Evaluation of a multiplexed oligonucleotide ligation assay for SARS-CoV-2 variant identification

BACKGROUND

SARS-CoV-2 variant surveillance informs vaccine composition and decisions to de-authorize antibody therapies. Though detailed genetic characterization requires whole-genome sequencing, targeted mutation analysis may complement pandemic surveillance efforts.

METHODS

This study investigated the qualitative performance of a multiplex oligonucleotide ligation assay targeting 19 spike mutations using 192 whole genome sequenced upper respiratory samples representing SARS-CoV-2 variants of concern.

RESULTS

Initial valid results were obtained from 95.8% [95% confidence interval (CI): 92.0 - 98.2; 184/192] of samples. All eight invalid samples were valid on repeat testing. When comparing SARS-CoV-2 oligonucleotide ligase assay SARS-CoV-2 variant calls with whole genome sequencing, overall positive percent agreement was 100% (95% CI: 98.1 - 100.0; 192/192), as was the positive and negative percent agreement for each of the tested variants; Gamma, Delta, Omicron BA.1, BA.2, and BA.4/BA.5.

CONCLUSIONS

This multiplexed oligonucleotide ligation assays demonstrated accurate SARS-CoV-2 variant typing compared to whole genome sequencing. Such an approach has the potential to provide improved turnaround compared to sequencing and more detailed mutation coverage than RT-qPCR.

Abstract 4351: Multiplex detection of G12/G13 KRAS mutations with an electrochemiluminescent hybridization assay

Purpose: Oncogenic Kirsten rat sarcoma virus (KRAS) mutations are the most prevalent cancer mutations in all human tumors. Also, genotyping the KRAS gene has become increasingly important with the emergence of new evidence highlighting differences in downstream signaling pathways, tumor microenvironment composition, treatment responses and prognoses linked to specific single nucleotide polymorphisms (SNPs) in the G12 or G13 codons. FDA approval of G12C-specific anti-KRAS drugs highlights the importance of the development of reliable SNP assays to interrogate the mutation status in a tumor sample. Currently available genotyping assays are based on NGS, PCR, or ddPCR. These methods can be time-consuming, costly, suffer from amplification bias, or require follow-up testing or bioinformatics skills to analyze. Building on Meso Scale Discovery’s (MSD) existing technology, we aimed to develop a method for the identification of eight KRAS SNPs located on the G12-G13 codons in a single reaction.

Methods: Ten-spot, 96-well N-PLEX plates were used for the study. SNP-specific upstream probes carrying unique 5′ leader sequences complementary to spot-specific captures on the N-PLEX plates were designed for eight KRAS genotypes (WT, G12R, G12C, G12S, G12A, G12D, G12V, G13D). Locus-specific downstream probes were 5’ phosphorylated for ligation and 3’ biotinylated for detection. Synthetic DNA targets were used as assay calibrators, and commercially available FFPE reference samples were tested for validation. DNA (10 ng) was PCR amplified with primers flanking the KRAS mutation sites. A multiplexed mixture of upstream and downstream probes was hybridized to the amplicons, and 30 cycles of ligation was performed using DNA ligase in a thermal cycler. Samples were subsequently hybridized to spot-specific capture oligonucleotides on the surface of the assay plates and detected with SULFO-TAG labeled streptavidin. Electrochemiluminescence readout was collected on an MSD imager.

Results: Optimization of probe concentrations and ligation temperature was performed to maximize signal-to-background ratios and assay specificity. Spike recovery experiments using artificial target DNA showed successful identification of KRAS mutant genotypes at spike levels as low as 0.1% over wild-type background. Validation experiments with gDNA extracted from FFPE reference samples confirmed that the multiplex SNP assay can accurately differentiate eight KRAS genotypes in samples with >0.4% tumor burden.

Conclusion: These data highlight a novel approach to simultaneously identify eight KRAS genotypes from 10 ng of DNA input in a single reaction within 4-5 hours. The assay is capable of identifying double mutants and can provide a semiquantitative assessment of tumor burden without the need for follow-up testing.

Citation Format: Annamaria Szabolcs, Timothy J. Break, Isaac H. Shin, Seth B. Harkins, Jacob N. Wohlstadter. Multiplex detection of G12/G13 KRAS mutations with an electrochemiluminescent hybridization assay. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4351.

Development and Characterization of V-PLEX® TH17 Cytokine. Assays

Th17 cytokines are important mediators of the host defense against infection and are increasingly investigated for their role in autoimmune disorders and immune regulation at mucosal surfaces. Here we describe the development, characterization, and analytical validation of a multiplexed immunoassay panel for seven Th17 cytokines, IL-17A, IL-21, IL-22, IL-23, IL-27, IL-31, and MIP-3alpha, on MSD’s V-PLEX platform.

To efficiently and rapidly identify potential antibody pairs, biotinylated capture antibodies and detection antibodies conjugated with SULFO-TAG™ label were screened on MSD’s U-PLEX® platform, which enables the solution phase assembly of capture antibody arrays. Subsequent development used printed arrays of capture antibodies. Antibody concentrations, calibrator curve linearity, dynamic range, specificity, matrix tolerance, and assay robustness were analyzed for each assay during development. Calibration curves demonstrated a three-log dynamic range while achieving a lower limit of quantitation (LLOQ) of less than 1 pg/mL for most assays. Control samples for the assays had CVs of less than 10%. Dilution linearity and spike recovery studies in serum, plasma, urine, and cell culture media were conducted to demonstrate matrix compatibility. Spiked matrix samples were typically found to recover between 80%–120% of the expected value. Cross-reactivity was shown to be less than 0.3% between assays within the panel and less than 0.5% when panned against more than 30 other blood-related biomarkers.

These validated, multiplexed assays provide sensitive measurement of Th17 cytokines in a variety of matrices and can be used as part of a researcher’s pre-clinical and clinical studies.

Abstract 3961: Methodological considerations in the preparation of biomimetic reference materials for ctDNA assays

Clinical utilization of cell-free DNA (cfDNA) has become commonplace for NIPS testing and has recently been more widely deployed to quantitate cell-free circulating tumor DNA (ctDNA) for use in cancer patient care longitudinally across the treatment spectrum from subclinical, to diagnosis and through treatment. The scarcity and unstable nature of the cfDNA analyte in human plasma is problematic and thus the lack of robust detection methods has limited clinical validation. In this work we sought to avoid the inherent limitations of plasma-based patient reference materials and developed a strategy to prepare a biomimetic reference material which is sufficiently equivalent to the cfDNA found in patients with malignant cancers. Thus far the scarcity and physical form of ctDNA in human plasma has attenuated the validation of assays for clinical utility. To this end, we have generated a biosynthetic construct with short DNA fragments containing relevant cancer mutation sequences, including single-nucleotide variations, insertions and deletions in BRAF, EGFR, KRAS, NRAS, PIK3CA or HER/ERBB2. The mutant fragments were titrated into normal human reference DNA, GM24385, and ultrasonically sheared to ∼160 bp. Precise allele frequency blends were verified by digital PCR (dPCR) prior to encapsulation to enhance stability and compatibility with commutable plasma. The reference material is formulated to 20 ng/mL of extractable DNA in modified Seracare Matribase™ to confer commutability in pre-analytic processes. These materials have been quantitated by dPCR and/or Next Generation Sequencing (NGS). A dilution panel was prepared at 10%, 5%, 2.5%, 1.25%, 0.1% allele frequency (mutant:normal DNA). Linearity (R2 = 0.9997) was observed by dPCR (measured vs. expected) and the NGS detected, Swift Accel-Amplicon 56G Oncology Panel (R2 = 0.997). Due to the low abundance of ctDNA, a characterized reference set is critical to validate assays that are developed with extremely low limit of detection. Data will be presented to show the breadth of this methodology and its utility in validating NGS and dPCR assays.

Citation Format: Seth B. Harkins, Farol L. Tomson, Bharathi Anekella, Russell Garlick. Methodological considerations in the preparation of biomimetic reference materials for ctDNA assays. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3961.

E-type delayed fluorescence of a phosphine-supported Cu2(mu-NAr2)2 diamond core: harvesting singlet and triplet excitons in OLEDs

A highly emissive bis(phosphine)diarylamido dinuclear copper(I) complex (quantum yield = 57%) was shown to exhibit E-type delayed fluorescence by variable temperature emission spectroscopy and photoluminescence decay measurement of doped vapor-deposited films. The lowest energy singlet and triplet excited states were assigned as charge transfer states on the basis of theoretical calculations and the small observed S(1)-T(1) energy gap. Vapor-deposited OLEDs doped with the complex in the emissive layer gave a maximum external quantum efficiency of 16.1%, demonstrating that triplet excitons can be harvested very efficiently through the delayed fluorescence channel. The function of the emissive dopant in OLEDs was further probed by several physical methods, including electrically detected EPR, cyclic voltammetry, and photoluminescence in the presence of applied current.

Multifrequency EPR studies of [Cu(1.5)Cu(1.5)](+) for Cu2(mu-NR2)2 and Cu2(mu-PR2)2 diamond cores

Multifrequency electron paramagnetic resonance (EPR) spectroscopy is used to explore the electronic structures of a series of dicopper complexes of the type {(LXL)Cu}(2)(+). These complexes contain two four-coordinate copper centers of highly distorted tetrahedral geometries linked by two [LXL](-) ligands featuring bridging amido or phosphido ligands and associated thioether or phosphine chelate donors. Specific chelating [LXL](-) ligands examined in this study include bis(2-tert-butylsulfanylphenyl)amide (SNS), bis(2-di-iso-butylphosphinophenyl)amide (PNP), and bis(2-di-iso-propylphosphinophenyl)phosphide (PPP). To better map the electronic coupling to copper, nitrogen, and phosphorus in these complexes, X-, S-, and Q-band EPR spectra have been obtained for each complex. The resulting EPR parameters implied by computer simulation are unusual for typical dicopper complexes and are largely consistent with previously published X-ray absorption spectroscopy and density functional theory data, where a highly covalent {Cu(2)(mu-XR(2))(2)}(+) diamond core has been assigned in which removal of an electron from the neutral {Cu(2)(mu-XR(2))(2)} can be viewed as ligand-centered to a substantial degree. To our knowledge, this is the first family of dicopper diamond core model complexes for which the compendium of X-, S-, and Q-band EPR spectra have been collected for comparison to Cu(A).

Nickel complexes of a pincer NN2 ligand: multiple carbon-chloride activation of CH2Cl2 and CHCl3 leads to selective carbon-carbon bond formation

A new pincer-type bis(amino)amine (NN2) ligand and its lithium and nickel complexes, including Ni(II) methyl, ethyl, and phenyl complexes, were synthesized. The Ni(II) alkyl complexes react cleanly with alkyl halides including chlorides to form C-C coupled products and Ni(II) halides. More interestingly, the Ni(II) alkyls undergo unprecedented reactions with CH2Cl2 and CHCl3 to cleave all the C-Cl bonds and replace them with C-C bonds. The reactions are highly selective and lead to the first efficient catalytic coupling of CH2Cl2 with alkyl Grignards. A conversion of 82% and a turnover number of 47 are achieved within minutes. Coupling of CD2Cl2 and 1,1-dichloro-3,3-dimethylbutane with nBuMgCl is also realized. Preliminary mechanistic study suggests a radical initiated process for these reactions.

Alpha-synuclein structures probed by 5-fluorotryptophan fluorescence and 19F NMR spectroscopy

Alpha-synuclein, the main protein component of fibrillar deposits found in Parkinson's disease, is intrinsically disordered in vitro. Site-specific information on the protein conformation has been obtained by biosynthetic incorporation of an unnatural amino acid, 5-fluorotryptophan (5FW), into the recombinant protein. Using fluorescence and 19F NMR spectroscopy, we have characterized three proteins with 5FW at positions 4, 39, and 94. Steady-state emission spectra (maxima at 353 nm; quantum yields approximately 0.2) indicate that all three indole side chains are exposed to the aqueous medium. Virtually identical single-exponential excited-state decays (tau approximately 3.4 ns) were observed in all three cases. Single 19F NMR resonances were measured for W4, W39, and W94 at -49.0 +/- 0.1 ppm. Our analysis of the spectroscopic data suggests that the protein conformations are very similar in the regions near the three sites.

Unexpected Photoisomerization of a Pincer-type Amido Ligand Leads to Facial Coordination at Pt(IV)

The divalent complex (BQA)PtMe undergoes oxidative addition with MeI to afford the octahedral complex cis-(mer-BQA)PtMe2I {(BQA)- = bis(8-quinolinyl)amide}. When this molecule is irradiated with visible light, it isomerizes to (fac-BQA)PtMe2I, where the BQA ligand adopts an unexpected facial coordination mode. The amide nitrogen in this molecule is sp3 hybridized and can be easily quarternized with HBF4, resulting in [H(fac-BQA)PtMe2I][BF4], with only minor perturbation to the coordination sphere.

Structural snapshots of a flexible Cu2P2 core that accommodates the oxidation states Cu(I)Cu(I), Cu1.5Cu1.5, and Cu(II)Cu(II)

The phosphido-bridged dicopper(I) complex {(PPP)Cu}2 has been synthesized and structurally characterized ([PPP]- = bis(2-di-iso-propylphosphinophenyl)phosphide). Cyclic voltammetry of {(PPP)Cu}2 in THF shows fully reversible oxidations at -1.02 V (Cu1.5Cu1.5/CuICuI) and -0.423 V (CuIICuII/Cu1.5Cu1.5). Chemical oxidation of {(PPP)Cu}2 by one electron yields the class III mixed-valence species [{(PPP)Cu}2]+ (EPR, UV-vis). Structural data establish an unexpectedly large change (0.538 A) in the Cu...Cu distance upon oxidation state. Oxidation of {(PPP)Cu}2 by two electrons yields the dication [{(PPP)Cu}2]2+, an antiferromagnetically coupled dicopper(II) complex. Maintenance of a pseudotetrahedral geometry that is midway between a square plane and an ideal tetrahedron at the copper centers, along with a high degree of flexibility at the phosphide hinges, allows for efficient access to CuICuI, Cu1.5Cu1.5, and CuIICuII redox states without the need for ligand exchange, substitution, or redistribution processes.

Synthesis and characterization of cationic iron complexes supported by the neutral ligands NPi-Pr3, NArPi-Pr3, and NSt-Bu3

This paper compares the local geometries, spin states, and redox properties of a series of iron complexes supported by neutral, tetradentate NP3 (tris(phosphine)amine) and NS3 (tris(thioether)amine) ligands. Our consideration of an Fe-mediated N2 fixation scheme similar to that proposed by Chatt for molybdenum motivates our interest in systems of these types. This report specifically describes the synthesis and characterization of cationic Fe(II) chloride complexes supported by the neutral ligands NPi-Pr3 (NPi-Pr3 = [N(CH2CH2P-i-Pr2)3]), NArPi-Pr3 (NArPi-Pr3 = [N(2-diisopropylphosphine-4-methylphenyl)3]), and NSt-Bu3 (NSt-Bu3 = [N(CH2CH2S-t-Bu)3]). The solid-state structures, electrochemistry, and magnetic properties of these complexes are reported. Whereas the NPi-Pr3 and NArPi-Pr3 ligands provide pseudotetrahedral S = 2 ferrous cations [Fe(NPi-Pr3)Cl]PF6 (1[PF6]) and [Fe(NArPi-Pr3)Cl]BPh4 (2[BPh4]) featuring a long Fe—N bond distance, the NSt-Bu3 ligand gives rise to a trigonal bipyramidal structure with a S = 1 ground state and a much shorter Fe–N interaction. The complexes 1[BPh4] and 2[BPh4] can be reduced under CO to give rise to the five-coordinate Fe(I) monocarbonyls [Fe(NPi-Pr3)CO]BPh4 (4[BPh4]) and [Fe(NArPi-Pr3)CO]BPh4 (5[BPh4]). The solid-state structures and electrochemistry of 4[BPh4] and 5[BPh4] are described, as is the EPR spectrum of 4[BPh4]. The synthesis and characterization of the hydride–dinitrogen complex [Fe(NPi-Pr3)(N2)(H)]PF6 (6[PF6]) has also been accomplished and its properties are also reported.Key words: nitrogenase, iron, polydentate phosphines, thioether ligands, N2 chemistry, nitrogen, Fe(I).

A Highly Emissive Cu2N2 Diamond Core Complex Supported by a [PNP]- Ligand

A Cu2N2 diamond core structure, {(PNP)CuI}2 (2), supported by a [PNP]- ligand (1) ([PNP]- = bis(2-(diisobutylphosphino)phenyl)amide) has been prepared. 2 is highly emissive at ambient temperature in both the solid and solution states and is characterized by a relatively long-lived excited state (tau > 10 mus) and an unusually high quantum yield (phi > 0.65). These observations are consistent with a low degree of structural reorganization between the ground state of 2 and its excited state *2, and also with a high degree of steric protection of the two copper centers of 2 afforded by the bulky [PNP]- ligand. An estimate for the excited-state reduction potential of *2 (ca. -3.2 V vs Fc+/Fc), and the availability of two well-separated and reversible ground-state redox processes, suggests that bimetallic copper systems of these types may be interesting candidates to consider for photochemically driving multielectron redox transformations.

Amido-bridged Cu2N2 diamond cores that minimize structural reorganization and facilitate reversible redox behavior between a Cu1Cu1 and a class III delocalized Cu1.5Cu1.5 species

A novel Cu(2)N(2) diamond core structure supported by an [SNS](-) ligand (1) ([SNS](-) = bis(2-tert-butylsulfanylphenyl)amido) has been prepared. This dicopper system exhibits a fully reversible one-electron redox process between a reduced Cu(1)Cu(1) complex, [[SNS][Cu]](2) (2), and a class III delocalized Cu(1.5)Cu(1.5) state, [[[SNS][Cu]](2)][B(3,5-(CF(3))(2)C(6)H(3))(4)] (3). Structural snapshots of both redox forms have been obtained to reveal remarkably little overall structural reorganization. The Cu...Cu bond distance nonetheless undergoes an appreciable compression (approximately 0.13 A) upon oxidation, providing a Cu...Cu distance of 2.4724(4) A in the mixed-valence state that is virtually identical to the Cu...Cu distance observed in the reduced form of the Cu(A) site of thiolate-bridged cytochrome c oxidase. Despite the low structural reorganization evident between 2 and 3, the [SNS](-) ligand is quite flexible. For example, square-planar geometries can prevail for divalent copper ions supported by [SNS](-) as evident from the crystal structure of [SNS]CuCl (4). Physical characterization for the mixed valence complex 3 includes electrochemical, magnetic (SQUID), EPR, and optical data. The complex has also been examined by density functional methods. An attempt was made to measure the rate of electron self-exchange k(s) between the Cu(1)Cu(1) and the Cu(1.5)Cu(1.5) complexes 2 and 3 by NMR line-broadening analysis in dichloromethane solution. While the system is certainly in the fast-exchange regime, the exchange process is too fast to be accurately measured by this technique. The value for k(s) can be bracketed with a conservative lower boundary of > or =10(7) M(-1) s(-1), a value that appears to be larger than other low molecular weight copper model complexes for which similar data is available. The unusually large magnitude of k(s) likely reflects the minimal structural reorganization that accompanies Cu(1)Cu(1) <--> Cu(1.5)Cu(1.5) interchange.

Pincer-like amido complexes of platinum, palladium, and nickel

The ligands bis(8-quinolinyl)amine (BQAH, 1), (2-pyridin-2-yl-ethyl)-(8-quinolinyl)amine (2-pyridin-2-yl-ethyl-QAH, 2), o-dimethylaminophenyl(8-quinolinyl)amine (o-(NMe2)Ph-QAH, 3), and 3,5-dimethylphenyl(8-quinolinyl)amine (3,5-Me2Ph-QAH, 4) have been prepared in high yield from aryl halide and amine precursors by palladium-catalyzed coupling reactions. Deprotonation of 1 with nBuLi in toluene affords the lithium amide complex [Li][BQA] (5), whose dimeric solid-state crystal structure is presented. Lithium amide 5 was transmetalated by TlOTf to afford the thallium(I) amido complex [Tl][BQA] (6). An X-ray structural study of 6 shows it to be a 1:1 complex of the BQA ligand and Tl. Entry into the group 10 chemistry of the parent ligand 1 was effected by both protolytic and metathetical strategies. Thus, the divalent chloride complexes (BQA)PtCl (7), (BQA)PdCl (8), and (BQA)NiCl (9) were prepared and fully characterized. An X-ray structural study for each of these three complexes shows them to be well-defined, square-planar complexes in which the auxiliary BQA ligand binds in a planar, eta(3)-fashion. For comparison, the reactivity of ligands 2-4 with (COD)PtCl2 was studied. While reaction with ligand 2 afforded an ill-defined product mixture, ligands 3 and 4 reacted with (COD)PtCl2 to generate the unusual alkyl complexes (o-(NMe2)Ph-QA)Pt(1,2-eta(2)-6-sigma-cycloocta-1,4-dienyl) (10) and (3,5-Me2Ph-QA)Pt(1,2-eta(2)-6-sigma-cycloocta-1,4-dienyl) (11), both of which have been structurally characterized.