A paternally derived inverted duplication of distal 14q with a terminal 14q deletion

Inference of putative cell-type-specific imprinted regulatory elements and genes during human neuronal differentiation

Genomic imprinting results in gene expression bias caused by parental chromosome of origin and occurs in genes with important roles during human brain development. However, the cell-type and temporal specificity of imprinting during human neurogenesis is generally unknown. By detecting within-donor allelic biases in chromatin accessibility and gene expression that are unrelated to cross-donor genotype, we inferred imprinting in both primary human neural progenitor cells and their differentiated neuronal progeny from up to 85 donors. We identified 43/20 putatively imprinted regulatory elements (IREs) in neurons/progenitors, and 133/79 putatively imprinted genes in neurons/progenitors. Although 10 IREs and 42 genes were shared between neurons and progenitors, most putative imprinting was only detected within specific cell types. In addition to well-known imprinted genes and their promoters, we inferred novel putative IREs and imprinted genes. Consistent with both DNA methylation-based and H3K27me3-based regulation of imprinted expression, some putative IREs also overlapped with differentially methylated or histone-marked regions. Finally, we identified a progenitor-specific putatively imprinted gene overlapping with copy number variation that is associated with uniparental disomy-like phenotypes. Our results can therefore be useful in interpreting the function of variants identified in future parent-of-origin association studies.

The embryo battle against adverse genomes: Are de novo terminal deletions the rescue of unfavorable zygotic imbalances?

De novo distal deletions are structural variants considered to be already present in the zygote. However, investigations especially in the prenatal setting have documented that they are often in mosaic with cell lines in which the same deleted chromosome shows different types of aberrations such as: 1) neutral copy variants with loss of heterozygosity that replace the deleted region with equivalent portions of the homologous chromosome and create distal uniparental disomy (UPD); 2) derivative chromosomes where the deleted one ends with the distal region of another chromosome or has the shape of a ring; 3) U-type mirror dicentric or inv-dup del rearrangements. Unstable dicentrics had already been entailed as causative of terminal deletions even when no trace of the reciprocal inv-dup del had been detected. To clarify the mechanism of origin of distal deletions, we examined PubMed using as keywords: complex/mosaic chromosomal deletions, distal UPD, U-type dicentrics, inv-dup del chromosomes, excluding the recurrent inv-dup del(8p)s which are known to originate by NAHR at the maternal meiosis. The literature has shown that U-type dicentrics leading to nearly complete trisomy and therefore incompatible with zygotic survival underlie many types of de novo unbalanced rearrangements, including terminal deletions. In the early embryo, the position of the postzygotic breaks of the dicentric, the different ways of acquiring telomeres by the broken portions and the selection of the most favorable cell lines in the different tissues determine the prevalence of one or the other rearrangement. Multiple lines with simple terminal deletions, inv-dup dels, unbalanced translocations and segmental UPDs can coexist in various mosaic combinations although it is rare to identify them all in the blood. Regarding the origin of the dicentric, among the 30 cases of non-recurrent inv-dup del with sufficient genotyping information, paternal origin was markedly prevalent with consistently identical polymorphisms within the duplication region, regardless of parental origin. The non-random parental origin made any postzygotic origin unlikely and suggested the occurrence of these dicentrics mainly in spermatogenesis. This study strengthens the evidence that non-recurrent de novo structural rearrangements are often secondary to the rescue of a zygotic genome incompatible with embryo survival.

Goyal-Naqvi Syndrome (Concurrent Trisomy 10p and Terminal 14q Deletion): A Review of the Literature

Goyal-Naqvi syndrome (GNS) is a newly documented clinical entity that comprises trisomy 10p and terminal 14q deletion, though trisomy 10p and terminal 14q deletion have been discovered as distinct conditions in 1974 and 1997, respectively. Nevertheless, to date, the total number of reported cases of each of these conditions is estimated to be in double digits. Both manifest as a constellation of features like craniofacial dysmorphism, hypotonia, intellectual impairment and global developmental delay. Characteristic facies include protruded forehead, hypertelorism, epicanthic folds, down slanting palpebral fissures, flat nasal bridge, long philtrum, thin upper lip, carp-shaped mouth, retro-micrognathia and low set ears. Besides, trisomy 10p is strikingly associated with clinodactyly and camptodactyly which aids in clinical diagnosis, apart from other musculoskeletal deformities like hip dysplasia and pes planus. Intersex conditions have been found to commonly co-exist. As other systems also display involvement frequently, trisomy 10p is a discernible multiple congenital anomalies/mental retardation (MCA/MR) syndrome. On the other hand, with terminal 14q deletion, increased risk of certain types of cancer was predicted as specific tumor suppressor genes are lost in the deletion and thus, screening was recommended. Genetic workup using techniques like fluorescence in situ hybridization (FISH), spectral karyotyping (SKY) and chromosomal microarray-based comparative genomic hybridization (CGH) was found to be helpful in diagnosis of trisomy 10p and 14q deletion. Prenatal diagnosis of these conditions has been well documented too. Intrauterine growth retardation has been observed to be related to trisomy 10p. There is a paucity of literature on the management of children diagnosed with trisomy 10p or with terminal 14q deletion. Although management of a child diagnosed with concomitant occurrence of trisomy 10p and terminal 14q deletion by a multidisciplinary approach emphasizing physiotherapeutic intervention has shown remarkable improvement in motor skills, the care of children diagnosed with these genetic aberrations needs further investigation. Documentation of more such cases will help to expand phenotypic spectrum for early identification and to delineate natural history for a life span approach. Early identification and intervention facilitate tapping of the maximum neuroplastic potential for better neurodevelopmental outcomes. We present a review of current literature on this novel syndrome to identify gaps in knowledge to build future research.

A Recurrent De Novo Terminal Duplication of 14q32 in Korean Siblings Associated with Developmental Delay and Intellectual Disability, Growth Retardation, Facial Dysmorphism, and Cerebral Infarction: A Case Report and Literature Review

The terminal 14q32 duplication has been reported often in association with other cytogenetic abnormalities, and individuals with this specific duplication showed varying degrees of developmental delay/intellectual disability (DD/ID) and growth retardation (GR), and distinct facial dysmorphisms. Herein, based on the limited cases of terminal duplication of 14q32 known to date, we present new affected siblings presenting with DD/ID, GR, and facial dysmorphism, as well as cerebral infarction caused by recurrent de novo der(14)t(14;14)(p11.2;q32.1) leading to terminal duplication of 14q32. We used coverage analysis generated via duo exome sequencing, performed chromosomal microarray (CMA) as a confirmatory test, and compared our findings with those reported previously. Coverage analysis generated via duo exome sequencing revealed a 17.2 Mb heterozygous duplication at chromosome 14q32.11-q32.33 with a Z ratio ranging between 0.5 and 1 in the proband and her elder brother. As a complementary method, CMA established a terminal duplication described as the arr[hg19]14q32.11q32.33(90,043,558_107,258,824)x3 in the proband and her elder brother; however, the parents and other siblings showed normal karyotyping and no abnormal gain or loss of CMA results. Five candidate genes, BCL11B, CCNK, YY1, DYNC1H1, and PACS2, were associated with the clinical phenotypes in our cases. Although the parents had normal chromosomes, two affected cases carrying terminal duplication of 14q32 can be explained by gonadal mosaicism. Further studies are needed to establish the association between cerebrovascular events and terminal duplication of chromosome 14q32, including investigation into the cytogenetics of patients with precise clinical descriptions.

Inv dup del(10p): Prenatal diagnosis and molecular cytogenetic characterization

OBJECTIVE

We present molecular cytogenetic characterization of prenatally detected inverted duplication and deletion of 10p [inv dup del(10p)].

CASE REPORT

A 39-year-old, primigravid woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age. Amniocentesis revealed a derivative chromosome 10 with additional material at the end of the short arm of one chromosome 10. Simultaneous array comparative genomic hybridization (aCGH) analysis revealed the result of arr 10p15.3 (136,361-451,013) × 1, 10p15.3p12.1 (536,704-25,396,900) × 3 [GRCh37 (hg19)] with a 0.31-Mb deletion of 10p15.3 encompassing ZMYND11 and DIP2C, and a 24.86-Mb duplication of 10p15.3p12.1. The pregnancy was subsequently terminated, and a female fetus was delivered with facial dysmorphism. Postnatal aCGH analysis showed that the umbilical cord had the same result as that of amniotic fluid, whereas the placenta had only the deletion of 10p15.3. Fluorescence in situ hybridization (FISH) analysis of the cord blood confirmed inverted duplication and deletion of 10p. The cord blood had a karyotype of 46,XX,der(10) del(10) (p15.3)dup(10) (p15.3p12.1)dn. Polymorphic DNA marker analysis confirmed a maternal origin of the chromosome 10 aberration.

CONCLUSION

Prenatal diagnosis of inv dup del(10p) with haploinsufficiency of ZMYND11 should include a genetic counseling of mental retardation and chromosome 10p15.3 microdeletion syndrome. aCGH, FISH and polymorphic DNA marker analysis are useful for perinatal investigation of inv dup del(10p).

Prenatal diagnosis and molecular cytogenetic characterization of a de novo unbalanced reciprocal translocation of der(9)t(9;14)(p24.2;q32.11) associated with 9p terminal deletion and 14q distal duplication

OBJECTIVE

We present molecular cytogenetic characterization of a prenatally detected derivative chromosome 9 [der(9)] of unknown origin.

CASE REPORT

A 35-year-old woman underwent amniocentesis at 18 weeks of gestation because of advanced maternal age, which revealed a der(9) chromosome of unknown origin. The parental karyotypes were normal. Array comparative genomic hybridization (aCGH) analysis revealed a 2.593 Mb deletion of 9p24.3-p24.2 encompassing DOCK8, KANK1, DMRT1, and VLDLR and a 16.65 Mb duplication of 14q32.11-q32.33 encompassing DLK1, RTL1, MEG3, RTL1as, and MEG8. Quantitative fluorescent polymerase chain reaction (QF-PCR) analysis using D9S937 (9p24.2) and D14S605 (14q32.2) showed a paternal origin of 9p24.2 deletion and a paternal origin of 14q32.2 duplication consistent with a paternal origin of the de novo aberrant chromosome of der(9)t(9p;14q). The fetal karyotype was 46,XX,der(9)t(9;14) (p24.2;q32.11). Metaphase fluorescence in situ hybridization (FISH) analysis using RP11-57K23 (14q32.33), RP11-31F19 (9p24.3), RP11-30O14 (9p21.1), and RP11-1105I14 (14q11.2) confirmed an unbalanced reciprocal translocation of der(9)t(9p;14q). We discuss 9p deletion syndrome and 14q duplication syndrome in this case.

CONCLUSION

Molecular cytogenetic techniques such as aCGH, FISH, and QF-PCR are useful in the determination of the origin and nature of a prenatally detected de novo derivative chromosome of unknown origin.

14q32.3-qter trisomic segment: a case report and literature review

BACKGROUND

Segmental duplication of the long arm of chromosome 14 (14q) has commonly been reported to affect the proximal segment of 14q, while distal duplication is a rare condition and often associated with segmental monosomy of other chromosomes.

CASE PRESENTATION

We report the clinical and genetic characterization of a 4-year-old male patient with 14q32.3-qter trisomy resulting from an adjacent segregation of a paternal reciprocal translocation (14;21)(q32.1;p12). The child shows minor facial anomalies, severe developmental delay, growth retardation, and a history of congenital hypothyroidism and neonatal transitory hyperglycemic crises.

CONCLUSIONS

To the best of our knowledge, only 15 other cases of segmental 14q trisomy were documented. We compared molecularly defined cases to identify a minimal common duplicated region and to find genes with a hypothetical role in the phenotype. The presented case supports the previous suggestion of a pure "distal 14q partial duplication" and underlines the clinical variability.

Clinical and genomic evaluation of 201 patients with Phelan-McDermid syndrome

This study is the first to describe age-related changes in a large cohort of patients with Phelan-McDermid syndrome (PMS), also known as 22q13 deletion syndrome. Over a follow-up period of up to 12 years, physical examinations and structured interviews were conducted for 201 individuals diagnosed with PMS, 120 patients had a focused, high-resolution 22q12q13 array CGH, and 92 patients' deletions were assessed for parent-of-origin. 22q13 genomic anomalies include terminal deletions of 22q13 (89 %), terminal deletions and interstitial duplications (9 %), and interstitial deletions (2 %). Considering different age groups, in older patients, behavioral problems tended to subside, developmental abilities improved, and some features such as large or fleshy hands, full or puffy eyelids, hypotonia, lax ligaments, and hyperextensible joints were less frequent. However, the proportion reporting an autism spectrum disorder, seizures, and cellulitis, or presenting with lymphedema or abnormal reflexes increased with age. Some neurologic and dysmorphic features such as speech and developmental delay and macrocephaly correlated with deletion size. Deletion sizes in more recently diagnosed patients tend to be smaller than those diagnosed a decade earlier. Seventy-three percent of de novo deletions were of paternal origin. Seizures were reported three times more often among patients with a de novo deletion of the maternal rather than paternal chromosome 22. This analysis improves the understanding of the clinical presentation and natural history of PMS and can serve as a reference for the prevalence of clinical features in the syndrome.

Large inverted duplications in the human genome form via a fold-back mechanism

Inverted duplications are a common type of copy number variation (CNV) in germline and somatic genomes. Large duplications that include many genes can lead to both neurodevelopmental phenotypes in children and gene amplifications in tumors. There are several models for inverted duplication formation, most of which include a dicentric chromosome intermediate followed by breakage-fusion-bridge (BFB) cycles, but the mechanisms that give rise to the inverted dicentric chromosome in most inverted duplications remain unknown. Here we have combined high-resolution array CGH, custom sequence capture, next-generation sequencing, and long-range PCR to analyze the breakpoints of 50 nonrecurrent inverted duplications in patients with intellectual disability, autism, and congenital anomalies. For half of the rearrangements in our study, we sequenced at least one breakpoint junction. Sequence analysis of breakpoint junctions reveals a normal-copy disomic spacer between inverted and non-inverted copies of the duplication. Further, short inverted sequences are present at the boundary of the disomic spacer and the inverted duplication. These data support a mechanism of inverted duplication formation whereby a chromosome with a double-strand break intrastrand pairs with itself to form a “fold-back” intermediate that, after DNA replication, produces a dicentric inverted chromosome with a disomic spacer corresponding to the site of the fold-back loop. This process can lead to inverted duplications adjacent to terminal deletions, inverted duplications juxtaposed to translocations, and inverted duplication ring chromosomes.

Chromosomes with large inverted duplications and terminal deletions cause neurodevelopmental disorders in children. These chromosome rearrangements typically involve hundreds of genes, leading to significant changes in gene dosage. Though inverted duplications adjacent to terminal deletions are a relatively common type of chromosomal imbalance, the DNA repair mechanism responsible for their formation is not known. In this study, we analyze the genomic organization of the largest collection of human inverted duplications. We find a common inverted duplication structure, consistent with a model that requires DNA to fold back and form a dicentric chromosome intermediate. These data provide insight into the formation of nonrecurrent inverted duplications in the human genome.

Infantile hypertrophic pyloric stenosis--genetics and syndromes

Infantile hypertrophic pyloric stenosis (IHPS) is a common condition in neonates that is characterized by an acquired narrowing of the pylorus. The aetiology of isolated IHPS is still largely unknown. Classic genetic studies have demonstrated an increased risk in families of affected infants. Several genetic studies in groups of individuals with isolated IHPS have identified chromosomal regions linked to the condition; however, these associations could usually not be confirmed in subsequent cohorts, suggesting considerable genetic heterogeneity. IHPS is associated with many clinical syndromes that have known causative mutations. Patients with syndromes associated with IHPS can be considered as having an extreme phenotype of IHPS and studying these patients will be instrumental in finding causes of isolated IHPS. Possible pathways in syndromic IHPS include: (neuro)muscular disorders; connective tissue disorders; metabolic disorders; intracellular signalling pathway disturbances; intercellular communication disturbances; ciliopathies; DNA-repair disturbances; transcription regulation disorders; MAPK-pathway disturbances; lymphatic abnormalities; and environmental factors. Future research should focus on linkage analysis and next-generation molecular techniques in well-defined families with multiple affected members. Studies will have an increased chance of success if detailed phenotyping is applied and if knowledge about the various possible causative pathways is used in evaluating results.

Inv dup del(9p): prenatal diagnosis and molecular cytogenetic characterization by fluorescence in situ hybridization and array comparative genomic hybridization

OBJECTIVE

To present molecular cytogenetic characterization of prenatally detected inverted duplication and deletion of 9p, or inv dup del(9p).

MATERIALS, METHODS, AND RESULTS

A 35-year-old primigravid woman underwent amniocentesis at 16 weeks of gestation because of advanced maternal age. Amniocentesis revealed a derivative chromosome 9, or der(9) with additional material at the end of the short arm of one chromosome 9. Parental karyotypes were normal. Level II ultrasound showed ventriculomegaly and normal male external genitalia. Repeated amniocentesis was performed at 20 weeks of gestation. Array comparative genomic hybridization revealed a 0.70-Mb deletion at 9p24.3 and an 18.36-Mb duplication from 9p24.3 to 9p22.1. The distal 9p deletion encompassed the genes of DOCK8, ANKRD15, FOXD4, DMRT1, and DMRT3. Fluorescence in situ hybridization analysis using bacterial artificial chromosome clone probes specific for 9p confirmed that the der(9) was derived from the inv dup del(9p). The karyotype of the fetus was 46,XY,inv dup del(9)(:p22.1-->p24.3::p24.3-->qter)dn or 46,XY,der(9) del(9)(p24.3) inv dup(9)(p22.1p24.3)dn. Polymorphic DNA marker analysis determined a maternal origin of the inv dup del(9p). A 512-g male fetus was subsequently terminated at 22 weeks of gestation with facial dysmorphism. The fetus had normal male external genitalia without sex reversal.

CONCLUSION

Fluorescence in situ hybridization and array comparative genomic hybridization are useful to determine the nature of a prenatally detected aberrant chromosome derived from the inv dup del. Male fetuses with inv dup del(9p) and haploinsufficiency of DMRT1 and DMRT3 may present normal male external genitalia without sex reversal.

Rearrangement of chromosome 14q with associated white matter disease

We report the case of a 29-month-old boy with spasticity and periventricular white matter changes on magnetic resonance imaging in whom a complex rearrangement consisting of a de novo duplication of 14q32.31q32.33 and deletion of 14q32.33 was identified by array-based comparative genomic hybridization. Our case replicates some of the previous features associated with chromosome 14q duplication and deletion while expanding its clinical spectrum with pyramidal tract dysfunction signs and neuroimaging features. Genomic lesions should be considered in cases of leukodystrophies, and genome-wide studies such as array-based comparative genomic hybridization could be considered in the assessment of undefined white matter disorders.

Molecular characterization of a new patient with a non-recurrent inv dup del 2q and review of the mechanisms for this rearrangement

We report on newborn baby with microcephaly, facial anomalies, congenital heart defects, hypotonia, wrist contractures, long fingers, adducted thumbs, and club feet. Cytogenetic studies revealed an inverted duplication with terminal deletion (inv dup del) of 2q in the patient and a paternal 2qter deletion polymorphism. Microsatellite markers demonstrated that the inv dup del was maternal in origin and intrachromosomal. Intra or interchromosomal rearrangements may cause this aberration either by a U-type exchange (end-to-end fusion), an unequal crossover between inverted repeats (non-allelic homologous recombination: NAHR), or through breakage-fusion-bridge (BFB) cycles leading to a sister chromatid fusion by non-homologous end joining (NHEJ). A high-resolution oligo array-CGH (244 K) defined the breakpoints and did not detect a single copy region with a size exceeding 12.93 Kb in the fusion site. The size of the duplicated segment was 38.75 Mb, extending from 2q33.1 to 2q37.3 and the size of the terminal deletion was 2.85 Mb in 2q37.3. Our results indicate that the inv dup del (2q) is likely a non-recurrent chromosomal rearrangement generated by a NHEJ mechanism. The major clinical characteristics associated with this 2q rearrangement overlap with those commonly found in patients with 2q duplication reported in the literature.

Inverted duplications deletions: underdiagnosed rearrangements??

Molecular techniques led to the discovery that several chromosome rearrangements interpreted as terminal duplications were in fact inverted duplications contiguous to terminal deletions. Inv dup del rearrangements originate through a symmetric dicentric chromosome that, after asymmetric breakage, generates an inv dup del and a deleted chromosome. In recurrent inverted duplications the dicentric chromosome is formed at meiosis through non-allelic homologous recombination. In non-recurrent inv dup del cases, dicentric intermediates are formed by non-homologous end joining or intrastrand annealing. Some authors hypothesized that in these cases the dicentric may have been formed directly in the zygote. Healing of the broken dicentric chromosomes can occur not only in a telomerase-dependent way but also through telomere capture and circularization thus creating translocated or ring inv dup del chromosomes. In all the cases reported up to now, the duplicated region was always longer than the deleted one, but we can safely assume that there is another group of rearrangements where the deleted region is longer than the duplicated portion. In general, in these cases, the cytogeneticist will suspect the presence of a deletion and confirm it by FISH with a subtelomeric probe, but he/she will almost certainly miss the duplication. It is likely that the conventional analysis techniques used until now have led to a substantial underestimate of the frequency of inv dup del rearrangements and that the widespread use of array-CGH in routine analysis will allow a more realistic estimate. Obviously, the concomitant presence of deletion and duplication has important consequences in genotype/phenotype correlations.

Molecular cytogenetic characterization of the first reported case of inv dup del 20p compatible with a U-type exchange model

Inverted duplications with terminal deletions have been reported for an increasing number of chromosome ends. The best characterized and most frequent rearrangement reported involves the short arm of chromosome 8. It derives from non-allelic homologous recombination (NAHR) between two inverted LCRs (low copy repeats) of the olfactory receptor (OR) gene cluster during maternal meiosis. We report here on the cytogenetic characterization of the first inversion duplication deletion involving the short arm of chromosome 20 (inv dup del 20p) in an 18-month-old boy presenting with clinical signs consistent with 20p trisomy syndrome. This abnormality was suspected on karyotyping, but high-resolution molecular cytogenetic investigations were required to define the breakpoints of the rearrangement and to obtain insight into the mechanism underlying its formation. The duplicated region was estimated to be 18.16 Mb in size, extending from 20p13 to 20p11.22, and the size of the terminal deletion was estimated at 2.02 Mb in the 20p13 region. No single copy region was detected between the deleted and duplicated segments. As neither LCR nor inversion was identified in the 20p13 region, the inv dup del (20p) chromosome abnormality probably did not arise by NAHR. The most likely mechanism involves a break in the 20p13 region, leading to chromosome instability and reparation by U-type exchange or end-to-end fusion.

Subtelomeric 6p deletion: clinical and array-CGH characterization in two patients

We report on two patients with de novo subtelomeric terminal deletion of chromosome 6p. Patient 1 is an 8-month-old female born with normal growth parameters, typical facial features of 6pter deletion, bilateral corectopia, and protruding tongue. She has severe developmental delay, profound bilateral neurosensory deafness, poor visual contact, and hypsarrhythmia since the age of 6 months. Patient 2 is a 5-year-old male born with normal growth parameters and unilateral hip dysplasia; he has a characteristic facial phenotype, bilateral embryotoxon, and moderate mental retardation. Further characterization of the deletion, using high-resolution array comparative genomic hybridization (array-CGH; Agilent Human Genome kit 244 K), revealed that Patient 1 has a 8.1 Mb 6pter-6p24.3 deletion associated with a contiguous 5.8 Mb 6p24.3-6p24.1 duplication and Patient 2 a 5.7 Mb 6pter-6p25.1 deletion partially overlapping with that of Patient 1. Complementary FISH and array analysis showed that the inv del dup(6) in Patient 1 originated de novo. Our results demonstrate that simple rearrangements are often more complex than defined by standard techniques. We also discuss genotype-phenotype correlations including previously reported cases of deletion 6p.

CGcgh: a tool for molecular karyotyping using DNA microarray-based comparative genomic hybridization (array-CGH)

Microarray-based comparative genomic hybridization (array-CGH) is a technique by which variations in copy numbers between two genomes can be analyzed using DNA microarrays. Array CGH has been used to survey chromosomal amplifications and deletions in fetal aneuploidies or cancer tissues. Herein we report a user-friendly, MATLAB-based, array CGH analyzing program, Chang Gung comparative genomic hybridization (CGcgh), as a standalone PC version. The analyzed chromosomal data are displayed in a graphic interface, and CGcgh allows users to launch a corresponding G-banding ideogram. The abnormal DNA copy numbers (gains and losses) can be identified automatically using a user defined window size (default value is 50 probes) and sequential student t-tests with sliding windows along with chromosomes. CGcgh has been tested in multiple karyotype-confirmed human samples, including five published cases and trisomies 13, 18, 21 and X from our laboratories, and 18 cases of which microarray data are available publicly. CGcgh can be used to detect the copy number changes in small genomic regions, which are commonly encountered by clinical geneticists. CGcgh works well for the data from cDNA microarray, spotted oligonucleotide microarrays, and Affymetrix Human Mapping Arrays (10K, 100K, 500K Array Sets). The program can be freely downloaded from http://www.mcu.edu.tw/department/biotec/en%5Fpage/CGcgh/ .

Recombinant chromosome 14 due to maternal pericentric inversion

Chromosome 14 is often involved in various chromosome rearrangements, most of them balanced. Human chromosome 14 is acrocentric, so its pericentric inversions are extremely rare (only few cases have been described in the literature). Here we report on a boy with congenital malformations and recombinant chromosome 14 inherited from his mother carrying a pericentric inversion. The proband's G-banded chromosome analysis revealed derivative chromosome 14. Comparative genomic hybridization analysis identified duplication of the terminal part of chromosome 14q ish cgh dup(14)(q32.1qter). This abnormality has been confirmed by custom BAC FISH analysis. His mother's karyotype was 46,XX,inv(14)(p11.2q32.1).

Inverted duplication with terminal deletion of 5p and no cat-like cry

We report on a 6-year-old boy referred for cytogenetics study. A few non-specific features were observed in the newborn: hypotonia, failure to thrive, seizures, pre-auricular skin tags. Cat-like cry was not identified. No remarkable facial dysmorphism, gastrointestinal, respiratory or cardiac abnormalities were identified. At age 4 years, speech and motor skill delays were apparent. Karyotyping and FISH analysis revealed a de novo rearranged chromosome 5p, with subtelomeric deletion of 5p and a duplication of the cri-du-chat critical region. Array CGH using sub-megabase resolution tiling-set (SMRT) array followed by FISH analysis with labeled BACs showed a deletion of 5pter to 5p15.31 (0-6.9 Mb) and an inverted duplication of the greater part of 5p15.31 to the distal end of 5p14.3 (6.9-19.9 Mb). Although very rare, inverted duplications with terminal deletion (inv dup del) have been reported at different chromosomal ends. Our finding adds a second patient of inv dup del 5p to this growing list, and the potential causative mechanisms for this rearrangement are discussed. Review of the mapping information of cri-du-chat patients and the comparison with a previously reported patient suggested that the critical region for cat-like cry is located within a 0.6 Mb region.

Molecular cytogenetic characterization of terminal 14q32 deletions in two children with an abnormal phenotype and corpus callosum hypoplasia

Among previously reported cases of 14q terminal deletions, only 11 have dealt with pure terminal deletion of 14q (14q3-14qter) and the break points were mapped by fluorescent in situ hybridisation (FISH) or genotyping in only four of them. Thanks to a collaborative study on behalf of the 'Association des Cytogeneticiens de langue Française'(ACLF), we report two patients with terminal deletion of the long arm of chromosome 14, del(14)(q32.2) and del(14)(q32.32), diagnosed by subtelomere screening. In the two cases, a thick nuchal skinfold was detected by early ultrasound with normal prenatal karyotype. Their postnatal phenotype included large forehead, narrow palpebral fissures, epicanthic folds, upturned tip of the nose, narrow mouth and thin upper lip, microretrognathia, prominent earlobes, hypotonia, delayed psychomotor development and hypoplastic corpus callosum. By physical mapping using FISH, the size of the deletions was measured for patients 1 and 2: 6.55+/-1.05 and 4.67+/-0.10 Mb, respectively. The paternal origin of the deleted chromosome 14 was established by genotyping of microsatellites for patient 1 and the phenotype of terminal del(14)(q32) was compared to maternal uniparental disomy 14.

Ring chromosome formation as a novel escape mechanism in patients with inverted duplication and terminal deletion

Ring chromosomes are rare cytogenetic findings and are associated at phenotypic level with mental retardation and congenital abnormalities. Features specific for ring chromosome syndromes often overlap with the features of terminal deletions for the corresponding chromosomes. Here, we report a case of a ring chromosome 14 which was identified by conventional cytogenetics and shown to have a terminal deletion and an additional inverted duplication with a triplication by using large insert clone and oligo array-comparative genomic hybridization (array-CGH), fluorescence in situ hybridization (FISH) and multiplex ligation-dependent probe amplification (MLPA). The combination of an inverted duplication with a terminal deletion in a ring chromosome is of special interest for the described syndromes of chromosome 14. The presented findings might explain partly overlapping clinical features described in terminal deletion, duplication and ring chromosome 14 cases, as these rearrangements can be easily overlooked when performing GTG-banding only. Furthermore, we suggest that ring chromosome formation can act as an alternative chromosome rescue next to telomere healing and capture, particularly for acrocentric chromosomes. To our knowledge, this is the first time an inverted duplication with a terminal deletion in a ring chromosome is identified and characterized using high-resolution molecular karyotyping. Systematic evaluation of ring chromosomes by array-CGH might be especially useful in distinguishing cases with a duplication/deletion from those with a deletion only.