Identifying low-level sequence variants via next generation sequencing to aid stable CHO cell line screening

2015 ◽  
Vol 31 (4) ◽  
pp. 1077-1085 ◽  
Author(s):  
Sheng Zhang ◽  
Lisa Bartkowiak ◽  
Bernard Nabiswa ◽  
Pratibha Mishra ◽  
John Fann ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Cell Line ◽  
Sequence Variants ◽  
Next Generation ◽  
Cho Cell ◽  
Low Level ◽  
Level Sequence ◽  
Cho Cell Line ◽  
Generation Sequencing

Next-Generation Sequencing Of The BCR-ABL1 Kinase Domain May Be Beneficial In Decision Making Among Chronic Myeloid Leukemia Patients With Tyrosine Kinase Inhibitor Resistance

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 384-384 ◽  
Author(s):  
Yucel Erbilgin ◽  
Ahmet Emre Eskazan ◽  
Ozden Hatirnaz Ng ◽  
Ayse Salihoglu ◽  
Tugrul Elverdi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Myeloid Leukemia ◽  
Kinase Inhibitor ◽  
Kinase Domain ◽  
Next Generation ◽  
Time Points ◽  
Low Level ◽  
Development Of Resistance ◽  
Tki Resistance ◽  
Generation Sequencing

Abstract Background and Aim BCR-ABL1 mutation testing is recommended for chronic myeloid leukemia (CML) patients who have suboptimal response and/or treatment failure with tyrosine kinase inhibitor (TKI) therapy. BCR-ABL1 mutations in the kinase domain (KD) of ABL1 account for at least 40-50% of all TKI resistant cases. Thus, detection of low-level mutations after development of resistance may offer critical information to guide subsequent therapy selection. The current gold standard for BCR-ABL1 mutation detection is Sanger sequencing (SS), which has an analytical sensitivity of approximately 10-20%. In this study, our aim was to detect low level BCR-ABL1 variants in follow up samples of CML patients with TKI resistance using next-generation sequencing (NGS) approach. Methods Eight patients with CML who were resistant to imatinib had been routinely sequenced with SS for BCR-ABL1 KD mutations between December 2009 and December 2012. We then retrospectively analyzed these samples with NGS. RT and long range PCR was performed to amplify BCR-ABL1 fusion transcripts and the PCR products sequenced bidirectional after library preparation. We performed a fusion transcript based BCR-ABL1 mutation assay using Roche 454 amplicon deep-sequencing technology that is suited for detecting low level variants in pooled amplicon samples. Sequencing data was analyzed with GS Amplicon Variant Analyzer (AVA) software, and the variant frequency cut-off was adjusted to 1%. Results Clinical features, sequencing results, and the outcomes of the patients were summarized in Table 1. Four patients were male, and the median age was 37 years (range, 20-60 years). The patients were all in chronic phase at the time of the diagnosis. After imatinib resistance, 4 patients had received dasatinib (DAS), and 2 were given nilotinib (NIL) as second line TKI treatment. The remaining two patients had both received DAS and NIL (Table 1). In a set of 20 clinical samples, at different time points, NGS not only identified all the mutations detected by SS, but additionally identified low level variants present between 1 – 28.12 %. T315I and E255K/V were the most common mutations, which were detected in four patients, both by SS and NGS at the same time points (Table 1). Two patients (patient #1 and #4) had T315I, and they both progressed to blastic phase and died. E255K was detected in patients #2 and #3, and patient #2 had achieved and maintained complete cytogenetic and major molecular responses with 100 mg daily DAS, whereas patient #3 had received both NIL and DAS, but she was deceased due to myeloid blastic crisis. Among 4 patients (patients #5, #6, #7, and #8), mutation analysis was performed at eleven different time points, and these patients were wild-type with SS. We also did not detect any clinically significant mutations in these patients by NGS. Most probably mechanisms other than KD mutations were responsible for the TKI resistance among these four patients. Conclusions Polyclonal mutations in BCR-ABL1 KD are commonly identified in TKI resistant patients. Thus, detection of low-level mutations after development of resistance offers critical information to guide subsequent therapy selection. An inappropriate kinase inhibitor selection could highly increase the risk of treatment failure with clonal expansion of the resistant mutant. In our imatinib resistant cohort, we detected low level variants accompany to known mutations which may constitute background genetic variations. Although we had expected to detect mutations earlier by NGS (i.e. before these mutations can be detected by SS), we did not observe such finding in our patients. The patients' samples may not show a stable mutation spectrum between time points. Hence, it is not always possible to spot a mutation before patients show resistance to therapy. Regular NGS analysis might detect these mutations in earlier phases, which might help clinicians to choose the most suitable individual treatment modality for the patients. Acknowledgment The authors would like to thank the Interlaboratory Robustness of Next-generation sequencing (IRON) Phase II study group members, especially to Simona Soverini and Alexander Kohlmann who designed BCR-ABL primers and plates. We also would like to thank the Research Fund of the Istanbul University (Project no. 24244) and Turkish Society of Hematology for supporting the study. Disclosures: Sayitoglu: Roche Diagnostics: Research Support Other.

Performance of next-generation sequencing for detection of clinically actionable genetic variants in cancer.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. 11099-11099
Author(s):  
Mohammed Omar Hussaini ◽  
Ian S. Hagemann ◽  
Teresa Mary Cox ◽  
Christina Lockwood ◽  
Karen Seibert ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Variants ◽  
Simultaneous Detection ◽  
Genetic Alterations ◽  
Sequence Variants ◽  
Tumor Type ◽  
Cancer Genes ◽  
Next Generation ◽  
Therapeutic Implications ◽  
Generation Sequencing

11099 Background: Next-generation sequencing (NGS) allows for simultaneous detection of numerous actionable somatic variants in cancer. We have implemented a clinical NGS panel to detect genetic alterations in 25 genes with established roles in cancer and report here the frequency of clinically actionable genetic variants in a variety of cancer types. Methods: NGS testing was performed in a CAP-certified, CLIA-licensed environment on DNA extracted from FFPE tissue in 209 cases spanning 41 histologic tumor types. DNA was enriched by hybrid capture and sequenced to >1,000x average coverage on Illumina sequencers with 2x101bp or 2x150bp reads. Variants were called using clinically validated parameters using the Genome Analysis Toolkit, Pindel, and the custom-written Clinical Genomicist Workstation. Results: Non-small cell lung cancer (45%), pancreatic cancer (10%), and colorectal cancer (8%) were the most common tumors sent for NGS analysis. An average of 3 (range 1- 16) non-synonymous, non-SNP sequence variants per case (SNVs and indels) were detected in the 130kb exonic target. Variants were most commonly seen in TP53, KRAS, and EGFR. 27% of cases (56/209) had one or more variants with therapeutic implications for the tumor type tested (e.g., EGFR mutation in NSCLC). 15% of cases (32/209) showed actionable variants not generally associated with the malignancy tested (e.g., detection of an activating KITvariant in thymic carcinoma). 10% of cases (21/209) had variants that were prognostically significant but not directly targetable. Some cases (9%) had variants that were prognostic/diagnostic and targetable. In 117 cases (56% of total), no therapeutically or prognostically significant variants were identified. Overall, in 92 cases (44%), NGS testing yielded information with therapeutic (majority), prognostic, or diagnostic ramifications. Conclusions: We found that 44% of unselected cancer cases have clinically relevant sequence variants in a set of 25 commonly mutated cancer genes. Our data suggest that clinical NGS testing may serve as an integral tool in realizing the potential of precision medicine in oncology.

scholarly journals Sensitive Monitoring of BCR-ABL1 Kinase Domain Mutations By Next Generation Sequencing for Optimizing Clinical Decisions in Philadelphia-Positive Acute Lymphoblastic Leukemia in the Graaph-2014 Trial

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1295-1295 ◽  
Author(s):  
Jean-Michel Cayuela ◽  
Francois Lay ◽  
Yves Chalandon ◽  
Philippe Rousselot ◽  
Xavier Thomas ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Acute Lymphoblastic Leukemia ◽  
Limit Of Detection ◽  
Lymphoblastic Leukemia ◽  
Intensive Therapy ◽  
Kinase Domain ◽  
Rapid Expansion ◽  
Next Generation ◽  
Low Level ◽  
Generation Sequencing

A high proportion of Ph-positive Acute Lymphoblastic Leukemia (Ph+ ALL) patients still undergo relapses despite the use of Tyrosine Kinase Inhibitors (TKIs) in addition to chemotherapy as frontline therapy. In this leukemia subtype, the role of BCR-ABL1 kinase domain (KD) mutations as a driver of resistance to TKIs has already been documented by previous studies and such mutations have been reported in up to 80% of the patients at relapse. Next-generation sequencing (NGS) has been proposed to characterize these mutations with a higher sensitivity than Sanger. We report here a prospective study aiming at detecting potentially resistant cell populations by NGS in Ph+ ALL patients enrolled in the GRAAPH 2014-trial. Between March 2016 and February 2019, 156 patients aged 18 to 59 years with newly diagnosed Ph+ and/or BCR-ABL1 positive ALL have been included in the GRAAPH 2014 trial (NCT02619630). BCR-ABL1 isoforms were E1A2 69%, B2A2/B3A2 29%, atypical 2%. After a prephase of steroid, treatment consisted of 4 blocks of chemotherapy + nilotinib. 118 patients (76%) underwent allogeneic or autologous stem cell transplantation (SCT). 22 medullary relapses were recorded within a median time of 9 months (range, 2 - 35). Blood and marrow samples harvested at diagnosis, after each treatment block, before and 3 months after SCT, and at relapse, were sequenced if BCR-ABL1/ABL1 ratio were above 0.001. Mutated BCR-ABL1 transcripts were detected by sequencing the KD of BCR-ABL1 transcripts by NGS with a limit of detection (LOD) of 0.03. T315I allele specific oligonucleotide (ASO) droplet digital RT-PCR (ddRT-PCR) with a LOD of 0.0005 was also performed at diagnosis on a subset of 63 patients, including 5 who have subsequently developed a T315I clone. NGS. At diagnosis, no KD mutation was found by NGS in pretreatment samples of 137 patients. During follow-up (FU), only 12 mutations were found by NGS in 7 out of the 88 patients tested (81, 45, 30, 20, 19, 9 after block 1, 2, 3, 4, before and 3 months after SCT, respectively). Mutations were T315I (N=6), Y253H (N=1), E255K (N=2), E255V (N=1), Q252H (N=1), Y253F (N=1). At relapse, 16 mutations were identified by NGS in 12 patients out of the 17 tested (71%). Mutations were T315I (N=7), Y253H (N=n=3), F359V (N=2), E255K (N=1), E255V (N=1), Q252H (N=1), Y253F (N=1). More than 1 mutated clone were present in 2 patients (E255V+T315I+F359V and Y253H+F359V), and a compound mutation was found in 1 patient (Q252H/Y253F). Out of the 7 patients found mutated during FU, 5 have relapsed with a rapid expansion (1 to 3 months) of the mutated clone. One patient harboring a sub-clonal (10%) E255K at MRD1 has relapsed 9 months later without any detectable mutation. One patient identified with 3 mutated clones (E255K 10%, E255V 10%, T315I 80%) underwent SCT and has not relapsed so far. We failed to anticipate expansion of any mutated clone in the 7 remaining patients found mutated at relapse. T315I ASO ddRT-PCR on diagnostic samples. Low-level T315I mutated BCR-ABL1 transcripts (0.00051 to 0.0013) were detected in 14 out of 63 patients (24%) tested. Only one has expanded a T315I clone later on. In the context of the GRAAPH 2014 trial, 71% of the 17 relapses tested so far were associated with BCR-ABL1 KD mutations. Expansion of the mutated clone could have been characterized before the onset of hematological relapses in only 5 out of 12 patients (42%). Unfortunately in these cases, lags between first detection and relapse were very short (1 to 3 months). On the contrary, occurrences of relapses associated with expansion of KD-mutated clones could not have been anticipated in 58%. All mutations identified, including T315I, F359V, E255K/V and Y253F/H, Q252H/Y253F are known for conferring resistance to nilotinib. NGS is a valuable method for KD mutation detection in Ph+ ALL. It allows a quantitative characterization of KD mutations at relapse. However in our hands and in the context of an intensive therapy combining chemotherapy, nilotinib and SCT, its enhanced sensitivity as compared to Sanger (3% vs 20%) does not translate into the capacity of anticipating expansion of KD-mutated clones. Moreover, in this study, NGS did not detect any mutation in pre-therapeutic samples while T315I mutated BCR-ABL1 transcripts were found at low-level in 24% of these samples by ddRT-PCR. However it should be emphasized that when detected, low-level T315I mutated sub-clones present at diagnosis failed to expand in most instances. Disclosures Cayuela: Incyte: Honoraria, Speakers Bureau; Novartis: Consultancy, Honoraria, Speakers Bureau. Chalandon:Pfizer: Consultancy, Honoraria; Bristol-Myers Squibb: Consultancy, Honoraria; Incyte Biosciences: Consultancy, Honoraria; Novartis: Consultancy, Honoraria. Rousselot:Pfizer: Research Funding. Thomas:PFIZER: Honoraria; ABBVIE: Honoraria; INCYTE: Honoraria; DAICHI: Honoraria. Huguet:Amgen: Honoraria; Servier: Honoraria; Jazz Pharmaceuticals: Honoraria; BMS: Honoraria; Pfizer: Honoraria; Incyte Biosciences: Honoraria; Novartis: Honoraria. Chevallier:Incyte: Consultancy, Honoraria; Jazz Pharmaceuticals: Honoraria; Daiichi Sankyo: Honoraria. Boissel:NOVARTIS: Consultancy. Vey:Novartis: Consultancy, Honoraria; Janssen: Honoraria. Berthon:PFIZER: Other: DISCLOSURE BOARD; JAZZPHARMACEUTICAL: Other: DISCLOSURE BOARD; CELGEN: Other: DISCLOSURE BOARD.

scholarly journals Whole-Exome Sequencing for Diagnosis of Turner Syndrome: Toward Next-Generation Sequencing and Newborn Screening

2017 ◽  
Vol 102 (5) ◽  
pp. 1529-1537 ◽  
Author(s):  
David R. Murdock ◽  
Frank X. Donovan ◽  
Settara C. Chandrasekharappa ◽  
Nicole Banks ◽  
Carolyn Bondy ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Newborn Screening ◽  
Exome Sequencing ◽  
Turner Syndrome ◽  
Whole Exome Sequencing ◽  
Genomic Research ◽  
Next Generation ◽  
Low Level ◽  
Whole Exome ◽  
Generation Sequencing

Abstract Context: Turner syndrome (TS) is due to a complete or partial loss of an X chromosome in female patients and is not currently part of newborn screening (NBS). Diagnosis is often delayed, resulting in missed crucial diagnostic and therapeutic opportunities. Objectives: This study sought to determine if whole-exome sequencing (WES) as part of a potential NBS program could be used to diagnose TS. Design, Setting, Patients: Karyotype, chromosomal microarray, and WES were performed on blood samples from women with TS (n = 27) enrolled in the Personalized Genomic Research study at the National Institutes of Health. Female control subjects (n = 37) and male subjects (n = 27) also underwent WES. Copy number variation was evaluated using EXCAVATOR2 and B allele frequency was calculated from informative single nucleotide polymorphisms. Simulated WES data were generated for detection of low-level mosaicism and complex structural chromosome abnormalities. Results: We detected monosomy for chromosome X in all 27 TS samples, including 1 mosaic for 45,X/46,XX and another with previously unreported material on chromosome Y. Sensitivity and specificity were both 100% for the diagnosis of TS with no false-positive or false-negative results. Using simulated WES data, we detected isochromosome Xq and low-level mosaicism as low as 5%. Conclusion: We present an accurate method of diagnosing TS using WES, including cases with low-level mosaicism, isochromosome Xq, and cryptic Y-chromosome material. Given the potential use of next-generation sequencing for NBS in many different diseases and syndromes, we propose WES can be used as a screening test for TS in newborns.

scholarly journals Characterization of mutations and sequence variants in the D21S11 locus by next generation sequencing

2014 ◽  
Vol 8 (1) ◽  
pp. 68-72 ◽  
Author(s):  
Eszter Rockenbauer ◽  
Stine Hansen ◽  
Martin Mikkelsen ◽  
Claus Børsting ◽  
Niels Morling
Keyword(s):  
Next Generation Sequencing ◽  
Sequence Variants ◽  
Next Generation ◽  
Generation Sequencing
Sign in / Sign up

Export Citation Format

Share Document