Structural Chromosomal Rearrangements Require Nucleotide-Level Resolution: Lessons from Next-Generation Sequencing in Prenatal Diagnosis.

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.

Monochorionic diamniotic twin gestations discordant for markedly enlarged nuchal translucency.

OBJECTIVE: To assess karyotypes and outcomes of monochorionic diamniotic (MCDA) twin pregnancies discordant for markedly enlarged nuchal translucency (NT) in the first trimester. METHOD: Brigham and Women's Hospital's ultrasound database was queried to identify all MCDA gestations in which one twin had NT ≥ 3.5 mm and the co-twin had normal NT. Cytogenetic results, ultrasound findings, and pregnancy outcomes were reviewed. RESULTS: Of 162 MCDA twin pairs, 11 were discordant for NT ≥ 3.5. Chromosomal abnormalities were present in three cases: one twin pair was concordant for trisomy 18; one pair discordant for mosaic trisomy 2; and one pair discordant for confined placental mosaicism (CPM) (high frequency tetraploidy). Adverse outcomes for twins with euploid or unknown karyotypes included twin reverse arterial perfusion (TRAP) sequence, growth discordance, and esophageal atresia with tracheoesophageal fistula. CONCLUSION: Postfertilization nondisjunction leading to mosaicism in one fetus, discordant phenotypes yet concordant karyotypes, and discordance for CPM were documented phenomena, supporting karyotyping of both twins. In this case series, discordant NT was a marker for chromosome abnormalities, as well as for complications specific to monochorionic gestations, including TRAP sequence, amniotic fluid discordance, and structural anomalies. Nonetheless, normal fetal anatomy and karyotype were the most common outcomes.

The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies.

Despite the clinical significance of balanced chromosomal abnormalities (BCAs), their characterization has largely been restricted to cytogenetic resolution. We explored the landscape of BCAs at nucleotide resolution in 273 subjects with a spectrum of congenital anomalies. Whole-genome sequencing revised 93% of karyotypes and demonstrated complexity that was cryptic to karyotyping in 21% of BCAs, highlighting the limitations of conventional cytogenetic approaches. At least 33.9% of BCAs resulted in gene disruption that likely contributed to the developmental phenotype, 5.2% were associated with pathogenic genomic imbalances, and 7.3% disrupted topologically associated domains (TADs) encompassing known syndromic loci. Remarkably, BCA breakpoints in eight subjects altered a single TAD encompassing MEF2C, a known driver of 5q14.3 microdeletion syndrome, resulting in decreased MEF2C expression. We propose that sequence-level resolution dramatically improves prediction of clinical outcomes for balanced rearrangements and provides insight into new pathogenic mechanisms, such as altered regulation due to changes in chromosome topology.