Disease-associated mosaic variation in clinical exome sequencing: a two-year pediatric tertiary care experience

Abstract

Exome sequencing (ES) has become an important tool in pediatric genomic medicine, improving identification of disease-associated variation due to assay breadth. Depth is also afforded by ES, enabling detection of lower-frequency mosaic variation compared to Sanger sequencing in the studied tissue, thus enhancing diagnostic yield. Within a pediatric tertiary-care hospital, we report two years of clinical ES data from probands evaluated for genetic disease to assess diagnostic yield, characteristics of causal variants, and prevalence of mosaicism among disease-causing variants. Exome-derived, phenotype-driven variant data from 357 probands was analyzed concurrent with parental ES data, when available. Blood was the source of nucleic acid. Sequence read alignments were manually reviewed for all assessed variants. Sanger sequencing was used for suspected de novo or mosaic variation. Clinical provider notes were reviewed to determine concordance between laboratory-reported data and the ordering provider's interpretation of variant-associated disease causality. Laboratory-derived diagnostic yield and provider-substantiated diagnoses had 91.4% concordance. The cohort returned 117 provider-substantiated diagnoses among 115 probands for a diagnostic yield of 32.2%. De novo variants represented 64.9% of disease-associated variation within trio analyses. Among the 115 probands, five harbored disease-associated somatic mosaic variation. Two additional probands were observed to inherit a disease-associated variant from an unaffected mosaic parent. Among inheritance patterns, de novo variation was the most frequent disease etiology. Somatic mosaicism is increasingly recognized as a significant contributor to genetic disease, particularly with increased sequence depth attainable from ES. This report highlights the potential and importance of detecting mosaicism in ES.

MIPP-Seq: ultra-sensitive rapid detection and validation of low-frequency mosaic mutations

“…Mosaic mutations contribute to a wide range of genetic disorders beyond cancers including those impacting hematological [ 52 ], muscular [ 53 ], cardiovascular [ 54 , 55 ], and neurological [ 4 , 25 , 26 , 50 , 56 , 57 ] systems, but their identification and validation often remain challenging. Here we describe MIPP-Seq as a comprehensive method for the detection, quantification, and validation of known and novel genetic mutations across a wide range of AAFs and tissue types.…”

“…Furthermore, the costs associated with the highly scalable MIPP-Seq approach can be tenfold lower than ddPCR due to the combination of minimal optimization, ability to assess hundreds of mutations per sequencing run, use of standard primer synthesis, and a streamlined analytical pipeline. Thus, MIPP-Seq provides a scalable and rapid strategy for consistently precise estimation of AAFs which is broadly applicable to clinical and research studies of mosaic and germline mutations in human disease [ 4 , 26 , 29 , 50 , 53 , 54 , 56 , 57 ] and normal development [ 18 , 20 , 25 , 37 ]. In particular, the ability to utilize MIPP-Seq on multiple sequencing platforms and to simultaneously assess hundreds of variants with little optimization allows for a substantial reduction in the cost to validate any given allele.…”

Enhanced MAPK1 Function Causes a Neurodevelopmental Disorder within the RASopathy Clinical Spectrum

“…WES data processing, sequence alignment to GRCh37, and variant filtering and prioritization by allele frequency, predicted functional impact, and inheritance models were performed using the indicated pipeline (UMCUGenetics/IAP; subject 5) or as previously reported. [23][24][25][26][27][28][29] WES data output is summarized in Table S2. The de novo origin of the MAPK1 mutations was confirmed by Sanger sequencing in all cases (primer sequences are available on request).…”

Genome sequencing identifies three molecular diagnoses including a mosaic variant in the COL2A1 gene in an individual with Pol III–related leukodystrophy and Feingold syndrome

“…Genome sequencing (GS) can detect multiple variant types in a single assay, including SNVs, CNVs, indels, mitochondrial variants, and short tandem repeats (STRs) (Dolzhenko et al, 2017;Gross et al, 2019;Roller et al, 2016). In addition, somatic mosaicism identified through ES and GS has been reported in several studies (Miller et al 2020;Rodin et al 2021).…”