinephrine levels compared with those of control mice. After acute cold stress, the PGD mice continued to show structural and glucocorticoid secretion abnormalities resulting in a late response to the environmental change. Thus, our study indicates that PGD manipulations affect adrenal development, result in structural and functional abnormalities of the adrenals in the offspring and influence their reactivity and adaptability to cold stress.

The impact of next-generation sequencing technology on preimplantation genetic diagnosis and screening

Largely because of efforts required to complete the Human Genome Project, DNA sequencing has undergone a steady transformation with still-ongoing developments of high-throughput sequencing machines for which the cost per reaction is falling drastically. Similarly, the fast-changing landscape of reproductive technologies has been improved by genetic approaches. Preimplantation genetic diagnosis and screening were established more than two decades ago for selecting genetically normal embryos to avoid inherited diseases and to give the highest potential to achieve stable pregnancies. Most recent additions to the IVF practices (blastocyst/trophectoderm biopsy, embryo vitrification) and adoption of new genetics tools such as array comparative genome hybridization have allowed setting up more precise and efficient programs for clinical embryo diagnosis. Nevertheless, there is always room for improvements. Remarkably, a recent explosion in the release of advanced sequencing benchtop platforms, together with a certain maturity of bioinformatics tools, has set the target goal of sequencing individual cells for embryo diagnosis to be a realistically feasible scenario for the near future. Next-generation sequencing technology should provide the opportunity to simultaneously analyze single-gene disorders and perform an extensive comprehensive chromosome screening/diagnosis by concurrently sequencing, counting, and accurately assembling millions of DNA reads.

Chromosome microarrays in human reproduction

BACKGROUND

Chromosome microarray (CMA) testing allows automatic and easy identification of large chromosomal abnormalities detectable by conventional cytogenetics as well as the detection of submicroscopic chromosomal imbalances.

METHODS

A PubMed search was performed in order to review the current use of CMA testing in the field of human reproduction. Articles discussing the use of CMA in the preimplantation setting, ongoing pregnancies, miscarriages and patients with reproductive disorders were considered.

RESULTS

A high rate of concordance between conventional methods of detecting chromosomal abnormalities [e.g. fluorescence in situ hybridization (FISH), karyotyping] and CMA was reported in the prenatal setting with CMA providing more comprehensive and detailed results as it investigates the whole genome at higher resolution. In preimplantation genetic screening, CMA is replacing FISH and the selection of embryos based on CMA has already resulted in live births. For ongoing pregnancies and miscarriages, CMA eliminates tissue culture failures and artifacts and allows a quick turnaround time. The detection of submicroscopic imbalances [or copy number variants (CNVs)] is beneficial when the imbalance has a clear clinical consequence but is challenging for previously undescribed imbalances, particularly for ongoing pregnancies. Recurrent CNVs have been documented in patients with reproductive disorders; however, the application of CMA in this field is still limited.

CONCLUSIONS

CMA enhances reproductive medicine as it facilitates better understanding of the genetic aspects of human development and reproduction and more informed patient management. Further clinical validation of CMA in the prenatal setting, creation of practice guidelines and catalogs of newly discovered submicroscopic imbalances with clinical outcomes are areas that will require attention in the future.

Abnormal development at early postimplantation stage in mouse embryos after preimplantation genetic diagnosis

Preimplantation genetic diagnosis (PGD) is an established procedure for the genetic analysis of embryos. To assess the effect of the procedure on early embryonic development, we generated a murine experimental system, including mice implanted with biopsied in vitro cultured embryos, control mice implanted with in vitro cultured embryos without biopsy, and mice with naturally conceived embryos. Embryos at the 7.5-dpc stage were isolated from all three groups and the embryo implantation rate, the survival rate of implanted embryos, and the developmental stage of surviving embryos were carefully assessed and compared among all three groups. We found the implantation rate was similar between biopsied and control group embryos (67.92% vs. 66.67%). However, the survival rate of implanted embryos in the biopsied group (49.31%) was significantly lower than that of the control (60.91%) and normal groups (96.24%) at 7.5 dpc. In addition, the survival rate of control group embryos was significant lower than that of normal group embryos. Classification of the precise developmental stages of randomly selected live implanted embryos at 7.5 dpc revealed no differences among the three groups. Our results indicate that blastomere biopsy does not adversely affect embryo implantation. The PGD procedure, in particular blastomere biopsy, increases the rate of embryo death at 4.5-7.5 dpc, but does not affect the development of surviving 7.5 dpc embryos.

Whole genome amplification in preimplantation genetic diagnosis

Preimplantation genetic diagnosis (PGD) refers to a procedure for genetically analyzing embryos prior to implantation, improving the chance of conception for patients at high risk of transmitting specific inherited disorders. This method has been widely used for a large number of genetic disorders since the first successful application in the early 1990s. Polymerase chain reaction (PCR) and fluorescent in situ hybridization (FISH) are the two main methods in PGD, but there are some inevitable shortcomings limiting the scope of genetic diagnosis. Fortunately, different whole genome amplification (WGA) techniques have been developed to overcome these problems. Sufficient DNA can be amplified and multiple tasks which need abundant DNA can be performed. Moreover, WGA products can be analyzed as a template for multi-loci and multi-gene during the subsequent DNA analysis. In this review, we will focus on the currently available WGA techniques and their applications, as well as the new technical trends from WGA products.

Singling out genetic disorders and disease

Preimplantation genetic diagnosis (PGD) involves testing of single cells biopsied from oocytes and/or embryos generated in vitro. As only embryos unaffected for a given genetic condition are transferred to the uterus, it avoids prenatal diagnosis and termination of pregnancy. Follow-up data from PGD pregnancies, deliveries and children show an acceptable live birth rate and, so far, no detrimental effects of the procedure have been observed. Of course, the long-term health outcome is currently unknown. PGD was first performed in 1990 and remained an experimental procedure for a number of years. Now, two decades later, it is regarded as an established alternative to prenatal diagnosis: its use has expanded, the range of applications has broadened, and continuous technical progress in single-cell testing has led to high levels of efficiency and accuracy. The current gold standard methods (single-cell multiplex-PCR for monogenic diseases and interphase fluorescence in situ hybridization for chromosomal aberrations) are being replaced by single-cell whole genome amplification and array technology. These generalized methods substantially reduce the pre-PGD workload and allow more automated genome-wide analysis. The implementation of laboratory accreditation schemes brings the field at the same level of routine diagnostics. This article reviews the state of the art and considers indications, accuracy and current technical changes in the field of PGD.

Somatic genomic variations in early human prenatal development

Only 25 to 30% of conceptions result in a live birth. There is mounting evidence that the cause for this low fecundity is an extremely high incidence of chromosomal rearrangements occurring in the cleavage stage embryo. In this review, we gather all recent evidence for an extraordinary degree of mosaicisms in early embryogenesis. The presence of the rearrangements seen in the cleavage stage embryos can explain the origins of the placental mosaicisms seen during chorion villi sampling as well as the chromosomal anomalies seen in early miscarriages. Whereas these rearrangements often lead to implantation failure and early miscarriages, natural selection of the fittest cells in the embryo is the likely mechanism leading to healthy fetuses.

Preimplantation genetic screening: an effective testing for infertile and repeated miscarriage patients?

Aneuploidy in pregnancy is known to increase with advanced maternal age (AMA) and associate with repeated implantation failure (RIF), and repeated miscarriage (RM). Preimplantation genetic screening (PGS) has been introduced into clinical practice, screening, and eliminating aneuploidy embryos, which can improve the chance of conceptions for infertility cases with poor prognosis. These patients are a good target group to assess the possible benefit of aneuploidy screening. Although practiced widely throughout the world, there still exist some doubts about the efficacy of this technique. Recent randomized trials were not as desirable as we expected, suggesting that PGS needs to be reconsidered. The aim of this review is to discuss the efficacy of PGS.

The role of preimplantation genetic diagnosis in diagnosing embryo aneuploidy

PURPOSE OF REVIEW

Use of preimplantation genetic diagnosis to improve in-vitro fertilization outcomes is reviewed.

RECENT FINDINGS

Many embryos produced in vitro contain chromosomal abnormalities and have little potential for forming a viable pregnancy. The most commonly used method for preimplantation genetic diagnosis involves embryo biopsy on day 3 of development, followed by fluorescence in-situ hybridization analysis of 5-12 chromosomes. However, positive results have been more common with single-cell biopsy and the analysis of nine or more chromosomes, including 15, 16, 21, and 22. Comparative genomic hybridization, array-comparative genomic hybridization, and single-nucleotide polymorphism arrays analyze all chromosomes and, although technically demanding and requiring experience for successful use, improve the selection potential of preimplantation genetic diagnosis and minimize error rates. Recent data suggest that biopsy at the blastocyst stage may allow sampling of representative genetic material without compromising embryo viability. The optimal strategy for aneuploidy screening using preimplantation genetic diagnosis seems to be blastocyst biopsy at 5 days and comprehensive chromosome analysis (comparative genomic hybridization, array-comparative genomic hybridization, single-nucleotide polymorphism array).

SUMMARY

The use of preimplantation genetic diagnosis to assist the identification and preferential transfer of healthy euploid embryos should improve implantation rates, reduce miscarriages and trisomic offspring, and ultimately lead to an increase in live birth rates.

IVF/ICSI with or without preimplantation genetic screening for aneuploidy in couples without genetic disorders: a systematic review and meta-analysis

PURPOSE

To assess the efficacy of preimplantation genetic screening to increase ongoing pregnancy rates in couples without known genetic disorders.

METHODS

Systematic review and meta-analysis of randomized controlled trials. Two reviewers independently determined study eligibility and extracted data.

RESULTS

Ten randomized trials (1,512 women) were included. The quality of evidence was moderate. Meta-analyses using a random-effects model suggest that PGS has a lower rate of ongoing pregnancies (risk ratio=0.73, 95% confidence interval 0.62-0.87) and a lower rate of live births (risk ratio=0.76, 95% confidence interval 0.64-0.91) than standard in vitro fertilization/intracytoplasmic sperm injection.

CONCLUSIONS

In women with poor prognosis or in general in vitro fertilization program, in vitro fertilization/intracytoplasmic sperm injection with preimplantation genetic screening for aneuploidy does not increase but instead was associated with lower rates of ongoing pregnancies and live births. The use of preimplantation genetic screening in daily practice does not appear to be justified.

Oocyte karyotyping by comparative genomic hybridization [correction of hybrydization] provides a highly reliable method for selecting "competent" embryos, markedly improving in vitro fertilization outcome: a multiphase study

OBJECTIVE

To assess the karyotypic relationship between prefertilized/postfertilized oocytes and embryos using comparative genomic hybridization (CGH) on polar body-1 (PB-1), PB2, and blastomere biopsies and to evaluate IVF outcomes after transfer of blastocysts derived from euploid oocytes.

DESIGN

Prospective cohort.

SETTING

Medical center.

PATIENT(S)

Phase1: Fourteen oocyte donors (23-29 years). Phase 2: Forty-one healthy embryo recipients aged 29-43 years free of endometrial implantation dysfunction. In 30 cases own eggs were used. Eleven women used donated oocytes.

INTERVENTION(S)

Phase 1: PB-1 biopsies followed intracytoplasmic sperm injection (ICSI), PB-2, and day 3 blastomere biopsies. Phase 2: PB-1 biopsy followed by ICSI using normal sperm and the subsequent embryo transfer of < or =2 blastocysts derived from euploid oocytes. Comparative genomic hybridization on all DNA derived from phase 1 and 2 biopsies.

MAIN OUTCOME MEASURE(S)

Pregnancy and implantation rate.

RESULT(S)

Phase 1: 39% of oocytes and 88% of zygotes were euploid; >95% progressed to blastocysts. Mosaicism as evidenced by euploid oocytes developing into aneuploid zygotes or embryos occurred in 13% of concepti. Phase 2: Six of 30 women using own eggs, who failed to produce euploid oocytes, were cancelled. Thirty-five women underwent embryo transfers with < or =2 (mean, 1.3 +/- 0.7) blastocysts derived from euploid oocytes. The ongoing pregnancy/implantation rates per embryo transfer were 74% and 82%, respectively.

CONCLUSION(S)

Transferring euploid embryos markedly improved IVF outcome. These findings, if corroborated, could initiate a paradigm shift in assisted reproductive technology (ART).

The cytogenetics of preimplantation human development: insights provided by traditional and novel techniques

Our understanding of the incidence and origin of chromosome abnormalities in human preimplantation embryos is very limited due to the necessary ethical constraints involved in studying such material and the limited data ultimately produced. Several studies have addressed this issue, however, using techniques such as interphase fluorescence in situ hybridisation, modified G-banding preparation and the use of single-cell comparative genomic hybridisation (CGH). This review discusses the use of these techniques in assessing chromosome abnormalities in this, the earliest of human developmental stages. In addition, the prospects for the clinical use of CGH are discussed.

Incidence and spectrum of chromosome abnormalities in spontaneous abortions: New insights from a 12-year study

PURPOSE

Despite advances in harvesting and culturing techniques, analysis of the impact of these improvements on the observed frequency of chromosomal abnormalities in spontaneous abortions (SAB) has not been determined. We sought to evaluate the effect of these refinements on the success rate of our cultures and on the resulting frequency of detected chromosomal abnormalities.

METHODS

Between 1990 and 2002, 2301 specimens obtained from the products of conception (POC) of SABs were submitted to our laboratory for cytogenetic analysis. Due to refinements in specimen processing and culture techniques introduced at the end of 1997, our data were analyzed for two periods: Period A from 1990 through 1997 with 907 eligible specimens and Period B from 1998 through 2002 with 1273 eligible specimens.

RESULTS

Modifications in physician communication and sample processing contributed to significant improvements in the culture success rate and in the ratio of male-to-female cases with normal karyotypes. Additionally, increased detection of trisomic, triploid, and multiple aneuploid cases in Period B resulted in a significant increase in the percentage of cases with abnormal karyotypes (42.8% in Period A vs. 65.8% in Period B). Monosomy X accounted for < 10% of all abnormalities in Period B. Eighty five multiple aneuploid karyotypes, including 57 double trisomies, comprised 7.7% of our 1099 abnormal cases. These karyotypes were detected predominantly in POCs from the older women in our study. This collection of multiple aneuploidies is the largest published to date and includes abnormalities not reported in prior studies. We also present a table empirically derived from the data in Period B that indicates the likelihood of a specific abnormal karyotype based on maternal age. The table can be utilized by health care providers, who counsel patients after a spontaneous miscarriage.

CONCLUSION

Improvements in laboratory technique have led to reduced contamination and growth failure of POCs, irrespective of maternal age. This in turn has led to a more balanced male-to-female ratio and to the detection of an increased number of abnormal cases.

Numerical chromosomal abnormalities in equine embryos produced in vivo and in vitro

Chromosomal aberrations are often listed as a significant cause of early embryonic death in the mare, despite the absence of any concrete evidence for their involvement. The current study aimed to validate fluorescent in situ hybridization (FISH) probes to label specific equine chromosomes (ECA2 and ECA4) in interphase nuclei and thereby determine whether numerical chromosome abnormalities occur in horse embryos produced either in vivo (n = 22) or in vitro (IVP: n = 20). Overall, 75% of 36,720 and 88% of 2,978 nuclei in the in vivo developed and IVP embryos were analyzable. Using a scoring system in which extra FISH signals were taken to indicate increases in ploidy and "missing" signals were assumed to be "false negatives," 98% of the cells were scored as diploid and the majority of embryos (30/42: 71%) were classified as exclusively diploid. However, one IVP embryo was recorded as entirely triploid and a further seven IVP and four in vivo embryos were classified as mosaics containing diploid and polyploid cells, such that the incidence of apparently mixoploid embryos tended to be higher for IVP than in vivo embryos (P = 0.118). When the number of FISH signals per nucleus was examined in more detail for 11 of the embryos, the classification as diploid or polyploid was largely supported because 2,174 of 2,274 nuclei (95.6%) contained equal numbers of signals for the two chromosomes. However, the remaining 100 cells (4.4%) had an uneven number of chromosomes and, while it is probable that many were artefacts of the FISH procedure, it is also likely that a proportion were the result of other types of aneuploidy (e.g., trisomy, monosomy, or nullisomy). These results demonstrate that chromosomally abnormal cells are present in morphologically normal equine conceptuses and suggest that IVP may increase their likelihood. Definitive distinction between polyploidy, aneuploidy and FISH artefacts would require the use of more than one probe per chromosome and/or probes for more than two chromosomes.

Preimplantation genetic diagnosis and chromosome analysis of blastomeres using comparative genomic hybridization

Numerical chromosome errors are known to be common in early human embryos and probably make a significant contribution to early pregnancy loss and implantation failure in IVF patients. Over recent years fluorescent in situ hybridization (FISH) has been used to document embryonic aneuploidies. Many IVF laboratories perform preimplantation genetic diagnosis (PGD) with FISH to select embryos that are free from some aneuploidies in an attempt to improve implantation, pregnancy and live birth rates in particular categories of IVF patients. The usefulness of FISH is limited because only a few chromosomes can be detected simultaneously in a single biopsied cell. Complete karyotyping at the single cell level can now be achieved by comparative genomic hybridization (CGH). CGH enables not only enumeration of all chromosomes but gives a more complete picture of the entire length of each chromosome and has demonstrated that chromosomal breakages and partial aneuploidies exist in embryos. CGH has provided invaluable information about the extent of mosaicism and aneuploidy of all chromosomes in early human conceptuses. CGH has been applied to clinical PGD and has resulted in the birth of healthy babies from embryos whose full karyotype was determined in the preimplantation phase.

Detection of an interstitial deletion of 2q21-22 by high resolution comparative genomic hybridization in a child with multiple congenital anomalies and an apparent balanced translocation

Various molecular cytogenetic techniques are currently available to accurately characterize chromosome rearrangements in patients with multiple congenital anomalies. Among these is comparative genomic hybridization (CGH) whose main advantage is the ability to perform a whole genome scan without prior knowledge of the underlying chromosome abnormality. It has been used mostly in the area of cancer cytogenetics, but its role in clinical genetics is now expanding to even include preimplantation genetic diagnosis. We have used this method to reveal an interstitial deletion in a patient with multiple anomalies, who had for years been thought to have a de novo balanced translocation involving chromosomes 1 and 2. A review of published reports suggests that there is significant phenotypic and genetic heterogeneity in the small group of patients including our own with interstitial deletions of 2q21-q22.

Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize

Study of the maize (Zea mays L.) somatic chromosomes (2n = 20) has been difficult because of a lack of distinguishing characteristics. To identify all maize chromosomes, a multicolor fluorescence in situ hybridization procedure was developed. The procedure uses tandemly repeated DNA sequences to generate a distinctive banding pattern for each of the 10 chromosomes. Fluorescence in situ hybridization screening trials of nonsubtracted or subtracted PCR libraries resulted in the isolation of microsatellite 1-26-2, subtelomeric 4-12-1, and 5S rRNA 2-3-3 clones. These three probes, plus centromeric satellite 4 (Cent4), centromeric satellite C (CentC), knob, nucleolus-organizing region (NOR), pMTY9ER telomere-associated sequence, and tandemly repeated DNA sequence 1 (TR-1) were used as a mixture for hybridization to root-tip chromosomes. All 10 chromosomes were identified by the banding and color patterns in the 14 examined lines. There was significant quantitative variation among lines for the knob, microsatellite, TR-1, and CentC signals. The same probe mixture identifies meiotic pachytene, late prophase I, and metaphase I chromosomes. The procedure could facilitate the study of chromosomal structure and behavior and be adapted for other plant species.

Preimplantation genetic diagnosis

Preimplantation genetic diagnosis (PGD) was introduced at the beginning of the 1990s as an alternative to prenatal diagnosis, to prevent termination of pregnancy in couples with a high risk for offspring affected by a sex-linked genetic disease. At that time, embryos obtained in vitro were tested to ascertain their sex, and only female embryos were transferred. Since then, techniques for genetic analysis at the single-cell level, involving assessment of first and second polar bodies from oocytes or blastomeres from cleavage-stage embryos, have evolved. Fluorescence in-situ hybridisation (FISH) has been introduced for the analysis of chromosomes and PCR for the analysis of genes in cases of monogenic diseases. In-vitro culture of embryos has also improved through the use of sequential media. Here, we provide an overview of indications for, and techniques used in, PGD, and discuss results obtained with the technique and outcomes of pregnancies. A brief review of new technologies is also included.

A tiling resolution DNA microarray with complete coverage of the human genome

We constructed a tiling resolution array consisting of 32,433 overlapping BAC clones covering the entire human genome. This increases our ability to identify genetic alterations and their boundaries throughout the genome in a single comparative genomic hybridization (CGH) experiment. At this tiling resolution, we identified minute DNA alterations not previously reported. These alterations include microamplifications and deletions containing oncogenes, tumor-suppressor genes and new genes that may be associated with multiple tumor types. Our findings show the need to move beyond conventional marker-based genome comparison approaches, that rely on inference of continuity between interval markers. Our submegabase resolution tiling set for array CGH (SMRT array) allows comprehensive assessment of genomic integrity and thereby the identification of new genes associated with disease.

Quantitative Analysis of Nucleic Acids - the Last Few Years of Progress

DNA and RNA quantifications are widely used in biological and biomedical research. In the last ten years, many technologies have been developed to enable automated and high-throughput analyses. In this review, we first give a brief overview of how DNA and RNA quantifications are carried out. Then, five technologies (microarrays, SAGE, differential display, real time PCR and real competitive PCR) are introduced, with an emphasis on how these technologies can be applied and what their limitations are. The technologies are also evaluated in terms of a few key aspects of nucleic acids quantification such as accuracy, sensitivity, specificity, cost and throughput.

Materno-fetal Immunogenetic Disparity: The Biological Basis for In vitro Fertilization Treatment in Patients with Unexplained Recurrent Abortion?

PROBLEM

The majority of women with recurrent miscarriage have no discernible cause but it has been postulated that immunologic aberrations may be the cause in most of such cases. Also, it has been stressed that deliberate modification of the maternal host defense system can improve the chances of success. We tested the hypothesis that it is possible to potentiate maternal immune functions so as to improve reproductive performance by replacing several embryos into the uterus, thus favoring the recognition of fetal antigens.

METHOD OF STUDY

A total of 57 couples with three or more (mean 5.52; range 3-12) consecutive first-trimester spontaneous clinical abortions of unknown etiology were treated with in vitro fertilization (IVF) and embryo transfer for a total of 84 cycles. Patients underwent IVF after combined gonadotropin-releasing hormone agonist/gonadotropin treatment for ovarian stimulation, and up to four embryos were replaced into the uterus.

RESULTS

There were 32 pregnancies (three of them after frozen-thawed embryo transfers) and 26 (81%) of them were viable gestations. Overall, patients had a previous obstetric history of 315 pregnancy losses and 15 live-born babies. Thus, the probability of having a live baby before treatment was 4.54% (95% CI, 2.78-7.36) a figure significantly lower (P < 0.0001) than that observed under IVF treatment (81%; 95% CI, 64.53-91.01). None of selected variables potentially related with the outcome of pregnancy after IVF and embryo transfer in recurrent aborters (including pre-implantation genetic diagnosis) was found to be associated with miscarriage.

CONCLUSIONS

This study shows that replacement of several embryos after IVF is a useful treatment in the prevention of unexplained recurrent spontaneous abortion thus providing further evidence for immunologically modifiable pregnancy loss.

Genomic microarrays in human genetic disease and cancer

Alterations in the genome that lead to changes in DNA sequence copy number are a characteristic of solid tumors and are found in association with developmental abnormalities and/or mental retardation. Comparative genomic hybridization (CGH) can be used to detect and map these changes. Recent improvements in the resolution and sensitivity of CGH have been possible through implementation of microarray-based CGH (array CGH). Here we discuss the performance characteristics of different array platforms and review some of the recent applications of array CGH in cancer and medical genetics.