Clinical Diagnosis by Whole-Genome Sequencing of a Prenatal Sample

Abstract

SUMMARY Conventional cytogenetic testing offers low-resolution detection of balanced karyotypic abnormalities but cannot provide the precise, gene-level knowledge required to predict outcomes. The use of high-resolution whole-genome deep sequencing is currently impractical for the purpose of routine clinical care. We show here that whole-genome “jumping libraries” can offer an immediately applicable, nucleotide-level complement to conventional genetic diagnostics within a time frame that allows for clinical action. We performed large-insert sequencing of DNA extracted from amniotic-fluid cells with a balanced de novo translocation. The amniotic-fluid sample was from a patient in the third trimester of pregnancy who underwent amniocentesis because of severe polyhydramnios after multiple fetal anomalies had been detected on ultrasonography. Using a 13-day sequence and analysis pipeline, we discovered direct disruption of CHD7, a causal locus in the CHARGE syndrome (coloboma of the eye, heart anomaly, atresia of the choanae, retardation, and genital and ear anomalies). Clinical findings at birth were consistent with the CHARGE syndrome, a diagnosis that could not have been reliably inferred from the cytogenetic breakpoint. This case study illustrates the potential power of customized whole-genome jumping libraries when used to augment prenatal karyotyping.

Genome-Wide Sequencing for Prenatal Detection of Fetal Single-Gene Disorders

“…For other regions, alignment to the reference sequence cannot be resolved. These include breakpoints of balanced translocations and inversions, which can evade detection, unless paired-end sequencing is performed, wherein both sides of a fragment are linked together and sequenced in a way that the sequence is part of a single read (Talkowski et al 2012). It has been estimated that at least one exon of up to 3000 genes has a highly homologous pseudoexon and some genes have entire pseudogenes (Xue et al 2014).…”

“…Genomic sequencing was performed, which revealed disruption of CHD7, the gene involved in CHARGE syndrome. This diagnosis was achieved in 13 d by paired-end sequencing of large-insert (2-kb) fragments of a whole-genome "jumping library" (Talkowski et al 2012). Filges et al also sequenced the exomes of a trio (affected fetus and both parents) for a family with one healthy child and two affected fetuses with recurrent intrauterine growth restriction, brain abnormalities (including microcephaly), renal and genitourinary abnormalities.…”

Systematic review of accuracy of prenatal diagnosis for abnormal chromosome diseases by microarray technology

“…There were 118 studies obtained from the key word search. After screening titles and abstracts, 8 studies related to microarray prenatal diagnosis were obtained and selected for further screening by reading the full text (Lim et al, 2010;Chiu et al, 2010;Papoulidis et al, 2012;Stumm et al, 2012;Talkowski et al, 2012;Schmid et al, 2013;Simpson, 2013;Vaiopoulos et al, 2013). Among these, 2 studies were disease case reports and 5 investigated microarray techniques for different fields but did not judge noninvasive prenatal accuracy at a large scale; therefore, these studies were excluded.…”

Personalized Medicine: Impact on Patient Care in Genetic Counseling

“…WGS technologies were used to complement standard cytogenetic analyses on an amniotic fluid sample in order to specifically discover disruption of the CHD7 gene, which causes CHARGE syndrome [16]. Although this prenatal diagnosis relied on amniocentesis, an invasive procedure with inherent risks, it has now been shown that WGS of a human fetus may soon be clinically feasible using noninvasive techniques.…”