title: Universal Haplotype-Based Noninvasive Prenatal Testing for Single Gene Diseases.
abstract: BACKGROUND
  Researchers have developed approaches for the noninvasive prenatal testing of single gene diseases. One approach that allows for the noninvasive assessment of both maternally and paternally inherited mutations involves the analysis of single nucleotide polymorphisms (SNPs) in maternal plasma DNA with reference to parental haplotype information. In the past, parental haplotypes were resolved by complex experimental methods or inferential approaches, such as through the analysis of DNA from other affected family members. Recently, microfluidics-based linked-read sequencing technology has become available and allows the direct haplotype phasing of the whole genome rapidly. We explored the feasibility of applying this direct haplotyping technology in noninvasive prenatal testing.
  
  
  METHODS
  We first resolved the haplotypes of parental genomes with the use of linked-read sequencing technology. Then, we identified SNPs within and flanking the genes of interest in maternal plasma DNA by targeted sequencing. Finally, we applied relative haplotype dosage analysis to deduce the mutation inheritance status of the fetus.
  
  
  RESULTS
  Haplotype phasing and relative haplotype dosage analysis of 12 out of 13 families were successfully achieved. The mutational status of these 12 fetuses was correctly classified.
  
  
  CONCLUSIONS
  High-throughput linked-read sequencing followed by maternal plasma-based relative haplotype dosage analysis represents a streamlined approach for noninvasive prenatal testing of inherited single gene diseases. The approach bypasses the need for mutation-specific assays and is not dependent on the availability of DNA from other affected family members. Thus, the approach is universally applicable to pregnancies at risk for the inheritance of a single gene disease.
authors.affiliation: Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China.
authors.forename: Winnie W I
authors.initials: WW
authors.lastname: Hui
authors.affiliation: Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China.|Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
authors.forename: Peiyong
authors.initials: P
authors.lastname: Jiang
authors.affiliation: Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China.
authors.forename: Yu K
authors.initials: YK
authors.lastname: Tong
authors.affiliation: Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China.
authors.forename: Wing-Shan
authors.initials: WS
authors.lastname: Lee
authors.affiliation: Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.
authors.forename: Yvonne K Y
authors.initials: YK
authors.lastname: Cheng
authors.affiliation: Department of Pediatrics, Icahn School of Medicine at Mount Sinai, NY.
authors.forename: Maria I
authors.initials: MI
authors.lastname: New
authors.affiliation: Department of Obstetrics and Gynaecology, Royal Free London NHS Foundation Trust, London, UK.|Katharine Dormandy Haemophilia Centre and Thrombosis Unit, Royal Free London NHS Foundation Trust, London, UK.
authors.forename: Rezan A
authors.initials: RA
authors.lastname: Kadir
authors.affiliation: Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China.|Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
authors.forename: K C Allen
authors.initials: KC
authors.lastname: Chan
authors.affiliation: Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.
authors.forename: Tak Y
authors.initials: TY
authors.lastname: Leung
authors.affiliation: Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China.|Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
authors.forename: Y M Dennis
authors.initials: YM
authors.lastname: Lo
authors.affiliation: Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China; rossachiu@cuhk.edu.hk.|Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
authors.forename: Rossa W K
authors.initials: RW
authors.lastname: Chiu
mesh_terms: D004247:DNA / Q000097:blood / Q000235:genetics*; D005260:Female; D030342:Genetic Diseases, Inborn / Q000097:blood / Q000235:genetics*; D040181:Genetic Diseases, X-Linked / Q000097:blood / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D008297:Male; D046210:Microfluidic Analytical Techniques; D009154:Mutation; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011247:Pregnancy; D011296:Prenatal Diagnosis; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA