Clinical whole genome sequencing as a first-tier test at a resource-limited dysmorphology clinic in Mexico

Abstract

Patients with rare, undiagnosed, or genetic disease (RUGD) often undergo years of serial testing, commonly referred to as the "diagnostic odyssey". Patients in resource-limited areas face even greater challenges-a definitive diagnosis may never be reached due to difficulties in gaining access to clinicians, appropriate specialists, and diagnostic testing. Here, we report on a collaboration of the Illumina iHope Program with the Foundation for the Children of the Californias and Hospital Infantil de Las Californias, to enable deployment of clinical whole genome sequencing (cWGS) as first-tier test in a resource-limited dysmorphology clinic in northern Mexico. A total of 60 probands who were followed for a suspected genetic diagnosis and clinically unresolved after expert examination were tested with cWGS, and the ordering clinicians completed a semi-structured survey to investigate change in clinical management resulting from cWGS findings. Clinically significant genomic findings were identified in 68.3% (n = 41) of probands. No recurrent molecular diagnoses were observed. Copy number variants or gross chromosomal abnormalities accounted for 48.8% (n = 20) of the diagnosed cases, including a mosaic trisomy and suspected derivative chromosomes. A qualitative assessment of clinical management revealed 48.8% (n = 20) of those diagnosed had a change in clinical course based on their cWGS results, despite resource limitations. These data suggest that a cWGS first-tier testing approach can benefit patients with suspected genetic disorders.

Fig. 1

Case selection criteria. Chart review of previously evaluated individuals was performed by the clinician team. Probands who were diagnosed with a recognizable pattern of malformation (e.g., isolated Down syndrome), received counseling, and discharged from clinic were excluded from referral to the iHope Program. Probands with acquired disease (e.g.,: suspected environmental exposures) or isolated features (e.g.,: individuals with cleft lip with or without cleft palate) were typically also excluded. Probands with prior non-diagnostic molecular or cytogenic testing were included if all other criteria were met. Resulting families who were eligible for the iHope Program were contacted, offered cWGS, and scheduled to attend a Genome Day. Upon completion of a Genome Day visit, whole-blood samples were transported to the clinical laboratory for cWGS. Dx: diagnosis; cWGS: clinical whole genome sequencing

Fig. 2

Proportion of variant types observed in cases where molecular diagnoses were achieved. Number of probands with small variants (including SNVs and indels), copy number/chromosomal variants (including CNVs, derivative chromosomes, aneuploidies, and UPD), and multiple variant types (SNVs and another variant type in a single case) are noted. SNV: single nucleotide variant, indel: insertions and deletions, UPD: uniparental disomy, CNV: copy number variant