Single-Tube qPCR Detection and Quantitation of Hotspot Mutations Down to 0.01% Variant Allele Fraction

Author(s):  
Kerou Zhang ◽  
Luis Rodriguez ◽  
Lauren Yuxuan Cheng ◽  
Michael Wang ◽  
David Yu Zhang
2021 ◽  
pp. 510-524
Author(s):  
Jeffrey C. Thompson ◽  
Erica L. Carpenter ◽  
Benjamin A. Silva ◽  
Jamie Rosenstein ◽  
Austin L. Chien ◽  
...  

PURPOSE Although the majority of patients with metastatic non–small-cell lung cancer (mNSCLC) lacking a detectable targetable mutation will receive pembrolizumab-based therapy in the frontline setting, predicting which patients will experience a durable clinical benefit (DCB) remains challenging. MATERIALS AND METHODS Patients with mNSCLC receiving pembrolizumab monotherapy or in combination with chemotherapy underwent a 74-gene next-generation sequencing panel on blood samples obtained at baseline and at 9 weeks. The change in circulating tumor DNA levels on-therapy (molecular response) was quantified using a ratio calculation with response defined by a > 50% decrease in mean variant allele fraction. Patient response was assessed using RECIST 1.1; DCB was defined as complete or partial response or stable disease that lasted > 6 months. Progression-free survival and overall survival were recorded. RESULTS Among 67 patients, 51 (76.1%) had > 1 variant detected at a variant allele fraction > 0.3% and thus were eligible for calculation of molecular response from paired baseline and 9-week samples. Molecular response values were significantly lower in patients with an objective radiologic response (log mean 1.25% v 27.7%, P < .001). Patients achieving a DCB had significantly lower molecular response values compared to patients with no durable benefit (log mean 3.5% v 49.4%, P < .001). Molecular responders had significantly longer progression-free survival (hazard ratio, 0.25; 95% CI, 0.13 to 0.50) and overall survival (hazard ratio, 0.27; 95% CI, 0.12 to 0.64) compared with molecular nonresponders. CONCLUSION Molecular response assessment using circulating tumor DNA may serve as a noninvasive, on-therapy predictor of response to pembrolizumab-based therapy in addition to standard of care imaging in mNSCLC. This strategy requires validation in independent prospective studies.


2020 ◽  
Vol 20 (9) ◽  
pp. e569-e578
Author(s):  
Wasithep Limvorapitak ◽  
Jeremy Parker ◽  
Curtis Hughesman ◽  
Kelly McNeil ◽  
Lynda Foltz ◽  
...  

PLoS ONE ◽  
2018 ◽  
Vol 13 (11) ◽  
pp. e0206632 ◽  
Author(s):  
David M. Vossen ◽  
Caroline V. M. Verhagen ◽  
Reidar Grénman ◽  
Roelof J. C. Kluin ◽  
Marcel Verheij ◽  
...  

2019 ◽  
Vol 36 (5) ◽  
pp. 1351-1359 ◽  
Author(s):  
Liam F Spurr ◽  
Nawaf Alomran ◽  
Pavlos Bousounis ◽  
Dacian Reece-Stremtan ◽  
N M Prashant ◽  
...  

Abstract Motivation By testing for associations between DNA genotypes and gene expression levels, expression quantitative trait locus (eQTL) analyses have been instrumental in understanding how thousands of single nucleotide variants (SNVs) may affect gene expression. As compared to DNA genotypes, RNA genetic variation represents a phenotypic trait that reflects the actual allele content of the studied system. RNA genetic variation at expressed SNV loci can be estimated using the proportion of alleles bearing the variant nucleotide (variant allele fraction, VAFRNA). VAFRNA is a continuous measure which allows for precise allele quantitation in loci where the RNA alleles do not scale with the genotype count. We describe a method to correlate VAFRNA with gene expression and assess its ability to identify genetically regulated expression solely from RNA-sequencing (RNA-seq) datasets. Results We introduce ReQTL, an eQTL modification which substitutes the DNA allele count for the variant allele fraction at expressed SNV loci in the transcriptome (VAFRNA). We exemplify the method on sets of RNA-seq data from human tissues obtained though the Genotype-Tissue Expression (GTEx) project and demonstrate that ReQTL analyses are computationally feasible and can identify a subset of expressed eQTL loci. Availability and implementation A toolkit to perform ReQTL analyses is available at https://github.com/HorvathLab/ReQTL. Supplementary information Supplementary data are available at Bioinformatics online.


2020 ◽  
Author(s):  
NM Prashant ◽  
Nawaf Alomran ◽  
Yu Chen ◽  
Hongyu Liu ◽  
Pavlos Bousounis ◽  
...  

SummarySCReadCounts is a method for a cell-level estimation of the sequencing read counts bearing a particular nucleotide at genomic positions of interest from barcoded scRNA-seq alignments. SCReadCounts generates an array of outputs, including cell-SNV matrices with the absolute variant-harboring read counts, as well as cell-SNV matrices with expressed Variant Allele Fraction (VAFRNA); we demonstrate its application to estimate cell level expression of somatic mutations and RNA-editing on cancer datasets. SCReadCounts is benchmarked against GATK and Samtools and is freely available as a 64-bit self-contained binary distribution (Linux), along with MacOS and Python installation.Availabilityhttps://github.com/HorvathLab/NGS/tree/master/SCReadCountsSupplementary InformationSCReadCounts_Supplementary_Data.zip


Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 4286-4286
Author(s):  
Wasithep Limvorapitak ◽  
Jeremy Parker ◽  
Lynda Foltz ◽  
Aly Karsan

Abstract Introduction: JAK2V617F mutation is one of the major criteria in the diagnosis of myeloproliferative neoplasms (MPN). The disease phenotype and outcomes are dependent on variant allele fraction (VAF) of JAK2V617F. Recently, a new entity termed clonal hematopoiesis of indeterminate potential (CHIP) defines patients with normal cell counts and VAF of at least 2%. Outcomes of patients with <2% VAF are scarce and we aimed to retrospectively study characteristics and outcomes of patients with JAK2V617F VAF < 2% compared to patients with VAF 2-10%. Methods: The study population included all patients in the province of British Columbia with JAK2V617F testing performed during 2010-2015. We compared the patient characteristics, disease phenotypes, overall survival (OS), thrombosis-free survival (TFS) and cumulative incidence of thrombotic events between patients with VAF <2% and 2-10%. Parallel real-time quantitative polymerase chain reaction (RQ-PCR) for wild type JAK2 and JAK2V617F was used as detection method. MPN diagnoses were based on the treating physicians' assessment. Results: We identified 216 patients with JAK2V617F VAF < 10%. Twenty-seven patients were excluded due to missing follow-up data. A total of 189 patients were included for final analysis (89 patients with VAF <2% and 100 patients with VAF 2-10%). Patient characteristics, diagnoses and outcomes are shown in the Table. Patients with JAK2V617F >2% have significantly higher rate of splenomegaly, higher platelet counts and higher MPN diagnoses. Ten patients (10.0%) with VAF 2-10% had no hematologic diagnoses, consistent with CHIP, while 24 patients (27.0%) with VAF <2% had no hematologic diagnoses. There were no differences in all outcomes measured including thrombotic complications, progression to hematologic or solid cancers and death. The median follow-up time for the whole cohort was 5.2 years with interquartile range (IQR) 3.5-6.6 years. The 5-year OS were 81.0% for VAF < 2% and 81.7% for VAF 2-10%, log-rank P = 0.922. TFS at 5 years were 71.2% and 69.5%, respectively (P = 0.982). The 5-year cumulative incidences of thrombotic complications (considering death as a competing event) were 8.8% and 11.3%, respectively (Pepe-Mori P = 0.574). Further analysis by clinical diagnoses classified patients into polycythemia vera (PV) 40 (21.2%), essential thrombocythemia (ET) 99 (52.3%), primary myelofibrosis or MPN, NOS (PMF/MPN) 16 (8.5%) and clonal hematopoiesis of indeterminate potential (CHIP) or no hematologic diagnosis 34 (18.0%). Patients with PMF/MPN were significantly older than patients with other diagnoses (median age PV 64.2, ET 64.3, PMF/MPN 80.7 and CHIP 54.1 years, P=0.019). The 5-year OS were: PV 91.4%, ET 90.0%, PMF/MPN 31.3% and CHIP/no hematologic diagnoses 58.7%, P<0.001. TFS at 5 years were 83.1%, 74.7%, 25.0%and 57.4%, respectively, P<0.001. Conclusion: Patients with JAK2V617F VAF < 2% have less splenomegaly and are less likely to have a diagnosis of MPN compared to patients with VAF 2-10%. However, the incidence of thrombotic events was similar between patients with VAF < 2% and 2-10%. In the combined VAF < 10% cohort, PMF/MPN patients were older and had the worst survival outcomes. The mortality in this PMF/MPN group was mostly unrelated to MPN diagnoses. Interestingly, patients with CHIP/no hematologic diagnoses in this study have the next worse OS and TFS. This could be explained by selection bias for performing JAK2 testing in acute or chronically ill patients with reactive changes in the peripheral blood. Table. Table. Disclosures Foltz: Gilead: Research Funding; Novartis: Consultancy, Honoraria, Research Funding; Promedior: Research Funding; Incyte: Research Funding.


Lung Cancer ◽  
2019 ◽  
Vol 131 ◽  
pp. 86-89 ◽  
Author(s):  
Grainne M. O’Kane ◽  
Geoffrey Liu ◽  
Tracy L. Stockley ◽  
Muqdas Shabir ◽  
Tong Zhang ◽  
...  

2020 ◽  
Author(s):  
Hongyu Liu ◽  
N M Prashant ◽  
Liam F. Spurr ◽  
Pavlos Bousounis ◽  
Nawaf Alomran ◽  
...  

AbstractRecently, pioneering eQTLs studies on single cell RNA-seq (scRNA-seq) data have revealed new and cell-specific regulatory SNVs. Because eQTLs correlate genotypes and gene expression across multiple individuals, they are confined to SNVs with sufficient population frequency. Here, we present an alternative sc-eQTL approach – scReQTL - wherein we substitute the genotypes with expressed Variant Allele Fraction (VAFRNA) at heterozygous SNV sites. Our approach employs the advantage that, when estimated from multiple cells, VAFRNA can be used to assess effects of rare SNVs in a single individual. ScReQTLs are enriched in known genetic interactions, therefore can be used to identify novel regulatory SNVs.


2021 ◽  
pp. mcs.a006119
Author(s):  
Christopher L Sudduth ◽  
Dennis J Konczyk ◽  
Patrick J Smits ◽  
Whitney Eng ◽  
Alyaa Al-Ibraheemi ◽  
...  

Bockenheimer disease is a venous malformation involving all tissues of an extremity. Patients have significant morbidity and treatment is palliative. The purpose of this study was to identify the cause of Bockenheimer disease to develop pharmacotherapy for the condition. Paraffin-embedded tissue from 9 individuals with Bockenheimer disease obtained during a clinically-indicated operation underwent DNA extraction. Droplet digital PCR (ddPCR) was used to screen for variants most commonly associated with sporadic venous malformations [TEK (NM_000459.5:c.2740C>T; p.Leu914Phe), PIK3CA (NM_006218.4:c.1624G>A; p.Glu542Lys and NM_006218.4:c.3140A>G; p.His1047Arg)]. ddPCR detected a TEK L914F variant in all 9 patients (variant allele fraction 2%-13%). PIK3CA E542K and H1047R variants were not identified in the specimens. Sanger sequencing and restriction enzyme digestion confirmed variants identified by ddPCR. A pathogenic variant in the endothelial cell tyrosine kinase receptor TEK is associated with Bockenheimer disease. Pharmacotherapy targeting the TEK signaling pathway might benefit patients with the condition.


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