Genome Sequencing Evaluated in Children with Unexplained Medical Complexity

Collectively, rare genetic conditions are an important cause of severe pediatric morbidity and mortality. A genetic diagnosis can inform prognosis, anticipatory care, management, and reproductive planning. Rapid genome sequencing as a first-tier test in neonatal and pediatric intensive care units has been associated with a high diagnostic yield and potential health care cost savings.

A team of medical geneticists from The Hospital for Sick Children (Toronto, ON, Canada) and some colleagues recruited families taking part in a structured complex care program. Following medical record review, 143 families met eligibility criteria, and 54 of them were interested and met additional criteria. Patients were eligible if they were thought to have an underlying genetic condition that had not been identified through conventional genetic testing. In all, 138 individuals from 49 families underwent genome sequencing, including 40 parent-child trios.

Genome sequencing was performed using established methods, with high-quality DNA extracted from whole blood. In brief, library preparation was performed from 500 ng of DNA using the TruSeq Nano DNA Library Preparation Kit (Illumina Inc, San Diego, CA, USA) omitting the polymerase chain reaction amplification step, followed by sequencing on an Illumina HiSeq X platform. Single-nucleotide variations (SNVs) and indels were detected using Genome Analysis Toolkit, version 3.4-46 or version 3.7 (Broad Institute, Cambridge, MA, USA).

Genome sequencing detected all genomic variation previously identified by conventional genetic testing. A total of 15 probands (30.6%) received a new primary molecular genetic diagnosis after genome sequencing. Three individuals had novel diseases and an additional nine had either ultra-rare genetic conditions or rare genetic conditions with atypical features. At least 11 families received diagnostic information that had clinical management implications beyond genetic and reproductive counseling. One patient, for instance, had a maternally inherited single-exon duplication in the KDM6A gene on the X chromosome that causes Kabuki syndrome, which was not detected by chromosomal microarray analysis, exome sequencing, or a multiplex ligation-dependent probe amplification test of the gene.

The authors concluded that genome sequencing has high analytical and clinical validity and can result in new diagnoses in CMC even in the setting of extensive prior investigations. This clinical population may be enriched for ultra-rare and novel genetic disorders. Genome sequencing is a potentially first-tier genetic test for CMC. The study was published on September 22, 2020 in the journal JAMA Network Open.