Rapid Somatic Mutation Testing in Colorectal Cancer by Use of a Fully Automated System and Single-Use Cartridge: A Comparison with Next-Generation Sequencing

Background

Molecular tests have been increasingly used in the management of various cancers as more targeted therapies are becoming available as treatment options. The Idylla™ system is a fully integrated, cartridge-based platform that provides automated sample processing (deparaffinization, tissue digestion, and DNA extraction) and real-time PCR-based mutation detection with all reagents included in a single-use cartridge. This retrospective study aimed at evaluating both the Idylla KRAS and NRAS-BRAF-EGFR492 Mutation Assay cartridges (research use only) against next-generation sequencing (NGS) by using colorectal cancer (CRC) tissue samples.

Methods

Forty-four archived formalin-fixed paraffin-embedded (FFPE) CRC tissue samples previously analyzed by targeted NGS were tested on the Idylla system. Among these samples, 17 had a mutation in KRAS proto-oncogene, GTPase (KRAS), 5 in NRAS proto-oncogene, GTPase (NRAS), and 12 in B-Raf proto-oncogene, serine/threonine kinase (BRAF) as determined using the Ion AmpliSeq 50-gene Cancer Hotspot Panel v2. The remaining 10 samples were wild-type for KRAS, NRAS, and BRAF. Two 10-μm FFPE tissue sections were used for each Idylla run, 1 for the KRAS cartridge, and 1 for the NRAS-BRAF-EGFR492 cartridge. All cases met the Idylla minimum tumor content requirement for KRAS, NRAS, and BRAF (≥10%). Assay reproducibility was evaluated by testing commercial controls derived from human cell lines, which had an allelic frequency of 50% and were run in triplicate.

Results

The Idylla system successfully detected all mutations previously identified by NGS in KRAS (G12C, G12D, G12V, G13D, Q61K, Q61R, A146T), NRAS (G12V, G13R, Q61H), and BRAF (V600E). Compared with NGS, Idylla had a sensitivity of 100%. Analysis of the mutated commercial controls demonstrated agreement with the expected result for all samples and 100% reproducibility. The Idylla system produced results quickly with a turnaround time of approximately 2 h.

Conclusion

The Idylla system offers reliable and sensitive testing of clinically actionable mutations in KRAS, NRAS, and BRAF directly from FFPE tissue sections.

Identification of targetable molecular alterations in the NCI-COG Pediatric MATCH trial

10011

Background: The screening protocol for the NCI-Children’s Oncology Group (COG) Pediatric Molecular Analysis for Therapy Choice (MATCH) trial detects tumor alterations that are used to assign patients with treatment-refractory or recurrent cancers to phase 2 treatment arms of molecularly-targeted therapies. Methods: Patients age 1 to 21 years old with treatment-refractory or recurrent solid tumors, non-Hodgkin lymphomas, or histiocytic disorders treated at U.S. based COG sites are eligible. DNA and RNA extracted from FFPE tumor samples are sequenced using an Oncomine cancer gene panel for detection of mutations, amplifications, and fusions. Loss of SMARCB1, SMARCA4, and PTEN expression is detected by immunohistochemistry. Lists of actionable mutations (aMOIs) based upon available clinical and pre-clinical data are used a priori to determine eligibility for treatment arms. Results: Between 7/24/17 and 12/31/18, 422 patients with a median age of 13 years (range 1-21) were enrolled from 93 COG sites. Solid tumors comprised 71% (n = 300) of diagnoses, CNS tumors 24% (n = 101) and lymphomas/histiocytoses 5% (n = 21). A tumor sample was submitted for 390 patients, sequencing was attempted for 370 (95%), and results were confirmed for 357 (92%). Median turn-around time was 15 days. An aMOI for at least one of the 10 current treatment arms was identified in 112 patients (29%, 95% CI 24%-33%); 95 patients (24%, 95% CI 20%-29%) were assigned to a treatment arm with 39 patients (10%, 95% CI 7%-13%) enrolled to date. The aMOI rate was similar in patients less than 12 years of age (35%) compared to patients 12 years and older (25%). Actionable MAPK pathway alterations were found in 11% of patients (n = 41), most often HRAS/ KRAS/ NRAS mutations (n = 16), BRAF mutations or fusions (n = 14), or NF1 mutations (n = 11). Other genes with recurrent aMOIs included SMARCB1 (n = 14), ALK (n = 8), CDK4 (n = 8), PIK3CA (n = 7), PTEN (n = 7), FGFR1 (n = 5), and BRCA1/BRCA2 (n = 5). Conclusions: Approximately one-quarter of patients with tumor submitted for Pediatric MATCH screening have been assigned to an investigational therapy, facilitating the evaluation of molecularly-targeted agents in biomarker-positive pediatric cohorts through a collaborative nationwide study. Clinical trial information: NCT03155620.

Design and development of the molecular analysis for Therapy Choice (NCI-MATCH) Designated Laboratory Network

3016

Background: NCI-MATCH is a precision medicine trial that assigns treatment to refractory cancer patients by tumor mutation profile rather than by histology. After screening fresh tumor biopsies from nearly 6000 patients many treatment arms did not meet accrual due to the low prevalence of the eligible variants. NCI MATCH developed an approach to identify patients for the remaining arms utilizing a network of academic and commercial CLIA-certified labs that perform NGS assays as routine care at MATCH participating sites. Methods: Candidate labs were recruited through a notice in the Federal Register and posted on the NCI and ECOG ACRIN web sites. Twenty-seven labs (17 academic/10 commercial) submitted applications. After acceptance each lab analyzed a common set of 10 DNAs extracted from 8 cell lines and 2 clinical samples for concordance with the central NCI-MATCH NGS assay. Results: For the 17 labs with concordance results, a median of 8 (range 2 – 58) copy number variants (CNVs) were evaluated by the NGS assay of each DL, with the number evaluated depending on each lab’s clinical assay panel content. CNV concordance between central and DL assays, as measured by positive percent agreement (PPA), averaged 98.7% (range 87.5% - 100%) with the central assay as referent and 94.1% (range 77.8% – 100%) with the DL assay as referent. For single nucleotide variants (SNVs) and Insertion/deletions (Indels) combined, a median of 19 variants (range 11 – 26) were evaluated by each DL for concordance. PPA between central and DL assays averaged 98.0% (range 87.5% – 100%) and 98.6% (range 90.0% – 100%) with central and DL assay as referents, respectively. Strong correlations were observed between central and DL assays for both CNVs (median r = 0.93; 0.33 – 1.00) and SNV/Indels (median r = 0.98; 0.67 – 0.99). Conclusions: Our results suggest that different NGS assay platforms using diverse strategies for target enrichment and data analysis may still achieve high concordance if pre-analytical variables are minimized and the common genomic regions interrogated by each assay are well-understood. The designated lab network allows for a wider search for rare variants in tumors and provides a model for conducting future clinical trials. Clinical trial information: NCT02465060.

Screening for Human Papillomavirus in a Low- and Middle-Income Country

PURPOSE

Low- and middle-income countries have high incidences of cervical cancer linked to human papillomavirus (HPV), and without resources for cancer screenings these countries bear 85% of all cervical cancer cases. To address some of these needs, brigade-style screening combined with sensitive polymerase chain reaction–based HPV testing to detect common high-risk HPV genotypes may be necessary.

METHODS

We deployed an inexpensive DNA extraction technique and a real-time polymerase chain reaction–based HPV genotyping assay, as well as Papanicolaou testing, in a factory in San Pedro Sula, Honduras, where 1,732 women were screened for cervical cancer.

RESULTS

We found that 28% of participants were positive for high-risk HPV, with 26% of HPV-positive participants having more than one HPV infection. Moreover, the most common HPV genotypes detected were different than those routinely found in the United States.

CONCLUSION

This work demonstrates a deployable protocol for HPV screening in low- and middle-income countries with limited resources to perform cytopathology assessment of Pap smears.

Pancreatic cyst fluid harboring a KRAS mutation

A 55-yr-old woman presented with abdominal bloating for approximately 1 year. Imaging studies showed a cyst in the body of the pancreas with proximal pancreatic ductal dilation. An endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) was performed. Cytologic findings from the cyst fluid were consistent with a mucinous neoplastic cyst, and the possibility of malignancy could not be entirely excluded. A KRAS mutation analysis was performed on the cyst fluid using the Idylla system and circulating tumor KRAS (ctKRAS) cartridge (Biocartis, Mechelen, Belgium), which tests for actionable mutations in exons 2, 3, and 4 of the KRAS gene. Idylla testing detected a KRAS G12D mutation in the cyst fluid. The patient subsequently underwent a distal subtotal pancreatectomy with splenectomy. Microscopic examination of the resected tissue revealed an intraductal papillary mucinous neoplasm (IPMN) with an associated invasive carcinoma. KRAS testing on the resected tumor tissue confirmed the G12D mutation detected in the cyst fluid earlier. The described rapid testing of KRAS directly from the pancreatic cyst fluid can complement cytology assessment to classify pancreatic cysts more reliably and can potentially be of significant help when other cyst findings are nondiagnostic.

Design of peptide nucleic acid probes on plasmonic gold nanorods for detection of circulating tumor DNA point mutations

Here we present a gold nanorod-based platform for the sequence-specific detection of circulating tumor DNA (ctDNA) point mutations without the need for amplification or fluorescence labeling. Peptide nucleic acid probes complimentary to the G12V mutation in the KRAS gene were conjugated to gold nanorods, and the localized surface plasmon resonance absorbance through the sample was measured after exposure to synthetic ctDNA at various concentrations. Each step of the reaction was thoroughly controlled, starting from reagent concentrations and including conjugation, sonication, and incubation time. The platform was evaluated in both buffer and spiked healthy patient serum, demonstrating a linear working range below 125 nanograms of ctDNA per milliliter solution, and an effective limit of detection of 2 nanograms of ctDNA per milliliter. A clear distinction between mutant and wild type synthetic ctDNA was also found using this platform. In order to improve upon the selectivity of the sensor, a DNA hybridization simulation was performed to understand how the addition of mutations to the peptide nucleic acid probe could enhance the selectivity for capture of mutant over wild type sequences. The top candidate from the simulations, which had an additional mutation two base pairs away from the mutation of interest, had a significant impact on the selectivity between mutant and wild type capture. This paper provides a framework for sequence-specific capture of ctDNA, and a method of improving selectivity for desired point mutations through careful probe design.

Identifying aerosolized cyanobacteria in the human respiratory tract: A proposed mechanism for cyanotoxin-associated diseases

Cyanobacteria produce harmful toxins that have been associated with several acute conditions and chronic human diseases, like gastroenteritis, non-alcoholic liver disease, and amyotrophic lateral sclerosis. Aerosol from waterbodies appears to be a likely mechanism for exposure. We conducted a study of human biospecimens focused on the cyanobacterial aerosilization process by evaluating the extent to which cyanobacteria can invade the human respiratory tract. Our study suggests that humans routinely inhale aerosolized cyanobacteria, which can be harbored in the nostrils and the lungs. Using PCR, cyanobacteria were found at high frequencies in the upper respiratory tract (92.20%) and central airway (79.31%) of our study subjects. Nasal swabs were not predictive of bronchoalveolar lavage (BAL) when detecting inhaled cyanobacteria. Interestingly, we found no evidence that time of year was a significant factor for cyanobacteria positivity (BAL cytology p = 1.0 and PCR p = 1.0); (nasal swab cytology p = 0.051 and PCR p = 0.65). Additionally, we found that proximity to a waterbody was not a significant factor for cyanobacteria positivity in BAL and nasal swabs collected during cyanobacteria bloom season [May-October] (p = 0.46 and p = 0.38). These data suggest that cyanobacteria exposure may be a prevalent and chronic phenomenon not necessarily restricted to waterbodies alone. Sources of indoor exposure warrant future investigation. Given the widespread prevalence of cyanobacterial exposure in the airway, investigation of the aerosol spread of cyanotoxins, more specifically, is warranted. Our findings are consistent with the hypothesis that aerosol is a significant route for cyanobacteria exposure, and thus a likely route of transmission for cyanotoxin-associated human diseases.

Ductal Carcinoma in Situ Biomarkers in a Precision Medicine Era: Current and Future Molecular-Based Testing

Historically, ductal carcinoma in situ (DCIS) of the breast has been managed aggressively with surgery and radiotherapy because of a risk of progression to invasive ductal carcinoma. However, this treatment paradigm has been challenged by overtreatment concerns and evidence that suggests that DCIS can be stratified according to risk of recurrence or risk of progression to invasive disease. Traditional methods of risk stratification include histologic grade and hormone receptor status. Recent technological advancements have enabled an era of precision medicine, where DCIS can be molecularly analyzed by tools, such as next-generation DNA and RNA sequencing, to identify molecular biomarkers for risk stratification. These findings have led to the development of tools such as the Oncotype DX Breast DCIS Score, a gene expression-based assay with the potential to prevent overtreatment in low-risk disease.

Implementation of Multicolor Melt Curve Analysis for High-Risk Human Papilloma Virus Detection in Low- and Middle-Income Countries: A Pilot Study for Expanded Cervical Cancer Screening in Honduras

PURPOSE

Cervical cancer is a leading cause of cancer-related mortality in low- and middle-income countries (LMICs) and screening in LMICs is extremely limited. We aimed to implement on-site high-risk human papillomavirus (hrHPV) DNA testing in cohorts of women from an urban factory and from a rural village.

METHODS

A total of 802 women were recruited for this study in partnership with La Liga Contra el Cancer through the establishment of women's health resource fairs at two locations in Honduras: a textile factory (n = 401) in the city of San Pedro Sula and the rural village of El Rosario (n = 401) in Yoro. Participants received a routine cervical examination during which three sterile cytobrushes were used to collect cervical samples for testing. hrHPV genotyping was performed using a hrHPV genotyping assay and a real-time polymerase chain reaction instrument.

RESULTS

hrHPV status across all participants at both sites was 13% hrHPV positive and 67% hrHPV negative. When hrHPV status was compared across all three testing sites, hrHPV-positive rates were approximately equal among the factory (13%), village (12%), and confirmatory testing at Dartmouth-Hitchcock Medical Center (Lebanon, NH; 14%). hrHPV genotype was compared across sites, with HPV16 showing the highest infection rate (15%), followed by HPV59 (12%), and HPV68 (11%). There was a low prevalence of HPV18 observed in both populations compared with the hrHPV-positive population in the United States.

CONCLUSION

In collaboration with oncologists and pathologists from La Liga Contra el Cancer, we were able to provide a continuum of care once health-fair testing was performed. We established a method and implementation plan for hrHPV testing that is sustainable in LMICs.

Abstract B20: Cancer screening in rural Honduras: Maximizing impact with a multiorgan screening approach

Introduction: Poverty, poor health infrastructure, and rurality contribute to lack of cancer screening for most residents of Honduras (HN). We hypothesized that if community-identified barriers were mitigated, rural Hondurans would participate in cancer screening; initial low-tech screening methods would be useful in identifying high-risk individuals in a large group; and that we could operationalize an acceptable and effective multiorgan screening program. Our objective was to test multiorgan cancer-screening strategies for challenging rural environments such as our site in rural El Rosario, Honduras and develop a strategy that would be generalizable to rural sites in other low-income countries.

Methods: We conducted three cancer-screening projects (2013/n=449 women, 2016/n=389 women, 2017/n=299 men) by developing relationships with rural community leaders and Honduran oncologists. Together, we launched multiorgan screening events via a brigade-style medical outreach model designed to mitigate barriers to early detection of cancers. Key strategies: 1) a screening cascade system and low-tech methods to identify high-risk individuals for further screening; 2) triage for findings requiring additional workup, rather than focusing on making a definitive cancer diagnosis; 3) inserting cancer education into the participants' experience; and 4) multiorgan screening to maximize cancer prevention with little additional use of resources. Community-identified barriers were transportation, cost, fear, and inconvenience; we negotiated an array of minimalist and highly effective community-based strategies to mitigate the barriers. In 2013 and 2016 we screened women for cancers including cervix, breast, oropharynx, and thyroid, and in 2017 screened men for testicular, oropharynx, skin, prostate, and colon cancers. Post-study, participants with suspicious findings were connected with follow-up care at a cancer center in HN. On-site screening methods ranged from no-tech, including surveys, clinical breast exams, throat palpation for thyroid, digital rectal exam for prostate, physical exam of testes, and visual skin inspection for skin cancer; to mid-tech, including telepathology for oral cancer, fecal occult blood test for colon cancer, and PSA for prostate; and high-tech PCR screening for high-risk HPV (hrHPV). Well-trained HN medical students staffed the screening areas; their participation is intended to increase long-term screening capacity in HN. Community leaders were responsible for promoting the screening clinic by training teens who traveled to villages to introduce the opportunity.

Results: Participants came via a free bus, horse, motorbike, and on foot from 31 (2013), 40 (2016), and 38 (2017) different communities. Median age and years of education were 38/5 (2013), 40/6 (2016), and 47/4 (2017). Almost every participant completed all screenings. We found 11 types of hrHPV; in 2013/8.4% and 2016/12.5% were positive for 1 or more types. Referrals for breast follow-up were 2013/2.7% and 2016/4.4%. In 2017 (men), 26 referrals were: skin screening/2; testicular exams/2; colon/2; oropharynx/0; and 20 men for clinical prostate follow-up by a screening cascade of survey, digital rectal exam, and PSA. 249 men self-identified based on ASCO colon standards and brought stool samples for FOBT/4 tested positive. We used oral consent and focus groups for post-event evaluation. Comments reflected satisfaction with the medical students, convenience of a free bus, and protection of participants' privacy.

Conclusion: With community engagement and attention to planning for organized and rapid throughput, large-scale multiorgan cancer screening is feasible in low-income rural communities. Despite low expectation of male participation because it is “common knowledge” that Honduran males avoid clinics, our experience demonstrates that with mitigation of barriers, men will participate.

Citation Format: Linda Skewes Kennedy, Kayla A. Marra, Ethan Phillip Marshall LaRochelle, Mary D. Chamberlin, Kathleen D. Lyons, Suyapa A. Bejarano, Gregory J. Tsongalis. Cancer screening in rural Honduras: Maximizing impact with a multiorgan screening approach [abstract]. In: Proceedings of the Tenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2017 Sep 25-28; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2018;27(7 Suppl):Abstract nr B20.

Rural distribution of human papilloma virus in low- and middle-income countries

Cervical cancer rates in low- and middle-income countries (LMICs) are higher than in developed countries and account for 80% of an estimated 500,000 new cases annually. Factors that contribute to this are that diagnostic and prevention strategies designed for developed countries suffer from the combination of low vaccination rates and limitations due to lack of consistent access to both healthcare and supplies. Here we: 1) improve upon our LMIC deployable HPV test and 2) determine both the high and low-risk HPV genotype prevalence in an isolated Honduran population. We found an unexpected HPV distribution with an abundance of HPV 52 and HPV 72 infections. In this context, molecular testing using a LMIC deployable approach for the detection of HPV can aid in both the triage of HPV positive cytology-based follow up and provide information regarding HPV genotype distribution in support of vaccination strategies.

Pharmacogenetics of Opioid Use and Implications for Pain Management

BACKGROUND

Opioid analgesics are frequently prescribed to manage acute and chronic pain, but individual differences in opioid response make effective pain control in all patients an elusive goal. Furthermore, the risk of addiction following opioid consumption varies among individual patients. Although many psychosocial factors contribute to an individual's opioid response and risk for addiction, a strong genetic component has also been demonstrated.

CONTENT

Opioids undergo substantial enzymatic modification that can generate metabolites with either increased or decreased opioid activity relative to the parent compound. To elicit their analgesic effect, parent compounds and active metabolites must be transported into the central nervous system where they bind to opioid receptors and inhibit neurotransmission. Inherited genetic variants that alter the function of proteins involved in these processes have been associated with differences in opioid response and risk for addiction. Detection of these variants can help guide opioid selection, inform dosing decisions, or encourage use of a nonopioid analgesic.

SUMMARY

Whereas some genetic variants are clearly associated with differences in opioid response and have been included in consensus clinical practice guidelines, the impact of other variants on opioid response remains unclear. Studies performed to date have generated promising results, but inconsistent findings, reimbursement challenges, and the lack of robust decision support tools have hampered widespread adoption of pharmacogenetic testing to guide pain management treatment decisions. Future work involving the simultaneous evaluation of large numbers of variants and demonstration of a clear clinical benefit provided by pharmacogenetic testing will be required to overcome these obstacles.

Genomic characterization of patient-derived xenograft models established from fine needle aspirate biopsies of a primary pancreatic ductal adenocarcinoma and from patient-matched metastatic sites

N-of-1 trials target actionable mutations, yet such approaches do not test genomically-informed therapies in patient tumor models prior to patient treatment. To address this, we developed patient-derived xenograft (PDX) models from fine needle aspiration (FNA) biopsies (FNA-PDX) obtained from primary pancreatic ductal adenocarcinoma (PDAC) at the time of diagnosis. Here, we characterize PDX models established from one primary and two metastatic sites of one patient. We identified an activating KRAS G12R mutation among other mutations in these models. In explant cells derived from these PDX tumor models with a KRAS G12R mutation, treatment with inhibitors of CDKs (including CDK9) reduced phosphorylation of a marker of CDK9 activity (phospho-RNAPII CTD Ser2/5) and reduced viability/growth of explant cells derived from PDAC PDX models. Similarly, a CDK inhibitor reduced phospho-RNAPII CTD Ser2/5, increased apoptosis, and inhibited tumor growth in FNA-PDX and patient-matched metastatic-PDX models. In summary, PDX models can be constructed from FNA biopsies of PDAC which in turn can enable genomic characterization and identification of potential therapies.

Somatic Mutation Analysis of Human Cancers: Challenges in Clinical Practice

Somatic mutation analysis of human cancers has become the standard of practice. Whether screening for single gene variants or sequencing hundreds of cancer-related genes, this genomic information is the basis for precision medicine initiatives in oncology. Genomic profiling results in information that allows oncologists to make a more educated selection of appropriate therapeutic strategies that more often combine traditional cytotoxic chemotherapy and radiation with novel targeted therapies. Here we discuss the nuances of implementing somatic mutation testing in a clinical setting.

Use of Biosynthetic Controls as Performance Standards for Next-Generation Sequencing Assays of Somatic Tumors: A Multilaboratory Study

BACKGROUND

Next-generation sequencing (NGS) assays are highly complex tests that can vary substantially in both their design and intended application. Despite their innumerous advantages, NGS assays present some unique challenges associated with the preanalytical process, library preparation, data analysis, and reporting. According to a number of professional laboratory organization, control materials should be included both during the analytical validation phase and in routine clinical use to guarantee highly accurate results. The SeraseqTM Solid Tumor Mutation Mix AF10 and AF20 control materials consist of 26 biosynthetic DNA constructs in a genomic DNA background, each containing a specific variant or mutation of interest and an internal quality marker at 2 distinct allelic frequencies of 10% and 20%, respectively. The goal of this interlaboratory study was to evaluate the Seraseq AF10 and AF20 control materials by verifying their performance as control materials and by evaluating their ability to measure quality metrics essential to a clinical test.

METHODS

Performance characteristics were assessed within and between 6 CLIA-accredited laboratories and 1 research laboratory.

RESULTS

Most laboratories detected all 26 mutations of interest; however, some discrepancies involving the internal quality markers were observed.

CONCLUSION

This interlaboratory study showed that the Seraseq AF10 and AF20 control materials have high quality, stability, and genomic complexity in variant types that are well suited for assisting in NGS assay analytical validation and monitoring routine clinical applications.

Development of HLA-B*57:01 Genotyping Real-Time PCR with Optimized Hydrolysis Probe Design

HLA-B*57:01 genotyping before abacavir (ABC) administration is a standard of care to avoid ABC-driven hypersensitivity reactions. Several HLA-B*57:01 tests have been developed, each with advantages and disadvantages. Some have limited accuracy, require special instrumentation, and/or are labor intensive and expensive. We developed a novel hydrolysis probe-based real-time PCR method of HLA-B*57:01 genotyping. Primer and probes were designed based on published sequence variations in exon 3 of HLA-B that distinguish HLA-B*57:01 from ABC-insensitive alleles such as HLA-B*57:03 and HLA-B*58:01. We designed PCR primers to amplify HLA-B*57:01 along with closely related alleles, such as HLA-B*57:03, directly from genomic DNA. Most ABC-insensitive alleles, including HLA-B*58:01, would not produce any products in the PCR reaction. Our hydrolysis probes enable differentiation of HLA-B*57:01 from the other amplified, but ABC-insensitive, alleles. In addition to using real-time PCR, we used restriction enzymes to generate differential digestion patterns that led to the development of an HLA-B*57:01 PCR-restriction fragment length polymorphism marker. When used to genotype a set of 75 selected clinical samples, our real-time PCR assay demonstrated 100% accuracy in distinguishing between the HLA-B*57:01-positive and -negative alleles when results were compared to those of sequence-specific oligonucleotide probe typing and reference laboratory testing. Our newly developed test will allow clinical laboratories with real-time PCR capabilities to perform HLA-B*57:01 genotyping in a timely and economical manner.

The Case for Laboratory Developed Procedures: Quality and Positive Impact on Patient Care

An explosion of knowledge and technology is revolutionizing medicine and patient care. Novel testing must be brought to the clinic with safety and accuracy, but also in a timely and cost-effective manner, so that patients can benefit and laboratories can offer testing consistent with current guidelines. Under the oversight provided by the Clinical Laboratory Improvement Amendments, laboratories have been able to develop and optimize laboratory procedures for use in-house. Quality improvement programs, interlaboratory comparisons, and the ability of laboratories to adjust assays as needed to improve results, utilize new sample types, or incorporate new mutations, information, or technologies are positive aspects of Clinical Laboratory Improvement Amendments oversight of laboratory-developed procedures. Laboratories have a long history of successful service to patients operating under Clinical Laboratory Improvement Amendments. A series of detailed clinical examples illustrating the quality and positive impact of laboratory-developed procedures on patient care is provided. These examples also demonstrate how Clinical Laboratory Improvement Amendments oversight ensures accurate, reliable, and reproducible testing in clinical laboratories.

Molecular matching and treatment strategies for lung cancer at Dartmouth-Hitchcock Medical Center: A three year review of a molecular tumor board

e20585

Background: Matching of actionable tumor mutations with targeted therapy has been shown to increase response rates and prolong survival in lung cancer patients. Drug development and trials targeting genetic alterations are expanding rapidly. We describe the role of a Molecular Tumor Board (MTB) in the design of molecularly informed treatment strategies in our lung cancer patient population. Methods: DNA from tumor specimens was sequenced to identify coding mutations using a 50-gene targeted next-generation sequencing panel (Ampliseq v2). Cases were evaluated by a multidisciplinary MTB that included medical oncologists, hematologists, molecular and anatomic pathologists, genetic counselors, and basic science researchers who suggested a course of treatment based on the patient’s molecular findings. Results: During a three-year period, 88 patients were presented to the MTB. Of these, 21 patients had lung cancer (23.9%). All patients lacked common (indicated for FDA approved drug) activating EGFR and ALK mutations. One patient was stage IIIb, all others were stage IV; 18 had previously received at least one prior line of therapy (range 0-5). Suggestions for treatment with a targeted therapy were made for 19 of 21 (90.5%) and four patients underwent treatment with a MTB-suggested targeted agent (21.1%); two as part of a clinical trial. One patient received targeted therapy for 27 months before his disease eventually progressed. Barriers to treatment with targeted therapy included: ineligibility for study (n = 2), lack of interest in study/distance to travel (n = 2), lack of disease progression (n = 2), death/hospice enrollment (n = 5), decision to treat with immunotherapy (n = 3), and unknown (n = 1). Conclusions: For the majority of lung cancer patients, the MTB was able to provide suggestions based on targetable genetic alterations. The largest barriers to treatment were death and hospice enrollment indicating that molecular testing and presentation to the MTB at earlier stages of disease may increase the number of patients who ultimately are eligible for treatment with a targeted agent.

miRNA analysis in pancreatic cancer: the Dartmouth experience

Pancreatic cancer is considered one of the most lethal cancers being the fourth leading cause of cancer deaths in adults in the United States because of the lack of early signs and symptoms and the lack of early detection. Pancreatic ductal adenocarcinoma (PDAC) is the most common histological type among pancreatic cancers, representing 80%-90% of all solid tumors of the pancreas. The majority of PDAC develops from three precursor lesions: pancreatic intraepithelial neoplasia, intraductual papillary mucinous neoplasm and mucinous cystic neoplasm. Although histologic tissue evaluation remains the gold standard for diagnosis, endoscopic ultrasound-guided fine needle aspiration has become the preferred modality for obtaining pathologic confirmation. At Dartmouth-Hitchcock Medical Center (DHMC),we have developed and validated a microRNA (miRNA) panel for patients with pancreatic diseases that can be used in association with the gold standard method for diagnosis. miRNAs have an important role in biological processes, such as apoptosis, metabolism, cell growth and differentiation. In cancer, miRNAs can be classified as either oncogenic or tumor suppressor according to their function in the carcinogenic process. In this study, we describe the expression of many miRNA in benign and malignant pancreatic tissues as well as their clinical significance. For this reason, miRNAs have been considered potential biomarkers of pancreatic diseases that could potentially contribute to an early diagnosis, predict disease progression, accurately monitor disease, contribute to better treatment strategies and reduce mortality by improving disease management.

Feasibility Study of Molecular Profiling of Gastric Cancer Specimens From Rwanda

Abstract 51

Background:

Gastric cancer is associated with high mortality in Rwanda. Geographic or genetic differences may lead to variations in somatic mutations and novel therapies. Overseas collaboration to determine gastric cancer molecular profiles is paramount. We undertook this work to determine the feasibility of collaboration between researchers in Rwanda and the United States by creating a research platform for gastric and other cancers in Rwanda.

Methods:

Patients consented for biopsy. Cases that were confirmed as gastric adenocarcinoma were included. Formalin-fixed paraffin-embedded tissue blocks or eight unstained sections (4 μm) were transported to the United States. DNA extraction and library preparation was performed by using 50 ng gDNA. Samples were normalized, pooled, and sequenced by using the Pillar NGS SLIMamp Lung Hot Spot Panel (Pillar Biosciences, Natick, MA). FASTq files were uploaded to Pillar Biosciences to perform sequence alignment, annotation, and variant classification.

Results:

Fifty-seven samples were received and 35 were excluded because of low DNA yield or quality (18 and 17, respectively). Mutations were detected in nine (41%) of 22 samples. One sample contained three mutations, other cases had one to two mutations identified. In total, 12 mutations were identified: TP53 (four), SMAD4 (two), ERBB4 (two; S341L and D228N), PTEN (two; K267RfsTer9 and C136Y), FBXW7 (one), and KRAS (one).

Conclusion:

Overseas collaboration for the molecular profiling of gastric cancer samples is feasible. Quality improved with larger biopsies or tissue blocks. Frequency of mutations is lower than expected. ERBB4 mutations identified are not known to be pathogenic. PTEN mutations are considered pathogenic—a potential target for therapy in larger trials. A larger fusion panel may be more effective in identifying potential targets. Funding: Pillar Biosciences provided reagents for sequencing.

AUTHORS' DISCLOSURES OF POTENTIAL CONFLICTS OF INTEREST

Mary D. Chamberlin Research Funding: Pillar Biosciences Belson Rugwizangoga No relationship to disclose Francine B. DeAbreu No relationship to disclose Eric Rutaganda No relationship to disclose Vincent Dusabejambo No relationship to disclose Oswald Habyarimana No relationship to disclose Steve Bensen No relationship to disclose Gregory J. Tsongalis Honoraria: Roche, ChromaCode, Foundation Medicine, Physician Choice Labs Consulting or Advisory Role: Baystate Health System, Jackson Laboratory for Genomic Medicine (Inst) Research Funding: Qiagen, Illumina, QuanDx, Leica Biosystems, Abbott Molecular, Affymetrix