title: Validation of two-channel sequencing-by-synthesis for noninvasive prenatal testing of fetal whole and partial chromosome aberrations.
abstract: OBJECTIVE
  To validate Illumina's two-channel NextSeq 500 sequencing system for noninvasive prenatal testing (NIPT) of fetal whole chromosome and partial aberrations.
  
  
  METHODS
  A total of 162 plasma samples, previously sequenced for NIPT on a SOLiD 5500xl platform, were sequenced on the NextSeq 500 using 75-bp single-end sequencing, followed by analysis using the WISECONDOR algorithm.
  
  
  RESULTS
  For whole chromosome aneuploidy detection, all samples were classified correctly (in total 3× T13, 3× T18, 8× T21 and 145× euploid). Three partial aberrations (36-Mb terminal loss of 5p, 14-Mb gain on 18p and 33-Mb terminal loss of 13q) were also correctly identified. Fetal fractions in 34 male samples sequenced on both the SOLiD 5500xl and NextSeq 500 platform showed no significant difference. To test robustness, two sample sets, containing both euploid and aneuploid samples, were sequenced on different NextSeq 500 machines, revealing identical results. With unchanged laboratory flow, the NIPT turnaround time could be reduced from 15-16 calendar days to 7-8 calendar days, after switching from the SOLiD 5500xl to the NextSeq 500 platform.
  
  
  CONCLUSIONS
  The NextSeq 500 platform can be used for NIPT to detect both whole and partial chromosome aberrations. It has fast turnaround times and is suitable for mid-sized laboratories.
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.|Genomics Technology Center, Radboud University Medical Center, Nijmegen, The Netherlands.|Prenatal Screening Foundation Nijmegen Region, Nijmegen, The Netherlands.
authors.forename: Kornelia
authors.initials: K
authors.lastname: Neveling
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
authors.forename: Djie
authors.initials: D
authors.lastname: Tjwan Thung
authors.affiliation: Prenatal Screening Foundation Nijmegen Region, Nijmegen, The Netherlands.|Department of Obstetrics and Gynecology, Radboud University Medical Center, Nijmegen, The Netherlands.
authors.forename: Lean
authors.initials: L
authors.lastname: Beulen
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.|Genomics Technology Center, Radboud University Medical Center, Nijmegen, The Netherlands.
authors.forename: Wendy
authors.initials: W
authors.lastname: van Rens-Buijsman
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
authors.forename: Ingrid
authors.initials: I
authors.lastname: Gomes
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.|Genomics Technology Center, Radboud University Medical Center, Nijmegen, The Netherlands.
authors.forename: Simone
authors.initials: S
authors.lastname: van den Heuvel
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
authors.forename: Hanneke
authors.initials: H
authors.lastname: Mieloo
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
authors.forename: Irma
authors.initials: I
authors.lastname: Derks-Prinsen
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
authors.forename: Ellen
authors.initials: E
authors.lastname: Kater-Baats
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
authors.forename: Brigitte H W
authors.initials: BH
authors.lastname: Faas
mesh_terms: D000653:Amniotic Fluid / Q000737:chemistry / Q000378:metabolism; D002824:Chorionic Villi / Q000737:chemistry / Q000378:metabolism; D002869:Chromosome Aberrations; D025063:Chromosome Disorders / Q000175:diagnosis*; D004247:DNA / Q000032:analysis / Q000097:blood; D005260:Female; D005333:Fetus / Q000378:metabolism; D005820:Genetic Testing / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D011247:Pregnancy; D011296:Prenatal Diagnosis / Q000379:methods*
chemical_list: D004247:DNA