Jonathan J. Waters

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 Downs 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 Downs 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.

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

Abstract 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 Downs Syndrome.

QF-PCR as a stand-alone test for prenatal samples: the first 2 years' experience in the London region.

To analyse the results of the first 2 years of a QF‐PCR stand‐alone testing strategy for the prenatal diagnosis of aneuploidy in the London region and to determine the advantages and disadvantages of this policy.

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.

Trends in cytogenetic prenatal diagnosis in the UK: results from UKNEQAS external audit, 1987-1998.

The aim of this audit was to evaluate trends in mean reporting time, culture success rate and abnormality rate for conventional cytogenetic prenatal diagnoses for amniotic fluid samples (AFS) and chorionic villus samples (CVS) in the UK. Anonymized data in the form of retrospective external audits were obtained from UKNEQAS in Clinical Cytogenetics annual reports, for AFS (1987–1997/98) and CVS (1988–1997/98). UK laboratories providing a prenatal service by referral criteria applicable at local level participated in the scheme.

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.

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

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.

Confined placental mosaicism: implications for fetal chromosomal analysis using microarray comparative genomic hybridization

The utility of array comparative genomic hybridization (CGH) testing in prenatal diagnosis has been recently described1,2 with potential advantages, including improved detection of pathogenic chromosomal rearrangements following rapid analysis of uncultured chorionic villi or amniocytes. Whilst some of the technical difficulties encountered in the prenatal setting, such as DNA extraction for rapid results and interpretation of calls, have already been discussed, others, such as confined placental mosaicism (CPM) are yet to be evaluated.

The idic(15) syndrome: Expanding the phenotype

The Idic(15) Syndrome: Expanding the Phenotype Elizabeth Caruana Galizia, Rodger Palmer, Jonathan J. Waters, Matthias J. Koepp, Raoul C.M. Hennekam, and Sanjay M. Sisodiya* Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, Queen Square, London, United Kingdom North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Trust, London, United Kingdom Department of Pediatrics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands