Identification of copy number variants in miscarriages from couples with idiopathic recurrent pregnancy loss.

BACKGROUND: Recurrent pregnancy loss (RPL), defined as two or more miscarriages, affects 3-5% of couples trying to establish a family. Despite extensive evaluation, no factor is identified in ∼40% of cases. In this study, we investigated the possibility that submicroscopic chromosomal changes, not detectable by conventional cytogenetic analysis, exist in miscarriages with normal karyotypes (46,XY or 46,XX) from couples with idiopathic RPL. METHODS: Array comparative genomic hybridization (array-CGH) was used to assess for DNA copy number variants (CNVs) in 26 miscarriages with normal karyotypes. Parental array-CGH analysis was performed to determine if miscarriage CNVs were de novo or inherited. RESULTS: There were 11 unique (previously not described) CNVs, all inherited, identified in 13 miscarriages from 8 couples. The maternal origin of two CNVs was of interest as they involved the imprinted genes TIMP2 and CTNNA3, which are only normally expressed from the maternal copy in the placenta. Two additional cohorts, consisting of 282 women with recurrent miscarriage (RM) and 61 fertile women, were screened for these two CNVs using a Quantitative Multiplex Fluorescent PCR of Short Fragments assay. One woman with RM, but none of the fertile women, carried the CTNNA3-associated CNV. CONCLUSIONS: This preliminary study shows that array-CGH is useful for detecting CNVs in cases of RPL. Further investigations of CNVs, particularly those involving genes that are imprinted in placenta, in women with RPL could be worthwhile.

Genomic changes detected by array CGH in human embryos with developmental defects.

Developmental abnormalities of human embryos can be visualized in utero using embryoscopy. Our previous embryoscopic and genetic evaluations detected developmental abnormalities in the majority of both euploid (74%) and aneuploid or polyploid (90%) miscarriages. Since we found the pattern of morphological changes to be similar in euploid and non-euploid embryos, we proposed that lethal submicroscopic changes, not detected by standard chromosome testing, may be responsible for miscarriage of euploid embryos. Whole genome oligo and bacterial artificial chromosome array comparative genome hybridization (CGH) was used to screen for submicroscopic chromosomal changes (DNA copy number variants or CNVs) in 17 euploid embryonic miscarriages, with a range of developmental abnormalities documented by embryoscopy. The CNV breakpoints were refined using a custom array (Agilent) with high resolution coverage of the CNVs. Six unique CNVs, previously not reported, were identified in 5 of the 17 embryos (29% of all cases or 50% of cases studied with higher resolution arrays). All six unique CNVs were <250 kb in size. On the basis of parental array CGH analysis, a de novo origin of a CNV was determined for one embryo (at 13q32.1) and suspected for another (at 10p15.3). Three CNVs, at Xq28, 1q25.3 and 7p14.3, were inherited and a CNV at 17p13.1 was of unknown origin. The genes contained within these unique CNVs will be discussed, with specific reference to rearrangements of syntaxin and tryptophan-aspartic acid (WD) repeat genes. Our report describes for the first time, de novo and inherited unique CNVs in euploid human embryos with specific developmental defects.

Autologous bone marrow transplantation for children with AML in first remission.

In Children's cancer group (CCG) 2891, newly diagnosed patients with AML were randomized between standard and intensive timing induction therapies. Patients in first remission who lacked an HLA matched family donor were randomized between an autologous bone marrow transplantation (ABMT) where marrow was purged with 4 hydroperoxycyclophosphamide and consolidation chemotherapy. One hundred and thirty seven patients received an ABMT. Myeloid and platelet engraftment occurred at a median of 44 and 42 days, respectively. Disease-free survival (DFS), relapse-free survival and overall survival at 8 years post induction were 47% (95% confidence interval (CI): 38-55), 50% (CI: 42-59) and 55% (CI: 46-63), respectively. Multivariate analysis of DFS showed WBC <50 000/microl and having received intensively timed induction therapy were associated with improved DFS. Recipients who received intensive timed induction therapy and whose WBC was less than 50 000/microl had a DFS at 8 years of 62% (CI: 49-73). Conversely, recipients who received intensive timed induction therapy patients whose WBC was > or =50 000/microl had a DFS of 33% (CI: 17-50), P=0.003. The results confirm previous studies that ABMT is effective post remission therapy for pediatric patients with AML in first remission.

Prenatally detected trisomy 20 mosaicism.

BACKGROUND: Trisomy 20 is one of the more common mosaic trisomies detected on amniocentesis and presents with a normal outcome in over 90% of reported cases. Trisomic cells are almost never confirmed in newborn blood and are only rarely found in other fetal or placental samples. Nonetheless, some abnormal outcomes have been reported, including unexplained fetal demise, intrauterine growth restriction, and multiple congenital anomalies. Because of the lack of molecular studies on such cases, it is unknown whether the origin of trisomy or presence of uniparental disomy (UPD) could have some influence on outcome. METHODS: We present data on six cases of trisomy mosaicism, two detected by chorionic villous sampling (CVS) and four by amniocentesis (AF), submitted to our laboratory for molecular studies. RESULTS AND CONCLUSIONS: A meiotic origin of the trisomy could be confirmed in only one of these cases. In addition, uniparental disomy was excluded in all four cases for which parents were available for testing. The four cases with low levels of trisomy in amniotic fluid (0%, 10%, 11%, and 12%) were associated with a normal outcome. The remaining two cases of trisomy 20 had high levels of trisomy in amniotic fluid (96% and 58%) and had abnormal outcomes (developmental delay in one and stillbirth with IUGR and severe oligohydramnios in the other). Including previously published cases, there is a clear association with the level of trisomy and outcome, with only 4% abnormal outcomes when <40% trisomic cells were detected. Higher levels of trisomy were also observed in male fetuses as compared to female fetuses (p = 0.01); however, there were no sex differences in frequency of abnormal outcomes.

Effects of triploidy on early human development.

OBJECTIVE: The morphologic features of 18 triploid embryos are described. METHOD: Embryoscopic examination of the embryo in cases of missed abortion before instrumental evacuation from the uterus. Cytogenetic and histologic analysis of the chorionic villi. RESULTS: Seventeen out of 18 triploid embryos showed structural defects on embryoscopic examination. The most common defects were facial anomalies (n = 15), limb abnormalities (n = 13), microcephaly (n = 11) and neural tube defects (n = 10); 3 embryos were classified as growth disorganized. Placenta of 12 grossly abnormal embryos was diagnosed as partial hydatidiform moles on histological examination. CONCLUSIONS: The grossly abnormal development of the embryo observed in 12 partial hydatidiform moles indicate that, in aborted triploid embryos, the presence of two paternal genomes might have both placental and embryonic consequences. Transcervical embryoscopy in cases of missed abortion can serve as a central component in additional studies using molecular determination of parental origin of triploidy to establish the true proportion of diandric triploidy among grossly abnormal triploid embryos.

Transcervical fetoscopic diagnosis of structural defects in four first-trimester monochorionic twin intrauterine deaths.

OBJECTIVE: While chromosomal abnormalities are often the cause of early failed pregnancies, other mechanisms could be involved in monochorionic twin intrauterine deaths, that might be screened for careful morphological analysis. METHODS: Transcervical fetoscopy prior to instrumental evacuation of the uterus was performed in four first-trimester monochorionic twin intrauterine deaths. RESULTS: We present fetoscopic and cytogenetic findings in four cases of monochorionic twin intrauterine deaths. In the first, generalized abnormal embryonic development observed in both twins was a manifestation of trisomy 20. The second (thoracophagus) and third (acardius) pair of twins had anomalies peculiar to multiple gestations. The fourth pair of twins was remarkable because of the concordance for the observed limb-reduction defects. CONCLUSION: Malformations of first-trimester monochorionic twin intrauterine deaths might cover a wide spectrum of etiologies from abnormal chromosomes and single gene defects to rare duplication anomalies. Their detection by careful morphological analysis and the identification of a specific mechanism provides valuable information for genetic counseling and prenatal investigation in a future pregnancy.

Embryoscopic and cytogenetic analysis of 233 missed abortions: factors involved in the pathogenesis of developmental defects of early failed pregnancies.

BACKGROUND: While chromosomal abnormalities are often the cause of missed abortions, other defects could be involved, which might be screened for by transcervical embryoscopy. METHODS: A total of 272 patients with missed abortion underwent transcervical embryoscopy prior to dilatation and curettage, together with cytogenetic analysis of chorionic villi, using either standard G-banding cytogenetic techniques or comparative genomic hybridization in combination with flow cytometry analysis. RESULTS: Visualization of the embryo or early fetus (12 cases) was successful in 233 patients, and karyotyping in 221. Among 233 examined cases, 33 had normal external features, 71 were classified as growth-disorganized and 129 had either isolated or multiple defects, including holoprosencephaly, anencephaly, encephalocele, spina bifida, microcephaly, facial dysplasia, limb reduction defect, cleft hand, syndactyly, pseudosyndactly, polydactyly, various forms of cleft lip and an amniotic adhesion. Of the 165 cases with an abnormal karyotype, there were 46 grossly disorganized embryos, 98 multiple defects, six single defects and 15 morphologically normal cases. Of the 56 cases with a normal karyotype, there were 20 grossly disorganized embryos, 16 multiple defects, four single defects and 16 morphologically normal cases. CONCLUSIONS: A total of 75% of the cases with missed abortion had an abnormal karyotype, 18% had a morphological defect with a normal karyotype, while no embryonic or chromosomal abnormality could be diagnosed in 7% of the cases. Correlation of morphological and cytogenetic findings in spontaneous abortion specimens could provide valuable information for genetic counselling and prenatal care in future pregnancies in couples with a history of repeated pregnancy loss.

Clinical aspects, prenatal diagnosis, and pathogenesis of trisomy 16 mosaicism.

INTRODUCTION: Analysis of data from cases of trisomy mosaicism can provide insight for genetic counselling after prenatal diagnosis and for the elucidation of the pathogenesis of trisomy during pregnancy. METHODS: Statistical analysis was carried out on data from 162 cases of pregnancies with prenatal diagnosis of trisomy 16 mosaicism. RESULTS: The majority of cases resulted in live birth (66%) with an average gestational age of 35.7 weeks and average birth weight of -1.93 standard deviations from the population mean. Among the live births 45% had at least one malformation, the most common being VSD, ASD, and hypospadias. The level of trisomy on direct CVS (cytotrophoblast) was associated with more severe intrauterine growth restriction (IUGR) and higher risk of malformation, while the level of trisomy on cultured CVS (chorionic villous stroma) was associated only with more severe IUGR. Similarly, the presence of trisomy on amniocentesis (amniotic fluid) was associated with both IUGR and malformation, while the presence of trisomy in the amniotic mesenchyme was associated only with IUGR. Surprisingly, the degree of trisomy in placental tissues appeared to be independent of the degree of trisomy in amniotic fluid and amniotic mesenchyme. The sex of the fetus was not associated with any outcome variables, although there was an excess of females (sex ratio = 0.45) that may be explained by selection against male mosaic trisomy 16 embryos before the time of CVS (approximately 9-12 weeks). CONCLUSION: The levels of trisomy in different fetal-placental tissues are significant predictors of some measures of outcome in mosaic trisomy 16 pregnancies.

Skewed X-chromosome inactivation is associated with trisomy in women ascertained on the basis of recurrent spontaneous abortion or chromosomally abnormal pregnancies.

An increase in extremely skewed X-chromosome inactivation (XCI) (> or = 90%) among women who experienced recurrent spontaneous abortion (RSA) has been previously reported. To further delineate the etiology of this association, we have evaluated XCI status in 207 women who experience RSA. A significant excess of trisomic losses was observed among the women who had RSA with skewed XCI versus those without skewed XCI (P=.02). There was also a significant excess of boys among live births in this group (P=.04), which is contrary to expectations if the cause of skewed XCI was only that these women carried X-linked lethal mutations. To confirm the association between skewed XCI and the risk of trisomy, an independent group of 53 women, ascertained on the basis of a prenatal diagnosis of trisomy mosaicism, were investigated. Only cases for which the trisomy was shown to be of maternal meiotic origin were included. The results show a significantly higher level of extreme skewing (> or = 90%) in women whose pregnancies involved placental trisomy mosaicism (17%) than in either of two separate control populations (n=102 and 99) (P=.02 compared with total control subjects). An additional 11 cases were ascertained on the basis of one or more trisomic-pregnancy losses. When all women in the present study with a trisomic pregnancy (n=103) were considered together, skewed XCI was identified in 18%, as compared with 7% in all controls (n=201) (P=.005). This difference was more pronounced when a cutoff of extreme skewing of 95% was used (10% vs. 1.5% skewed; P=.002). Maternal age was not associated with skewing in either the patient or control populations and therefore cannot account for the association with trisomy. Previous studies have shown that a reduced ovarian reserve is associated with increased risk of trisomic pregnancies. We hypothesize that the association between skewed XCI and trisomic pregnancies is produced by a common mechanism that underlies both and that involves a reduction of the size of the follicular pool.

Evidence for imprinting on chromosome 16: the effect of uniparental disomy on the outcome of mosaic trisomy 16 pregnancies.

Although a number of infants with maternal uniparental disomy of chromosome 16 (upd(16)mat) have been reported, the evidence for imprinting on chromosome 16 is not yet conclusive. To test the hypothesis that upd(16)mat has a distinct phenotype, which would support the existence of imprinted gene(s) on chromosome 16, statistical analysis was performed on a large series (n = 83) of mosaic trisomy 16 cases with molecular determination of uniparental disomy status. The incidence of upd(16)mat was 40%, which is consistent with the expected one third from random chromosome loss during trisomy rescue (P = 0.262). In pairwise comparisons, upd(16)mat was found to be associated with fetal growth restriction (P = 0.029) and with increased risk of major malformation (RR = 1.43; P = 0.053). Regression modeling showed that the effect of upd(16)mat on fetal/neonatal weight and malformation is independent of the degree of trisomy detected in the fetus. Regression modeling to control for the degree of trisomy detected in the placenta was not possible due to limited sample size. We conclude that upd(16)mat is associated with more severe growth restriction, and possibly, with higher risk of malformation. Our hypothesis is that imprinted gene(s) exist on chromosome 16 and that abnormal expression of these gene(s) in upd(16)mat cells during development results in decreased cell proliferation. Although we do not advocate prenatal testing for upd(16), studies on the long-term outcome of upd(16)mat neonates is necessary for counseling purposes.

Amnion rupture sequence in a first trimester missed abortion.

We report the diagnosis of amnion rupture sequence made by sonography and fetoscopy during the first trimester of gestation in a case of missed abortion. The investigation revealed a demised fetus with the characteristics of 9 weeks of development. The early fetus had an amnion adhesion at the tip of the nose and strands of amnion wrapped around the terminal phalanges of both feet. No defects in addition to the face and limb involvement were identified. The karyotype was normal: 46,XX. In the reported case, fetoscopy allowed confirmation of the sonographic diagnosis of an amnion rupture sequence in the first trimester of gestation and consequently helped to clarify the cause of abortion in this case of early fetal demise.

Transcervical embryoscopy in missed abortion.

PURPOSE: The present study was conducted to determine the usefulness of transcervical embryoscopy in diagnosing localized and systemic defects in embryonic morphogenesis of missed abortions. METHODS: The study population consisted of 24 women with the final diagnosis of missed abortion. Prior to the instrumental evacuation of the uterus a rigid hysteroscope was passed transcervically into the amniotic cavity to obtain a detailed view of the embryo. Karyotyping was attempted in all cases included in this study. RESULTS: An embryo could be visualized in 19 cases. Ten embryos showed multiple developmental defects. CONCLUSIONS: In cases of early failure of pregnancy, embryoscopy permits visualization of the embryo in utero, unaffected by the damage usually caused by its instrumental evacuation or spontaneous passage. This technique can be a helpful tool for pathologists and geneticists in enhancing their understanding of human embryonic malformations, but more importantly, it improves clinical care and follow-up, especially in cases of repeated abortions.

Two cases of confined placental mosaicism for chromosome 4, including one with maternal uniparental disomy.

Two cases of trisomy 4 mosaicism are reported including one with molecularly confirmed uniparental disomy (UPD) of chromosome 4. Cytogenetic analysis of a chorionic villus sample (CVS) in Case 1 showed complete trisomy 4 in trophoblast and diploidy in chorionic stroma. Amniotic fluid analysis demonstrated a 46,XX complement. After intrauterine fetal death at 30 weeks, molecular analysis confirmed the presence of trisomy 4 of maternal meiotic origin, while fetal tissues showed maternal UPD for chromosome 4. Cultured CVS in Case 2 revealed trisomy 4 in 2/30 cells analyzed. This pregnancy resulted in a healthy livebirth with biparental inheritance of chromosome 4. Molecularly confirmed UPD4 has not been previously reported, and therefore, although the adverse outcome in Case 1 is likely due to the trisomy 4 in the placenta, an imprinting effect associated with UPD4 cannot be excluded.

Comparative genomic hybridization: a new tool for reproductive pathology.

OBJECTIVE: To demonstrate the effectiveness of comparative genomic hybridization (CGH) for analysis of reproductive pathology specimens in clinical cytogenetics laboratories. DESIGN: A total of 856 CGH analyses were performed on various placental and fetal tissues derived from 368 specimens of spontaneous abortions and on placentas from 219 pregnancies with live-born infants. The live-born infants were clinically evaluated as normally developed, with either a normal birth weight or with intrauterine growth restriction; some live-born infants had an abnormal prenatal triple screen with normal cytogenetic results on amniotic fluid cell cultures. RESULTS: Comparative genomic hybridization analysis was successfully performed on 856 samples from spontaneously aborted specimens and term placentas. Failure of analysis occurred in 1.6% of samples and was due to an insufficient amount of tissue for DNA extraction. Comparative genomic hybridization identified aneuploidy in 53% of spontaneous abortion samples and 3.1% of term placentas. CONCLUSIONS: Comparative genomic hybridization analysis is a useful clinical tool for detection of aneuploidy in placental and fetal tissues. It provides a genome-wide screen while eliminating tissue culture failures, culture artifacts, and maternal cell contamination. We present practical guidelines for interpreting CGH profiles derived from human reproductive specimens.

Confined placental mosaicism and genomic imprinting.

The concept of confined placental mosaicism and its relationship to genomic imprinting and uniparental disomy is explained in this chapter. Clinically significant imprinting syndromes, such as Prader-Willi syndrome, Angelman syndrome, Beckwith-Wiedemann syndrome, Silver-Russell syndrome and transient neonatal diabetes mellitus, potentially associated with confined placental mosaicism are described and referenced. Non-Mendelian inheritance of recessive mutations in uniparental disomy is illustrated. Both skewed X chromosome inactivation and isolated gonadal mosaicism are outlined as newly recognized consequences of post-zygotic chromosomal mutation and confined placental mosaicism. Clinical management of pregnancies with confined placental mosaicism is proposed as well as future research directions in the field of confined placental mosaicism and its consequences.

Comparative genomic hybridization: a new approach to screening for intrauterine complete or mosaic aneuploidy.

In the practice of clinical genetics chromosomal aneuploidy in both mosaic and nonmosaic forms has long been recognized as a cause of abnormal prenatal and postnatal development. Traditionally, cytogenetic analysis of cultured lymphocytes has been used as a standard test for detection of constitutional aneuploidies. As lymphocytes represent only one lineage, chromosomal mosaicism expressed in other tissues often remains undetected. The purpose of this study was to assess the utilization of molecular cytogenetic analysis for detection of chromosomal aneuploidy in placental tissues. Using placentas from 100 pregnancies with viable nonmalformed livebirths, both trophoblast and chorionic stroma were analyzed using comparative genomic hybridization (CGH). In all cases with an indication of chromosomal imbalance by CGH, fluorescence in situ hybridization (FISH) analysis was performed to confirm the presence of aneuploidy. To differentiate between constitutional aneuploidy and confined placental mosaicism (CPM), amniotic membrane was analyzed by CGH and FISH techniques. Our results demonstrated five placentas with CPM for chromosomes 2, 4, 12, 13, and 18, respectively, and two constitutional nonmosaic aneuploidies (47,XXX and 47,XXY). Molecular cytogenetic studies of human placental tissues enables easy analysis of both embryonic (amnion) and extraembryonic (chorion) cell lineages. Detection at birth of chromosomal defects affecting intrauterine placental and fetal development is important because these chromosomal defects may continue to have an influence on postnatal development.

Pathogenesis of chromosomal mosaicism and its effect on early human development.

Constitutional chromosomal mosaicism is the result of postfertilization mitotic error, the mechanism of which is not fully understood. The distribution of mosaicism in the conceptus depends on the timing, cell lineage(s) involved, cell viability, and chromosome involved. The developmental consequences of mosaicism also are related to its meiotic or somatic type. Meiotic mosaicism often is associated with a more severely adverse effect on the conceptus (see trisomy zygote rescue) due to the presence of uniparental disomy in the embryo/fetus and/or to dysfunction of a trisomic placenta. As mosaicism can be tissue specific, the result of a normal karyotype in cultured lymphocytes does not exclude the presence of mosaicism elsewhere in the conceptus. Mosaicism can best be detected by a combination of traditional cytogenetic analysis with molecular cytogenetic techniques such as comparative genomic hybridization and fluorescence in situ hybridization.

Comparative genomic hybridization in combination with flow cytometry improves results of cytogenetic analysis of spontaneous abortions.

More than 50% of spontaneous abortions (SAs) have abnormal chromosomes; the most common abnormalities are trisomy, sex chromosome monosomy, and polyploidy. Conventional cytogenetic analysis of SAs depends on tissue culturing and is associated with a significant tissue culture failure rate and contamination by maternally derived cells. Comparative genomic hybridization (CGH), in combination with flow cytometry (FCM), can detect numerical and unbalanced structural chromosomal abnormalities associated with SAs while avoiding the technical problems associated with tissue culture. Routine cytogenetic and CGH analysis was performed independently on tissue from 301 SAs. Samples shown to be chromosomally balanced by CGH were analyzed by FCM to determine ploidy. Of 253 samples successfully analyzed by both approaches, there was an absolute correlation of results in 235 (92.8%). Of the 18 cases with discrepancies between cytogenetic and CGH/FCM results, an explanation could be found in 17. Twelve samples produced a 46,XX karyotype by cytogenetics, whereas CGH/FCM demonstrated aneuploidy/polyploidy or a male genome, indicating maternal contamination of the tissue cultures. In two cases, where tetraploidy was demonstrated by cytogenetics and diploidy by FCM, tissue culture artifact is implied. In three cases, CGH demonstrated an aneuploidy, and cytogenetics demonstrated hypertriploidy. In one unexplainable case, aneuploidy demonstrated by CGH could not be detected by repeat CGH analysis, conventional cytogenetic, or FISH analysis. These results demonstrate that CGH supplemented with FCM can readily identify chromosomal abnormalities associated with SAs and, by avoiding maternal contamination and tissue culture artifacts, can do so with a lower failure rate and more accuracy than conventional cytogenetic analysis.