Next-generation Sequencing Database Research Articles

Abstract PO5-10-06: A Pilot Study for Clinical Research Nurse Navigation at an Urban NCI-Designated Comprehensive Cancer Center

Abstract Background: Breast cancer is now the leading cause of cancer death for non-Hispanic Black women in Georgia with non-Hispanic Black women 40% more likely to die of breast cancer compared to White women. Inadequate representation of patients in clinical trials may contribute to health care inequity, though prior work has also shown disparate outcomes on similar clinical trials at Emory, suggesting differences in tumor biology may also be contributing to the disparity. Improving diversity in trial participation is imperative to better understand these differences, particularly with newer molecularly targeted therapies. We aimed to utilize Clinical Trials Nurse Navigation to increase clinical trial enrollment at an urban NCI-designated comprehensive care center in Atlanta, Georgia. Methods: A prospective pilot study was conducted investigating the role of a Clinical Research Nurse as a dedicated Clinical Trials Nurse Navigator to identify, pre-screen, and refer potential patients to both breast and next generation sequencing (NGS)-driven basket clinical trials at the Winship Cancer Institute at Emory University. The role also included centralizing all molecular data from patients with stage IV breast cancer into a database as a tool to refer patients to NGS-driven clinical trials. This role expands upon the Institute’s current research nursing scope to better meet the needs of our diverse patient population. Our catchment area is 35% non-Hispanic Black or African American. The nurse prescreened patients with stage IV breast cancer from breast oncology clinic templates and the breast NGS database to match them with clinical trials, with a particular emphasis on patients with stage IV triple negative breast cancer. The study began in January 2022 and is currently ongoing. Results: Since study initiation in January 2022, there has been a 27% increase in breast cancer clinical trial enrollment over a 12-month period. Over the last 6 months from January 2023, this has increased even further with 57 patients enrolled onto breast cancer clinical trials compared to a total enrollment of 70 patients onto breast cancer clinical trials in 2022 (Table 1). Of these patients, 11% enrolled in NGS-driven clinical trials in 2022 to present compared to 0% in 2021. Twenty-two (31.4%) non-Hispanic Black women enrolled onto breast cancer clinical trials in 2022 with another 21 (36.8%) non-Hispanic Black women enrolled thus far in 2023 (Table 1). Conclusion: Disparities in clinical trial enrollment may contribute to racial inequities in breast cancer outcomes. Implementation of clinical research nurse navigation has successfully improved clinical trial enrollment and diversity in clinical trial enrollment at our urban cancer center. Through increasing clinical trial prescreening, centralizing an NGS database, and dedicated nurse support to allow patients to navigate onto clinical trials, we achieved a 21% improvement in clinical trial enrollment from 2021 to 2022 and are on track to increase enrollment by 200% by the end of 2023. Clinical trials nurse navigators serve as an essential link between clinical trial patients and their providers, and should strongly be considered a key component of all clinical trials programs. Table 1 Breast Working Group Patient Enrollment by Race and Ethnicity, 2019-2023 Citation Format: Lizzie Huckaby, Maisey Ratcliffe, Madison Canning, Demetria Smith-Graziani, Kevin Kalinsky, Manali Bhave. A Pilot Study for Clinical Research Nurse Navigation at an Urban NCI-Designated Comprehensive Cancer Center [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-10-06.

Abstract B003: Real-world (RW) characterization and frequency of TSC1 and/or TSC2 alterations collected from tumor tissue and liquid biopsies from the Tempus genomic database in patients with advanced cancer

Abstract Background Tumor suppressor genes tuberous sclerosis complex subunit 1 and 2 (TSC1, TSC2) are critical negative regulators of mTORC1 activity. Patients (pts) harboring inactivating alterations in TSC1 and/or TSC2 (TSC1/2) in the AMPECT PEComa trial (NCT02494570) and in a pan-tumor Expanded Access Program (NCT03817515) demonstrated response to the mTORC1 inhibitor, nab-sirolimus. PRECISION I (NCT05103358), a currently enrolling tumor-agnostic study, will assess the clinical benefit of nab-sirolimus in pts with cancer with inactivating TSC1/2 alterations. To appreciate the potential for TSC1/2 targeted therapy, here we characterize TSC1/2 alterations across a large RW pt population with advanced cancer using data from tissue and liquid biopsies (LBs). Methods De-identified RW data for 154965 cancer pts profiled with the Tempus xT tumor DNA sequencing assay were obtained from the Tempus database (accessed 28 Apr 2023). Records included next-generation sequencing (NGS) data from the Tempus xT tumor DNA and/or xF LB sequencing assays. Somatic TSC1/2 variants were categorized as pathogenic/likely pathogenic mutations, deletions (copy number loss), or variants of uncertain significance (VUS). Inactivating TSC1/2 mutations and copy number variants were further characterized including frequency across primary vs metastatic tumor samples. Results Of the xT patients, pathogenic/likely pathogenic inactivating TSC1/2 alterations were identified in 2621 (1.7%) pts; TSC1/2 VUS (primarily missense) were identified in 9918 (6.4%) pts. Inactivating TSC1/2 variants consisted of frameshifts (35.9%), stop gains (35.8%), multihits (18.4%), deletions (7.0%), and missense mutations (3.0%), and were most frequently identified in urothelial carcinoma (UC) and pancreatic neuroendocrine tumor (each 8.4%), renal clear cell carcinoma (6.3%), hepatocellular carcinoma (HCC; 5.9%), and endometrial carcinoma (3.9%). Pathogenic TSC1 variants were more common (TSC1 56.6%; TSC2 43.4%), as was their detection among primary (~20380) vs metastatic (~70790) tumors (TSC1 1.1% vs 0.91%; TSC2 0.82% vs 0.60%). Of the 53502 xF pts with LB sequencing, inactivating TSC1/2 mutations were identified in 489 (0.9%) pts; TSC2 variants were slightly more common than TSC1 (TSC2 58.5%; TSC1 41.5%). The most common tumor types harboring inactivating TSC1/2 variants in LBs were HCC (5.2%), UC (3.6%), and gastrointestinal stromal tumor (2.1%). Conclusion In a large (N=154965) NGS database of pts with cancer, inactivating TSC1/2 variants occurred in about 1.7% of pts overall and were frequently identified in commonly occurring cancers. The frequency of TSC1/2 alterations and tumor types were generally consistent between tumor tissue samples and LBs. Consistency between primary vs metastatic samples suggests TSC1/2 alterations may not be acquired, although samples were not longitudinal. Additional research is needed to understand the clinical implications of these observations, but these RW observations suggest TSC1/2 alterations in cancer may be a reasonable therapeutic target. Citation Format: David J. Kwiatkowski, Norma A. Palma, Willis H. Navarro, Gopa Iyer. Real-world (RW) characterization and frequency of TSC1 and/or TSC2 alterations collected from tumor tissue and liquid biopsies from the Tempus genomic database in patients with advanced cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B003.

984. Detection of Mycobacterial Species from Specimens Submitted for Metagenomic Analysis

Abstract Background A national U.S. epidemic of non-tuberculous mycobacterial (NTM) infections is occurring at rates unseen over earlier decades, resulting in substantial numbers of pathogenic sequelae. Culture of mycobacteria is laborious, often requiring weeks for cultivation and speciation. Next generation sequencing (NGS) to detect NTM from clinical specimens has advantages over culture methods. From January 2018 to June 2022 we queried a large national NGS database to detect NTM rates and species. Methods DNA was isolated from 431,716 patient specimens collected from a variety of body sites: sputum, urine, sinus, wound or an unspecified swabs. Employing an Illumina’s 16S and ITS targeted-gene, deep sequencing approach, bacterial and/or fungal species resident in the specimen were determined. The identity and relative abundance of mycobacterial DNA recovered for each specimen were reported by species as the primary outcomes. Results Of the 431,716 specimens analyzed in this 4.5 year retrospective study, 0.001% (468) contained mycobacterial DNA. Forty different species of mycobacteria were detected with the most common frequency including: M abscessus, 40%; M mucogenicum, 13%; M. tuberculosis, 8.5% and M immunogenum 4.6%. M. avian and M. intracellulare were each detected in only 4% of the positive NTM specimens. 15% were other NTM species and 15% were not speciated NTM. Between 2018-2022 of the 468 NTM, the annual number of M. abscessus was 38, 53, 41 and 41, respectively. The concentration or relative abundance of mycobacterial DNA within each specimen varied from 4 to 100% of the total bacterial DNA recovered. Conclusion Over 4.5 years , NGS performed at a national molecular diagnostic laboratory detected 40 NTM species with a predominant fraction as M. abscessus (40%), supporting the clinical concern for an epidemic increase in M. abscessus infections during the last half decade. These data support the view that NGS metagenomics can uncover NTM epidemiological trends and implicate NTM infections. Disclosures Joseph F. John, Jr., MD, FACP, FIDSA, MicroGenDx: Advisor/Consultant Michael G. Schmidt, PhD, MicroGenDx: Advisor/Consultant Courtney L. Jarvis, PhD, MicroGenDX: Employee Niccole Diaz, BS, MicroGenDX: Advisor/Consultant Rick Martin, BS, MicroGenDX: Ownership Interest

A study of clinical and molecular characteristics in bilateral primary breast cancer.

Bilateral primary breast cancer (BPBC) is a rare type of breast cancer. Studies on the clinicopathologic and molecular characteristics of BPBC in a metastatic context are very limited. A total of 574 unselected metastatic breast cancer patients with clinical information were enrolled in our next-generation sequencing (NGS) database. Patients with BPBC from our NGS database were regarded as the study cohort. In addition, 1467 patients with BPBC and 2874 patients with unilateral breast cancer (UBC) from the Surveillance, Epidemiology, and End Results (SEER) public database were also analyzed to determine the characteristics of BPBC. Among the 574 patients enrolled in our NGS database, 20 (3.5%) patients had bilateral disease, comprising 15 (75%) patients with synchronous bilateral disease and 5 (25%) patients with metachronous bilateral disease. Eight patients had bilateral hormone receptor-positive (HR+)/human epidermal growth factor receptor-negative (HER2-) tumors, and three had unilateral HR+/HER2- tumors. More HR+/HER2- tumors and lobular components were found in BPBC patients than in UBC patients. The molecular subtype of the metastatic lesions in three patients was inconsistent with either side of the primary lesions, which suggested the importance of rebiopsy. Strong correlations in clinicopathologic features between the left and right tumors in BPBC were exhibited in the SEER database. In our NGS database, only one BPBC patient was found with a pathogenic germline mutation in BRCA2. The top mutated somatic genes in BPBC patients were similar to those in UBC patients, including TP53 (58.8% in BPBC and 60.6% in UBC) and PI3KCA (47.1% in BPBC and 35.9% in UBC). Our study suggested that BPBC may tend to be lobular carcinoma and have the HR+/HER2- subtype. Although our study did not find specific germline and somatic mutations in BPBC, more research is needed for verification.

Analysis of clinical features, genomic landscapes and survival outcomes in HER2-low breast cancer

BackgroundNovel human epidermal growth factor receptor 2 (HER2)-directed antibody–drug conjugates prompt the identification of the HER2-low subtype. However, the biological significance of HER2-low expression in breast cancer is unclear.MethodsClinical and genomic data of 579 metastatic breast cancer patients were reviewed from our next-generation sequencing (NGS) database and genomic analysis of early breast cancer patients from TCGA was also analyzed.FindingsFirst, the clinicopathological characteristics of HER2-low patients were profoundly influenced by HR status and no difference of prognosis was observed between HER2-low and HER2-zero patients when paired by HR status, but notably HER2-low patients showed similar metastatic patterns to HER2-positive patients in the HR-positive (HR+ ) subgroup, with more brain and initial lung metastases and more cases of de novo stage IV breast cancer than HER2-zero patients. Second, among patients with primary HER2-low or HER2-zero tumors, the discordance of HER2 status between primary and metastatic tumors was significant, with 48.4% of patients with HER2-zero primary tumors exhibiting HER2-low phenotype in metastatic tumors in the HR+ subgroup. Third, within HR+ and HR-negative subtypes, HER2-low and HER2-zero tumors showed no substantial differences in mutation alterations and copy number variations. Forth, germline BRCA2 mutations were observed only in HER2-low patients in our NGS database, especially in HR+ HER2-low tumors. Finally, three molecular subtypes based on genomic alterations in HER2-low breast cancer were identified, which provided novel insights into heterogeneity in HER2-low breast cancer.ConclusionsAfter correcting for HR expression, only marginal differences in clinical and molecular phenotypes were determined between HER2-low and HER2-zero breast cancer. Therefore, HER2-low breast cancer is insufficient to be defined as a distinct molecular entity, but rather a heterogenous disease.

Genomic, clinical characteristics, and treatment outcomes of patients with metastatic castration-sensitive prostate cancer with SPOP mutations: Analysis from the Kaiser Permanente Northern California Healthcare System.

261 Background: Androgen deprivation therapy (ADT) plus either Abiraterone, Docetaxel or Enzalutamide (ADE) improves overall survival (OS) of men with metastatic M1 castrate-sensitive prostate cancer (mCSPC), compared to ADT alone and is currently standard of care. Men with mCSPC with a point mutation of the speckle-type pox virus and zinc finger mutation (mutSPOP) derive superior response to ADT compared to wild type SPOP. The additive benefit of ADE to ADT in this subclass of CSPC is unclear. We sought to evaluate the benefit of therapy in patients with mutSPOP in a real-world setting. Methods: Between November 2017 and July 2022, 1002, patients in the Kaiser Permanente Northern California (KPNC) health system with advanced prostate cancer had tumor specimens examined by next generation sequencing (NGS). Of these patients, we retrospectively identified 70 mCSPC patients with mutSPOP. Patient records were reviewed to determine baseline characteristics, therapy for CSPC, subsequent therapy for Castrate Resistant Prostate Cancer (CRPC), and clinical outcome. The primary outcome was progression-free survival (PFS) for patients who received ADT alone or ADT plus ADE. PFS was defined as time to either PSA progression by PCWG2 criteria, clinical progression, or time to next line of therapy. Results: Median age for the 70 patients with mutSPOP was 75 years (range 50-91). Thirty-six (51%) were non-Hispanic white; 11 (16%) were African American; and 13 (19%) were Asian. F133 was the most frequently mutated allele (64%), TP53 was the most common co-mutated gene (27%), and mutations in MSH2, MSH6 and BRCA1 were identified in one patient each. Two patients had concurrent ERG fusion. Thirty-six patients (51%) had a Gleason score 8-10 and 48 (69%) were diagnosed with de-novo metastatic disease. Twenty-seven patients (39%) received ADT alone, 41 (59%) received ADT + ADE, 2 patients elected observation only. PFS was 28.1 months (mos) for ADT alone vs 35 for ADT+ADE (p=0.08). Twenty-nine patients (41%) received 2nd line therapy at CRPC; among them 24 received ADT plus Abiraterone or Enzalutamide. Median PFS for all the CRPC patients who received 2nd line treatment was 15mos. Median PFS for CRPC patients who received 2nd line treatment with Abiraterone, or Enzalutamide was 15.3 mos. Median overall survival for the entire group was 173 mos (95% CI 135-NR). Conclusions: In this real-world study within KPNC, we confirmed the durable benefit of ADT based therapy in patients with mutSPOP. Patients with mutSPOP derived similar benefit regardless of 1st line therapy (ADT vs ADT + ADE). We also noted durable responses to abiraterone or enzalutamide for CRPC after initial treatment with ADE for CSPC. Confirmation of these findings from an another large NGS database is ongoing and will be reported later.

Landscape of DNA damage response gene alterations in breast cancer: A comprehensive investigation.

DNA damage response (DDR) gene alterations are prevalent in breast cancer (BC) and important for treatment decisions. Intensive studies on DDR alterations in BC are still needed. The authors included 438 patients with metastatic breast cancer from their next-generation sequencing database and 1091 patients with early-stage breast cancer from The Cancer Genome Atlas (TCGA) database in the analysis to characterize molecular alterations in the DDR pathway. Germline DDR mutations were more prevalent in younger patients and those with HER2-negative cancers. Tumors with germline DDR mutations more commonly had somatic DDR mutations, especially those with germline Fanconi anemia (FA) pathway mutations. Notably, 66.67% (four of six) of patients with germline PALB2 mutations had tumors that harbored somatic PALB2 mutations. No differences in prognosis were observed in patients with germline or tumor somatic DDR mutations compared to patients and tumors that were wild-type. Compared to early BC, the frequency of somatic DDR mutations in metastatic cancers was significantly higher (24.89% vs. 16.02%, p<.001). Higher tumor mutation burdens were observed in cancers with somatic DDR mutations, but not in cancers with germline DDR mutations. Furthermore, tumors with somatic DDR mutations showed an abundance of anticancer immunological phenotypes. Somatic FA and mismatch repair pathway mutations were associated with increased expression of immune checkpoint molecules. Although most DDR genes were significantly positively associated with expression of proliferation-related genes, PARP3 expression was negatively correlated with MKI67 expression. Lower PARP3 expression was associated with a worse prognosis in TCGA database by multivariate Cox analysis. Patients with germline FA mutations more frequently have tumors with somatic DDR mutations. Somatic DDR mutations lead to anticancer immunological phenotypes in BC. No differences in prognosis according to germline or somatic DDR mutations were found.

Frequency, underdiagnosis, and heterogeneity of epidermal growth factor receptor exon 20 insertion mutations using real-world genomic datasets.

Epidermal growth factor receptor (EGFR) exon 20 insertion mutations (ex20ins) account for ≤ 12% of all EGFR-mutant nonsmall cell lung cancers. We analysed real-world datasets to determine the frequency of ex20ins variants, and the ability of polymerase chain reaction (PCR) and next-generation sequencing (NGS) to identify them. Three real-world United States NGS databases were used: GENIE, FoundationInsights, and GuardantINFORM. Mutation profiles consistent with in-frame EGFR ex20ins were summarized. GENIE, FoundationInsights, and GuardantINFORM datasets identified 180, 627, and 627 patients with EGFR ex20ins respectively. The most frequent insertion region of exon 20 was the near loop (~ 70%), followed by the far loop (~ 30%) and the helical (~ 3-6%) regions. GENIE, FoundationInsights, and GuardantINFORM datasets identified 41, 102, and 96 unique variants respectively. An analysis of variants projected that ~ 50% of EGFR ex20ins identified by NGS would have been missed by PCR-based assays. Given the breadth of EGFR ex20ins identified in the real-world US datasets, the ability of PCR to identify these mutations is limited. NGS platforms are more appropriate to identify patients likely to benefit from EGFR ex20ins-targeted therapies.

High expression of NLRP12 predicts poor prognosis in patients with intracranial glioma.

Intracranial gliomas are the most common primary central nervous system tumors in humans, and glioblastoma multiforme is the most malignant intracranial glioma. The nucleotide-binding domain leucine-rich repeat (NLR)-containing family are crucial regulators of inflammatory and innate immune responses. NLRP12 codes for the monarch-1 protein, which regulates immune responses in humans. Data from a next-generation sequencing database indicated that NLRP12 expression is increased in glioma cells. However, the relationship between NLRP12 levels and gliomas is unclear. To explore the role of NLRP12-related translation factors and proteins in glioma, we evaluated the clinical data and paraffin sections from glioma patients. The expression of NLRP12 was evaluated using immunohistochemical analysis, and clinical parameters were analyzed using chi-square and Kaplan-Meier survival tests. The degree of malignancy and prognosis highly correlated with NLRP12 levels. In addition, the siRNA-mediated downregulation of NLRP12 in glioma cell lines decreased proliferation, invasion, and migration. The levels of VEGF, N-cadherin, and cyclin D1 were downregulated after knockdown of NRLP12 in glioma cell lines, as observed using western blotting in vitro. Knockdown of NLRP12 attenuated the tumor progression in vivo. The expression of NLRP12 may be an independent prognostic factor and a potential target for the treatment of intracranial glioma.

Next generation sequencing (NGS) to identify relapsed gastrointestinal (GI) solid tumor patients with human leukocyte antigen (HLA) loss of heterozygosity (LOH) for future logic-gated CAR T therapy to reduce on target off tumor toxicity.

190 Background: Metastatic colorectal (CRC), pancreatic (PANC), and gastroesophageal (GE) cancers are the leading causes of GI cancer–related mortality (5-yr survival rate, 14%, 3% and ̃5-6%, respectively). T-cell immunotherapy targeting GI-associated tumor antigens has been attempted, but efficacy has been constrained by on-target off-tumor toxicity, limiting the therapeutic window. The Tmod (TM) platform is an AND-NOT logic-gated CAR T modular system, versions of which have a CEA- or MSLN-targeting CAR activator and a separate HLA-A*02-targeting blocker receptor to protect normal cells. Tmod CAR T exploits HLA LOH, common in GI malignancies (10-33% in primary solid tumors [TCGA]) and can kill tumor cells without harming healthy cells in vitro and in vivo. However, the prevalence of HLA LOH across GI tumors is unknown in the real-world setting. We utilized the Tempus xT oncology NGS database of patients with multiple GI tumors. From a standard-of-care NGS assay, GI cancer patients can be readily identified for HLA LOH and future treatment with Tmod CAR T therapy. Methods: The occurrence of HLA LOH in GI tumors of 1439 patients was assessed using paired germline and somatic DNA sequencing using a research assay [6]. CRC, PANC and GE patients with ≥ stage 3 were then extracted, and rates of HLA LOH were identified (ie, whether loss occurred across high-frequency HLA-A alleles). In addition, mutations in KRAS and BRAF, as well as MSI status were stratified to determine any association with HLA-A LOH. Results: HLA-A LOH was detected in 830 (17.3%) of all solid tumor records, and a similar proportion when all GI cancer records were analyzed (17.0%). For GI subtypes, these values ranged from 13.5% to 23.1% (Table). No high-frequency HLA-A allele (A*01, A*02, A*03, A*11) was more likely to be lost. Clinical biomarkers ( KRAS, BRAF and MSI status) were not associated with HLA-LOH. Conclusions: The frequency of HLA LOH among advanced solid tumor cancers in this dataset is 17.3%, with a range of 13.5-23% between CRC, PANC and GE. The HLA LOH frequency observed in these GI tumors is consistent with that in primary tumors from TCGA, which also used germline-matched and tumor samples. Clinical biomarkers were not associated with HLA LOH. Tempus NGS was able to identify HLA LOH, which can be used for Tmod CAR T therapy to an enhanced therapeutic window. Identification of these patients in BASECAMP-1 (NCT04981119) will enable novel Tmod CAR T therapy. [Table: see text]

The global prevalence and ethnic heterogeneity of primary ciliary dyskinesia gene variants: a genetic database analysis

Primary ciliary dyskinesia (PCD) is a motile ciliopathy characterised by otosinopulmonary infections. Inheritance is commonly autosomal recessive, with extensive locus and allelic heterogeneity. The prevalence is uncertain. Most genetic studies have been done in North America or Europe. The aim of the study was to estimate the worldwide prevalence and ethnic heterogeneity of PCD. We calculated the allele frequency of disease-causing variants in 29 PCD genes associated with autosomal recessive inheritance in 182 681 unique individuals to estimate the global prevalence of PCD in seven ethnicities (African or African American, Latino, Ashkenazi Jewish, Finnish, non-Finnish European, east Asian, and south Asian). We began by aggregating variants that had been interpreted by Invitae, San Francisco, CA, USA, a genetics laboratory with PCD expertise. We then determined the allele frequency of each variant (pathogenic, likely pathogenic, or variant of uncertain significance [VUS]) in the Genome Aggregation Database (gnomAD), a publicly available next-generation sequencing database that aggregates exome and genome sequencing information from a wide variety of large-scale projects and stratifies allele counts by ethnicity. Using the Hardy-Weinberg equilibrium equation, we were able to calculate a lower-end prevalence of PCD for each ethnicity by including only pathogenic and likely pathogenic variants; and upper-end prevalence by also including VUS. This approach was similar to previous work on Li-Fraumeni (TP53 variants) prevalence. We were not diagnosing PCD, but rather estimating prevalence based on known variants. The overall minimum global prevalence of PCD is calculated to be at least one in 7554 individuals, although this is likely to be an underestimate because some variants currently classified as VUS might be disease-causing and some pathogenic variants might not be detected by our methods. In the overall cohort, Invitae data could be included for variants without gnomAD data for a primary ethnicity. When using only gnomAD allele frequencies to calculate prevalence in individual ethnicities, the estimated prevalence of PCD was lower in each ethnicity compared with the overall cohort. This is because the overall cohort includes additional data from the Invitae database such as copy number variants and other variants not present in gnomAD. With gnomAD we found the expected PCD frequency to be higher in individuals of African ancestry than in most other populations (excluding VUS: 1 in 9906 in African or African American vs 1 in 10 388 in non-Finnish European vs 1 in 14 606 in east Asian vs 1 in 16 309 in Latino; including VUS: 1 in 106 in African or African American vs 1 in 178 in non-Finnish European vs 1 in 196 in Latino vs 1 in 188 in east Asian). In addition, we found that the top 5 genes most commonly implicated in PCD differed across ethnic ancestries and contrasted commonly published findings. PCD appears to be more common than has been recognised, particularly in individuals of African ancestry. We identified gene distributions that differ from those in previous European and North American studies. These results could have an international impact on case identification. Our analytic approach can be expanded as more PCD loci are identified, and could be adapted to study the prevalence of other inherited diseases. None.

Machine learning random forest for predicting oncosomatic variant NGS analysis

Since 2017, we have used IonTorrent NGS platform in our hospital to diagnose and treat cancer. Analyzing variants at each run requires considerable time, and we are still struggling with some variants that appear correct on the metrics at first, but are found to be negative upon further investigation. Can any machine learning algorithm (ML) help us classify NGS variants? This has led us to investigate which ML can fit our NGS data and to develop a tool that can be routinely implemented to help biologists. Currently, one of the greatest challenges in medicine is processing a significant quantity of data. This is particularly true in molecular biology with the advantage of next-generation sequencing (NGS) for profiling and identifying molecular tumors and their treatment. In addition to bioinformatics pipelines, artificial intelligence (AI) can be valuable in helping to analyze mutation variants. Generating sequencing data from patient DNA samples has become easy to perform in clinical trials. However, analyzing the massive quantities of genomic or transcriptomic data and extracting the key biomarkers associated with a clinical response to a specific therapy requires a formidable combination of scientific expertise, biomolecular skills and a panel of bioinformatic and biostatistic tools, in which artificial intelligence is now successful in developing future routine diagnostics. However, cancer genome complexity and technical artifacts make identifying real variants challenging. We present a machine learning method for classifying pathogenic single nucleotide variants (SNVs), single nucleotide polymorphisms (SNPs), multiple nucleotide variants (MNVs), insertions, and deletions detected by NGS from different types of tumor specimens, such as: colorectal, melanoma, lung and glioma cancer. We compared our NGS data to different machine learning algorithms using the k-fold cross-validation method and to neural networks (deep learning) to measure the performance of the different ML algorithms and determine which one is a valid model for confirming NGS variant calls in cancer diagnosis. We trained our machine learning with 70% of our data samples, extracted from our local database (our data structure had 7 parameters: chromosome, position, exon, variant allele frequency, minor allele frequency, coverage and protein description) and validated it with the 30% remaining data. The model offering the best accuracy was chosen and implemented in the NGS analysis routine. Artificial intelligence was developed with the R script language version 3.6.0. We trained our model on 70% of 102,011 variants. Our best error rate (0.22%) was found with random forest machine learning (ntree = 500 and mtry = 4), with an AUC of 0.99. Neural networks achieved some good scores. The final trained model with the neural network achieved an accuracy of 98% and an ROC-AUC of 0.99 with validation data. We tested our RF model to interpret more than 2000 variants from our NGS database: 20 variants were misclassified (error rate < 1%). The errors were nomenclature problems and false positives. After adding false positives to our training database and implementing our RF model routinely, our error rate was always < 0.5%. The RF model shows excellent results for oncosomatic NGS interpretation and can easily be implemented in other molecular biology laboratories. AI is becoming increasingly important in molecular biomedical analysis and can be very helpful in processing medical data. Neural networks show a good capacity in variant classification, and in the future, they may be useful in predicting more complex variants.

Molecular Insights into Clonal Hematopoiesis and Therapy-Related Myeloid Neoplasm in Patients with Multiple Myeloma and Cytopenia(s)

Background: Multiple myeloma (MM) is a clonal plasma cell neoplasm typically associated with chronic therapy and resultant potential toxicities, including clonal cytopenias, myelodysplastic syndrome (MDS), or therapy-related myeloid neoplasms (tMN). Early identification of myelodysplasia is important for patient management and outcome. Next generation sequencing (NGS) is playing an ever increasing role in this field. Materials and Methods: The retrospective study was approved by Moffitt institutional review board (IRB). We searched our in-house NGS database with ~6000 patients and clinical databases to identify the patients with MM and sustained cytopenia with accompanying NGS data. The NGS results were analyzed for associations with myeloma and myelodysplasia. Results: Of the 196 identified patients identified (Table 1), there were 114 males (58%) and 82 females (42%) with a median age of 68 years. Eighty-four myeloma patients with cytopenia (43%) were found to have one or more somatic mutations and 112 patients (57%) showed no mutations. The most frequently mutated genes are as following: TP53 (12%), DNMT3A (8%), TET2 (6%), ASXL1 (5%), KRAS (5%), ETV6 (3%), RUNX1 (2%), CUX1 (2%), BCOR (2%), SF3B1 (2%), ZRSR2 (2%), EZH2 (2%), IDH2 (2%), SRSF2 (2%), and BRAF (1%). We divided the patients into four groups according their disease status at the time of NGS testing: 1) patients with myeloma but no myelodysplasia (MM_Only, 105 patients and 53.57%); 2) Patients with myelodysplasia but no overt residual myeloma (Myelodysplasia_Only, 14 patients, 7.14%); 3) Patients with both myeloma and myelodysplasia (MM+Myelodysplasia, 27 patients, 13.78%); 4) Patients with neither myeloma or myelodysplasia (Negative_for_Both, 50 patients, 25.51%). The "Myelodysplasia" in this study is defined as having either overt morphologic dysplasia (&amp;gt;10% of the lineage cells), or equivocal dysplasia but having myeloid-related (non-myeloma) cytogenetic abnormalities. NGS results were not included in the classification to assess the added diagnostic value of NGS. The Mutational profiles of the four disease groups are displayed in Figure 1 and compared in Table 1 and 2. The MM+Myelodysplasia group showed highest percentage of mutations (88.89% of patients tested), followed by Myelodysplasia_Only group (57.14%) and MM_Only group (35.24%), with Negative_for_Both group showing the lowest mutation rate (30.00%). The average number of somatic mutations/case also followed the same order: 1.63, 1.00, 0.48, and 0.36, respectively. Of the 196 patients, 58 patients (29.59%) had no morphologic dysplasia or myeloid-related cytogenetic abnormalities but showed one or more somatic mutations by NGS. These patients harbored clonal cytopenia of uncertain significance (CCUS) clones and would have been missed without NGS testing. Of these 58 patients, retrospective review actually identified 7 patients with morphologic dysplasia and were reclassified as MDS. Further mutational analysis revealed the following interesting findings. ASXL1, DNMT3A, KRAS, and SF3B1 mutations showed highest frequencies in MM+Myelodysplaisa group when compared with other 3 groups (Table 2), indicating a close association with myelodysplasia development in patients with persistent myeloma. In contract, among the 4 groups, RUNX1 mutations were most common in Myelodysplasia_only patients, suggesting a potential alternative pathway for myelodysplasia development in patient with myeloma in remission. It is possible that presence of myeloma clones create different evolution pressure on neoplastic myeloid clones. TP53 mutations were present in MM_Only group, but were much more frequent in patients with MM+Myelodysplasia and Myelodysplasia_only groups. The presence of TP53 mutations might therefore suggest increased risk for myelodysplasia. Finally, TET2 were similar between these groups and therefore not of significant diagnostic value. Conclusion: NGS testing is valuable in identifying CCUS, MDS, or tMN in myeloma patients, especially in those with no morphologic or cytogenetic abnormalities. Statistically significant differences are seen in the mutational profiles of the four groups of patients, suggestive of different roles in myelodysplasia development. Further studies are necessary to better distinguish the origin of these mutations as being derived from the myeloma versus the myeloid components of the disease. Disclosures Hussaini: Stemline: Consultancy; Amgen: Consultancy; Janssen: Consultancy; Adaptive: Consultancy; Boston Biomedical: Consultancy. Shain:Karyopharm: Research Funding, Speakers Bureau; AbbVie: Research Funding; Takeda: Honoraria, Speakers Bureau; Sanofi/Genzyme: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Amgen: Speakers Bureau; GlaxoSmithKline: Speakers Bureau; Adaptive: Consultancy, Honoraria; BMS: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Janssen: Honoraria, Speakers Bureau; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Nishihori:Novartis: Other: Research support to institution; Karyopharm: Other: Research support to institution.

SKmDB: an integrated database of next generation sequencing information in skeletal muscle.

Skeletal muscles have indispensable functions and also possess prominent regenerative ability. The rapid emergence of Next Generation Sequencing (NGS) data in recent years offers us an unprecedented perspective to understand gene regulatory networks governing skeletal muscle development and regeneration. However, the data from public NGS database are often in raw data format or processed with different procedures, causing obstacles to make full use of them. We provide SKmDB, an integrated database of NGS information in skeletal muscle. SKmDB not only includes all NGS datasets available in the human and mouse skeletal muscle tissues and cells, but also provide preliminary data analyses including gene/isoform expression levels, gene co-expression subnetworks, as well as assembly of putative lincRNAs, typical and super enhancers and transcription factor hotspots. Users can efficiently search, browse and visualize the information with the well-designed user interface and server side. SKmDB thus will offer wet lab biologists useful information to study gene regulatory mechanisms in the field of skeletal muscle development and regeneration. Freely available on the web at http://sunlab.cpy.cuhk.edu.hk/SKmDB. Supplementary data are available at Bioinformatics online.

Clinical implications of next-generation sequencing in the treatment of brain cancer at a large academic institution.

e13521 Background: The use of next-generation sequencing (NGS) in clinical practice has increased the treatment (tx) options for cancer patients (pts). The expansion of genomic libraries used by NGS databases has resulted in increased identification of targetable genomic alterations (GAs). The aim of this study was to identify the clinical implications of genomic library expansion in the detection of GAs in pts with brain cancer at a large academic institution. Methods: We retrospectively analyzed 71 consecutive pts with brain cancer at the John Theurer Cancer Center that had NGS performed between 02/2014 and 09/2016. GAs were identified using the FoundationOne assay (Foundation Medicine, Cambridge, MA). GAs, number (n) of available genomic-directed tx and n of clinical trials were reviewed. The NGS assay interrogated 236 genes and introns of 19 genes until 09/2014, and subsequently was expanded to include 315 genes and introns of 28 genes. We compared median survival, n of GAs found, n of available trials, and n of tx available in pts who received NGS until 09/2014 (G1, n = 33) with pts who received NGS after 9/2014 (G2, n = 38). Results: Median survival was 30 months (range 19.9-40.1), median age was 62 years (range 26-82), the median n of GAs/sample was 5 (range 1-11). There was a significant positive correlation between n of GAs/sample and n of available trials and tx (r = .5, p = .00 and r = .3, p = .00, respectively). There was a negative correlation between survival and n of GAs (r = -.3, p = .02). G1 harbored 142 GAs with a median n of 4 GAs/sample (range 1-10), while G2 harbored 170 GAs with a median n of 5.5 GAs/sample (range 0-11). There was an absolute increase of 19.7% in GAs in G2 compared to G1. There was no difference in median overall survival. Conclusions: The expansion of genomic libraries increased the detection of GAs, and was positively correlated with the n of tx and clinical trials available for brain cancer pts. Survival was not affected by the expansion of the genomic library, but higher n of GAs was correlated with shorter survival. Expansions of NGS databases lead to increased n of potential tx options for brain cancer pts. Further studies are needed to investigate the impact of NGS targeted tx on survival.

Non-V600 BRAF Mutations Define a Clinically Distinct Molecular Subtype of Metastatic Colorectal Cancer.

Purpose Molecular diagnostic testing has become an integral part of the evaluation of patients with metastatic colorectal cancer (CRC). Expanded mutational testing, such as next-generation sequencing (NGS), often identifies mutations with unclear clinical or prognostic implications. One such example is BRAF mutations that occur outside of codon 600 (non-V600 BRAF mutations). Methods We conducted this multicenter, retrospective cohort study to characterize the clinical, pathologic, and survival implications of non-V600 BRAF mutations in metastatic CRC. We pooled patients in whom non-V600 BRAF mutations were identified from NGS databases at three large molecular genetics reference laboratories. Results A total of 9,643 patients with metastatic CRC underwent NGS testing. We identified 208 patients with non-V600 BRAF mutations, which occurred in 2.2% of all patients tested and accounted for 22% of all BRAF mutations identified. Cancers with non-V600 BRAF mutations, compared with cancers with V600E BRAF (V600E BRAF) mutations, were found in patients who were significantly younger (58 v 68 years, respectively), fewer female patients (46% v 65%, respectively), and patients who had fewer high-grade tumors (13% v 64%, respectively) or right-sided primary tumors (36% v 81%, respectively). Median overall survival was significantly longer in patients with non-V600 BRAF-mutant metastatic CRC compared with those with both V600E BRAF-mutant and wild-type BRAF metastatic CRC (60.7 v 11.4 v 43.0 months, respectively; P < .001). In multivariable analysis, non-V600 BRAF mutation was independently associated with improved overall survival (hazard ratio, 0.18; P < .001). Conclusion Non-V600 BRAF mutations occur in approximately 2.2% of patients with metastatic CRC and define a clinically distinct subtype of CRC with an excellent prognosis.

Molecular Characterization and Expression Analysis of P38 MAPK Gene and Protein in Aquatic Midge, Chironomus riparius (Diptera: Chironomidae), Exposed to Environmental Contaminants.

P38 Mitogen-activated protein kinase (MAPK), an important signaling protein involved in various cellular processes, including stress responses, has been well characterized in model organisms. P38 has been identified in a number of insects, including the genus Drosophila; however, its homologue in Chironomus riparius has not yet been identified. In this study, we identified and characterized p38 MAPK (Crp38) gene in C. riparius using a transcriptome database that was previously generated 454 GS-FLX pyrosequencing. Comparative and phylogenetic analyses were performed using the p38 homologue of other species, such as Drosophila melanogaster, Aedes aegypti, Bombyx mori, Caenorhabditis elegans, Homo sapiens, etc. Furthermore, to test its potential as a biomarker of environmental contamination, Crp38 gene expression was analyzed upon exposure to nonylphenol (NP), silver nanoparticles (AgNPs), and cadmium (Cd). Crp38 gene expression was up- or down-regulated depending on the concentration and exposure duration of chemicals. These results show the role of Crp38 gene in defense against environmental stresses, as well as its potential use as a biomarker for various environmental pollutants. We further synthesized p38 antibody based on the predicted amino acid sequence deduced from Crp38 cDNA and, using this customized antibody, examined p38 protein expression in Cd exposed C. riparius. Although transcriptional alteration was not translated to the protein level, this result showed the possible application of a protein level functional study using cDNA sequence information from next-generation sequencing database in nonmodel organisms.

The Clinical Next-Generation Sequencing Database: A Tool for the Unified Management of Clinical Information and Genetic Variants to Accelerate Variant Pathogenicity Classification.

ABSTRACTRecent advances in next‐generation sequencing (NGS) have given rise to new challenges due to the difficulties in variant pathogenicity interpretation and large dataset management, including many kinds of public population databases as well as public or commercial disease‐specific databases. Here, we report a new database development tool, named the “Clinical NGS Database,” for improving clinical NGS workflow through the unified management of variant information and clinical information. This database software offers a two‐feature approach to variant pathogenicity classification. The first of these approaches is a phenotype similarity‐based approach. This database allows the easy comparison of the detailed phenotype of each patient with the average phenotype of the same gene mutation at the variant or gene level. It is also possible to browse patients with the same gene mutation quickly. The other approach is a statistical approach to variant pathogenicity classification based on the use of the odds ratio for comparisons between the case and the control for each inheritance mode (families with apparently autosomal dominant inheritance vs. control, and families with apparently autosomal recessive inheritance vs. control). A number of case studies are also presented to illustrate the utility of this database.

The locked genomes: A perspective from Arabia

The locked genomes: A perspective from Arabia

Assessment of species diversity and distribution of an ancient diatom lineage using a DNA metabarcoding approach.

BackgroundContinuous efforts to estimate actual diversity and to trace the species distribution and ranges in the natural environments have gone in equal pace with advancements of the technologies in the study of microbial species diversity from microscopic observations to DNA-based barcoding. DNA metabarcoding based on Next Generation Sequencing (NGS) constitutes the latest advancement in these efforts. Here we use NGS data from different sites to investigate the geographic range of six species of the diatom family Leptocylindraceae and to identify possible new taxa within the family.Methodology/Principal FindingsWe analysed the V4 and V9 regions of the nuclear-encoded SSU rDNA gene region in the NGS database of the European ERA-Biodiversa project BioMarKs, collected in plankton and sediments at six coastal sites in European coastal waters, as well as environmental sequences from the NCBI database. All species known in the family Leptocylindraceae were detected in both datasets, but the much larger Illumina V9 dataset showed a higher species coverage at the various sites than the 454 V4 dataset. Sequences identical or similar to the references of Leptocylindrus aporus, L. convexus, L. danicus/hargravesii and Tenuicylindrus belgicus were found in the Mediterranean Sea, North Atlantic Ocean and Black Sea as well as at locations outside Europe. Instead, sequences identical or close to that of L. minimus were found in the North Atlantic Ocean and the Black Sea but not in the Mediterranean Sea, while sequences belonging to a yet undescribed taxon were encountered only in Oslo Fjord and Baffin Bay.Conclusions/SignificanceIdentification of Leptocylindraceae species in NGS datasets has expanded our knowledge of the species biogeographic distribution and of the overall diversity of this diatom family. Individual species appear to be widespread, but not all of them are found everywhere. Despite the sequencing depth allowed by NGS and the wide geographic area covered by this study, the diversity of this ancient diatom family appears to be low, at least at the level of the marker used in this study.