Refinements and considerations for trio whole-genome sequence analysis when investigating Mendelian diseases presenting in early childhood

Abstract

To facilitate early deployment of whole-genome sequencing (WGS) for severely ill children, a standardized pipeline for WGS analysis with timely turnaround and primary care pediatric uptake is needed. We developed a bioinformatics pipeline for comprehensive gene-agnostic trio WGS analysis of children suspected of having an undiagnosed monogenic disease that included detection and interpretation of primary genetic mechanisms of disease, including SNVs/indels, CNVs/SVs, uniparental disomy (UPD), imprinted genes, short tandem repeat expansions, mobile element insertions, SMN1/2 copy number calling, and mitochondrial genome variants. We assessed primary care practitioner experience and competence in a large cohort of 521 families (comprising 90% WGS trios). Children were identified by primary practitioners for recruitment, and we used the UK index of multiple deprivation to confirm lack of patient socio-economic status ascertainment bias. Of the 521 children sequenced, 176 (34%) received molecular diagnoses, with rates as high as 45% for neurology clinics. Twenty-three of the diagnosed cases (13%) required bespoke methods beyond routine SNV/CNV analysis. In our multidisciplinary clinician user experience assessment, both pediatricians and clinical geneticists expressed strong support for rapid WGS early in the care pathway, but requested further training in determining patient selection, consenting, and variant interpretation. Rapid trio WGS provides an efficacious single-pass screening test for children when deployed by primary practitioners in clinical settings that carry high a priori risk for rare pediatric disease presentations.

Keywords: genomics; mendelian disorders; paediatrics; rapid diagnostic whole genome; rare disease.

Figure 1

Comprehensive trio WGS bioinformatics pipeline Schema of the bioinformatics pipeline. The color corresponds to the main steps (variant calls and various filtering types). CNV, copy number variant; MEI, mobile elements insertion; MT, mitochondria; SNV, single-nucleotide variant; SV, structural variant; UPD, uniparental disomy.

Figure 2

Inheritance patterns of variants in diagnosed cases Distribution of inheritance patterns of variants in (A) all diagnosed cases and (B) split by genomic ethnicity.

Figure 3

Different mechanisms of disease found in the cohort (A) Proportion of the different inheritance and variant types identified in the cohort. Examples of cases with (B) spinal muscular atrophy from SMN1 deletion and truncation (exon 7 and 8 deletion), (C) Temple syndrome from maternal uniparental heterodisomy 14, and (D) congenital muscular dystrophy in the child due to a large expansion of a trinucleotide repeat expansion in the 3′ UTR of DMPK inherited from the mother. For the latter, ExpansionHunter detected heterozygous anchored repeat lengths of 5/15 in the father, 13/107 in the mother, and 5/92 in the child. ExpansionHunter DeNovo detected 9 times as many paired in-repeat reads in the child compared with the mother, indicating early-onset myotonic dystrophy (DM1) in the child. Triplet PCR in mother and child confirmed expansions in the pathogenic range.

Figure 4

NGC impact survey results: utility and challenges Results of the survey assessing the impact of the NGC project. Thirty-two pediatricians and clinical geneticists were asked to rate (A) advantages of the study as not, somewhat, or very useful and (B) challenges as not, somewhat, or very significant.