Pregnancy in Patients with the Fontan Operation

Improved survival rates for patients with a Fontan circulation has allowed more women with this complex cardiac physiology to contemplate pregnancy. However, pregnancy in women with a Fontan circulation is associated with a high risk of adverse maternal and fetal outcomes, high rates of miscarriage and preterm delivery. Factors associated with a successful pregnancy outcome are: younger age, normal body weight, absence of significant functional limitation, no Fontan-related complications, and well-functioning single ventricle physiology. Appropriate care with timely preconception counselling and regular, frequent clinical reviews by a multidisciplinary team based at a tertiary centre, improves the chance of a successful pregnancy. Empowerment of patients with education on their specific congenital cardiac condition and its projected trajectory, helps them make informed choices regarding their health, reproductive choices and assists them to achieve their life goals.

Improved outcomes of large B-cell lymphoma patients treated with CD19 CAR T in the UK over time

The success of CD19 Chimeric antigen receptor (CAR) T-cell therapy in large B-cell lymphoma (LBCL) has been partially offset by toxicity and logistical challenges, which off-the-shelf agents like CD20xCD3 bispecific antibodies might potentially overcome. However, when using CAR T outcomes as the 'standard-of-care comparator̕ for relapsed/refractory (r/r) LBCL, a potential learning curve with implementing a novel, complex therapy like CAR T needs to be considered. To address this, we analysed 726 UK patients intended to be treated with CD19 CAR T for r/r LBCL and compared outcomes between the first year of the national CAR T programme (Era 1; 2019) and the more recent treatment era (Era 2; 2020-2022). We identified significant improvements for Era 2 versus Era 1 in dropout rate (17% vs. 27%, p = 0.001), progression-free survival (1-year PFS 50% vs. 32%, p < 0.001) and overall survival (1-year OS 60% vs. 40%, p < 0.001). We also observed increased use of bridging therapy, improvement in bridging outcomes, more tocilizumab/corticosteroid use, reduced high-grade cytokine release syndrome (4% vs. 9%, p = 0.01) and intensive care unit admissions (20% vs. 32%, p = 0.001). Our results demonstrate significant improvement in CAR T outcomes over time, highlighting the importance of using up-to-date clinical data when comparing CAR T against new treatment options for r/r LBCL.

Abstract 5743: Comprehensive next generation sequencing profiling in combination with transcriptomic-based tumor molecular subtyping and harmonized TMB calculation using paired specimens from late-stage CRC patients

Background: Colorectal Cancer (CRC) can be classified into transcriptomics subtypes such as, stromal or immunogenic. A previously demonstrated consensus molecular subtype (CMS) classification method was utilized on CRC samples. We explored the potential clinical utility of combining a transcriptome derived subtypes approach with WES by demonstrating the association among subtypes and tumor characteristics such as whole exome based microsatellite instability (MSI), tumor mutational burden (TMB) and karyotype.

Methods: Tumor tissue and paired blood samples were collected from 19 late-stage, treatment-naïve colorectal cancer (CRC) patients. gDNA and RNA were extracted and analyzed by the Personalis® ImmunoID NeXT Platform®. RNA-seq results were normalized with the R DESeq2 package, with CRC CMS classification performed by the R package CMScaller. Somatic variants, copy number variants and MSI were evaluated using paired tumor/normal (T/N) samples. Copy number (CN) was characterized both genome-wide as a ploidy estimate and focally as the number of amplified regions. TMB was computed in alignment with the Friends of Cancer Research phase I guidelines.

Results: The most commonly mutated genes included TP53 (19/19), APC (16/19), and KRAS (9/19). CMScaller identified molecular subtypes (CMS1 immune/MSI n=1; CMS2 canonical/epithelial n=6; CMS3 metabolic/epithelial n=2; CMS4 mesenchyme/stromal n=8; unspecified n=2) in 17/19 samples. CMS2 and CMS4, the two most common molecular subtypes in this cohort, differed in terms of exome-wide MSI percent (p=0.03, Student’s t) and purity (p&lt;0.007, Student’s t). TMB, in silico ploidy estimates, and focal copy number changes were assessed for associations with tumor purity, with a significant association only between purity and ploidy (p=0.014; Bonferroni q=0.42; Student’s t) at the highest and lowest purity quartiles. Exome-wide percent unstable MSI was significantly associated with tumor purity (p=0.0053, lowest vs. highest quartile purity), with high purity tumors possessing more MSI. No association between TMB and Union for International Cancer Control stage was identified.

Conclusion: It has been demonstrated that the ImmunoID NeXT Platform’s transcriptomics capabilities enable CMS classification in most samples (17/19, 89%), an overall performance superior or comparable to previously reported results. An association between tumor purity and WES MSI using a broader exome-wide measurement was identified with transcriptomic based molecular subtyping. It has been corroborated that future comprehensive molecular classifiers can expand on transcriptomics based classification by leveraging DNA-based measurements to further delineate subtypes and eventually lead to biomarker driven precision oncology focused patient selection.

Citation Format: Danyi Wang, Lee McDaniel, Sean Boyle, Juergen Scheuenpflug, Zheng Feng. Comprehensive next generation sequencing profiling in combination with transcriptomic-based tumor molecular subtyping and harmonized TMB calculation using paired specimens from late-stage CRC patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5743.

Abstract 5021: Accurate quantification of infiltrating B cell composition and clone diversity in tumor samples

Tumors harbor a complex ecosystem of malignant, immune, and stromal cells. While malignant cells dictate much of the tumor biology, there is evidence that the tumor microenvironment (TME) also plays a major role in disease etiology. Given the complexity and abundance of the TME cellular composition, investigating the role of immune cell types will yield novel biomarkers for tumor progression and response to therapies.

The role of B cells as a prognostic biomarker remains elusive. For instance, infiltrating B cells in CRC have both positive and negative prognostic value. Thus, a scalable approach to quantify B cells and the B-cell receptor (BCR) repertoire could yield novel insights into the role of B cells in tumor biology. To address this, we have developed immune cell quantification (InfiltrateID࣪) and immune receptor repertoire profiling (RepertoireID࣪) methods as part of the ImmunoID NeXT Platform®, an augmented, immuno-oncology-optimized exome/transcriptome platform.

We estimate B cell abundance and BCR repertoire by profiling FFPE and PBMC samples using ImmunoID NeXT࣪. In expanding upon InfiltrateID to further estimate B cell abundance, here we regress the bulk RNA-seq readout from a reference signature from purified immune cell types. We also generate orthogonal quantifications of B cell abundance by profiling samples with cytometry by time of flight, single-cell RNA-seq, flow cytometry, and immunohistochemistry (IHC). We compare BCR results from ImmunoID NeXT to a standalone sequencing approach to evaluate the concordance of top clones. We then utilize BCR profiling from ImmunoID NeXT to analyze clonality and isotype composition in tumor samples.

We first use InfiltrateID to estimate absolute B cell fractions in over 50 samples. Overall, we observe a high correlation between InfiltrateID results and orthogonal data sets in both PBMC and tumor FFPE samples (R2=0.90). When comparing BCR results from RepertoireID to a standalone BCR sequencing method that profiles IgM and IgG, we identify 475 and 387 of the top 500 clones in IgG and IgM, respectively, with highly concordant abundances across all clones (R2&gt;0.72 and R2&gt;0.82 in IgM and IgG, respectively). Next, we use InfiltrateID to estimate absolute B cell fractions in over 650 samples from 14 tumor types. On average, samples display B cell fractions in agreement with the literature and IHC quantifications, with higher B cell fractions in lung, breast, and cervical tumors. We also observe a range of BCR clonality values across tumor types. Finally, we observe differences in B cell composition and repertoire diversity in tumor samples from patients who underwent checkpoint blockade therapy.

We show that InfiltrateID and RepertoireID accurately capture the composition and clone diversity of infiltrating B cells in tumor samples.

Citation Format: Fabio Navarro, Eric Levy, Pamela Milani, Qiang Li, Shruti Bhide, Upasana Dutta, Charles W. Abbott, Jose Jacob, Rena McClory, John West, John Lyle, Sean Boyle, Richard O. Chen. Accurate quantification of infiltrating B cell composition and clone diversity in tumor samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5021.

Abstract 5161: Exome-scale longitudinal tracking of emerging therapeutic resistance in GIST via analysis of circulating tumor DNA

Gastrointestinal stromal tumors (GIST) are lethal tumors characterized by constitutively activating mutations to KIT or PDGFRA. Transient disease control in the first-line setting is achieved via inhibition of tyrosine kinase signaling using the KIT inhibitor imatinib. As patients progress through subsequent lines of therapy a molecularly heterogeneous disease evolves, characterized by distinct subtypes and shifting repertoires of exon-specific KIT variants which directly impact treatment outcomes. Here, we use tumor-informed exome-scale liquid biopsy to identify and track the evolution of multiple resistance mechanisms in patients receiving tyrosine kinase inhibitors (TKIs) to address the unmet need of comprehensive understanding of GIST evolution in response to therapy.

Matched tumor, normal and serial plasma samples were obtained from 15 heavily pretreated metastatic GIST patients. Following baseline sample collection, all patients received systemic TKI therapy, and were monitored until disease progression. Exome-scale detection of somatic variants in cfDNA from longitudinal matched plasma samples was achieved using the NeXT Liquid BiopsyTM platform. The ImmunoID NeXT PlatformⓇ, an augmented exome/transcriptome platform and analysis pipeline which generates comprehensive tumor and immune data was used to profile paired tumor and normal samples.

Longitudinal whole exome sequencing of plasma identified dynamic shifts in existing clones harboring exon-specific KIT mutations, and evolution of new KIT mutations arising prior to identification of tumor progression using standard imaging techniques. We detected a correlation between the number of damaging mutations detected in baseline ctDNA and tumor exon 11 KIT mutation status, suggesting that plasma mutation profiles may be KIT-variant dependent. ctDNA from patients with shorter overall survival (OS) was enriched for variants in the PI3K-AKT and MAPK pathway, potentially contributing to immune evasion observed in those patients. Additional associations were observed between gene copy-number changes and OS (P = .0097). Previous studies have demonstrated that immune infiltration and activity may be KIT variant specific, here we broaden those findings, identifying a significant correlation between TCRɑ clonality and variants detected only in plasma (P = .04), as well as a significant association between TCRβ diversity and OS (HR = 2.55, log rank P = .04).

Comprehensive profiling of paired tumor tissue (WES and RNA-Seq) and WES of serially collected ctDNA sensitively and repeatedly identified evolving KIT mutations and other molecular alterations prior to radiologically confirmed disease progression. These findings suggest plasma-based monitoring of late-stage GIST malignancies may be useful for non-invasive disease tracking, providing treatment guidance prior to traditional approaches.

Citation Format: Charles W. Abbott, Niamh Coleman, Jing Wang, Josette Northcott, Jason Pugh, Dan Norton, Fábio C. Navarro, Lee D. McDaniel, Eric Levy, Rachel Marty Pyke, John Lyle, Jason Harris, Gabor Bartha, Filip Janku, John West, Richard O. Chen, Sean Boyle. Exome-scale longitudinal tracking of emerging therapeutic resistance in GIST via analysis of circulating tumor DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5161.

Abstract 5744: Characterization of sideness-related differentiated genetic alterations in stage I-IV colorectal cancer patients by using whole exome sequencing

Background: Although constituting a single organ, the right colon and left colon arise from midgut and hindgut embryonic precursors respectively. In the context of these embryonic origins, tumor laterality has been associated with differential microsatellite instability (MSI), aneuploidic karyotype, and loss of heterozygosity between the left and right colon. Differential genetic mutation profiles are not fully characterized in the context of left vs right laterality colorectal cancer (CRC). Therefore, we investigated associations between CRC anatomical site and somatic gene mutation patterns using whole exome sequencing.

Methods: Whole exome sequencing data were collected from 55 FFPE samples from different stages (stage I: 11, II: 9; III: 19, IV: 16), treatment-naive CRC patients using the Personalis® tumor-only ImmunoID NeXT Platform®, which captures somatic mutations (SNVs), copy number variants (CNVs), percent MSI in the exome, oncovirus detection, etc. The R package maftools was used to identify differential rates of mutation between samples resected from the rectum, left, and right colon respectively. Maftools-derived mutated gene lists, filtered to p&lt;0.5 and odds-ratio&gt;1, were assessed for pathway enrichment with Enrichr.

Results: APC and TP53 were the most commonly mutated genes in the entire cohort, with mutations seen in &gt;90% (APC) and &gt;75% (TP53) of samples respectively. Individual gene mutation frequency was not significantly different among the primary tumor locations (left colon; right colon; rectum) after Bonferroni multiple test correction, with FBXW7, APC, trending towards differential mutation between right colon tumors and left/rectal tumors. Maftools-derived mutated gene lists, filtered to p&lt;0.5 and odds-ratio&gt;1, were processed with Enrichr, identifying an enrichment of estrogen-related mutation events in right-sided vs rectal tumors (n=81 genes; Bioplanet 2019; q=5x10-4; WikiPathway 2021 Human; q&lt;5x10-6). In rectal tumors compared to right side, PI3K/AKT signaling mutations were more enriched (n=106 genes; Kyoto Encyclopedia of Genes and Genomes 2021; q&lt;4x10-6; MSigDB Hallmark 2020; q=9x10-3).

Conclusion: A statistically significant increase in frequencies of estrogen pathway gene mutations on right-sided tumors, and on PI3K/AKT mutations on rectal tumors, were identified. These are consistent with prior expression-based findings indicating the association of estrogen signaling with right-sided tumors, and increased AKT expression with left-sided CRCs. The whole exome sequencing based laterality associated genetic mutation results provided clinically applicable evidence that patients suffered from left versus right CRC tumors may benefit differential treatment therapies, and further investigation is ongoing to explore the potential correlation between tumor laterality and stage.

Citation Format: Danyi Wang, Lee McDaniel, Sean Boyle, Giuseppe Locatelli, Juergen Scheuenpflug, Zheng Feng. Characterization of sideness-related differentiated genetic alterations in stage I-IV colorectal cancer patients by using whole exome sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5744.

POS1468 PROGRESSIVE MULTIFOCAL LEUKOENCEPHALOPATHY IN A PATIENT WITH A BACKGROUND OF LUPUS NEPHRITIS AND CEREBRAL LUPUS

Background

Progressive multifocal leukocencephalopathy (PML) is a potentially fatal degenerative condition caused by reactivation of the human polyomavirus 2 (JC virus) in immunodeficient individuals. It is well recognised in individuals who have received Rituximab, but patients treated with other immunosuppressants are at risk also (1). Moreover, patients with SLE may be at increased risk, even when they are not taking immunosuppressants (1, 2).

Objectives

Describe the case of a patient with a history of lupus nephritis and cerebral lupus, on long-term Mycophenolate mofetil (MMF) and Prednisolone, diagnosed with PML complicated by immune reconstitution inflammatory syndrome (IRIS).

Methods

Case report.

Results

This patient first presented in 2010 at the age of 18 with ankle swelling and proteinuria. She had high ANA and anti-dsDNA titres, and renal biopsy showed class IV lupus nephritis. She went into remission on high dose Prednisolone and MMF and elected to stop her MMF. Four months later, she developed behaviour changes and worsening proteinuria. MRI showed a mild high signal lesion in the right cerebral hemisphere, and she was diagnosed with cerebral lupus. She recovered after treatment with IV methylprednisolone and MMF. Over the subsequent eight years, she had three flares of her lupus nephritis, with repeat biopsies in 2013 and 2018 showing active proliferative (class IVA) glomerulonephritis. Consequently she was treated with varying doses of oral Prednisolone and MMF for most of this period. She never received any B-cell depleting therapies.

In October 2020, she presented to A&E with numbness in her left face and down her left arm and leg. MRI demonstrated signal abnormalities in her right hemisphere, involving the cortex, white matter and leptomeninges. She was lymphopenic (0.58x10^9/L) with a low CD4 count of 136 cells/uL (normal range 620-1990 cells/uL). A recent dsDNA had risen to 70 IU/ml. Her cerebrospinal fluid revealed mildly raised white cells and a weakly positive JC virus PCR. The differential diagnoses included cerebral lupus, opportunistic infection and malignancy. During this period of diagnostic uncertainty, she was treated with an increased dose of oral Prednisolone and plasma exchange. She went on to have a brain biopsy that showed peri-vascular lymphocytic infiltration and JC virus was present in high copy numbers in the brain tissue (49221.8 IU/mL), confirming a diagnosis of PML. Her MMF was stopped but she continued a low dose Prednisolone with the addition of Hydroxychloroquine.

She was re-admitted two weeks after discharge in December 2020 with a right-sided headache, left facial weakness and loss of dexterity in her left hand. MRI showed evidence of IRIS in the right hemisphere with cerebral oedema causing midline shift. She was treated with IV Dexamethasone then Prednisolone 30 mg daily, with a gradual taper over a year.

She has made a good recovery with minimal neurological deficit; she had recurrent seizures which responded well to anticonvulsant therapy. Her SLE has not flared.

Conclusion

This describes a case of PML in the context of longstanding lupus nephritis, treated with prednisolone and MMF. Her longstanding lymphopenia with low CD4 counts were attributed to the combined consequences of active lupus and her cumulative immunosuppressive burden. CD4 lymphopenia is associated with PML in the HIV population, and may provide information about which patients on immunosuppressive treatments are at risk of developing PML (3). However, not enough is known to routinely screen patients and the counts of other lymphocyte subsets are likely to be important too.

The case highlights that PML can be associated with different immunosuppressants, other than B-cell depletion. The prompt diagnosis, facilitated by brain biopsy, and appropriate management led to a good medium-term outcome for this patient, showing that PML is eminently survivable.

References

[1]Calabrese LH, Molloy ES. ARD 2008;67:iii64-iii65

[2]Henegar CE et al. Lupus 2016;25(6):617-26

[3]Mills EA, Mao-Draayer Y. Front Immunol 2018;9:138

Disclosure of Interests

None declared

Oro-Naso-Sino-Orbital-Cutaneous Fistula From Prolonged Cocaine Use

Presentation We present the case of a 48-year-old man with nasal cellulitis and subsequent oro-naso-sino-orbital-cutaneous fistula from prolonged cocaine use. Diagnosis Initial laboratory investigations reported a raised white cell count (WBC) and C-Reactive Protein (CRP) and subsequently a positive atypical anti-neutrophil cytoplasm antibodies (ANCA) and positive anti-proteinase (PR3). Perihilar lung nodularity on chest imaging raised the possibility of a systemic autoimmune response. His urinalysis was positive for cocaine. Treatment He was commenced on Augmentin, Amphotericin B and Prednisolone. An obturator was created to manage the oro-nasal fistula. A subsequent naso-cutaneous defect was re-approximated. Daily nasal saline douche and abstinence of cocaine were recommended. Discussion Cocaine use in the community is rising and poses a challenge to multiple facets of our health care system.

19 Exome-scale liquid biopsy characterization of emerging immune resistance mechanisms in treatment-resistant GIST

Background

Metastatic gastrointestinal stromal tumors (GIST) are lethal tumors of the GI tract characterized by gain of function mutations in KIT or PDGFRα. Transient first-line control is achieved through the inhibition of tyrosine kinase signaling using the KIT inhibitor imatinib, though most patients progress after 2–3 years. Progression through successive lines of therapy results in a molecularly heterogeneous disease with diverse subtypes, driven by distinct collections of exon-specific KIT mutations which directly inform therapy decisions. To address the unmet need of comprehensive understanding of GIST, we used tumor-informed whole exome liquid biopsy to identify and track the evolution of multiple concurrent heterogeneous resistance mechanisms in individual patients receiving tyrosine kinase inhibitors (TKIs).

Methods

Baseline matched tumor, normal and longitudinal plasma samples were obtained from 15 metastatic, heavily pretreated GIST patients. Following baseline sample collection, all patients received systemic TKI therapy, and were monitored until disease progression. Paired tumor and normal samples were profiled using the ImmunoID NeXT Platform®, an augmented exome/transcriptome platform and analysis pipeline which generates comprehensive tumor and immune information. Exome-scale cfDNA profiling of matched plasma samples was performed using the NeXT Liquid BiopsyTM platform to detect somatic variants.

Results

Baseline solid tumor WES confirmed primary sensitizing KIT mutations in all 15 (100%) patients, and secondary KIT mutations in 7/15 patients (47%). Serial plasma whole exome sequencing identified evolution and expansion of clones harboring newly formed, druggable, exon-specific KIT mutations which evolved prior to identification of tumor progression using standard imaging techniques. In addition to these variants, we detected node-specific enrichment of PI3K-AKT and MAPK pathway mutations in plasma of patients with shorter overall survival (OS), which may contribute to the observed immune evasion. Accompanying these changes, we also detected significant association between gene copy-number profiles and duration of OS (P = 0.0097). Investigation of immune signatures using univariate cox modeling revealed a significant association between TCRβ diversity and reduced OS (HR = 2.55, log rank P = 0.04).

Conclusions

Comprehensive genomic profiling (WES and RNA-Seq) of paired tumor tissue and WES of serially collected ctDNA identified evolving druggable KIT mutations and other molecular alterations which preceded clinical disease progression. These findings suggest liquid biopsy-based monitoring of late-stage GIST malignancies may be useful for early identification of treatment resistance, providing treatment guidance prior to traditional approaches.

Ethics Approval

Ethics approval was granted by the MD Anderson Human Research Protection Program, and all participants gave informed consent prior to participation.

75 Comprehensive profiling of the tumor-immune microenvironment using an augmented transcriptome

Background

Comprehensive profiling of both the tumor and tumor microenvironment (TME) can help further our understanding of tumor progression and response to treatment. Many immune features can be extracted from transcriptomic data, including characterization of the immune infiltrate and profiling the diversity of immune receptors. To address this, we have developed multiple TME profiling features as part of the ImmunoID NeXT Platform®, an augmented, immuno-oncology-optimized exome/transcriptome platform designed to provide comprehensive information regarding the tumor and TME from a single FFPE tumor sample. These features including quantification of immune cell infiltration and profiling of the T-cell receptor (TCR) and B-cell receptor (BCR).

Methods

To develop our immune infiltrate quantification method, we profiled the transcriptomes of eight purified immune cell types using ImmunoID NeXT™ to develop platform-specific gene sets, and compared our transcriptome quantification to immune cell quantification with IHC. For TCR and BCR methods, we analyzed the reproducibility of clone results, and compared top clones to standalone TCR and BCR sequencing approaches. In addition, we characterized the immune content of over 800 tumor samples across 14 cancer types. Finally, we analyzed the immune features in a cohort of melanoma patients who underwent PD-1 blockade.

Results

We observe significant concordances between cell fractions by IHC and ImmunoID NeXT’s transcriptome-based scores in tumor FFPE samples for B cells, CD8+ T cells, and macrophages (R2>0.82, R2>0.75, and R2>0.52, respectively). For TCR and BCR methods, abundances of clones shared between subsequent curls of a tumor FFPE sample have very high concordances (R2>0.89, R2>0.92, and R2>0.76 for TRB, IgG, and IgA, respectively). Compared to the standalone approaches, we identify 100% of the top 500 TRB clones and 95% of the top 500 IgG clones, with highly concordant abundances (R2>0.94 and R2>0.82 for TRB and IgG, respectively) in a PBMC sample. We identify biologically-relevant immune signatures across tumor types by characterizing the immune features across over 800 tumor samples. Finally, in a melanoma cohort, TRB clonality and CD8+ T cell scores are significantly different in responders to checkpoint inhibition.

Conclusions

RNA sequencing can be used as a scalable approach to profile the immune composition in tumors. Such analysis can add to our understanding of the tumor-immune interaction, including studies of response to immunotherapy. We show that immune infiltrate quantification and TCR and BCR profiling – all part of the ImmunoID NeXT Platform – are able to accurately and effectively evaluate the composition and diversity of tumor-infiltrating immune cells.

20 Tumor-informed liquid biopsy monitoring of evolving therapeutic resistance mechanisms in head and neck squamous cell carcinoma patients receiving anti-PD-1 therapy

Background

Typical liquid biopsy panels offer a limited understanding of tumor biology, potentially under-representing the heterogeneity of resistance in late-stage cancers. Here, diminished scope can result in undetected, therapeutically-relevant biomarkers which respond dynamically to treatment, as well as potentially missed resistance mechanisms and pathway-level events. To address the challenges associated with identifying multiple concurrent heterogeneous resistance mechanisms in individual patients, we evaluated longitudinal exome-scale tumor-informed cell-free DNA (cfDNA) data from head and neck squamous cell carcinoma (HNSCC) patients receiving anti-PD1 therapy.

Methods

Pre- and post-intervention matched tumor, normal and plasma samples were retrospectively obtained from 15 stage II-IV HNSCC patients. Following baseline sample collection, all patients received a single dose of nivolumab or pembrolizumab. The primary tumor was then resected approximately one month later when possible, or a second biopsy collected where resection was impractical. Paired tumor and normal samples were then profiled using ImmunoID NeXT Platform®, an augmented exome/transcriptome platform and analysis pipeline. Exome-scale cfDNA profiling of matched plasma samples was performed using the NeXT Liquid BiopsyTM platform to detect somatic variants.

Results

Patient neoantigen presentation score (NEOPSTM) rapidly and significantly contracted following therapy (p=.00098). Novel neoantigens arising post-treatment which were predicted to be presented on lost HLA alleles were significantly higher in patients with longer overall survival (p=.019). Variant detection across same-patient serial cfDNA samples revealed significantly correlated VAFs (R=.62, p<.0001) despite significant contraction of mutational burden in solid tumor (p=.0039), suggesting complex clonal/subclonal dynamics. Investigation of the evolving tumor and cfDNA subclonal architecture revealed significant association between decreasing cellular prevalence and NOTCH signaling (q=.001) and the innate immune system (q=.002), while increasing cellular prevalence was associated with p53 signalling (q=.02) and hypoxia (q=.02). These findings were complimented by transcriptomic data which showed significant enrichment of multiple immune pathways across treatment.

Conclusions

We found that immune checkpoint blockade precipitates rapid evolution of the HNSCC tumor microenvironment. By leveraging comprehensive, tumor-informed liquid biopsy data we were able to identify contracting cellular populations enriched for NOTCH pathway mutations. Longer OS following either intervention was associated with an expansion of novel neoantigens predicted to be presented by lost HLA alleles. Our results suggest that tumor-informed liquid biopsy provides a more robust understanding of therapeutic response and resistance mechanisms than that attainable with typical liquid biopsy panels alone.

Ethics Approval

This study obtained ethics approval from Human Subjects Research at Stanford University. ID number is 40425. All participants gave informed consent prior to enrollment.

79 Extensively validated HLA LOH algorithm demonstrates an association between HLA LOH and genomic instability

Background

Human Leukocyte Antigen (HLA) genes are critical for the presentation of neoantigens to the immune system by cancer cells. Deletion of HLA alleles, known as HLA loss of heterozygosity (LOH), has been highlighted as a key immune escape mechanism. Validated algorithms to detect HLA LOH from sequencing data are critical for exploring the biological impact of HLA LOH and assessing its utility as a clinical biomarker.

Methods

We developed DASH (Deletion of Allele-Specific HLAs), a machine learning algorithm trained on data from 279 patients on the ImmunoID NeXT Platform using features that account for probe capture variability between alleles and incorporate information from the regions flanking each HLA gene. To understand the contribution of boosted sequencing in the HLA region of the ImmunoID NeXT Platform, we performed an in silico downsampling analysis. To assess DASH’s performance at variable tumor purities and HLA LOH subclonalities we identified three tumor-normal cell lines with HLA LOH and created in silico mixtures. Furthermore, after designing patient-specific primers for 21 patients that target specific alleles, we applied digital PCR (dPCR) to validate the HLA allele copy number status of the patients. Finally, we applied DASH to 611 patients spanning 15 tumor types.

Results

In cross validation analyses across patient samples, DASH achieved 98.7% specificity and 92.9% sensitivity while LOHHLA, a widely used algorithm, only reached 94.3% and 78.8%, respectively (figure 1). Downsampling analyses demonstrated that DASH benefits significantly from the boosted HLA sequencing on the ImmunoID NeXT Platform, dropping 0.06 in F-score after downsampling to the sequencing depth of other exome platforms. In cell line mixture analyses, DASH demonstrates greater than 99% specificity across all tumor purity and sub-clonality levels and greater than 98% sensitivity for above 27% tumor purity. Moreover, DASH demonstrated 100% sensitivity and specificity in dPCR experiments across 21 tumor samples with stable controls. We applied DASH to a large pan-cancer cohort and found that 18% of patients had HLA LOH (figure 2). We identified strong associations between HLA LOH and genomic instability. Moreover, we demonstrated relationships between HLA LOH and markers of immune pressure, such as a correlation with CD274 (PD-1) expression and allele-specific neoantigen enrichment for deleted HLA alleles.

Conclusions

DASH, a highly sensitive HLA LOH algorithm that has been extensively validated using cross validation, in silico downsampling, cell line mixtures and dPCR, has demonstrated the widespread impact of HLA LOH in a large pan-cancer cohort.

Abstract 79 Figure 1

Bar plots showing the sensitivity and specificities scores across ImmunoID NeXT cross validation samples between LOHHLA (blue) and DASH (green).

Abstract 79 Figure 2

Bar plots denoting the number of patients and the frequency of HLA LOH in each tumor type cohort. 95% confidence intervals are shown with the thin dark grey bars. Only cohorts with at least 10 patients are shown

Abstract LB057: Whole exome sequencing of tumor tissue and circulating tumor DNA ingastrointestinal stromal tumors (GIST)

Background: The discovery of oncogenic mutations as potential targets for cancer therapy has revolutionized the treatment of GIST and other cancers. However, adaptive resistance ultimately develops in nearly all patients, which emphasizes the need for a more detailed understanding of the underlying molecular profile. Methods: Using the Personalis ImmunoID NeXT Platform® (Personalis, Inc.; Menlo Park, CA), an augmented exome/transcriptome platform and analysis pipeline, we performed whole exome sequencing (WES) and whole transcriptome total RNA sequencing (RNA-Seq) of paired baseline tumor and normal tissue. NeXT Liquid Biopsy™ (Personalis, Inc.) was used for WES of plasma-derived ctDNA from serially collected samples collected at baseline, after 1 month and at progression to experimental systemic therapies in 15 patients with advanced/metastatic GIST. Results: WES of tumor tissue samples from all 15 patients confirmed underlying KIT mutation in all patients. There was large heterogeneity of other molecular alterations, which included therapeutically relevant molecular alterations, such as microsatellite instability-high (MSI-high) in 1 sample. RNA-Seq of tumor tissue revealed recurrent overexpression of GALR2, NY-ESO-1 and other genes involved in cancer progression, angiogenesis and anticancer immunity. Patients with response to systemic therapies demonstrated lower levels of cytolytic activity measured by CYT score in tumor tissue compared to patients without response (P=0.04). KIT mutations were detected in serially collected ctDNA samples from 12 (80%) of 15 patients. Quantity of KIT and other mutant ctDNA dynamically tracked the clonal evolution and clinical course during systemic therapy. Conclusions: Comprehensive genomic profiling (WES and RNA-Seq) of tumor tissue and WES of serially collected ctDNA is feasible and detects underlying druggable KIT mutations and other molecular alterations.

Citation Format: Niamh Coleman, Charles Abbot, Neeta Somaiah, Sarina Piha-Paul, Shubham Pant, Jordi Rodon, S. Greg Call, Sean Boyle, Funda Meric-Bernstam, Filip Janku. Whole exome sequencing of tumor tissue and circulating tumor DNA ingastrointestinal stromal tumors (GIST) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB057.

Abstract 555: Longitudinal exome-scale liquid biopsy monitoring of evolving therapeutic resistance mechanisms in head and neck squamous cell carcinoma patients receiving anti-PD-1 therapy

Background Typical liquid biopsy panels capture a relatively small number of variants, and likely under-represent the heterogeneity of resistance in late-stage cancers. This reduced scope can result in overlooked therapeutic biomarkers which respond dynamically to treatment, as well as potentially missed resistance mechanisms and pathway-level events. To address the challenges associated with identifying multiple concurrent heterogeneous resistance mechanisms in individual patients, we evaluated longitudinal whole exome sequencing of cell free DNA (cfDNA) and solid tumor biopsies from head and neck squamous cell carcinoma (HNSCC) patients that received anti-PD1 therapy. Using this approach, we identified evolving variant and pathway-level resistance mechanisms in cfDNA, as a complement to tumor biopsy derived information, and identified differences in putative neoantigens found in tissue and cfDNA.

Methods Pre- and post-intervention matched tumor, normal and plasma samples were obtained from a pilot cohort of 13 patients with HNSCC. Following baseline sample collection, all patients received a single dose of nivolumab. The primary tumor was then resected, approximately one month later when possible, or a second biopsy was collected where resection was impractical. Paired tumor and normal samples were profiled using ImmunoID NeXTTM, an augmented exome/transcriptome platform and analysis pipeline. Exome-scale cfDNA profiling of matched plasma samples was performed using the NeXT Liquid BiopsyTM platform to detect somatic variants. Data from these two platforms were then compared with corresponding clinical findings.

Results We observed a rapid evolution of the tumor microenvironment and disease mutation profile following therapy, with strong concordance detected between plasma and tumor variants at each timepoint. Post-therapy interrogation of cfDNA revealed dynamic changes in numerous oncogenes and clinically relevant pathways, such as ERK1/2 and MAPK, that were not observed in solid tumor. These findings suggest that single-lesion biopsy of the primary tumor misses co-occurring, clinically relevant resistance alterations. Median post-treatment neoantigen count was reduced in solid tumor, but increased in cfDNA. HLA-specific loss of heterozygosity (LOH) was identified in a number of subjects, likely resulting in reduced neoepitope presentation in those cases.

Conclusions Exome-wide somatic events were reliably detected in cfDNA, providing additional potential biomarkers to complement those identified in solid tumor. As we increase our cohort size, we expect that identification of biomarkers from both exome scale tissue biopsy and cfDNA will provide a more comprehensive view into therapeutic response and resistance mechanisms in HNSCC patients missed with typical liquid biopsy panels.

Citation Format: Charles W. Abbott, Nikita Bedi, Simo V. Zhang, Josette Northcott, Robin LI, Rachel Marty Pyke, Eric Levy, Rebecca Chernock, Mena Mansour, A. Dimitrios Colevas, John Lyle, John B. Sunwoo, Sean Boyle, Richard Chen. Longitudinal exome-scale liquid biopsy monitoring of evolving therapeutic resistance mechanisms in head and neck squamous cell carcinoma patients receiving anti-PD-1 therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 555.

OP0079 LIMB GIRDLE MUSCULAR DYSTROPHY TYPE 2B - A RARE MYOSITIS MIMIC

Background:

Proximal muscle weakness with associated raised creatine kinase (CK) commonly leads to referral to Rheumatology for the investigation of Idiopathic Inflammatory Myopathy (IIM). Some genetic myopathies can have a similar presentation with investigations that suggest inflammatory disease, leading to difficulty with accurate diagnosis (Amato & Brown, 2011; Harlan & Mammen, 2019).

Objectives:

To describe the case of a patient with Limb Girdle Muscular Dystrophy Type 2B (LGMD2B), whose initial presentation mimicked an inflammatory myopathy.

Methods:

Case report.

Results:

A 43-year-old patient was reviewed by Rheumatology due to proximal muscle weakness with a raised CK. Muscle biopsy was suggestive of inflammatory myopathy. Therefore, he was started on treatment with corticosteroids. Corticosteroid treatment resulted in no improvement in his weakness or CK. His diagnosis was reviewed, and he was referred to the Neurology and Genetics services. Following molecular genetic analysis, a diagnosis of Limb Girdle Muscular Dystrophy Type 2B was made.

Conclusion:

Muscle biopsies can suggest an inflammatory aetiology in some genetic myopathies (Amato & Brown, 2011; Harlan & Mammen, 2019). If a patient with suspected IIM presents with atypical features, or they do not respond as expected to treatment, then consider a genetic myopathy such as LGMD2B as a cause and involve the Neurology and Genetics services in the case.

References:

[1]Amato, A. A., & Brown, R. H., Jr. (2011). Dysferlinopathies. Handb Clin Neurol, 101, 111-118. https://doi.org/10.1016/b978-0-08-045031-5.00007-4

[2]Harlan, M & Mammen A. L (2019). Myositis Mimics: The Differential Diagnosis of Myositis. In: R. Aggarwal and C. V. Oddis (Eds.) Managing Myositis (pp. 209-223). Springer, Cham.

Disclosure of Interests:

None declared

Use of Acute Psychiatric Hospitalisation: A Study of the Factors Influencing Decisions to Arrange Acute Admission to Inpatient Mental Health Facilities

Background: Human decision-making involves a complex interplay of intra- and inter-personal factors. The decisions clinicians make in practise are subject to a wide range of influences. Admission to a psychiatric hospital is a major clinical intervention, but the decision-making processes involved in admissions remain unclear. Aims: To delineate the range of factors influencing clinicians' decisions to arrange acute psychiatric admissions. Methods: We undertook six focus groups with teams centrally involved in decisions to admit patients to hospital (crisis resolution home treatment, liaison psychiatry, approved mental health practitioners and consultant psychiatrists). The data were analysed using qualitative thematic analysis. Results: Our analysis of the data show a complex range of factors influencing decision-making that were categorised as those related to: (i) clinical and risk factors; (ii) fear/threat factors; (iii) interpersonal dynamics; (iv) contextual factors. Conclusions: Decisions to arrange acute admission to hospital are not just based on an appraisal of clinical and risk-related information. Emotional, interpersonal and contextual factors are also critical in decision-making. Delineating the breadth of factors that bear on clinical decision-making can inform approaches to (i) clinical decision-making research, (ii) the training and supervision of clinicians, and (iii) service delivery models.

Abstract 4278: A composite neoantigen score is more strongly associated with therapeutic response than tumor mutational burden in a cohort of late-stage anti-PD-1-treated melanoma patients

Checkpoint inhibitor therapy has demonstrated meaningful, if varied antitumor activity, with patient response influenced by a variety of biological factors, including complex interactions between the tumor and immune system. Thus, it is of increasing interest to identify composite biomarkers integrating multiple biological features to better predict immunotherapy response. In this study we use a comprehensive tumor immungenomics profiling platform to examine the effectiveness of our composite neoantigen score for stratifying patient response to checkpoint blockade therapy compared to tumor mutational burden and other biomarkers.Pre-treatment tumor/normal samples from 55 unresectable, stage III/IV melanoma patients who underwent anti-PD-1 therapy were characterized to assess factors influencing response. RECIST criteria were used to evaluate tumor response to therapy, with a median follow-up of 18 months. For each patient, a single paired FFPE tumor and normal blood sample was collected and profiled using Personalis' ImmunoID NeXT platform; an augmented exome/transcriptome platform and analysis pipeline, which produces comprehensive tumor mutation information, gene expression quantification, neoantigen characterization, HLA typing and LOH, TCR repertoire profiling and tumor microenvironment profiling. These data were then analyzed together with clinical outcome, and a composite neoantigen score computed for each patient along with other biomarkers such as tumor mutational burden (TMB).In this cohort, an elevated pretreatment composite neoantigen score combining neoantigen predictions adjusted based on resistance mechanisms that affect neoantigen presentation on the MHC complex was more strongly predictive of response to PD-1 blockade than TMB alone. This was true for both response and non-response via RECIST criteria and progression free survival. We also found that the composite neoantigen score was a stronger predictor of patient response when compared to neoantigen burden alone. Additionally, we observed increased response to anti-PD-1 therapy in patients with elevated pretreatment TCR clonality. Combining the composite neoantigen score and TCR clonality data revealed a significant association with non-response to therapy. Patients with high composite neoantigen score and TCR clonality that failed to achieve complete response revealed potential resistance mechanisms to anti-PD-1 therapy. Specifically, we identified patients with high expression of IDO1 or CTLA4, which may facilitate PD-1-independent immune escape. Additionally, we found patients with mutations within the antigen presentation machinery (APM), likely leading to loss of surface expression of the proteins, and in the case of B2M mutations, improper HLA class I folding and antigen presentation. These APM mutations likely result in reduced neoantigen presentation in these patients, facilitating tumor escape.In summary, our composite neoantigen score which integrates multiple components of MHC class I presentation into a single score, is more significantly associated with response to therapy than individual biomarkers such as tumor mutational burden. These findings highlight the promise of composite biomarkers for the optimization of anti-PD-1 therapy patient selection.

Citation Format: Charles W. Abbott, Eric Levy, Rachel Marty Pyke, Rena McClory, Sekwon Jang, Richard Chen, Sean Boyle. A composite neoantigen score is more strongly associated with therapeutic response than tumor mutational burden in a cohort of late-stage anti-PD-1-treated melanoma patients [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 4278.

Approaches to triage optimization in HPV primary screening: Extended genotyping and p16/Ki-67 dual-stained cytology-Retrospective insights from ATHENA

The objective of our study was to assess the performance of different triage strategies for high‐risk human papillomavirus (hrHPV)‐positive results utilizing either extended genotyping or a p16/Ki‐67 dual‐stained cytology (DS) approach, with or without partial genotyping. A subset of women with hrHPV infections participating in the Addressing the Need for Advanced HPV Diagnostics (ATHENA) study were analyzed to determine the number of cervical intraepithelial neoplasia grade 3 or worse (≥CIN3) cases detected, and the absolute risk for ≥CIN3 of each genotype. A clinical utility table was constructed to compare the impact of different triage strategies. In all, 2,339 women with single‐genotype hrHPV infections were identified. Among these were 171 ≥CIN3 cases. The U.S. Food and Drug Administration (FDA)‐approved algorithm (HPV16/18 positive, or 12‐other hrHPV positive and Pap positive, i.e., ≥ atypical squamous cells of undetermined significance) for primary HPV screening detected 132/171 (77.2%) ≥CIN3 cases and required 964 colposcopies (colposcopies per ≥CIN3 ratio: 7.3). An approach that uses DS instead of cytology in the FDA‐approved algorithm detected 147/171 (86.0%) ≥CIN3 cases, requiring 1,012 colposcopies (ratio: 6.9). Utilizing DS for triage of all hrHPV‐positive women identified 126/171 (73.7%) ≥CIN3 cases, requiring 640 colposcopies (ratio: 5.1). A strategy that detected HPV16/18/31/33/35+ captured 130/171 (76.0%) ≥CIN3 cases, requiring 1,025 colposcopies (ratio: 7.9). Inclusion of additional genotypes resulted in greater disease detection at the expense of higher colposcopy ratios. Substituting cytology with a DS triage approach improved disease detection and the colposcopy detection rate. Further reduction of colposcopy rates can be achieved by using DS without partial genotyping. Extended genotyping strategies can identify a comparable number of cases but requires an increased number of colposcopies.

What's new?

Among HPV‐positive women, the goal is to maximize the number of CIN3 or greater cases detected while minimizing colposcopies. These authors compared various combinations of genotyping and dual‐stained cytology (DS) as triage strategies. From a pool of 2,339 hrHPV+ women, 171 cases with ≥CIN3 were identified. Only one algorithm they tested boosted sensitivity over the current approach without reducing specificity. This method used DS to triage women who tested positive for 12‐other HPV, and referring HPV16/18+ patients directly to colposcopy. This approach caught 147 of the 171 cases, while reducing the number of colposcopies per case from 7.4 to 6.9.

Process evaluation of a cluster-randomised controlled trial of multi-component weight management programme in adults with intellectual disabilities and obesity

BACKGROUND

Providing effective weight management to adults with intellectual disabilities is necessary to challenge the high rates of obesity. The aim of this process evaluation was to explore the feasibility of conducting a full-scale clinical trial of the TAKE 5 multi-component weight management programme.

METHODS

The study was a 12-month pilot cluster-randomised controlled trial. Adults with intellectual disabilities and obesity were randomised to either TAKE 5, which included an energy deficit diet (EDD) or Waist Winners Too, based on health education principles. A mixed-methods process evaluation was conducted focussing on the reach, recruitment, fidelity, implementation, dose (delivered/received) and context.

RESULTS

The study successfully recruited adults with intellectual disabilities. Both weight management programmes were delivered with high fidelity and implemented as intended. Only one weight management programme, TAKE 5, demonstrated potential efficacy in reducing body weight and body composition. The effectiveness was largely attributed to the EDD and social support from carers.

CONCLUSIONS

The extensive process evaluation illustrated that a full-scale trial of a multi-component programme including an EDD is feasible and an acceptable approach to weight management for adults with intellectual disabilities and obesity.

Related to Anxiety: Arbitrarily Applicable Relational Responding and Experimental Psychopathology Research on Fear and Avoidance

Humans have an unparalleled ability to engage in arbitrarily applicable relational responding (AARR). One of the consequences of this ability to spontaneously combine and relate events from the past, present, and future may, in fact, be a propensity to suffer. For instance, maladaptive fear and avoidance of remote or derived threats may actually perpetuate anxiety. In this narrative review, we consider contemporary AARR research on fear and avoidance as it relates to anxiety. We first describe laboratory-based research on the emergent spread of fear- and avoidance-eliciting functions in humans. Next, we consider the validity of AARR research on fear and avoidance and address the therapeutic implications of the work. Finally, we outline challenges and opportunities for a greater synthesis between behavior analysis research on AARR and experimental psychopathology.

Abstract 546: Supporting neoantigen identification for personalized cancer vaccines trough analytical validation of an augmented content enhanced (ACE) transcriptome

The identification of neoantigens has become a critical step in the development of neoantigen-based personalized cancer vaccines and other immunotherapy applications. Since neoantigens can be generated from tumor specific mutations in any expressed gene, the first step in neoantigen identification typically involves deep sequencing of the tumor exome and transcriptome combined with exome sequencing of the matched normal. As personalized vaccines enter clinical trials, there is a growing need for strong analytical validation of these platforms.

To address this, we have developed the ACE Exome (~200X) and Transcriptome platforms for neoantigen identification which harness an augmented exome approach specifically designed to increase sensitivity for neoantigens in low complexity, difficult to sequence regions. To enable this platform for neoantigen based personalized cancer vaccines, we have performed a validation of both our ACE Exome (tumor and normal) and ACE transcriptome platforms for detecting DNA-based SNVs and Indels, as well as for RNA based small variant and fusion calls, variant types that are especially important for neoantigen identification. In this abstract, we describe the ACE Transcriptome validation.

To validate the ACE Transcriptome, we assessed analytical sensitivity (AS) and positive predictive accuracy (PPA). AS was calculated from a reference set of 894 SNVs and 19 indels across 11 tumor cancer cell lines with matched normals. The reference set was constructed based on previously observed variants in CCLE, COSMIC or had been validated by Sanger sequencing. PPA and limit of detection (LOD) were calculated in a series of tumor-normal dilutions representing allele frequencies ranging from 10% to 100%. For fusions, we further selected an additional 10 cell lines to test the detection of 16 previously characterized fusion events including several clinically actionable fusions (ALK and BCR-ABL1).

We report an analytical sensitivity for SNVs of &gt;99%, and a PPA of &gt;96% for small variants with &gt;=10% minor allele frequency (MAF). For fusion events, we report an analytical sensitivity of &gt;99%, with the detection of all 16 fusion events supported by at least 5 reads.

We demonstrate that our ACE Transcriptome assay and RNA cancer pipeline is a highly sensitive and robust platform for detecting small variants and fusions in the RNA.

Citation Format: Jennifer L. Yen, Sean Boyle, Ravi Alla, Jason Harris, Martina Lefterova, Richard Chen. Supporting neoantigen identification for personalized cancer vaccines trough analytical validation of an augmented content enhanced (ACE) transcriptome [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 546. doi:10.1158/1538-7445.AM2017-546

A Pilot Study Using Preoperative Cerebral Tissue Oxygen Saturation to Stratify Cardiovascular Risk in Major Non-Cardiac Surgery

This prospective pilot study evaluated whether low preoperative cerebral tissue oxygen saturation is associated with unfavourable outcomes after major elective non-cardiac surgery. Eighty-one patients over 60 years of age, American Society of Anesthesiologists physical status 3 or 4, were recruited. Resting cerebral tissue oxygen saturation was recorded on room air, and after oxygen supplementation, using cerebral oximetry. The primary outcome was 30-day major adverse event of combined mortality or severe morbidity, and the secondary outcome was 30-day new disability. Eleven patients (13.6%) suffered a major adverse event, and 28 patients (34.6%) experienced new disability. Room air cerebral tissue oxygen saturation was significantly different between patients who had a major adverse event, 67% (95% confidence interval [CI] 65–70) versus unaffected, 71% (95% CI 70–72; P=0.04). No statistical difference was found between patients for new disability (range 70%– 74%; P=0.73). Room air cerebral tissue oxygen saturation was significantly associated with major adverse events (odds ratio 1.36 (95% CI 1.03–1.79), P=0.03). Saturation levels ≤68% carried a positive likelihood ratio of 2.2 for death or severe morbidity, P=0.04. A definitive trial is required to confirm if cerebral oximetry can be used to stratify the cardiovascular risk of patients presenting for non-cardiac surgery.

Sharps and Needlestick Injuries Among Medical Students, Surgical Residents, Faculty, and Operating Room Staff at a Single Academic Institution

BACKGROUND

The hospital is a place of high risk for sharps and needlestick injuries (SNI) and such injuries are historically underreported.

METHODS

This institutional review board approved study compares the incidence of SNI among all surgical personnel at a single academic institution via an anonymous electronic survey distributed to medical students, surgical residents, general surgery attendings, surgical technicians, and operating room nurses.

RESULTS

The overall survey response rate was 37% (195/528). Among all respondents, 55% (107/195) had a history of a SNI in the workplace. The overall report rate following an initial SNI was 64%. Surgical staff reported SNIs more frequently, with an incidence rate ratio (IRR) of 1.33 (p = 0.085) when compared with attendings. When compared with surgical attendings, medical students (IRR of 2.86, p = 0.008) and residents (IRR of 2.21, p = 0.04) were more likely to cite fear as a reason for not reporting SNIs. Approximately 65% of respondents did not report their exposure either because of the time consuming process or the patient involved was perceived to be low-risk or both.

CONCLUSIONS

The 2 most common reasons for not reporting SNIs at our institution are because of the inability to complete the time consuming reporting process and fear of embarrassment or punitive response because of admitting an injury. Further research is necessary to mitigate these factors.

Attrition and weight loss outcomes for patients with complex obesity, anxiety and depression attending a weight management programme with targeted psychological treatment

The objective of the study is to investigate the effect of baseline anxiety and depression, using different definitions for caseness, on attrition and weight outcomes following a multidisciplinary weight management programme. The study design is a prospective observational study. The Hospital Anxiety and Depression Scale (HADS) was used to measure anxiety and depression with 'caseness' scoring ≥11 and severity ≥14. The participants were all patients who began a weight management programme between 1 October 2008 and 30 September 2009 (n = 1838). The setting was the Glasgow and Clyde Weight Management Service (GCWMS), a specialist multidisciplinary service, which aims to achieve a minimum of ≥5 kg weight loss. The results were as follows: patients with HADS score ≥14 were referred to the integrated psychology service for psychological assessment or intervention. Patients with caseness (HADS ≥11) for anxiety (33%) and depression (27%) were significantly younger, heavier, more socio-economically deprived and a higher proportion was female. There was a significant positive correlation between HADS anxiety and depression scores and increasing body mass index (r(2)  = 0.094, P < 0.001 and r(2)  = 0.175, P < 0.001, respectively). Attendance and completion was lower throughout follow-up amongst patients with anxiety or depression. More patients with HADS score ≥11 achieved ≥5 kg or ≥5% weight loss and by 12 months those with anxiety had a significantly higher mean weight loss (P = 0.032). Participants who scored for severe anxiety (HADS ≥14) achieved similar weight loss to those without, whilst participants who scored for severe depression achieved significantly greater weight loss than non-cases at 3, 6 and 12 months of follow-up (P < 0.01). Despite a less favourable case-mix of risk-factors for poor weight loss, patients who scored caseness for severe anxiety or depression and were offered additional psychological input achieved similar or better weight loss outcomes.

Abstract A2-39: Augmented targeted NGS in cancer diagnostics: Comparing gene panels and whole exome sequencing for accurate detection of driver mutations

With the advent of next-generation sequencing techniques, tumor mutations that guide therapeutic decisions can be identified on a large scale. The ability to accurately detect these mutations is often impaired by obstacles such as sequencing coverage gaps, small sample amount, low cellularity, and tumor heterogeneity. Two methods commonly used to interrogate the genomic profile of a tumor are: i) cancer gene panels, where a small number of genes (in the range of ~5-500, depending on the specific panel design) is assessed, and ii) cancer exome sequencing, where most human genes are evaluated. Additionally, tumor RNA can be studied to elucidate gene fusions and expression features that may impact treatment. Depending on the goals of the investigator, both methods have certain advantages and disadvantages. Differences between these assays must be clearly understood in order for cancer researchers to make the best decision to achieve their objective.

We developed a set of unique sequencing assays to augment and improve detection of major cancer mutations by enhancing coverage over known sequencing gaps and GC-rich regions. We utilize these protocols to create an accuracy and content enhanced whole-exome (ACE Exome) as well as an extended, augmented cancer gene panel (ACE Extended Cancer Panel), targeting over 1,300 cancer genes and 200 miRNA genes at very high depth. We compared these ACE assays to standard exome and gene panels currently available. We then compared the ACE panel to the ACE exome using a set of well-characterized cancer cell lines, cell line mixtures with known genomic perturbations, and primary tumor and matched normal pairs involved in drug resistance. We also performed whole-transcriptome and targeted RNA sequencing as companion assays to the DNA exome and panel, respectively. All data were analyzed using a cancer bioinformatics pipeline optimized for detection of low-representation small variants and indels, as well as somatic copy-number aberrations, gene expression and fusions.

The ACE assays were able to detect somatic variants with higher accuracy than standard assays across regions targeted by both. For example, a low-representation BRAF mutation detected by standard exome was confirmed as a false positive using the ACE exome due to 90 times more coverage over that region. Between the ACE assays, we found that 88% of somatic variants identified through ACE exome were also identified with our comprehensive panel within regions targeted by both. Conversely, more than half of the somatic variants discovered in the ACE panel were missed in the ACE exome due to insufficient read depth. For instance, the panel detected two EGFR variants known to be present at 1% that were missed in the ACE exome. About 20 times more somatic variants across some ~18,000 genes were detected in whole-exome that are not targeted on the augmented gene panel. These genes have not yet been associated with cancer in current literature, but may be of potential interest for discovery research. Copy number profiles, although more comprehensive in the exome, were recapitulated using the panel, despite large distances between panel targets. Finally, the integration of RNA analysis to the DNA panel was able to detect expression and fusion patterns. In particular, we detected a DNA mutation associated with resistance in a post-treatment specimen, but accompanying RNA data proved this mutant unexpressed and thereby unlikely to be the driver of resistance.

For NGS-based cancer analysis to effectively guide clinical decisions and research, accuracy across all relevant cancer genes is of paramount importance. An enhanced exome may offer a solution for researchers interested in novel cancer associations who desire broad, even coverage. A comprehensive, high-depth panel targeting a large set of genes associated with cancer, accompanied by RNA analysis, may accomplish research goals across a wide range of translational cancer research.

Citation Format: Elena Helman, Michael James Clark, Sean Boyle, Richard Chen, Shujun Luo, Christian Haudenschild, Jason Harris, Gabor Bartha, Deanna Church, John West. Augmented targeted NGS in cancer diagnostics: Comparing gene panels and whole exome sequencing for accurate detection of driver mutations. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-39.

The Role of Human Papillomavirus Genotyping in Cervical Cancer Screening: A Large-Scale Evaluation of the cobas HPV Test

BACKGROUND

The cobas HPV Test ("cobas"; Roche Molecular Systems) detects HPV16 and HPV18 individually, and a pool of 12 other high-risk (HR) HPV types. The test is approved for (i) atypical squamous cells of undetermined significance (ASC-US) triage to determine need for colposcopy, (ii) combined screening with cytology ("cotesting"), and (iii) primary HPV screening.

METHODS

To assess the possible value of HPV16/18 typing, >17,000 specimens from a longitudinal cohort study of initially HPV-positive women (HC2, Qiagen) were retested with cobas. To study accuracy, cobas genotyping results were compared with those of an established method, the Linear Array HPV Genotyping Test (LA, Roche Molecular Systems). Clinical value of the typing strategy was evaluated by linking the cobas results (supplemented by other available typing results) to 3-year cumulative risks of CIN3+.

RESULTS

Grouped hierarchically (HPV16, else HPV18, else other HR types, else negative), the κ statistic for agreement between cobas and LA was 0.86 [95% confidence interval (CI), 0.86-0.87]. In all three scenarios, HPV16-positive women were at much higher 3-year risk of CIN3+ than HPV16-negative women: women ages 21 and older with ASC-US (14.5%; 95% CI, 13.5%-15.5% vs. 3.5%; 95% CI, 3.3-3.6); women ages 30 years and older that were HPV-positive cytology-negative (10.3%; 95% CI, 9.6-11.1 vs. 2.3%; 95% CI, 2.2-2.4); and all women 25 years and older that were HPV-positive (18.5%; 95% CI, 17.8-19.2 vs. 4.3%; 95% CI, 4.2-4.4).

CONCLUSION

The cobas and LA results show excellent agreement. The data support HPV16 typing.

IMPACT

HPV16 typing is useful in the management of HPV-positive/cytology-negative women in cotesting, of all HPV-positive women in primary HPV testing, and perhaps in the management of HPV-positive women with ASC-US. Cancer Epidemiol Biomarkers Prev; 24(9); 1304-10.

PRC2-independent chromatin compaction and transcriptional repression in cancer

The silencing of large chromosomal regions by epigenetic mechanisms has been reported to occur frequently in cancer. Epigenetic marks, such as histone methylation and acetylation, are altered at these loci. However, the mechanisms of formation of such aberrant gene clusters remain largely unknown. Here, we show that, in cancer cells, the epigenetic remodeling of chromatin into hypoacetylated domains covered with histone H3K27 trimethylation is paralleled by changes in higher-order chromatin structures. Using fluorescence in situ hybridization, we demonstrate that regional epigenetic silencing corresponds to the establishment of compact chromatin domains. We show that gene repression is tightly correlated to the state of chromatin compaction and not to the levels of H3K27me3-its removal through the knockdown of EZH2 does not induce significant gene expression nor chromatin decompaction. Moreover, transcription can occur with intact high-H3K27me3 levels; treatment with histone deacetylase inhibitors can relieve chromatin compaction and gene repression, without altering H3K27me3 levels. Our findings imply that compaction and subsequent repression of large chromatin domains are not direct consequences of PRC2 deregulation in cancer cells. By challenging the role of EZH2 in aberrant gene silencing in cancer, these findings have therapeutical implications, notably for the choice of epigenetic drugs for tumors with multiple regional epigenetic alterations.

Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum-associated degradation pathway

PURPOSE

The endoplasmic reticulum-associated degradation pathway is responsible for the translocation of misfolded proteins across the endoplasmic reticulum membrane into the cytosol for subsequent degradation by the proteasome. To define the phenotype associated with a novel inherited disorder of cytosolic endoplasmic reticulum-associated degradation pathway dysfunction, we studied a series of eight patients with deficiency of N-glycanase 1.

METHODS

Whole-genome, whole-exome, or standard Sanger sequencing techniques were employed. Retrospective chart reviews were performed in order to obtain clinical data.

RESULTS

All patients had global developmental delay, a movement disorder, and hypotonia. Other common findings included hypolacrima or alacrima (7/8), elevated liver transaminases (6/7), microcephaly (6/8), diminished reflexes (6/8), hepatocyte cytoplasmic storage material or vacuolization (5/6), and seizures (4/8). The nonsense mutation c.1201A>T (p.R401X) was the most common deleterious allele.

CONCLUSION

NGLY1 deficiency is a novel autosomal recessive disorder of the endoplasmic reticulum-associated degradation pathway associated with neurological dysfunction, abnormal tear production, and liver disease. The majority of patients detected to date carry a specific nonsense mutation that appears to be associated with severe disease. The phenotypic spectrum is likely to enlarge as cases with a broader range of mutations are detected.