June 1, 2021  |  

Single Molecule Real-Time (SMRT) Sequencing of genes implicated in autosomal recessive diseases.

In today’s clinical diagnostic laboratories, the detection of the disease causing mutations is either done through genotyping or Sanger sequencing. Whether done singly or in a multiplex assay, genotyping works only if the exact molecular change is known. Sanger sequencing is the gold standard method that captures both known and novel molecular changes in the disease gene of interest. Most clinical Sanger sequencing assays involve PCR-amplifying the coding sequences of the disease target gene followed by bi-directional sequencing of the amplified products. Therefore for every patient sample, one generates multiple amplicons singly and each amplicon leads to two separate sequencing reactions. Single Molecule, Real-Time (SMRT) sequencing offers several advantages to Sanger sequencing including long read lengths, first-in-first-out processing, fast time to result, high-levels of multiplexing and substantially reduced costs. For our first proof-of-concept experiment, we queried 3 known disease-associated mutations in de-identified clinical samples. We started off with 3 autosomal recessive diseases found at an increased frequency in the Ashkenazi Jewish population: Tay Sachs disease, Niemann-Pick disease and Canavan disease. The mutated gene in Tays Sachs is HEXA, Niemann-Pick is SMPD1 and Canavan is ASPA. Coding exons were amplified in multiple (6-13) amplicons for each gene from both non-carrier and carriers. Amplicons were purified, concentrations normalized, and combined prior to SMRTbell™ Library prep. A single SMRTbell library was sequenced for each gene from each patient using standard Pacific Biosciences C2 chemistry and protocols. Average read lengths of 4,000 bp across samples allowed for high-quality Circular Consensus Sequences (CCS) across all amplicons (all less than 1 kb). This high quality CCS data permitted the clean partitioning of reads from a patient in the presence of heterozygous events. Using non-carrier sequencing as a control, we were able to correctly identify the known events in carrier genes. This suggests the potential utility of SMRT sequencing in a clinical setting, enabling a cost-effective method of replacing targeted mutation detection with sequencing of the entire gene.


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