9p Duplication Research Articles

Chromosomal scan of single sperm cells by combining fluorescence-activated cell sorting and next-generation sequencing.

The purpose of this study was to develop a feasible approach for single sperm isolation and chromosome analysis by next-generation sequencing (NGS). Single sperm cells were isolated from semen samples of normozoospermic male and an infertile reciprocal translocation (RcT) carrier with the 46,XY,t(7;13)(p12;q12.1) karyotype using the optimized fluorescence-activated cell sorting (FACS) technique. Genome profiling was performed using NGS. Following whole-genome amplification, NGS,and quality control, the final chromosome analysis was performed on 31 and 6 single cell samples derived from the RcT carrier and normozoospermic male, respectively. All sperm cells from normozoospermic male showed a normal haploid 23-chromosome profile. For the RcT carrier, the sequencing data revealed that 64.5% of sperm cells harbored different variants of chromosome aberrations, involving deletion of 7p or 7q, duplication of 7p, and duplication of 13q, which is concordant with the expected chromosome segregation patterns observed in balanced translocation carriers. In one sample, a duplication of 9q was also detected. We optimized FACS protocol for simple and efficient isolation of single human sperm cells that subsequently enabled a successful genome-wide chromosome profiling and identification of segmental aneuploidies from these individual cells, following NGS analysis. This approach may be useful for analyzing semen samples of infertile men or chromosomal aberration carriers to facilitate the reproductive risk assessment.

Derivative chromosomes involving 5p large rearranged segments went unnoticed with the use of conventional cytogenetics

BackgroundIn countries where comparative genomic hybridization arrays (aCGH) and next generation sequencing are not widely available due to accessibility and economic constraints, conventional 400–500-band karyotyping is the first-line choice for the etiological diagnosis of patients with congenital malformations and intellectual disability. Conventional karyotype analysis can rule out chromosomal alterations greater than 10 Mb. However, some large structural abnormalities, such as derivative chromosomes, may go undetected when the analysis is performed at less than a 550-band resolution and the size and banding pattern of the interchanged segments are similar. Derivatives frequently originate from inter-chromosomal exchanges and sometimes are inherited from a parent who carries a reciprocal translocation.Case presentationWe present two cases with derivative chromosomes involving a 9.1 Mb 5p deletion/14.8 Mb 10p duplication in the first patient and a 19.9 Mb 5p deletion/ 18.5 Mb 9p duplication in the second patient. These long chromosomal imbalances were ascertained by aCGH but not by conventional cytogenetics. Both patients presented with a deletion of the Cri du chat syndrome region and a duplication of another genomic region. Each patient had a unique clinical picture, and although they presented some features of Cri du chat syndrome, the phenotype did not conclusively point towards this diagnosis, although a chromosomopathy was suspected.ConclusionsThese cases highlight the fundamental role of the clinical suspicion in guiding the approach for the etiological diagnosis of patients. Molecular cytogenetics techniques, such as aCGH, should be considered when the clinician suspects the presence of a chromosomal imbalance in spite of a normal karyotype.

Chromosomal rearrangements in the 11p15 imprinted region: 17 new 11p15.5 duplications with associated phenotypes and putative functional consequences

BackgroundThe 11p15 region contains two clusters of imprinted genes. Opposite genetic and epigenetic anomalies of this region result in two distinct growth disturbance syndromes: Beckwith-Wiedemann (BWS) and Silver-Russell syndromes (SRS)....

The behavioural phenotype of Potocki-Lupski syndrome: a cross-syndrome comparison

BackgroundPotocki-Lupski syndrome (PTLS) and Smith-Magenis syndrome (SMS) are related genomic disorders, as duplication 17p11.2 (associated with PTLS) is the reciprocal recombination product of the SMS microdeletion. While SMS has a relatively well-delineated behavioural phenotype, the behavioural profile in PTLS is less well defined, despite purported associations with autism spectrum disorder (ASD) and the suggestion that some behaviours may be diametric to those seen in SMS.MethodsCaregivers of individuals with PTLS (N = 34; M age = 12.43, SD = 6.78) completed online behavioural questionnaires, including the Challenging Behaviour Questionnaire (CBQ), the Activity Questionnaire (TAQ), the Repetitive Behaviour Questionnaire (RBQ), the Mood, Interest and Pleasure Questionnaire-Short Form (MIPQ-S) and the Social Communication Questionnaire (SCQ), which assesses behaviours associated with ASD. Individuals with PTLS were matched on age and adaptive functioning to individuals with SMS (N = 31; M age = 13.61, SD = 6.85) and individuals with idiopathic ASD (N = 33; M age = 12.04, SD = 5.85) from an existing dataset.ResultsIndividuals with PTLS and SMS were less impaired than those with idiopathic ASD on the communication and reciprocal social interaction subscales of the SCQ, but neither syndrome group differed from idiopathic ASD on the restricted, repetitive and stereotyped behaviours subscale. On the repetitive behaviour measure, individuals with PTLS and idiopathic ASD scored higher than individuals with SMS on the compulsive behaviour subscale. Rates of self-injury and property destruction were significantly lower in PTLS and idiopathic ASD than in SMS. No between-syndrome differences were found in relation to overactivity or mood; however, impulsivity was greater in SMS than in PTLS.ConclusionsFindings suggest some overlap in the behavioural phenotype of PTLS and features of ASD symptomatology; however, the overall profile of behaviours in PTLS appears to be divergent from both idiopathic ASD and SMS. Relative to idiopathic ASD, PTLS is not characterised by communication or social interaction deficits. However, restricted and repetitive behaviours were evident in PTLS, and these may be characterised specifically by compulsive behaviours. While several behavioural differences were identified between PTLS and SMS, there was little evidence of diametric behavioural phenotypes, particularly in relation to social behaviour.

Incomplete penetrance, variable expressivity, or dosage insensitivity in four families with directly transmitted unbalanced chromosome abnormalities.

The direct transmission of microscopically visible unbalanced chromosome abnormalities (UBCAs) is rare and usually has phenotypic consequences. Here we report four families in which a normal phenotype was initially found in one or more family members. Each UBCA was interpreted with regard to overlapping examples and factors previously associated with transmitted imbalances including incidental ascertainment, low gene density, benign copy number variation (CNV) content, and gene relatedness. A 4.56 Mb deletion of 8p23.1-p23.2 was thought to be causal in the affected proband but showed incomplete penetrance in her mother and sibling (Family 1). Incomplete penetrance was also associated with a 10.88 Mb duplication of 13q21.31-q22.1 (Family 3) and dosage insensitivity with a 17.6 Mb deletion of 22pter-q11.21 (Family 4) that were both ascertained at prenatal diagnosis and each found in 4 unaffected family members. The 22pter-q11.21 deletion is part of a region with high benign CNV content and supports the mapping of cat eye syndrome to a 600 kb interval of 22q11.1-q11.21. Low gene densities of less than 2.0 genes/Mb were found in each of these three families but only after segmentally duplicated genes were excluded from the deletions of 8p and 22q. In contrast, gene density was average and variable expressivity associated with a 3.59 Mb duplication of 8p23.1 incidentally ascertained for paternal infertility (Family 2). Our results indicate that a greater degree of direct parental transmission, incomplete penetrance, and variable expression are features of both sub-microscopic CNVs and UBCAs with relatively low gene and high benign CNV content.

De novo paternal origin duplication of chromosome 11p15.5: report of two Chinese cases with Beckwith-Wiedemann syndrome

BackgroundThe molecular etiology of Beckwith-Wiedemann syndrome (BWS) is complex and heterogeneous. Several subtypes of epigenetic-genetic alterations including aberrant methylation patterns, segmental uniparental disomy, single gene mutations, and copy number changes have been described. An integrated molecular approach to analyze the epigenetic-genetic alterations is required for accurate diagnosis of BWS.Case presentationWe reported two Chinese cases with BWS detected by genome-wide copy number analysis and locus-specific methylation profiling. Prenatal analysis on cord blood of patient 1 showed a de novo paternal origin duplication spanning 896Kb at 11p15.5. Patient 2 was referred at 2-month old and the genetic analysis showed a de novo 228.8Kb deletion at 11p15.5 telomeric end and a de novo duplication of 2.5 Mb at 11p15.5–15.4. Both the duplications are of paternal origin with gain of methylation at the imprinting center 1 and thus belong to the subgroup of a low tumor risk.ConclusionResults from these two cases and other reported cases from literature indicated that paternally derived duplications at 11p15.5 region cause BWS. Combined chromosome microarray analysis and methylation profiling provided reliable diagnosis for this subtype of BWS. Characterization of genetic defects in BWS patients could lead to better understanding the genetic mechanisms of this clinically and genetically heterogeneous disorder.

Genetic study of a fetus with 9p direct duplication deletion syndrome

To use next generation sequencing (NGS) to identify unknown abnormality of chromosome 9 in a fetus and explore its mechanism. A pregnant woman with abnormal fetal ultrasound finding underwent amniocentesis for G-banded chromosomal analysis. Karyotyping was also performed on peripheral blood samples derived from its parents. Fetal blood sample was obtained for NGS testing to identify abnormality unrecognized by karyotyping. Analysis of amniocytes has revealed a 46,XX,der(9)(?::p21 to qter) karyotype, while both parents had a normal karyotype. NGS analysis of the fetus revealed a 20.67 Mb duplication (4 454 279-25 126 275) at 9p21.3p24.2, which overlapped with that of the 9p duplication syndrome, and a 4.43 Mb deletion at 9p24.2p24.3 (10 001-4 442 364), which partially overlapped with that of 9p deletion syndrome and 46,XY sex reversal 4 region. Comparison of the sequencing data with reference genome database indicated direct duplication of 9p21.3p24.2, which was also supported by review of the morphology of chromosome 9p. Therefore, the karyotype of the fetus was verified to be 46,XX,der(9) dir dup(9)(p21.3p24.2), del(9)(p24.2p24.3). Combined G-banded karyotyping and NGS can identify dir dup del(9p) with accuracy. Delineation of the mechanism of dir dup del(9p) and its genotype-phenotype correlation may facilitate genetic counseling and estimation of recurrence risk.

Postzygotic telomere capture causes segmental UPD, duplication and deletion of chromosome 8p in a patient with intellectual disability and obesity

Using SNP array and FISH analysis, a patient with moderate intellectual disability and obesity was found to harbour an atypical 1.6 Mb inverted duplication on 8p23.1, directly flanked by a distally located interstitial deletion of 2.3 Mb and a terminal segmental uniparental disomy. The duplicated and deleted regions lie exactly between the two segmental duplication regions.These segmental duplications on chromosome 8p23.1 are known to be involved in chromosomal rearrangements because of mutual homology and homology to other genomic regions. Genomic instability mediated by these segmental duplications is generally caused by non-allelic homologous recombination, resulting in deletions, reciprocal duplications, inversions and translocations.Additional analysis of the parental origin of the fragments of this atypical inverted duplication/interstitial deletion shows paternal contribution in the maternal derivate chromosome 8. Combined with the finding that the normal chromosome 8 carries an inversion in 8p23.1 we hypothesize that a double strand break in 8p23.1 of the maternal chromosome was postzygotically repaired with the paternal inverted copy resulting in a duplication, deletion and segmental uniparental disomy, with no particular mediation of the 8p23.1 segmental duplication regions in recombination.

Prenatal diagnosis of paternal duplication of 11p15.5→14.3: Its implication of Beckwith–Wiedemann syndrome

ObjectiveTo characterize a prenatally detected chromosomal aberration with molecular cytogenetic approaches and explore its relationship with Beckwith–Wiedemann syndrome (BWS). Case reportA 33-year-old woman, gravida 2, para 0, was referred to our prenatal clinic at 20+ weeks due to an abnormal amniocentesis karyotyping finding, which showed 46,XY,add(11)(q24.2)dn. The mother conceived through in vitro fertilization–intracytoplasmic sperm injection (IVF-ICSI), then embryo transfer. Fetal ultrasound revealed a left-sided congenital diaphragmatic hernia, overgrowth of the fetus, and an enlarged placenta. After genetic counseling and careful deliberation by the family, the pregnancy was subsequently terminated at 22+ weeks of gestation, delivering a fetus weighing 810 g (85th to 90th centile) and a placenta of 325 g (85th to 90th centile). To further delineate the nature of the rearrangement involved in the defective chromosome 11, repeat chromosomal analyses, including array comparative genomic hybridization (aCGH) test and quantitative fluorescence–polymerase chain reaction (QF-PCR) using short tandem repeat (STR) markers, were performed by sampling fetal tissue. The final result confirmed a diagnosis of 46,XY,del(11)(q24.3q25),dup(11)(p14.3p15.5). The abnormal chromosome 11 was inherited from the father and the duplicated segment involved 11p15.5, a critical imprinting region for BWS. ConclusionWe presented a prenatally detected chromosomal aberration characterized by paternal duplication of chromosome 11p15.5, which strongly related to the phenotypic manifestation of BWS.

Study of copy number variations in children with unexplained mental retardation/brain development delay

Objective By using array-based single nucleotide polymorphisms comparative genomic hybri-dization (SNP-aCGH) to detect and fine mapping copy number variations (CNVs) in children with unexplained mental retardation/brain development delay(MR/BD), then the CNVs were analyzed to determine diagnosis and offer genetic counseling, finally to discuss the application of SNP-aCGH in genetic diagnosis of MR/BD with unknown causes. Methods Ninety-two children with unexplained MR/BD were recruited.SNP-aCGH was used to get CNVs from the whole genome-wide, and the correlation of CNVs and phenotype was analyzed to definit disease genes or pat-hogenic fragment.Statistics was performed to analyze the common phenotype between positive cases(case with CNVs) and negative cases. Results (1) The CNVs were detected in 10 cases with a detection rate of 10.86%, from which 8 cases showed subtelomeric aberration, 5 cases without subtelomeric aberration, and the rate was 8.70%, 5.40%, respectively.The CNVs related to MR/BD involved 10 different subtelomeric regions (9p, 21q, 3p, 2p, 15q, 4p, 12p, 22q, 16p, 17p), and 7 different regions without subtelomeric (1p, 4q, 2p, 14q, 15q, 12q, 22q). The deletions involved 11 zones (size: 1.05-8.80 Mb), and duplications referred to 8 zones(size: 1.33-31.25 Mb). (2)One case was diagnosed as 9p duplication syndrome, for candidate genes: DOCK8, VLDLR.A case was detected with a gene fracture(CRBN). One case was diagnosed as Coffin-Siris syndrome combined with a deletion of 15q26.3-qter, for candidate genes: SOX11 and LINS1, respectively.One case referred to 12p13.3 deletion syndrome, for candidate genes: ELKS, ERC1.One case referred to 22q13.2-qter deletion, for candidate genes: SHANK3.Two cases were diagnosed as ATR-16 syndrome with 17p13.3 deletion syndrome, their candidate genes: HBA1, HBA2, SOX8 for the former, YWHAE, LIS1 for the latter.(3)There were statistically significant differences in comparison of positive cases to the negative ones for growth delay, internal organs deformity, low birth weight infant(LBW) and premature infant(all P<0.05). Conclusions (1)Besides MR/BD in different degrees in all the positive cases, they also showed growth delay, a portion of them with internal organs deformity, low birth weight infant and premature infant.(2)Subtelomeric aberrations are related to MR/BD, while the submicroscopic rearrangement in regions without subtelomeric is suspiciously pathogenic, and need to be further studied.(3)SNP-aCGH can fine mapping the region of CNVs by high resolution from the whole genome-wide, which does contribute to limit the zones for finding pathogenic region and candidate genes, as well as to offer a technology platform for investigating about the correlation of phenotype and genes or CNVs. Key words: Mental retardation/brain development delay; Single nucleotide polymorphisms comparative geno-mic hybridization; Phenotype analysis

Prenatal diagnosis of partial monosomy 5p (5p15.1→pter) and partial trisomy 7p (7p15.2→pter) associated with cystic hygroma, abnormal skull development, and ventriculomegaly

ObjectivePrenatal diagnosis of concomitant chromosome 5p deletion syndrome and chromosome 7p duplication syndrome in a fetus with abnormal prenatal ultrasound is presented. Case ReportA 34-year-old woman was referred for amniocentesis at 22 weeks of gestation because of an irregular-shaped skull, bilateral ventriculomegaly, and nuchal cystic hygroma. Amniocentesis revealed a derivative chromosome 5 with a distal 5p deletion and an addendum of an extra unknown chromosomal segment at the breakpoint of 5p. Cytogenetic analysis of parental bloods revealed a karyotype of 46, XX, t(5;7)(p15.1;p15.2) in the mother and a karyotype of 46,XY in the father. The karyotype of the fetus was 46, XX, der(5) t(5;7)(p15.1;p15.2)mat consistent with partial monosomy 5p (5p15.1→pter) and partial trisomy 7p (7p15.2→pter). A malformed fetus was subsequently delivered with an irregular-shaped skull, a large anterior fontanelle, brachycephaly, hypertelorism, a high and prominent forehead, a large nuchal cystic hygroma, large low-set ears, a short and flattened nose, and micrognathia. Array comparative genomic hybridization analysis of the placenta revealed the result of arr 5p15.33p15.1 (22,179-18,133,327)×1.0, 7p22.3p15.2 (54,215-25,551,540)×3.0, indicating an 18.11-Mb deletion of 5p (5p15.33-p15.1) and a 22.5-Mb duplication of 7p (7p22.3-p15.2). Cord blood sampling revealed a karyotype of 46, XX, der(5)t(5;7) (p15.1;p15.2)mat. ConclusionFetuses with 5p deletion syndrome and 7p duplication syndrome may present ventriculomegaly, abnormal skull development, and cystic hygroma on prenatal ultrasound.

Deletion and duplication of 16p11.2 are associated with opposing effects on visual evoked potential amplitude.

BackgroundDuplication and deletion of the chromosomal region 16p11.2 cause a broad range of impairments, including intellectual disability, language disorders, and sensory symptoms. However, it is unclear how changes in 16p11.2 dosage affect cortical circuitry during development. The aim of this study was to investigate whether the visual evoked potential (VEP) could be used as a noninvasive quantitative measure of cortical processing in children with 16p11.2 copy number variation.MethodsPattern-reversal VEPs were successfully recorded in 19 deletion carriers, 9 duplication carriers, and 13 typically developing children between the ages of 3 and 14 years. The stimulus was a black and white checkerboard (60’) that reversed contrast at 2 Hz. VEP responses were extracted from continuous EEG recorded using a high-density elasticized electrode net.ResultsQuantitative analysis of the VEP waveform revealed that, relative to controls, deletion carriers displayed increased amplitude and duplication carriers displayed diminished amplitude. Latencies of the VEP waveform components were unaffected by 16p11.2 status. P1 amplitude did not correlate with age, IQ, or head circumference.ConclusionsThe results of this study suggest that recording VEP is a useful method to assay cortical processing in children with 16p11.2 copy number variation. There is a gene dosage-dependent effect on P1 amplitude that merits further investigation. The VEP is directly translatable to animal models, offering a promising way to probe the neurobiological mechanisms underlying cortical dysfunction in this developmental disorder.

Prenatal Array Comparative Genomic Hybridization in Fetuses With Structural Cardiac Anomalies.

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

Attenuated Phenotype in a Patient with Prader-Willi Syndrome and Duplication 16P11.2 Detected by Chromosomal Microarray

ABSTRACT Objective: We report an unusual case of Prader-Willi Syndrome (PWS) presenting with clinical signs and symptoms suggestive of Angelman Syndrome (AS), without exclusive features of PWS. Methods: A deletion in the 15q11-13 region is associated with 2 distinctive genetic syndromes depending on the parent of origin: AS and PWS. AS is characterized by developmental delays, seizures, microcephaly, movement or balance disorders, speech disorders, and happy demeanor. PWS is characterized by hypotonia, hyperphagia, and developmental delays. An 11.5-year-old female was evaluated for developmental delay with cognitive disabilities, minimal speech, echolalia, and continuous hand motions. The patient had a pleasant but minimally interactive demeanor. Results: Chromosomal microarray analysis revealed a 5.02 Mb interstitial deletion of 15q11.2>q13.1 (base pairs 21,192,943 to 26,213,571), consistent with PWS or AS, and a 604 kb interstitial duplication of 16p11.2 (base pairs 29,530,197 to 30,134,432). Based on h...

A large Indian family with rearrangement of chromosome 4p16 and 3p26.3 and divergent clinical presentations

BackgroundThe deletion of the chromosome 4p16.3 Wolf-Hirschhorn syndrome critical region (WHSCR-2) typically results in a characteristic facial appearance, varying intellectual disability, stereotypies and prenatal onset of growth retardation, while gains of the same chromosomal region result in a more variable degree of intellectual deficit and dysmorphism. Similarly the phenotype of individuals with terminal deletions of distal chromosome 3p (3p deletion syndrome) varies from mild to severe intellectual deficit, micro- and trigonocephaly, and a distinct facial appearance.Methods and resultsWe investigated a large Indian five-generation pedigree with ten affected family members in which chromosomal microarray and fluorescence in situ hybridization analyses disclosed a complex rearrangement involving chromosomal subregions 4p16.1 and 3p26.3 resulting in a 4p16.1 deletion and 3p26.3 microduplication in three individuals, and a 4p16.1 duplication and 3p26.3 microdeletion in seven individuals. A typical clinical presentation of WHS was observed in all three cases with 4p16.1 deletion and 3p26.3 microduplication. Individuals with a 4p16.1 duplication and 3p26.3 microdeletion demonstrated a range of clinical features including typical 3p microdeletion or 4p partial trisomy syndrome to more severe neurodevelopmental delay with distinct dysmorphic features.ConclusionWe present the largest pedigree with complex t(4p;3p) chromosomal rearrangements and diverse clinical outcomes including Wolf Hirschorn-, 3p deletion-, and 4p duplication syndrome amongst affected individuals.Electronic supplementary materialThe online version of this article (doi:10.1186/s12881-015-0251-5) contains supplementary material, which is available to authorized users.

MG-138 Co-occurrence of cohen syndrome with 16p11.2 duplication: The exome sequencing approach

Background The recurrent duplication of 16p11.2 (dup16p11.2) is associated with a broad spectrum of neurocognitive phenotypes with incomplete penetrance and variable expressivity. Objective To explore the possibility of co-occurrence of other genetic alterations in the genome that could explain the variability in the clinical phenotypes of dup16p11.2 cases. Methods We used whole exome sequencing with Illumina HiSeq 2000 to screen the mutational load of a trio family involving a boy with idiopathic ID/ASD who inherited dup16p11.2 from his healthy mother. Golden Helix SVS v8.1.5 software was used for data analysis. We excluded all variants outside the exonic regions (except variants at canonical splice sites), synonymous and common autosomal dominant or X-linked variants (>1% MAF), or autosomal recessive variants (>5% MAF). Seven bioinformatics tools predicted functional damaging and conservation scores of remaining variants. Their expression pattern and role in disease based in literature were also considered. Result After filtering, two compound heterozygous variants of VPS13B (8q22.2) at canonical splice sites were detected in the proband, confirmed by Sanger sequencing. Nucleotide changes of c.1426–1 and c.4157+1 were inherited from the mother and father, respectively. VPS13B protein is required for Golgi integrity and function and involved in vesicle-mediated sorting and intracellular protein transport. Mutations and/or CNVs in VPS13B cause the autosomal recessive Cohen syndrome with which the proband’s phenotype is consistent (ID, ASD, postnatal microcephaly, facial gestalt, retinal dystrophy, body habitus, joint hypermobility and episodic neutropenia). Conclusion Our study showed that variable expressivity among cases with 16p11.2 duplication may be due to the presence of other disease causing variants.

Genetic testing in inherited neuropathies: what and when to test

Genetic testing in inherited neuropathies: What and when to test Professor Mary M Reilly, MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London UK There are now more than 80 identified causative genes for the inherited neuropathies. This makes it challenging for clinicians to decide which genes to test and in what order for an individual patient. Despite the advent of next generation sequencing, careful phenotyping is still the first step in acheiving an accurate genetic diagnosis. Most diagnostic laboratories are using next generation sequencing techniques (NGS) and have developed disease-specific, or mulit-gene, testing panels which employ NGS to regions of the exome that contain known inherited neuropathy genes. These disease-specific panels are currently the best method for simultaneously screening a large number of CMT genes and, until the coverage of WES (whole exome sequencing) and WGS (whole genome sequencing) improves, they are likely to remain a comprehensive tool in genetic diagnosis of patients with CMT. In the case of a patient with sporadic or autosomal dominant CMT1 and with the typical homogenous motor conduction slowing, we still recommend testing for the 17p duplication with conventional methods as a first step. Otherwise we use a targeted CMT panel approach depending on the phenotype. We use WES for those patients who still do not have a genetic diagnosis but this currently is still done in the research side of our service. Careful in depth phenotyping remains crucial not only in choosing what tests to do but in helping to determine if variants identified by genetic testing are pathogenic which is currently the major diagnostic challenge.

De Novo Duplication of 7p21.1p22.2 in a Child with Autism Spectrum Disorder and Craniofacial Dysmorphism.

The duplication of the short arm of chromosome 7 as de novo is extremely rare. The phenotype spectrum varies depending on the region of duplication. We report a case of de novo duplication of chromosomal region 7p21.1p22.2 in a three-year-old male child with autism who presented to the Sultan Qaboos University Hospital in Muscat, Oman, in January 2012. The patient was diagnosed with craniofacial dysmorphism, global developmental delay, hypotonia and bilateral cryptorchidism. The duplication was detected by conventional G-banded karyotype analysis/fluorescence in situ hybridisation and confirmed by array comparative genomic hybridisation. To the best of the authors' knowledge, this is the first report of chromosomal region 7p21.1 involvement in an autistic patient showing features of a 7p duplication phenotype. Identifying genes in the duplicated region using molecular techniques is recommended to promote characterisation of the phenotype and associated condition. It may also reveal the possible role of these genes in autism spectrum disorder.

Distal 3p duplication and terminal 7q deletion associated with nuchal edema and cyclopia in a fetus and a review of the literature

ObjectiveTo present perinatal detection of distal 3p duplication and terminal 7q deletion associated with nuchal edema and cyclopia in a fetus, and to review the literature. Materials and methodsA 32-year-old, G9P0, woman who had experienced eight spontaneous abortions was found to have fetal nuchal edema, alobar holoprosencephaly, and cyclopia by prenatal ultrasound at 15 weeks of gestation. The pregnancy was subsequently terminated, and a malformed fetus was delivered with cyclopia. Molecular and conventional cytogenetic analyses were made to determine the genetic pathogenesis of fetal abnormalities. ResultsThe father had a karyotype of 46,XY,t(3;7)(p22.1;q36.1). The mother had a karyotype of 46,XX. The fetus had a karyotype of 46,XY,der(7)t(3;7)(p22.1;q36.1)pat. The analysis of array comparative genomic hybridization analysis revealed a 43.68-Mb duplication of 3p26.3-3p22.1 encompassing CHL1 and CNTN4, and an 8.66-Mb deletion of 7q36.1-7q36.3 encompassing SHH in the fetus. ConclusionSimultaneous occurrence of 7q deletion and 3p duplication can be associated with alobar holoprosencephaly. For the couple with a parental translocation involving 7q and 3p, prenatal ultrasound should include a detailed investigation of central nervous system anomalies.

Analysis of invdupdel(8p) rearrangement: Clinical, cytogenetic and molecular characterization.

Inverted duplication 8p associated with deletion of the short arms of chromosome 8 (invdupdel[8p]) is a relatively uncommon complex chromosomal rearrangement, with an estimated incidence of 1 in 10,000-30,000 live borns. The chromosomal rearrangement consists of a deletion of the telomeric region (8p23-pter) and an inverted duplication of the 8p11.2-p22 region. Clinical manifestations of this disorder include severe to moderate intellectual disability and characteristic facial features. In most cases, there are also CNS associated malformations and congenital heart defects. In this work, we present the cytogenetic and molecular characterization of seven children with invdupdel(8p) rearrangements. Subsequently, we have carried out genotype-phenotype correlations in these seven patients. The majority of our patients carry a similar deletion but different size of duplications; the latter probably explaining the phenotypic variability among them. We recommend that complete clinical evaluation and detailed chromosomal microarray studies should be undertaken, enabling appropriate genetic counseling.