Diagnostic implications of genetic copy number variation in epilepsy plus.

OBJECTIVE: Copy number variations (CNVs) represent a significant genetic risk for several neurodevelopmental disorders including epilepsy. As knowledge increases, reanalysis of existing data is essential. Reliable estimates of the contribution of CNVs to epilepsies from sizeable populations are not available. METHODS: We assembled a cohort of 1255 patients with preexisting array comparative genomic hybridization or single nucleotide polymorphism array based CNV data. All patients had "epilepsy plus," defined as epilepsy with comorbid features, including intellectual disability, psychiatric symptoms, and other neurological and nonneurological features. CNV classification was conducted using a systematic filtering workflow adapted to epilepsy. RESULTS: Of 1097 patients remaining after genetic data quality control, 120 individuals (10.9%) carried at least one autosomal CNV classified as pathogenic; 19 individuals (1.7%) carried at least one autosomal CNV classified as possibly pathogenic. Eleven patients (1%) carried more than one (possibly) pathogenic CNV. We identified CNVs covering recently reported (HNRNPU) or emerging (RORB) epilepsy genes, and further delineated the phenotype associated with mutations of these genes. Additional novel epilepsy candidate genes emerge from our study. Comparing phenotypic features of pathogenic CNV carriers to those of noncarriers of pathogenic CNVs, we show that patients with nonneurological comorbidities, especially dysmorphism, were more likely to carry pathogenic CNVs (odds ratio = 4.09, confidence interval = 2.51-6.68; P = 2.34 × 10-9 ). Meta-analysis including data from published control groups showed that the presence or absence of epilepsy did not affect the detected frequency of CNVs. SIGNIFICANCE: The use of a specifically adapted workflow enabled identification of pathogenic autosomal CNVs in 10.9% of patients with epilepsy plus, which rose to 12.7% when we also considered possibly pathogenic CNVs. Our data indicate that epilepsy with comorbid features should be considered an indication for patients to be selected for a diagnostic algorithm including CNV detection. Collaborative large-scale CNV reanalysis leads to novel declaration of pathogenicity in unexplained cases and can promote discovery of promising candidate epilepsy genes.

The population impact of screening for Down syndrome: audit of 19 326 invasive diagnostic tests in England and Wales in 2008.

OBJECTIVE: Pregnant women who receive a high screening risk result for Down, Edwards or Patau syndrome are offered diagnostic tests that carry a risk of miscarriage. This study determined how many women had such tests per syndrome diagnosis. METHOD: The number of tests per Down, Edwards or Patau syndrome diagnosis adjusted for maternal and gestational age at diagnosis was calculated using routine data from 18 (95%) cytogenetic laboratories in England and Wales in 2008. RESULTS: There were 19,326 tests that identified 1118 diagnoses of Down syndrome and 615 of Edwards and Patau syndromes. There were eight chorionic villus samplings (CVS) per syndrome diagnosis compared with 16 amniocenteses (gestational age adjusted). The lowest number of tests per diagnosis (three for CVSs and for amniocentesis) resulted from an abnormal ultrasound scan. Among pregnant women, 2.9% had an invasive diagnostic test. If a CVS and an amniocentesis increase the risk of a miscarriage by 1% and 0.5%, respectively, approximately one miscarriage for every 14 Down, Edwards or Patau syndrome diagnosis would have occurred. CONCLUSION: A simple measurement of the population impact of screening for Down syndrome can be calculated using data already collected. Annual estimates should be produced to monitor the national fetal anomaly screening programme. © 2012 John Wiley & Sons, Ltd.

Sotos syndrome, infantile hypercalcemia, and nephrocalcinosis: a contiguous gene syndrome.

Sotos syndrome is characterized by overgrowth, a typical facial appearance, and learning difficulties. It is caused by heterozygous mutations, including deletions, of NSD1 located at chromosome 5q35. Here we report two unrelated cases of Sotos syndrome associated with nephrocalcinosis. One patient also had idiopathic infantile hypercalcemia. Genetic investigations revealed heterozygous deletions at 5q35 in both patients, encompassing NSD1 and SLC34A1 (NaPi2a). Mutations in SLC34A1 have previously been associated with hypercalciuria/nephrolithiasis. Our cases suggest a contiguous gene deletion syndrome including NSD1 and SLC34A1 and provide a potential genetic basis for idiopathic infantile hypercalcemia.

A Novel Variant in the TBC1D24 Lipid-Binding Pocket Causes Autosomal Dominant Hearing Loss: Evidence for a Genotype-Phenotype Correlation.

Background: Hereditary hearing loss is a disorder with high genetic and allelic heterogeneity. Diagnostic screening of candidate genes commonly yields novel variants of unknown clinical significance. TBC1D24 is a pleiotropic gene associated with recessive DOORS syndrome, epileptic encephalopathy, myoclonic epilepsy, and both recessive and dominant hearing impairment. Genotype-phenotype correlations have not been established to date but could facilitate diagnostic variant assessment and elucidation of pathomechanisms. Methods and Results: Whole-exome and gene panel screening identified a novel (c.919A>C; p.Asn307His) causative variant in TBC1D24 in two unrelated Caucasian families with Autosomal dominant (AD) nonsyndromic late-onset hearing loss. Protein modeling on the Drosophila TBC1D24 ortholog Skywalker crystal structure showed close interhelix proximity (6.8Å) between the highly conserved residue p.Asn307 in α18 and the position of the single known pathogenic dominant variation (p.Ser178Leu) in α11 that causes a form of deafness with similar clinical characteristics. Conclusion: Genetic variants affecting two polar hydrophilic residues in neighboring helices of TBC1D24 cause AD nonsyndromic late-onset hearing loss. The spatial proximity of the affected residues suggests the first genotype-phenotype association in TBC1D24-related disorders. Three conserved residues in α18 contribute to the formation of a functionally relevant cationic phosphoinositide binding pocket that regulates synaptic vesicle trafficking which may be involved in the molecular mechanism of disease.

Inherited 2q23.1 microdeletions involving the MBD5 locus.

BACKGROUND: Microdeletions of 2q23.1 disrupting MBD5 and loss of function mutations of MBD5 cause MBD5-Associated Neurodevelopmental disorders (MAND). Nearly all reported patients have been isolated cases of de novo origin. METHODS: This study investigates three families with inherited MBD5 mutations from three different Regional Genetics Centres in the UK. RESULTS: Two of the parents in the study had MBD5 deletions in a mosaic form. The parent with an MBD5 deletion in an apparently nonmosaic form has a psychiatric disorder in the absence of developmental delay or dysmorphism. CONCLUSIONS: Inherited forms of MBD5 deletions are rare, but do occur, especially in a mosaic form. The phenotypic spectrum of MAND may be wider than previously thought.

Ring Chromosome 17 Not Involving the Miller-Dieker Region: A Case with Drug-Resistant Epilepsy.

Chromosomal abnormalities are often identified in people with neurodevelopmental disorders including intellectual disability, autism, and epilepsy. Ring chromosomes, which usually involve gene copy number loss, are formed by fusion of subtelomeric or telomeric chromosomal regions. Some ring chromosomes, including ring 14, 17, and 20, are strongly associated with seizure disorders. We report an individual with a ring chromosome 17, r(17)(p13.3q25.3), with a terminal 17q25.3 deletion and no short arm copy number loss, and with a phenotype characterized by intellectual disability and drug-resistant epilepsy, including a propensity for nonconvulsive status epilepticus.

Prenatal detection of Down's syndrome by rapid aneuploidy testing for chromosomes 13, 18, and 21 by FISH or PCR without a full karyotype: a cytogenetic risk assessment.

BACKGROUND: In 2004, the UK National Screening Committee (UKNSC) recommended that new screening programmes for Down's syndrome need not include karyotyping and can offer prenatal diagnosis for the syndrome with FISH (fluorescence in-situ hybridisation) or PCR as rapid diagnostic tests. The UKNSC also recommended that FISH or PCR tests should only include trisomies 13, 18, and 21. We undertook a retrospective cytogenetic audit to assess the probable clinical effect of these proposed policy changes. METHODS: 23 prenatal cytogenetic laboratories from the UK public sector submitted data for amniotic fluid or chorionic villus samples referred from April, 1999, to March, 2004. We obtained data for the details of all abnormal karyotypes by reason for referral and assessed the efficiency of FISH and PCR rapid tests for the detection of chromosome abnormalities. FINDINGS: Of 119,528 amniotic fluid and 23,077 chorionic villus samples, rapid aneuploidy testing replacement of karyotyping would have resulted in about one in 100 and one in 40 samples having an undetected abnormal karyotype, respectively. Of these missed results, 293 (30%) of 1006 amniotic fluid samples and 152 (45%) of 327 chorionic villus samples were associated with a substantial risk of an abnormal phenotypic outcome. Of 34,995 amniotic fluid and 3049 chorionic villus samples that had karyotyping and a rapid test on the same sample, none of the three technologies was completely reliable to detect an abnormal karyotype, but the best protocol for an interpretable result was PCR and karyotyping or FISH and karyotyping. INTERPRETATION: Replacement of full karyotyping with rapid testing for trisomies 13, 18, and 21 after a positive screen for Down's syndrome will result in substantial numbers of liveborn children with hitherto preventable mental or physical handicaps, and represents a substantial change in the outcome quality of prenatal testing offered to couples in the UK.

De Novo Interstitial Microdeletion at 1q32.1 in a 10-Year-Old Boy with Developmental Delay and Dysmorphism.

A 10-year-old boy was referred with developmental delay and dysmorphism. Genomewide aCGH microarray analysis detected a de novo 3.7 Mb deletion at 1q32.1: arr 1q32.1(199,985,888-203,690,832)x1 dn [build HG19]. This first report of a deletion in this region implies a critical role for dosage-sensitive genes within 1q32.1 in neurological development. This is consistent with previously reported duplications of this region in patients with a similar phenotype.

Trisomy 21 mid-trimester amniotic fluid induced pluripotent stem cells maintain genetic signatures during reprogramming: implications for disease modeling and cryobanking.

Trisomy 21 is the most common chromosomal abnormality and is associated primarily with cardiovascular, hematological, and neurological complications. A robust patient-derived cellular model is necessary to investigate the pathophysiology of the syndrome because current animal models are limited and access to tissues from affected individuals is ethically challenging. We aimed to derive induced pluripotent stem cells (iPSCs) from trisomy 21 human mid-trimester amniotic fluid stem cells (AFSCs) and describe their hematopoietic and neurological characteristics. Human AFSCs collected from women undergoing prenatal diagnosis were selected for c-KIT(+) and transduced with a Cre-lox-inducible polycistronic lentiviral vector encoding SOX2, OCT4, KLF-4, and c-MYC (50,000 cells at a multiplicity of infection (MOI) 1-5 for 72 h). The embryonic stem cell (ESC)-like properties of the AFSC-derived iPSCs were established in vitro by embryoid body formation and in vivo by teratoma formation in RAG2(-/-), γ-chain(-/-), C2(-/-) immunodeficient mice. Reprogrammed cells retained their cytogenetic signatures and differentiated into specialized hematopoietic and neural precursors detected by morphological assessment, immunostaining, and RT-PCR. Additionally, the iPSCs expressed all pluripotency markers upon multiple rounds of freeze-thawing. These findings are important in establishing a patient-specific cellular platform of trisomy 21 to study the pathophysiology of the aneuploidy and for future drug discovery.

Array comparative genomic hybridization: results from an adult population with drug-resistant epilepsy and co-morbidities.

BACKGROUND: The emergence of array comparative genomic hybridization (array CGH) as a diagnostic tool in molecular genetics has facilitated recognition of microdeletions and microduplications as risk factors for both generalised and focal epilepsies. Furthermore, there is evidence that some microdeletions/duplications, such as the 15q13.3 deletion predispose to a range of neuropsychiatric disorders, including intellectual disability (ID), autism, schizophrenia and epilepsy. We hypothesised that array CGH would reveal relevant findings in an adult patient group with epilepsy and complex phenotypes. METHODS: 82 patients (54 from the National Hospital for Neurology and Neurosurgery and 28 from King's College Hospital) with drug-resistant epilepsy and co-morbidities had array CGH. Separate clinicians ordered array CGH and separate platforms were used at the two sites. RESULTS: In the two independent groups we identified copy number variants judged to be of pathogenic significance in 13.5% (7/52) and 20% (5/25) respectively, noting that slightly different selection criteria were used, giving an overall yield of 15.6%. Sixty-nine variants of unknown significance were also identified in the group from the National Hospital for Neurology and Neurosurgery and 5 from the King's College Hospital patient group. CONCLUSION: We conclude that array CGH be considered an important investigation in adults with complicated epilepsy and, at least at present for selected patients, should join the diagnostic repertoire of clinical history and examination, neuroimaging, electroencephalography and other indicated investigations in generating a more complete formulation of an individual's epilepsy.

Complete discrepancy between QF-PCR analysis of uncultured villi and karyotyping of cultured cells in the prenatal diagnosis of trisomy 21 in three CVS.

OBJECTIVE: To investigate complete discrepancies in the prenatal diagnosis of trisomy 21 between QF-PCR analysis of uncultured villi and karyotyping of cultured cells in three chorion villus samples. METHODS: Clinical details were obtained from all three patients. Follow-up studies were undertaken where possible by evaluation of chromosome 21 copy number with QF-PCR, interphase FISH, MLPA and karyotyping, and by post-mortem examination. RESULTS: Case 1: severe oligohydramnios and microcephaly on scan. QF-PCR: trisomy 21; MLPA: trisomy 21; cultured karyotype: 46,XY[48]. Placental and fetal tissue results and post-mortem examination indicated a euploid fetus with trisomy 21 mosaicism confined to the placenta. Case 2: Down screen risk 1:16; NT = 4.4 mm; absent nasal bone (Caucasian mother). QF-PCR: disomy 21; cultured karyotype: 47,XY,+ 21[23]. Neck thickening noted at delivery-post-mortem refused, no fetal tissue available. Placental tissue indicated mosaicism for trisomy 21. Case 3: Down screen risk 1:91; NT = 6.7 mm. QF-PCR: disomy 21; cultured karyotype: 46,XX,der(21;21)(q10;q10)[60]. No follow-up possible. PCR genotyping of cultured cells confirmed sample identity in all three cases. Chromosome 21 markers observed by PCR were biallelic in all three cases, indicating that a mitotic error could account for the presence of the abnormal cell lines in each case. CONCLUSION: QF-PCR analysis of uncultured villi and cultured karyotyping may rarely show complete discrepancy in the prediction of fetal trisomy 21 in CVS. Within-biopsy sample mosaicism, together with the testing of different cell populations, provide an explanation for these results. Practical ways to minimise the risk of such discrepancy are proposed.

Complete discrepancy between abnormal fetal karyotypes predicted by QF-PCR rapid testing and karyotyped cultured cells in a first-trimester CVS.

A chorion villus sample (CVS) biopsied at 11 weeks' gestation for raised nuchal translucency, revealed monosomy X (presumptive 45,X karyotype) by QF-PCR for rapid aneuploidy testing for chromosomes 13, 18, 21, X and Y. Long-term culture gave the karyotype: 47,XY,+ 21[66]/49,XYY,+ 21,+ 21 [22]. This discrepancy prompted redigestion of the combined residual villus fragments from the original QF-PCR assay. The repeat QF-PCR assay identified the presence of trisomy 21 and a Y chromosome consistent with a 47,XY,+ 21 karyotype. A double non-disjunction event early in embryogenesis in a 47,XY,+ 21 conceptus with subsequent cell lineage compartmentalisation of the three observed cell lines (45,X; 47,XY,+ 21 and 49,XYY,+ 21,+ 21) would account for these results. This is the first reported case to describe complete discrepancy at diagnosis between abnormal karyotypes detected by QF-PCR rapid aneuploidy testing and a cultured karyotype in the same CVS.

Fetal nuchal translucency scan and early prenatal diagnosis of chromosomal abnormalities by rapid aneuploidy screening: observational study.

OBJECTIVE: To investigate an approach for the analysis of samples obtained in screening for trisomy 21 that retains the advantages of quantitative fluorescent polymerase chain reaction (qf-PCR) over full karyotyping and maximises the detection of clinically significant abnormalities. DESIGN: Observational study. SETTING: Tertiary referral centre. SUBJECTS: 17,446 pregnancies, from which chorionic villous samples had been taken after assessment of risk for trisomy 21 by measurement of fetal nuchal translucency (NT) thickness at 11 to 13(+6) weeks of gestation. INTERVENTIONS: Analysis of chorionic villous samples by full karyotyping and by qf-PCR for chromosomes 13, 18, 21, X, and Y. MAIN OUTCOME MEASURE: Detection of clinically significant chromosomal abnormalities. RESULTS: The fetal karyotype was normal in 15,548 (89.1%) cases and abnormal in 1898 (10.9%) cases, including 1722 with a likely clinically significant adverse outcome. Karyotyping all cases would lead to the diagnosis of all clinically significant abnormalities, and a policy of relying entirely on qf-PCR would lead to the diagnosis of 97.9% of abnormalities. An alternative strategy whereby qf-PCR is the main method of analysis and full karyotyping is reserved for those cases with a minimum fetal NT thickness of 4 mm would require full karyotyping in 10.1% of the cases, would identify 99.0% of the significant abnormalities, and would cost 60% less than full karyotyping for all. CONCLUSIONS: In the diagnosis of chromosomal abnormalities after first trimester screening for trisomy 21, a policy of qf-PCR for all samples and karyotyping only if the fetal NT thickness is increased would reduce the economic costs, provide rapid delivery of results, and identify 99% of the clinically significant chromosomal abnormalities.

The future of prenatal diagnosis: rapid testing or full karyotype? An audit of chromosome abnormalities and pregnancy outcomes for women referred for Down's Syndrome testing.

OBJECTIVE: To assess the implications of a change in prenatal diagnosis policy from full karyotype analysis to rapid trisomy testing for women referred primarily for increased risk of Down's Syndrome. DESIGN: Retrospective collection and review of data. SETTING: The four London Regional Genetics Centres. POPULATION: Pregnant women (32,674) in the London area having invasive prenatal diagnosis during a six-year three-month period. METHODS: Abnormal karyotypes and total number of samples referred for raised maternal age, raised risk of Down's Syndrome following serum screening or maternal anxiety were collected. Abnormal karyotypes detected by molecular trisomy detection were removed, leaving cases with residual abnormal karyotypes. These were assessed for their clinical significance. Pregnancy outcomes were ascertained by reviewing patient notes or by contacting obstetricians or general practioners. MAIN OUTCOME MEASURES: Proportion of prenatal samples with abnormal karyotypes that would not have been detected by rapid trisomy testing, and the outcome of those pregnancies with abnormal karyotypes. RESULTS: Results from 32,674 samples were identified, of which 24,891 (76.2%) were from women referred primarily for Down's Syndrome testing. There were 118/24,891 (0.47%) abnormal sex chromosome karyotypes. Of the samples with autosomal abnormalities that would not be detected by rapid trisomy testing, 153/24,891 (0.61%) were in pregnancies referred primarily for Down's Syndrome testing. Of these, 98 (0.39%) had a good prognosis (46/98 liveborn, 3/98 terminations, 1/98 intrauterine death, 1/98 miscarriage, 47/98 not ascertained); 37 (0.15%) had an uncertain prognosis (20/37 liveborn, 5/37 terminations; 12/37 not ascertained) and 18 (0.07%) had a poor prognosis (1/18 liveborn, 2/18 miscarriage, 11/18 terminations, 4/18 not ascertained). CONCLUSIONS: For pregnant women with a raised risk of Down's Syndrome, a change of policy from full karyotype analysis to rapid trisomy testing would result in the failure to detect chromosome abnormalities likely to have serious clinical significance in approximately 0.06% (1 in 1659) cases. However, it should be noted that this figure may be higher (up to 0.12%; 1 in 833) if there were fetal abnormalities in some of the pregnancies in the uncertain prognosis group for which outcome information was not available.

Prenatal diagnosis by rapid aneuploidy detection and karyotyping: a prospective study of the role of ultrasound in 1589 second-trimester amniocenteses.

BACKGROUND: Reliable methods are available for rapid aneuploidy detection (RAD) for the prenatal diagnosis of trisomies 21, 18 and 13. This study examines the potential advantages and limitations of using RAD as a replacement rather than as an adjunct to traditional karyotyping. METHODS: One thousand five hundred and eighty-nine consecutive pregnancies referred for cytogenetic assessment were offered RAD (FISH or QF-PCR) as an adjunct to traditional karyotyping. The results of these two processes were compared, and the effects of three policies for cytogenetic evaluation were determined: RAD alone, a combination of RAD for all and traditional karyotyping for cases with ultrasound anomalies or a policy of RAD and traditional karyotyping in all cases. RESULTS: RAD was uninformative because of maternal-cell contamination in 37 (2.3%) cases compared to 4 (0.3%) cases of culture failure in traditional karyotyping. RAD and traditional karyotyping results were concordant in 1526 of 1548 (98.6%) cases. All non-mosaic cases of trisomies 21, 18 and 13 and cases of triploidy were correctly identified by RAD, and there were no false-positive diagnoses. The gold standard of a traditional karyotype in each case would have detected all chromosomal abnormalities. A policy of RAD alone would have identified 60 of 73 (82%) clinically important chromosomal abnormalities. The addition of a full karyotype for cases with evidence of ultrasound abnormalities would have improved detection to 95%. CONCLUSION: A policy offering RAD to all patients, but restricting traditional karyotyping to cases with ultrasound anomalies, would reduce the number of traditional karyotypes requested by 70%, but maintain a 95% detection rate for all clinically important chromosomal abnormalities. Further studies are required to determine whether similar results could be obtained in district general hospital units and to determine whether this approach would be acceptable to health professionals and patients.

Prenatal screening for Down syndrome in England and Wales and population-based birth outcomes.

OBJECTIVE: Whether the introduction of antenatal screening for Down syndrome in England and Wales with serum biochemistry or ultrasound has led to improvements in patient outcomes is unknown. The purpose of this study was to relate pregnancy outcomes to the dominant method used for prenatal Down syndrome screening. STUDY DESIGN: For the years 1989 through 1999, England and Wales were divided into geographically defined areas where specific hospitals, health authorities, and cytogenetic laboratories provided maternity care for well-defined populations. For each year from 1989 through 1999, the dominant Down syndrome screening method that was used in each area was determined. Outcomes for area-years that used serum biochemistry or ultrasound (first or second trimester) were compared with area-years that used advanced maternal age as the dominant screening method. The percent of Down syndrome cases that were diagnosed prenatally (effectiveness) and the number of invasive prenatal tests that were performed to diagnose each Down syndrome case prenatally (efficiency) were compared. RESULTS: There were 5,980,519 births and 335,184 referrals for prenatal karyotyping (amniocentesis and chorionic villus sampling) that occurred in the area-years studied, of which 12,047 pregnancies were diagnosed as Down syndrome; 5393 cases of Down syndrome (45%) were diagnosed prenatally. Invasive testing increased from 4.4% of pregnancies in 1989 to 6.4% in 1997 and declined slightly in 1999 (5.8%). Prenatal diagnosis of Down syndrome cases rose from 28% in 1989 to 53% in 1999, and the number of invasive tests that were performed to diagnose each Down syndrome case fell from 89.7 to 47.7 (P [for trend]<.0001). Areas with serum or ultrasound as the dominant screening method detected 50% more Down syndrome cases in prenatally (52% and 53% vs 36%; P<.0001) and performed fewer invasive procedures to diagnose each Down syndrome case (60.7 and 52.0 vs 88.0; P<.0001) compared with areas in which advanced maternal age screening was dominant, despite serving populations with similar mean/median maternal ages. CONCLUSION: In clinical practice, screening programs for Down syndrome that were based on maternal serum biochemistry or ultrasound were more effective and efficient than the screening programs that used advanced maternal age alone.