A cytogenetic survey of 14,069 newborn infants. I. Incidence of chromosome abnormalities

Disorders of sex development: a study of 194 cases

OBJECTIVE

To study the clinical profile and the management of patients with disorders of sex development (DSD).

DESIGN AND SETTING

Retrospective study from a tertiary care hospital of North India.

METHODS AND PATIENTS

One hundred ninety-four patients of DSD registered in the Endocrine clinic of Postgraduate Institute of Medical Education and Research, Chandigarh between 1995 and 2014 were included.

RESULTS

One hundred and two patients (52.5%) had 46,XY DSD and seventy-four patients (38.1%) had 46,XX DSD. Sex chromosome DSD was identified in seven (3.6%) patients. Of 102 patients with 46,XY DSD, 32 (31.4%) had androgen insensitivity syndrome and 26 (25.5%) had androgen biosynthetic defect. Of the 74 patients with 46,XX DSD, 52 (70.27%) had congenital adrenal hyperplasia (CAH) and eight (10.8%) had ovotesticular DSD. Five patients with sex chromosome DSD had mixed gonadal dysgenesis. Excluding CAH, majority of the patients (90%) presented in the post-pubertal period. One-fourth of the patients with simple virilising CAH were reared as males because of strong male gender identity and behaviour and firm insistence by the parents. Corrective surgeries were performed in twenty patients (20%) of 46,XY DSD without hormonal evaluation prior to the presentation.

CONCLUSION

Congenital adrenal hyperplasia is the most common DSD in the present series. Most common XY DSD is androgen insensitivity syndrome, while CAH is the most common XX DSD. Delayed diagnosis is a common feature, and corrective surgeries are performed without seeking a definite diagnosis.

Historical and Clinical Perspectives on Chromosomal Translocations

Chromosomal translocations, rearrangements involving the exchange of segments between chromosomes, were documented in humans in 1959. The first accurately reported clinical phenotype resulting from a translocation was that of Down syndrome. In a small percentage of Down syndrome cases, an extra 21q is provided by a Robertsonian translocation chromosome, either occurring de novo or inherited from a phenotypically normal parent with the translocation chromosome and a balanced genome of 45 chromosomes. Balanced translocations, including both Robertsonian and reciprocal translocations, are typically benign, but meiosis in germ cells with balanced translocations may result in meiotic arrest and subsequent infertility, or in unbalanced gametes, with attendant risks of miscarriage and unbalanced progeny. Most reciprocal translocations are unique. A few to several percent of translocations disrupt haploinsufficient genes or their regulatory regions and result in clinical phenotypes. Balanced translocations from patients with clinical phenotypes have been valuable in mapping disease genes and in illuminating cis-regulatory regions. Mapping of discordant mate pairs from long-insert, low-pass genome sequencing now permits efficient and cost-effective discovery and nucleotide-level resolution of rearrangement breakpoints, information that is absolutely necessary for interpreting the etiology of clinical phenotypes in patients with rearrangements. Pathogenic translocations and other balanced chromosomal rearrangements constitute a class of typically highly penetrant mutation that is cryptic to both clinical microarray and exome sequencing. A significant proportion of rearrangements include additional complexity that is not visible by conventional karyotype analysis. Some proportion of patients with negative findings on exome/genome sequencing and clinical microarray will be found to have etiologic balanced rearrangements only discoverable by genome sequencing with analysis pipelines optimized to recover rearrangement breakpoints.

The establishment and application of preimplantation genetic haplotyping in embryo diagnosis for reciprocal and Robertsonian translocation carriers

Background

Preimplantation genetic diagnosis (PGD) is now widely used to select embryos free of chromosomal copy number variations (CNV) from chromosome balanced translocation carriers. However, it remains a difficulty to distinguish in embryos between balanced and structurally normal chromosomes efficiently.

Methods

For this purpose, genome wide preimplantation genetic haplotyping (PGH) analysis was utilized based on single nucleotide polymorphism (SNP) microarray. SNPs that are heterozygous in the carrier and, homozygous in the carrier’s partner and carrier’s family member are defined as informative SNPs. The haplotypes including the breakpoint regions, the whole chromosomes involved in the translocation and the corresponding homologous chromosomes are established with these informative SNPs in the couple, reference and embryos. In order to perform this analysis, a reference either a translocation carrier’s family member or one unbalanced embryo is required. The positions of translocation breakpoints are identified by molecular karyotypes of unbalanced embryos. The recombination of breakpoint regions in embryos could be identified.

Results

Eleven translocation families were enrolled. 68 blastocysts were analyzed, in which 42 were unbalanced or aneuploid and the other 26 were balanced or normal chromosomes. Thirteen embryos were transferred back to patients. Prenatal cytogenetic analysis of amniotic fluid cells was performed. The results predicted by PGH and karyotypes were totally consistent.

Conclusions

With the successful clinical application, we demonstrate that PGH was a simple, efficient, and popularized method to distinguish between balanced and structurally normal chromosome embryos.

Electronic supplementary material

The online version of this article (10.1186/s12920-017-0294-x) contains supplementary material, which is available to authorized users.

Rare X Chromosome Abnormalities in Systemic Lupus Erythematosus and Sjögren's Syndrome

OBJECTIVE

Sjögren's syndrome (SS) and systemic lupus erythematosus (SLE) are related by clinical and serologic manifestations as well as genetic risks. Both diseases are more commonly found in women than in men, at a ratio of ~10 to 1. Common X chromosome aneuploidies, 47,XXY and 47,XXX, are enriched among men and women, respectively, in either disease, suggesting a dose effect on the X chromosome.

METHODS

We examined cohorts of SS and SLE patients by constructing intensity plots of X chromosome single-nucleotide polymorphism alleles, along with determining the karyotype of selected patients.

RESULTS

Among ~2,500 women with SLE, we found 3 patients with a triple mosaic, consisting of 45,X/46,XX/47,XXX. Among ~2,100 women with SS, 1 patient had 45,X/46,XX/47,XXX, with a triplication of the distal p arm of the X chromosome in the 47,XXX cells. Neither the triple mosaic nor the partial triplication was found among the controls. In another SS cohort, we found a mother/daughter pair with partial triplication of this same region of the X chromosome. The triple mosaic occurs in ~1 in 25,000-50,000 live female births, while partial triplications are even rarer.

CONCLUSION

Very rare X chromosome abnormalities are present among patients with either SS or SLE and may inform the location of a gene(s) that mediates an X dose effect, as well as critical cell types in which such an effect is operative.

Molecular characterisation of a case of dicentric Y presented as nonobstructive azoospermia with testicular early maturation arrest

The dicentric Y chromosome is the most common cytogenetically visible structural abnormality of Y chromosome. The sites of break and fusion of dicentric Y are variable, but break and fusion at Yq12 (proximal to the pseudoautosomal region 2/PAR 2) is very rare. Dicentric Y chromosome is unstable during cell division and likely to generate chromosomal mosaicism. Here, we report a case of infertile male with nonmosaic 46,XY where chromosome Y was dicentric with break and fusion at Yq12 (proximal to PAR 2). Clinical presentation of the case was nonobstructive azoospermia due to early maturation arrest at the primary spermatocyte stage. Various molecular techniques such as FISH, STS-PCR and DNA microarray were carried out to characterise genetic defect leading to testicular maturation arrest in the patient. The break and fusion was found at Yq12 (proximal to PAR 2) and resulted in near total duplication of Y chromosome (excluding PAR 2). The reason for maturation arrest seems due to CNVs of PARs (gain in PAR 1 and loss of PAR 2) and azoospermia factors (gain).

Centromere structure and function analysis in wheat-rye translocation lines

1RS.1BL translocations are centric translocations formed by misdivision and have been used extensively in wheat breeding. However, the role that the centromere plays in the formation of 1RS.1BL translocations is still unclear. Fluorescence in situ hybridization (FISH) was applied to detect the fine structures of the centromeres in 130 1RS.1BL translocation cultivars. Immuno-FISH, chromatin immunoprecipitation (ChIP)-qPCR and RT-PCR were used to investigate the functions of the hybrid centromeres in 1RS.1BL translocations. New 1R translocations with different centromere structures were created by misdivision and pollen irradiation to elucidate the role that the centromere plays in the formation of 1RS.1BL translocations. We found that all of the 1RS.1BL translocations detected contained hybrid centromeres and that wheat-derived CENH3 bound to both the wheat and rye centromeres in the 1RS.1BL translocation chromosomes. Moreover, a rye centromere-specific retrotransposon was actively transcribed in 1RS.1BL translocations. The frequencies of new 1RS hybrid centromere translocations and group-1 chromosome translocations were higher during 1R misdivision. Our study demonstrates the hybrid nature of the centromere in 1RS.1BL translocations. New 1R translocations with different centromere structures were created to help understand the fusion centromere used for wheat breeding and for use as breeding material for the improvement of wheat.

Hypospadias in a male infant with an unusual mosaic 45,X/46,X,psu idic(Y)(p11.32)/46,XY and haploinsufficiency of SHOX: A case report

A male newborn presented with hypospadias and differential testicular volumes. Short femur length was detected four times during pregnancy, at 23, 31, 32 and 33 weeks, by ultrasonographic examination. Chromosome analysis was performed on peripheral lymphocytes obtained from the infant and his parents. Fluorescent in situ hybridization (FISH), using sex determining region Y (SRY)/DXZ1 and DYZ3 probes, was performed to verify the deletion of the SRY gene (located on Yp11.3 region) and the activation of Y chromosomal centromeres. Single nucleotide polymorphism (SNP)-array comparative genomic hybridization (CGH) was used to detect copy number variations in the infant. The results revealed a ~2.2 Mb mircodeletion on Yp11.32 containing the short stature homeobox (SHOX) gene. According to the above examinations, the abnormal Y chromosome of the patient was identified as a dicentric derivate of the Y chromosome with pseudoinactivation of one of the two centromeres. The karyotype is therefore: 45,X[20]/46,X,idic(Y)(p11.3).ish psu idic(Y)(p11.3) (SRY++, DYZ3++). array Yp11.32 (118,551–2,393,500)x0[26]/46,X,ishY(SRY+, DYZ3+)[4]. The combination of cytogenetic, FISH and SNP-array CGH technologies was beneficial for diagnosing the karyotype accurately, predicting the prognosis, and preparing an effective treatment plan for the patient.

Cross-sectional study shows that impaired bone mineral status and metabolism are found in nonmosaic triple X syndrome

AIM

The effect of a supernumerary X chromosome on bones has not been reported, and this study evaluated bone mineral status and metabolism in nonmosaic triple X syndrome.

METHODS

This cross-sectional study comprised 19 girls, with a median age of 10.9 years, with nonmosaic triple X syndrome and a control group matched for age and body size. We studied ionised and total calcium, phosphate, parathyroid hormone (PTH), 25-hydroxyvitamin D (25(OH)D), 1,25-dihydroxyvitamin D, osteocalcin, bone alkaline phosphatase levels and urinary deoxypyridinoline concentrations. We also measured the phalangeal amplitude-dependent speed of sound (AD-SoS) and the bone transmission time (BTT) Z-scores.

RESULTS

Patients with nonmosaic triple X syndrome showed significantly reduced AD-SoS (p < 0.005) and BTT Z-scores (p < 0.0001) compared to the control group, and these results persisted when we divided the sample into prepubertal and pubertal patients (p < 0.05). These patients also had significantly reduced ionised calcium (p < 0.005) and 25(OH)D levels (p < 0.005) and higher phosphate (p < 0.0001) and PTH (p < 0.0001) levels.

CONCLUSION

Subjects with nonmosaic triple X syndrome exhibited a significant impairment in bone mineral status and metabolism similar to other X polisomy, such as Klinefelter's syndrome. This suggests the presence of a primary bone deficit and the need for regular and close monitoring of these subjects.

Clinical outcomes for couples containing a reciprocal chromosome translocation carrier without preimplantation genetic diagnosis

OBJECTIVE

To evaluate the pregnancy outcomes of couples containing a carrier of a reciprocal chromosome translocation (RCT) after assisted reproductive technology without preimplantation genetic diagnosis.

METHODS

A retrospective study was performed using data for couples with an RCT carrier and control couples with a normal karyotype (1:4 ratio) who underwent assisted reproductive technology cycles at a Chinese fertility center in 2010-2011. The embryos were fertilized via in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI). Only the first pick-up cycles were used for analysis. Clinical variables were compared.

RESULTS

Compared with the control group (n=164), the RCT group (n=41) had a marginally lower clinical pregnancy rate (46.3% [19/41] vs 54.3% [89/164]), implantation rate (21.7% [23/106] vs 26.9% [118/438]), multiple-gestation pregnancy rate (21.1% [4/19] vs 32.6% [29/89]), and delivery rate (36.6% [15/41] vs 47.6% [78/164]), whereas the spontaneous abortion rate was slightly higher (21.1% [4/19] vs 12.4% [11/89]). However, none of these differences were significant.

CONCLUSION

The clinical outcomes for RCT carriers were acceptable after IVF/ICSI without performing preimplantation genetic diagnosis, indicating that this approach might comprise a feasible alternative fertility treatment for RCT carriers.

Prenatal evaluation of a fetus with trisomy 18 and additional balanced de novo Rob(13;14)

The main aim of this work is to present unusual case with full trisomy 18 and additional robertsonian translocation- Rob (13;14) detected through abnormalities found in prenatal ultrasound examination. A 26 years-old pregnant women with no family history of any reproductive failure underwent level II ultrasound screening in 19 weeks of gestation. Polyhydramnios, intrauterine growth retardation, hydrocephalus, enlarged lateral ventricles, club foot and cardiac defect were found. Amniocentesis was indicated considering the high likelihood of a chromosomal aberration. Abnormal karyotype was detected 46, XY, der(13;14)(q10;q10), +18. Karyotypes of parents were normal, what confirmed de novo origin of this aberration. Pregnancy was terminated. In postnatal examination fetus demonstrated intrauterine groth retardation and a lot of dysmorphic features characteristic for trisomy 18: microcephaly, prominent occiput, very low set and posteriorly rotated ears, hypertelorism, small mouth, small recessed mandible, a high narrow palate, broad nasal bridge, low-set ears, preauricilar skin appendage, clenched fingers clinodactyly of Vth fingers and club foot. In conclusion it is worth to say that our described fetus demonstrated rather typical for trisomy 18 ultrasonographic features. Balanced Rob (13;14) gives no phenotypic expression. Possible interchromosomal effect in complex chromosomal aberration formation such as Rob (13;14) with trisomy 18 was discussed.

Chromosomal analysis of blastocysts from balanced chromosomal rearrangement carriers

Balanced chromosomal rearrangements (CRs) are among the most common genetic abnormalities in humans. In the present study, we have investigated the degree of consistency between the chromosomal composition of the blastocyst inner cell mass (ICM) and trophectoderm (TE) in carriers with balanced CR, which has not been previously addressed. As a secondary aim, we have also evaluated the validity of cleavage-stage preimplantation genetic diagnosis (PGD) based on fluorescence in situ hybridization (FISH) of blastocysts from CR carriers. Blastocyst ICM and TE were screened for chromosomal aneuploidy and imbalance of CR-associated chromosomes based on whole-genome copy number variation analysis by low-coverage next-generation sequencing (NGS) following single-cell whole-genome amplification by multiple annealing and looping-based amplification cycling. The NGS results were analyzed without knowledge of cleavage-stage FISH results. NGS results for blastocyst ICM and TE from CR carriers were 86.49% (32/37) consistent. Of the 1702 (37×46) chromosomes examined, 99.47% (1693/1702) showed consistency. However, only 40.0% (18/45) of all embryos had consistent results for chromosomes involved in CR, as determined by blastocyst NGS and cleavage-stage FISH. Of the 85 CR-affected chromosomes analyzed by FISH, 37.65% (32/85) were incongruous with NGS results, with 87.5% (28/32) showing imbalanced composition by FISH but balanced composition by NGS. These results indicate that chromosomal composition of blastocyst ICM and TE in balanced CR carriers is highly consistent, and that PGD based on cleavage-stage FISH is inaccurate; therefore, using blastocyst TE biopsies for NGS-based PGD is recommended for identifying chromosomal imbalance in embryos from balanced CR carriers.

Identifying Robertsonian Translocation Carriers by Microarray-Based DNA Analysis

OBJECTIVE

To develop a noninvasive prenatal testing improvement that allows identification of Robertsonian translocation carriers.

METHODS

Blood samples from 191 subjects, including 7 pregnant and 9 non-pregnant Robertsonian translocation carriers, were analyzed for fetal trisomy and Robertsonian translocation status. Digital Analysis of Selected Regions (DANSR™) assays targeting sequences common to the p arms of 5 acrocentric chromosomes were developed and added to existing DANSR assays. DANSR products were hybridized onto a custom DNA microarray for DNA analysis. The Fetal-Fraction Optimized Risk of Trisomy Evaluation (FORTE™) algorithm measures the fraction of fetal DNA and accounts for both the fetal and maternal fractions in the cell-free DNA sample to determine Robertsonian risk. The expectation in a Robertsonian translocation carrier is that DANSR assays on acrocentric p arms should have a concentration 20% less than that of controls.

RESULTS

The FORTE algorithm correctly classified the fetal trisomy status and maternal Robertsonian translocation status in all 191 samples. Sixteen samples had a Robertsonian risk score above 99%, while 175 samples had a Robertsonian risk score below 0.01%.

CONCLUSIONS

Robertsonian translocations are the most common chromosomal translocations and can have significant reproductive consequences. A maternal screen for Robertsonian translocation carriers would provide women valuable information regarding the risk of fetal trisomy.

Mechanisms of germ line genome instability

During meiosis, numerous DNA double-strand breaks (DSBs) are formed as part of the normal developmental program. This seemingly destructive behavior is necessary for successful meiosis, since repair of the DSBs through homologous recombination (HR) helps to produce physical links between the homologous chromosomes essential for correct chromosome segregation later in meiosis. However, DSB formation at such a massive scale also introduces opportunities to generate gross chromosomal rearrangements. In this review, we explore ways in which meiotic DSBs can result in such genomic alterations.

Constitutional abnormalities of chromosome 21 predispose to iAMP21-acute lymphoblastic leukaemia

In addition to Down syndrome, individuals with other constitutional abnormalities of chromosome 21 have an increased risk of developing childhood acute lymphoblastic leukaemia (ALL). Specifically, carriers of the Robertsonian translocation between chromosomes 15 and 21, rob(15;21) (q10; q10)c, have ∼2,700 increased risk of developing ALL with iAMP21 (intrachromosomal amplification of chromosome 21). In these patients, chromosome 15 as well as chromosome 21 is involved in the formation of iAMP21, referred to here as der(21)(15;21). Individuals with constitutional ring chromosomes involving chromosome 21, r(21)c, are also predisposed to iAMP21-ALL, involving the same series of mutational processes as seen in sporadic- and der(21)(15;21)-iAMP21 ALL. Evidence is accumulating that the dicentric nature of the Robertsonian and ring chromosome is the initiating factor in the formation of the complex iAMP21 structure. Unravelling these intriguing predispositions to iAMP21-ALL may provide insight into how other complex rearrangements arise in cancer.

Cytogenetic analysis of chromosomal abnormalities in Sri Lankan children

BACKGROUND

Cytogenetic analysis is a valuable investigation in the diagnostic work up of children with suspected chromosomal disorders. The objective of this study was to describe the prevalence of various types of chromosomal abnormalities in Sri Lankan children undergoing cytogenetic analysis.

METHODS

Cytogenetic reports of 1554 consecutive children with suspected chromosomal disorders who underwent karyotyping in two genetic centers in Sri Lanka from January 2006 to December 2011 were reviewed retrospectively.

RESULTS

A total of 1548 children were successfully karyotyped. Abnormal karyotypes were found in 783 (50.6%) children. Numerical and structural abnormalities accounted for 90.8% and 9.2%, respectively. Down syndrome was the commonest aneuploidy identified. Other various autosomal and sex chromosomal aneuploidies as well as micro-deletion syndromes were also detected.

CONCLUSIONS

The prevalence of chromosomal abnormalities in Sri Lankan children undergoing cytogenetic analysis for suspected chromosomal disorders was relatively higher than that in Caucasian and other Asian populations.

Perspectives in Pediatric Pathology, Chapter 5. Gonadal Dysgenesis

One of the most challenging areas in pediatric testicular pathology is the appropriate understanding and pathological diagnosis of disorders of sexual development (DSD), and in particular, the issue of gonadal dysgenesis. Here we present the main concepts necessary for their understanding and appropriate classification, with extensive genetic correlations.

Morphometric analysis and developmental comparison of embryos from carriers with balanced chromosomal rearrangements in preimplantation genetic diagnosis cycles

The morphological parameters of embryos from 22 carriers with balanced chromosomal rearrangements (CRs) were quantified and evaluated to determine their possible link to chromosomal composition. The morphometric characteristics of 168 embryos diagnosed by fluorescence in situ hybridisation were measured using an imaging tool and then analysed retrospectively. The mean zygotic diameter of normal-balanced embryos was significantly smaller compared with that of abnormal embryos (P=0.015). In addition, the reduction in total cytoplasmic volume for Day-3 embryos was significantly lower in normal or balanced embryos than in abnormal embryos (P=0.027). Moreover, the pronuclear volumes of embryos that failed to reach the blastocyst stage were significantly smaller compared with those of blastocysts (P=0.016). These findings indicate that morphometric characteristics are correlated with developmental outcomes as well as with chromosomal composition in embryos from balanced CR carriers. However, an effective indicator of developmental outcomes may not accurately reflect chromosomal composition. Combining morphometric and traditional qualitative assessment may increase the precision and standardisation of embryo evaluation as well as contributing to improved efficiency of preimplantation genetic diagnosis by selecting embryos with high developmental potential and preferentially testing embryos predicted to have a low risk of chromosomal imbalance.

Robertsonian translocations: an overview of 872 Robertsonian translocations identified in a diagnostic laboratory in China

Robertsonian translocations (ROBs) have an estimated incidence rate of 1/1000 births, making this type of rearrangement the most common structural chromosomal abnormalities seen in the general population. In this study, we reports 872 cases of ROBs from 205,001 specimens karyotyped postnatally in a single accredited laboratory in China, including 583 balanced ROBs, 264 unbalanced ROBs, 9 mosaic ROBs, and 18 complex ROBs. Ninety-three percent of the balanced ROBs observed were adults with infertility, miscarriage, or offspring(s) with known chromosomal abnormalities. Significant excess of females were found to be carriers of balanced ROBs with an adjusted male/female ratio of 0.77. Ninety-eight percent of the unbalanced ROBs observed were children with variable referral reasons. Almost all of the unbalanced ROBs involved chromosome 21 except a single ROB with [46,XX,der(13;14),+13] identified in a newborn girl with multiple congenital anomalies. Multiple novel ROB karyotypes were reported in this report. This study represents the largest collections of ROBs in Chinese population.

Prenatal screening of cytogenetic anomalies - a Western Indian experience

Background

Children born with congenital anomalies present a very high rate of perinatal death and neonatal mortality. Cytogenetic analysis is a convincing investigation along with clinical suspicion and biochemical screening tests. The current study was designed to characterize the prevalence and types of chromosomal abnormalities in high risk prenatal samples using different cytogenetic techniques.

Methods

This study was conducted on a total of 1,728 prenatal samples (1,324 amniotic fluids, 366 chorionic villi and 38 cord blood samples) from 1994 to 2014 at Institute of Human Genetics, Ahmedabad, India. Conventional karyotyping was conducted with GTG-banding. Molecular approaches were used (fluorescence in situ hybridization = FISH and/ or array-comparative genomic hybridization = aCGH) when indicated to detect karyotypic abnormalities.

Results

Abnormal karyotypes were detected in 125/1,728 (7.2%) cases. Trisomy 21 was the most common abnormality detected in 46 (2.7%) followed by trisomy 18 in 11 (0.6%) and trisomy 13 in 2 (0.1%) samples. Besides, structural abnormalities such as reciprocal and Robertsonian translocation were detected in 20 [1.2%] cases. Turner syndrome was diagnosed in seven (0.4%) cases; in six (0.34%) cases there was an inversion in the Y-chromosome. Heteromorphic variants were diagnosed in 22 (1.3%) cases. Finally, small supernumerary marker chromosomes (sSMC) were found in six (0.34%) cases.

Conclusion

Conventional GTG-banding along with molecular cytogenetic techniques is useful in detecting genomic alterations and rearrangements. Comprehensive characterization of chromosomal rearrangements like sSMC has the potential to save potentially healthy fetuses from being terminated.

Blood Spotlight on iAMP21 acute lymphoblastic leukemia (ALL), a high-risk pediatric disease

Intrachromosomal amplification of chromosome 21 (iAMP21) defines a distinct cytogenetic subgroup of childhood B-cell precursor acute lymphoblastic leukemia. Breakage-fusion-bridge cycles followed by chromothripsis and other complex structural rearrangements of chromosome 21 underlie the mechanism giving rise to iAMP21. Patients with iAMP21 are older (median age 9 years), with a low white cell count. They have a high relapse rate when treated as standard risk. Recent studies have shown improved outcome on intensive therapy. Molecular targets for therapy are being sought.

Local adaptation and the evolution of chromosome fusions

We use forward and coalescent models of population genetics to study chromosome fusions that reduce the recombination between two locally adapted loci. Under a continent-island model, a fusion spreads and reaches a polymorphic equilibrium when it causes recombination between locally adapted alleles to be less than their selective advantage. In contrast, fusions in a two-deme model always spread; whether it reaches a polymorphic equilibrium or becomes fixed depends on the relative recombination rates of fused homozygotes and heterozygotes. Neutral divergence around fusion polymorphisms is markedly increased, showing peaks at the point of fusion and at the locally adapted loci. Local adaptation could explain the evolution of many of chromosome fusions, which are some of the most common chromosome rearrangements in nature.

Analysis of the gene coding for steroidogenic factor 1 (SF1, NR5A1) in a cohort of 50 Egyptian patients with 46,XY disorders of sex development

OBJECTIVE

Steroidogenic factor 1 (SF1, NR5A1) is a key transcriptional regulator of genes involved in the hypothalamic-pituitary-gonadal axis. Recently, SF1 mutations were found to be a frequent cause of 46,XY disorders of sex development (DSD) in humans. We investigate the frequency of NR5A1 mutations in an Egyptian cohort of XY DSD.

DESIGN

Clinical assessment, endocrine evaluation and genetic analysis of 50 Egyptian XY DSD patients (without adrenal insufficiency) with a wide phenotypic spectrum.

METHODS

Molecular analysis of NR5A1 gene by direct sequencing followed by in vitro functional analysis of the two novel missense mutations detected.

RESULTS

Three novel heterozygous mutations of the coding region in patients with hypospadias were detected. p.Glu121AlafsX25 results in severely truncated protein, p.Arg62Cys lies in DNA-binding zinc finger, whereas p.Ala154Thr lies in the hinge region of SF1 protein. Transactivation assays using reporter constructs carrying promoters of anti-Müllerian hormone (AMH), CYP11A1 and TESCO core enhancer of Sox9 showed that p.Ala154Thr and p.Arg62Cys mutations result in aberrant biological activity of NR5A1. A total of 17 patients (34%) harboured the p.Gly146Ala polymorphism.

CONCLUSION

We identified two novel NR5A1 mutations showing impaired function in 23 Egyptian XY DSD patients with hypospadias (8.5%). This is the first study searching for NR5A1 mutations in oriental patients from the Middle East and Arab region with XY DSD and no adrenal insufficiency, revealing a frequency similar to that in European patients (6.5-15%). We recommend screening of NR5A1 in patients with hypospadias and gonadal dysgenesis. Yearly follow-ups of gonadal function and early cryoconservation of sperms should be performed in XY DSD patients with NR5A1 mutations given the risk of future fertility problems due to early gonadal failure.

Constitutional and somatic rearrangement of chromosome 21 in acute lymphoblastic leukaemia

Changes in gene dosage are a major driver of cancer, known to be caused by a finite, but increasingly well annotated, repertoire of mutational mechanisms. This can potentially generate correlated copy-number alterations across hundreds of linked genes, as exemplified by the 2% of childhood acute lymphoblastic leukaemia (ALL) with recurrent amplification of megabase regions of chromosome 21 (iAMP21). We used genomic, cytogenetic and transcriptional analysis, coupled with novel bioinformatic approaches, to reconstruct the evolution of iAMP21 ALL. Here we show that individuals born with the rare constitutional Robertsonian translocation between chromosomes 15 and 21, rob(15;21)(q10;q10)c, have approximately 2,700-fold increased risk of developing iAMP21 ALL compared to the general population. In such cases, amplification is initiated by a chromothripsis event involving both sister chromatids of the Robertsonian chromosome, a novel mechanism for cancer predisposition. In sporadic iAMP21, breakage-fusion-bridge cycles are typically the initiating event, often followed by chromothripsis. In both sporadic and rob(15;21)c-associated iAMP21, the final stages frequently involve duplications of the entire abnormal chromosome. The end-product is a derivative of chromosome 21 or the rob(15;21)c chromosome with gene dosage optimized for leukaemic potential, showing constrained copy-number levels over multiple linked genes. Thus, dicentric chromosomes may be an important precipitant of chromothripsis, as we show rob(15;21)c to be constitutionally dicentric and breakage-fusion-bridge cycles generate dicentric chromosomes somatically. Furthermore, our data illustrate that several cancer-specific mutational processes, applied sequentially, can coordinate to fashion copy-number profiles over large genomic scales, incrementally refining the fitness benefits of aggregated gene dosage changes.

Uniparental disomy in Robertsonian translocations: strategies for uniparental disomy testing

Robertsonian translocations (ROBs) are whole arm rearrangements involving the acrocentric chromosomes 13-15 and 21-22 and carriers are at increased risk for aneuploidy and thus uniparental disomy (UPD). Chromosomes 14 and 15 are imprinted with expression of genes dependent on the parental origin of the chromosome. Correction of a trisomic or monosomic conceptus for chromosomes 14 or 15 would lead to one of the established UPD 14mat/pat or UPD 15 (Prader-Willi/Angelman) syndromes (PWS/AS). In view of this, prenatal UPD testing should be considered for balanced carriers of a ROB, fetuses with a familial or de novo balanced ROB that contains chromosome 14 or 15 or with a normal karyotype when a parent is a carrier of a balanced ROB with a 14 or 15. Individuals with congenital anomalies and an abnormal phenotype and carry a ROB involving the two imprinted chromosomes should also be UPD tested.

Nucleolar organization, ribosomal DNA array stability, and acrocentric chromosome integrity are linked to telomere function

The short arms of the ten acrocentric human chromosomes share several repetitive DNAs, including ribosomal RNA genes (rDNA). The rDNA arrays correspond to nucleolar organizing regions that coalesce each cell cycle to form the nucleolus. Telomere disruption by expressing a mutant version of telomere binding protein TRF2 (dnTRF2) causes non-random acrocentric fusions, as well as large-scale nucleolar defects. The mechanisms responsible for acrocentric chromosome sensitivity to dysfunctional telomeres are unclear. In this study, we show that TRF2 normally associates with the nucleolus and rDNA. However, when telomeres are crippled by dnTRF2 or RNAi knockdown of TRF2, gross nucleolar and chromosomal changes occur. We used the controllable dnTRF2 system to precisely dissect the timing and progression of nucleolar and chromosomal instability induced by telomere dysfunction, demonstrating that nucleolar changes precede the DNA damage and morphological changes that occur at acrocentric short arms. The rDNA repeat arrays on the short arms decondense, and are coated by RNA polymerase I transcription binding factor UBF, physically linking acrocentrics to one another as they become fusogenic. These results highlight the importance of telomere function in nucleolar stability and structural integrity of acrocentric chromosomes, particularly the rDNA arrays. Telomeric stress is widely accepted to cause DNA damage at chromosome ends, but our findings suggest that it also disrupts chromosome structure beyond the telomere region, specifically within the rDNA arrays located on acrocentric chromosomes. These results have relevance for Robertsonian translocation formation in humans and mechanisms by which acrocentric-acrocentric fusions are promoted by DNA damage and repair.

Phenotypic differences in mosaic Klinefelter patients as compared with non-mosaic Klinefelter patients

OBJECTIVE

To determine whether men with Klinefelter syndrome (KS) have the same phenotype as men with mosaic KS.

DESIGN

Subject identification via prospectively collected database.

SETTING

Male infertility specialty clinic.

PATIENT(S)

Men undergoing a fertility evaluation from 2005 to 2012 at a single male infertility specialty clinic and having a karyotype demonstrating KS (mosaic or non-mosaic).

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

Testicular size, and semen and hormone parameters, genetic evaluation, and signs of testosterone (T) deficiency using validated questionnaires.

RESULT(S)

Of 86 men identified with KS, 6 (6.7%) were mosaic KS, and 80 (93.3%) were non-mosaic KS. Men with mosaic KS had lower baseline luteinizing hormone (LH) levels (10.31 IU/L ± 5.52 vs. 19.89 IU/L ± 6.93), lower estradiol levels (58.71 ± 31.10 pmol/L vs. 108.57 ± 43.45 pmol/L), larger mean testicular volumes (11 ± 7.3 mL vs. 6.35 ± 3.69 mL), and a higher mean total sperm count (4.43 ± 9.86 M/mL vs. 0.18 ± 1.17 M/mL). A higher proportion of men with mosaic KS had sperm in the ejaculate: 3 (50%) of 6 versus 3 (3.75%) of 80. The Sexual Health Inventory for Men (SHIM) and Androgen Deficiency in the Aging Male (ADAM) questionnaire scores were not different between groups.

CONCLUSION(S)

Men with mosaic KS seem to be more well androgenized than their non-mosaic KS counterparts, both with respect to hormones and sperm in the ejaculate.

Radiation effects on human heredity

In experimental organisms such as fruit flies and mice, increased frequencies in germ cell mutations have been detected following exposure to ionizing radiation. In contrast, there has been no clear evidence for radiation-induced germ cell mutations in humans that lead to birth defects, chromosome aberrations, Mendelian disorders, etc. This situation exists partly because no sensitive and practical genetic marker is available for human studies and also because the number of people exposed to large doses of radiation and subsequently having offspring was small until childhood cancer survivors became an important study population. In addition, the genome of apparently normal individuals seems to contain large numbers of alterations, including dozens to hundreds of nonfunctional alleles. With the number of mutational events in protein-coding genes estimated as less than one per genome after 1 gray (Gy) exposure, it is unsurprising that genetic effects from radiation have not yet been detected conclusively in humans.

Coexistence of Ankylosing Spondylitis and Klinefelter's Syndrome

Ankylosing spondylitis is a chronic inflammatory disease characterized by inflammatory lower back pain and morning stiffness and accompanied by spine and sacroiliac joint involvement. Klinefelter's syndrome is a genetic condition that only affects males. Affected males have an extra X chromosome. This paper reports a 30-years-old male on followup with the diagnosis of Klinefelters syndrome. The patient admitted with complaints of inflammatory lower back, and neck pain and morning stiffness and was diagnosed with ankylosing spondylitis. Nonsteroidal anti-inflammatory drug and salazopyrine treatment resulted in significant regression in his complaints.

The clinical application of array CGH for the detection of chromosomal defects in 20,126 unselected newborns

Background

Array comparative genomic hybridization (CGH) is a powerful tool for detecting unbalanced chromosomal alterations. To validate the usefulness of array CGH in newborn screening, we examined 20,126 unselected infants. In addition, the number of newborns analyzed with array CGH is the largest one ever reported.

Findings

A total of 20,126 unselected newborns were investigated with array CGH and cytogenetic analyses. The analyses revealed 87 cases with chromosome abnormalities. Of these, 53 cases had significant chromosome aneuploidies, including trisomy 13, trisomy 21, 47,XXY or 45,X, and the other 34 cases presented partial chromosomal deletions or duplications.

Conclusions

In this study, we show that array CGH is an appropriate tool for the screening of chromosomal abnormalities in newborns, especially for the infants without distinct clinical features.

Effect of arsenic contaminated drinking water on human chromosome: a case study

Arsenic contamination of ground water has become a serious problem all over the world. Large number of people from Uttar Pradesh, Bihar and West Bengal of India are suffering due to consumption of arsenic contaminated drinking water. Study was carried out on 30 individuals residing in Ballia District, UP where the maximum concentration of arsenic was observed around 0.37 ppm in drinking water. Blood samples were collected from them to find out the problem related with arsenic. Cytogenetic study of the blood samples indicates that out of 30, two persons developed Klinefelter syndrome.

Identification and molecular cytogenetic characterization of a novel complex Y chromosome rearrangement in a boy with disorder of sexual development

Ambiguous genitalia or disorder of the sexual development is a birth defect where the external genitals do not have the typical appearance of either a male or female. Here we report a boy with ambiguous genitalia and short stature. The cytogenetic analysis by G-banding revealed a small Y chromosome and an additional material on the 15p arm. Further, molecular cytogenetic analysis by Fluorescence in situ hybridization (FISH) using whole chromosome paint probes showed the presence of Y sequences on the 15p arm, confirming that it is a Y;15 translocation. Subsequent, FISH with centromere probe Y showed two signals depicting the presence of two centromeres and differing with a balanced translocation. The dicentric nature of the derivative 15 chromosome was confirmed by FISH with both 15 and Y centromeric probes. Further, the delineation of the Y chromosomal DNA was also done by quantitative real time PCR. Additional Y-short tandem repeat typing was performed to find out the extent of deletion on small Y chromosome. Fine mapping was carried out with 8 Y specific BAC clones which helped in defining the breakpoint regions. MLPA was performed to check the presence or absence of subtelomeric regions and SHOX regions on Y. Finally array CGH helped us in confirming the breakpoint regions. In our study we identified and characterized a novel complex Y chromosomal rearrangement with a complete deletion of the Yq region and duplication of the Yp region with one copy being translocated onto the15p arm. This is the first report of novel and unique Y complex rearrangement showing a deletion, duplication and a translocation in the same patient. The possible mechanism of the rearrangement and the phenotype-genotype correlation are discussed.

Detailed analysis of an idic(Y)(q11.21) in a mosaic karyotype

Abnormalities involving sex chromosomes account for approximately 0.5% of live births. The phenotypes of individuals with mosaic cell lines that exhibit structural aberrations of the X and Y chromosomes are variable and difficult to predict. Phenotypes associated with sex chromosome mosaicism vary from females with Turner syndrome to males with infertility, and include individuals with ambiguous genitalia. In this study, we report a 17-year-old male with phenotypic features of Klinefelter syndrome with an isodicentric Y chromosome and a final karyotype of 45,X[4]/46,X,idic(Y)(q11.21)[95]/47,XX,+idic(Y)(q11.21)[1]. Application of high resolution molecular cytogenetic techniques as well as molecular studies revealed two copies of the sex-determining region of Y chromosome (SRY) gene and two centromers. Additionally, the breakpoint in Yq11.21 was narrowed down between positions 13.4 and 14.3 MB (hg18). We present a patient with partial disomy of Ypter to Yq11.21 in the majority of the patient cells, showing phenotypic features of Klinefelter syndrome. The syndrome may have occurred due to a more prominent presence of the cell line 47,XX,+idic(Y)(q11.21) detected only once in 1% of the peripheral blood cells. This finding may prove helpful in similar cases with symptoms of Klinefelter syndrome, but which exhibit an absence of the cell line 47,XXY in peripheral blood.

46 XY gonadal dysgenesis in adulthood 'pitfalls of late diagnosis'

Disorders of sex development (DSD) include congenital conditions where developments of chromosomal, gonadal or anatomical sex are atypical. Ostrer in 2000, reported a prevalence of 1:20 000 for 46 XY DSD and complete gonadal dysgenesis. A 21-year-old patient consulted for sexual ambiguity at the out-patient department of the Philippine general hospital. At birth, the perceived female external genitalia and clitoromegaly, led the parents to register and eventually rear the patient as a female. At puberty, he developed masculine features and growth of phallus. Patient was more interested in male activities and began to identify himself as male in the community. The discrepancy between his birth certificate and his male gender jeopardised his ambition to become a policeman; this led him to seek medical consult. On physical examination, he was phenotypically male. The external genitalia showed the phallus length of 3.5 cm and perineoscrotal hypospadias. Chromosomal sex was normal 46 XY with neither numerical nor structural aberrations in all cell lines, serum testosterone was low and gonadotrophins were elevated. Whole abdominal CT scan showed bilaterally undescended testes and a 4.5 cm blind vaginal pouch seen on genitogram. Bilateral orchidectomy with first stage repair of hypospadias was performed. On histopathology, the right testis was fibrotic and the left testis showed minimal testicular tissue with absent spermatids. The clinical, endocrine, cytogenetic and histopathologic data are consistent with gonadal dysgenesis syndrome.

Rare chromosome abnormalities, prevalence and prenatal diagnosis rates from population-based congenital anomaly registers in Europe

The aim of this study is to quantify the prevalence and types of rare chromosome abnormalities (RCAs) in Europe for 2000-2006 inclusive, and to describe prenatal diagnosis rates and pregnancy outcome. Data held by the European Surveillance of Congenital Anomalies database were analysed on all the cases from 16 population-based registries in 11 European countries diagnosed prenatally or before 1 year of age, and delivered between 2000 and 2006. Cases were all unbalanced chromosome abnormalities and included live births, fetal deaths from 20 weeks gestation and terminations of pregnancy for fetal anomaly. There were 10,323 cases with a chromosome abnormality, giving a total birth prevalence rate of 43.8/10,000 births. Of these, 7335 cases had trisomy 21,18 or 13, giving individual prevalence rates of 23.0, 5.9 and 2.3/10,000 births, respectively (53, 13 and 5% of all reported chromosome errors, respectively). In all, 473 cases (5%) had a sex chromosome trisomy, and 778 (8%) had 45,X, giving prevalence rates of 2.0 and 3.3/10,000 births, respectively. There were 1,737 RCA cases (17%), giving a prevalence of 7.4/10,000 births. These included triploidy, other trisomies, marker chromosomes, unbalanced translocations, deletions and duplications. There was a wide variation between the registers in both the overall prenatal diagnosis rate of RCA, an average of 65% (range 5-92%) and the prevalence of RCA (range 2.4-12.9/10,000 births). In all, 49% were liveborn. The data provide the prevalence of families currently requiring specialised genetic counselling services in the perinatal period for these conditions and, for some, long-term care.

Sex chromosome aneuploidies among men with systemic lupus erythematosus

About 90% of patients with systemic lupus erythematosus (SLE) are female. We hypothesize that the number of X chromosomes, not sex, is a determinate of risk of SLE. Number of X chromosomes was determined by single nucleotide typing and then confirmed by karyotype or fluorescent in situ hybridization in a large group of men with SLE. Presence of an sry gene was assessed by RT-PCR. We calculated 96% confidence intervals using the Adjusted Wald method, and used Bayes' theorem to estimate the prevalence of SLE among 47,XXY and 46,XX men. Among 316 men with SLE, 7 had 47,XXY and 1 had 46,XX. The rate of Klinefelter's syndrome (47,XXY) was statistically different from that found in control men and from the known prevalence in the population. The 46,XX man had an sry gene, which encodes the testes determining factor, on an X chromosome as a result of an abnormal crossover during meiosis. In the case of 46,XX, 1 of 316 was statistically different from the known population prevalence of 1 in 20,000 live male births. A previously reported 46,XX man with SLE had a different molecular mechanism in which there were no common gene copy number abnormalities with our patient. Thus, men with SLE are enriched for conditions with additional X chromosomes. Especially since 46,XX men are generally normal males, except for infertility, these data suggest the number of X chromosomes, not phenotypic sex, is responsible for the sex-bias of SLE.

Preimplantation genetic diagnosis in female and male carriers of reciprocal translocations: clinical outcome until delivery of 312 cycles

Carriers of reciprocal translocations (rcp) are known to be at risk for reproductive difficulties. Preimplantation genetic diagnosis (PGD) is one of the options these carriers have to try in order to fulfil their desire to have a child. In the present study, we retrospectively looked at the results of 11 years (1997-2007) of PGD for rcp in our center to improve the reproductive counseling of these carriers. During this period 312 cycles were performed for 69 male and 73 female carriers. The mean female age was 32.8 years, the mean male age 35.8 years. Most carriers were diagnosed with a translocation because of fertility problems or recurrent miscarriages, and most of them opted for PGD to avoid these problems. In 150 of the 312 cycles, embryo transfer (ET) was feasible and 40 women had a successful singleton or twin pregnancy. This gives a live birth delivery rate of 12.8% per started cycle and of 26.7% per cycle with ET. Owing to the large number of abnormal embryos, PGD cycles for rcp often lead to cancellation of ET, explaining the low success rate when expressed per cycle with oocyte pick-up. Once ET was feasible, the live birth delivery rate was similar to that of PGD in general at our center. PGD is therefore an established option for specific reciprocal translocation carriers.

Ethical and legal aspects of management for disorders of sex development

Intense controversy surrounds the management of disorders of sex development, particularly in relation to the validity of parental consent for genital surgery and the removal of gonadal tissue carried out during infancy or childhood. Past practices have been heavily criticised on ethical grounds by patient advocacy organisations, who have demanded a moratorium on these kinds of operations unless authorised by a court. Some doctors and hospital administrators have been influenced by the controversy and have referred cases to the Family Court of Australia, where a series of judgements have now established legal precedents that apply across Australia, restricting the circumstances in which parents can give consent for surgery. An alternative approach is to use a hospital-based Clinical Ethics Response Group and, if necessary, Clinical Ethics Committee, which has lay and legal representatives as well as health professionals, as a semi-independent committee of review. Finding a solution that protects the human rights and best interests of children is an ongoing challenge.