EACH study: Evaluation of Array Comparative genomic Hybridisation and non-invasive prenatal diagnosis using cell free fetal DNA in prenatal diagnosis of fetal anomalies

The study will evaluate the efficacy of prenatal array CGH and address the hypothesis that array CGH detects more de novo pathogenic chromosomal imbalances than standard karyotyping. It will also evaluate NIPD for Down’s syndrome. DESIGN: Multicentre experimental study with cost analysis and qualitative sub-study POPULATION: Trios (fetus+parents) will be recruited from 11 Fetal Medicine Centres across England & Wales. Fetuses with (a) structural anomaly identified at the 11-14 or 18-21 week screening scan or (b) isolated nuchal translucency >3mm identified at the 11-14 week screening scan, undergoing karyotyping. INTERVENTIONS: Cell free DNA will be extracted from maternal plasma samples for non-invasive prenatal diagnosis (NIPD) of Down’s syndrome. In all cases with a normal PCR aCGH using either either a 60K or 135 K oligonucleotide array will be performed on fetal DNA extracted from villi or amniocytes in 6 molecular cytogenetic laboratories. Where the array identifies a putative copy number variant (CNV), further studies on parental/fetal DNA will be conducted using parent versus parent (sex mis-matched array), FISH or MLPA. Standard amniocyte/chorion villus G-banded karyotyping will be performed in all cases as per current clinical guidelines. OUTCOMES: Primary – (1) Detection of pathogenic chromosomal imbalances by karyotyping and pathogenic CNVs by by array CGH. CNVs will be defined as pathogenic, benign or of uncertain clinical significance based on size, gene content and inheritance pattern. (2) sensitivity and specificity of NIPD for Down’s syndrome. Secondary - (a) Detection of chromosome imbalances and CNVs of uncertain clinical significance; (b) Turn-around times for array CGH, karyotyping and NIPD; (c) Costs to NHS and personal social services of array CGH and karyotyping and cost per additional pathogenic CNV detected by array CGH (and associated follow up testing) relative to karyotyping; (d) Parent and health professional attitudes to array CGH: a qualitative sub-study will determine views on array CGH and desirability and feasibility of replacing karyotyping with array CGH in prenatal diagnosis. SAMPLE SIZE AND ANALYSIS: A sample of 500 cases from each of the target populations will give in excess of 90% power to detect a difference in detection rates at the 5% significance level assuming that karyotyping and array CGH detect pathogenic imbalances in 5% and 10% of cases respectively. For the qualitative sub-study, semi-structured in-depth interviews will be undertaken in 12-15 health professionals and 12-15 parents. Using the Wilson method and 1500 cases for evaluation of NIPD, for a sensitivity of 100% the 95% CI will be 97.7-100%. TIMETABLE & PROJECT TEAM: The team led by Robson (Fetal Medicine) and Chitty (Genetics) includes expertise in Clinical Genetics, Molecular Cytogenetics, Health Economics, Statistics and Sociology as well as lay representation. Team members have collaborated extensively on prior/current NIHR grants. The large number of collaborating centres ensures that the study can be completed over 3 years.