P262: Transformative care through genome sequencing: Insights from the first 100 patients in the CincyKidsSeq Study

Methods: Patients with an undiagnostic genetic disorder, despite extensive evaluation, were included in the study.Detailed phenotype and investigation results were systematically documented in a predefined proforma.A reanalysis of previously performed genomic data was done for all enrolled patients.Exome sequencing (ES) was done if not done previously, and genome sequencing (GS) for those with inconclusive exome results.Genomic data analysis was performed using advanced in-house bioinformatics pipeline to identify mobile element insertion (MEI), triplet repeats, SNVs, SVs, and CNVs.Variants were classified as per ACMG/AMP guidelines.Additional tests and functional analysis were carried out as indicated and possible.Diagnostic yield was calculated only for pathogenic and likely pathogenic variants.Results: The study included 326 patients (168 males, 152 females, and 6 fetuses) aged in-utero to 45 years.Positive family history with consanguinity was present in 37/326 (11%) families and without consanguinity in 29 (9%).Consanguinity was present in 30 families (9%) without additional affected family members.ES was done for 226 patients, while 100 patients underwent GS.A definite molecular diagnosis was established in 134/326 (41%) patients.The diagnostic yield of ES and GS was 44% (99 of 226) and 34%, respectively.A reanalysis of the previous data confirmed a diagnosis of 27.2%.One hundred and forty-six variants in 107 genes were identified, 120 pathogenic or likely pathogenic, and 26 variants of uncertain significance.The additional yield by GS included structural variants in TUBGCP6 and SUMF1, missense promoter variant in GJC2 and TNFRSF1A genes, triplet repeats in ATXN2, deep intronic indel and SNV in IDS & SERPINF1, respectively.A homozygous MEI in RECQL4 and a heterozygous MEI in GNPTAB were identified.The identification of the above gene variants was supported by the consistent clinical phenotype identified in these patients.Where the phenotype was not specific for a clinically diagnosable disorder, GS aided diagnosis in two patients by identifying pathogenic variants in SEPSECS and NOP56 genes.Optical genome mapping confirmed an inversion of IDS gene in a clinical and biochemically diagnosed MPS2 patient.Additionally, the I-UDP supported discovery of variants in six candidate genes, for which functional studies are ongoing.Conclusion: Rationalizing diagnostic tests is essential in developing countries like India, which have out-of-pocket healthcare expenditures.In this study, we demonstrate the role of ES in the clinical diagnostic algorithm and the importance of data reanalysis before embarking on GS.The I-UDP addressed the unmet needs of undiagnosed patients with diagnostic odysseys for whom availability of advanced diagnostic tests and expertise is challenging.The importance of deep phenotyping and development of enhanced workflows for genetic variant identification through collaborative learning with the UDNI is a strongly supportive framework in countries with limited access and expertise for advanced genomic testing.