Teledermatology in practice: Report of Mayo Clinic experience.

Background: Delivery of dermatologic care through telemedicine was accelerated by the COVID-19 pandemic. We sought to analyze the teledermatology experience across Mayo Clinic's health care system to identify strengths and limitations of teledermatology. Methods: Electronic health records of dermatology televisits were reviewed from multiple U.S. Mayo Clinic sites from January 2020 through January 2021. Results: A total of 13,181 dermatology televisits were conducted in 6468 unique patients. Patients were primarily female (60.2%), and mean age of all patients was 34.1 years. Synchronous / live video conferencing visits were the most common (40.0%) telecare modality. Synchronous / live audio conferencing and asynchronous / store-and-forward visits comprised 33.0% and 27.0% of appointments. In total, 3944 televisits (29.9%) were successfully concluded via a single appointment. An in-person appointment was needed for 1693 patients (26.2%) after their initial televisit. For patients with a single televisit, synchronous / live video conferencing was the most common virtual modality (58.0% vs 32.2% of patients with multiple visits, p < 0.001). Patients needing in-person follow-up visits were slightly older than those who did not (mean [SD], 38.8 [22.3] vs 35.0 [23.6] years; p < 0.001) but without any sex-based difference. Around one-third of patients needed an in-person follow-up visit after their initial asynchronous / store-and-forward visit which was higher when compared with synchronous / live audio and video conferencing. Conclusion: Single dermatology televisits effectively managed nearly one-third of patients who did not require in-person follow-up. An initial synchronous / live video conferencing was more likely to yield a single clinical encounter, whereas asynchronous / store-and-forward visits required more in-person follow-up. Future studies are required that focus on dermatology-specific cost, diagnoses, access, quality of care, and outcomes.

The predictive value of imaging studies in evaluating regional lymph node involvement in Merkel cell carcinoma.

BACKGROUND: Merkel cell carcinoma (MCC) is a rare cutaneous neuroendocrine malignancy with high potential for nodal or distant metastatic spread. Little information exists on sensitivity and specificity of various imaging techniques when compared with the gold standard of histopathologic evaluation of the lymph node basin. OBJECTIVE: We sought to further understand the value of various imaging modalities in the staging and initial workup of patients with MCC. METHODS: Of 240 patients with primary MCC evaluated between 1981 and 2008, 99 had diagnostic imaging at initial presentation with biopsy-proven cutaneous MCC and had histopathologic nodal evaluation within 4 weeks of the initial scan. We conducted a retrospective chart review of these identified patients. RESULTS: Computed tomography (n = 69) demonstrated a sensitivity of 47%, specificity of 97%, positive predictive value of 94%, and negative predictive value of 68% in detecting nodal basin involvement. Fluorine-18-fluorodeoxyglucose positron emission tomography scan (n = 33) demonstrated a sensitivity of 83%, specificity of 95%, positive predictive value of 91%, and negative predictive value of 91% in detecting nodal basin involvement. Magnetic resonance imaging (n = 10) demonstrated a sensitivity of 0%, specificity of 86%, positive predictive value of 0%, and negative predictive value of 67% in detecting nodal basin involvement. LIMITATIONS: This was a retrospective study with small sample size. CONCLUSION: Use of fluorine-18-fluorodeoxyglucose positron emission tomography in the evaluation of a regional lymph node basin in primary MCC is significantly more sensitive and equally specific when compared with traditional computed tomography. Both fluorine-18-fluorodeoxyglucose positron emission tomography and computed tomography are more sensitive than clinical examination alone.

Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample.

BACKGROUND: Accurate detection of somatic mutations is challenging but critical in understanding cancer formation, progression, and treatment. We recently proposed NeuSomatic, the first deep convolutional neural network-based somatic mutation detection approach, and demonstrated performance advantages on in silico data. RESULTS: In this study, we use the first comprehensive and well-characterized somatic reference data sets from the SEQC2 consortium to investigate best practices for using a deep learning framework in cancer mutation detection. Using the high-confidence somatic mutations established for a cancer cell line by the consortium, we identify the best strategy for building robust models on multiple data sets derived from samples representing real scenarios, for example, a model trained on a combination of real and spike-in mutations had the highest average performance. CONCLUSIONS: The strategy identified in our study achieved high robustness across multiple sequencing technologies for fresh and FFPE DNA input, varying tumor/normal purities, and different coverages, with significant superiority over conventional detection approaches in general, as well as in challenging situations such as low coverage, low variant allele frequency, DNA damage, and difficult genomic regions.

Personalized genome assembly for accurate cancer somatic mutation discovery using tumor-normal paired reference samples.

BACKGROUND: The use of a personalized haplotype-specific genome assembly, rather than an unrelated, mosaic genome like GRCh38, as a reference for detecting the full spectrum of somatic events from cancers has long been advocated but has never been explored in tumor-normal paired samples. Here, we provide the first demonstrated use of de novo assembled personalized genome as a reference for cancer mutation detection and quantifying the effects of the reference genomes on the accuracy of somatic mutation detection. RESULTS: We generate de novo assemblies of the first tumor-normal paired genomes, both nuclear and mitochondrial, derived from the same individual with triple negative breast cancer. The personalized genome was chromosomal scale, haplotype phased, and annotated. We demonstrate that it provides individual specific haplotypes for complex regions and medically relevant genes. We illustrate that the personalized genome reference not only improves read alignments for both short-read and long-read sequencing data but also ameliorates the detection accuracy of somatic SNVs and SVs. We identify the equivalent somatic mutation calls between two genome references and uncover novel somatic mutations only when personalized genome assembly is used as a reference. CONCLUSIONS: Our findings demonstrate that use of a personalized genome with individual-specific haplotypes is essential for accurate detection of the full spectrum of somatic mutations in the paired tumor-normal samples. The unique resource and methodology established in this study will be beneficial to the development of precision oncology medicine not only for breast cancer, but also for other cancers.

Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies.

BACKGROUND: The cancer genome is commonly altered with thousands of structural rearrangements including insertions, deletions, translocation, inversions, duplications, and copy number variations. Thus, structural variant (SV) characterization plays a paramount role in cancer target identification, oncology diagnostics, and personalized medicine. As part of the SEQC2 Consortium effort, the present study established and evaluated a consensus SV call set using a breast cancer reference cell line and matched normal control derived from the same donor, which were used in our companion benchmarking studies as reference samples. RESULTS: We systematically investigated somatic SVs in the reference cancer cell line by comparing to a matched normal cell line using multiple NGS platforms including Illumina short-read, 10X Genomics linked reads, PacBio long reads, Oxford Nanopore long reads, and high-throughput chromosome conformation capture (Hi-C). We established a consensus SV call set of a total of 1788 SVs including 717 deletions, 230 duplications, 551 insertions, 133 inversions, 146 translocations, and 11 breakends for the reference cancer cell line. To independently evaluate and cross-validate the accuracy of our consensus SV call set, we used orthogonal methods including PCR-based validation, Affymetrix arrays, Bionano optical mapping, and identification of fusion genes detected from RNA-seq. We evaluated the strengths and weaknesses of each NGS technology for SV determination, and our findings provide an actionable guide to improve cancer genome SV detection sensitivity and accuracy. CONCLUSIONS: A high-confidence consensus SV call set was established for the reference cancer cell line. A large subset of the variants identified was validated by multiple orthogonal methods.

Atypical fibroxanthoma in the setting of chronic lymphocytic leukemia and other non-Hodgkin lymphomas.

BACKGROUND: Atypical fibroxanthoma (AFX) is a rare cutaneous malignancy of older adults. Little is known about the behavior of AFX in the setting of chronic lymphocytic leukemia (CLL) and non-Hodgkin lymphoma (NHL). OBJECTIVE: To further understand the development, characteristics, and behavior of AFX in the setting of concomitant CLL and other types of NHL. METHODS AND MATERIALS: Study approval was obtained from the Mayo Clinic Institutional Review Board. The master diagnosis index was queried from January 1, 1980, through December 31, 2008, to identify patients with AFX and CLL or other types of NHL. A retrospective chart review was conducted. RESULTS: Ten patients were identified with AFX and NHL. These patients did not show a greater risk of recurrence, metastasis, or death than that found in previous case reports. Of these 10 patients, four had AFX and CLL. The outcomes of these patients were no different from those of patients with AFX and other types of lymphoma. CONCLUSIONS: AFX did not demonstrate aggressive features such as recurrence or metastasis in patients with concomitant CLL or other NHL. More studies are needed to definitively characterize the behavior of AFX in this patient population.

Unusual cutaneous manifestations of B-cell chronic lymphocytic leukemia.

BACKGROUND: B-cell chronic lymphocytic leukemia (B-CLL) is a low-grade lymphoproliferative disorder with characteristic histomorphologic features and an identifiable immunophenotype. The skin can be involved in the context of known disease, but cutaneous signs are rarely the presenting findings. OBJECTIVE: Evaluation of unusual clinical cutaneous presentations of B-CLL. METHODS: We conducted a retrospective case series analysis of 3 patients with unusual cutaneous clinicopathologic presentations of B-cell chronic lymphocytic leukemia, including erythematous plaques, angiomatosis/telangiectasia, and erosive skin changes, respectively, without a previous clinical history of chronic lymphocytic lymphoma. Main outcome measures were clinical cutaneous presentations and histopathologic results in the diagnosis of underlying disease. RESULTS: In the 3 cases, lesion locations were the lower cheek, lower extremity, and penis (groin region). Histomorphologic testing showed mild to dense perivascular and periadnexal lymphoid aggregates throughout the dermis and extending into the panniculus, consistent with B-CLL. The diagnosis was confirmed with immunohistochemical studies that showed coexpression of CD5 and CD20 in the neoplastic lymphocytic infiltrate. LIMITATIONS: None. CONCLUSION: Cutaneous manifestations are an uncommon presentation of subclinical B-CLL. Cutaneous changes were the presenting features of underlying lymphoma in all 3 cases, highlighting the importance of maintaining a high index of suspicion for a lymphoproliferative process in cases with unusual or atypical clinicopathologic features. Additional investigations into the behavior of B-CLL in the skin may elucidate further the evolution of cutaneous lesions in this disease.