The Development of an Infrastructure to Facilitate the Use of Whole Genome Sequencing for Population Health

The clinical use of genomic analysis has expanded rapidly resulting in an increased availability and utility of genomic information in clinical care. We have developed an infrastructure utilizing informatics tools and clinical processes to facilitate the use of whole genome sequencing data for population health management across the healthcare system. Our resulting framework scaled well to multiple clinical domains in both pediatric and adult care, although there were domain specific challenges that arose. Our infrastructure was complementary to existing clinical processes and well-received by care providers and patients. Informatics solutions were critical to the successful deployment and scaling of this program. Implementation of genomics at the scale of population health utilizes complicated technologies and processes that for many health systems are not supported by current information systems or in existing clinical workflows. To scale such a system requires a substantial clinical framework backed by informatics tools to facilitate the flow and management of data. Our work represents an early model that has been successful in scaling to 29 different genes with associated genetic conditions in four clinical domains. Work is ongoing to optimize informatics tools; and to identify best practices for translation to smaller healthcare systems.

POS0731 CLINICAL ASSOCIATIONS OF COGNITIVE DYSFUNCTION IN SYSTEMIC LUPUS ERYTHEMATOSUS (SLE)

Background:

Cognitive symptoms are commonly reported by SLE patients, but the prevalence and clinical associations of cognitive dysfunction (CD) is poorly understood.

Objectives:

To examine the relationship between SLE disease parameters and CD.

Methods:

Patients with SLE were consecutively recruited from 2018-2020. Cognitive assessment was performed using the one-hour conventional neuropsychiatric test battery recommended by the American College of Rheumatology for SLE1. Three binary definitions of CD and seven cognitive test z-scores were included in analysis. Clinical parameters included disease activity (SLEDAI-2K) and damage (SDI). Multivariate regression analysis was performed to determine associations with cognitive endpoints using variables with p <0.1 on univariate testing; likelihood ratio tests were used to select for inclusion from collinear pairs. A subgroup univariate analysis was performed to look for associations with interferon gene signature (IGS) and metabolic indices.

Results:

91 SLE patients and 48 age, sex, and premorbid IQ matched controls were recruited. The median (range) age was 45 (21-64) and median disease duration 13 years (0.2-39). 60% were Caucasian and the rest predominantly Asian, and all had good English proficiency. Prevalence of CD varied based on definition used; 18% had ≥2 cognitive domains ≥2 SD below the healthy control mean, whereas 48% were considered impaired if this threshold was reduced to ≥1.5 SD below. Age and premorbid IQ were significantly associated with multiple cognitive endpoints, and SDI was associated with four endpoints including the most severe definition of CD. Increased parity and past strokes correlated with poorer cognition in two endpoints. In contrast, clinical variables such as SLEDAI, antiphospholipid antibodies and past seizures only correlated with one endpoint each. There were no associations with other antibodies or any medications including glucocorticoids. Subgroup analysis showed univariate associations of CD with increased waist circumference, hypertriglyceridemia and low IGS.

Conclusion:

Clinical associations of CD in SLE vary according to the cognitive domain or impairment definition used. SDI was the disease-related factor most consistently associated with CD, while IGS was negatively and metabolic features positively associated with CD. Studies of CD in SLE should use standardised methods to determine CD.

References:

[1]Liang et al. The American College of Rheumatology nomenclature and case definitions for neuropsychiatric lupus syndromes. Arthritis Rheum. 1999;42(4).

Table 1.

Multivariate Analysis of Clinical Predictors of Cognitive Dysfunction in SLE

Cognitive Dysfunction Definitions1Individual Cognitive Domains (Tests)2 domains-1.5 SD1 domain-2 SD2 domains-2 SDVisual Memory(ROCF recall)Verbal Memory(CVLT 1-5)Verbal Fluency(COWAT FAS)Working Memory(LNS score)Processing Speed(Coding score)Complex attention(TMT B time)Psychomotor Speed(Finger tap)Odds ratio(logistic regression)Coefficient (linear regression)Age1.06*1.06*-0.03*-0.014*-0.03**Premorbid IQ0.89**0.86**0.85*0.056**0.044**0.072**0.028**0.026*0.05**0.017SLEDAI0.860.89Time-adjusted mean SLEDAI0.14**-0.012PGA0.79**0.44SDI1.91*-0.25**-0.15**-0.22**Past stroke or TIA7.9413.19*-0.97**Past seizures-0.65*-0.24Methotrexate-0.23Anti Ro0.22Anti-cardiolipin0.38*Any APLS abs0.037**Parity2.21**-0.05-0.051-0.22**Substance use2.58-0.49*-0.62*

1Impairment defined by number of cognitive domains either 1.5 or 2 SD below healthy control group mean*p value <0.05 **p value <0.005 Abbreviations: SLEDAI - SLE Disease Activity Index, PGA - Physician global assessment, SDI - SLE International Collaborating Clinics Damage Index, TIA - Transient Ischaemic Attack, abs - Antibodies, APLS - Antiphospholipid Syndrome, ROCF - Rey-Ostrrieth Complex Figure Test, CVLT - California Verbal Learning Test, COWAT - Controlled Oral Word Association Test, LNS and Coding - Letter Number Sequencing & Coding subsets of Wechsler Adult Intelligence Scale IV, TMT - Trail Making Test

Acknowledgements:

We would like to acknowledge the patients who contribute to the Australian Lupus Registry and Biobank (ALRB) and participated in this study. The ALRB has received sponsorship from AstraZeneca, UCB and Arthritis Victoria.

Disclosure of Interests:

None declared

Immune related biomarkers in biliary tract cancers (BTC)

e16191

Background: Biliary tract cancers are aggressive tumors with limited treatment options. Several ongoing clinical trials are currently exploring role of immune therapy in advanced BTC. Programmed death-ligand 1 (PD-L1), tumor mutational burden (TMB), and microsatellite instability (MSI) are commonly used immune related-biomarkers. Herein, we analyzed the TMB, MSI and PD-L1 expression in advanced BTC. Methods: We retrospectively evaluated the association of TMB, MSI and PD-L1 expression with survival and related treatment outcomes. Results: The immune mediated biomarkers were reported in a total of 62 BTC patients (pts). The mean age of the pts is 73 (range 32-83) years, with predominant females (59%) and Caucasians (82%). The most common histology noted was intrahepatic cholangiocarcinoma (67%) followed by extrahepatic cholangiocarcinoma (18%) and gallbladder carcinoma (15%). Approximately, 40% received 2 or more lines of therapy while 20% of patients didn’t receive any treatment and over. The treatment regimen included gemcitabine-based regimen (35%), 5FU based regimen (18%), immune therapy (15%) and targeted therapy (6%). The TMB was low in 52 pts (83%), intermediate 7 pts (11%) and high in 2 pts (3%). MSI is stable in 55 pts (89%) and PD-L1 expression is negative in 29 pts (47%) and positive in 23 pts (37%). Conclusions: Our data suggests the BTC’s have in general low TMB, are microsatellite stable and have low PD-L1 expression. The potential prognostic and predictive value of these immune related- biomarkers need to be validated in larger studies.

The Relationship Between Architectural Modularity and Platform Scale Up Performance: The Moderating Effects of Strategic Flexibility and Technology Turbulence

The emergence of digital platforms has had a deep impact on the way firms design and position their products. An open architecture is a key to successfully scale up platforms in terms of usage. Architectural modularity is an important feature that facilitates openness of platforms. Successful scaling of platforms needs a digital infrastructure layer that facilitates collaboration and creation and hence the role of modular systems in the development of platform ecosystems has increased substantially. In this paper, we study the relationship between modular architectures and platform scale up performance from a survey data of managers in the semiconductor industry with 232 data points. The findings from our study show that the scale-up performance of platforms has an inverted U-shaped relationship with modularity. We also find that the strategic flexibility of firms positively moderates this relationship.

The degree of flexibility that system architecture should have is not only an important technical decision but is important from a business perspective as well. Ambiguity in terms of interfaces and the functionality of modules reduces the possibility of ex-ante specification of contracting terms and incentives and monitoring of incentives. The link between architectural modularity and the relationship to performance is important as this enables us to examine questions related to the success of task partitioning at an industry level.

Abstract 5454: A data driven pipeline to detect somatic mutations in oncology

The analysis of Next Generation Sequencing (NGS) data relies on workflows that integrate different bioinformatics tools. Designing workflows that are assay agnostic and have a robust computational framework for result generation in a timely manner is particularly important for clinical applications of NGS. These technologies play an important role in classifying a patient's tumor at a molecular level however, there is still a need to develop workflows that generate consistent mutation profiles for oncology. We developed a bioinformatics tool to analyze DNA and RNA sequencing data in a single pipeline and to specifically detect somatic mutations in oncology clinical workflows. Our automated pipeline report contains extensive quality metrics for each sample and generates a robust mutation annotation and filtration module vital for clinical use. We use data driven filters and algorithms that predict the effectiveness of mutations to filter out mutations of poor quality or mutations without clinical significance. We applied our pipeline to standard cell lines and various cancer FFPE samples acquired from the Intermountain Healthcare Biorepository. Our pipeline successfully processes different mutation classes including Single Nucleotide Variants (SNVs), small (&lt;20 bp) and large (&gt;21 bp) insertions and deletions (InDels), gene fusions, and exon skipping mutations. In addition, we established a reference set that allows us to call Copy Number Variants (CNVs) in a gene panel designed to detect clinically relevant mutations in lung cancers. Comparison of this pipeline to a validated external workflow yield high concordance of clinically significant mutations. We conclude that our pipeline offers a sensitive and specific methodology to analyze DNA and RNA sequencing data to clinically relevant results from low input amplicon-based assays for various solid tumor cancer types.

Citation Format: Katherine Shortt, Christopher Johnson, Archana Ramesh, Tom Neuwerth, Chris Giauque, Sharanya Raghunath. A data driven pipeline to detect somatic mutations in oncology [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5454.

DNA damage repair (DDR) pathway defects in gastrointestinal (GI) malignancies

647

Background: The clinical significance of the genomic alterations associated with DDR pathway in GI tumors (besides MMR defects) is largely unknown. These patients can potentially derive benefit from targeted therapy with poly ADP ribose polymerase (PARP) inhibitors, which have already shown promising activity in ovarian, breast and prostate cancers. In this study, we investigated the frequency and clinical significance of DDR repair defects (other than MMR defects) in GI tumors. Methods: We performed a retrospective analysis of all patients who had tumor next generation sequencing performed between January 2013 and August 2017 on GI cancers harboring DDR pathway defects. Data including demographics, clinical history, and treatment were extracted from patients' records. Results: Of 299 patients with GI tumors sequenced, 35 cases (12%) were noted to have DDR defects. The most commonly mutated genes – 6 (17%) BRCA2, 5 (14%) PALB2, 4 (11%) ATM, 3 (8.6%) BRCA1, 2 (5.7%) each of NBN, MUTYH, ERCC3, PARP1 amplification and 1 (2.8%) each of ERCC2, CDK12, and PARP2 amplification. Two patients had both ATM and BRCA2 mutations. Combination of ATM and MRE11, ATM and BRCA1, BRCA1 and ERCC6, BRCA2 and CDK12 were noted in 1 patient each. Of the 23 patients with available clinical data, the median age at diagnosis was 65 (range 30–85) years with male and female prevalence rates of 60.8% and 39.2%, respectively. Stage at diagnosis was I (n = 3), II (n = 3), III (n = 8), and IV (n = 9). The primary site of tumor was found in 8 (34.8%) colon, 4 (17.4%) liver, 4 (17.4%) pancreas, 2 (8.7%) esophagus, 2 (8.7%) anus, 2 (8.7%) appendix, 1 (4.3%) rectum. Seventeen patients received platinum‐based therapy, 7 were treated with PARP inhibitors and 5 patients received both platinum and PARP inhibitor. Median overall survival from diagnosis for patients with stage I/II was 65.3 months, stage III was 23.1 months, and stage IV was 22.4 months. The median survival of patients treated with olaparib was 24.5 months. Conclusions: DDR pathway defects in GI tumors are uncommon. However, they can potentially be targeted with PARP inhibitors with durable survival. Future clinical trials are warranted to explore the role to PARP inhibitors in these unique subset of patients.

Utility of next-generation sequencing in clinical decision making in hepatocellular carcinoma (HCC)

295

Background: HCC is a heterogeneous disease with diverse genomic alterations. The prior genomic studies have identified common alterations in TERT, P53, WNT pathways. However, most of these alterations are not targetable with current FDA approved targeted agents. In this study, we determine the clinical impact of targeted next generation sequencing in patients with advanced HCC. Methods: We retrospectively assessed all patients with gastrointestinal (GI) malignancies who have undergone next generation sequencing (NGS) between January 2013 and August 2017. The primary endpoint is to determine the frequency of clinically actionable mutations in HCC. Secondary endpoint is to identify number of patients eligible for current FDA approved targeted agents. Results: Of the 299 consecutive GI tumors sequenced, 29 cases were identified as HCC. Clinically actionable mutations were noted in 22 of 29 patients (pts) (76%). Most pts (52%) were found to harbor more than one potentially actionable genetic alterations (n = 15). The common pathways involved: P53 in 9 pts (22%), cell-cycle regulation in 7 pts (17.1%) and mitogen-activated protein kinase in 6 pts (14.6%). Other pathways involved were DNA repair in 4 pts (9.8%), WNT in 3 pts (7.3%), MYC in 3 pts (7.3%), NOTCH in 2 pts (4.9%), HNPCC in 2 pts (4.9%), APC in 2 pts (4.9%), phosphatidylinositol 3-kinase-AKT-mTOR in 1 patient (pt) (2.4%), BRINP in 1 pt (2.4%) and angiogenesis in 1 pt (2.4%). We noted 10 pts (34.5%) harbor alterations that could potentially be targeted with FDA approved treatments such as palbociclib (for CCND1/2 amplification), PARP inhibitors (for DNA repair defects), and immunotherapy (for MMR defects) on precision medicine clinical trials such as TAPUR or MATCH. Conclusions: Mutational profiling using a targeted NGS panel identified clinically actionable alterations in nearly 75% of advanced HCC patients. Almost one third of these patients were potential candidates for current FDA approved treatments. NGS and enrollment in clinical trials should be considered in all fit patients with HCC who had progression on current standard of care treatments.

Cell cycle checkpoint defects in gastrointestinal malignancies

680

Background: Cyclin Dependent Kinases (CDKs) play a significant role in cell cycle regulation. Aberrations involving the cell cycle pathway genes can lead to uncontrolled cell proliferation and genomic instability. These could potentially be targeted with CDK4/6 inhibitors. The frequency and type of these alterations in GI tumors is largely unknown. Methods: We analyzed the frequency of abnormalities in cell cycle genes in patients with diverse GI malignancies (colorectal, liver, pancreas, gastroesophageal, anal, appendix) that underwent next generation sequencing from January 2013 to August 2017. Results: Aberrations in the cell cycle pathway were identified in 33 of 299 (11%) of cancers. The frequency of aberrations was as follows: CDKN2A/B in 10 (30.3%), CCND1 in 7 patients (pts) (21.2%), CCND2 in 2 pts (6%), CEBPA in 2 pts (6%), CDK6 in 2 pts (6%), CDK8 in 2 pts (6%) and CDK2 in 1 (3%). Alteration involving multiple genes of cell cycle noted in 7 patients (21.2%) with combination of CCND1 and CDKN2A being most common combination. The cell cycle checkpoint defects were most frequently seen in 9 pts with colon (27%), 8 pts with hepatobiliary (27%), 8 pts with pancreatic (24%), 7 pts with esophageal (21%), and less commonly in small bowel (6%) and GIST (6%). Conclusions: The alterations in the cell cycle pathway are most common in certain GI tumors mainly colon, pancreatic, hepatobiliary and esophageal tumors. Future clinical trials exploring the potential role of targeted agents such as CDK4/6 inhibitors alone or in combination with other targeted agents such as MEK inhibitors requires further exploration in these tumors.

Abstract 5359: An ultrasensitive and highly reproducible hybridization capture-based Next-Generation Sequencing clinical assay to enable precision oncology in patients with solid tumors

Sequencing whole cancer exome and whole genome provides useful information to study cancer evolution. However, cost and amount of data may become overwhelming. Enrichment capture-based methods to design custom targeted gene panel have rapidly evolved recently in cancer genomics arena. Custom targeted gene sequencing entails several advantages (i.e., better quality, ethical, affordable, technically suitable, personalized and reimbursable) for cancer patients over whole exome and whole genome sequencing. With this in mind, and to enable precision oncology in patients with solid tumors, we developed ICG100 2.0 panel, a hybridization capture-based next-generation sequencing assay for targeted sequencing of all exons and flanking introns of 162 commonly mutated cancer genes in formalin-fixed, paraffin-embedded (FFPE) tumors. To establish ICG100 2.0 panel, we compared three commercially available capture based technologies and evaluated reproducibility, sensitivity, specificity and the detection limit for low-frequency variants using internally developed bioinformatics pipeline. Cell lines, reference standards/synthetic DNA and solid tumor samples with the known genetic information was utilized in this analysis. Results were derived from MiSeq and NextSeq platforms and cross-compared on other platforms, including MassArray and ddPCR for establishing concordance and uniformity. Intra and interrun replicates were utilized to assess the quality, precision and reproducibility of variant calling. Mean depth of coverage was observed at &gt;300X with &gt;99% sensitivity and specificity. These findings and observations will guide other clinical laboratories to establish new assay that require less DNA input, enzyme based fragmentation and reduced preparation time. While we show that the three capture based methods (after comparison) had an overall accuracy in SNP and CNV detection similar to each other with minor differences, we describe an approach to assess and establish the best assay from the clinical standpoint to guide treatment decisions and match cancer patients to the most appropriate clinical trials.

Citation Format: Moises Hernandez, Sara King, Sharanya Raghunath, Christopher Johnson, David Loughmiller, Lincoln Nadauld, Pravin J. Mishra. An ultrasensitive and highly reproducible hybridization capture-based Next-Generation Sequencing clinical assay to enable precision oncology in patients with solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5359. doi:10.1158/1538-7445.AM2017-5359

Abstract 3625: Beyond SNPs: Utilizing NGS methods to detect copy number alterations at high sensitivity in clinical cancer samples

The emergence of novel technologies, including Next-Generation Sequencing, has enabled the identification of actionable variants in clinical specimens, which can then be targeted with molecular therapeutics in a precision medicine approach. In human cancers, Single Nucleotide Polymorphisms (SNPs) have become powerful predictors of response to certain targeted therapies. However, Copy Number Alterations (CNAs) also represent a major class of clinically actionable variants that are frequently identified in clinical cancer samples. CNAs account for more than one third of all actionable mutations. A major question in the clinical application of technologies such as NGS is whether CNAs are faithfully detected; a particularly important question given the prevalence of actionable CNAs in cancer samples. To address this question we prepared tumor samples from eleven distinct patients and compared CNA detection on two different NGS platforms. As an orthogonal method for validation, we compared the CNA detection results to Fluorescent In Situ Hybridization (FISH) performed on the same samples. We observed 20 copy number amplification events across the eleven patient samples according to FISH analysis. By comparison, our internal NGS assay, termed ICG100, detected 19/20 (94%) amplification events, whereas an external, commercially available NGS-based test detected only 12/20 (59%) amplification events. Of the seven amplification events that were not identified by the external NGS test, six were considered clinically actionable variants. These findings highlight the discrepancies that exist amongst NGS library preparation chemistries and their abilities to accurately detect CNAs. The relevance of these findings is particularly underscored by the clinically actionable nature of the variants that were discordantly detected, including a high-level ERBB2 amplification.

Citation Format: Sharanya Raghunath, Jackie Wayne, Aimee Shamo, Patrick Bradley, Moises Hernandez Abanto, David Loughmiller, Jason Gillman, Derrick S. Haslem, Gary Stone, Pravin Mishra, Lincoln D. Nadauld. Beyond SNPs: Utilizing NGS methods to detect copy number alterations at high sensitivity in clinical cancer samples. [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 3625.

Abstract 3650: Multi-pronged approach to establish control standards for somatic mutations in next generation sequencing (NGS) oncology test

In recent years, somatic mutation testing via Next Generation Sequencing (NGS) has emerged as a powerful tool to detect targetable mutations in diseases such as cancer. These include mutations such as BRAF V600E, which can lead to targeted drug therapy; therefore, improving the standard of care in cancer diagnostics. To generate clinically meaningful results, we need to define standards that can be applied to laboratories performing somatic testing on tumor samples. With ongoing debate about the use of positive or negative controls in somatic testing assays, we designed an experiment to test the concordance of clinically actionable mutations commonly seen in tumor testing. We use cell line controls and commercially engineered DNA to validate concordance of mutations at specific allelic ratios. Our results depict an experiment design to determine if a genomic test can detect actionable mutations with high levels of accuracy and precision.

In this study, we designed a multi-pronged approach to evaluate the need for control standards by the ICG100 clinical NGS panel. To establish a baseline negative control, we performed concordance testing on the NA12878 cell line. We compared SNPs, insertions and deletions found using our methodology to the variants reports by NIST. We found our results to be concordant with NIST at a sensitivity of 92% and a specificity of 93%. To establish a baseline for positive controls, we utilized commercially engineered DNA which contains variants spiked-in at known allelic frequencies. This allowed us to determine if the ICG100 panel was able to retrieve specific somatic mutations. We were able to detect high confidence somatic mutations, such as BRAFV600E, as well as BRAF V600G which was spiked in at a lower expect allelic frequency of 4%. Moreover, we are able to detect with high confidence mutations such as ALK F1174L, EGFR G719S, PIK3CA H1047R, and MET Y1247D, and we were able to reproduce the results across multiple cell lines. Overall, our results show the need to utilize controls as standard protocol which can help assess the proficiency of a clinical assay. With rapid advances is NGS testing methodologies, there is a need for establishing standardized controls that asses the performance of a somatic tumor testing.

Citation Format: Christopher Johnson, Sharanya Raghunath, Jackie Wayne, Aimee Shamo, Patrick Bradley, Moises Hernandez, David Loughmiller, Jason Gillman, Derrick Haslem, Gary Stone, Lincoln Nadauld, Pravin J. Mishra. Multi-pronged approach to establish control standards for somatic mutations in next generation sequencing (NGS) oncology test. [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 3650.

Abstract 1114: Genomics in cancer patient care: Bench to bedside and beyond

Burgeoning sequencing technologies and the slow pace to use genomics data clinically has been largely hampered by lack of unestablished clinical utilities. There is an immediate need to store, analyze and retrieve meaningful clinical information from high throughput genomics data. At Intermountain Cancer Genomics (ICG) we created a complete translational pipeline that integrates these major core aspects: a clinical laboratory that generates data targeted within our gene panel, a bioinformatics pipeline that accounts for the quality of the data and further generates a set of variants that can be interpreted and targeted clinically to improve the quality of a patient's life.

At the ICG clinical laboratory we have developed a comprehensive ICG100 targeted sequencing panel under CLIA-CAP guidelines. DNA extracted from patient's tumor specimen gets sequenced for the entire coding region of 96 cancer-related genes which are often altered in cancer. These targeted regions are sequenced on Illumina's MiSeq sequencing platform using an in-solution, oligo-capture sequencing method. This test offers high coverage (&gt;100X) and detects all classes of genomic alterations, including indels, translocations, copy number alterations (CNAs), and point mutations across the exons of 96 genes. This approach is viable and well-suited for all sample types including FFPE, fresh tissue and plasma.

We have developed a comprehensive bio-analytics pipeline that accommodates the diverse variants generated by the unique sequencing chemistry. Comparison of ICG100 to a commercially available CLIA-certified sequencing test that also detects copy number alterations, reveals high concordance across the spectrum of variant types. In addition, the ICG100 test detected 10 additional CNAs across 6 separate samples that were not identified in the commercially available test, suggesting an increased sensitivity with ICG100.

This integrated service utilizes a collaborative molecular tumor board that consist of subject expert scientists and physicians. Interdisciplinary tumor board suggests effective treatment options based on genomics data and clinical relevance. ‘Actionable’ genomic alterations are categorized as such if linked to an approved therapy in the solid tumor examined or another solid tumor. This test can be ordered by oncologist through a simple web-based interface where genomic results and molecular tumor board interpretation can be viewed. Additionally, oncologists can make a treatment selection and order drug at their convenience.

The ICG100 test therefore not only is cost-effective but offers higher sensitivity, coverage, superior ability for clinical management with identification of actionable CNAs, genomics-driven personalized treatment and precision cancer care.

Citation Format: Sharanya Raghunath, David Loughmiller, Aimee Shamo, Jackie Wayne, Patrick Bradley, Jason Gillman, Gary Stone, Derrick Haslem, Lincoln Nadauld, Pravin J. Mishra. Genomics in cancer patient care: Bench to bedside and beyond. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1114. doi:10.1158/1538-7445.AM2015-1114

Canine urothelial carcinoma: genomically aberrant and comparatively relevant

Urothelial carcinoma (UC), also referred to as transitional cell carcinoma (TCC), is the most common bladder malignancy in both human and canine populations. In human UC, numerous studies have demonstrated the prevalence of chromosomal imbalances. Although the histopathology of the disease is similar in both species, studies evaluating the genomic profile of canine UC are lacking, limiting the discovery of key comparative molecular markers associated with driving UC pathogenesis. In the present study, we evaluated 31 primary canine UC biopsies by oligonucleotide array comparative genomic hybridization (oaCGH). Results highlighted the presence of three highly recurrent numerical aberrations: gain of dog chromosome (CFA) 13 and 36 and loss of CFA 19. Regional gains of CFA 13 and 36 were present in 97 % and 84 % of cases, respectively, and losses on CFA 19 were present in 77 % of cases. Fluorescence in situ hybridization (FISH), using targeted bacterial artificial chromosome (BAC) clones and custom Agilent SureFISH probes, was performed to detect and quantify these regions in paraffin-embedded biopsy sections and urine-derived urothelial cells. The data indicate that these three aberrations are potentially diagnostic of UC. Comparison of our canine oaCGH data with that of 285 human cases identified a series of shared copy number aberrations. Using an informatics approach to interrogate the frequency of copy number aberrations across both species, we identified those that had the highest joint probability of association with UC. The most significant joint region contained the gene PABPC1, which should be considered further for its role in UC progression. In addition, cross-species filtering of genome-wide copy number data highlighted several genes as high-profile candidates for further analysis, including CDKN2A, S100A8/9, and LRP1B. We propose that these common aberrations are indicative of an evolutionarily conserved mechanism of pathogenesis and harbor genes key to urothelial neoplasia, warranting investigation for diagnostic, prognostic, and therapeutic applications.

Cutaneous manifestations of chikungunya fever: observations made during a recent outbreak in south India

BACKGROUND; Chikungunya fever is an Aedes mosquito-borne Arbo viral illness with significant morbidity.

METHODS

In a recent outbreak of the disease in south India, the dermatologic manifestations of 145 patients attending a tertiary care hospital were recorded.

RESULTS

All age groups were affected, including newborns. Some of the cutaneous features were observed during the acute stage of the illness, and others during convalescence or thereafter. Pigmentary changes were found to be the most common cutaneous finding (42%), followed by maculopapular eruption (33%) and intertriginous aphthous-like ulcers (21.37%). Lesions with significant morbidity were generalized vesiculobullous eruptions (2.75%), found only in infants, lymphedema, and intertriginous aphthous-like ulcers. Exacerbation of existing dermatoses, such as psoriasis, and unmasking of undiagnosed Hansen's disease were observed. A perivascular lymphocytic infiltrate was a consistent histopathologic finding in all types of skin lesions. All patients responded well to symptomatic, conservative treatment.

CONCLUSIONS

The cutaneous findings hitherto not reported may be the result of the African genotype of the virus detected during this outbreak in India.