Estimating tumor mutation burden using next-generation sequencing assay

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Background: High tumor mutation burden is a promising biomarker shown in some cancer types to predict positive response to immune checkpoint inhibitors. We show the ability of a targeted cancer research panel to estimate tumor mutation burden per megabase. Methods: We present a single sample analysis workflow for estimating tumor mutation burden from FFPE research samples. Our assay utilizes a PCR-based target enrichment panel that interrogates 409 known key cancer genes covering ~1.7 megabase of genomic space. Our customized workflow requires only 20 ng of input DNA, and enables a 2 day turn-around time from sample to the result. The ease of our workflow enables less than 60 minutes of hands-on time for automated library preparation and templating on a batch of 8 samples. Next-generation Sequencing is performed using high throughput semiconductor sequencing platform to achieve sufficient depth (~500x coverage) and accuracy. Our custom analysis pipeline calls variants with optimized parameters on the tumor sample only, with no matched normal sample required, and applies filters to remove germ-line variants and background noise. Results: Through in silico analysis performed on The Cancer Genome Atlas (TCGA) data we demonstrate that the panel achieves high sensitivity ( > 90%) and specificity ( > 95%) necessary to separate high and low mutation burden samples. Our workflow provides clear separation between allele ratio of somatic and germ-line variants. Our filters consistently eliminate ~98% of germ-line variants from the set of all variants called in single sample analysis workflow. Evidence from tumor-normal analyses on matched tumor and normal samples suggests that our single sample analysis, on the tumor sample only, detects somatic mutations with high sensitivity and specificity with residual of < 3% germ-line variants. Our pipeline identifies mutational signatures consistent with specific mechanisms such as spontaneous deamination of 5-methyl-cytosine, as well as base-damage from FFPE processing. Conclusions: A simple workflow has been developed on the Ion Torrent sequencing platform to estimate per megabase somatic mutational burden from a single tumor FFPE sample. This solution can help advance research in immuno-oncology.

Somatic mutation burden in cancer samples determined by targeted next generation sequencing

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Background: High somatic mutation burden in tumor tissues is associated with the presentation of neoantigens that promote immune responses particularly in the context of immune checkpoint therapies. Herein, we characterize the ability of targeted cancer research panels to generate estimates of somatic mutation burden. Methods: Somatic mutation data from > 8000 cancer samples obtained from The Cancer Genome Atlas (TCGA) was curated and standardized, and the number of single nucleotide variants (SNVs) in exonic regions of each sample determined. Next, the number of SNVs associated with target regions of two Ion AmpliSeq cancer panels (Oncomine Comprehensive Assay [OCA, 146 genes, 0.35 MB]; Comprehensive Cancer Panel [CCP, 409 genes, 1.7 MB]) was likewise determined and the frequency of mutation counts in the exome and the panel target regions was compared. Mutation counts of samples containing truncating mutations in mismatch repair (MMR) and other DNA repair genes were characterized. A facile workflow with less than 60 minutes of hands-on time was developed to estimate mutation counts for a batch of 8 samples using the Ion Chef for automated library preparation and templating followed by sequencing on the Ion S5. Results: The sensitivity of targeted panels in estimating somatic mutation burden was positively correlated with panel size. The area under the Receiver Operating Characteristic (ROC) curve showed that CCP had > 90% sensitivity and > 95% specificity to differentiate high and low mutation burden based on informatics analysis of TCGA data. As expected, truncating mutations in MMR genes were associated with higher somatic mutation counts in colorectal tumor tissue. Using data generated from OCA and CCP, we characterized a set of filters that provided a good estimate of somatic mutation counts when applied to a tumor-only workflow. Conclusions: A simple workflow was developed on the Ion Torrent sequencing platform to estimate somatic mutation burden in cancer samples. The methods described herein will help advance research in immuo-oncology.

Abstract 4933: Sanger sequencing of low amount of genomic DNA and FFPE DNA with PCR primers derived from the Ion AmpliSeq cancer hotspot panel

The introduction of defined Ion AmpliSeq™ panels for detection and characterization of actionable mutations occurring in tumor tissue has the potential to revolutionize translational oncology research.

The Ion Ampliseq™ cancer hotspot panel version 2 (CHP v2) by Ion Torrent includes 207 actionable mutation targets present in 50 genes and the more comprehensive Ion Oncomine™ cancer panel (OCP) contains over 2000 mutations. A hallmark of these Ion Torrent Ampliseq cancer panels is the low amount of input DNA needed which is critical when the clinical specimen material is limited such as with fine needle biopsy or FFPE samples. Typically, 10 ng of DNA obtained from these sources is sufficient to produce informative sequencing data. Often, cancer-causing or promoting mutations are detected at relatively low allele frequencies like 10-20% compared to the major normal allele. Many researchers wish to verify these findings of low frequency mutations by an orthologous method such as traditional dye-fluorescent Sanger sequencing on a capillary electrophoresis (CE) instrument such as the Applied Biosystems 3500 genetic analyzer. To that end, we have developed a workflow that enables the amplification and traditional Sanger sequencing of individual Ion AmpliSeq targets directly from the AmpliSeq library starting material.

The method requires a retainer of 1 μl (∼ 5%) of the original AmpliSeq preamplification material. A dilution of this aliquot is used as template source for individualized PCR/sequencing reactions. We show that a random selection of 48 targets from the CHPv2 panel could be successfully amplified and Sanger-sequenced from an Ion Torrent Ampliseq library originally prepared from 10 ng of FFPE DNA. Furthermore, we show the successful Sanger-re-sequencing of all individual 24 targets covering the TP53 exons from the same sample processed and pre-amplified with the OncoMine AmpliSeq panel.

Taken together, this method will enable researchers to reflex-test potential mutations of interest from very material-limited specimen using Sanger CE sequencing.

Citation Format: Edgar H. Schreiber, Adam Broomer, Mark Andersen, Kamini Varma. Sanger sequencing of low amount of genomic DNA and FFPE DNA with PCR primers derived from the Ion AmpliSeq cancer hotspot panel. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4933. doi:10.1158/1538-7445.AM2015-4933

Abstract 5076: Rapid assessment of AML genes for mutation detection and copy number variation

Targeted sequencing using the Ion AmpliSeq™ Library kit combined with the Ion PGM™ sequencing instrument is a fast and effective method to identify genetic variants in cancer samples. A new targeted primer panel for amplification of genes involved in Acute Myeloid Leukemia (AML) has been developed by Life Technologies. The panel covers 19 genes characterized using over 300 specific primer pairs in two highly multiplexed PCRs. To demonstrate the coverage efficiency, we evaluated libraries prepared from whole blood and isolated genomic DNA. When libraries from 4 individuals were run on a single Ion 318™ Chip, the average coverage depth was &gt;3000x, with &gt;97% of the target bases covered &gt;500X. Additionally, &gt;90% of reads were on-target. The panel was tested on control samples and analyzed using the Ion Reporter™ Software, and expected variants, including copy number variations (CNVs) were detected with high sensitivity and specificity.

Citation Format: Mark Andersen, Kate Rhodes, Steve Roman, Cristina VanLoy, Adam Broomer, Michael Allen, Denise Topacio, Guoying Liu, Fiona Hyland. Rapid assessment of AML genes for mutation detection and copy number variation. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5076. doi:10.1158/1538-7445.AM2014-5076

Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes

BACKGROUND

Duplications and deletions in the human genome can cause disease or predispose persons to disease. Advances in technologies to detect these changes allow for the routine identification of submicroscopic imbalances in large numbers of patients.

METHODS

We tested for the presence of microdeletions and microduplications at a specific region of chromosome 1q21.1 in two groups of patients with unexplained mental retardation, autism, or congenital anomalies and in unaffected persons.

RESULTS

We identified 25 persons with a recurrent 1.35-Mb deletion within 1q21.1 from screening 5218 patients. The microdeletions had arisen de novo in eight patients, were inherited from a mildly affected parent in three patients, were inherited from an apparently unaffected parent in six patients, and were of unknown inheritance in eight patients. The deletion was absent in a series of 4737 control persons (P=1.1x10(-7)). We found considerable variability in the level of phenotypic expression of the microdeletion; phenotypes included mild-to-moderate mental retardation, microcephaly, cardiac abnormalities, and cataracts. The reciprocal duplication was enriched in nine children with mental retardation or autism spectrum disorder and other variable features (P=0.02). We identified three deletions and three duplications of the 1q21.1 region in an independent sample of 788 patients with mental retardation and congenital anomalies.

CONCLUSIONS

We have identified recurrent molecular lesions that elude syndromic classification and whose disease manifestations must be considered in a broader context of development as opposed to being assigned to a specific disease. Clinical diagnosis in patients with these lesions may be most readily achieved on the basis of genotype rather than phenotype.

A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures

We report a recurrent microdeletion syndrome causing mental retardation, epilepsy and variable facial and digital dysmorphisms. We describe nine affected individuals, including six probands: two with de novo deletions, two who inherited the deletion from an affected parent and two with unknown inheritance. The proximal breakpoint of the largest deletion is contiguous with breakpoint 3 (BP3) of the Prader-Willi and Angelman syndrome region, extending 3.95 Mb distally to BP5. A smaller 1.5-Mb deletion has a proximal breakpoint within the larger deletion (BP4) and shares the same distal BP5. This recurrent 1.5-Mb deletion contains six genes, including a candidate gene for epilepsy (CHRNA7) that is probably responsible for the observed seizure phenotype. The BP4-BP5 region undergoes frequent inversion, suggesting a possible link between this inversion polymorphism and recurrent deletion. The frequency of these microdeletions in mental retardation cases is approximately 0.3% (6/2,082 tested), a prevalence comparable to that of Williams, Angelman and Prader-Willi syndromes.

Filter-based PNA in situ hybridization for rapid detection, identification and enumeration of specific micro-organisms

AIMS

A method for rapid and simultaneous detection, identification and enumeration of specific micro-organisms using Peptide Nucleic Acid (PNA) probes is presented.

METHODS AND RESULTS

The method is based on a membrane filtration technique. The membrane filter was incubated for a short period of time. The microcolonies were analysed by in situ hybridization, using peroxidase-labelled PNA probes targeting a species-specific rRNA sequence, and visualized by a chemiluminescent reaction. Microcolonies were observed as small spots of light on film, thereby providing simultaneous detection, identification and enumeration. The method showed 95-100% correlation to standard plate counts along with definitive identification due to the specificity of the probe.

CONCLUSION

Using the same protocol, results were generated approximately three times faster than culture methods for Gram-positive and -negative bacterial species and yeast species.

SIGNIFICANCE AND IMPACT OF THE STUDY

The method is an improvement on the current membrane filtration technique, providing rapid determination of the level of specific pathogens, spoilage or indicator micro-organisms.

Identification of Dekkera bruxellensis (Brettanomyces) from wine by fluorescence in situ hybridization using peptide nucleic acid probes

A new fluorescence in situ hybridization method using peptide nucleic acid (PNA) probes for identification of Brettanomyces is described. The test is based on fluorescein-labeled PNA probes targeting a species-specific sequence of the rRNA of Dekkera bruxellensis. The PNA probes were applied to smears of colonies, and results were interpreted by fluorescence microscopy. The results obtained from testing 127 different yeast strains, including 78 Brettanomyces isolates from wine, show that the spoilage organism Brettanomyces belongs to the species D. bruxellensis and that the new method is able to identify Brettanomyces (D. bruxellensis) with 100% sensitivity and 100% specificity.

Rapid detection, identification, and enumeration of Pseudomonas aeruginosa in bottled water using peptide nucleic acid probes

A new chemiluminescent in situ hybridization (CISH) method that provides simultaneous detection, identification, and enumeration of Pseudomonas aeruginosa in bottled water within 1 working day has been developed. Individual micro-colonies of P. aeruginosa were detected directly on membrane filters following 5 h of growth by use of soybean peroxidase-labeled peptide nucleic acid (PNA) probes targeted to a species-specific sequence in P. aeruginosa rRNA. Within each micro-colony, reaction of the peroxidase with a chemiluminescent substrate generated light that was subsequently captured by film or with a digital camera system. Each spot of light represented one micro-colony of P. aeruginosa. Sensitivity and specificity for the identification of P. aeruginosa were 100% as determined by testing 28 P. aeruginosa strains and 17 other bacterial species that included closely related Pseudomonas species. Furthermore, the number of micro-colonies of P. aeruginosa represented by light spots correlated with counts of visible colonies following sustained growth. We conclude that PNA CISH speeds up traditional membrane filtration techniques and adds the specificity of PNA probe technology to generate fast and definitive results.