| Literature DB >> 26824862 |
Michael Parks1, Samantha Court1, Siobhan Cleary1, Samuel Clokie1, Julie Hewitt1, Denise Williams1, Trevor Cole1, Fiona MacDonald1, Mike Griffiths1, Stephanie Allen1.
Abstract
OBJECTIVE: Development of an accurate and affordable test for the non-invasive prenatal diagnosis of Duchenne and Becker muscular dystrophies (DMD/BMD) to implement in clinical practice.Entities:
Mesh:
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Year: 2016 PMID: 26824862 PMCID: PMC4864947 DOI: 10.1002/pd.4781
Source DB: PubMed Journal: Prenat Diagn ISSN: 0197-3851 Impact factor: 3.050
Figure 1Workflow and processing steps of samples obtained from group 1 and group 2 patients. As group 1 patients consisted of individuals who were not at risk of Duchenne and Becker muscular dystrophies pregnancy, the final outcomes of the test were labelled as simply haplotype A or B
Figure 2(A) The diagram summarises what is required to conduct relative haplotype dosage (RHDO) analysis for non‐invasive prenatal diagnosis of X‐linked disorders. The cumulative sequencing counts of SNP alleles are used to determine the proband and maternal haplotypes. SNPs that are heterozygous in the mother are informative and are used in the RHDO analysis. The allelic imbalance between the two haplotypes in the maternal cell‐free DNA (cfDNA) is used to calculate the fetal fraction (which has been set at 10% in this case). In this diagram, haplotype A is over‐represented in the maternal cfDNA, indicating that it has been inherited by the fetus. (B) SPRTs are used in RHDO analysis to determine the statistical significance of the allelic imbalance within a haplotype block. Cumulative sequencing counts of SNP alleles from plasma cfDNA (right table) are fed into the SPRT in order of chromosome position until a classification is made. Haplotype blocks are then plotted onto the dystrophin gene and provide the final outcome of the test (diagram). RHDO analysis is conducted from 5′ to 3′ and 3′ to 5′ in order to include all informative SNPs in the analysis and to better estimate the position of recombination sites
Figure 3Diagram of the Xp21.2 locus on chromosome X containing the dystrophin gene, represented by the light blue highlighted area. The red dots indicate the chromosome position of SNPs with AvHet >0.4, which were targeted through capture‐based DNA library enrichment for non‐invasive prenatal diagnosis of Duchenne and Becker muscular dystrophies. The brown triangles indicate the chromosome position of all 79 exons contained in the dystrophin gene. The light blue crosses indicate the position of the markers routinely used in our laboratory for linkage analysis in Duchenne and Becker muscular dystrophies families
Summary of tests conducted on patients from groups 1 and 2
| Family | Group | Mutation | Outcome | Gestation | Fetal fraction (%) | PND outcome | Reference haplotype | Informative SNPs used | Haplotype blocks (forward / reverse) | Classification accuracy (%) | Average sequencing depth of informative SNPs used |
|---|---|---|---|---|---|---|---|---|---|---|---|
| A | 1 | NA | HapA | 13 w + 3 d | 5.27 | NA | CVS | 422 | 15/14 | 100 | 160 |
| B | 1 | NA | HapA | 11 w + 6 d | 15.19 | NA | CVS | 383 | 15/15 | 100 | 193 |
| C | 1 | NA | HapA | 12 w + 5 d | 18.05 | NA | CVS | 365 | 15/15 | 100 | 52 |
| D | 1 | NA | HapA | 13 w + 2 d | 5.83 | NA | CVS | 286 | 10/10 | 100 | 114 |
| E | 1 | NA | HapA | 13 w | 26.62 | NA | CVS | 441 | 17/17 | 100 | 59 |
| F | 1 | NA | HapA | 11 w + 4 d | 3.55 | NA | CVS | 441 | 15/15 | 90 | 247 |
| G | 1 | NA | HapA | 13 w + 3 d | 14.84 | NA | CVS | 337 | 13/13 | 100 | 53 |
| H | 2 | Del ex45 | Affected | 8 w + 4 d | 9.48 | Affected | Affected son | 325 | 12/11 | 100 | 48 |
| I | 2 | Del ex43 | Unaffected | 12 + 3 d | 13.00 | Unaffected | Affected brother | 318 | 7/7 | 100 | 11 |
Prenatal diagnosis was conducted by invasive means on group 2 patients. The informative SNPs used represent SNPs which are heterozygous in the mother and comply with RHDO parameters (appendix D, supporting information). The numbers of haplotype blocks identified in the forward and reverse RHDO analysis are kept separate. The classification accuracy represents the percentage of haplotype blocks which showed an expected inheritance pattern. The average sequencing depth has been calculated on the informative SNPs used for the RHDO analysis.
Figure 4(A) Family tree of family H. (B) Diagram of relative haplotype dosage (RHDO) analysis results for family H, showing the chromosome position of the dystrophin gene, its exons, the informative SNPs identified and the mutation. Haplotype blocks are represented as red and blue arrows depending on whether they show an overrepresentation (red) or under‐representation (blue) of the affected haplotype. (C) Diagram of RHDO analysis results for family I. The switch from over‐representation to under‐representation of the affected haplotype indicates that a recombination event has taken place. The comparison between SNP alleles sequenced from the chorionic villus sampling (CVS) and the proband DNA samples is represented in the diagram by blue dots where unmatching alleles were observed and by red dots where matching alleles were found. (D) Family tree of family I. (E) Linkage analysis on family members of family I using Duchenne muscular dystrophy (DMD) markers. The marker name and size for both alleles are shown along the dystrophin gene region under each family member tested