scholarly journals Detection of genomic alterations in breast cancer with circulating tumour DNA sequencing

2019 ◽  
Author(s):  
Dimitrios Kleftogiannis ◽  
Danliang Ho ◽  
Jun Xian Liew ◽  
Polly Poon ◽  
Anna Gan ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Solid Tumour ◽  
Copy Number Variations ◽  
Healthy Individuals ◽  
Plasma Dna ◽  
Single Nucleotide Variants ◽  
Genomic Alterations ◽  
Single Nucleotide ◽  
Target Region ◽  
Circulating Tumour Dna

AbstractAnalysis of circulating cell-free DNA (cfDNA) data has opened new opportunities for characterizing tumour mutational landscapes with many applications in genomic-driven oncology. We developed a customized targeted cfDNA sequencing approach for breast cancer (BC) using unique molecular identifiers (UMIs) for error correction. Our assay, spanning a 284.5 kb target region, is combined with freely-available bioinformatics pipelines that provide ultra-sensitive detection of single nucleotide variants (SNVs), and reliable identification of copy number variations (CNVs) directly from plasma DNA. In a cohort of 35 BC patients, our approach detected actionable driver and clonal SNVs at low (~0.5%) frequency levels in cfDNA that were concordant (83.3%) with sequencing of primary and/or metastatic solid tumour sites. We also detected ERRB2 gene CNVs used for HER2 subtype classification with 80% precision compared to immunohistochemistry. Further, we evaluated fragmentation profiles of cfDNA in BC and observed distinct differences compared to data from healthy individuals. Our results show that the developed assay addresses the majority of tumour associated aberrations directly from plasma DNA, and thus may be used to elucidate genomic alterations in liquid biopsy studies.

scholarly journals Detection of genomic alterations in breast cancer with circulating tumour DNA sequencing

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Dimitrios Kleftogiannis ◽  
Danliang Ho ◽  
Jun Xian Liew ◽  
Polly S. Y. Poon ◽  
Anna Gan ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Low Frequency ◽  
Copy Number Variations ◽  
Plasma Dna ◽  
Bioinformatics Pipeline ◽  
Genomic Alterations ◽  
Target Region ◽  
Variant Frequency ◽  
Circulating Tumour Dna ◽  
Reference Samples

Abstract Analysis of circulating cell-free DNA (cfDNA) has opened new opportunities for characterizing tumour mutational landscapes with many applications in genomic-driven oncology. We developed a customized targeted cfDNA sequencing approach for breast cancer (BC) using unique molecular identifiers (UMIs) for error correction. Our assay, spanning a 284.5 kb target region, is combined with a novel freely-licensed bioinformatics pipeline that provides detection of low-frequency variants, and reliable identification of copy number variations (CNVs) directly from plasma DNA. We first evaluated our pipeline on reference samples. Then in a cohort of 35 BC patients our approach detected actionable driver and clonal variants at low variant frequency levels in cfDNA that were concordant (77%) with sequencing of primary and/or metastatic solid tumour sites. We also detected ERRB2 gene CNVs used for HER2 subtype classification with 80% precision compared to immunohistochemistry. Further, we evaluated fragmentation profiles of cfDNA in BC and observed distinct differences compared to data from healthy individuals. Our results show that the developed assay addresses the majority of tumour associated aberrations directly from plasma DNA, and thus may be used to elucidate genomic alterations in liquid biopsy studies.

scholarly journals Identifying Genomic Alterations in Stage IV Breast Cancer Patients using MammaSeq™: An International Collaborative Study

2020 ◽  
Author(s):  
Osama Shiraz Shah ◽  
Atilla Soran ◽  
Mustafa Sahin ◽  
Serdar Ugras ◽  
Esin Celik ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cancer Patients ◽  
Clinical Significance ◽  
Copy Number ◽  
Stage Iv ◽  
Copy Number Variations ◽  
Breast Cancer Patients ◽  
Genomic Alterations ◽  
Single Nucleotide ◽  
Stage Iv Breast Cancer

ABSTRACTBackgroundIdentification of genomic alterations present in cancer patients may aid in cancer diagnosis and prognosis and may identify therapeutic targets. In this study, we aimed to identify clinically actionable variants present in stage IV breast cancer (BC) samples.Materials and MethodsDNA was extracted from formalin fixed paraffin embedded (FFPE) samples of BC (n=41). DNA was sequenced using MammaSeq™, a BC specific next generation sequencing panel targeting 79 genes and 1369 mutations. Ion Torrent Suite 4.0 was used to make variant calls on the raw data and the resulting single nucleotide variants were annotated using CRAVAT toolkit. SNVs were filtered to remove common polymorphisms and somatic variants. CNVkit was employed to identify copy number variations. The Precision Medicine Knowledgebase (PMKB) and OncoKB Precision Oncology Database were used to associate clinical significance with the identified variants.ResultsA total of 41 Turkish BC patient samples were sequenced (read depth of 94 – 13340, median of 1529). These samples were from patients diagnosed with various BC subtypes including invasive ductal carcinoma (IDC), invasive lobular carcinoma (ILC), apocrine BC and micropapillary BC. In total, 59 different alterations (49 SNVs and 10 CNVs) were identified. From these, 8 alterations (3 CNVs – ERBB2, FGFR1 and AR copy number gains and 5 SNVs – IDH1.R132H, TP53.E204*, PI3KCA.E545K, PI3KCA.H1047R and PI3KCA.R88Q) were identified to have some clinical significance by PMKB and OncoKB. Moreover, the top five genes with most SNVs included PIK3CA, TP53, MAP3K1, ATM and NCOR1. Additionally, copy number gains and losses were found in ERBB2, GRB7, IGFR1, AR, FGFR1, MYC and IKBKB, and BRCA2, RUNX1 and RB1 respectively.ConclusionWe identified 59 unique alterations in 38 genes in 41 stage IV BC tissue samples using MammaSeq™. Ten of these alterations were found to have some clinical significance by OncoKB and PKMB. This study highlights the potential use of cancer specific NGS panels in clinic to get better insight into the patient-specific genomic alterations.Highlights- 41 stage IV stage breast cancer patients of Turkish descent were sequenced using MammaSeq™- 49 single nucleotide variations and 10 copy number variations identified- PIK3CA and TP53 mutations were present in 24% and 17% of the samples respectively- 37% of the samples had ERBB2/GRB7 gains and 7% had loss of BRCA2/RB1 locus- Eight clinically significant alterations were identifiedMicro AbstractWe performed targeted sequencing using DNA from FFPE samples of 41 stage IV breast cancer patients using MammaSeq™, a breast cancer gene specific targeted sequencing panel. In total, 49 single nucleotide variations (SNVs) and 10 copy number variations (CNVs) were identified. Eight alterations (3 CNVs – ERBB2, FGFR1 and AR copy number gains and 5 SNVs – IDH1.R132H, TP53.E204*, PI3KCA.E545K, PI3KCA.H1047R and PI3KCA.R88Q) were identified to have clinical significance by PMKB and OncoKB databases.

scholarly journals Combination of Genome-Wide Polymorphisms and Copy Number Variations of Pharmacogenes in Koreans

2021 ◽  
Vol 11 (1) ◽  
pp. 33
Author(s):  
Nayoung Han ◽  
Jung Mi Oh ◽  
In-Wha Kim
Keyword(s):  
Copy Number ◽  
Genome Wide Association Study ◽  
Copy Number Gain ◽  
Copy Number Variations ◽  
Gene Gain ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Haplotype Blocks ◽  
Genome Wide ◽  
Control And Prevention

For predicting phenotypes and executing precision medicine, combination analysis of single nucleotide variants (SNVs) genotyping with copy number variations (CNVs) is required. The aim of this study was to discover SNVs or common copy CNVs and examine the combined frequencies of SNVs and CNVs in pharmacogenes using the Korean genome and epidemiology study (KoGES), a consortium project. The genotypes (N = 72,299) and CNV data (N = 1000) were provided by the Korean National Institute of Health, Korea Centers for Disease Control and Prevention. The allele frequencies of SNVs, CNVs, and combined SNVs with CNVs were calculated and haplotype analysis was performed. CYP2D6 rs1065852 (c.100C>T, p.P34S) was the most common variant allele (48.23%). A total of 8454 haplotype blocks in 18 pharmacogenes were estimated. DMD ranked the highest in frequency for gene gain (64.52%), while TPMT ranked the highest in frequency for gene loss (51.80%). Copy number gain of CYP4F2 was observed in 22 subjects; 13 of those subjects were carriers with CYP4F2*3 gain. In the case of TPMT, approximately one-half of the participants (N = 308) had loss of the TPMT*1*1 diplotype. The frequencies of SNVs and CNVs in pharmacogenes were determined using the Korean cohort-based genome-wide association study.

scholarly journals Unsuspected somatic mosaicism for FBN1 gene contributes to Marfan syndrome

2021 ◽  
Author(s):  
Pauline Arnaud ◽  
Hélène Morel ◽  
Olivier Milleron ◽  
Laurent Gouya ◽  
Christine Francannet ◽  
...  
Keyword(s):  
Marfan Syndrome ◽  
Somatic Mosaicism ◽  
Variant Calling ◽  
Copy Number Variations ◽  
Pathogenic Variant ◽  
Single Nucleotide Variants ◽  
Bioinformatics Analyses ◽  
Single Nucleotide ◽  
Fbn1 Gene ◽  
Pathogenic Variants

Abstract Purpose Individuals with mosaic pathogenic variants in the FBN1 gene are mainly described in the course of familial screening. In the literature, almost all these mosaic individuals are asymptomatic. In this study, we report the experience of our team on more than 5,000 Marfan syndrome (MFS) probands. Methods Next-generation sequencing (NGS) capture technology allowed us to identify five cases of MFS probands who harbored a mosaic pathogenic variant in the FBN1 gene. Results These five sporadic mosaic probands displayed classical features usually seen in Marfan syndrome. Combined with the results of the literature, these rare findings concerned both single-nucleotide variants and copy-number variations. Conclusion This underestimated finding should not be overlooked in the molecular diagnosis of MFS patients and warrants an adaptation of the parameters used in bioinformatics analyses. The five present cases of symptomatic MFS probands harboring a mosaic FBN1 pathogenic variant reinforce the fact that apparently asymptomatic mosaic parents should have a complete clinical examination and a regular cardiovascular follow-up. We advise that individuals with a typical MFS for whom no single-nucleotide pathogenic variant or exon deletion/duplication was identified should be tested by NGS capture panel with an adapted variant calling analysis.

Circulating tumor DNA (ctDNA) in patients with advanced adrenocortical carcinoma.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 4585-4585
Author(s):  
Bassel Nazha ◽  
Hiba I. Dada ◽  
Leylah Drusbosky ◽  
Jacqueline T Brown ◽  
Deepak Ravindranathan ◽  
...  
Keyword(s):  
Adrenocortical Carcinoma ◽  
Treatment Options ◽  
Genomic Data ◽  
Circulating Tumor Dna ◽  
Copy Number Variations ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Entire Cohort ◽  
Genomic Landscape ◽  
Ctdna Analysis

4585 Background: Adrenocortical Carcinoma (ACC) is a rare and aggressive malignancy with poor prognosis and limited treatments in the advanced setting. Molecular pathways with tumor suppressor genes (e.g. TP53, CDKN2A) and oncogenes (e.g. CTNNB1 and RAS) are implicated in oncogenesis. To our knowledge, the genomic landscape of ctDNA alterations for ACC has not been described in a large cohort. We report plasma-based ctDNA alterations in patients with advanced ACC. Methods: We retrospectively evaluated genomic data from 102 patients with ACC who had ctDNA testing between 12/2016 – 10/2020 using Guardant360 (Guardant Health, CA). ctDNA analysis interrogated single nucleotide variants (SNV), fusions, indels and copy number variations (CNV) of up to 83 genes. We evaluated the frequency of genomic alterations, the landscape of co-occurring mutations, and pathogenic or likely pathogenic alterations with potential targeted therapies. The prevalence of alterations identified in ctDNA were compared to those detected in tissue using a publicly available database (cBioPortal). Results: The median age was 54 years (range 24-81), and 55% of patients were male. Among the entire cohort, 84 pts (82.4%) had ≥1 somatic alteration detected. Mutations were most frequently detected in TP53 (52%), EGFR (23%), CTNNB1 (18%), MET (18%), and ATM (14%). The frequencies detected in ctDNA were similar to the results detected in tissue. Pathogenic and/or likely pathogenic mutations in therapeutically relevant alterations were observed in 36 patients (35%), including EGFR, BRAF, MET, CDKN2A, and CDK4/6 (Table 1). The most frequently co-occurring mutations were EGFR + TP53 (14%), EGFR + MET (11%), BRAF + MET (10%). Conclusions: Blood-based ctDNA profiling in advanced ACC provided comprehensive genomic data in most patients, with a similar profile to tumor tissue analyses. Over one third of patients had actionable mutations with approved therapies in other cancers. This approach might inform the development of personalized treatment options for this aggressive malignancy.[Table: see text]

Circulating cell-free DNA (ctDNA) assessments before, during, and after neoadjuvant therapy (NAC) in nonmetastatic inflammatory breast cancer (IBC).

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e12113-e12113
Author(s):  
Carolyn S. Hall ◽  
Salyna Meas ◽  
Vanessa Nicole Sarli ◽  
Anthony Lucci
Keyword(s):  
Breast Cancer ◽  
Pathologic Complete Response ◽  
Copy Number Variants ◽  
Residual Tumor ◽  
Complete Response ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Cell Free Dna ◽  
Free Dna ◽  
Circulating Cell Free Dna

e12113 Background: : IBC is a rare and aggressive subtype of breast cancer. A significant number of IBC patients who achieve pathologic complete response (no residual tumor in breast and axillary nodes, pCR) relapse after NAC. We hypothesized that circulating cell-free DNA (ctDNA) identified in blood before, during, and after NAC would identify novel ctDNA targets. Methods: Plasma ctDNA was extracted from 43 non-metastatic IBC patients (IRB: LAB04-0698) pre, mid, and post-NAC. The Oncomine Pan Cancer ctDNA Assay (ThermoFisher) was used for library preparation, and high throughput next generation sequencing was performed on a GeneStudio S5XL System (ThermoFisher), following manufacturer’s directions. ThermoFisher Ion Reporter 5.10 Software was used to analyze single nucleotide variants (SNVs), and copy number variants (CNVs). Results: Seventeen patients had pre-NAC ctDNA assessments; 7/17 (41%) had PIK3CA SNVs; 5/7 also had MYC or FGFR2 CNVs. Five of 17 (29%) had TP53 SNVs; 2/5 also had FGFR2 CNVs. Ten patients had mid-NAC ctDNA assessments; 9/10 (90%) had PIK3CA SNVs; 5/9 also had FGFR2 CNVs, 2/9 had FGFR2 and FGFR3 CNVs, 2/9 also had TP53 SNVs, 1/9 had FGFR2 and ERB2 CNVs. Thirty-one patients had post-NAC ctDNA assessments; 5/31 (16%) had PIK3CA SNVs; 2/5 had FGFR2 CNVs, 1/5 also had a TP53 mutation and an FGFR2 CNV, 1/5 had FGFR2 CNV, and FGFR3 CNV. Six of 31 (19%) had TP53 SNVs, 1/6 had CCND1 CNVs, no CNVs were detected in 6 patients with TP53 SNVs. Six of 31 (19%) had MAP2K1 SNVs. Three of 31 (10%) had MET SNVs; 1/3 had CCND3 CNVs, no CNVs were detected in 2 patients with MET SNVs. No SNVs or CNVs were detected in 10/31 (32%) of patients post NAC. Conclusions: ctDNA assessments before, during, and after NAC identified novel targets that could be tested in future adjuvant therapies trials in IBC patients who remain at high risk for relapse.

Detection of Copy Number Variations in Breast Cancer Samples Using Single-nucleotide Polymorphism-targeted Massively Multiplexed PCR

2014 ◽  
Vol 207 (6) ◽  
pp. 287
Author(s):  
Joshua E. Babiarz ◽  
Bernhard G. Zimmermann ◽  
Tudor Constantin ◽  
Ryan Swenerton ◽  
Eser Kirkizlar ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Single Nucleotide Polymorphism ◽  
Copy Number ◽  
Copy Number Variations ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Multiplexed Pcr

scholarly journals Ultra-sensitive mutation detection and genome-wide DNA copy number reconstruction by error corrected circulating tumour DNA sequencing

2017 ◽  
Author(s):  
Sonia Mansukhani ◽  
Louise J. Barber ◽  
Sing Yu Moorcraft ◽  
Michael Davidson ◽  
Andrew Woolston ◽  
...  
Keyword(s):  
Error Correction ◽  
Copy Number ◽  
Parallel Evolution ◽  
Tumour Tissue ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Target Region ◽  
Circulating Free Dna ◽  
Genome Wide ◽  
Variant Frequency

AbstractMinimally invasive circulating free DNA (cfDNA) analysis can portray cancer genome landscapes but highly sensitive and specific genetic approaches are necessary to accurately detect mutations with often low variant frequencies. We developed a targeted cfDNA sequencing technology using novel off-the-shelf molecular barcodes for error correction, in combination with custom solution hybrid capture enrichment. Modelling based on cfDNA yields from 58 patients shows that our assay, which requires 25ng of cfDNA input, should be applicable to >95% of patients with metastatic colorectal cancer. Sequencing of a 163.3 kb target region including 32 genes detected 100% of single nucleotide variants with 0.15% variant frequency in cfDNA spike-in experiments. Molecular barcode error correction reduced false positive mutation calls by 98.6%. In a series of 28 patients with metastatic colorectal cancers, 80 out of 91 (88%) mutations previously detected by tumour tissue sequencing were called in the cfDNA. Call rates were similar for single nucleotide variants and small insertions/deletions. Mutations only called in cfDNA but not detectable in matched tumour tissue included, among others, a subclonal resistance driver mutation to anti-EGFR antibodies in theKRASgene, multiple activatingPIK3CAmutations in each of two patients (indicative of parallel evolution), andTP53mutations originating from clonal haematopoiesis. Furthermore, we demonstrate that cfDNA off-target read analysis allows the reconstruction of genome wide copy number aberration profiles from 71% of these 28 cases. This error-corrected ultra-deep cfDNA sequencing assay with a target region that can be readily customized enables broad insights into cancer genomes and evolution.

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