Article

Genetics in Medicine (2011) 13, 913–920; doi:10.1097/GIM.0b013e3182368a0e

DNA sequencing of maternal plasma to detect Down syndrome: An international clinical validation study

Glenn E Palomaki1, Edward M Kloza1, Geralyn M Lambert-Messerlian1, James E Haddow1, Louis M Neveux1, Mathias Ehrich2, Dirk van den Boom2, Allan T Bombard2,3,4, Cosmin Deciu3, Wayne W Grody5, Stanley F Nelson6 and Jacob A Canick1

  1. 1Division of Medical Screening and Special Testing, Department of Pathology and Laboratory Medicine, Women & Infants Hospital, Alpert Medical School of Brown University, Providence, Rhode Island
  2. 2Sequenom Inc., San Diego, California
  3. 3Sequenom Center for Molecular Medicine, San Diego, California
  4. 4Department of Reproductive Medicine, University of California at San Diego, San Diego, California
  5. 5Departments of Pathology and Laboratory Medicine, Pediatrics, and Human Genetics, Pathology and Laboratory Medicine, and Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, California
  6. 6Departments of Human Genetics, Pathology and Laboratory Medicine, and Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, California

Correspondence: Glenn E. Palomaki, PhD, Division of Medical Screening and Special Testing, Department of Pathology and Laboratory Medicine, Women & Infants Hospital, 70 Elm Street, 2nd Floor, Providence, Rhode Island 02903. E-mail: gpalomaki@ipmms.org.

Disclosure: Palomaki and Canick (Co-Principal Investigators) were members of the Sequenom Clinical Advisory Board for 6 months and resigned when the study was funded. Van den Boom, Ehrich, Bombard, and Deciu are employees and shareholders of Sequenom, Inc.

Role of the Sponsor: Sequenom Center for Molecular Medicine (SCMM) was responsible for developing an internally validated laboratory developed test (LDT) for detecting Down syndrome in maternal plasma using MPSS and for providing clinical interpretation of the test results. SCMM also identified, equipped, and trained an independent laboratory to test a subset of samples through a separate contract with UCLA. The sponsor did not control study design, identify, or communicate with Enrollment Sites, thaw or test samples prior to the formal testing period, have access to patient information prior to all testing being completed, analyze study results, prepare drafts of the manuscript, or have final decisions on manuscript content.

Supplemental digital content is available for this article. Direct URL citations appear in the printed text and are provided in the HTML and PDF versions of this article on the journal's Web site (www.geneticsinmedicine.org).

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Abstract

Purpose: Prenatal screening for Down syndrome has improved, but the number of resulting invasive diagnostic procedures remains problematic. Measurement of circulating cell-free DNA in maternal plasma might offer improvement.

Methods: A blinded, nested case-control study was designed within a cohort of 4664 pregnancies at high risk for Down syndrome. Fetal karyotyping was compared with an internally validated, laboratory-developed test based on next-generation sequencing in 212 Down syndrome and 1484 matched euploid pregnancies. None had been previously tested. Primary testing occurred at a CLIA-certified commercial laboratory, with cross validation by a CLIA-certified university laboratory.

Results: Down syndrome detection rate was 98.6% (209/212), the false-positive rate was 0.20% (3/1471), and the testing failed in 13 pregnancies (0.8%); all were euploid. Before unblinding, the primary testing laboratory also reported multiple alternative interpretations. Adjusting chromosome 21 counts for guanine cytosine base content had the largest impact on improving performance.

Conclusion: When applied to high-risk pregnancies, measuring maternal plasma DNA detects nearly all cases of Down syndrome at a very low false-positive rate. This method can substantially reduce the need for invasive diagnostic procedures and attendant procedure-related fetal losses. Although implementation issues need to be addressed, the evidence supports introducing this testing on a clinical basis.

Keywords:

Down syndrome; prenatal screening; massively parallel shotgun sequencing; fetal DNA; clinical validation; detection rate; false-positive rate