Advances in next-generation sequencing and emerging technologies for hematologic malignancies

Innovations in molecular diagnostics have often evolved through the study of hematologic malignancies. Examples include the pioneering characterization of the Philadelphia chromosome by cytogenetics in the 1970s, the implementation of polymerase chain reaction for high-sensitivity detection and monitoring of mutations and, most recently, targeted next- generation sequencing to drive the prognostic and therapeutic assessment of leukemia. Hematologists and hematopath- ologists have continued to advance in the past decade with new innovations improving the type, amount, and quality of data generated for each molecule of nucleic acid. In this review article, we touch on these new developments and discuss their implications for diagnostics in hematopoietic malignancies. We review advances in sequencing platforms and library preparation chemistry that can lead to faster turnaround times, novel sequencing techniques, the development of mobile laboratories with implications for worldwide benefits, the current status of sample types, improvements to quality and reference materials, bioinformatic pipelines, and the integration of machine learning and artificial intelligence into mol- ecular diagnostic tools for hematologic malignancies.

Tumor Mutational Burden Testing in Solid Tumors

A 58-year-old man with diabetes, chronic kidney disease, and JAK2-positive myeloproliferative neoplasm is referred for newly diagnosed oligometastatic prostate cancer with substantial urinary symptoms. What would you do next?

Feature extraction of time series data on functional near-infrared spectroscopy and comparison of deep learning performance for classifying patients with Alzheimer's-related mild cognitive impairment: a post-hoc analysis of a diagnostic interventional trial

OBJECTIVE

This study aimed to define a method of classifying patients with mild cognitive impairment caused by Alzheimer's disease by the retrieval of functional near-infrared spectroscopy (fNIRS) signal characteristics obtained during olfactory stimulation and the validation of deep learning findings.

PATIENTS AND METHODS

Participants were recruited for the study from March 02 and August 30, 2021. A total of 78 participants met the criteria for categorization. The Mini-Mental State Examination and the Seoul Neuropsychological Scale were used to distinguish between patients with mild Alzheimer's disease-related cognitive impairment and healthy controls. fNIRS data received during olfactory stimulation were used to create 1,680 time-series sample values. A total of 150 indices with a p-value ≤ 0.1 were used as deep learning features to construct the result values for 120 models accounting for all conceivable combinations of data ratios.

RESULTS

For this trial, 78 participants were recruited for the original intervention trial. The average accuracy of the 120 deep-learning models for classifying patients with Alzheimer's-related mild cognitive impairment ranged from 0.78 to 0.90. Sensitivity ranged from 0.88 to 0.96 for the 120 models, while specificity ranged from 0.86 to 0.94. The F1 scores ranged from 0.74 to 0.88. At 0.78 to 0.90, the precision and recall were equivalent.

CONCLUSIONS

This trial using a deep-learning model found that the representative value extracted from the time series data of each channel could distinguish between healthy people and patients with mild cognitive impairment caused by Alzheimer's disease.

Ethnic and sex differences in the distributions of body mass index and waist circumference among adults: a binationally representative study in South Korea and the United States

OBJECTIVE

The ethnic and sex differences in the distributions of body mass index (BMI) and waist circumference (WC) among adults are largely unknown. Therefore, we aimed to investigate the percentiles of BMI and WC in groups divided according to age, sex, and ethnicity.

PATIENTS AND METHODS

We conducted a population-based binational study of adults aged ≥20 years based on data from two sources: US National Health and Nutrition Examination Survey (2015 to 2020) and Korea National Health and Nutrition Examination Survey (2016 to 2019).

RESULTS

Weight, height, and WC were measured in 13,144 American adults and 30,191 Korean adults. Overall, BMI increased at younger ages and decreased at older ages, which indicates a reversed U-shaped relationship, and differed in terms of age, sex, and ethnicity. Women in the other Hispanic, non-Hispanic white, non-Hispanic black, and "other ethnic groups" showed a common BMI peak at ages 50-54 years. The patterns of WC distribution were similar to those of BMI distribution.

CONCLUSIONS

In this binational representative study, we found varied distributions of ethnic and sex differences in BMI and WC. Considering the differences in these distributions may help improve individual and personalized treatment strategies.

17-year trends of body mass index, overweight, and obesity among adolescents from 2005 to 2021, including the COVID-19 pandemic: a Korean national representative study

OBJECTIVE

There is a lack of pediatric studies that have analyzed trends in mean body mass index (BMI) and the prevalence of obesity and overweight over a period that includes the mid-stage of the COVID-19 pandemic. Thus, we aimed to investigate trends in BMI, overweight, and obesity among Korean adolescents from 2005 to 2021, including the COVID-19 pandemic.

SUBJECTS AND METHODS

We used data from the Korea Youth Risk Behavior Web-based Survey (KYRBS), which is nationally representative of South Korea. The study included middle- and high-school students between the ages of 12 and 18. We examined trends in mean BMI and prevalence of obesity and/or overweight during the COVID-19 pandemic and compared these to those of pre-pandemic trends in each subgroup by gender, grade, and residential region.

RESULTS

Data from 1,111,300 adolescents (mean age: 15.04 years) were analyzed. The estimated weighted mean BMI was 20.48 kg/m2 (95% CI, 20.46-20.51) between 2005 and 2007, and this was 21.61 kg/m2 (95% CI, 21.54-21.68) in 2021. The prevalence of overweight and obesity was 13.1% (95% CI, 12.9-13.3%) between 2005 and 2007 and 23.4% (95% CI, 22.8-24.0%) in 2021. The mean BMI and prevalence of obesity and overweight have gradually increased over the past 17 years; however, the extent of change in mean BMI and in the prevalence of obesity and overweight during the pandemic was distinctly less than before. The 17-year trends in the mean BMI, obesity, and overweight exhibited a considerable rise from 2005 to 2021; however, the slope during the COVID-19 pandemic (2020-2021) was significantly less prominent than in the pre-pandemic (2005-2019).

CONCLUSIONS

These findings enable us to comprehend long-term trends in the mean BMI of Korean adolescents and further emphasize the need for practical prevention measures against youth obesity and overweight.

Development of a Syphilis-Specific Molecular Assay

Syphilis is a sexually transmitted disease caused by the spirochete Treponema pallidum subspecies pallidum. Rates of infection have been rising for 20 years, with nearly 39,000 cases of primary and secondary syphilis reported in the United States in 2019. Early diagnosis is critical for preventing disease progression and transmission but remains challenging. Dark-field microscopy is laborious and unavailable in most clinical laboratories. Serology, the mainstay of diagnosis and monitoring, may be nonreactive in up to 47% of patients with early primary syphilis. Immunofluorescence and immunohistochemistry can be difficult to interpret due to cross-reactivity and nonspecific staining.

Given these limitations, nucleic acid amplification testing (NAAT) via polymerase chain reaction (PCR) is an attractive diagnostic tool. It offers the possibility of high sensitivity and specificity; detection across a wide variety of specimens; and applicability to early primary lesions, extragenital sites, and late-stage syphilis. However, no FDA-approved T. pallidum NAATs exist, and few commercial laboratory-developed tests are available. Due to this lack, clinicians have turned to broad-range bacterial PCR targeting the 16S rRNA gene offered by our molecular microbiology reference laboratory, particularly for detection in formalin-fixed paraffin-embedded tissue. To understand usage patterns, we searched the laboratory information system, revealing 45 specimens (representing 40 unique patients) in which T. pallidum was detected by this assay. We identified an additional 4 specimens from 2 patients in whom syphilis was suspected. The results of gold-standard testing were available for 19 cases, yielding a positive percent agreement of ~73% and negative percent agreement of 100%. These findings both highlight the utility of a molecular assay and suggest an organism-specific assay could increase sensitivity.

To build on the promise of PCR-based T. pallidum diagnostics, we developed an assay targeting tprCDFI, a 400bp region conserved across four paralogous genes and unique to T. pallidum. We hypothesized that the multiple copies of tprCDFI will increase the assay’s analytical sensitivity as compared with the single-copy tp47 and two-copy 16S rRNA loci. Ten candidate primer pairs were evaluated bioinformatically for species-specificity and five were chosen for empiric testing. Two primer sets successfully detected both synthetic DNA target and gDNA extracted from two clinical isolates and two laboratory strains (Nichols, SS14) of T. pallidum. The analytes were spiked into 50ng of human gDNA to simulate patient matrix. Preliminary experiments showed a limit of detection of 40 or fewer genomes per reaction. Studies are under way to determine analytical sensitivity, specificity, and limit of detection and to compare the performance of the tprCDFI primers with those for 16S rRNA and tp47 genes before proceeding to clinical validation in a variety of pluri- and paucicellular specimens.

Comparison of Cervical Cancer Screen Results on Female-to-Male Transgender Patients With Female Patients

OBJECTIVES

There are limited data on cervical screen results from female-to-male (FTM) transgender patients. Herein, we compiled demographic information and cervical screen testing on FTM transgender patients and compared with age-appropriate controls.

METHODS

A search of our previous and current databases was performed for Papanicolaou (Pap) tests from patients taking testosterone and/or with a diagnosis of gender dysphoria, transsexualism, or transvestism. Patient data were reviewed. Relative risks of abnormal Pap smear and human papillomavirus (HPV) infection were calculated against age-matched controls.

RESULTS

Eighty-nine Pap tests from FTM transgender individuals were identified, with a mean age of 31.3 years (range, 21-60 years). The Pap test diagnoses were distributed as follows: negative for intraepithelial lesion (n = 84, 94.4%), atypical squamous cells of undetermined significance (n = 0), low-grade intraepithelial lesion (n = 4, 4.5%), and high-grade squamous intraepithelial lesion (n = 1, 1.1%). Fifty (56.2%) patients had concurrent high-risk HPV testing with four (8%) positive results. Relative risk was 0.625 (95% confidence interval [CI], 0.25-1.59; P = .32) for an abnormal Pap test and 0.55 (95% CI, 0.19-1.52; P = .24) for HPV compared with 267 age-matched controls. Of note, 13.5% of patients older than 21 years had documentation of never having a prior Pap test in our medical record.

CONCLUSIONS

In our study, FTM transgender individuals were not at a higher or lower risk of HPV infection or abnormal Pap test result compared with women. However, larger studies are needed to support our findings.

A Novel NIPBL-NACC1 Gene Fusion Is Characteristic of the Cholangioblastic Variant of Intrahepatic Cholangiocarcinoma

We report a novel NIPBL-NACC1 gene fusion in a rare primary hepatic neoplasm previously described as the "cholangioblastic variant of intrahepatic cholangiocarcinoma." The 2 index cases were identified within our consultation files as morphologically distinctive primary hepatic neoplasms in a 24-year-old female and a 54-year-old male. The neoplasms each demonstrated varied architecture, including trabecular, organoid, microcystic/follicular, and infiltrative glandular patterns, and biphasic cytology with large, polygonal eosinophilic cells and smaller basophilic cells. The neoplasms had a distinctive immunoprofile characterized by diffuse labeling for inhibin, and patchy labeling for neuroendocrine markers (chromogranin and synaptophysin) and biliary marker cytokeratin 19. RNA sequencing of both cases demonstrated an identical fusion of NIBPL exon 8 to NACC1 exon 2, which was further confirmed by break-apart fluorescence in situ hybridization assay for each gene. Review of a tissue microarray including 123 cases originally diagnosed as well-differentiated neuroendocrine neoplasm at one of our hospitals resulted in identification of a third case with similar morphology and immunophenotype in a 52-year-old male, and break-apart fluorescence in situ hybridization probes confirmed rearrangement of both NIPBL and NACC1. Review of The Cancer Genome Atlas (TCGA) sequencing data and digital images from 36 intrahepatic cholangiocarcinomas (www.cbioportal.org) revealed one additional case with the same gene fusion and the same characteristic solid, trabecular, and follicular/microcystic architectures and biphasic cytology as seen in our genetically confirmed cases. The NIPBL-NACC1 fusion represents the third type of gene fusion identified in intrahepatic cholangiocarcinoma, and correlates with a distinctive morphology described herein.

Pediatric Idiopathic Basal Ganglia Calcification and Spherocytosis With Chromosome 8p11 Deletion

Idiopathic basal ganglia calcification (IBGC), also known as Fahr disease, is a rare neurodegenerative disorder characterized by the accumulation of extensive parenchymal and vascular calcifications in the basal ganglia, with variable calcifications elsewhere in the brain. Typically, IBGC presents with neurologic and psychiatric symptoms in middle-aged adults. Recent genetic studies have identified alterations in 4 genes causing IBGC, including alterations in SLC20A2 on chromosome 8p11.2. Currently, there are no clinical descriptions of patients with IBGC occurring within the context of a complex genetic syndrome. Here, we present a case of pediatric 8p11 deletion with IBGC, hereditary spherocytosis, vitreoretinopathy, and focal cortical dysplasia. We review multiple cases of IBGC with pediatric onset due to SLC20A2 deletion in the literature, and raise the consideration of IBGC in the evaluation of pediatric patients with 8p11.2 deletion syndromes.

The Effect of Total Cost Information on Consumer Treatment Decisions: An Experimental Survey

BACKGROUND

Unrestrained use of expensive, high-risk interventions runs counter to the idea of a limited medical commons.

OBJECTIVE

To examine the effect of displaying the total first-year cost of implanting a left ventricular assist device (LVAD) on a hypothetical treatment decision and whether this effect differs when choosing for oneself versus for another person.

DESIGN

We conducted an online survey in February 2016. The survey described the clinical course of end-stage heart failure and the risks and benefits of an LVAD. Participants were randomized to 1 of 4 scenarios, which varied by patient identity (oneself versus another person) and description of total cost.

MEASUREMENTS

This study measured acceptance of LVAD implantation. Reasoning and attitudes were secondarily explored.

RESULTS

We received 1211 valid responses. The mean age was 38.3 y (±12.8); 53.5% were female and 84.4% were white. Participants were more likely to accept an LVAD when shown the total cost (66.2% v. 58.0%, P = 0.003) or when choosing for another (68.0 % v. 56.4%, P < 0.001). Open-ended responses indicated that acceptors wanted to extend survival while decliners feared poor quality of life with LVAD therapy. Acceptors and decliners agreed that consumers can help lower the cost of health care, but decliners were more likely to consider cost when making health care decisions ( P < 0.001).

LIMITATIONS

Limitations include the use of a hypothetical scenario, the use of paid participants, and differences between the respondents and the typical patient facing an LVAD decision.

CONCLUSIONS

In this sample, being shown the total cost increased the likelihood of accepting an expensive, high-risk treatment. The results question how well consumers understand the relationship between expensive treatments and the commons.

Beyond the Chief Complaint: Our Patients' Worries

Fourth-year medical students at the University of Colorado School of Medicine distributed cards to patients in the emergency department asking, "What Worries You Most?" The patients' responses provided insight about their most pressing concerns, often unrelated to their "chief complaints."

Lung cancer: current therapies and new targeted treatments

Lung cancer is the most frequent cause of cancer-related deaths worldwide. Every year, 1·8 million people are diagnosed with lung cancer, and 1·6 million people die as a result of the disease. 5-year survival rates vary from 4-17% depending on stage and regional differences. In this Seminar, we discuss existing treatment for patients with lung cancer and the promise of precision medicine, with special emphasis on new targeted therapies. Some subgroups, eg-patients with poor performance status and elderly patients-are not specifically addressed, because these groups require special treatment considerations and no frameworks have been established in terms of new targeted therapies. We discuss prevention and early detection of lung cancer with an emphasis on lung cancer screening. Although we acknowledge the importance of smoking prevention and cessation, this is a large topic beyond the scope of this Seminar.

The University of California, Irvine experience with tomotherapy using the Peacock system

Our institutional experience using the Peacock system for intensity-modulated radiation therapy (IMRT) is summarized. Over 100 patients were treated using this system, which is fitted to a Clinac 600C linac. Both cranial and extracranial lesions have been treated using this modality. Immobilization is achieved either with the Talon system for cranial sites or an Aquaplast cast. Target volumes up to 500 cm3 have been treated. Multiple lesions (up to 3) were treated in one setup. The range of dose/fractionation schemes used was 15 Gy/1 fx (radiosurgical treatment) - 80 Gy/40 fx. Dose validation studies were carried out using film and ion chamber dosimetry in a specially designed phantom. Optimal dose distributions were attainable using inverse treatment planning for IMRT delivery. These were found to encompass the target volumes accurately using dose validation phantom studies. Immobilization methods used were accurate to within 1 mm, as evidenced by daily portal films. IMRT using the Peacock system offers the advantage of delivery of conformal therapy to high doses safely and accurately. This provides the opportunity for dose escalation studies, retreatment of previously treated tumors, as well as treating multiple targets in one setup. The system may be fitted to a conventional linac without major modifications.