Comparison of Optical Genome Mapping With Conventional Diagnostic Methods for Structural Variant Detection in Hematologic Malignancies

Background

Structural variants (SVs) are currently analyzed using a combination of conventional methods; however, this approach has limitations. Optical genome mapping (OGM), an emerging technology for detecting SVs using a single-molecule strategy, has the potential to replace conventional methods. We compared OGM with conventional diagnostic methods for detecting SVs in various hematologic malignancies.

Methods

Residual bone marrow aspirates from 27 patients with hematologic malignancies in whom SVs were observed using conventional methods (chromosomal banding analysis, FISH, an RNA fusion panel, and reverse transcription PCR) were analyzed using OGM. The concordance between the OGM and conventional method results was evaluated.

Results

OGM showed concordance in 63% (17/27) and partial concordance in 37% (10/27) of samples. OGM detected 76% (52/68) of the total SVs correctly (concordance rate for each type of SVs: aneuploidies, 83% [15/18]; balanced translocation, 80% [12/15] unbalanced translocation, 54% [7/13] deletions, 81% [13/16]; duplications, 100% [2/2] inversion 100% [1/1]; insertion, 100% [1/1]; marker chromosome, 0% [0/1]; isochromosome, 100% [1/1]). Sixteen discordant results were attributed to the involvement of centromeric/telomeric regions, detection sensitivity, and a low mapping rate and coverage. OGM identified additional SVs, including submicroscopic SVs and novel fusions, in five cases.

Conclusions

OGM shows a high level of concordance with conventional diagnostic methods for the detection of SVs and can identify novel variants, suggesting its potential utility in enabling more comprehensive SV analysis in routine diagnostics of hematologic malignancies, although further studies and improvements are required.

Association Between Aortic Valve Sclerosis and Clonal Hematopoiesis of Indeterminate Potential

Background

The mechanism and medical treatment target for degenerative aortic valve disease, including aortic stenosis, is not well studied. In this study, we investigated the effect of clonal hematopoiesis of indeterminate potential (CHIP) on the development of aortic valve sclerosis (AVS), a calcified aortic valve without significant stenosis.

Methods

Participants with AVS (valves ≥2 mm thick, high echogenicity, and a peak transaortic velocity of <2.5 m/sec) and an age- and sex-matched control group were enrolled. Twenty-four CHIP genes with common variants in cardiovascular disease were used to generate a next-generation sequencing panel. The primary endpoint was the CHIP detection rate between the AVS and control groups. Inverse-probability treatment weighting (IPTW) analysis was performed to adjust for differences in baseline characteristics.

Results

From April 2020 to April 2022, 187 participants (125 with AVS and 62 controls) were enrolled; the mean age was 72.6±8.5 yrs, and 54.5% were male. An average of 1.3 CHIP variants was observed. CHIP detection, defined by a variant allele frequency (VAF) of ≥0.5%, was similar between the groups. However, the AVS group had larger CHIP clones: 49 (39.2%) participants had a VAF of ≥1% (vs. 13 [21.0%] in the control group; P=0.020), and 25 (20.0%) had a VAF of ≥2% (vs. 4 [6.5%]; P=0.028). AVS is independently associated with a VAF of ≥1% (adjusted odds ratio: 2.44, 95% confidence interval: 1.11-5.36; P=0.027). This trend was concordant and clearer in the IPTW cohort.

Conclusions

Participants with AVS more commonly had larger CHIP clones than age- and sex-matched controls. Further studies are warranted to identify causality between AVS and CHIP.

Investigation of PARP Inhibitor Resistance Based on Serially Collected Circulating Tumor DNA in Patients With BRCA-Mutated Ovarian Cancer

PURPOSE

Patient-specific molecular alterations leading to PARP inhibitor (PARPi) resistance are relatively unexplored. In this study, we analyzed serially collected circulating tumor DNA (ctDNA) from patients with BRCA1/2 mutations who received PARPis to investigate the resistance mechanisms and their significance in postprogression treatment response and survival.

EXPERIMENTAL DESIGN

Patients were prospectively enrolled between January 2018 and December 2021 (NCT05458973). Whole-blood samples were obtained before PARPi administration and serially every 3 months until progression. ctDNA was extracted from the samples and sequenced with a 531-gene panel; gene sets for each resistance mechanism were curated.

RESULTS

Fifty-four patients were included in this analysis. Mutation profiles of genes in pre-PARPi samples indicating a high tumor mutational burden and alterations in genes associated with replication fork stabilization and drug efflux were associated with poor progression-free survival on PARPis. BRCA hypomorphism and reversion were found in 1 and 3 patients, respectively. Among 29 patients with matched samples, mutational heterogeneity increased postprogression on PARPis, showing at least one postspecific mutation in 89.7% of the patients. These mutations indicate non-exclusive acquired resistance mechanisms-homologous recombination repair restoration (28%), replication fork stability (34%), upregulated survival pathway (41%), target loss (10%), and drug efflux (3%). We observed poor progression-free survival with subsequent chemotherapy in patients with homologous recombination repair restoration (P = 0.003) and those with the simultaneous involvement of two or more resistance mechanisms (P = 0.040).

CONCLUSIONS

Analysis of serial ctDNAs highlighted multiple acquired resistance mechanisms, providing valuable insights for improving postprogression treatment and survival.

Copy-number analysis by base-level normalization: An intuitive visualization tool for evaluating copy number variations

Next-generation sequencing (NGS) facilitates comprehensive molecular analyses that help with diagnosing unsolved disorders. In addition to detecting single-nucleotide variations and small insertions/deletions, bioinformatics tools can identify copy number variations (CNVs) in NGS data, which improves the diagnostic yield. However, due to the possibility of false positives, subsequent confirmation tests are generally performed. Here, we introduce Copy-number Analysis by BAse-level NormAlization (CABANA), a visualization tool that allows users to intuitively identify candidate CNVs using the normalized single-base-level read depth calculated from NGS data. To demonstrate how CABANA works, NGS data were obtained from 474 patients with neuromuscular disorders. CNVs were screened using a conventional bioinformatics tool, ExomeDepth, and then we normalized and visualized those data at the single-base level using CABANA, followed by manual inspection by geneticists to filter out false positives and determine candidate CNVs. In doing so, we identified 31 candidate CNVs (7%) in 474 patients and subsequently confirmed all of them to be true using multiplex ligation-dependent probe amplification. The performance of CABANA was deemed acceptable by comparing its diagnostic yield with previous data about neuromuscular disorders. Despite some limitations, we expect CABANA to help researchers accurately identify CNVs and reduce the need for subsequent confirmation testing.

Optical genome mapping identifies clinically relevant genomic rearrangements in prostate cancer biopsy sample

Background

Prostate cancer (PCa) is characterized by complex genomic rearrangements such as the ETS oncogene family fusions, yet the clinical relevance is not well established. While paneled genetic tests of DNA repair genes are recommended in advanced PCa, conventional genomic or cytogenetic tools are not ideal for genome-wide screening of structural variations (SVs) such as balanced translocation due to cost and/or resolution issues.

Methods

In this study, we tested the feasibility of whole-genome optical genomic mapping (OGM), a newly developed platform for genome-wide SV analysis to detect complex genomic rearrangements in consecutive unselected PCa samples from MRI/US-fusion targeted biopsy.

Results

We tested ten samples, and nine (90%) passed quality check. Average mapping rate and coverage depth were 58.1 ± 23.7% and 157.3 ± 97.7×, respectively (mean ± SD). OGM detected copy number alterations such as chr6q13 loss and chr8q12-24 gain. Two adjacent tumor samples were distinguished by inter/intra-chromosomal translocations, revealing that they’re from the same ancestor. Furthermore, OGM detected large deletion of chr13q13.1 accompanied by inter-chromosomal translocation t(13;20)(q13.1;p13) occurring within BRCA2 gene, suggesting complete loss of function.

Conclusion

In conclusion, clinically relevant genomic SVs were successfully detected in PCa samples by OGM. We suggest that OGM can complement panel sequencing of DNA repair genes BRCA1/2 or ATM in high-risk PCa.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12935-022-02728-2.

Diagnostic Performance of Multidetector Computerized Tomography in the Detection of Abdominal Complications Early and Late After Liver Transplantation: A 10-Year Experience

BACKGROUND

Multidetector computerized tomography (MDCT) is considered to be a fast noninvasive diagnostic technique for the evaluation of postoperative complications in patients with liver transplantation (LT). However, its role has not been fully established in the diagnosis for detecting complications after liver transplantation. The aim of this work was to evaluate the diagnostic performance of MDCT for detecting abdominal complications in the early and late periods after LT.

METHODS

We retrospectively enrolled 75 patients who had undergone LT from March 2006 to January 2010, followed by MDCT from March 2006 to November 2017. Patients were divided into 2 groups according to the timing after LT: within the first 3 months (early period) or ≥3 months after LT (late period). We evaluated vascular, biliary, and other complications on MDCT. Angiography, endoscopic retrograde cholangiography, and percutaneous transhepatic cholangiography were used as reference standards.

RESULTS

We initially found 77 complications in 45 patients (60.0%) with the use of MDCT. After comparison with the reference standards, 83 complications were diagnosed in 49 patients (65.3%). Forty-seven complications (34 vascular, 10 biliary, 3 other complications) were diagnosed in 33 patients (44.0%) during the early period, and 36 complications (6 vascular, 20 biliary, 10 other complications) were detected in 27 patients (36.0%) in the late period. The sensitivity, specificity, and diagnostic accuracy of MDCT for diagnosing overall complications were, respectively, 93.6%, 90.2%, and 92.0% in the early period (for vascular complications: 97.1%, 92.6%, and 94.3%,; for biliary complications: 80.0%, 100%, and 97.7%) and 77.8%, 98.1%, and 89.8% in the late period (for vascular complications: 83.3%, 100%, and 98.9%; for biliary complications: 65.0%, 98.6%, and 90.9%).

CONCLUSIONS

Although MDCT in the late period should be interpreted with caution in patients with suspected biliary complication, MDCT is a reliable diagnostic technique for the identification of early and late abdominal complications after LT.

Prognostic significance of CD44s expression in bile duct carcinomas

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Background: CD44 is a surface glycoprotein and has a key role for surface hyaluronan receptor, which is associated with adhesion and metastasis in many solid tumors. There are CD44 standard isoform (CD44s) and ten variant isoforms (CD44v1–10). CD44s and CD44 variant 6 (CD44v6) were evaluated to clarify the applicable prognostic factor in patients with bile duct carcinomas. Methods: A retrospective study was performed in bile duct carcinomas. Immunohistochemical stain was done with primary antibodies for CD44 (Novocastra, Newcastle upon Tyne, UK) and CD44v6 (Novocastra) using automated machine (Vision Biosystems, Mount Waverley, VIC, Australia) and bond polymer detection system with counterstain (Vision Biosystems) in paraffin embedded tissues. The extent of staining categorized as 0% (none), <10% (weak), 10%-50% (moderate), and >50% (strong). Clinical characteristics including age, sex, stage, grade and overall survival were reviewed. Results: Ninety six patients (M:F=35:61) were evaluated and the median age of these patients was 64 years old (37∼86). The rate of overexpression (>10%) of CD44s was 50% and the rate of CD44v6 expression was 16.9%. With median 34.2 months of follow up, the overall survival of total 96 patients was 12.2 months. The Cox proportional hazards test identified CD44s overexpression. (HR:2.379, 95% CI:1.195–4.736, p=0.014) and the stage as prognostic factors. But the expression of CD44v6 (weak vs. moderate to strong, HR:3.983, 95%CI:0.295–1.588, p=0.377) showed no prognostic significance on overall survival. Conclusion: CD44s overexpression can be a poor prognostic marker in bile duct carcinomas. And there is a potential to apply postoperative investigational or aggressive therapy in this poor prognostic group.

No significant financial relationships to disclose.

EGFR mutations and human papillomavirus in squamous cell carcinoma of tongue and tonsil

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Background: Some studies reported the presence of somatic mutation of EGFR in head and neck cancer. Human papillomavirus (HPV) was associated with some types of head and neck cancer. We performed this study to determine clinical significance of EGFR mutation and its association with HPV infection in patients with tongue and tonsil cancer. Methods: We sequenced exons 18–21 of EGFR TK domain and HPV typing was performed using the HPV DNA chip in tissues of patients with tongue and tonsil cancer. Univariate and multivariate analysis was performed. Results: Eighty-one patients were included. We detected EGFR mutation in 10 (12%) patients. Mutation was significantly frequent in never-smoker (21% versus 5%; P = 0.031). The mutation frequency did not differ between tongue and tonsil cancer (12% vs. 13%, respectively; P = 0.978). There was no difference between female and male (12% vs. 14%, respectively; P = 0.754). Eleven of 81 (14%) patients were HPV positive. HPV positivity was more common in young (<60 years) than older (≥60 years) patients (20% vs. 3%, respectively; P = 0.039). Patients with tonsil cancer showed more frequent HPV positivity than tongue cancer (42% vs. 2%, respectively; P < 0.001). There was no association between HPV positivity and EGFR mutation. In terms of disease-free survival, patients with EGFR mutation had better survival independently of stage and primary site (hazard ratio, 0.246; 95% CI, 0.075 to 0.802). Conclusions: We did not find association between EGFR mutation and HPV positivity. Patients with EGFR mutation showed better outcome in tongue and tonsil cancer. These results suggest that EGFR mutation may be a prognostic factor in patients with head and neck cancer.

No significant financial relationships to disclose.

A molecular dynamics computer simulation study of room-temperature ionic liquids. I. Equilibrium solvation structure and free energetics

Solvation in 1-ethyl-3-methylmidazolium chloride and in 1-ethyl-3-methylimidazolium hexafluorophosphate near equilibrium is investigated via molecular dynamics computer simulations with diatomic and benzenelike molecules employed as probe solutes. It is found that electrostriction plays an important role in both solvation structure and free energetics. The angular and radial distributions of cations and anions become more structured and their densities near the solute become enhanced as the solute charge separation grows. Due to the enhancement in structural rigidity induced by electrostriction, the force constant associated with solvent configuration fluctuations relevant to charge shift and transfer processes is also found to increase. The effective polarity and reorganization free energies of these ionic liquids are analyzed and compared with those of highly polar acetonitrile. Their screening behavior of electric charges is also investigated.

A molecular dynamics computer simulation study of room-temperature ionic liquids. II. Equilibrium and nonequilibrium solvation dynamics

The molecular dynamics (MD) simulation study of solvation structure and free energetics in 1-ethyl-3-methylimidazolium chloride and 1-ethyl-3-methylimidazolium hexafluorophosphate using a probe solute in the preceding article [Y. Shim, M. Y. Choi and H. J. Kim, J. Chem. Phys. 122, 044510 (2005)] is extended to investigate dynamic properties of these liquids. Solvent fluctuation dynamics near equilibrium are studied via MD and associated time-dependent friction is analyzed via the generalized Langevin equation. Nonequilibrium solvent relaxation following an instantaneous change in the solute charge distribution and accompanying solvent structure reorganization are also investigated. Both equilibrium and nonequilibrium solvation dynamics are characterized by at least two vastly different time scales--a subpicosecond inertial regime followed by a slow diffusive regime. Solvent regions contributing to the subpicosecond nonequilibrium relaxation are found to vary significantly with initial solvation configurations, especially near the solute. If the solvent density near the solute is sufficiently high at the outset of the relaxation, subpicosecond dynamics are mainly governed by the motions of a few ions close to the solute. By contrast, in the case of a low local density, solvent ions located not only close to but also relatively far from the solute participate in the subpicosecond relaxation. Despite this difference, linear response holds reasonably well in both ionic liquids.

Critical behavior of a strain percolation model for metals

Extensive simulations of a strain percolation model for a deforming metal have been performed to examine its strain behavior. We find that the total strain exhibits critical power-law behavior that is well explained by two-dimensional percolation theory. Near the critical point, most of the strained cells organize themselves around a state having the minimum or at least marginally stable strain regardless of the initial conditions. A strain much greater than the minimum stable strain generally decays to a lower value when transmitted to an unstrained cell. The universal behavior of the total strain in the system is a consequence of the self-organizing character of the strain in the critical cluster. Although the probability distributions for the total strain and cluster size appear to exhibit nonuniversal behavior, this may merely represent a transient response before crossover to a true asymptotic, universal behavior occurs. Other critical aspects of the model are also discussed.

Noise-enhanced temporal association in neural networks

We consider a network of globally coupled neuronal oscillators subject to random force, and investigate numerically dynamic responses to external periodic driving. The order parameter, which measures the overlap between the configuration of the system and embedded patterns, is found to exhibit stochastic resonance behavior, as manifested by the signal-to-noise ratio (SNR). The optimal noise level at which the SNR reaches its maximum is found to depend on the driving frequency. On the other hand, as the randomness in the driving amplitude is increased, the system undergoes a transition from the memory-retrieval state to the mixed-memory one. The noise effects on the temporal-association state in the absence of external periodic driving are also investigated, revealing similar noise-enhanced resonance.

Consumer misperceptions of diet quality

OBJECTIVE

This study compares consumers' self-perceived diet quality with calculated diet quality to assess the degree of consumer misperception regarding one's own diet quality and to identify factors associated with such misperception.

DESIGN

The perceived diet quality was measured by consumers' self-perception of the overall healthfulness of their diet. The calculated diet quality was measured by the Healthy Eating Index, a 10-component indicator of overall diet quality developed from 3 consecutive days of 1-day 24-hour dietary recall and 2-day diet record.

SUBJECTS/SETTINGS

Measures of perceived and calculated diet quality were obtained for a sample of 2862 household meal planners/preparers from the 1989-90 Continuing Survey of Food Intake by Individuals and the Diet and Health Knowledge Survey.

OUTCOME

Dietary misperception was assessed by classifying respondents based on categories of perceived and calculated diet quality into three groups: optimists, realists, and pessimists.

STATISTICAL ANALYSES

Bivariate statistical tests and multivariate logistic regression were used for comparing the characteristics of optimists with the other two groups.

RESULTS

An estimated 40% of the population of household meal planner/preparers were optimists who perceived the quality of their diets to be better than their calculated diet quality. In multivariate analysis, household size, gender, education, smoking status, perceived health status, importance of nutrition in grocery shopping, and belief about the need for dietary change were found to be significant predictors of being optimistic about diet quality. Nutritionists and health professionals need to be aware of this misperception and alert dietary optimists about their false perceptions of diet quality.

Dynamic finite-size scaling of the normalized height distribution in kinetic surface roughening

Using well-known simple growth models, we have studied the dynamic finite-size scaling theory for the normalized height distribution of a growing surface. We find a simple functional form that explains size-dependent behavior of the skewness and kurtosis in the transient regime, and obtain the transient- and long-time values of the skewness and kurtosis for the models. Scaled distributions of the models are obtained, and the shape of each distribution is discussed in terms of the interfacial width, skewness, and kurtosis, and compared with those for other models. Exponents eta(+) and eta(-), which characterize the form of the distribution, are determined from an exponential fitting of scaling functions. Our detailed results reveal that eta(+)+eta(-) approximately 4 for a model obeying usual scaling in contrast to eta(+)+eta(-)<4 with eta(-)=1 for a model exhibiting anomalous scaling as well as multiscaling. Since we obtain eta(+)+eta(-) approximately 4 for a model exhibiting anomalous scaling but no multiscaling, we conclude that the deviation from eta(+)+eta(-) approximately 4 is due to the presence of multiscaling behavior in a model.

Map dynamic ranges versus duration of hearing loss in cochlear implantees

In order to assess the relationship of factors such as age, cause of deafness, use of hearing aids, duration of hearing loss, and age at onset of hearing loss, with the size of map dynamic ranges (DRs), 34 postlingually and 8 prelingually deaf users of the Nucleus cochlear implant system were analyzed according to the sizes of map DRs. Lack of auditory stimulation for a longer period than 10 years might be one of the most important factors associated with a reduced map DR. Use of hearing aids was associated with larger map DRs. Small map DRs were found across a range of age, age at onset, and duration of hearing loss. Cause of deafness did not appear to be related to map DRs.

Arterial windkessel parameter estimation: a new time-domain method

We developed and validated a new, more accurate, and easily applied method for calculating the parameters of the three-element Windkessel to quantitate arterial properties and to investigate ventriculoarterial coupling. This method is based on integrating the governing differential equation of the three-element Windkessel and solving for arterial compliance. It accounts for the interaction between characteristic impedance and compliance, an important phenomenon that has been ignored by previously implemented methods. The new integral method was compared with four previously published methods as well as a new independent linear least-squares analysis, using ascending aortic micromanometric and volumetric flow measurements from eight dogs. The parameters calculated by the new integral method were found to be significantly different from those obtained by the previous methods but did not differ significantly from maximum likelihood estimators obtained by a linear least-squares approach. To assess the accuracy of parameter estimation, pressure and flow waveforms were reconstructed in the time domain by numerically solving the governing differential equation of the three-element Windkessel model. Standard deviations of reconstructed waveforms from the experimental ensemble-averaged waveforms, which solely reflect the relative accuracy of the Windkessel parameters given by the various methods, were calculated. The new integral method invariably yielded the smallest error. These results demonstrate the improved accuracy of our new integral method in estimating arterial parameters of the three-element Windkessel.

Ejection load changes in aortic stenosis. Observations made after balloon aortic valvuloplasty

To investigate complementarity and competitiveness between the intrinsic and extrinsic components of the total left ventricular systolic load, hemodynamic data from 18 elderly subjects with severe aortic stenosis were analyzed before and after balloon dilation of the stenosed aortic valve. Multisensor micromanometric pressure measurements allowed calculation (simplified Bernoulli equation) of the ejection velocity and aortic input impedance spectra. Despite a 32% increase in the aortic valve area (from 0.56 +/- 0.04 to 0.74 +/- 0.05 cm2 [mean +/- SEM], p < 0.01), the peak left ventricular systolic pressure fell by only 12% (from 189 +/- 10 to 167 +/- 8 mm Hg, p < 0.01). This was accompanied by an increase in the impedance at the same cardiac output. In a subset of patients (n = 9) in whom the peak aortic systolic pressure rose after valvuloplasty (from 115 +/- 10 to 128 +/- 12 mm Hg, p < 0.01), a 40% increase in the aortic valve area was accompanied by a marked increase in the aortic input impedance. In this subset, the steady component of the aortic input impedance increased by 24% (from 960 +/- 96 to 1,188 +/- 134 dyne.sec/ml, p < 0.05), and the characteristic impedance increased by 25% (from 106 +/- 13 to 132 +/- 19 dyne.sec/ml, p < 0.05). Because of an increased aortic impedance acutely following the procedure, the total left ventricular systolic load after balloon dilation of the stenotic valve was only slightly decreased despite a significant increase in aortic valve area. This represents an example of complementarity and competitiveness between the intrinsic and extrinsic components of the total systolic ventricular load. It may explain why improvement in left ventricular performance may be modest acutely following balloon aortic valvuloplasty.