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Jin B, Wang Y, Zhang B, Xu H, Lu X, Sang X, Wang W, Mao Y, Chen P, Wang S, Qian Z, Wang Y, Du S. Immune checkpoint inhibitor-related molecular markers predict prognosis in extrahepatic cholangiocarcinoma. Cancer Med 2023; 12:20470-20481. [PMID: 37814942 PMCID: PMC10652350 DOI: 10.1002/cam4.6441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 10/11/2023] Open
Abstract
BACKGROUND Therapeutic approaches for extrahepatic cholangiocarcinoma (EHCC) are limited, due to insufficient understanding to biomarkers related to prognosis and drug response. Here, we comprehensively assess the molecular characterization of EHCC with clinical implications. METHODS Whole-exome sequencing (WES) on 37 tissue samples of EHCC were performed to evaluate genomic alterations, tumor mutational burden (TMB) and microsatellite instability (MSI). RESULTS Mutation of KRAS (16%) was significantly correlated to poor OS. ERBB2 mutation was associated with improved OS. ERBB2, KRAS, and ARID1A were three potentially actionable targets. TMB ≥10 mutations per megabase was detected in 13 (35.1%) cases. Six patients (16.2%) with MSIsensor scores ≥10 were found. In multivariate Cox analysis, patients with MSIsensor sore exceed a certain threshold (MSIsensor score ≥0.36, value approximately above the 20th percentile as thresholds) showed a significant association with the improved OS (HR = 0.16; 95% CI: 0.056-0.46, p < 0.001), as well as patients with both TMB ≥3.47 mutations per megabase (value approximately above the 20th percentile) and MSIsensor score ≥0.36. CONCLUSIONS TMB and MSI are potential biomarkers associated with better prognosis for EHCC patients. Furthermore, our study highlights important genetic alteration and potential therapeutic targets in EHCC.
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Affiliation(s)
- Bao Jin
- Department of Liver Surgery, Peking Union Medical College HospitalChinese Academy of Medical Sciences& Peking Union Medical CollegeBeijingChina
| | - Yuxin Wang
- Department of Liver Surgery, Peking Union Medical College HospitalChinese Academy of Medical Sciences& Peking Union Medical CollegeBeijingChina
| | - Baoluhe Zhang
- Department of Liver Surgery, Peking Union Medical College HospitalChinese Academy of Medical Sciences& Peking Union Medical CollegeBeijingChina
| | - Haifeng Xu
- Department of Liver Surgery, Peking Union Medical College HospitalChinese Academy of Medical Sciences& Peking Union Medical CollegeBeijingChina
| | - Xin Lu
- Department of Liver Surgery, Peking Union Medical College HospitalChinese Academy of Medical Sciences& Peking Union Medical CollegeBeijingChina
| | - Xinting Sang
- Department of Liver Surgery, Peking Union Medical College HospitalChinese Academy of Medical Sciences& Peking Union Medical CollegeBeijingChina
| | - Wenze Wang
- Department of Pathology, Peking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Yilei Mao
- Department of Liver Surgery, Peking Union Medical College HospitalChinese Academy of Medical Sciences& Peking Union Medical CollegeBeijingChina
| | | | - Shun Wang
- Beidou Precision Medicine InstituteGuangzhouChina
| | - Zhirong Qian
- Beidou Precision Medicine InstituteGuangzhouChina
| | - Yingyi Wang
- Department of Medical Oncology, Peking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
| | - Shunda Du
- Department of Liver Surgery, Peking Union Medical College HospitalChinese Academy of Medical Sciences& Peking Union Medical CollegeBeijingChina
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Hook PW, Timp W. Beyond assembly: the increasing flexibility of single-molecule sequencing technology. Nat Rev Genet 2023; 24:627-641. [PMID: 37161088 PMCID: PMC10169143 DOI: 10.1038/s41576-023-00600-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 05/11/2023]
Abstract
The maturation of high-throughput short-read sequencing technology over the past two decades has shaped the way genomes are studied. Recently, single-molecule, long-read sequencing has emerged as an essential tool in deciphering genome structure and function, including filling gaps in the human reference genome, measuring the epigenome and characterizing splicing variants in the transcriptome. With recent technological developments, these single-molecule technologies have moved beyond genome assembly and are being used in a variety of ways, including to selectively sequence specific loci with long reads, measure chromatin state and protein-DNA binding in order to investigate the dynamics of gene regulation, and rapidly determine copy number variation. These increasingly flexible uses of single-molecule technologies highlight a young and fast-moving part of the field that is leading to a more accessible era of nucleic acid sequencing.
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Affiliation(s)
- Paul W Hook
- Department of Biomedical Engineering, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Winston Timp
- Department of Biomedical Engineering, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
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3
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Váradi A, Kaszab E, Kardos G, Prépost E, Szarka K, Laczkó L. Rapid genotyping of targeted viral samples using Illumina short-read sequencing data. PLoS One 2022; 17:e0274414. [PMID: 36112576 PMCID: PMC9481040 DOI: 10.1371/journal.pone.0274414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/30/2022] [Indexed: 11/19/2022] Open
Abstract
The most important information about microorganisms might be their accurate genome sequence. Using current Next Generation Sequencing methods, sequencing data can be generated at an unprecedented pace. However, we still lack tools for the automated and accurate reference-based genotyping of viral sequencing reads. This paper presents our pipeline designed to reconstruct the dominant consensus genome of viral samples and analyze their within-host variability. We benchmarked our approach on numerous datasets and showed that the consensus genome of samples could be obtained reliably without further manual data curation. Our pipeline can be a valuable tool for fast identifying viral samples. The pipeline is publicly available on the project’s GitHub page (https://github.com/laczkol/QVG).
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Affiliation(s)
- Alex Váradi
- Department of Metagenomics, University of Debrecen, Debrecen, Hungary
- Department of Laboratory Medicine, University of Pécs, Pécs, Hungary
| | - Eszter Kaszab
- Department of Metagenomics, University of Debrecen, Debrecen, Hungary
- Veterinary Medical Research Institute, Budapest, Hungary
| | - Gábor Kardos
- Department of Metagenomics, University of Debrecen, Debrecen, Hungary
| | - Eszter Prépost
- Department of Metagenomics, University of Debrecen, Debrecen, Hungary
| | - Krisztina Szarka
- Department of Metagenomics, University of Debrecen, Debrecen, Hungary
| | - Levente Laczkó
- Department of Metagenomics, University of Debrecen, Debrecen, Hungary
- ELKH-DE Conservation Biology Research Group, Debrecen, Hungary
- * E-mail:
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4
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HIV-1 Drug Resistance Assay Using Ion Torrent Next Generation Sequencing and On-Instrument End-to-End Analysis Software. J Clin Microbiol 2022; 60:e0025322. [PMID: 35699434 DOI: 10.1128/jcm.00253-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HIV-1 antiretroviral therapy management requires sequencing the protease, reverse transcriptase, and integrase portions of the HIV-1 pol gene. Most resistance testing is performed with Sanger sequencing, which has limited ability to detect minor variants. Next generation sequencing (NGS) platforms enable variant detection at frequencies as low as 1% allowing for earlier detection of resistance and modification of therapy. Implementation of NGS assays in the clinical laboratory is hindered by complicated assay design, cumbersome wet bench procedures, and the complexity of data analysis and bioinformatics. We developed a complete NGS protocol and companion analysis and reporting pipeline using AmpliSeq multiplex PCR, Ion Torrent S5 XL sequencing, and Stanford's HIVdb resistance algorithm. Implemented as a Torrent Suite software plugin, the pipeline runs automatically after sequencing. An optimum variant frequency threshold of 10% was determined by comparing Sanger sequences of archived samples from ViroSeq testing, resulting in a sensitivity of 98.2% and specificity of 99.0%. The majority (91%) of drug resistance mutations were detected by both Sanger and NGS, with 1.7% only by Sanger and 7.3% only by NGS. Variant calls were highly reproducible and there was no cross-reactivity to VZV, HBV, CMV, EBV, and HCV. The limit of detection was 500 copies/mL. The NGS assay performance was comparable to ViroSeq Sanger sequencing and has several advantages, including a publicly available end-to-end analysis and reporting plugin. The assay provides a straightforward path for implementation of NGS for HIV drug resistance testing in the laboratory setting without additional investment in bioinformatics infrastructure and resources.
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Testing the Ion AmpliSeq™ HID Y-SNP Research Panel v1 for performance and resolution in admixed South Americans of haplogroup Q. Forensic Sci Int Genet 2022; 59:102708. [DOI: 10.1016/j.fsigen.2022.102708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 11/18/2022]
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Wang XQ, Goytain A, Dickson BC, Nielsen TO. Advances in Sarcoma Molecular Diagnostics. Genes Chromosomes Cancer 2022; 61:332-345. [DOI: 10.1002/gcc.23025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 01/10/2022] [Accepted: 01/15/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Xue Qi Wang
- Faculty of Medicine University of British Columbia Vancouver Canada
- Genetic Pathology Evaluation Centre, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver Canada
| | - Angela Goytain
- Genetic Pathology Evaluation Centre, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver Canada
| | - Brendan C. Dickson
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital; Department of Laboratory Medicine and Pathobiology University of Toronto Toronto ON Canada
| | - Torsten Owen Nielsen
- Genetic Pathology Evaluation Centre, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver Canada
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Schwabl P, Maiguashca Sánchez J, Costales JA, Ocaña-Mayorga S, Segovia M, Carrasco HJ, Hernández C, Ramírez JD, Lewis MD, Grijalva MJ, Llewellyn MS. Culture-free genome-wide locus sequence typing (GLST) provides new perspectives on Trypanosoma cruzi dispersal and infection complexity. PLoS Genet 2020; 16:e1009170. [PMID: 33326438 PMCID: PMC7743988 DOI: 10.1371/journal.pgen.1009170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/02/2020] [Indexed: 12/30/2022] Open
Abstract
Analysis of genetic polymorphism is a powerful tool for epidemiological surveillance and research. Powerful inference from pathogen genetic variation, however, is often restrained by limited access to representative target DNA, especially in the study of obligate parasitic species for which ex vivo culture is resource-intensive or bias-prone. Modern sequence capture methods enable pathogen genetic variation to be analyzed directly from host/vector material but are often too complex and expensive for resource-poor settings where infectious diseases prevail. This study proposes a simple, cost-effective 'genome-wide locus sequence typing' (GLST) tool based on massive parallel amplification of information hotspots throughout the target pathogen genome. The multiplexed polymerase chain reaction amplifies hundreds of different, user-defined genetic targets in a single reaction tube, and subsequent agarose gel-based clean-up and barcoding completes library preparation at under 4 USD per sample. Our study generates a flexible GLST primer panel design workflow for Trypanosoma cruzi, the parasitic agent of Chagas disease. We successfully apply our 203-target GLST panel to direct, culture-free metagenomic extracts from triatomine vectors containing a minimum of 3.69 pg/μl T. cruzi DNA and further elaborate on method performance by sequencing GLST libraries from T. cruzi reference clones representing discrete typing units (DTUs) TcI, TcIII, TcIV, TcV and TcVI. The 780 SNP sites we identify in the sample set repeatably distinguish parasites infecting sympatric vectors and detect correlations between genetic and geographic distances at regional (< 150 km) as well as continental scales. The markers also clearly separate TcI, TcIII, TcIV and TcV + TcVI and appear to distinguish multiclonal infections within TcI. We discuss the advantages, limitations and prospects of our method across a spectrum of epidemiological research.
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Affiliation(s)
- Philipp Schwabl
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Jalil Maiguashca Sánchez
- Centro de Investigación para la Salud en América Latina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Jaime A. Costales
- Centro de Investigación para la Salud en América Latina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Sofía Ocaña-Mayorga
- Centro de Investigación para la Salud en América Latina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Maikell Segovia
- Laboratorio de Biología Molecular de Protozoarios, Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Hernán J. Carrasco
- Laboratorio de Biología Molecular de Protozoarios, Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Carolina Hernández
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Michael D. Lewis
- London School of Hygiene & Tropical Medicine, Keppel Street, London, United Kingdom
| | - Mario J. Grijalva
- Centro de Investigación para la Salud en América Latina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Infectious and Tropical Disease Institute, Biomedical Sciences Department, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, United States of America
| | - Martin S. Llewellyn
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
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