Quantifying single nucleotide variant detection sensitivity in exome sequencing

BACKGROUND: The targeted capture and sequencing of genomic regions has rapidly demonstrated its utility in genetic studies. Inherent in this technology is considerable heterogeneity of target coverage and this is expected to systematically impact our sensitivity to detect genuine polymorphisms. To fully interpret the polymorphisms identified in a genetic study it is often essential to both detect polymorphisms and to understand where and with what probability real polymorphisms may have been missed. RESULTS: Using down-sampling of 30 deeply sequenced exomes and a set of gold-standard single nucleotide variant (SNV) genotype calls for each sample, we developed an empirical model relating the read depth at a polymorphic site to the probability of calling the correct genotype at that site. We find that measured sensitivity in SNV detection is substantially worse than that predicted from the naive expectation of sampling from a binomial. This calibrated model allows us to produce single nucleotide resolution SNV sensitivity estimates which can be merged to give summary sensitivity measures for any arbitrary partition of the target sequences (nucleotide, exon, gene, pathway, exome). These metrics are directly comparable between platforms and can be combined between samples to give “power estimates” for an entire study. We estimate a local read depth of 13X is required to detect the alleles and genotype of a heterozygous SNV 95% of the time, but only 3X for a homozygous SNV. At a mean on-target read depth of 20X, commonly used for rare disease exome sequencing studies, we predict 5–15% of heterozygous and 1–4% of homozygous SNVs in the targeted regions will be missed. CONCLUSIONS: Non-reference alleles in the heterozygote state have a high chance of being missed when commonly applied read coverage thresholds are used despite the widely held assumption that there is good polymorphism detection at these coverage levels. Such alleles are likely to be of functional importance in population based studies of rare diseases, somatic mutations in cancer and explaining the “missing heritability” of quantitative traits

Structure Optimization and Their Biodistribution in Tumor-bearing Mice on FAP and αⅤβ3 Dual Targeting Molecular Probes

Fibroblast activation protein (FAP) is a crucial biomarker for the activation of tumor associated fibroblasts, served as an excellent target for both the diagnosis and treatment of cancer. In recent years, a variety of quinoline-based FAP inhibitors (FAPIs) have been developed, such as FAPI-02, FAPI-04 and FAPI-46, which were used to positron emission tomography (PET) imaging for clinical patients. However, high expression of FAP also occurs in chronic inflammation, fibrosis, arthritis, atherosclerotic plaques and cardiac fibrosis, which results in a compromised sensitivity/selectivity in distinguishing cancers from other FAP-positive diseases, such as chronic inflammation and fibrosis. Additionally, integrin receptor αⅤβ3 highly expresses on the surface of various tumor cells and neovascular endothelial cells, including those in lung cancer, glioblastoma, breast cancer, and osteosarcoma, but absent in resting endothelial cells of normal tissues. Integrin receptor αⅤβ3 plays an important role in regulating tumor growth, angiogenesis, local invasiveness, and metastatic potential. However, RGD-based radiotracers, including multimeric RGD peptides with enhanced integrin-targeting efficiency have only moderate tumor uptake. Based on this, in this paper two heterologous dimeric radiotracers, 68Ga-FAPI-RGD-01 and 68Ga-FAPI-RGD-02, were designed and synthesized, which are based on the quinoline-based FAPI-02 for targeting FAP, a cyclic RGD peptide for targeting αⅤβ3, a 1,4,7-triazacyclononanetriacetic acid (NOTA) group for radionuclide labeling, and poly (ethylene glycol) linker. And then, the two radiotracers were used to study the microPET imaging and preliminary biodistribution in U87MG tumor-bearing mice. The excellent in vitro stability of both 68Ga-FAPI-RGD-01 and 68Ga-FAPI-RGD-02 was confirmed through high-performance liquid chromatography analysis, which could maintain radiochemical purity over 95% in PBS buffer solution or in serum medium for at least 4 h. The radiotracers also show favorable binding affinity and specificity through affinity assays of protein and receptor in vitro, and microPET imaging of U87MG tumor-bearing mice in vivo. Subsequently, the pharmacokinetics of the two radiotracers were assessed in healthy ICR mice, microPET imaging and biodistribution were performed in U87MG tumor-bearing mice, and comparing the performance of the 68Ga-FAPI-RGD-01 and 68Ga-FAPI-RGD-02 tracers. Compared to 68Ga-FAPI-RGD-01, 68Ga-FAPI-RGD-02 exhibits higher tumor uptake and lower uptake in the heart, liver, kidneys, and muscle tissues. In addition, compared to FAPI-02, RGD, and FAPI-02+RGD blocking groups, the tumor uptake and retention of 68Ga-FAPI-RGD-02 is very much higher than these blocking groups through microPET imaging studies. It is indicated that superior pharmacokinetic performance and tumor imaging effect for 68Ga-FAPI-RGD-02, demonstrating its enormous potential in clinical disease diagnosis

DISC1 genetics, biology and psychiatric illness

Psychiatric disorders are highly heritable, and in many individuals likely arise from the combined effects of genes and the environment. A substantial body of evidence points towards DISC1 being one of the genes that influence risk of schizophrenia, bipolar disorder and depression, and functional studies of DISC1 consequently have the potential to reveal much about the pathways that lead to major mental illness. Here, we review the evidence that DISC1 influences disease risk through effects upon multiple critical pathways in the developing and adult brain

CMS physics technical design report : Addendum on high density QCD with heavy ions

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