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Sultana GNN, Akter F, Israfil SMH, Ray UC, Jahan RA, Ali MS, Din SA, Rahman S, Halim R, Alam MS. Quantitative analysis of serum cell-free DNA as a predictive and prognostic marker in breast cancer patients. Front Oncol 2023; 13:1171412. [PMID: 37427131 PMCID: PMC10324030 DOI: 10.3389/fonc.2023.1171412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/23/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction According to the GLOBOCAN (Global Cancer Observatory) 2020 report, 13,028 new cases of breast cancer (19%) were diagnosed in the United States, and 6,783 of them succumbed to the disease, making it the most common cancer among women. The clinical stage at the time of diagnosis is one of the most significant survival predictors in breast cancer. With delayed illness detection comes a lower survival rate. The prognosis of breast cancer may be predicted using circulating cell-free DNA (cfDNA), a non-invasive diagnosis technique. Objective This study aimed to determine the most sensitive and effective method for detecting changes in cfDNA levels and for using cfDNA as a diagnostic and prognostic marker of breast cancer. Methods The potential function of serum cfDNA levels as a marker for early breast cancer diagnosis was investigated using UV spectrophotometric, fluorometric, and real-time qPCR assays. Results This research suggests that the most successful way to measure the amount of cfDNA described decades ago could be used as a "liquid biopsy" to track cancer in real time. The RT-qPCR (ALU115) method produced the most statistically significant results (p=0.000). At the threshold concentration of 395.65 ng/ml of cfDNA, the ROC curve reflects the maximum AUC= 0.7607, with a sensitivity of 0.65 and specificity of 0.80. Conclusion For a preliminary assessment of total circulating cfDNA, a combination of all of the above techniques will be most efficacious. Based on our results, we conclude that the RT-qPCR technique combined with fluorometric measurement can identify a statistically significant difference in cfDNA levels between cohorts of breast cancer patients and healthy controls.
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Affiliation(s)
| | - Ferdowsi Akter
- Department of Clinical Pharmacy and Pharmacology, University of Dhaka, Dhaka, Bangladesh
| | - S. M. Hasan Israfil
- Department of Pharmaceutical Chemistry, University of Dhaka, Dhaka, Bangladesh
| | - Utpal Chandra Ray
- Genetic and Cytology Laboratory, Invent Technologies, Banani, Dhaka, Bangladesh
| | - Rumana Akther Jahan
- Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Mohammad Shawkat Ali
- Department of Clinical Pharmacy and Pharmacology, University of Dhaka, Dhaka, Bangladesh
| | - Salim Al Din
- Genetic and Cytology Laboratory, Invent Technologies, Banani, Dhaka, Bangladesh
| | - Shafiqur Rahman
- Institute of Statistical Research and Training, University of Dhaka, Dhaka, Bangladesh
| | - Rezaul Halim
- Genetic and Cytology Laboratory, Invent Technologies, Banani, Dhaka, Bangladesh
| | - Mohammad Sahajadul Alam
- Department of Surgical Oncology, National Institute of Cancer Research and Hospital, Dhaka, Bangladesh
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2
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Zhang X, Chen J. HIV Reservoir: How to Measure It? Curr HIV/AIDS Rep 2023; 20:29-41. [PMID: 37004676 DOI: 10.1007/s11904-023-00653-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2023] [Indexed: 04/04/2023]
Abstract
PURPOSEOF REVIEW In the current quest for a complete cure for HIV/AIDS, the persistence of a long-lived reservoir of cells carrying replication-competent proviruses is the major challenge. Here, we describe the main elements and characteristics of several widely used assays of HIV latent reservoir detection. RECENT FINDINGS To date, researchers have developed several different HIV latent reservoir detection assays. Among them, the in vitro quantitative viral outgrowth assay (QVOA) has been the gold standard for assessing latent HIV-1 viral load. The intact proviral DNA assay (IPDA) based on PCR also demonstrated the predominance of defective viruses. However, these assays all have some drawbacks and may still be inadequate in detecting the presence of ultralow levels of latent virus in many patients who were initially thought to have been cured, but eventually showed viral rebound. An accurate and precise measurement of the HIV reservoir is therefore needed to evaluate curative strategies, aimed to functional cure or sterilizing cure.
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Affiliation(s)
- Xinyu Zhang
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jun Chen
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
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3
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Microvascular Experimentation in the Chick Chorioallantoic Membrane as a Model for Screening Angiogenic Agents including from Gene-Modified Cells. Int J Mol Sci 2021; 23:ijms23010452. [PMID: 35008876 PMCID: PMC8745510 DOI: 10.3390/ijms23010452] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 02/07/2023] Open
Abstract
The chick chorioallantoic membrane (CAM) assay model of angiogenesis has been highlighted as a relatively quick, low cost and effective model for the study of pro-angiogenic and anti-angiogenic factors. The chick CAM is a highly vascularised extraembryonic membrane which functions for gas exchange, nutrient exchange and waste removal for the growing chick embryo. It is beneficial as it can function as a treatment screening tool, which bridges the gap between cell based in vitro studies and in vivo animal experimentation. In this review, we explore the benefits and drawbacks of the CAM assay to study microcirculation, by the investigation of each distinct stage of the CAM assay procedure, including cultivation techniques, treatment applications and methods of determining an angiogenic response using this assay. We detail the angiogenic effect of treatments, including drugs, metabolites, genes and cells used in conjunction with the CAM assay, while also highlighting the testing of genetically modified cells. We also present a detailed exploration of the advantages and limitations of different CAM analysis techniques, including visual assessment, histological and molecular analysis along with vascular casting methods and live blood flow observations.
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Plasma DNA Integrity as a Prognostic Biomarker for Colorectal Cancer Chemotherapy. JOURNAL OF ONCOLOGY 2021; 2021:5569783. [PMID: 34135960 PMCID: PMC8175143 DOI: 10.1155/2021/5569783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/18/2021] [Indexed: 12/24/2022]
Abstract
Objectives To verify whether the concentrations and integrity index of circulating cell-free DNA (cfDNA) in serum may be clinically useful for the progression monitoring of colorectal cancer (CRC) patients. Methods Serum samples were collected from 76 primary CRC patients who underwent surgery, including 60 with chemotherapy and 43 with follow-up. Long (247 bp) and short (115 bp) DNA fragments in serum were detected by real-time quantitative PCR by amplifying the ALU repeats. Ten serum traditional biomarkers levels were detected by chemiluminescence immunoassay assay. Results The median DNA integrity index (ALU247/ALU115) of serum DNA in the preoperative group was significantly higher than those in the postchemotherapy and the follow-up groups, while cfDNA concentration (ALU115) was significantly lower in the preoperative group compared with the postchemotherapy and the follow-up groups. CEA and CA242 were significantly lower in the postoperative group than in the preoperative group. Conclusions Serum DNA integrity index (ALU247/115) may prove to be a promising candidate biomarker for prognostic prediction of CRC who underwent chemotherapy and during short-term follow-up.
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Strnadová K, Španko M, Dvořánková B, Lacina L, Kodet O, Shbat A, Klepáček I, Smetana K. Melanoma xenotransplant on the chicken chorioallantoic membrane: a complex biological model for the study of cancer cell behaviour. Histochem Cell Biol 2020; 154:177-188. [PMID: 32232553 DOI: 10.1007/s00418-020-01872-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2020] [Indexed: 12/11/2022]
Abstract
The globally increasing incidence of cancer, including melanoma, requires novel therapeutic strategies. Development of successful novel drugs is based on clear identification of the target mechanisms responsible for the disease progression. The specific cancer microenvironment represents a critically important aspect of cancer biology, which cannot be properly studied in simplistic cell culture conditions. Among other traditional options, the study of melanoma cell growth on the chicken chorioallantoic membrane offers several significant advantages. This model offers increased complexity compared to usual in silico culture models and still remains financially affordable. Using this model, we studied the growth of three established human melanoma cell lines: A2058, BLM, G361. The combination of histology, immunohistochemistry with the application of human-specific antibodies, intravascular injection of contrast material such as filtered Indian ink, Mercox solution and phosphotungstic acid, and X-ray micro-CT and live-cell monitoring was employed. Melanoma cells spread well on the chicken chorioallantoic membrane. However, invasion into the stroma of the chorioallantoic membrane and the limb primordium graft was rare. The melanoma cells also significantly influenced the architecture of the blood vessel network, resulting in the orientation of the vessels to the site of the tumour cell inoculation. The system of melanoma cell culture on the chorioallantoic membrane is suitable for the study of melanoma cell growth, particularly of rearrangement of the host vascular pattern after cancer cell implantation. The system also has promising potential for further development.
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Affiliation(s)
- Karolína Strnadová
- Institute of Anatomy, First Faculty of Medicine, Charles University, 12800, Prague, Czech Republic.,BIOCEV, First Faculty of Medicine, Charles University, 25250, Vestec, Czech Republic
| | - Michal Španko
- Institute of Anatomy, First Faculty of Medicine, Charles University, 12800, Prague, Czech Republic.,Department of Stomatology, First Faculty of Medicine, Charles University, 12800, Prague, Czech Republic
| | - Barbora Dvořánková
- Institute of Anatomy, First Faculty of Medicine, Charles University, 12800, Prague, Czech Republic.,BIOCEV, First Faculty of Medicine, Charles University, 25250, Vestec, Czech Republic
| | - Lukáš Lacina
- Institute of Anatomy, First Faculty of Medicine, Charles University, 12800, Prague, Czech Republic. .,BIOCEV, First Faculty of Medicine, Charles University, 25250, Vestec, Czech Republic. .,Department of Dermatovenereology, First Faculty of Medicine, Charles University, 12808, Prague, Czech Republic.
| | - Ondřej Kodet
- Institute of Anatomy, First Faculty of Medicine, Charles University, 12800, Prague, Czech Republic.,BIOCEV, First Faculty of Medicine, Charles University, 25250, Vestec, Czech Republic.,Department of Dermatovenereology, First Faculty of Medicine, Charles University, 12808, Prague, Czech Republic
| | - Andrej Shbat
- Institute of Anatomy, First Faculty of Medicine, Charles University, 12800, Prague, Czech Republic
| | - Ivo Klepáček
- Institute of Anatomy, First Faculty of Medicine, Charles University, 12800, Prague, Czech Republic
| | - Karel Smetana
- Institute of Anatomy, First Faculty of Medicine, Charles University, 12800, Prague, Czech Republic. .,BIOCEV, First Faculty of Medicine, Charles University, 25250, Vestec, Czech Republic.
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Wisse RPL, Kuiper JJW, Radstake TRD, Broen JCA. Quantification of Double Stranded DNA Breaks and Telomere Length as Proxies for Corneal Damage and Replicative Stress in Human Keratoconus Corneas. Transl Vis Sci Technol 2019; 8:10. [PMID: 31372311 PMCID: PMC6660185 DOI: 10.1167/tvst.8.4.10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 05/17/2019] [Indexed: 12/17/2022] Open
Abstract
Purpose The pathogenesis of keratoconus (KC) is multifactorial, and associated with oxidative stress and subsequent DNA damage. We investigate differences in DNA damage and replicative stress in patients with KC, and in healthy and diseased controls. Methods We obtained 64 corneal buttons from 27 patients with KC after corneal transplant surgery, 21 with a decompensated graft (DG), and 16 healthy controls (HC). The amount of intact Alu elements per genome copy as measured by quantitative polymerase chain reaction (qPCR) was used to quantify intact DNA. Telomere length was measured as a proxy for replicative stress. In addition, telomerase reverse transcriptase (hTERT) gene expression level was assessed. Results Mean (± standard deviation [SD]) DNA damage was similar between the KC (5.56 ± 14.08), DG (3.16 ± 8.22), and HC (3.51 ± 6.66) groups (P = 0.807). No associations were found between DNA damage and patient age (P = 0.523), atopic constitution (P = 0.240), or contact lens wear (P = 0.393). Telomere length differed (P = 0.034), most notably in the KC group, and hTERT was not detected in any corneal sample. Three cross-linked (CXL) KC corneas did not contain significantly more DNA damage (×2.6, P = 0.750). Conclusions Based on these findings, differences in actual corneal DNA damage in KC could not be identified, and the longer telomere length in KC did not support replicative stress as a major etiologic factor in the pathogenesis of KC. Future longitudinal investigations on KC etiology should assess progressively early cases to better comprehend the cellular and molecular processes preceding the archetypical morphologic changes. Translational Relevance The standard treatment for progressive keratoconus promotes the crosslinking of collagen fibers through ultraviolet radiation and the subsequent formation of reactive oxygen species. Our study helps to underline the safety of this treatment approach.
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Affiliation(s)
- Robert P L Wisse
- Department of Ophthalmology, University Medical Center Utrecht, The Netherlands
| | - Jonas J W Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, The Netherlands.,Ophthalmo-Immunology group, Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, The Netherlands
| | - Timothy R D Radstake
- Department of Rheumatology & Clinical Immunology, Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, The Netherlands
| | - Jasper C A Broen
- Department of Rheumatology & Clinical Immunology, Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, The Netherlands
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Jiang Y, Zong W, Ju S, Jing R, Cui M. Promising member of the short interspersed nuclear elements ( Alu elements): mechanisms and clinical applications in human cancers. J Med Genet 2019; 56:639-645. [PMID: 30852527 DOI: 10.1136/jmedgenet-2018-105761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/13/2019] [Accepted: 01/31/2019] [Indexed: 12/11/2022]
Abstract
Alu elements are one of most ubiquitous repetitive sequences in human genome, which were considered as the junk DNA in the past. Alu elements have been found to be associated with human diseases including cancers via events such as amplification, insertion, recombination or RNA editing, which provide a new perspective of oncogenesis at both DNA and RNA levels. Due to the prevalent distribution, Alu elements are widely used as target molecule of liquid biopsy. Alu-based cell-free DNA shows feasible application value in tumour diagnosis, postoperative monitoring and adjuvant therapy. In this review, the special tumourigenesis mechanism of Alu elements in human cancers is discussed, and the application of Alu elements in various tumour liquid biopsy is summarised.
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Affiliation(s)
- Yun Jiang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.,Medical college, Nantong University, Nantong, Jiangsu, China
| | - Wei Zong
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China.,Medical college, Nantong University, Nantong, Jiangsu, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Rongrong Jing
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Ming Cui
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
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8
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Hao TB, Shi W, Shen XJ, Qi J, Wu XH, Wu Y, Tang YY, Ju SQ. Circulating cell-free DNA in serum as a biomarker for diagnosis and prognostic prediction of colorectal cancer. Br J Cancer 2014; 111:1482-9. [PMID: 25157833 PMCID: PMC4200099 DOI: 10.1038/bjc.2014.470] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 07/07/2014] [Accepted: 07/16/2014] [Indexed: 12/15/2022] Open
Abstract
Background: To verify whether the concentrations and integrity index of circulating cell-free DNA (ccf-DNA) in serum may be clinically useful for the diagnosis and progression monitoring of colorectal cancer (CRC) patients. Methods: Serum samples were collected from 104 with primary CRC, 85 with operated CRC, 16 with recurrent/metastatic CRC, 63 patients with intestinal polyps and 110 normal controls. Long (247 bp) and short (115 bp) DNA fragments in serum were detected by real-time quantitative PCR by amplifying the ALU repeats (ALU-qPCR). Serum carcinoembryonic antigen (CEA) level was detected by ARCHITECT assay. Results: The median absolute serum ALU115 and ALU247/115 in primary CRC group was significantly higher than those in intestinal polyp and normal control groups (both P<0.0001), in recurrent/metastatic CRC was significantly higher compared with primary CRC (P=0.0021, P=0.0018) or operated CRC (P<0.0001, respectively) and during follow-up, ALU115 and ALU247/115 were increased before surgery and decreased significantly after surgery. Conclusions: Combined detection of ALU115, ALU247/115 and CEA could improve the diagnostic efficiency for CRC. Serum DNA concentrations and integrity index may be valuable in early complementary diagnosis and monitoring of progression and prognosis of CRC.
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Affiliation(s)
- T B Hao
- Medical School of Nantong University, Nantong 226000, Jiangsu Province, China
| | - W Shi
- Surgical Comprehensive Laboratory, Affiliated Hospital of Nantong University, Nantong 226000, Jiangsu Province, China
| | - X J Shen
- Surgical Comprehensive Laboratory, Affiliated Hospital of Nantong University, Nantong 226000, Jiangsu Province, China
| | - J Qi
- Surgical Comprehensive Laboratory, Affiliated Hospital of Nantong University, Nantong 226000, Jiangsu Province, China
| | - X H Wu
- Surgical Comprehensive Laboratory, Affiliated Hospital of Nantong University, Nantong 226000, Jiangsu Province, China
| | - Y Wu
- Medical School of Nantong University, Nantong 226000, Jiangsu Province, China
| | - Y Y Tang
- Medical School of Nantong University, Nantong 226000, Jiangsu Province, China
| | - S Q Ju
- 1] Surgical Comprehensive Laboratory, Affiliated Hospital of Nantong University, Nantong 226000, Jiangsu Province, China [2] Center of Laboratory Medicine, Affiliated Hospital of Nantong University, 20 Xisi Street, Nantong 226000, Jiangsu Province, China
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9
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Cardelli M, Marchegiani F, Provinciali M. Alu insertion profiling: array-based methods to detect Alu insertions in the human genome. Genomics 2012; 99:340-6. [PMID: 22495107 DOI: 10.1016/j.ygeno.2012.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 03/15/2012] [Accepted: 03/23/2012] [Indexed: 10/28/2022]
Abstract
The analysis of the genetic variability associated to Alu sequences was hampered by the absence of genome-wide methodologies able to efficiently detect new polymorphisms/mutations among these repetitive elements. Here we describe two Alu insertion profiling (AIP) methods based on the hybridization of Alu-flanking genomic fragments on tiling microarrays. Protocols are designed to preferentially detect active Alu subfamilies. We tested AIP methods by analyzing chromosomes 1 and 6 in two genomic samples. In genomic regions covered by array-features, with a sensitivity of 2% (AIP1) -4% (AIP2) and 5% (AIP1) -8% (AIP2) for the old J and S Alu lineages respectively, we obtained a sensitivity of 67% (AIP1) -90% (AIP2) for the young Ya subfamily. Among the loci showing sample-to-sample differences, 5 (AIP1) -8 (AIP2) were associated to known Alu polymorphisms. Moreover, we were able to confirm by PCR and DNA sequencing 4 new intragenic Alu elements, polymorphic in 10 additional individuals.
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Affiliation(s)
- Maurizio Cardelli
- Advanced Technology Center for Aging Research, Scientific Technological Area, INRCA-IRCCS, Ancona, Italy
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Cardelli M, Nicoli M, Bazzani A, Franceschi C. Application of Wavelet Packet Transform to detect genetic polymorphisms by the analysis of inter-Alu PCR patterns. BMC Bioinformatics 2010; 11:593. [PMID: 21143911 PMCID: PMC3012677 DOI: 10.1186/1471-2105-11-593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 12/09/2010] [Indexed: 11/30/2022] Open
Abstract
Background The analysis of Inter-Alu PCR patterns obtained from human genomic DNA samples is a promising technique for a simultaneous analysis of many genomic loci flanked by Alu repetitive sequences in order to detect the presence of genetic polymorphisms. Inter-Alu PCR products may be separated and analyzed by capillary electrophoresis using an automatic sequencer that generates a complex pattern of peaks. We propose an algorithmic method based on the Haar-Walsh Wavelet Packet Transformation (WPT) for an efficient detection of fingerprint-type patterns generated by PCR-based methodologies. We have tested our algorithmic approach on inter-Alu patterns obtained from the genomic DNA of three couples of monozygotic twins, expecting that the inter-Alu patterns of each twins couple will show differences due to unavoidable experimental variability. On the contrary the differences among samples of different twins are supposed to originate from genetic variability. Our goal is to automatically detect regions in the inter-Alu pattern likely associated to the presence of genetic polymorphisms. Results We show that the WPT algorithm provides a reliable tool to identify sample to sample differences in complex peak patterns, reducing the possible errors and limits associated to a subjective evaluation. The redundant decomposition of the WPT algorithm allows for a procedure of best basis selection which maximizes the pattern differences at the lowest possible scale. Our analysis points out few classifying signal regions that could indicate the presence of possible genetic polymorphisms. Conclusions The WPT algorithm based on the Haar-Walsh wavelet is an efficient tool for a non-supervised pattern classification of inter-ALU signals provided by a genetic analyzer, even if it was not possible to estimate the power and false positive rate due to the lacking of a suitable data base. The identification of non-reproducible peaks is usually accomplished comparing different experimental replicates of each sample. Moreover, we remark that, albeit we developed and optimized an algorithm able to analyze patterns obtained through inter-Alu PCR, the method is theoretically applicable to whatever fingerprint-type pattern obtained analyzing anonymous DNA fragments through capillary electrophoresis, and it could be usefully applied on a wide range of fingerprint-type methodologies.
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Affiliation(s)
- Maurizio Cardelli
- Italian National Research Centers on Aging (I.N.R.C.A.), Ancona, Italy
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