Clinical and molecular characterization of an almost complete ring chromosome 4 in two sisters, with recurrence due to gonadal mosaicism

Autosomal ring chromosomes are rare cytogenetic findings that arise from breakage and fusion of the chromosome ends. Rings are mitotically unstable, usually sporadic and associated with a 'ring syndrome', characterized by a variable phenotype: growth retardation, no significant dysmorphisms and normal to moderately disabled intelligence. We describe the clinical features and molecular characterization of two sisters with ring chromosome 4. Karyotype analysis was performed on both sisters and parents. Chromosome microarray was performed on both sisters to delineate the breakpoint imbalance. Both sisters had a large ring 4 chromosome in the majority of cells analyzed on karyotype. Microarray results were identical in the sisters, showing a 55.8 kb duplication on the terminal 4p arm and a 1.5 Mb deletion on the terminal 4q arm. No genes of interest were identified in these regions. Parental karyotypes on lymphocytes and fibroblasts were normal, with no finding of mosaicism for the ring 4 chromosome. Polymorphic marker analysis revealed the maternal origin of the ring. To our knowledge, this is the first reported instance of a ring 4 chromosome recurring in siblings after extensive parental testing, which suggests this was due to maternal gonadal mosaicism.

Failure of NIPT to detect constitutional chromoanasynthesis involving chromosome 21 in a case of fetal hydrops-A case report

We report a case of a de novo ring 21 complex chromosomal rearrangement in a fetus presenting with hydrops. Noninvasive prenatal testing (NIPT) failed to detect the imbalance. This case highlights the need to understand the various limitations and strengths of NIPT technology when counseling patients.

Prenatal Array Comparative Genomic Hybridization in Fetuses With Structural Cardiac Anomalies

OBJECTIVES

To examine the diagnostic performance of array comparative genomic hybridization (CGH) for fetal cardiac anomalies in two medium-sized Canadian prenatal genetics clinics.

METHODS

We prospectively recruited 22 pregnant women with fetal structural cardiac anomalies, normal rapid aneuploidy detection, and FISH for 22q11.2 testing for array CGH analysis.

RESULTS

One case had an 8p deletion that was also visible on karyotype and included the GATA4 gene, which has been associated with congenital heart disease. Two cases had inherited pathogenic copy number variants (CNVs) of variable expressivity and penetrance: one was a duplication of 16p11.2 and the other a deletion of 15q11.2. One case had the incidental finding of being a carrier of a recessive disease unrelated to the cardiac anomaly.

CONCLUSIONS

Of these prospectively recruited cases of fetal cardiac anomalies, 14% had a pathogenic result on array CGH. Pathogenic CNVs of variable penetrance and expressivity were a significant proportion of the positive results identified. These CNVs are generally associated with neurodevelopmental issues and may or may not have been associated with the fetus' underlying congenital heart disease. Array CGH increases the diagnostic yield in this group of patients; however, certain CNVs remain a challenge for counselling in the prenatal setting.

A 2q24.3q31.1 microdeletion found in a patient with Filippi-like syndrome phenotype: a case report

Filippi syndrome is characterized by developmental delay, growth failure, cryptorchidism, bilateral hand and foot syndactyly, and facial dysmorphism. The 2q24q31 contiguous deletion syndrome has similarly been associated with hand and foot anomalies, growth retardation, microcephaly, characteristic facies with a broad prominent nasal root and thin alae nasi, and intellectual disability. We present a patient with this deletion who has a Filippi-like phenotype, which may be the first causative cytogenetic result in this syndrome. This suggests the importance of array comparative genomic hybridization in evaluation of patients with Filippi syndrome, and suggests that the inheritance may not always be autosomal recessive.

Disruption of the ASTN2/TRIM32 locus at 9q33.1 is a risk factor in males for autism spectrum disorders, ADHD and other neurodevelopmental phenotypes

Rare copy number variants (CNVs) disrupting ASTN2 or both ASTN2 and TRIM32 have been reported at 9q33.1 by genome-wide studies in a few individuals with neurodevelopmental disorders (NDDs). The vertebrate-specific astrotactins, ASTN2 and its paralog ASTN1, have key roles in glial-guided neuronal migration during brain development. To determine the prevalence of astrotactin mutations and delineate their associated phenotypic spectrum, we screened ASTN2/TRIM32 and ASTN1 (1q25.2) for exonic CNVs in clinical microarray data from 89 985 individuals across 10 sites, including 64 114 NDD subjects. In this clinical dataset, we identified 46 deletions and 12 duplications affecting ASTN2. Deletions of ASTN1 were much rarer. Deletions near the 3' terminus of ASTN2, which would disrupt all transcript isoforms (a subset of these deletions also included TRIM32), were significantly enriched in the NDD subjects (P = 0.002) compared with 44 085 population-based controls. Frequent phenotypes observed in individuals with such deletions include autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), speech delay, anxiety and obsessive compulsive disorder (OCD). The 3'-terminal ASTN2 deletions were significantly enriched compared with controls in males with NDDs, but not in females. Upon quantifying ASTN2 human brain RNA, we observed shorter isoforms expressed from an alternative transcription start site of recent evolutionary origin near the 3' end. Spatiotemporal expression profiling in the human brain revealed consistently high ASTN1 expression while ASTN2 expression peaked in the early embryonic neocortex and postnatal cerebellar cortex. Our findings shed new light on the role of the astrotactins in psychopathology and their interplay in human neurodevelopment.

Canadian College of Medical Geneticists guidelines for the indications, analysis, and reporting of cancer specimens

The Canadian College of Medical Geneticists (ccmg) is a national organization of medical and laboratory geneticists. The mission of the ccmg is to establish and maintain high-quality professional and ethical standards for medical genetics services in Canada and to help to ensure that service of the highest quality is delivered to the Canadian public.Cancer cytogenetics is one of the sections of practice of the ccmg. The ccmg Cytogenetic Committee has, therefore, put forward guidelines to provide oncologists and ccmg cytogeneticists with a comprehensive review of the cytogenetic diagnostic tests that are recommended as a minimum standard of care for tumours of hematopoietic and lymphoid tissues and for tumours of soft tissue and bone. The guidelines were approved by the ccmg board of directors in June 2010.

Application of microarray-based comparative genomic hybridization in prenatal and postnatal settings: three case reports

Microarray-based comparative genomic hybridization (array CGH) is a newly emerged molecular cytogenetic technique for rapid evaluation of the entire genome with sub-megabase resolution. It allows for the comprehensive investigation of thousands and millions of genomic loci at once and therefore enables the efficient detection of DNA copy number variations (a.k.a, cryptic genomic imbalances). The development and the clinical application of array CGH have revolutionized the diagnostic process in patients and has provided a clue to many unidentified or unexplained diseases which are suspected to have a genetic cause. In this paper, we present three clinical cases in both prenatal and postnatal settings. Among all, array CGH played a major discovery role to reveal the cryptic and/or complex nature of chromosome arrangements. By identifying the genetic causes responsible for the clinical observation in patients, array CGH has provided accurate diagnosis and appropriate clinical management in a timely and efficient manner.

CCMG guidelines: prenatal and postnatal diagnostic testing for uniparental disomy

The aim of this statement is to provide clinicians, cytogeneticists and molecular geneticists of the Canadian College of Medical Geneticists (CCMG) a comprehensive review of the role of UPD in constitutional genetic diagnosis and to provide a guideline as to when investigation for UPD is recommended. Members of the CCMG Cytogenetics, Molecular Genetics, Clinical Practice, and Prenatal Diagnosis committees reviewed the relevant literature on uniparental disomy (UPD) in constitutional genetic diagnosis (May 2010). Guidelines were developed for UPD testing in Canada. The guidelines were circulated for comment to the CCMG members at large and following appropriate modification, approved by the CCMG Board of Directors (July 2010).

Goldenhar phenotype in a child with distal 22q11.2 deletion and intracranial atypical teratoid rhabdoid tumor

Chromosome-specific low copy repeats (LCRs) are implicated in several clinically significant microdeletion and microduplication syndromes. The well-recognized phenotype of DiGeorge/velocardiofacial syndrome (DG/VCF) results from deletions of the long arm of chromosome 22 (22q11.2) mediated by the proximal LCRs in this region. More recent evidence suggests that the distal LCRs within 22q11.2 are also implicated in microdeletions and microduplications with less characterized phenotypes. Here we report on an infant diagnosed with Goldenhar syndrome (GS) phenotype who developed an atypical teratoid rhabdoid tumor (AT/RT) of the brain due to a distal deletion of the chromosome 22q11.2 region encompassing the INI1/SMARCB1 tumor suppressor. We also discuss the phenotype of patients with germline deletions of this region and the possible implication of the 22q11.2 region in the GS.

Unusual segregation products in sperm from a pericentric inversion 17 heterozygote

Chromosome segregation and interchromosomal effect were studied in spermatozoa from a carrier of a pericentric chromosome 17 inversion, 46,XY,inv(17)(p13.1q25.3). Sperm chromosome segregation, lymphocytes of the inversion carrier, and cells from his offspring were analysed by multicolour fluorescence in situ hybridization. The frequency of balanced sperm was 73%. An unusual segregation of recombinants was observed, viz. deletion of the p arm (14.6%) or duplication of the p arm with the presence of one q arm (8.4%), instead of the expected recombinants, viz. duplication of one arm with deletion of the other and vice versa. These unusual recombinants were explained by the position of the 17q breakpoint, which was between the q arm telomere-associated repeats and the unique q subtelomere region. The offspring of the donor were found to have a 17p deletion including the Miller-Dieker critical region, similar to the most frequent recombinant sperm class. The disomy frequency was significantly increased for chromosome 17 compared with other autosomes, suggesting that pairing and recombination of the inversion may predispose to non-disjunction. There was no significant difference between the frequencies of aneuploidy for chromosomes 13, 21, X and Y in the chromosome inversion heterozygote compared with controls. Thus, this unique pericentric inversion of chromosome 17 produces unusual recombinant products; no evidence was apparent of an interchromosomal effect in any of the tested chromosomes.

Microduplication and triplication of 22q11.2: a highly variable syndrome

22q11.2 microduplications of a 3-Mb region surrounded by low-copy repeats should be, theoretically, as frequent as the deletions of this region; however, few microduplications have been reported. We show that the phenotype of these patients with microduplications is extremely diverse, ranging from normal to behavioral abnormalities to multiple defects, only some of which are reminiscent of the 22q11.2 deletion syndrome. This diversity will make ascertainment difficult and will necessitate a rapid-screening method. We demonstrate the utility of four different screening methods. Although all the screening techniques give unique information, the efficiency of real-time polymerase chain reaction allowed the discovery of two 22q11.2 microduplications in a series of 275 females who tested negative for fragile X syndrome, thus widening the phenotypic diversity. Ascertainment of the fragile X-negative cohort was twice that of the cohort screened for the 22q11.2 deletion. We also report the first patient with a 22q11.2 triplication and show that this patient's mother carries a 22q11.2 microduplication. We strongly recommend that other family members of patients with 22q11.2 microduplications also be tested, since we found several phenotypically normal parents who were carriers of the chromosomal abnormality.

Duplication of the 22q11.2 region associated with congenital cardiac disease

The DiGeorge, or velocardiofacial, syndrome has been aetiologically linked to heterozygous deletion of the q11.2 region of chromosome 22. It is the most common of the microdeletion syndromes, and is associated with malformations involving the ventricular outflow tracts. Duplication of the 22q11.2 region has also been reported, adding to a growing list of syndromes involving genomic deletion or duplication that cause disease by decreasing or increasing the gene dosage. We report two cases of congenital cardiac disease associated with microduplications of 22q11.2, and discuss the evidence to date for the potential clinical significance of this genetic defect.

Analysis of chromosome segregation in sperm from a chromosome 2 inversion heterozygote and assessment of an interchromosomal effect

Using fluorescence in situ hybridization (FISH) analysis, the chromosome segregation of a pericentric inversion of chromosome 2 was studied in spermatozoa. An interchromosomal effect (ICE) was also determined for chromosomes 13, 21, X, and Y. This chromosome inversion included more than 2/3 of the total length of the chromosome and the breaks points were in G-light bands. The frequency of non-recombinant sperm was 55.9%, and that of recombinant sperm was 34.5% (with a 1:1 ratio of duplication of the p arm and deletion of the q arm and vice versa). There was a significantly increased frequency of disomy for chromosome 2 (0.6%) compared to the other autosomes, suggesting that pairing and recombination of the inversion may predispose to nondisjunction. There was no significant difference between the frequencies of aneuploidy for chromosomes 13, 21, X, and Y for the chromosome inversion heterozygote compared to control donors. Thus we did not find evidence for an ICE.

A comparison of the frequency of sperm chromosome abnormalities in men with mild, moderate, and severe oligozoospermia

Infertile men undergoing intracytoplasmic sperm injection have an increased frequency of chromosome abnormalities in their sperm. Men with low sperm concentration (oligozoospermia) have an increased risk of sperm chromosome abnormalities. This study was initiated to determine whether men with severe oligozoospermia (<10(6) sperm/ml) have a higher frequency of chromosome abnormalities in their sperm compared with men with moderate (1-9 x 10(6) sperm/ml) or mild (10-19 x 10(6) sperm/ml) oligozoospermia. Multicolor fluorescence in situ hybridization analysis was performed using DNA probes specific for chromosomes 13, 21, X, and Y (with chromosome 1 as an autosomal control for the sex chromosomes). Aneuploidy and disomy frequencies were assessed from a total of 603,011 sperm from 30 men: 10 in each of the categories. The mean frequencies of disomy for the patients with mild, moderate, and severe oligozoospermia were 0.17%, 0.24%, and 0.30%, respectively, for chromosome 13 and 0.22%, 0.44%, and 0.58%, respectively, for chromosome 21. For the sex chromosomes, the mean frequencies of disomy for mild, moderate, and severe oligozoospermia were 0.25%, 1.04%, and 0.68%, respectively, for XY, 0.047%, 0.08%, and 0.10%, respectively, for XX, and 0.04%, 0.06%, and 0.09%, respectively, for YY. The frequencies for diploidy also increased from 0.4% for mild to 1.20% for moderate to 1.24% for severe oligozoospermia. There was a significant inverse correlation between the frequency of sperm chromosome abnormalities and the sperm concentration for XY, XX, and YY disomy and diploidy. These results demonstrate that men with severe oligozoospermia have an elevated risk for chromosome abnormalities in their sperm, particularly sex chromosome abnormalities.

Analysis of aneuploidy in spermatozoa from testicular biopsies from men with nonobstructive azoospermia

Testicular sperm biopsy combined with intracytoplasmic sperm injection (ICSI) allows men with azoospermia the possibility of fathering a child. However, little information exists on the risk of chromosome abnormalities in their sperm. Multicolor fluorescence in situ hybridization (FISH) analysis was used to determine the frequency of sperm diploidy and disomy for the sex chromosomes in six men with normal karyotypes and non-obstructive azoospermia. A new method using microwave decondensation and codenaturation of sperm nuclei yielded a much larger number of sperm nuclei for FISH analysis than our previous study of men with azoospermia. A total of 59916 sperm were analyzed; more than 9000 sperm were scored for each man. The men with nonobstructive azoospermia had an increased frequency of sperm chromosomal disomy for YY, XY, total sex chromosomal disomy, and diploidy compared with 18 normal controls, but only YY disomy reached statistical significance. One infertile man had a frequency of 3.8% XY disomy and 4.3% diploidy, which was 13-fold and 7-fold higher than control donors, respectively. Our results suggest that some men with nonobstructive azoospermia have a significantly increased frequency of sex chromosomal abnormalities than normal men, but that the overall frequency of abnormalities is similar to that found in infertile men with abnormal semen parameters.

Chromosome abnormalities in sperm from infertile men with asthenoteratozoospermia

Research over the past few years has clearly demonstrated that infertile men have an increased frequency of chromosome abnormalities in their sperm. These studies have been further corroborated by an increased frequency of chromosome abnormalities in newborns and fetuses from pregnancies established by intracytoplasmic sperm injection. Most studies have considered men with any type of infertility. However, it is possible that some types of infertility have an increased risk of sperm chromosome abnormalities, whereas others do not. We studied 10 men with a specific type of infertility, asthenozoospermia (poor motility), by multicolor fluorescence in situ hybridization analysis to determine whether they had an increased frequency of disomy for chromosomes 13, 21, XX, YY, and XY, as well as diploidy. The patients ranged in age from 28 to 42 yr (mean 34.1 yr); they were compared with 18 normal control donors whose ages ranged from 23 to 58 yr (mean 35.6 yr). A total of 201 416 sperm were analyzed in the men with asthenozoospermia, with a minimum of 10 000 sperm analyzed per chromosome probe per donor. There was a significant increase in the frequency of disomy in men with asthenozoospermia compared with controls for chromosomes 13 and XX. Thus, this study indicates that infertile men with poorly motile sperm but normal concentration have a significantly increased frequency of sperm chromosome abnormalities.

Aneuploid spermatozoa in infertile men: teratozoospermia

We and others have demonstrated that infertile men who are candidates for intracytoplasmic sperm injection (ICSI) have an increased frequency of chromosomal abnormalities in their sperm. Reports based on prenatal diagnosis of ICSI pregnancies have confirmed the increased frequency of chromosomal abnormalities in offspring. Most studies to date have lumped various types of infertility together. However, it is quite likely that some subsets of infertility have an increased risk of sperm chromosomal abnormalities whereas others do not. We have studied nine men with severe teratozoospermia (WHO, 1992 criteria, 0-13% morphologically normal forms) by multicolour fluorescence in situ hybridisation (FISH) analysis to determine if they have an increased frequency of disomy for chromosomes 13, 21, XX, YY, and XY, as well as diploidy. All of the men also had aesthenozoospermia (< 50% forward progression) but none of the men had oligozoospermia (<20 x 10(6) sperm/ml). The patients ranged in age from 20 to 49 years (mean 33.2 years) in comparison to 18 normal control donors who were 23 to 58 years (mean 35.6 years). The control donors had normal semen parameters and no history of infertility. A total of 180,566 sperm were scored in the teratozoospermic men with a minimum of 10,000 sperm analyzed/donor/chromosome probe. There was a significant increase in the frequency of disomy in teratozoospermic men compared to controls for chromosomes 13 (.23 vs.13%), XX (.13 vs.05%), and XY (.50 vs.30%) (P <.0001, 2-tailed Z statistic). This study indicates that men with teratozoospermia and aesthenozoospermia but with normal concentrations of sperm have a significantly increased frequency of sperm chromosomal abnormalities.

Association between congenital foot anomalies and gestational age at amniocentesis

OBJECTIVES

Our objectives were to confirm the reported association between early amniocentesis and congenital foot anomalies as well as to report, for the first time, on the outcome of amniocenteses performed during the 13th and 14th weeks of gestation.

METHODS

We conducted a triple cohort retrospective study of 4457 amniocenteses. Cohort definitions: early amniocentesis (EA), 11 weeks and 0/7 days to 12 weeks to 6/7 days; early midtrimester amniocentesis (EMA), 13 weeks and 0/7 days to 14 weeks and 6/7 days; and midtrimester amniocentesis (MA), 15 weeks and 0/7 days to 19 weeks and 6/7 days. Outcome measures were obtained by searching the Alberta Congenital Anomalies Surveillance System (ACASS) database for children born with foot anomalies represented by International Classification of Diseases version 9 (ICD-9) codes 754.5, 754.6 and 754.7.

RESULTS

Incidences of congenital foot anomalies were: EA 11/980 (1.1%), EMA 11/2515 (0.4%), and MA 1/962 (0.1%). There is a significant difference between the EA and EMA cohorts (p=0.019) and between the EA and MA cohorts (p=0.003); however, these data suggest there is no difference between EMA and MA cohorts (p=0.11).

CONCLUSIONS

Our incidence of congenital foot anomalies of 1.1% for women who underwent EA is similar to previously reported data, which further validates this association; however, our data also suggest that the foot anomaly risk may be limited to amniocenteses performed before the 13th week of gestation.

Chromosome analysis of spermatozoa extracted from testes of men with non-obstructive azoospermia

Infertile men with azoospermia now have the possibility of fathering children by testicular sperm extraction combined with intracytoplasmic sperm injection. However, there are concerns about the risk of chromosomal abnormalities in their spermatozoa. We have studied aneuploidy frequencies for chromosomes 13, 21, X and Y by multicolour fluorescence in-situ hybridization (FISH) in testicular spermatozoa extracted from three men with non-obstructive azoospermia. The men were 34-37 years of age and had normal follicle-stimulating hormone (FSH) concentrations and normal 46,XY somatic karyotypes. A total of 3324 spermatozoa was analysed. The infertile patients had an elevated frequency of disomy for chromosomes 13, 21, XY disomy compared to controls but none of these reached statistical significance. Also there was no significant difference in the sex ratio or the frequency of diploidy in azoospermic patients compared to normal control donors. This first report on chromosomal aneuploidy in spermatozoa extracted from testes of patients with non-obstructive azoospermia suggests that some azoospermic men do not have a substantially increased risk of chromosomally abnormal spermatozoa.

Trisomy 16pter to 16q12.1 and monosomy 22pter to 22q11.2 resulting from adjacent-2 segregation of a maternal complex chromosome rearrangement

We report on a 16-week-old male fetus with partial trisomy 16 and partial monosomy 22 resulting from 3:3 adjacent-2 segregation of a maternal balanced complex chromosome translocation involving chromosomes 5, 16, and 22. The karyotype of the 29-year-old phenotypically normal mother was 46,XX,t(5;16;22)(q31.3;q12.1;q11.2). The karyotype of the fetus was 46,XY,der (5)t(5;16;22)(q31.3;q12.1;q11.2),+der(16) t(5;16;22)mat,-22. The fetus had multiple congenital anomalies, including bilateral cleft lip and palate.