title: Detection of microdeletion 22q11.2 in a fetus by next-generation sequencing of maternal plasma.
abstract: BACKGROUND
  Efforts have been undertaken recently to assess the fetal genome through analysis of circulating cell-free (ccf) fetal DNA obtained from maternal plasma. Sequencing analysis of such ccf DNA has been shown to enable accurate prenatal detection of fetal aneuploidies, including trisomies of chromosomes 21, 18, and 13. We sought to extend these analyses to examine subchromosomal copy number variants through the sequencing of ccf DNA. We examined a clinically relevant genomic region, chromosome 22q11.2, the location of a series of well-characterized deletion anomalies that cause 22q11.2 deletion syndrome.
  
  
  METHODS
  We sequenced ccf DNA isolated from maternal plasma samples obtained from 2 patients with confirmed 22q11.2 deletion syndrome and from 14 women at low risk for fetal chromosomal abnormalities. The latter samples were used as controls, and the mean genomic coverage was 3.83-fold. Data were aligned to the human genome, repetitive regions were removed, the remaining data were normalized for GC content, and z scores were calculated for the affected region.
  
  
  RESULTS
  The median fetal DNA contribution for all samples was 18%, with the affected samples containing 17%-18% fetal DNA. Using a technique similar to that used for sequencing-based fetal aneuploidy detection from maternal plasma, we detected a statistically significant loss of representation of a portion of chromosome 22q11.2 in both of the affected fetal samples. No such loss was detected in any of the control samples.
  
  
  CONCLUSIONS
  Noninvasive prenatal diagnosis of subchromosomal fetal genomic anomalies is feasible with next-generation sequencing.
authors.affiliation: Sequenom Center for Molecular Medicine, San Diego, CA, USA.
authors.forename: Taylor J
authors.initials: TJ
authors.lastname: Jensen
authors.forename: Zeljko
authors.initials: Z
authors.lastname: Dzakula
authors.forename: Cosmin
authors.initials: C
authors.lastname: Deciu
authors.forename: Dirk
authors.initials: D
authors.lastname: van den Boom
authors.forename: Mathias
authors.initials: M
authors.lastname: Ehrich
mesh_terms: D002872:Chromosome Deletion; D002892:Chromosomes, Human, Pair 22 / Q000235:genetics; D004247:DNA / Q000097:blood / Q000235:genetics*; D005240:Feasibility Studies; D005260:Female; D005333:Fetus; D005865:Gestational Age; D006801:Humans; D011247:Pregnancy; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA