1
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Wang Z, Huang C, Fan W, Sun S, Li K, Liu X, Pu J, Zhang G, Li X. Case report: EGFR fusion mutation combined with EGFR amplification responds to EGFR-TKI therapy. Front Oncol 2024; 14:1347282. [PMID: 38595815 PMCID: PMC11003264 DOI: 10.3389/fonc.2024.1347282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/07/2024] [Indexed: 04/11/2024] Open
Abstract
Given their good antitumor effects, epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) are standard first-line therapy for EGFR-sensitive mutations, including exon 19 deletions and exon 21 L858R mutations. EGFR fusion mutations and EGFR amplification are very rare in non-small cell lung cancer (NSCLC). We describe 2 patients with NSCLC harboring EGFR fusion mutations (EGFR-MACF1 and EGFR-GNAT3) combined with EGFR amplification. Both patients received EGFR-TKI treatment, and 1 of them showed an antitumor response.
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Affiliation(s)
- Zhulin Wang
- Department of Thoracic Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
- Department of Thoracic Surgery, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Chunyao Huang
- Department of Thoracic Surgery, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Wenbo Fan
- Department of Thoracic Surgery, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Shaowu Sun
- Department of Thoracic Surgery, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Kaiyuan Li
- Department of Thoracic Surgery, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xu Liu
- Department of Thoracic Surgery, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jiangtao Pu
- Department of Thoracic Surgery, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Guoqing Zhang
- Department of Thoracic Surgery, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiangnan Li
- Department of Thoracic Surgery, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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2
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Chung IH, Huang YS, Fang TH, Chen CH. Whole Genome Sequencing Revealed Inherited Rare Oligogenic Variants Contributing to Schizophrenia and Major Depressive Disorder in Two Families. Int J Mol Sci 2023; 24:11777. [PMID: 37511534 PMCID: PMC10380944 DOI: 10.3390/ijms241411777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/12/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Schizophrenia and affective disorder are two major complex mental disorders with high heritability. Evidence shows that rare variants with significant clinical impacts contribute to the genetic liability of these two disorders. Also, rare variants associated with schizophrenia and affective disorders are highly personalized; each patient may carry different variants. We used whole genome sequencing analysis to study the genetic basis of two families with schizophrenia and major depressive disorder. We did not detect de novo, autosomal dominant, or recessive pathogenic or likely pathogenic variants associated with psychiatric disorders in these two families. Nevertheless, we identified multiple rare inherited variants with unknown significance in the probands. In family 1, with singleton schizophrenia, we detected four rare variants in genes implicated in schizophrenia, including p.Arg1627Trp of LAMA2, p.Pro1338Ser of CSMD1, p.Arg691Gly of TLR4, and Arg182X of AGTR2. The p.Arg691Gly of TLR4 was inherited from the father, while the other three were inherited from the mother. In family 2, with two affected sisters diagnosed with major depressive disorder, we detected three rare variants shared by the two sisters in three genes implicated in affective disorders, including p.Ala4551Gly of FAT1, p.Val231Leu of HOMER3, and p.Ile185Met of GPM6B. These three rare variants were assumed to be inherited from their parents. Prompted by these findings, we suggest that these rare inherited variants may interact with each other and lead to psychiatric conditions in these two families. Our observations support the conclusion that inherited rare variants may contribute to the heritability of psychiatric disorders.
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Affiliation(s)
- I-Hang Chung
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan
| | - Yu-Shu Huang
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan
- Department of Psychiatry, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Ting-Hsuan Fang
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan
| | - Chia-Hsiang Chen
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan 333, Taiwan
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3
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Kleinfelder K, Villella VR, Hristodor AM, Laudanna C, Castaldo G, Amato F, Melotti P, Sorio C. Theratyping of the Rare CFTR Genotype A559T in Rectal Organoids and Nasal Cells Reveals a Relevant Response to Elexacaftor (VX-445) and Tezacaftor (VX-661) Combination. Int J Mol Sci 2023; 24:10358. [PMID: 37373505 DOI: 10.3390/ijms241210358] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Despite the promising results of new CFTR targeting drugs designed for the recovery of F508del- and class III variants activity, none of them have been approved for individuals with selected rare mutations, because uncharacterized CFTR variants lack information associated with the ability of these compounds in recovering their molecular defects. Here we used both rectal organoids (colonoids) and primary nasal brushed cells (hNEC) derived from a CF patient homozygous for A559T (c.1675G>A) variant to evaluate the responsiveness of this pathogenic variant to available CFTR targeted drugs that include VX-770, VX-809, VX-661 and VX-661 combined with VX-445. A559T is a rare mutation, found in African-Americans people with CF (PwCF) with only 85 patients registered in the CFTR2 database. At present, there is no treatment approved by FDA (U.S. Food and Drug Administration) for this genotype. Short-circuit current (Isc) measurements indicate that A559T-CFTR presents a minimal function. The acute addition of VX-770 following CFTR activation by forskolin had no significant increment of baseline level of anion transport in both colonoids and nasal cells. However, the combined treatment, VX-661-VX-445, significantly increases the chloride secretion in A559T-colonoids monolayers and hNEC, reaching approximately 10% of WT-CFTR function. These results were confirmed by forskolin-induced swelling assay and by western blotting in rectal organoids. Overall, our data show a relevant response to VX-661-VX-445 in rectal organoids and hNEC with CFTR genotype A559T/A559T. This could provide a strong rationale for treating patients carrying this variant with VX-661-VX-445-VX-770 combination.
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Affiliation(s)
- Karina Kleinfelder
- Cystic Fibrosis Laboratory "D. Lissandrini", Department of Medicine, Division of General Pathology, University of Verona, 37134 Verona, Italy
| | - Valeria Rachela Villella
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80138 Napoli, Italy
- CEINGE-Advanced Biotechnologies Franco Salvatore, 80145 Naples, Italy
| | - Anca Manuela Hristodor
- Cystic Fibrosis Centre, Azienda Ospedaliera Universitaria Integrata Verona, 37126 Verona, Italy
| | - Carlo Laudanna
- Cystic Fibrosis Laboratory "D. Lissandrini", Department of Medicine, Division of General Pathology, University of Verona, 37134 Verona, Italy
| | - Giuseppe Castaldo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80138 Napoli, Italy
- CEINGE-Advanced Biotechnologies Franco Salvatore, 80145 Naples, Italy
| | - Felice Amato
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80138 Napoli, Italy
| | - Paola Melotti
- Cystic Fibrosis Centre, Azienda Ospedaliera Universitaria Integrata Verona, 37126 Verona, Italy
| | - Claudio Sorio
- Cystic Fibrosis Laboratory "D. Lissandrini", Department of Medicine, Division of General Pathology, University of Verona, 37134 Verona, Italy
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4
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Jiang Y, Fang X, Xiang Y, Fang T, Liu J, Lu K. Afatinib for the Treatment of NSCLC with Uncommon EGFR Mutations: A Narrative Review. Curr Oncol 2023; 30:5337-5349. [PMID: 37366888 DOI: 10.3390/curroncol30060405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 06/28/2023] Open
Abstract
Afatinib, the world's first irreversible ErbB family (containing four different cancer cell epidermal growth factor receptors, including EGFR, HER2, ErbB3, and ErbB4) inhibitor, is a second-generation oral epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI). It can be used as a first-line treatment for locally advanced or metastatic non-small-cell lung cancer (NSCLC) with an EGFR-sensitive mutation or for patients with locally advanced or metastatic squamous lung cancer whose disease progresses during or after platinum-containing chemotherapy. Currently, with the use of third-generation EGFR-TKIs, afatinib is no longer clinically indicated as the first choice for patients with NSCLC who have EGFR-sensitive mutations. However, afatinib showed a considerable inhibitory effect in NSCLC patients with uncommon EGFR mutations (G719X, S768I, and L861Q) according to a combined post hoc analysis of the LUX-Lung2/3/6 trials. With the development of genetic testing technology, the detection rate of uncommon EGFR mutations is increasing. The aim of this paper is to describe in detail the sensitivity of rare EGFR mutations to afatinib and to provide information and a reference for those suffering from advanced NSCLC who have uncommon EGFR mutations.
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Affiliation(s)
- Yingying Jiang
- Department of Oncology, Nanjing Medical University, Nanjing 210029, China
| | - Xiaoxu Fang
- Department of Oncology, Nanjing Medical University, Nanjing 210029, China
| | - Yan Xiang
- Department of Oncology, Nanjing Medical University, Nanjing 210029, China
| | - Tingwen Fang
- Department of Oncology, Nanjing Medical University, Nanjing 210029, China
| | - Jingwen Liu
- Department of Oncology, Nanjing Medical University, Nanjing 210029, China
| | - Kaihua Lu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
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5
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Kulkarni AA, Fujioka N, Reinhardt L, Patel MR, Kratzke RA. Exceptional response to afatinib in a patient with persistent G719A EGFR-mutant NSCLC. Lung Cancer Manag 2022; 11:LMT54. [PMID: 35463918 PMCID: PMC9024393 DOI: 10.2217/lmt-2021-0001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/11/2022] [Indexed: 11/28/2022] Open
Abstract
We present a patient with metastatic NSCLC harboring a compound EGFR mutation with co-occurring G719A and T790M mutation. T790M mutation was treatment emergent mutation when patient was on early generation tyrosine kinase inhibitors. Initial Guardant 360 showed that G719A was the dominant clone. Following, osimertinib, the patient had only a radiographic disease stabilization and then developed both clinical and radiographic progression. On progression, T790M was undetectable but G719A continued to be the dominant clone. Subsequent administration of afatinib led to a clinical and radiological response. To our knowledge, this is the first case report describing co-occurrence of EGFR G719A and T790M mutations and the clonal evolution during treatment with anti-EGFR therapies. Drugs taken by mouth that target the EGFR gene are very effective in patients with NSCLC who have common mutations (changes) that affect the EGFR gene (known as ‘sensitizing mutations’). However, some patients may have less common mutations that can cause their response to these drugs to vary. In rare cases, a patient may have two different EGFR mutations that affect their response to these drugs in different ways. In this Case Report we present a patient with advanced NSCLC who had both T790M (a common mutation) and G719A (an uncommon mutation). T790M was most likely a resistance mutation following treatment with gefitnib. Subsequent treatment with osimertinib gave short-term benefit and liquid biopsy (examination of fluid from the patient’s body) carried out when the disease progressed showed the T790M clone had been eliminated but that the G719A mutation was still present. Treatment with afatinib then led to long-term treatment response. This case highlights the potential for using liquid biopsy for monitoring changes in mutations in EGFR-mutant NSCLC.
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Affiliation(s)
- Amit A Kulkarni
- Department of Medicine, Division of Hematology, Oncology & Transplantation, University of Minnesota, MN 55455, USA
| | - Naomi Fujioka
- Department of Medicine, Division of Hematology, Oncology & Transplantation, University of Minnesota, MN 55455, USA
| | - Lucia Reinhardt
- Department of Medicine, Division of Hematology, Oncology & Transplantation, University of Minnesota, MN 55455, USA
| | - Manish R Patel
- Department of Medicine, Division of Hematology, Oncology & Transplantation, University of Minnesota, MN 55455, USA
| | - Robert A Kratzke
- Department of Medicine, Division of Hematology, Oncology & Transplantation, University of Minnesota, MN 55455, USA
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6
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Lopes-Pacheco M, Bacalhau M, Ramalho SS, Silva IAL, Ferreira FC, Carlile GW, Thomas DY, Farinha CM, Hanrahan JW, Amaral MD. Rescue of Mutant CFTR Trafficking Defect by the Investigational Compound MCG1516A. Cells 2022; 11:136. [PMID: 35011698 DOI: 10.3390/cells11010136] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 01/27/2023] Open
Abstract
Although some therapeutic progress has been achieved in developing small molecules that correct F508del-CFTR defects, the mechanism of action (MoA) of these compounds remain poorly elucidated. Here, we investigated the effects and MoA of MCG1516A, a newly developed F508del-CFTR corrector. MCG1516A effects on wild-type (WT) and F508del-CFTR were assessed by immunofluorescence microscopy, and biochemical and functional assays both in cell lines and in intestinal organoids. To shed light on the MoA of MCG1516A, we evaluated its additivity to the FDA-approved corrector VX-661, low temperature, genetic revertants of F508del-CFTR (G550E, R1070W, and 4RK), and the traffic-null variant DD/AA. Finally, we explored the ability of MCG1516A to rescue trafficking and function of other CF-causing mutations. We found that MCG1516A rescues F508del-CFTR with additive effects to VX-661. A similar behavior was observed for WT-CFTR. Under low temperature incubation, F508del-CFTR demonstrated an additivity in processing and function with VX-661, but not with MCG1516A. In contrast, both compounds promoted additional effects to low temperature to WT-CFTR. MCG1516A demonstrated additivity to genetic revertant R1070W, while VX-661 was additive to G550E and 4RK. Nevertheless, none of these compounds rescued DD/AA trafficking. Both MCG1516A and VX-661 rescued CFTR processing of L206W- and R334W-CFTR with greater effects when these compounds were combined. In summary, the absence of additivity of MCG1516A to genetic revertant G550E suggests a putative binding site for this compound on NBD1:NBD2 interface. Therefore, a combination of MCG1516A with compounds able to rescue DD/AA traffic, or mimicking the actions of revertant R1070W (e.g., VX-661), could enhance correction of F508del-CFTR defects.
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7
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Ramalho SS, Silva IAL, Amaral MD, Farinha CM. Rare Trafficking CFTR Mutations Involve Distinct Cellular Retention Machineries and Require Different Rescuing Strategies. Int J Mol Sci 2021; 23:24. [PMID: 35008443 DOI: 10.3390/ijms23010024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 12/12/2022] Open
Abstract
Most of the ~2100 CFTR variants so far reported are very rare and still uncharacterized regarding their cystic fibrosis (CF) disease liability. Since some may respond to currently approved modulators, characterizing their defect and response to these drugs is essential. Here we aimed characterizing the defect associated with four rare missense (likely Class II) CFTR variants and assess their rescue by corrector drugs. We produced CFBE cell lines stably expressing CFTR with W57G, R560S, H1079P and Q1100P, assessed their effect upon CFTR expression and maturation and their rescue by VX-661/VX-445 correctors. Results were validated by forskolin-induced swelling assay (FIS) using intestinal organoids from individuals bearing these variants. Finally, knock-down (KD) of genes previously shown to rescue F508del-CFTR was assessed on these mutants. Results show that all the variants preclude the production of mature CFTR, confirming them as Class II mutations. None of the variants responded to VX-661 but the combination rescued H1079P- and Q1100P-CFTR. The KD of factors that correct F508del-CFTR retention only marginally rescued R560S- and H1079P-CFTR. Overall, data evidence that Class II mutations induce distinct molecular defects that are neither rescued by the same corrector compounds nor recognized by the same cellular machinery, thus requiring personalized drug discovery initiatives.
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8
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Drenner K, Basu GD, Goodman LJ, Ozols AA, LoBello JR, Royce T, Gordon MS, Borazanci EH, Steinbach MA, Trent J, Sharma S. The value of comprehensive genomic sequencing to maximize the identification of clinically actionable alterations in advanced cancer patients: a case series. Oncotarget 2021; 12:1836-1847. [PMID: 34504655 PMCID: PMC8416559 DOI: 10.18632/oncotarget.28046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/27/2021] [Indexed: 01/10/2023] Open
Abstract
Purpose: We present seven cases of advanced cancer patients who initially underwent tumor testing utilizing smaller, panel-based tests, followed by a variety of therapeutic treatments which ultimately resulted in progression of their disease. These cases demonstrate the value of utilizing WES/RNA seq and characterization following disease progression in these patients and the determination of clinically targetable alterations as well as acquired resistance mutations. Materials and Methods: All patients are part of an IRB approved observational study. WES and RNA sequencing were performed, using GEM ExTra® on tumor and blood samples obtained during routine clinical care. To accurately determine somatic versus germline alterations the test was performed with paired normal testing from peripheral blood. Results: The presented cases demonstrate the clinical impact of actionable findings uncovered using GEM ExTra® in patients with advanced disease who failed many rounds of treatment. Unique alterations were identified resulting in newly identified potential targeted therapies, mechanisms of resistance, and variation in the genomic characterization of the primary versus the metastatic tumor. Conclusions: Taken together our results demonstrate that GEM ExTra® maximizes detection of actionable mutations, thus allowing for appropriate treatment selection for patients harboring both common and rare genomic alterations.
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Affiliation(s)
- Kevin Drenner
- Translational Genomic Research Institute (Tgen), Phoenix, AZ 85004, USA.,These authors contributed equally to this work
| | - Gargi D Basu
- Ashion Analytics, LLC, Phoenix, AZ 85004, USA.,These authors contributed equally to this work
| | | | | | | | | | | | | | | | - Jeffrey Trent
- Translational Genomic Research Institute (Tgen), Phoenix, AZ 85004, USA
| | - Sunil Sharma
- Translational Genomic Research Institute (Tgen), Phoenix, AZ 85004, USA
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9
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Kaplinski L, Möls M, Puurand T, Pajuste FD, Remm M. KATK: Fast genotyping of rare variants directly from unmapped sequencing reads. Hum Mutat 2021; 42:777-786. [PMID: 33715282 DOI: 10.1002/humu.24197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 11/06/2022]
Abstract
KATK is a fast and accurate software tool for calling variants directly from raw next-generation sequencing reads. It uses predefined k-mers to retrieve only the reads of interest from the FASTQ file and calls genotypes by aligning retrieved reads locally. KATK does not use data about known polymorphisms and has NC (no call) as the default genotype. The reference or variant allele is called only if there is sufficient evidence for their presence in data. Thus it is not biased against rare variants or de-novo mutations. With simulated datasets, we achieved a false-negative rate of 0.23% (sensitivity 99.77%) and a false discovery rate of 0.19%. Calling all human exonic regions with KATK requires 1-2 h, depending on sequencing coverage.
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Affiliation(s)
- Lauris Kaplinski
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Märt Möls
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Tarmo Puurand
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Fanny-Dhelia Pajuste
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maido Remm
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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10
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Wheeler DA, Takebe N, Hinoue T, Hoadley KA, Cardenas MF, Hamilton AM, Laird PW, Wang L, Johnson A, Dewal N, Miller V, Piñeyro D, Castro de Moura M, Esteller M, Shen H, Zenklusen JC, Tarnuzzer R, McShane LM, Tricoli JV, Williams PM, Lubensky I, O'Sullivan-Coyne G, Kohn EC, Little RF, White J, Malik S, Harris L, Weil C, Chen AP, Karlovich C, Rodgers B, Shankar L, Jacobs P, Nolan T, Hu J, Muzny DM, Doddapaneni H, Korchina V, Gastier-Foster J, Bowen J, Leraas K, Edmondson EF, Doroshow JH, Conley BA, Ivy SP, Staudt LM. Molecular Features of Cancers Exhibiting Exceptional Responses to Treatment. Cancer Cell 2021; 39:38-53.e7. [PMID: 33217343 PMCID: PMC8478080 DOI: 10.1016/j.ccell.2020.10.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/23/2020] [Accepted: 10/13/2020] [Indexed: 12/21/2022]
Abstract
A small fraction of cancer patients with advanced disease survive significantly longer than patients with clinically comparable tumors. Molecular mechanisms for exceptional responses to therapy have been identified by genomic analysis of tumor biopsies from individual patients. Here, we analyzed tumor biopsies from an unbiased cohort of 111 exceptional responder patients using multiple platforms to profile genetic and epigenetic aberrations as well as the tumor microenvironment. Integrative analysis uncovered plausible mechanisms for the therapeutic response in nearly a quarter of the patients. The mechanisms were assigned to four broad categories-DNA damage response, intracellular signaling, immune engagement, and genetic alterations characteristic of favorable prognosis-with many tumors falling into multiple categories. These analyses revealed synthetic lethal relationships that may be exploited therapeutically and rare genetic lesions that favor therapeutic success, while also providing a wealth of testable hypotheses regarding oncogenic mechanisms that may influence the response to cancer therapy.
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Affiliation(s)
- David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Naoko Takebe
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Katherine A Hoadley
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Maria F Cardenas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alina M Hamilton
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Linghua Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Ninad Dewal
- Foundation Medicine Inc, Cambridge, MA 02141, USA
| | | | - David Piñeyro
- Josep Carreras Leukaemia Research Institute, Badalona, 08916 Barcelona, Catalonia, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain
| | - Manuel Castro de Moura
- Josep Carreras Leukaemia Research Institute, Badalona, 08916 Barcelona, Catalonia, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute, Badalona, 08916 Barcelona, Catalonia, Spain; Centro de Investigacion Biomedica en Red Cancer (CIBERONC), 28029 Madrid, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), 08007 Barcelona, Catalonia, Spain
| | - Hui Shen
- Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | - Roy Tarnuzzer
- Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Lisa M McShane
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - James V Tricoli
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Paul M Williams
- Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Irina Lubensky
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Elise C Kohn
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Richard F Little
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jeffrey White
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Shakun Malik
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Lyndsay Harris
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Carol Weil
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alice P Chen
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Chris Karlovich
- Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Brian Rodgers
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Lalitha Shankar
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Paula Jacobs
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tracy Nolan
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Viktoriya Korchina
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Jay Bowen
- Nationwide Children's Hospital, Columbus, OH 43205, USA
| | | | - Elijah F Edmondson
- Pathology and Histology Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21701, USA
| | - James H Doroshow
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Barbara A Conley
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - S Percy Ivy
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Louis M Staudt
- Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA.
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11
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Yue L, Wentao L, Xin Z, Jingjing H, Xiaoyan Z, Na F, Tonghui M, Dalin L. Human epidermal growth factor receptor 2-positive metastatic breast cancer with novel epidermal growth factor receptor -ZNF880 fusion and epidermal growth factor receptor E114K mutations effectively treated with pyrotinib: A case report. Medicine (Baltimore) 2020; 99:e23406. [PMID: 33371069 PMCID: PMC7748359 DOI: 10.1097/md.0000000000023406] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 10/30/2020] [Indexed: 11/26/2022] Open
Abstract
INTRODUCTION In about 15% to 20% of breast cancer cases, human epidermal growth factor receptor 2 (HER2) over-expression or gene-amplification is associated with poor prognosis. Thanks to the development of target therapies, HER2 positive patients can be managed using HER2-targeting drugs. There are several kinds ofHER2 inhibitors, such as trastuzumab, lapatinib, and pyrotinib. Pyrotinib which exert different functions, of note, the latest generation of the drug, is an irreversible small-molecule tyrosine kinase inhibitor targeting epidermal growth factor receptor (EGFR) (HER1) and/or HER2 and/or HER4. Both lapatinib and pyrotinib potentially target EGFR and/or HER2, but in some instances, induces different responses of patients with EGFR and/or HER2 mutations. This is attributed to the different mutations in EGFR and HER2 genes, which may form distinct types of HER2 dimers, with different binding capacities to drugs. PATIENT CONCERNS Five years ago, a patient underwent a radical mastectomy in an external hospital. Results of the resection histopathology revealed an invasive ductal carcinoma, pT3N0M0, stage IIB, HER2 positive. The lady patient received 6 cycles of adjuvant chemotherapy and was subjected to adjuvant trastuzumab therapy for 1 year. After a regular 1-year follow-up and in March 2018, she complained of chest pain and visited our hospital. We diagnosed her with metastatic breast cancer, positive for HER2. DIAGNOSIS positron emission tomography/computed tomography showed multiple metastases in the lung and sternum, while the breast lesions did not progress, the curative effect of which we evaluated as a progressive disease. Then, lapatinib integrated with chemotherapy was administered to the patient. After 5 cycles of the treatment, the patient experienced lower back pain. Through CT examination, it was revealed that she had multiple metastases in the lung and sternum, in addition to new metastases in the lumbar spine and right lobe of the liver. Moreover, magnetic resonance imaging revealed multiple metastases in the brain, and the disease further progressed. The results of circulating tumor DNA assays showed that other than HER2 amplification, novel EGFR-ZNF880 fusion and EGFR E114K mutations developed. INTERVENTIONS The patient was administered with a combination of pyrotinib with chemotherapy. OUTCOMES After 2 months of pyrotinib treatment, the metastases of the lung, sternum, lumbar spine, and right lobe of the liver disappeared. Also, the size of the brain metastases reduced while bone metastases were relieved. The curative effect was evaluated as a partial response. Following the results of circulating tumor DNA assays, HER2 amplification, EGFR-ZNF880 fusion, and EGFR E114K mutations disappeared. However, since a small lesion was present in the brain, the patient was subjected to radiotherapy in the head. Notably, after 9 months treatment with pyrotinib, enhanced CT indicated that tumors in the breast, liver, both lungs, brain, and bone were under control. The patient continually received oral pyrotinib, however, a new brain lesion appeared 6 months later. Overall, we managed to regulate the efficacy of pyrotinib for up to 15 months. CONCLUSION This case report demonstrates that EGFR-ZNF880 fusion and EGFR E114K mutations may contribute or lead to the formation of a special HER2 dimer, which is rapidly resistant to lapatinib but sensitive to pyrotinib. Of note, this is the first report that such a new fusion has been found.
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Affiliation(s)
- Li Yue
- Oncology Department, Harbin Medical University Cancer Hospital, Heilongjiang
| | - Liu Wentao
- Oncology Department, Harbin Medical University Cancer Hospital, Heilongjiang
| | - Zhang Xin
- Department of Translational Medicine, Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Huang Jingjing
- Department of Translational Medicine, Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Zhang Xiaoyan
- Department of Translational Medicine, Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Fu Na
- Oncology Department, Harbin Medical University Cancer Hospital, Heilongjiang
| | - Ma Tonghui
- Department of Translational Medicine, Genetron Health (Beijing) Technology, Co. Ltd., Beijing, China
| | - Li Dalin
- Oncology Department, Harbin Medical University Cancer Hospital, Heilongjiang
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12
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Laselva O, McCormack J, Bartlett C, Ip W, Gunawardena TNA, Ouyang H, Eckford PDW, Gonska T, Moraes TJ, Bear CE. Preclinical Studies of a Rare CF-Causing Mutation in the Second Nucleotide Binding Domain (c.3700A>G) Show Robust Functional Rescue in Primary Nasal Cultures by Novel CFTR Modulators. J Pers Med 2020; 10:jpm10040209. [PMID: 33167369 PMCID: PMC7712331 DOI: 10.3390/jpm10040209] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022] Open
Abstract
The combination therapies ORKAMBITM and TRIKAFTATM are approved for people who have the F508del mutation on at least one allele. In this study we examine the effects of potentiator and corrector combinations on the rare mutation c.3700A>G. This mutation produces a cryptic splice site that deletes six amino acids in NBD2 (I1234-R1239del). Like F508del it causes protein misprocessing and reduced chloride channel function. We show that a novel cystic fibrosis transmembrane conductance regulator CFTR modulator triple combination (AC1, corrector, AC2-2, co-potentiator and AP2, potentiator), rescued I1234-R1239del-CFTR activity to WT-CFTR level in HEK293 cells. Moreover, we show that although the response to ORKAMBI was modest in nasal epithelial cells from two individuals homozygous for I1234-R1239del-CFTR, a substantial functional rescue was achieved with the novel triple combination. Interestingly, while both the novel CFTR triple combination and TRIKAFTATM treatment showed functional rescue in gene-edited I1234-R1239del-CFTR-expressing HBE cells and in nasal cells from two CF patients heterozygous for I1234-R1239del/W1282X, nasal cells homozygous for I1234-R1239del-CFTR showed no significant response to the TRIKAFTATM combination. These data suggest a potential benefit of CFTR modulators on the functional rescue of I1234-R1239del -CFTR, which arises from the rare CF-causing mutation c.3700A>G, and highlight that patient tissues are crucial to our full understanding of functional rescue in rare CFTR mutations.
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Affiliation(s)
- Onofrio Laselva
- Programme in Molecular Medicine, Hospital for Sick Children, Toronto, ON M5G 8X4, Canada; (O.L.); (J.M.); (T.N.A.G.); (P.D.W.E.)
- Department of Physiology, University of Toronto, Toronto, ON M5G 8X4, Canada
| | - Jacqueline McCormack
- Programme in Molecular Medicine, Hospital for Sick Children, Toronto, ON M5G 8X4, Canada; (O.L.); (J.M.); (T.N.A.G.); (P.D.W.E.)
| | - Claire Bartlett
- Programme in Translational Medicine, Hospital for Sick Children, Toronto, ON M5G 8X4, Canada; (C.B.); (W.I.); (H.O.); (T.G.); (T.J.M.)
| | - Wan Ip
- Programme in Translational Medicine, Hospital for Sick Children, Toronto, ON M5G 8X4, Canada; (C.B.); (W.I.); (H.O.); (T.G.); (T.J.M.)
| | - Tarini N. A. Gunawardena
- Programme in Molecular Medicine, Hospital for Sick Children, Toronto, ON M5G 8X4, Canada; (O.L.); (J.M.); (T.N.A.G.); (P.D.W.E.)
| | - Hong Ouyang
- Programme in Translational Medicine, Hospital for Sick Children, Toronto, ON M5G 8X4, Canada; (C.B.); (W.I.); (H.O.); (T.G.); (T.J.M.)
| | - Paul D. W. Eckford
- Programme in Molecular Medicine, Hospital for Sick Children, Toronto, ON M5G 8X4, Canada; (O.L.); (J.M.); (T.N.A.G.); (P.D.W.E.)
| | - Tanja Gonska
- Programme in Translational Medicine, Hospital for Sick Children, Toronto, ON M5G 8X4, Canada; (C.B.); (W.I.); (H.O.); (T.G.); (T.J.M.)
- Department of Paediatrics, University of Toronto, Toronto, ON M5G 8X4, Canada
| | - Theo J. Moraes
- Programme in Translational Medicine, Hospital for Sick Children, Toronto, ON M5G 8X4, Canada; (C.B.); (W.I.); (H.O.); (T.G.); (T.J.M.)
- Department of Paediatrics, University of Toronto, Toronto, ON M5G 8X4, Canada
| | - Christine E. Bear
- Programme in Molecular Medicine, Hospital for Sick Children, Toronto, ON M5G 8X4, Canada; (O.L.); (J.M.); (T.N.A.G.); (P.D.W.E.)
- Department of Physiology, University of Toronto, Toronto, ON M5G 8X4, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 8X4, Canada
- Correspondence: ; Tel.: +1-416-816-5981
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13
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Tong YR, Geng C, Guan YZ, Zhao YH, Ren HT, Yao FX, Ling C, Wang DC, Chen L, Cui LY, Zhang SY, Dai Y. A Comprehensive Analysis of 2013 Dystrophinopathies in China: A Report From National Rare Disease Center. Front Neurol 2020; 11:572006. [PMID: 33101180 PMCID: PMC7554367 DOI: 10.3389/fneur.2020.572006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/24/2020] [Indexed: 12/17/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are X-linked recessive neuromuscular disorders caused by mutations in DMD. A high-quality database of DMD/BMD is essential not only for clinical practice but also for fundamental research. Here, we aimed to build the largest Chinese national dystrophinopathy database using the National Rare Diseases Registry System of China. Peking Union Medical College Hospital (PUMCH) was the National Rare Diseases Center of China. This research involved 2013 patients with dystrophinopathies, whose diagnoses were confirmed; they were registered and followed up at PUMCH from March 2011 to December 2018. Family history, clinical signs, and treatment data were reported for patients with DMD and BMD at different rates. All six serum biochemical indexes could accurately distinguish between DMD and BMD patients. Copy number variations were the most frequent mutation type (79.2% in DMD and 84.3% in BMD), of which large deletions accounted for 88.4 and 88.6%, large duplications accounted for 11.6 and 11.4% in DMD and BMD, respectively. An exon deletion hotspot, located in exons 45-54, was observed in DMD, and intron 44 was the most frequent deletion starting point (26.5%). Duplication and single nucleotide variations appeared to be uniformly distributed among all exons. Eleven patients were identified to have ultrarare mutation types. Eleven other patients suffered from two separate mutations simultaneously, some of which may have taken place via dependent mechanisms. Thus, we have established the largest hospital-based Chinese dystrophinopathy database via the National Rare Diseases Registry System. This study provides valuable information for further diagnostic and therapeutic studies of dystrophinopathy.
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Affiliation(s)
- Yuan-Ren Tong
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chang Geng
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yu-Zhou Guan
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yan-Huan Zhao
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hai-Tao Ren
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Feng-Xia Yao
- Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chao Ling
- Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dan-Chen Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lin Chen
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Li-Ying Cui
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shu-Yang Zhang
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yi Dai
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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14
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Zybert K, Wozniacki L, Tomaszewska-Sobczyńska A, Wertheim-Tysarowska K, Czerska K, Ołtarzewski M, Sands D. Clinical characteristics of rare CFTR mutations causing cystic fibrosis in Polish population. Pediatr Pulmonol 2020; 55:2097-2107. [PMID: 32442342 DOI: 10.1002/ppul.24823] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 04/19/2020] [Accepted: 04/23/2020] [Indexed: 01/04/2023]
Abstract
INTRODUCTION More than 2000 mutations have been identified since the discovery of the CFTR gene in 1989. However, only 346 mutations have been classified as cystic fibrosis (CF)-causing mutations. Due to the increasing number of mutations and poor correlation between the genotype and phenotype, there is an urgent need to determine the mutations that are pathogenic, nonpathogenic, or lead to variable symptoms. AIM The aim of the study was to present the clinical characteristics of Polish patients with rare and novel CFTR mutations, with an attempt to determine the pathogenicity status of those variants. MATERIALS AND METHODS The group included 13 patients born between September 2006 and May 2019, who underwent CF newborn screening and in whom two CFTR mutations, including at least one rare or a novel mutation, were identified. RESULTS We identified 13 patients with mutations in both alleles of the CFTR gene, one of which was at least rare in Polish population (R289NfsX17, I618RfsX2, T682KfsX40, S1347PfsX13, W356X, E33X, dup.16,17A) or was a mutation of unknown clinical consequences (H199R, L468P, A1217E, Q359R, T1036I, W1282R). None of them were described in the CFTR2 database. In all examined patients, sweat tests were elevated. The diagnosed patients presented with a wide spectrum of clinical symptoms. Broad clinical characteristics and test results are presented. CONCLUSION Pathogenic mutations are H199R, L468P, A1217E, Q359R, T1036I, W1282R, R289NfsX17, I618RfsX2, T682KfsX40, S1347PfsX13, W356X, E33X, dup.16,17A. Every patient with a mutation of unknown clinical consequences in one CFTR allele requires attentive follow-up.
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Affiliation(s)
- Katarzyna Zybert
- Department of Cystic Fibrosis, Institute of Mother and Child, Warsaw, Poland.,Warsaw Cystic Fibrosis Centre, Dziekanow Lesny Paediatric Hospital, Lomianki, Poland
| | - Lukasz Wozniacki
- Department of Cystic Fibrosis, Institute of Mother and Child, Warsaw, Poland.,Warsaw Cystic Fibrosis Centre, Dziekanow Lesny Paediatric Hospital, Lomianki, Poland
| | - Agnieszka Tomaszewska-Sobczyńska
- MedGen Medical Centre, Warsaw, Poland.,Department of Screening and Metabolic Diagnostics, Institute of Mother and Child, Warsaw, Poland
| | | | | | - Mariusz Ołtarzewski
- Department of Screening and Metabolic Diagnostics, Institute of Mother and Child, Warsaw, Poland
| | - Dorota Sands
- Department of Cystic Fibrosis, Institute of Mother and Child, Warsaw, Poland.,Warsaw Cystic Fibrosis Centre, Dziekanow Lesny Paediatric Hospital, Lomianki, Poland
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15
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Ye J, Tong Y, Lv J, Peng R, Chen S, Kuang L, Su K, Zheng Y, Zhang T, Zhang F, Jin L, Yang X, Wang H. Rare mutations in the autophagy-regulating gene AMBRA1 contribute to human neural tube defects. Hum Mutat 2020; 41:1383-1393. [PMID: 32333458 DOI: 10.1002/humu.24028] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/24/2020] [Accepted: 04/19/2020] [Indexed: 01/31/2023]
Abstract
Neural tube defects (NTDs) are severe congenital malformations caused by failed neural tube closure. Recently, autophagy is revealed to play a vital role in neuroepithelium development and neurulation. Autophagy and beclin 1 regulator 1 (Ambra1) is a crucial regulator of autophagy initiation, and its deficiency in mice leads to exencephaly and/or spina bifida. However, the genetic contribution of AMBRA1 to the etiology of human NTDs remains unknown. In this study, we identified five rare missense mutations of AMBRA1 in 352 NTDs cases, which were absent in 224 matched controls. Western blotting and fluorescence puncta counting for MAP1LC3A/LC3 in HEK293T cells suggested that four of the mutations (AMBRA1 p.Thr80Met, p.Leu274Phe, p.Ser743Phe, and p.Met884Val) affected autophagy initiation to various extents. Furthermore, these four mutations also displayed loss-of-function effects compared with wild-type AMBRA1 when we injected messenger RNA (mRNA) to overexpress or rescue ambra1a-morpholino oligos (MO) knockdown in zebrafish. It is intriguing that trehalose, a natural disaccharide, could rescue ambra1a-MO knockdown in a dose-dependent manner independently or together with AMBRA1 mRNA. Taken together, our findings suggest that rare mutations of the autophagy regulator gene AMBRA1 may contribute to the etiology of human neural tube defects, and trehalose is a promising treatment for a subset of NTDs caused by autophagy impairment.
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Affiliation(s)
- Jianhong Ye
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China.,The MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Youli Tong
- The MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Jiashun Lv
- The MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Rui Peng
- Key Laboratory of Reproduction Regulation of NPFPC, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Shuxia Chen
- The MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Lele Kuang
- The MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.,Department of Assisted Reproduction, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Ke Su
- The MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Yufang Zheng
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China.,Key Laboratory of Reproduction Regulation of NPFPC, Institute of Reproduction and Development, Fudan University, Shanghai, China.,Institute of Developmental Biology and Molecular Medicine, Fudan University, Shanghai, China
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, The Capital Institute of Pediatrics, Beijing, China
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China.,Key Laboratory of Reproduction Regulation of NPFPC, Institute of Reproduction and Development, Fudan University, Shanghai, China.,Children's Hospital of Fudan University, Shanghai, China
| | - Li Jin
- The MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Xueyan Yang
- The MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Hongyan Wang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China.,Key Laboratory of Reproduction Regulation of NPFPC, Institute of Reproduction and Development, Fudan University, Shanghai, China.,Children's Hospital of Fudan University, Shanghai, China
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16
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Shen CH, DeKosky BJ, Guo Y, Xu K, Gu Y, Kilam D, Ko SH, Kong R, Liu K, Louder MK, Ou L, Zhang B, Chao CW, Corcoran MM, Feng E, Huang J, Normandin E, O'Dell S, Ransier A, Rawi R, Sastry M, Schmidt SD, Wang S, Wang Y, Chuang GY, Doria-Rose NA, Lin B, Zhou T, Boritz EA, Connors M, Douek DC, Karlsson Hedestam GB, Sheng Z, Shapiro L, Mascola JR, Kwong PD. VRC34-Antibody Lineage Development Reveals How a Required Rare Mutation Shapes the Maturation of a Broad HIV-Neutralizing Lineage. Cell Host Microbe 2020; 27:531-543.e6. [PMID: 32130953 PMCID: PMC7467872 DOI: 10.1016/j.chom.2020.01.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/31/2019] [Accepted: 01/30/2020] [Indexed: 01/07/2023]
Abstract
Rare mutations have been proposed to restrict the development of broadly neutralizing antibodies against HIV-1, but this has not been explicitly demonstrated. We hypothesized that such rare mutations might be identified by comparing broadly neutralizing and non-broadly neutralizing branches of an antibody-developmental tree. Because sequences of antibodies isolated from the fusion peptide (FP)-targeting VRC34-antibody lineage suggested it might be suitable for such rare mutation analysis, we carried out next-generation sequencing (NGS) on B cell transcripts from donor N123, the source of the VRC34 lineage, and functionally and structurally characterized inferred intermediates along broadly neutralizing and poorly neutralizing developmental branches. The broadly neutralizing VRC34.01 branch required the rare heavy-chain mutation Y33P to bind FP, whereas the early bifurcated VRC34.05 branch did not require this rare mutation and evolved less breadth. Our results demonstrate how a required rare mutation can restrict development and shape the maturation of a broad HIV-1-neutralizing antibody lineage.
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Affiliation(s)
- Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brandon J DeKosky
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Chemical & Petroleum Engineering and Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66045, USA
| | - Yicheng Guo
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Kai Xu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ying Gu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Divya Kilam
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sung Hee Ko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Ou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cara W Chao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Martin M Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Eric Feng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jesse Huang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erica Normandin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy Ransier
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mallika Sastry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen D Schmidt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yiran Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bob Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eli A Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark Connors
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Zizhang Sheng
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Lawrence Shapiro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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17
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Bonvicini C, Scassellati C, Benussi L, Di Maria E, Maj C, Ciani M, Fostinelli S, Mega A, Bocchetta M, Lanzi G, Giacopuzzi E, Ferraboli S, Pievani M, Fedi V, Defanti CA, Giliani S, Frisoni GB, Ghidoni R, Gennarelli M. Next Generation Sequencing Analysis in Early Onset Dementia Patients. J Alzheimers Dis 2020; 67:243-256. [PMID: 30530974 PMCID: PMC6398561 DOI: 10.3233/jad-180482] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background: Early onset dementias (EOD) are rare neurodegenerative dementias that present before 65 years. Genetic factors have a substantially higher pathogenetic contribution in EOD patients than in late onset dementia. Objective: To identify known and/or novel rare variants in major candidate genes associated to EOD by high-throughput sequencing. Common-risk variants of apolipoprotein E (APOE) and prion protein (PRNP) genes were also assessed. Methods: We studied 22 EOD patients recruited in Memory Clinics, in the context of studies investigating genetic forms of dementia. Two methodological approaches were applied for the target-Next Generation Sequencing (NGS) analysis of these patients. In addition, we performed progranulin plasma dosage, C9Orf72 hexanucleotide repeat expansion analysis, and APOE genotyping. Results: We detected three rare known pathogenic mutations in the GRN and PSEN2 genes and eleven unknown-impact mutations in the GRN, VCP, MAPT, FUS, TREM2, and NOTCH3 genes. Six patients were carriers of only common risk variants (APOE and PRNP), and one did not show any risk mutation/variant. Overall, 69% (n = 9) of our early onset Alzheimer’s disease (EAOD) patients, compared with 34% (n = 13) of sporadic late onset Alzheimer’s disease (LOAD) patients and 27% (n = 73) of non-affected controls (ADNI, whole genome data), were carriers of at least two rare/common risk variants in the analyzed candidate genes panel, excluding the full penetrant mutations. Conclusion: This study suggests that EOD patients without full penetrant mutations are characterized by higher probability to carry polygenic risk alleles that patients with LOAD forms. This finding is in line with recently reported evidence, thus suggesting that the genetic risk factors identified in LOAD might modulate the risk also in EOAD.
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Affiliation(s)
- Cristian Bonvicini
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Catia Scassellati
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Luisa Benussi
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Emilio Di Maria
- Department of Health Sciences, University of Genova and Division of Medical Genetics, Galliera Hospital, Genova, Italy
| | - Carlo Maj
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy.,Institute for Genomic Statistics and Bioinformatics, Bonn, Germany
| | - Miriam Ciani
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy.,Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Silvia Fostinelli
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Anna Mega
- Laboratory Alzheimer's Neuroimaging and Epidemiology, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Martina Bocchetta
- Laboratory Alzheimer's Neuroimaging and Epidemiology, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy.,Dementia Research Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Gaetana Lanzi
- A. Nocivelli' Institute for Molecular Medicine Spedali Civili and University of Brescia, Brescia, Italy
| | - Edoardo Giacopuzzi
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy.,Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Sergio Ferraboli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Michela Pievani
- Laboratory Alzheimer's Neuroimaging and Epidemiology, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | | | - Carlo Alberto Defanti
- Fondazione Europea Ricerca Biomedica, Centro di Eccellenza Alzheimer, Ospedale Briolini Gazzaniga, Bergamo, Italy
| | - Silvia Giliani
- A. Nocivelli' Institute for Molecular Medicine Spedali Civili and University of Brescia, Brescia, Italy
| | | | - Giovanni Battista Frisoni
- Laboratory Alzheimer's Neuroimaging and Epidemiology, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy.,Laboratory of Neuroimaging of Aging (LANVIE), University Hospitals and University of Geneva, Geneva, Switzerland; Department of Internal Medicine, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Roberta Ghidoni
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Massimo Gennarelli
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy.,Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
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18
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Tang W, Stimson MR, Basu S, Heckbert SR, Cushman M, Pankow JS, Folsom AR, Pankratz N. Burden of rare exome sequence variants in PROC gene is associated with venous thromboembolism: a population-based study. J Thromb Haemost 2020; 18:445-453. [PMID: 31680443 PMCID: PMC7787541 DOI: 10.1111/jth.14676] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/13/2019] [Accepted: 10/30/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Rare coding mutations underlying deficiencies of antithrombin and proteins C and S contribute to familial venous thromboembolism (VTE). It is uncertain whether rare variants play a role in the etiology of VTE in the general population. OBJECTIVES We conducted a deep whole-exome sequencing (WES) study to investigate the associations between rare coding variants and the risk of VTE in two population-based prospective cohorts. PATIENTS/METHODS Whole-exome sequencing was performed in the Longitudinal Investigation of Thromboembolism Etiology (LITE), which combines the Atherosclerosis Risk in Communities (ARIC) study (316 incident VTE events among 3159 African Americans [AAs] and 458 incident VTEs among 7772 European Americans [EAs]) and the Cardiovascular Healthy Study (CHS; 60 incident VTEs among 1751 EAs). We performed gene-based tests of rare variants (allele frequency < 1%, exome-wide significance P < 1.47 × 10-6 ) separately in each study and ancestry group, and meta-analyzed the results for the EAs in ARIC and CHS. RESULTS In the meta-analysis of EAs, we identified one gene, PROC, in which the burden of rare, coding variants was significantly associated with increased risk of VTE (HR = 5.42 [3.11, 9.42] for carriers versus non-carriers, P = 2.27 × 10-9 ). In ARIC EAs, carriers of the PROC rare variants had on average 0.75 standard deviation (SD) lower concentrations of plasma protein C and 0.28 SD higher D-dimer (P < .05) than non-carriers. Adjustment for low protein C status did not eliminate the association of PROC burden with VTE. In AAs, rare coding PROC variants were not associated with VTE. CONCLUSIONS Rare coding variants in PROC contribute to increased VTE risk in EAs in this general population sample.
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Affiliation(s)
- Weihong Tang
- Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States
| | - Mary Rachel Stimson
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis, Minnesota, United States
| | - Saonli Basu
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States
| | - Susan R. Heckbert
- Department of Epidemiology, University of Washington, Seattle, Washington, United States
| | - Mary Cushman
- Department of Pathology, University of Vermont, Burlington, Vermont, United States
| | - James S. Pankow
- Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States
| | - Aaron R. Folsom
- Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis, Minnesota, United States
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19
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Yadav R, Saini A, Agarwal P, Kapoor P, Aggarwal AN, Sethi S. A Rare D94F Change in gyrA Gene of Multidrug-Resistant Mycobacterium tuberculosis Possibly Contributing to an Unfavorable Treatment Outcome. Antimicrob Agents Chemother 2019; 63:e01312-19. [PMID: 31501146 DOI: 10.1128/AAC.01312-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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20
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Russo A, Franchina T, Ricciardi G, Battaglia A, Picciotto M, Adamo V. Heterogeneous Responses to Epidermal Growth Factor Receptor (EGFR) Tyrosine Kinase Inhibitors (TKIs) in Patients with Uncommon EGFR Mutations: New Insights and Future Perspectives in this Complex Clinical Scenario. Int J Mol Sci 2019; 20:E1431. [PMID: 30901844 DOI: 10.3390/ijms20061431] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 12/18/2022] Open
Abstract
Uncommon Epidermal Growth Factor Receptor (EGFR) mutations represent a distinct and highly heterogeneous subgroup of Non-Small Cell Lung Cancers (NSCLCs), that accounts for approximately 10% of all EGFR-mutated patients. The incidence of uncommon EGFR mutations is growing, due to the wider adoption of next-generation sequencing (NGS) for diagnostic purposes, which enables the identification of rare variants, usually missed with available commercial kits that only detect a limited number of EGFR mutations. However, the sensitivity of uncommon mutations to first- and second-generation EGFR Tyrosine Kinase Inhibitors (TKIs) is widely heterogeneous and less well known, compared with classic mutations (i.e., exon 19 deletions and exon 21 L858R point mutation), since most of the pivotal studies with EGFR TKIs in the first line, with few exceptions, excluded patients with rare and/or complex variants. Recently, the third generation EGFR TKI osimertinib further revolutionized the therapeutic algorithm of EGFR-mutated NSCLC, but its role in patients harboring EGFR mutations besides exon 19 deletions and/or L858R is largely unknown. Therefore, a better knowledge of the sensitivity of uncommon mutations to currently available EGFR TKIs is critical to guiding treatment decisions in clinical practice. The aim of this paper is to provide a comprehensive overview of the treatment of NSCLC patients harboring uncommon EGFR mutations with currently approved therapies and to discuss the emerging therapeutic opportunities in this peculiar subgroup of patients, including chemo-immunotherapy combinations, next-generation EGFR TKIs, and novel targeted agents.
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21
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Ahn EH, Lee SH. Detection of Low-Frequency Mutations and Identification of Heat-Induced Artifactual Mutations Using Duplex Sequencing. Int J Mol Sci 2019; 20:E199. [PMID: 30625989 PMCID: PMC6337315 DOI: 10.3390/ijms20010199] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/28/2018] [Accepted: 01/03/2019] [Indexed: 12/12/2022] Open
Abstract
We present a genome-wide comparative and comprehensive analysis of three different sequencing methods (conventional next generation sequencing (NGS), tag-based single strand sequencing (e.g., SSCS), and Duplex Sequencing for investigating mitochondrial mutations in human breast epithelial cells. Duplex Sequencing produces a single strand consensus sequence (SSCS) and a duplex consensus sequence (DCS) analysis, respectively. Our study validates that although high-frequency mutations are detectable by all the three sequencing methods with the similar accuracy and reproducibility, rare (low-frequency) mutations are not accurately detectable by NGS and SSCS. Even with conservative bioinformatical modification to overcome the high error rate of NGS, the NGS frequency of rare mutations is 7.0 × 10-4. The frequency is reduced to 1.3 × 10-4 with SSCS and is further reduced to 1.0 × 10-5 using DCS. Rare mutation context spectra obtained from NGS significantly vary across independent experiments, and it is not possible to identify a dominant mutation context. In contrast, rare mutation context spectra are consistently similar in all independent DCS experiments. We have systematically identified heat-induced artifactual variants and corrected the artifacts using Duplex Sequencing. Specific sequence contexts were analyzed to examine the effects of neighboring bases on the accumulation of heat-induced artifactual variants. All of these artifacts are stochastically occurring rare mutations. C > A/G > T, a signature of oxidative damage, is the most increased (170-fold) heat-induced artifactual mutation type. Our results strongly support the claim that Duplex Sequencing accurately detects low-frequency mutations and identifies and corrects artifactual mutations introduced by heating during DNA preparation.
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Affiliation(s)
- Eun Hyun Ahn
- Department of Pathology, University of Washington, Seattle, WA 98195, USA.
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA.
| | - Seung Hyuk Lee
- Department of Pathology, University of Washington, Seattle, WA 98195, USA.
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22
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Moassas F, Alabloog A, Murad H. Description of a Rare β-Globin Gene Mutation: -86 (C>G) (HBB: c.-136C>G) Observed in a Syrian Family. Hemoglobin 2018; 42:203-205. [PMID: 30173596 DOI: 10.1080/03630269.2018.1500918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We present the description of a β-thalassemia (β-thal) -86 (C>G) (HBB: c.-136C>G) mutation in a Syrian family from Damascus, As-Suwayda Province, Syria, who was referred to the laboratory for prenatal diagnosis (PND). The mutation was found in the mother in a homozygous state, while it was in the father and in the amniotic fluid sample in a heterozygous state. This mutation is located at -86 within the proximal CACCC box in the promoter of the β-globin gene and is possibly linked with a phenotype of β+-thal. Polymerase chain reaction-restriction fragment length polymorphism (PCR/RFLP) analysis indicated that the -86 mutation was linked with haplotype I [+ - - - - + +]. We propose that Lebanon may be the origin of this mutation. To the best of our knowledge, this is the first report describing this mutation in As-Suwayda Province. These findings provide novel information on the region-specificity of this mutation in southwestern Syria.
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Affiliation(s)
- Faten Moassas
- a Molecular Biology and Biotechnology Department, Human Genetics Division , Atomic Energy Commission of Syria , Damascus , Syria
| | - Ayman Alabloog
- a Molecular Biology and Biotechnology Department, Human Genetics Division , Atomic Energy Commission of Syria , Damascus , Syria
| | - Hossam Murad
- a Molecular Biology and Biotechnology Department, Human Genetics Division , Atomic Energy Commission of Syria , Damascus , Syria
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23
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Trubini S, Ubiali A, Paties CT, Cavanna L. Novel BRAF mutation in melanoma: A case report. Mol Clin Oncol 2018; 8:460-462. [PMID: 29456854 DOI: 10.3892/mco.2018.1555] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 11/17/2017] [Indexed: 11/05/2022] Open
Abstract
In melanoma, a number of specific genetic and genomic aberrations have been identified to be important in tumorigenesis. In particular, the mutant B-Raf proto-oncogene, Serine/Threonine kinase (BRAF) gene is the target of tailored therapy with kinase inhibitor molecules. Identification of the array of mutations in patients with melanoma will be useful in determining a genetic profile of the tumor with potential implications for treatment decisions. A rare aminoacidic insertion in codon 599 of the BRAF gene (c.1797_1798insACA, T599insT) was detected by using both direct (Sanger) sequencing and pyrosequencing techniques in a metastatic melanoma of a female elderly patient. As suggested in other clinical contexts including pilocytic astrocytoma, papillary thyroid carcinomas and anaplastic thyroid carcinomas, this unusual mutation may be associated with a modified spatial structure of activated P-loop, resulting in a constitutional activation of the BRAF protein. The patient died shortly following the test, thus no biological therapy was performed. Comparable data regarding treatment of melanoma patients with rare BRAF mutations is lacking, and the response to BRAF inhibitors requires further investigation.
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Affiliation(s)
- Serena Trubini
- Onco-Hematologic Department, Ospedale Guglielmo da Saliceto, I-49-29121 Piacenza, Italy
| | - Alessandro Ubiali
- Onco-Hematologic Department, Ospedale Guglielmo da Saliceto, I-49-29121 Piacenza, Italy
| | - Carlo Terenzio Paties
- Onco-Hematologic Department, Ospedale Guglielmo da Saliceto, I-49-29121 Piacenza, Italy
| | - Luigi Cavanna
- Onco-Hematologic Department, Ospedale Guglielmo da Saliceto, I-49-29121 Piacenza, Italy
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24
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Liu HL, Han G, Peng M, Weng YM, Yuan JP, Yang GF, Yu JM, Song QB. Efficacy of EGFR tyrosine kinase inhibitors in non-small cell lung cancer patients harboring different types of EGFR mutations: A retrospective analysis. Curr Med Sci 2017; 37:864-72. [PMID: 29270745 DOI: 10.1007/s11596-017-1819-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 09/13/2017] [Indexed: 10/18/2022]
Abstract
With the development of molecular pathology, many types of epidermal growth factor receptor (EGFR) mutations have been identified. The efficacy of EGFR tyrosine kinase inhibitors (EGFR-TKIs) in non-small cell lung cancer (NSCLC) patients with different types of EGFR mutations, especially in patients with single rare mutations or complex mutations (co-occurrence of two or more different mutations), has not been fully understood. This study aimed to examine the efficacy of EGFR-TKIs in NSCLC patients with different types of EGFR mutations. Clinical data of 809 NSCLC patients who harbored different types of EGFR mutations and treated from January 2012 to October 2016 at Renmin Hospital and Zhongnan Hospital, Wuhan, were retrospectively reviewed. The clinical characteristics of these patients and the efficacy of EGFR-TKIs were analyzed. Among these patients, 377 patients had only the EGFR del-19 mutation, 362 patients the EGFR L858R mutation in exon 21, 33 patients single rare mutations and 37 patients complex mutations. Among these 809 patients, 239 patients were treated with EGFR-TKIs. In all the 239 patients, the disease control rate (DCR) was 93.7% with two patients (0.2%) achieving complete response (CR), the median progression free survival (PFS) was 13.0 months (95% confidence interval [CI], 11.6-14.4 months), and the median overall survival (OS) was 55.0 months (95% CI, 26.3-83.7 months). Subgroup analysis revealed that the DCR in patients harboring single rare or complex mutations of EGFR was significantly lower than in those with del-19 or L858R mutation (P<0.001). Patients with classic mutations (del-19 and/or L858R mutations) demonstrated longer PFS (P<0.001) and OS (P=0.017) than those with uncommon mutations (single rare and/or complex mutations). Furthermore, the patients with single rare mutations had shorter median OS than in those with other mutations. Multivariate Cox regression analysis identified that the type of EGFR mutations was an independent risk factor for PFS (hazard ratio [HR]=0.308, 95% CI, 0.191-0.494, P<0.001) and OS (HR=0.221, 95% CI, 0.101-0.480, P<0.001). The results suggest that the single rare or complex EGFR mutations confer inferior efficacy of EGFR-TKIs treatment to the classic mutations. The prognosis of the single rare EGFR mutations is depressing. EGFR-TKIs may be not a good choice for NSCLC patients with single rare mutations of EGFR. Further studies in these patients with uncommon mutations (especially for the patients with single rare mutations) are needed to determine a better precision treatment.
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25
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Sitzmann AF, Hagelstrom RT, Tassone F, Hagerman RJ, Butler MG. Rare FMR1 gene mutations causing fragile X syndrome: A review. Am J Med Genet A 2017; 176:11-18. [PMID: 29178241 DOI: 10.1002/ajmg.a.38504] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 09/21/2017] [Accepted: 09/24/2017] [Indexed: 12/16/2022]
Abstract
Fragile X syndrome (FXS) is the most common inherited form of intellectual disability, typically due to CGG-repeat expansions in the FMR1 gene leading to lack of expression. We identified a rare FMR1 gene mutation (c.413G>A), previously reported in a single patient and reviewed the literature for other rare FMR1 mutations. Our patient at 10 years of age presented with the classical findings of FXS including intellectual disability, autism, craniofacial findings, hyperextensibility, fleshy hands, flat feet, unsteady gait, and seizures but without the typical CGG-repeat expansion. He had more features of FXS than the previously reported patient with the same mutation. Twenty individuals reported previously with rare missense or nonsense mutations or other coding disturbances of the FMR1 gene ranged in age from infancy to 50 years; most were verbal with limited speech, had autism and hyperactivity, and all had intellectual disability. Four of the 20 individuals had a mutation within exon 15, three within exon 5, and two within exon 2. The FMR1 missense mutation (c.413G>A) is the same as in a previously reported male where it was shown that there was preservation of the post-synaptic function of the fragile X mental retardation protein (FMRP), the encoded protein of the FMR1 gene was preserved. Both patients with this missense mutation had physical, cognitive, and behavioral features similarly seen in FXS.
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Affiliation(s)
- Adam F Sitzmann
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, Kansas
| | - Robert T Hagelstrom
- Human Genetics Laboratory, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, University of California-Davis Medical Center, Sacramento, California.,MIND Institute, University of California-Davis Medical Center, Sacramento, California
| | - Randi J Hagerman
- MIND Institute, University of California-Davis Medical Center, Sacramento, California.,Department of Pediatrics, University of California-Davis Medical Center, Sacramento, California
| | - Merlin G Butler
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, Kansas
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26
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Jakaitiene A, Avino M, Guarracino MR. Beta-Binomial Model for the Detection of Rare Mutations in Pooled Next-Generation Sequencing Experiments. J Comput Biol 2016; 24:357-367. [PMID: 27632638 DOI: 10.1089/cmb.2016.0106] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Against diminishing costs, next-generation sequencing (NGS) still remains expensive for studies with a large number of individuals. As cost saving, sequencing genome of pools containing multiple samples might be used. Currently, there are many software available for the detection of single-nucleotide polymorphisms (SNPs). Sensitivity and specificity depend on the model used and data analyzed, indicating that all software have space for improvement. We use beta-binomial model to detect rare mutations in untagged pooled NGS experiments. We propose a multireference framework for pooled data with ability being specific up to two patients affected by neuromuscular disorders (NMD). We assessed the results comparing with The Genome Analysis Toolkit (GATK), CRISP, SNVer, and FreeBayes. Our results show that the multireference approach applying beta-binomial model is accurate in predicting rare mutations at 0.01 fraction. Finally, we explored the concordance of mutations between the model and software, checking their involvement in any NMD-related gene. We detected seven novel SNPs, for which the functional analysis produced enriched terms related to locomotion and musculature.
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Affiliation(s)
- Audrone Jakaitiene
- 1 Bioinformatics and Biostatistics Center, Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University , Vilnius, Lithuania
| | - Mariano Avino
- 2 High Performance Computing and Networking Institute , National Research Council, Naples, Italy
| | - Mario Rosario Guarracino
- 2 High Performance Computing and Networking Institute , National Research Council, Naples, Italy
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27
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Chorostowska-Wynimko J, Struniawski R, Sliwinski P, Wajda B, Czajkowska-Malinowska M. The national alpha-1 antitrypsin deficiency registry in Poland. COPD 2016; 12 Suppl 1:22-6. [PMID: 25938287 DOI: 10.3109/15412555.2015.1021915] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The alpha-1 antitrypsin deficiency (AATD) targeted screening program, together with the National Registry, were established in Poland in 2010 soon after the AATD diagnostics became available. Between 2010 and 2014 a total of 2525 samples were collected from respiratory patients countrywide; 55 patients with severe AAT deficiency or rare mutations were identified and registered, including 36 PiZZ subjects (65%). The majority of AATD patients were diagnosed with COPD (40%) or emphysema (7%), but also with bronchial asthma (16%) and bronchiectasis (13%). Therefore, the registry has proved instrumental in setting-up the AATD-dedicated network of respiratory medical centres in Poland. Since augmentation therapy is not reimbursed in our country, the smoking cessation guidance, optimal pharmacotherapy of respiratory symptoms as well the early detection, and effective treatment of exacerbations is absolutely essential.
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Affiliation(s)
- Joanna Chorostowska-Wynimko
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases , Warsaw , Poland
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28
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Orton RJ, Wright CF, Morelli MJ, King DJ, Paton DJ, King DP, Haydon DT. Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data. BMC Genomics 2015; 16:229. [PMID: 25886445 PMCID: PMC4425905 DOI: 10.1186/s12864-015-1456-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 03/09/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND RNA viruses have high mutation rates and exist within their hosts as large, complex and heterogeneous populations, comprising a spectrum of related but non-identical genome sequences. Next generation sequencing is revolutionising the study of viral populations by enabling the ultra deep sequencing of their genomes, and the subsequent identification of the full spectrum of variants within the population. Identification of low frequency variants is important for our understanding of mutational dynamics, disease progression, immune pressure, and for the detection of drug resistant or pathogenic mutations. However, the current challenge is to accurately model the errors in the sequence data and distinguish real viral variants, particularly those that exist at low frequency, from errors introduced during sequencing and sample processing, which can both be substantial. RESULTS We have created a novel set of laboratory control samples that are derived from a plasmid containing a full-length viral genome with extremely limited diversity in the starting population. One sample was sequenced without PCR amplification whilst the other samples were subjected to increasing amounts of RT and PCR amplification prior to ultra-deep sequencing. This enabled the level of error introduced by the RT and PCR processes to be assessed and minimum frequency thresholds to be set for true viral variant identification. We developed a genome-scale computational model of the sample processing and NGS calling process to gain a detailed understanding of the errors at each step, which predicted that RT and PCR errors are more likely to occur at some genomic sites than others. The model can also be used to investigate whether the number of observed mutations at a given site of interest is greater than would be expected from processing errors alone in any NGS data set. After providing basic sample processing information and the site's coverage and quality scores, the model utilises the fitted RT-PCR error distributions to simulate the number of mutations that would be observed from processing errors alone. CONCLUSIONS These data sets and models provide an effective means of separating true viral mutations from those erroneously introduced during sample processing and sequencing.
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Affiliation(s)
- Richard J Orton
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom.
- Medical Research Council-University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom.
| | | | - Marco J Morelli
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia at the IFOM-IEO Campus, Via Adamello 16, Milano, 20139, Italy.
| | - David J King
- Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK.
| | - David J Paton
- Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK.
| | - Donald P King
- Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK.
| | - Daniel T Haydon
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom.
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Martin PM, Yang X, Robin N, Lam E, Rabinowitz JS, Erdman CA, Quinn J, Weiss LA, Hamilton SP, Kwok PY, Moon RT, Cheyette BNR. A rare WNT1 missense variant overrepresented in ASD leads to increased Wnt signal pathway activation. Transl Psychiatry 2013; 3:e301. [PMID: 24002087 PMCID: PMC3784764 DOI: 10.1038/tp.2013.75] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 07/23/2013] [Accepted: 07/24/2013] [Indexed: 01/01/2023] Open
Abstract
Wnt signaling, which encompasses multiple biochemical pathways that regulate neural development downstream of extracellular Wnt glycoprotein ligands, has been suggested to contribute to major psychiatric disorders including autism spectrum disorders (ASD). We used next-generation sequencing and Sequenom genotyping technologies to resequence 10 Wnt signaling pathway genes in 198 ASD patients and 240 matched controls. Results for single-nucleotide polymorphisms (SNPs) of interest were confirmed in a second set of 91 ASD and 144 control samples. We found a significantly increased burden of extremely rare missense variants predicted to be deleterious by PolyPhen-2, distributed across seven genes in the ASD sample (3.5% in ASD vs 0.8% in controls; Fisher's exact test, odds ratio (OR)=4.37, P=0.04). We also found a missense variant in WNT1 (S88R) that was overrepresented in the ASD sample (8 A/T in 267 ASD (minor allele frequency (MAF)=1.69%) vs 1 A/T in 377 controls (MAF=0.13%), OR=13.0, Fisher's exact test, P=0.0048; OR=8.2 and P=0.053 after correction for population stratification). Functional analysis revealed that WNT1-S88R is more active than wild-type WNT1 in assays for the Wnt/β-catenin signaling pathway. Our findings of a higher burden in ASD of rare missense variants distributed across 7 of 10 Wnt signaling pathway genes tested, and of a functional variant at the WNT1 locus associated with ASD, support that dysfunction of this pathway contributes to ASD susceptibility. Given recent findings of common molecular mechanisms in ASD, schizophrenia and affective disorders, these loci merit scrutiny in other psychiatric conditions as well.
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Affiliation(s)
- P-M Martin
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
| | - X Yang
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
| | - N Robin
- Department of Pharmacology and Howard Hughes Medical Institute, University of Washington School of Medicine, University of Washington, Seattle, WA, USA
| | - E Lam
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - J S Rabinowitz
- Department of Pharmacology and Howard Hughes Medical Institute, University of Washington School of Medicine, University of Washington, Seattle, WA, USA
| | - C A Erdman
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - J Quinn
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - L A Weiss
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - S P Hamilton
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - P-Y Kwok
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - R T Moon
- Department of Pharmacology and Howard Hughes Medical Institute, University of Washington School of Medicine, University of Washington, Seattle, WA, USA
| | - B N R Cheyette
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA,Department of Psychiatry, University of California, Rock Hall Room 284D, 1550 4th Street, San Francisco, CA 94158-2324, USA. E-mail:
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Stefl S, Nishi H, Petukh M, Panchenko AR, Alexov E. Molecular mechanisms of disease-causing missense mutations. J Mol Biol 2013; 425:3919-36. [PMID: 23871686 DOI: 10.1016/j.jmb.2013.07.014] [Citation(s) in RCA: 187] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 07/04/2013] [Accepted: 07/10/2013] [Indexed: 12/23/2022]
Abstract
Genetic variations resulting in a change of amino acid sequence can have a dramatic effect on stability, hydrogen bond network, conformational dynamics, activity and many other physiologically important properties of proteins. The substitutions of only one residue in a protein sequence, so-called missense mutations, can be related to many pathological conditions and may influence susceptibility to disease and drug treatment. The plausible effects of missense mutations range from affecting the macromolecular stability to perturbing macromolecular interactions and cellular localization. Here we review the individual cases and genome-wide studies that illustrate the association between missense mutations and diseases. In addition, we emphasize that the molecular mechanisms of effects of mutations should be revealed in order to understand the disease origin. Finally, we report the current state-of-the-art methodologies that predict the effects of mutations on protein stability, the hydrogen bond network, pH dependence, conformational dynamics and protein function.
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Affiliation(s)
- Shannon Stefl
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
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