Sequencing of the olfactory receptor subgenome
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REPOSITORIES: dbGaP
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Project description:Since the development of the third-generation aromatase inhibitors (AIs), anastrozole, letrozole and exemestane, these agents have been the subject of intensive research to determine their optimal use in advanced breast cancer. Not only have they replaced progestins in second-line therapy and challenged the role of tamoxifen in first-line, but there is also evidence for a lack of cross-resistance between the steroidal and nonsteroidal AIs, meaning that they may be used in sequence to obtain prolonged clinical benefit. Many questions remain, however, as to the best sequence of the two types of AIs and of the other available agents, including tamoxifen and fulvestrant, in different patient groups.
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Project description:The standard DNA sequencing methods for use in conjunction with commercially available sequencing kits are effective in sequencing a majority of templates. However, templates rich in dinucleotide and tetranucleotide repeats and a telomeric DNA containing tandem repeats are difficult to sequence adequately using these methods. Base compression artifacts due to formation of secondary structure on the nascent strands and slippage of the DNA polymerase accompanied by premature chain termination in homopolymer and short tandem repeat regions of DNA are commonly encountered problems in sequencing core laboratories. In an attempt to sequence such repeat regions of telomeric DNA templates using dye terminator chemistry, we investigated the effect of increasing the annealing time and temperature in combination with the use of denaturing conditions. Specifically, we compared the commonly used ABI PRISM BigDye, dGTP BigDye, and DYEnamic ET terminator chemistries for sequencing telomeric DNA templates rich in CA- and AACCCC-type repeats and for sequencing a template rich in dinucleotide (GT and CT) and tetranucleotide repeats. The routine reaction protocol was modified by adding either 1 M 1-carboxy-N,N,N-trimethylmethanaminium inner salt (betaine) or 5% dimethyl sulfoxide (DMSO) as denaturants in the reaction mixture. In addition, the annealing and denaturation times were increased to allow successful primer extension for linear growth of sequencing reaction product. Many of the artifacts in sequencing are known to be due to reduced stability of the hybrid formed between the template and the nascent strand. The effects of using denaturants to break secondary structures in the nascent chain and of increasing the denaturation and annealing times are discussed.We were able to sequence DNA templates with tandem repeats that failed to sequence under routine reaction conditions.
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Project description:The clinical translation of next-generation sequencing has created a paradigm shift in the diagnostic assessment of individuals with suspected rare genetic diseases. Whole-exome sequencing (WES) simultaneously examines the majority of the coding portion of the genome and is rapidly becoming accepted as an efficient alternative to clinical Sanger sequencing for diagnosing genetically heterogeneous disorders. Among reports of the clinical and diagnostic utility of WES, few studies to date have directly compared its concordance to Sanger sequencing, which is considered the clinical "gold standard". We performed a direct comparison of 391 coding and noncoding polymorphisms and variants of unknown significance identified by clinical Sanger sequencing to the WES results of 26 patients. Of the 150 well-covered coding variants identified by Sanger sequencing, 146 (97.3%) were also reported by WES. Nine genes were excluded from the comparison due to consistently low coverage in WES, which might be attributed to the use of older exome capture kits. We performed confirmatory Sanger sequencing of discordant variants; including five variants with discordant bases and four with discordant zygosity. Confirmatory Sanger sequencing supported the original Sanger report for three of the five discordant bases, one was shown to be a false positive supporting the WES data, and one result differed from both the Sanger and WES data. Two of the discordant zygosity results supported Sanger and the other two supported WES data. We report high concordance for well-covered coding variants, supporting the use of WES as a screening tool for heterogeneous disorders, and recommend the use of supplementary Sanger sequencing for poorly-covered genes when the clinical suspicion is high. Importantly, despite remaining difficulties with achieving complete coverage of the whole exome, 10 (38.5%) of the 26 compared patients were diagnosed through WES.
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Project description:Sequencing technology has achieved great advances in the past decade. Studies have previously shown the quality of specific instruments in controlled conditions. Here, we developed a method able to retroactively determine the error rate of most public sequencing datasets. To do this, we utilized the overlaps between reads that are a feature of many sequencing libraries. With this method, we surveyed 1943 different datasets from seven different sequencing instruments produced by Illumina. We show that among public datasets, the more expensive platforms like HiSeq and NovaSeq have a lower error rate and less variation. But we also discovered that there is great variation within each platform, with the accuracy of a sequencing experiment depending greatly on the experimenter. We show the importance of sequence context, especially the phenomenon where preceding bases bias the following bases toward the same identity. We also show the difference in patterns of sequence bias between instruments. Contrary to expectations based on the underlying chemistry, HiSeq X Ten and NovaSeq 6000 share notable exceptions to the preceding-base bias. Our results demonstrate the importance of the specific circumstances of every sequencing experiment, and the importance of evaluating the quality of each one.
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