CloneRetriever: An Automated Algorithm to Identify Clonal B and T Cell Gene Rearrangements by Next-Generation Sequencing for the Diagnosis of Lymphoid Malignancies

BACKGROUND

Clonal immunoglobulin and T-cell receptor rearrangements serve as tumor-specific markers that have become mainstays of the diagnosis and monitoring of lymphoid malignancy. Next-generation sequencing (NGS) techniques targeting these loci have been successfully applied to lymphoblastic leukemia and multiple myeloma for minimal residual disease detection. However, adoption of NGS for primary diagnosis remains limited.

METHODS

We addressed the bioinformatics challenges associated with immune cell sequencing and clone detection by designing a novel web tool, CloneRetriever (CR), which uses machine-learning principles to generate clone classification schemes that are customizable, and can be applied to large datasets. CR has 2 applications-a "validation" mode to derive a clonality classifier, and a "live" mode to screen for clones by applying a validated and/or customized classifier. In this study, CR-generated multiple classifiers using 2 datasets comprising 106 annotated patient samples. A custom classifier was then applied to 36 unannotated samples.

RESULTS

The optimal classifier for clonality required clonal dominance ≥4.5× above background, read representation ≥8% of all reads, and technical replicate agreement. Depending on the dataset and analysis step, the optimal algorithm yielded sensitivities of 81%-90%, specificities of 97%-100%, areas under the curve of 91%-94%, positive predictive values of 92-100%, and negative predictive values of 88%-98%. Customization of the algorithms yielded 95%-100% concordance with gold-standard clonality determination, including rescue of indeterminate samples. Application to a set of unknowns showed concordance rates of 83%-96%.

CONCLUSIONS

CR is an out-of-the-box ready and user-friendly software designed to identify clonal rearrangements in large NGS datasets for the diagnosis of lymphoid malignancies.

Feasibility of Cell-Free DNA Collection and Clonal Immunoglobulin Sequencing in South African Patients With HIV-Associated Lymphoma

PURPOSE

Diagnosis of AIDS lymphoma in low-resource settings, like South Africa, is often delayed, leaving patients with limited treatment options. In tuberculosis (TB) endemic regions, overlapping signs and symptoms often lead to diagnostic delays. Assessment of plasma cell-free DNA (cfDNA) by next-generation sequencing (NGS) may expedite the diagnosis of lymphoma but requires high-quality cfDNA.

METHODS

People living with HIV with newly diagnosed aggressive B-cell lymphoma and those with newly diagnosed TB seeking care at Chris Hani Baragwanath Academic Hospital and its surrounding clinics, in Soweto, South Africa, were enrolled in this study. Each participant provided a whole blood specimen collected in cell-stabilizing tubes. Quantity and quality of plasma cfDNA were assessed. NGS of the immunoglobulin heavy chain was performed.

RESULTS

Nine HIV+ patients with untreated lymphoma and eight HIV+ patients with TB, but without lymphoma, were enrolled. All cfDNA quantity and quality metrics were similar between the two groups, except that cfDNA accounted for a larger fraction of recovered plasma DNA in patients with lymphoma. The concentration of cfDNA in plasma also trended higher in patients with lymphoma. NGS of immunoglobulin heavy chain showed robust amplification of DNA, with large amplicons (> 250 bp) being more readily detected in patients with lymphoma. Clonal sequences were detected in five of nine patients with lymphoma, and none of the patients with TB.

CONCLUSION

This proof-of-principle study demonstrates that whole blood collected for cfDNA in a low-resource setting is suitable for sophisticated sequencing analyses, including clonal immunoglobulin NGS. The detection of clonal sequences in more than half of patients with lymphoma shows promise as a diagnostic marker that may be explored in future studies.

Abstract 5671: Alignment of TMB measured on clinical samples: Phase IIB of the Friends of Cancer Research TMB Harmonization Project

Introduction:

Tumor mutational burden (TMB) is the number of somatic mutations per megabase in a tumor's genome and has shown promise as a predictive biomarker of response to immune checkpoint inhibitors across several cancers. TMB is typically measured by whole exome sequencing (WES TMB) or by targeted next-generation sequencing gene panels (panel TMB). As more assays are developed to estimate TMB, harmonization is emerging as an unmet need and is a key goal of the Friends of Cancer Research (Friends) TMB Harmonization Project. Phase I of the Harmonization Project demonstrated correlation between panel TMB and WES TMB using TCGA data and defined theoretical sources of variability across panels. In phase IIA, sustainable TMB reference standard materials generated from human derived cell lines were used to characterize variability in TMB measurements across panels and assessed for utility in TMB alignment. Phase IIB aims to characterize variability in TMB measurements in clinical samples and to establish best practices for estimating and aligning TMB in order to improve consistency across panels.

Methods:

Fifteen laboratories (16 targeted gene panels) at different stages of development participated in phase IIB. Thirty formalin-fixed paraffin-embedded (FFPE) samples with >30% tumor content were acquired; tumor DNA was isolated by a single reference lab. TMB values were calculated for DNA extracted from lung (N=10), bladder (N=10), and gastric tumors (N=10) using WES and a uniform bioinformatics pipeline agreed upon by all Consortium members. DNA samples were also sent to all laboratories, and each used their own sequencing and bioinformatics pipelines to estimate TMB from the genes represented in their respective panels. For each tumor sample, a median across panel TMB estimates was calculated; individual panel TMB estimates were translated to fold-changes relative to the sample median to quantify variability. Association between WES TMB (reference) and panel TMB will be assessed by regression analysis; dependence of association on cancer type was investigated.

Results:

A subset of tumor samples (9 bladder, 7 lung, and 5 gastric) was analyzed using 11 panels at the time of abstract submission. Median panel TMB values ranged 0.60 - 40.26 across samples, with median of median values of 5.35. Fold-change from sample-level medians ranged 0x - 6.67x. Assessment of these clinical samples by WES and all 16 gene panels, as well as regression analysis results, are forthcoming.

Conclusions:

The Friends TMB Harmonization Project has made substantial progress in characterization of TMB measurement variability and association between WES TMB and panel TMB. These are important steps toward alignment of TMB estimates generated by different gene panels which may improve the interpretation of findings within clinical development programs and ultimately enhance the usefulness of this predictive biomarker in clinical decision making.

Citation Format: Diana M. MERINO, Laura M. Yee, Lisa M. McShane, P. Mickey Williams, Tomas Vilimas, Rajesh Patidar, J. Carl Barrett, Shu-Jen Chen, Jen-Hao Cheng, Jeffrey M. Conroy, Dinesh Cyanam, Kenneth R. Eyring, David A. Fabrizio, Vincent Funari, Elizabeth P. Garcia, Sean T. Glenn, Christopher D. Gocke, Vikas Gupta, Lisa M. Haley, Matthew D. Hellmann, Laurel Keefer, Lauryn R. Keeler, Brett Kennedy, Alexander J. Lazar, Laura E. MacConaill, Kristen L. Meier, Arnaud Papin, Naiyer A. Rizvi, Ethan Sokol, Phillip Stafford, John F. Thompson, Warren Tom, Victor J. Weigman, Mingchao Xie, Chen Zhao, Mark D. Stewart, Jeff Allen. Alignment of TMB measured on clinical samples: Phase IIB of the Friends of Cancer Research TMB Harmonization Project [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5671.

Circulating Tumor DNA as a Clinical Test in Resected Pancreatic Cancer

PURPOSE

In research settings, circulating tumor DNA (ctDNA) shows promise as a tumor-specific biomarker for pancreatic ductal adenocarcinoma (PDAC). This study aims to perform analytical and clinical validation of a KRAS ctDNA assay in a Clinical Laboratory Improvement Amendments (CLIA) and College of American Pathology-certified clinical laboratory.

EXPERIMENTAL DESIGN

Digital-droplet PCR was used to detect the major PDAC-associated somatic KRAS mutations (G12D, G12V, G12R, and Q61H) in liquid biopsies. For clinical validation, 290 preoperative and longitudinal postoperative plasma samples were collected from 59 patients with PDAC. The utility of ctDNA status to predict PDAC recurrence during follow-up was assessed.

RESULTS

ctDNA was detected preoperatively in 29 (49%) patients and was an independent predictor of decreased recurrence-free survival (RFS) and overall survival (OS). Patients who had neoadjuvant chemotherapy were less likely to have preoperative ctDNA than were chemo-naïve patients (21% vs. 69%; P < 0.001). ctDNA levels dropped significantly after tumor resection. Persistence of ctDNA in the immediate postoperative period was associated with a high rate of recurrence and poor median RFS (5 months). ctDNA detected during follow-up predicted clinical recurrence [sensitivity 90% (95% confidence interval (CI), 74%-98%), specificity 88% (95% CI, 62%-98%)] with a median lead time of 84 days (interquartile range, 25-146). Detection of ctDNA during postpancreatectomy follow-up was associated with a median OS of 17 months, while median OS was not yet reached at 30 months for patients without ctDNA (P = 0.011).

CONCLUSIONS

Measurement of KRAS ctDNA in a CLIA laboratory setting can be used to predict recurrence and survival in patients with PDAC.

Validation Strategy for Ultrasensitive Mutation Detection

BACKGROUND

Ultrasensitive detection of low-abundance DNA point mutations is a challenging molecular biology problem, because nearly identical mutant and wild-type molecules exhibit crosstalk. Reliable ultrasensitive point mutation detection will facilitate early detection of cancer and therapeutic monitoring of cancer patients.

OBJECTIVE

The objective of this study was to develop a method to correct errors in low-level cell line mixes.

MATERIALS AND METHODS

We tested sample mixes with digital-droplet PCR (ddPCR) and next-generation sequencing.

RESULTS

We introduced two corrections: baseline variant allele frequency (VAF) in the parental cell line was used to correct for copy number variation; and haplotype counting was used to correct errors in cell counting and pipetting. We found ddPCR to have better correlation for detecting low-level mutations without applying any correction (R² = 0.80) and be more linear after introducing both corrections (R² = 0.99).

CONCLUSIONS

The VAF correction was found to be more significant than haplotype correction. It is imperative that various technologies be evaluated against each other and laboratories be provided with defined quality control samples for proficiency testing.

The role of low (< or = 1 mM) phosphate concentrations in regulation of mitochondrial permeability: modulation of matrix free Ca2+ concentration

Under a variety of conditions, the permeability of the inner mitochondrial membrane to small solutes can be nonselectively increased. A classic mitochondrial permeability transition (MPT) was originally identified based on its dependence on matrix Ca2+ and its extreme sensitivity to cyclosporin A (CsA). It is now clear, however, that several additional and distinct processes can also produce increases in mitochondrial permeability. Both mitochondrial signal peptides (P. M. Sokolove and K. W. Kinnally, 1996, Arch. Biochem. Biophys. 336, 69-76) and butylated hydroxytoluene (BHT) (P. M. Sokolove and L. M. Haley, 1996, J. Bioenerg. Biomembr. 28, 199-206), for example, induce permeability increases that are relatively CsA insensitive and that persist in the presence of EGTA. Inorganic phosphate (Pi) appears to play a key role in each of these permeability increases. High (>1 mM) Pi levels facilitate the classic MPT, while Pi concentrations below 1 mM stimulate the permeability increase induced by signal peptides and inhibit that triggered by BHT. The effect of high Pi concentrations can most probably be explained by exchange of the anion for matrix ADP and the resulting alleviation of ADP-mediated inhibition of the MPT (R. G. Lapidus and P. M. Sokolove, 1994, J. Biol. Chem. 269, 18931-18936). In the experiments reported here, the mechanisms underlying the effects of low Pi concentrations on mitochondrial permeability were investigated, by monitoring mitochondrial volume, with the following results: (1) A hitherto unrecognized ability of Pi (<1 mM) to increase the lag preceding induction of the classic MPT by diamide, phenylarsine oxide, and t-butylhydroperoxide was identified. (2) Data were obtained suggesting that all of the effects of low Pi concentration, stimulation of signal peptide-induced swelling, blockade of BHT-induced swelling, and delay of the classic MPT, can be attributed to the capacity of the anion to complex Ca2+ in the mitochondrial matrix. (3) Differences in the responses of these three systems for enhancing mitochondrial permeability to experimental manipulation indicate that matrix Ca2+ plays more than one role in the regulation of mitochondrial permeability. An additional important finding is the observation that failure of EGTA to alter a mitochondrial process need not mean that the process is Ca2+ independent. In a multicompartment system, absence of EGTA action may instead reflect failure of the chelator to gain access to regulatory Ca2+.

Butylated hydroxytoluene and inorganic phosphate plus Ca2+ increase mitochondrial permeability via mutually exclusive mechanisms

Mitochondria undergo a permeability transition (PT)2, i.e., become nonselectively permeable to small solutes, in response to a wide range of conditions/compounds. In general, opening of the permeability transition pore (PTP) is Ca2+- and P(i)-dependent and is blocked by cyclosporin A (CsA), trifluoperazine (TFP), ADP, and butylated hydroxytoluene (BHT). Gudz and coworkers have reported [7th European Bioenergetics Conference, EBEC Short Reports (1992) 7, 125], however, that, under some conditions, BHT increases mitochondrial permeability via a process that may not share all of these characteristics. Specifically, they determined that the BHT-induced permeability transition was independent of Ca2+ and was insensitive to CsA. We have used mitochondrial swelling to compare in greater detail the changes in permeability induced by BHT and by Ca2+ plus P(i) with the following results. (1) The dependence of permeability on BHT concentration is triphasic: there is a threshold BHT concentration (ca. 60 nmol BHT/ mg mitochondrial protein) below which no increase occurs; BHT enhances permeability in an intermediate concentration range; and at high BHT concentrations (>120 nmol/mg) permeability is again reduced. (2) The effects of BHT depend on the ratio of BHT to mitochondrial protein. (3) Concentrations of BHT too low to induce swelling block the PT induced by Ca2+ and P(i). (4) The dependence of the Ca2+-triggered PT on P(i) concentration is biphasic. Below a threshold of 50-100 mu M, no swelling occurs. Above this threshold swelling increases rapidly. (5) P(i) levels too low to support the Ca2+-induced PT inhibit BHT-induced swelling. (6) Swelling induced by BHT can be stimulated by agents and treatments that block the PT induced by Ca2+ plus P(i). These data suggest that BHT and Ca2+ plus P(i) increase mitochondrial permeability via two mutually exclusive mechanisms.