title: Optimal detection of fetal chromosomal abnormalities by massively parallel DNA sequencing of cell-free fetal DNA from maternal blood.
abstract: BACKGROUND
  Massively parallel DNA sequencing of cell-free fetal DNA from maternal blood can detect fetal chromosomal abnormalities. Although existing algorithms focus on the detection of fetal trisomy 21 (T21), these same algorithms have difficulty detecting trisomy 18 (T18).
  
  
  METHODS
  Blood samples were collected from 1014 patients at 13 US clinic locations before they underwent an invasive prenatal procedure. All samples were processed to plasma, and the DNA extracted from 119 samples underwent massively parallel DNA sequencing. Fifty-three sequenced samples came from women with an abnormal fetal karyotype. To minimize the intra- and interrun sequencing variation, we developed an optimized algorithm by using normalized chromosome values (NCVs) from the sequencing data on a training set of 71 samples with 26 abnormal karyotypes. The classification process was then evaluated on an independent test set of 48 samples with 27 abnormal karyotypes.
  
  
  RESULTS
  Mapped sites for chromosomes of interest in the sequencing data from the training set were normalized individually by calculating the ratio of the number of sites on the specified chromosome to the number of sites observed on an optimized normalizing chromosome (or chromosome set). Threshold values for trisomy or sex chromosome classification were then established for all chromosomes of interest, and a classification schema was defined. Sequencing of the independent test set led to 100% correct classification of T21 (13 of 13) and T18 (8 of 8) samples. Other chromosomal abnormalities were also identified.
  
  
  CONCLUSIONS
  Massively parallel sequencing is capable of detecting multiple fetal chromosomal abnormalities from maternal plasma when an optimized algorithm is used.
authors.affiliation: Verinata Health, Inc., San Carlos, CA, USA.
authors.forename: Amy J
authors.initials: AJ
authors.lastname: Sehnert
authors.forename: Brian
authors.initials: B
authors.lastname: Rhees
authors.forename: David
authors.initials: D
authors.lastname: Comstock
authors.forename: Eileen
authors.initials: E
authors.lastname: de Feo
authors.forename: Gabrielle
authors.initials: G
authors.lastname: Heilek
authors.forename: John
authors.initials: J
authors.lastname: Burke
authors.forename: Richard P
authors.initials: RP
authors.lastname: Rava
mesh_terms: D000293:Adolescent; D000328:Adult; D000465:Algorithms; D002474:Cell-Free System; D002869:Chromosome Aberrations; D002877:Chromosomes, Human / Q000235:genetics*; D002882:Chromosomes, Human, Pair 13 / Q000235:genetics; D002887:Chromosomes, Human, Pair 18 / Q000235:genetics; D002891:Chromosomes, Human, Pair 21 / Q000235:genetics; D004247:DNA / Q000097:blood / Q000235:genetics*; D005260:Female; D005333:Fetus; D006801:Humans; D008875:Middle Aged; D011247:Pregnancy; D011296:Prenatal Diagnosis / Q000379:methods*; D017422:Sequence Analysis, DNA; D012730:Sex Chromosomes / Q000235:genetics; D014314:Trisomy / Q000175:diagnosis; D014427:Twins; D055815:Young Adult
chemical_list: D004247:DNA