title: Non-invasive prenatal diagnosis of spinal muscular atrophy by relative haplotype dosage.
abstract: Although technically possible, few clinical laboratories across the world have implemented non-invasive prenatal diagnosis (NIPD) for selected single-gene disorders, mostly owing to the elevated costs incurred. Having previously proven that NIPD for X-linked disorders can be feasibly implemented in clinical practice, we have now developed a test for the NIPD of an autosomal-recessive disorder, spinal muscular atrophy (SMA). Cell-free DNA was extracted from maternal blood and prepared for massively parallel sequencing on an Illumina MiSeq by targeted capture enrichment of single-nucleotide polymorphisms across a 6 Mb genomic window on chromosome 5 containing the SMN1 gene. Maternal, paternal and proband DNA samples were also tested for haplotyping purposes. Sequencing data was analysed by relative haplotype dosage (RHDO). Six pregnant SMA carriers and 10 healthy pregnant donors were recruited through the NIPSIGEN study. Inheritance of the maternally and paternally derived alleles of the affected SMN1 gene was determined in the foetus by RHDO analysis for autosomal-recessive disorders. DNA from the proband (for SMA carriers) or an invasively obtained foetal sample (for healthy pregnant donors) was used to identify the maternal and paternal reference haplotypes associated with the affected SMN1 gene. Results for all patients correlated with known outcomes and showed a testing specificity and sensitivity of 100%. On top of showing high accuracy and reliability throughout the stages of validation, our novel test for NIPD of SMA is also affordable and viable for implementation into clinical service.
authors.affiliation: West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK.
authors.forename: Michael
authors.identifier: 0000-0001-8240-0603
authors.initials: M
authors.lastname: Parks
authors.affiliation: West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK.
authors.forename: Samantha
authors.initials: S
authors.lastname: Court
authors.affiliation: West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Bowns
authors.affiliation: West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK.
authors.forename: Siobhan
authors.initials: S
authors.lastname: Cleary
authors.affiliation: West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK.
authors.forename: Samuel
authors.initials: S
authors.lastname: Clokie
authors.affiliation: West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham, UK.
authors.forename: Julie
authors.initials: J
authors.lastname: Hewitt
authors.affiliation: West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham, UK.
authors.forename: Denise
authors.initials: D
authors.lastname: Williams
authors.affiliation: West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham, UK.
authors.forename: Trevor
authors.initials: T
authors.lastname: Cole
authors.affiliation: West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK.
authors.forename: Fiona
authors.initials: F
authors.lastname: MacDonald
authors.affiliation: West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK.
authors.forename: Mike
authors.initials: M
authors.lastname: Griffiths
authors.affiliation: West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Allen
mesh_terms: D016022:Case-Control Studies; D005260:Female; D005820:Genetic Testing / Q000379:methods* / Q000592:standards; D006239:Haplotypes; D006579:Heterozygote; D006801:Humans; D008297:Male; D009134:Muscular Atrophy, Spinal / Q000175:diagnosis* / Q000235:genetics; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D011247:Pregnancy; D011296:Prenatal Diagnosis / Q000379:methods* / Q000592:standards; D012680:Sensitivity and Specificity; D055533:Survival of Motor Neuron 1 Protein / Q000235:genetics
chemical_list: C526471:SMN1 protein, human; D055533:Survival of Motor Neuron 1 Protein