title: Structural Chromosomal Rearrangements Require Nucleotide-Level Resolution: Lessons from Next-Generation Sequencing in Prenatal Diagnosis.
abstract: In this exciting era of "next-gen cytogenetics," integrating genomic sequencing into the prenatal diagnostic setting is possible within an actionable time frame and can provide precise delineation of balanced chromosomal rearrangements at the nucleotide level. Given the increased risk of congenital abnormalities in newborns with de novo balanced chromosomal rearrangements, comprehensive interpretation of breakpoints could substantially improve prediction of phenotypic outcomes and support perinatal medical care. Herein, we present and evaluate sequencing results of balanced chromosomal rearrangements in ten prenatal subjects with respect to the location of regulatory chromatin domains (topologically associated domains [TADs]). The genomic material from all subjects was interpreted to be "normal" by microarray analyses, and their rearrangements would not have been detected by cell-free DNA (cfDNA) screening. The findings of our systematic approach correlate with phenotypes of both pregnancies with untoward outcomes (5/10) and with healthy newborns (3/10). Two pregnancies, one with a chromosomal aberration predicted to be of unknown clinical significance and another one predicted to be likely benign, were terminated prior to phenotype-genotype correlation (2/10). We demonstrate that the clinical interpretation of structural rearrangements should not be limited to interruption, deletion, or duplication of specific genes and should also incorporate regulatory domains of the human genome with critical ramifications for the control of gene expression. As detailed in this study, our molecular approach to both detecting and interpreting the breakpoints of structural rearrangements yields unparalleled information in comparison to other commonly used first-tier diagnostic methods, such as non-invasive cfDNA screening and microarray analysis, to provide improved genetic counseling for phenotypic outcome in the prenatal setting.
authors.affiliation: Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Zehra
authors.initials: Z
authors.lastname: Ordulu
authors.affiliation: Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA.
authors.forename: Tammy
authors.initials: T
authors.lastname: Kammin
authors.affiliation: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA 02142, USA.
authors.forename: Harrison
authors.initials: H
authors.lastname: Brand
authors.affiliation: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA.
authors.forename: Vamsee
authors.initials: V
authors.lastname: Pillalamarri
authors.affiliation: Harvard Medical School, Boston, MA 02115, USA; Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA 02142, USA.
authors.forename: Claire E
authors.initials: CE
authors.lastname: Redin
authors.affiliation: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA.
authors.forename: Ryan L
authors.initials: RL
authors.lastname: Collins
authors.affiliation: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA.
authors.forename: Ian
authors.initials: I
authors.lastname: Blumenthal
authors.affiliation: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA.
authors.forename: Carrie
authors.initials: C
authors.lastname: Hanscom
authors.affiliation: Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA.
authors.forename: Shahrin
authors.initials: S
authors.lastname: Pereira
authors.affiliation: Department of Psychiatry, Prenatal Diagnosis Center, David Geffen School of Medicine, University of California, Los Angeles, Medical Plaza, Los Angeles, CA 90095, USA.
authors.forename: India
authors.initials: I
authors.lastname: Bradley
authors.affiliation: Department of Psychiatry, Prenatal Diagnosis Center, David Geffen School of Medicine, University of California, Los Angeles, Medical Plaza, Los Angeles, CA 90095, USA.
authors.forename: Barbara F
authors.initials: BF
authors.lastname: Crandall
authors.affiliation: Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA.
authors.forename: Pamela
authors.initials: P
authors.lastname: Gerrol
authors.affiliation: Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Hayden
authors.affiliation: Department of Pediatrics, Connecticut Children's Medical Center, University of Connecticut, Farmington, CT 06030, USA.
authors.forename: Naveed
authors.initials: N
authors.lastname: Hussain
authors.affiliation: Department of Obstetrics and Gynecology, Kaplan Medical Center, Rehovot 76100, Israel.
authors.forename: Bibi
authors.initials: B
authors.lastname: Kanengisser-Pines
authors.affiliation: Department of Pathology and Laboratory Medicine, UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Sibel
authors.initials: S
authors.lastname: Kantarci
authors.affiliation: Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
authors.forename: Brynn
authors.initials: B
authors.lastname: Levy
authors.affiliation: New York Presbyterian Hospital, Columbia University Medical Center, New York, NY 10032, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Macera
authors.affiliation: Department of Pathology and Laboratory Medicine, UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Fabiola
authors.initials: F
authors.lastname: Quintero-Rivera
authors.affiliation: Department of Maternal Fetal Medicine, Columbia University Medical Center, New York, NY 10032, USA.
authors.forename: Erica
authors.initials: E
authors.lastname: Spiegel
authors.affiliation: Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Texas Medical School at Houston, Houston, TX 77030, USA.
authors.forename: Blair
authors.initials: B
authors.lastname: Stevens
authors.affiliation: Regional Obstetrical Consultants, Chattanooga, TN 37403, USA.
authors.forename: Janet E
authors.initials: JE
authors.lastname: Ulm
authors.affiliation: Department of Genetics and Development, Columbia University, New York, NY 10032, USA; Department of Pediatrics, Columbia University, New York, NY 10032, USA.
authors.forename: Dorothy
authors.initials: D
authors.lastname: Warburton
authors.affiliation: Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Louise E
authors.initials: LE
authors.lastname: Wilkins-Haug
authors.affiliation: Department of Pediatrics, Clinical Genetics Services, New York University School of Medicine, New York, NY 10003, USA.
authors.forename: Naomi
authors.initials: N
authors.lastname: Yachelevich
authors.affiliation: Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA 02142, USA; Department of Genetics, Harvard Medical School, Boson, MA 02115, USA.
authors.forename: James F
authors.initials: JF
authors.lastname: Gusella
authors.affiliation: Harvard Medical School, Boston, MA 02115, USA; Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA 02142, USA; Departments of Psychiatry and Pathology, Massachusetts General Hospital, Boston, MA 02114, USA.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Talkowski
authors.affiliation: Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA 02142, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Evolution and Genomic Science, School of Biological Sciences, University of Manchester, Manchester Academic Health Science Center, Manchester 03101, UK. Electronic address: cmorton@partners.org.
authors.forename: Cynthia C
authors.initials: CC
authors.lastname: Morton
mesh_terms: D000483:Alleles; D002869:Chromosome Aberrations; D002874:Chromosome Mapping; D000013:Congenital Abnormalities / Q000175:diagnosis / Q000235:genetics*; D005260:Female; D005786:Gene Expression Regulation; D015321:Gene Rearrangement; D005820:Genetic Testing; D015894:Genome, Human; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007621:Karyotyping; D008297:Male; D009711:Nucleotides / Q000235:genetics*; D011247:Pregnancy; D011296:Prenatal Diagnosis / Q000379:methods*; D055758:SOX9 Transcription Factor / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D014178:Translocation, Genetic
chemical_list: D009711:Nucleotides; D055758:SOX9 Transcription Factor; C527932:SOX9 protein, human