Unusual suspects in hereditary melanoma: POT1, POLE, BAP1.

Systematic literature searches on POT1/POLE/BAP1 found that limited skin phenotypic characteristics have been documented in mutation carriers; 248 variants were annotated, and high-cluster variant regions associated with cutaneous melanoma were found in all three genes. Genotype-phenotype correlations can be used to identify patient disease predisposition based on mutation position and cluster regions.

POT1 and multiple primary melanomas: the dermatological phenotype.

POT1 is the second most frequently reported gene (after CDKN2A) in familial melanoma. Pathogenic variants are associated with earlier onset and/or multiple primary melanomas (MPMs). To date, POT1 phenotypical reports have been largely restricted to associated malignancies, and description of the dermatological landscape has been limited. We identified 10 variants in n=18 of 384 (4.7%) unrelated individuals (n=13 MPMs; n=5 single primary melanomas) of European ancestry. Five variants were rare (minor allele frequency <0.001) or novel (two loss-of-function (LOF), one splice acceptor and two missense) and were predicted to be functionally significant, in five unrelated probands with MPMs (≥3 melanomas). We performed three-dimensional total body photography on both individuals with confirmed pathogenic LOF variants to characterise the dermatological phenotype. Total body naevus counts (≥2 mm diameter) were significantly higher (p=7.72×10-12) in carriers compared with a control population. Majority of naevi were on the probands' back and lower limb regions, where only mild to moderate ultraviolet (UV) damage was observed. Conversely, the head/neck region, where both probands exhibited severe UV damage, had comparably fewer naevi. We hypothesise that carriage of functionally significant POT1 variants is associated with increased naevus counts generally, and naevi >5 mm in diameter specifically and the location of these are independent of UV damage.

The MC1R r allele does not increase melanoma risk in MITF E318K carriers.

BACKGROUND: Population-wide screening for melanoma is not cost-effective, but genetic characterization could facilitate risk stratification and targeted screening. Common Melanocortin-1 receptor (MC1R) red hair colour (RHC) variants and Microphthalmia-associated transcription factor (MITF) E318K separately confer moderate melanoma susceptibility, but their interactive effects are relatively unexplored. OBJECTIVES: To evaluate whether MC1R genotypes differentially affect melanoma risk in MITF E318K+ vs. E318K- individuals. MATERIALS AND METHODS: Melanoma status (affected or unaffected) and genotype data (MC1R and MITF E318K) were collated from research cohorts (five Australian and two European). In addition, RHC genotypes from E318K+ individuals with and without melanoma were extracted from databases (The Cancer Genome Atlas and Medical Genome Research Bank, respectively). χ2 and logistic regression were used to evaluate RHC allele and genotype frequencies within E318K+/- cohorts depending on melanoma status. Replication analysis was conducted on 200 000 general-population exomes (UK Biobank). RESULTS: The cohort comprised 1165 MITF E318K- and 322 E318K+ individuals. In E318K- cases MC1R R and r alleles increased melanoma risk relative to wild type (wt), P < 0.001 for both. Similarly, each MC1R RHC genotype (R/R, R/r, R/wt, r/r and r/wt) increased melanoma risk relative to wt/wt (P < 0.001 for all). In E318K+ cases, R alleles increased melanoma risk relative to the wt allele [odds ratio (OR) 2.04 (95% confidence interval 1.67-2.49); P = 0.01], while the r allele risk was comparable with the wt allele [OR 0.78 (0.54-1.14) vs. 1.00, respectively]. E318K+ cases with the r/r genotype had a lower but not significant melanoma risk relative to wt/wt [OR 0.52 (0.20-1.38)]. Within the E318K+ cohort, R genotypes (R/R, R/r and R/wt) conferred a significantly higher risk compared with non-R genotypes (r/r, r/wt and wt/wt) (P < 0.001). UK Biobank data supported our findings that r did not increase melanoma risk in E318K+ individuals. CONCLUSIONS: RHC alleles/genotypes modify melanoma risk differently in MITF E318K- and E318K+ individuals. Specifically, although all RHC alleles increase risk relative to wt in E318K- individuals, only MC1R R increases melanoma risk in E318K+ individuals. Importantly, in the E318K+ cohort the MC1R r allele risk is comparable with wt. These findings could inform counselling and management for MITF E318K+ individuals.

Artificial Intelligence for the Classification of Pigmented Skin Lesions in Populations with Skin of Color: A Systematic Review.

BACKGROUND: While skin cancers are less prevalent in people with skin of color, they are more often diagnosed at later stages and have a poorer prognosis. The use of artificial intelligence (AI) models can potentially improve early detection of skin cancers; however, the lack of skin color diversity in training datasets may only widen the pre-existing racial discrepancies in dermatology. OBJECTIVE: The aim of this study was to systematically review the technique, quality, accuracy, and implications of studies using AI models trained or tested in populations with skin of color for classification of pigmented skin lesions. METHODS: PubMed was used to identify any studies describing AI models for classification of pigmented skin lesions. Only studies that used training datasets with at least 10% of images from people with skin of color were eligible. Outcomes on study population, design of AI model, accuracy, and quality of the studies were reviewed. RESULTS: Twenty-two eligible articles were identified. The majority of studies were trained on datasets obtained from Chinese (7/22), Korean (5/22), and Japanese populations (3/22). Seven studies used diverse datasets containing Fitzpatrick skin type I-III in combination with at least 10% from black Americans, Native Americans, Pacific Islanders, or Fitzpatrick IV-VI. AI models producing binary outcomes (e.g., benign vs. malignant) reported an accuracy ranging from 70% to 99.7%. Accuracy of AI models reporting multiclass outcomes (e.g., specific lesion diagnosis) was lower, ranging from 43% to 93%. Reader studies, where dermatologists' classification is compared with AI model outcomes, reported similar accuracy in one study, higher AI accuracy in three studies, and higher clinician accuracy in two studies. A quality review revealed that dataset description and variety, benchmarking, public evaluation, and healthcare application were frequently not addressed. CONCLUSIONS: While this review provides promising evidence of accurate AI models in populations with skin of color, the majority of the studies reviewed were obtained from East Asian populations and therefore provide insufficient evidence to comment on the overall accuracy of AI models for darker skin types. Large discrepancies remain in the number of AI models developed in populations with skin of color (particularly Fitzpatrick type IV-VI) compared with those of largely European ancestry. A lack of publicly available datasets from diverse populations is likely a contributing factor, as is the inadequate reporting of patient-level metadata relating to skin color in training datasets.

Response to 'The essential role of dermatology publications in enhancing professional diversity, equity and inclusion'.

LINKED ARTICLE: Burgin et al. Br J Dermatol 2021; 185:473-4.

Anatomic Distribution of Cherry Angiomas in the General Population.

BACKGROUND: Cherry angiomas are common benign vascular skin lesions of unknown aetiology, found largely on the trunk. However, their exact anatomic distribution besides their truncal predisposition, and how they manifest in the general population, has not been characterised. METHODS: Three-dimensional (3D) total body imaging was obtained from 163 adult participants of a general population cohort study in Brisbane, Australia. Demographic, phenotypic, and sun behaviour characteristics were collected using a standard questionnaire along with history of melanoma and keratinocyte cancers. Cherry angiomas were identified using an automated classification algorithm with a sensitivity of 87% and a specificity of 99%, developed specifically for this study population. RESULTS: The 3D total body images of 163 participants were analysed. Participants had a median age of 57 years and 61% were male. On average, males had more angiomas than females (median of 16 vs. 12) and the number and size of cherry angiomas increased with age. In addition to male sex and age, an increase in angiomas was associated with Caucasian ancestry other than British/Irish only, fair skin colour opposed to medium/olive, having green/hazel eyes compared to blue/grey, and personal history of melanoma. The most common site for cherry angiomas was the front trunk, followed by the back. Interestingly, although males had more angiomas overall, females had more angiomas on the legs. CONCLUSION: Describing the distribution of cherry angiomas by body site is an important step towards further understanding of the aetiology of angiomas. While personal history of melanoma is associated with an increased number of cherry angiomas, whether this association is prognostic, co-occurs with development of melanoma, or is merely fortuitous requires further investigation.

Development of a Checklist Tool to Assess the Quality of Skin Lesion Images Acquired by Consumers Using Sequential Mobile Teledermoscopy.

BACKGROUND: Mobile teledermoscopy is an emerging technology that involves imaging and digitally sending dermoscopic images of skin lesions to a clinician for assessment. High-quality, consistent images are required for accurate telediagnoses when monitoring lesions over time. To date there are no tools to assess the quality of sequential images taken by consumers using mobile teledermoscopy. The purpose of this study was to develop a tool to assess the quality of images acquired by consumers. METHODS: Participants imaged skin lesions that they felt were concerning at baseline, 1-, and 2-months. A checklist to assess the quality of consumer sequential imaging of skin lesions was developed based on the International Skin Imaging Collaboration guidelines. A scale was implemented to grade the quality of the images: 0 (low) to 18 (very high). Intra- and inter-reliability of the checklist was assessed using Bland-Altman analysis. Using this checklist, the consistency with which 85 sets of images were scored by 2 evaluators were compared using Kappa statistics. Items with a low Kappa value <0.4 were removed. RESULTS: After reliability testing, 5 of the items were removed due to low Kappa values (<0.4) and the final checklist included 13 items surveying: lesion selection; image orientation; lighting; field of view; focus and depth of view. Participants had a mean age of 41 years (range 19-73), and 67% were female. Most participants (84%, n = 71/85) were able to select and image the correct lesion over time for both the dermoscopic and overview images. Younger participants (<40 years old) scored significantly higher (8.1 ± 2.1) on the imaging checklist compared to older participants (7.1 ± 2.4; p = 0.037). Participants had most difficulty with consistent image orientation. CONCLUSIONS: This checklist could be used as a triage tool to filter images acquired by consumers prior to telediagnosis evaluation, which would improve the efficiency and accuracy of teledermatology and teledermoscopy processes. It may also be used to provide feedback to the consumers to improve image acquisition over time.

The Additive Value of 3D Total Body Imaging for Sequential Monitoring of Skin Lesions: A Case Series.

BACKGROUND: Timely diagnosis is the cornerstone of melanoma morbidity and mortality reduction. 2D total body photography and dermoscopy are routinely used to assist with early detection of skin malignancies. Polarized 3D total body photography is a novel technique that enables fast image acquisition of almost the entire skin surface. We aimed to determine the added value of 3D total body photography alongside dermoscopy for monitoring cutaneous lesions. METHODS: Lesion images from high-risk individuals were assessed for long-term substantial changes via dermoscopy and 3D total body photography. Three case studies are presented demonstrating how 3D total body photography may enhance lesion analysis alongside traditional dermoscopy. RESULTS: 3D total body photography can assist clinicians by presenting cutaneous lesions in their skin ecosystem, thereby providing additional clinical context and enabling a more holistic assessment to aid dermoscopy interpretation. For lesion cases where previous dermoscopy is unavailable, corresponding 3D images can substitute for baseline dermoscopy. Additionally, 3D total body photography is not susceptible to artificial stretch artefacts. CONCLUSION: 3D total body photography is valuable alongside dermoscopy for monitoring cutaneous lesions. Furthermore, it is capable of surveilling almost the entire skin surface, including areas not traditionally monitored by sequential imaging.

Reproducible Naevus Counts Using 3D Total Body Photography and Convolutional Neural Networks.

BACKGROUND: The number of naevi on a person is the strongest risk factor for melanoma; however, naevus counting is highly variable due to lack of consistent methodology and lack of inter-rater agreement. Machine learning has been shown to be a valuable tool for image classification in dermatology. OBJECTIVES: To test whether automated, reproducible naevus counts are possible through the combination of convolutional neural networks (CNN) and three-dimensional (3D) total body imaging. METHODS: Total body images from a study of naevi in the general population were used for the training (82 subjects, 57,742 lesions) and testing (10 subjects; 4,868 lesions) datasets for the development of a CNN. Lesions were labelled as naevi, or not ("non-naevi"), by a senior dermatologist as the gold standard. Performance of the CNN was assessed using sensitivity, specificity, and Cohen's kappa, and evaluated at the lesion level and person level. RESULTS: Lesion-level analysis comparing the automated counts to the gold standard showed a sensitivity and specificity of 79% (76-83%) and 91% (90-92%), respectively, for lesions ≥2 mm, and 84% (75-91%) and 91% (88-94%) for lesions ≥5 mm. Cohen's kappa was 0.56 (0.53-0.59) indicating moderate agreement for naevi ≥2 mm, and substantial agreement (0.72, 0.63-0.80) for naevi ≥5 mm. For the 10 individuals in the test set, person-level agreement was assessed as categories with 70% agreement between the automated and gold standard counts. Agreement was lower in subjects with numerous seborrhoeic keratoses. CONCLUSION: Automated naevus counts with reasonable agreement to those of an expert clinician are possible through the combination of 3D total body photography and CNNs. Such an algorithm may provide a faster, reproducible method over the traditional in person total body naevus counts.

Breast cancer polygenic risk scores: a 12-month prospective study of patient reported outcomes and risk management behavior.

PURPOSE: To prospectively assess patient reported outcomes and risk management behavior of women choosing to receive (receivers) or decline (decliners) their breast cancer polygenic risk score (PRS). METHODS: Women either unaffected or affected by breast cancer and from families with no identified pathogenic variant in a breast cancer risk gene were invited to receive their PRS. All participants completed a questionnaire at study enrollment. Receivers completed questionnaires at two weeks and 12 months after receiving their PRS, and decliners a second questionnaire at 12 months post study enrollment. RESULTS: Of the 208 participants, 165 (79%) received their PRS. Among receivers, there were no changes in anxiety or distress following testing. However, compared to women with a low PRS, those with a high PRS reported greater genetic testing-specific distress, perceived risk, decisional regret, and less genetic testing-positive response. At 12 months, breast screening and uptake of risk-reducing strategies were consistent with current Australian guidelines of breast cancer risk management. Reasons for declining PRS included being unable to attend the appointment in person and concerns over potential emotional response. CONCLUSION: The outcomes of the study provide insight into women's responses to receiving PRS and highlight the issues that need to be addressed in the associated model of genetic counseling.

An Australian tertiary hospital analysis of outpatient dermatology clinical and demographic characteristics.

OBJECTIVES: Literature on dermatology outpatient demographic and clinical data is limited, and the few studies on this topic are mainly conducted overseas, with medical systems and case mix different to Australia. This study presents demographic data relating to dermatology public outpatient referrals to a tertiary hospital in Brisbane, Australia, and determines what additional structured data should be collected to formulate and evaluate initiatives to address service issues such as referral quality, triage process and wait times. METHODS: A four-year retrospective audit was undertaken, summarising all referrals (n = 7140) and clinical dermatology encounters (n = 53 844) between January 2016 and December 2019 at Princess Alexandra Hospital (PAH), the largest hospital in Metro South Health (MSH), serving a population of one million. PAH has one of the two largest public dermatology clinics in Queensland and is the only dermatology service within MSH. RESULTS: Patient demographic data, wait time by triage category, referral rates over time and encounter durations were collected. Structured diagnostic data (e.g. ICD-10 coding) of the provisional diagnosis, comorbidities, medications and the final diagnosis are not collected in a structured format and would be a valuable addition. CONCLUSIONS: The clinical burden of public dermatology is increasing. Both collection and analysis of structured data pertaining to the referrals and encounters are important to help formulate, implement and evaluate initiatives that aim to improve health service provision in this area.

Epidemic surveillance in a low resource setting: lessons from an evaluation of the Solomon Islands syndromic surveillance system, 2017.

BACKGROUND: Solomon Islands is one of the least developed countries in the world. Recognising that timely detection of outbreaks is needed to enable early and effective response to disease outbreaks, the Solomon Islands government introduced a simple syndromic surveillance system in 2011. We conducted the first evaluation of the system and the first exploration of a national experience within the broader multi-country Pacific Syndromic Surveillance System to determine if it is meeting its objectives and to identify opportunities for improvement. METHODS: We used a multi-method approach involving retrospective data collection and statistical analysis, modelling, qualitative research and observational methods. RESULTS: We found that the system was well accepted, highly relied upon and designed to account for contextual limitations. We found the syndromic algorithm used to identify outbreaks was moderately sensitive, detecting 11.8% (IQR: 6.3-25.0%), 21.3% (IQR: 10.3-36.8%), 27.5% (IQR: 12.8-52.3%) and 40.5% (IQR: 13.5-65.7%) of outbreaks that caused small, moderate, large and very large increases in case presentations to health facilities, respectively. The false alert rate was 10.8% (IQR: 4.8-24.5%). Rural coverage of the system was poor. Limited workforce, surveillance resourcing and other 'upstream' health system factors constrained performance. CONCLUSIONS: The system has made a significant contribution to public health security in Solomon Islands, but remains insufficiently sensitive to detect small-moderate sized outbreaks and hence should not be relied upon as a stand-alone surveillance strategy. Rather, the system should sit within a complementary suite of early warning surveillance activities including event-based, in-patient- and laboratory-based surveillance methods. Future investments need to find a balance between actions to address the technical and systems issues that constrain performance while maintaining simplicity and hence sustainability.

A method for near full-length amplification and sequencing for six hepatitis C virus genotypes.

BACKGROUND: Hepatitis C virus (HCV) is a rapidly evolving RNA virus that has been classified into seven genotypes. All HCV genotypes cause chronic hepatitis, which ultimately leads to liver diseases such as cirrhosis. The genotypes are unevenly distributed across the globe, with genotypes 1 and 3 being the most prevalent. Until recently, molecular epidemiological studies of HCV evolution within the host and at the population level have been limited to the analyses of partial viral genome segments, as it has been technically challenging to amplify and sequence the full-length of the 9.6 kb HCV genome. Although recent improvements have been made in full genome sequencing methodologies, these protocols are still either limited to a specific genotype or cost-inefficient. RESULTS: In this study we describe a genotype-specific protocol for the amplification and sequencing of the near-full length genome of all six major HCV genotypes. We applied this protocol to 122 HCV positive clinical samples, and had a successful genome amplification rate of 90%, when the viral load was greater than 15,000 IU/ml. The assay was shown to have a detection limit of 1-3 cDNA copies per reaction. The method was tested with both Illumina and PacBio single molecule, real-time (SMRT) sequencing technologies. Illumina sequencing resulted in deep coverage and allowed detection of rare variants as well as HCV co-infection with multiple genotypes. The application of the method with PacBio RS resulted in sequence reads greater than 9 kb that covered the near full-length HCV amplicon in a single read and enabled analysis of the near full-length quasispecies. CONCLUSIONS: The protocol described herein can be utilised for rapid amplification and sequencing of the near-full length HCV genome in a cost efficient manner suitable for a wide range of applications.

Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells.

Heterogeneity of T cells is a hallmark of a successful adaptive immune response, harnessing the vast diversity of antigen-specific T cells into a coordinated evolution of effector and memory outcomes. The T cell receptor (TCR) repertoire is highly diverse to account for the highly heterogeneous antigenic world. During the response to a virus multiple individual clones of antigen specific CD8+ (Ag-specific) T cells can be identified against a single epitope and multiple epitopes are recognised. Advances in single-cell technologies have provided the potential to study Ag-specific T cell heterogeneity at both surface phenotype and transcriptome levels, thereby allowing investigation of the diversity within the same apparent sub-population. We propose a new method (VDJPuzzle) to reconstruct the native TCRαß from single cell RNA-seq data of Ag-specific T cells and then to link these with the gene expression profile of individual cells. We applied this method using rare Ag-specific T cells isolated from peripheral blood of a subject who cleared hepatitis C virus infection. We successfully reconstructed productive TCRαß in 56 of a total of 63 cells (89%), with double α and double ß in 18, and 7% respectively, and double TCRαß in 2 cells. The method was validated via standard single cell PCR sequencing of the TCR. We demonstrate that single-cell transcriptome analysis can successfully distinguish Ag-specific T cell populations sorted directly from resting memory cells in peripheral blood and sorted after ex vivo stimulation. This approach allows a detailed analysis of the TCR diversity and its relationship with the transcriptional profile of different clones.

Incident Hepatitis C Virus Genotype Distribution and Multiple Infection in Australian Prisons.

Hepatitis C virus (HCV) is a highly diverse pathogen that is classified into seven distinct genotypes. Simultaneous or sequential reinfection with multiple HCV genotypes is recognized in high-risk populations, such as injecting drug users (IDUs). Multiple infection is of clinical concern as different genotypes have various sensitivities to current antiviral therapies. Therefore, a better understanding of the frequency of multiple infection and of the genotypes currently being transmitted is clinically relevant. An Australian cohort of IDUs (n = 123), identified with primary incident infection, was followed for multiple infection by regular HCV RNA testing between 2005 and 2013. A total of 354 samples were tested. Sequencing of primary incident infections revealed that genotype 3a was the most common circulating genotype, followed by genotype 1a. Examination of longitudinally collected samples identified complex patterns of multiple infection, including reinfection and superinfection. In those with multiple infection, there was no apparent evidence of homotypic immunity conferring protection against reinfection of the same subtype. This study revealed frequent multiple infection in a high-risk prisoner cohort, illustrating the complex nature of HCV infection and reinfection and highlighting the need for pan-genotypic antiviral therapies.

Structural characteristics of the optic nerve head influencing human retinal venous pulsations.

The relationship between structural characteristics of the optic nerve head and venous pulsations in the human eye remain unknown. Using photoplethysmographic techniques we investigated whether properties of the human retinal veins and their surrounding structures influence venous pulsation. 448 locations of venous pulsation were analysed from 26 normal human eyes. Green channel densitometry derived from video recordings of venous pulsations were used to generate a map of venous pulsation amplitudes along retinal veins. Optical coherence tomography was used to perform quantitative measurements of tissue characteristics at sites of high and low amplitude points as well as in a second analysis, at maximal amplitude pulsation sites from superior and inferior halves of the eyes. Structural characteristics measured included venous diameter, distance from pulsation point to cup margin, vessel length from pulsation point to vein exit, tissue thickness overlying vein, optic disc diameter and presence of a proximal arteriovenous crossing. Increasing venous pulsation amplitudes were associated with larger applied ophthalmodynamometry force, increasing venous diameter, and decreasing absolute cup margin distance (all p < 0.001). Increasing distance of maximal amplitude pulsation point to cup margin was associated with the presence of a proximal arteriovenous crossing, increasing venous diameter, and decreasing tissue depth (all p ≤ 0.001). Venous diameter and tissue depth alter venous compliance, which is likely to be a major factor determining sites of venous pulsation.

Optimizing donor selection for public cord blood banking: influence of maternal, infant, and collection characteristics on cord blood unit quality.

BACKGROUND: Banked unrelated donor umbilical cord blood (CB) has improved access to hematopoietic stem cell transplantation for patients without a suitably matched donor. In a resource-limited environment, ensuring that the public inventory is enriched with high-quality cord blood units (CBUs) addressing the needs of a diverse group of patients is a priority. Identification of donor characteristics correlating with higher CBU quality could guide operational strategies to increase the yield of banked high-quality CBUs. STUDY DESIGN AND METHODS: Characteristics of 5267 CBUs donated to the Carolinas Cord Blood Bank, a public bank participating in the National Cord Blood Inventory, were retrospectively analyzed. Eligible CBUs, collected by trained personnel, were processed using standard procedures. Routine quality and potency metrics (postprocessing total nucleated cell count [post-TNCC], CD34+, colony-forming units [CFUs]) were correlated with maternal, infant, and collection characteristics. RESULTS: High-quality CBUs were defined as those with higher post-TNCC (>1.25 × 10(9)) with CD34+ and CFUs in the upper quartile. Factors associated with higher CD34+ or CFU content included a shorter interval from collection to processing (<10 hr), younger gestational age (34-37 weeks; CD34+ and CFUs), Caucasian race, higher birthweight (>3500 g), and larger collection volumes (>80 mL). CONCLUSIONS: We describe characteristics identifying high-quality CBUs, which can be used to inform strategies for CBU collection for public banks. Efforts should be made to prioritize collections from larger babies born before 38 weeks of gestation. CBUs should be rapidly transported to the processing laboratory. The lower quality of CBUs from non-Caucasian donors highlights the challenges of building a racially diverse public CB inventory.