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Seroussi E. Estimating Copy-Number Proportions: The Comeback of Sanger Sequencing. Genes (Basel) 2021; 12:283. [PMID: 33671263 PMCID: PMC7922598 DOI: 10.3390/genes12020283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 12/28/2022] Open
Abstract
Determination of the relative copy numbers of mixed molecular species in nucleic acid samples is often the objective of biological experiments, including Single-Nucleotide Polymorphism (SNP), indel and gene copy-number characterization, and quantification of CRISPR-Cas9 base editing, cytosine methylation, and RNA editing. Standard dye-terminator chromatograms are a widely accessible, cost-effective information source from which copy-number proportions can be inferred. However, the rate of incorporation of dye terminators is dependent on the dye type, the adjacent sequence string, and the secondary structure of the sequenced strand. These variable rates complicate inferences and have driven scientists to resort to complex and costly quantification methods. Because these complex methods introduce their own biases, researchers are rethinking whether rectifying distortions in sequencing trace files and using direct sequencing for quantification will enable comparable accurate assessment. Indeed, recent developments in software tools (e.g., TIDE, ICE, EditR, BEEP and BEAT) indicate that quantification based on direct Sanger sequencing is gaining in scientific acceptance. This commentary reviews the common obstacles in quantification and the latest insights and developments relevant to estimating copy-number proportions based on direct Sanger sequencing, concluding that bidirectional sequencing and sophisticated base calling are the keys to identifying and avoiding sequence distortions.
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Affiliation(s)
- Eyal Seroussi
- Institute of Animal Science, Agricultural Research Organization (ARO), HaMaccabim Road, P.O.B 15159, Rishon LeTsiyon 7528809, Israel
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2
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Melchionda F, Stanciu F, Buscemi L, Pesaresi M, Tagliabracci A, Turchi C. Searching the undetected mtDNA variants in forensic MPS data. Forensic Sci Int Genet 2020; 49:102399. [PMID: 33038616 DOI: 10.1016/j.fsigen.2020.102399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/27/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
The efficiency of MPS in forensic mtDNA analysis has been thoroughly proven, although a reliable and well established data evaluation still remains a critical point. Numerous bioinformatics tools have been developed, but most of them require specific operating systems and high costs, while free open-source programs with user-friendly interfaces are few. In this study, 43 full mtGenomes were sequenced using the Ion Personal Genome Machine™ (PGM™) System and analyzed utilizing the plug-in Variant Caller (TVC) of the Ion Torrent Software Suite and the mtDNA-Server (mDS), a free web-based mitochondrial analysis tool for MPS data. The outcomes of these two different analysis tools were compared to variants noted after manual inspection of the aligned reads performed using Integrative Genomics Viewer (IGV). The comparison highlighted the presence of thirty-nine discordant variant calls, which were resolved by Sanger sequencing that confirmed the presence of all variants, except for 7 deletions. The combined adoption of IGV and Sanger type sequencing confirmatory steps, in addition of TVC and mDS analysis, resulted in a more accurate variants assignment with the detection of 32 additional true polymorphisms, which were noted in the final dataset. Regarding the heteroplasmy issue, out of a total of thirty heteroplasmic variants, twenty-eight were detected by the TVC, while the mDS detected twenty-two. Overall, none of the used bioinformatics tools were the perfect choice and a secondary analysis with an expert's opinion in complete mtGenome MPS data evaluation is still required in forensic genetic analysis.
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Affiliation(s)
- Filomena Melchionda
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Florin Stanciu
- Romanian National DNA Database, National Forensic Science Institute, General Inspectorate of Romanian Police, Bucharest, Romania.
| | - Loredana Buscemi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Mauro Pesaresi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Adriano Tagliabracci
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Chiara Turchi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
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3
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Palencia-Madrid L, Vinueza-Espinosa D, Baeta M, Rocandio AM, de Pancorbo MM. Validation of a 52-mtSNP minisequencing panel for haplogroup classification of forensic DNA samples. Int J Legal Med 2020; 134:929-936. [PMID: 32030455 DOI: 10.1007/s00414-020-02264-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 01/31/2020] [Indexed: 11/25/2022]
Abstract
Mitochondrial DNA (mtDNA) is a useful tool in forensic investigation as it provides information about the matrilineal ancestry of individuals. In addition, mtDNA can be analyzed when the analysis of other nuclear markers is underperforming. Recently, we developed a minisequencing panel for the simultaneous analysis of 52 mtDNA SNPs to classify maternal lineages into the main haplogroups and their phylogeographic origin. In order to make this panel suitable for forensic genetics laboratories, a validation study has been performed in accordance with the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines, including species specificity, reproducibility, sensitivity, and stability tests. The results demonstrate that the panel of 52 mtDNA SNPs is highly sensitive, since it enables to obtain complete genetic profiles of samples containing minimal amounts of DNA (1 pg). Furthermore, it provides sufficient genetic information to detect the matrilineal biogeographical origin of highly degraded samples, i.e., ancient dating skeletal remains, and samples with the presence of inhibitors, such as hematin and humic acid. In addition, this panel can detect mixtures in samples whose mtDNA haplogroups of contributors are different. Overall, the results of this study demonstrate the suitability of this minisequencing panel of 52 mtDNA SNPs to be used in forensic cases, with samples of low amount or degraded DNA.
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Affiliation(s)
- Leire Palencia-Madrid
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Diana Vinueza-Espinosa
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
- Laboratori d'ADN antic, Unitat d'Antropologia biològica, Departament de Biologia Animal, de Biologia Vegetal i Ecologia, Facultat Biociències, Universitat Autònoma de Barcelona, Bellaterra, Cerdanyola del Vallès, Spain
| | - Miriam Baeta
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Ana M Rocandio
- Department of Nutrition and Food Sciences, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain.
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4
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Get it off, but keep it: Efficient cleaning of hair shafts with parallel DNA extraction of the surface stain. Forensic Sci Int Genet 2019; 45:102210. [PMID: 31812096 DOI: 10.1016/j.fsigen.2019.102210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 01/10/2023]
Abstract
The analysis of hair samples is a common task in forensic investigations. Material transferred to the surface of a hair during a crime challenges the analysis as it has to be removed efficiently. However, the removal of the stain can also lead to a loss of information on stain contributors. DNA analysis of the stain itself might thus be helpful for the forensic investigation. The aim of this study was the examination of different methods to remove common biological surface stains completely from human hair shafts without hampering the parallel DNA extraction of the cleaned hair shaft and the isolated surface stain (blood, saliva, vaginal secretion, semen, and skin flocks). Four different methods of cleaning (water, lysis buffer, swabbing, NaClO) were compared to their cleaning efficiency as well as their success of mtDNA analysis of three hair donors and the original five stains on the hair. In order to test the suitability of this procedure for future analysis methods, a selection of samples were also sequenced with MPS. Additionally, nuclear DNA analysis of the stain DNA was performed using a screening STR assay to test the potential success for detection of a STR profile. The most efficient removal of the stain was achieved using NaClO, however compromising further analysis of the stain DNA. The best results for cleaning and parallel stain analysis were obtained using a swab moistened with 0.5 % SDS for surface cleaning. Especially water failed to remove stains efficiently, leading to a high amount of mixed mtDNA in the DNA extracts. MPS showed an increased sensitivity for detection of minute mixtures.
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5
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Desmyter S, Dognaux S, Noel F, Prieto L. Base specific variation rates at mtDNA positions 16093 and 16183 in human hairs. Forensic Sci Int Genet 2019; 43:102142. [PMID: 31437782 DOI: 10.1016/j.fsigen.2019.102142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/25/2019] [Accepted: 08/11/2019] [Indexed: 10/26/2022]
Abstract
Small variations between haplotypes detected in different tissues from the same individual have been previously described. These differences complicate the interpretation of mtDNA results in real forensic casework. mtDNA haplotypes detected in hair strands collected at the crime scene have to be frequently compared with haplotypes of reference samples (buccal swabs) from victims or suspects. Nucleotide position 16093 is a well-known hot spot where differences can accumulate between different tissues of the same individual. Intra individual variation was also detected at positions 16182 and 16183 in haplotypes showing an uninterrupted HV1 poly-C stretch (with 16189C). In order to better characterize the type of variation in these positions between buccal cells and hair strands from the same individual, we have performed Sanger sequencing in 25-28 hair strands (411 in total) from 15 individuals showing either an uninterrupted HV1 polyC-stretch (16189C) or 16093C/Y in their buccal cells. The results have been evaluated by also taking into account our previous results published in [19]. We have found that no variation among hair strands was detected in individuals showing T16093 in buccal cells, while variation in hair strands (T16093, 16093C and 16093Y) were detected in individuals showing 16093C or 16093Y in buccal cells. Regarding nucleotide positions 16182 and 16183 in combination with an uninterrupted polyC-stretch, no variation was detected in hairs from individuals showing A16182 16183C in their buccal cells. In contrast, individuals A16182 A16183 showed hair strands with A16182 16183 M and A16182 16183C. And finally, individuals with 16182C 16183C showed some variation in a small amount of their hair strands (some hairs with 16182 M 16183C). These results can be relevant for forensic practitioners when comparing reference samples with hair strands, which is the type of sample most tested by using mtDNA analysis in forensic casework.
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Affiliation(s)
- Stijn Desmyter
- NICC - Belgian Institute for Forensic Science and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium.
| | - Sophie Dognaux
- NICC - Belgian Institute for Forensic Science and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium
| | - Fabrice Noel
- NICC - Belgian Institute for Forensic Science and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium
| | - Lourdes Prieto
- Instituto de Ciencias Forenses. Grupo de Medicina Xenómica. Universidade de Santiago de Compostela, Spain; Laboratorio ADN. Comisaría General de Policía Científica, Madrid, Spain
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6
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Abicht A, Scharf F, Kleinle S, Schön U, Holinski-Feder E, Horvath R, Benet-Pagès A, Diebold I. Mitochondrial and nuclear disease panel (Mito-aND-Panel): Combined sequencing of mitochondrial and nuclear DNA by a cost-effective and sensitive NGS-based method. Mol Genet Genomic Med 2018; 6:1188-1198. [PMID: 30406974 PMCID: PMC6305657 DOI: 10.1002/mgg3.500] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/27/2018] [Accepted: 10/10/2018] [Indexed: 01/21/2023] Open
Abstract
Background The diagnosis of mitochondrial disorders is challenging because of the clinical variability and genetic heterogeneity of these conditions. Next‐Generation Sequencing (NGS) technology offers a robust high‐throughput platform for nuclear and mitochondrial DNA (mtDNA) analyses. Method We developed a custom Agilent SureSelect Mitochondrial and Nuclear Disease Panel (Mito‐aND‐Panel) capture kit that allows parallel enrichment for subsequent NGS‐based sequence analysis of nuclear mitochondrial disease‐related genes and the complete mtDNA genome. Sequencing of enriched mtDNA simultaneously with nuclear genes was compared with the separated sequencing of the mitochondrial genome and whole exome sequencing (WES). Results The Mito‐aND‐Panel permits accurate detection of low‐level mtDNA heteroplasmy due to a very high sequencing depth compared to standard diagnostic procedures using Sanger sequencing/SNaPshot and WES which is crucial to identify maternally inherited mitochondrial disorders. Conclusion We established a NGS‐based method with combined sequencing of the complete mtDNA and nuclear genes which enables a more sensitive heteroplasmy detection of mtDNA mutations compared to traditional methods. Because the method promotes the analysis of mtDNA variants in large cohorts, it is cost‐effective and simple to setup, we anticipate this is a highly relevant method for sequence‐based genetic diagnosis in clinical diagnostic applications.
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Affiliation(s)
- Angela Abicht
- Medical Genetic Center Munich, Munich, Germany.,Department of Neurology, Friedrich-Baur-Institute, Klinikum der Ludwig-Maximilians-Universität München, Munich, Germany
| | | | | | | | | | - Rita Horvath
- Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, UK
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7
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Kluesner MG, Nedveck DA, Lahr WS, Garbe JR, Abrahante JE, Webber BR, Moriarity BS. EditR: A Method to Quantify Base Editing from Sanger Sequencing. CRISPR J 2018; 1:239-250. [PMID: 31021262 PMCID: PMC6694769 DOI: 10.1089/crispr.2018.0014] [Citation(s) in RCA: 266] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas9-Cytidine deaminase fusion enzymes—termed “base editors”—allow targeted editing of genomic deoxycytidine to deoxythymidine (C:G→T:A) without the need for double-stranded break induction. Base editors represent a paradigm shift in gene editing technology due to their unprecedented efficiency to mediate targeted, single-base conversion. However, current analysis of base editing outcomes rely on methods that are either imprecise or expensive and time-consuming. To overcome these limitations, we developed a simple, cost-effective, and accurate program to measure base editing efficiency from fluorescence-based Sanger sequencing, termed “EditR.” We provide EditR as a free online tool or downloadable desktop application requiring a single Sanger sequencing file and guide RNA sequence. EditR is more accurate than enzymatic assays, and provides added insight to the position, type, and efficiency of base editing. Furthermore, EditR is likely amenable to quantify base editing from the recently developed adenosine deaminase base editors that act on either DNA (adenosine deaminase base editors [ABEs]) or RNA (REPAIRs) (catalyzes A:T→G:C). Collectively, we demonstrate that EditR is a robust, inexpensive tool that will facilitate the broad application of base editing technology, thereby fostering further innovation in this burgeoning field.
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Affiliation(s)
- Mitchell G Kluesner
- 1 Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota.,2 Department of Pediatrics, University of Minnesota , Minneapolis, Minnesota.,3 Center for Genome Engineering, University of Minnesota , Minneapolis, Minnesota
| | - Derek A Nedveck
- 4 Department of Plant Biology, University of Minnesota , Minneapolis, Minnesota
| | - Walker S Lahr
- 1 Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota.,2 Department of Pediatrics, University of Minnesota , Minneapolis, Minnesota.,3 Center for Genome Engineering, University of Minnesota , Minneapolis, Minnesota
| | - John R Garbe
- 5 Genomics Center, University of Minnesota , Minneapolis, Minnesota
| | - Juan E Abrahante
- 6 Informatics Institute, University of Minnesota , Minneapolis, Minnesota
| | - Beau R Webber
- 1 Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota.,2 Department of Pediatrics, University of Minnesota , Minneapolis, Minnesota.,3 Center for Genome Engineering, University of Minnesota , Minneapolis, Minnesota
| | - Branden S Moriarity
- 1 Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota.,2 Department of Pediatrics, University of Minnesota , Minneapolis, Minnesota.,3 Center for Genome Engineering, University of Minnesota , Minneapolis, Minnesota
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8
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Recent Advances in Detecting Mitochondrial DNA Heteroplasmic Variations. Molecules 2018; 23:molecules23020323. [PMID: 29401641 PMCID: PMC6017848 DOI: 10.3390/molecules23020323] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 01/27/2018] [Accepted: 01/31/2018] [Indexed: 12/31/2022] Open
Abstract
The co-existence of wild-type and mutated mitochondrial DNA (mtDNA) molecules termed heteroplasmy becomes a research hot point of mitochondria. In this review, we listed several methods of mtDNA heteroplasmy research, including the enrichment of mtDNA and the way of calling heteroplasmic variations. At the present, while calling the novel ultra-low level heteroplasmy, high-throughput sequencing method is dominant while the detection limit of recorded mutations is accurate to 0.01% using the other quantitative approaches. In the future, the studies of mtDNA heteroplasmy may pay more attention to the single-cell level and focus on the linkage of mutations.
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9
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Ma EYT, Ratnasingham S, Kremer SC. Machine Learned Replacement of N-Labels for Basecalled Sequences in DNA Barcoding. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:191-204. [PMID: 28092571 DOI: 10.1109/tcbb.2016.2598752] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This study presents a machine learning method that increases the number of identified bases in Sanger Sequencing. The system post-processes a KB basecalled chromatogram. It selects a recoverable subset of N-labels in the KB-called chromatogram to replace with basecalls (A,C,G,T). An N-label correction is defined given an additional read of the same sequence, and a human finished sequence. Corrections are added to the dataset when an alignment determines the additional read and human agree on the identity of the N-label. KB must also rate the replacement with quality value of in the additional read. Corrections are only available during system training. Developing the system, nearly 850,000 N-labels are obtained from Barcode of Life Datasystems, the premier database of genetic markers called DNA Barcodes. Increasing the number of correct bases improves reference sequence reliability, increases sequence identification accuracy, and assures analysis correctness. Keeping with barcoding standards, our system maintains an error rate of percent. Our system only applies corrections when it estimates low rate of error. Tested on this data, our automation selects and recovers: 79 percent of N-labels from COI (animal barcode); 80 percent from matK and rbcL (plant barcodes); and 58 percent from non-protein-coding sequences (across eukaryotes).
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Hairy matters: MtDNA quantity and sequence variation along and among human head hairs. Forensic Sci Int Genet 2016; 25:1-9. [PMID: 27484846 DOI: 10.1016/j.fsigen.2016.07.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 07/20/2016] [Accepted: 07/23/2016] [Indexed: 01/31/2023]
Abstract
Hairs from the same donor have been found to differ in mtDNA sequence within and among themselves and from other tissues, which impacts interpretation of results obtained in a forensic setting. However, little is known on the magnitude of this phenomenon and published data on systematic studies are scarce. We addressed this issue by generating mtDNA control region (CR) profiles of >450 hair fragments from 21 donors by Sanger-type sequencing (STS). To mirror forensic scenarios, we compared hair haplotypes from the same donors to each other, to the corresponding buccal swab reference haplotypes and analyzed several fragments of individual hairs. We also investigated the effects of hair color, donor sex and age, mtDNA haplogroup and chemical treatment on mtDNA quantity, amplification success and variation. We observed a wide range of individual CR sequence variation. The reference haplotype was the only or most common (≥75%) hair haplotype for most donors. However, in two individuals, the reference haplotype was only found in about a third of the investigated hairs, mainly due to differences at highly variable positions. Similarly, most hairs revealed the reference haplotype along their entire length, however, about a fifth of the hairs contained up to 71% of segments with deviant haplotypes, independent of the longitudinal position. Variation affected numerous positions, typically restricted to the individual hair and in most cases heteroplasmic, but also fixed (i.e. homoplasmic) substitutions were observed. While existing forensic mtDNA interpretation guidelines were found still sufficient for all comparisons to reference haplotypes, some comparisons between hairs from the same donor could yield false exclusions when those guidelines are strictly followed. This study pinpoints the special care required when interpreting mtDNA results from hair in forensic casework.
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11
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Naue J, Hörer S, Sänger T, Strobl C, Hatzer-Grubwieser P, Parson W, Lutz-Bonengel S. Evidence for frequent and tissue-specific sequence heteroplasmy in human mitochondrial DNA. Mitochondrion 2014; 20:82-94. [PMID: 25526677 DOI: 10.1016/j.mito.2014.12.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 12/02/2014] [Accepted: 12/09/2014] [Indexed: 10/24/2022]
Abstract
Mitochondrial point heteroplasmy is a common event observed not only in patients with mitochondrial diseases but also in healthy individuals. We here report a comprehensive investigation of heteroplasmy occurrence in human including the whole mitochondrial control region from nine different tissue types of 100 individuals. Sanger sequencing was used as a standard method and results were supported by cloning, minisequencing, and massively parallel sequencing. Only 12% of all individuals showed no heteroplasmy, whereas 88% showed at least one heteroplasmic position within the investigated tissues. In 66% of individuals up to 8 positions were affected. The highest relative number of heteroplasmies was detected in muscle and liver (79%, 69%), followed by brain, hair, and heart (36.7%-30.2%). Lower percentages were observed in bone, blood, lung, and buccal cells (19.8%-16.2%). Accumulation of position-specific heteroplasmies was found in muscle (positions 64, 72, 73, 189, and 408), liver (position 72) and brain (partial deletion at position 71). Deeper analysis of these specific positions in muscle revealed a non-random appearance and position-specific dependency on age. MtDNA heteroplasmy frequency and its potential functional importance have been underestimated in the past and its occurrence is ubiquitous and dependent at least on age, tissue, and position-specific mutation rates.
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Affiliation(s)
- Jana Naue
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstrasse 9, D-79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, D-79104 Freiburg, Germany.
| | - Steffen Hörer
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstrasse 9, D-79104 Freiburg, Germany.
| | - Timo Sänger
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstrasse 9, D-79104 Freiburg, Germany.
| | - Christina Strobl
- Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, A-6020 Innsbruck, Austria.
| | - Petra Hatzer-Grubwieser
- Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, A-6020 Innsbruck, Austria.
| | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, A-6020 Innsbruck, Austria; Penn State Eberly College of Science, University Park, PA, USA.
| | - Sabine Lutz-Bonengel
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstrasse 9, D-79104 Freiburg, Germany.
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12
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Quantitative assessment of heteroplasmy of mitochondrial genome: perspectives in diagnostics and methodological pitfalls. BIOMED RESEARCH INTERNATIONAL 2014; 2014:292017. [PMID: 24818137 PMCID: PMC4003915 DOI: 10.1155/2014/292017] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/14/2014] [Indexed: 11/17/2022]
Abstract
The role of alterations of mitochondrial DNA (mtDNA) in the development of human pathologies is not understood well. Most of mitochondrial mutations are characterized by the phenomenon of heteroplasmy which is defined as the presence of a mixture of more than one type of an organellar genome within a cell or tissue. The level of heteroplasmy varies in wide range, and the expression of disease is dependent on the percent of alleles bearing mutations, thus allowing consumption that an upper threshold level may exist beyond which the mitochondrial function collapses. Recent findings have demonstrated that some mtDNA heteroplasmic mutations are associated with widely spread chronic diseases, including atherosclerosis and cancer. Actually, each etiological mtDNA mutation has its own heteroplasmy threshold that needs to be measured. Therefore, quantitative evaluation of a mutant allele of mitochondrial genome is an obvious methodological challenge, since it may be a keystone for diagnostics of individual genetic predisposition to the disease. This review provides a comprehensive comparison of methods applicable to the measurement of heteroplasmy level of mitochondrial mutations associated with the development of pathology, in particular, in atherosclerosis and its clinical manifestations.
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13
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Seneca S, Vancampenhout K, Van Coster R, Smet J, Lissens W, Vanlander A, De Paepe B, Jonckheere A, Stouffs K, De Meirleir L. Analysis of the whole mitochondrial genome: translation of the Ion Torrent Personal Genome Machine system to the diagnostic bench? Eur J Hum Genet 2014; 23:41-8. [PMID: 24667782 DOI: 10.1038/ejhg.2014.49] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 02/14/2014] [Accepted: 02/19/2014] [Indexed: 11/09/2022] Open
Abstract
Next-generation sequencing (NGS), an innovative sequencing technology that enables the successful analysis of numerous gene sequences in a massive parallel sequencing approach, has revolutionized the field of molecular biology. Although NGS was introduced in a rather recent past, the technology has already demonstrated its potential and effectiveness in many research projects, and is now on the verge of being introduced into the diagnostic setting of routine laboratories to delineate the molecular basis of genetic disease in undiagnosed patient samples. We tested a benchtop device on retrospective genomic DNA (gDNA) samples of controls and patients with a clinical suspicion of a mitochondrial DNA disorder. This Ion Torrent Personal Genome Machine platform is a high-throughput sequencer with a fast turnaround time and reasonable running costs. We challenged the chemistry and technology with the analysis and processing of a mutational spectrum composed of samples with single-nucleotide substitutions, indels (insertions and deletions) and large single or multiple deletions, occasionally in heteroplasmy. The output data were compared with previously obtained conventional dideoxy sequencing results and the mitochondrial revised Cambridge Reference Sequence (rCRS). We were able to identify the majority of all nucleotide alterations, but three false-negative results were also encountered in the data set. At the same time, the poor performance of the PGM instrument in regions associated with homopolymeric stretches generated many false-positive miscalls demanding additional manual curation of the data.
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Affiliation(s)
- Sara Seneca
- 1] Center for Medical Genetics, UZ Brussel, Vrije Universiteit Brussel (VUB), Brussels, Belgium [2] Research Group Reproduction and Genetics, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Kim Vancampenhout
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Rudy Van Coster
- Department of Pediatrics, Division of Neurology and Metabolism, University Hospital Ghent, Ghent University, Ghent, Belgium
| | - Joél Smet
- Department of Pediatrics, Division of Neurology and Metabolism, University Hospital Ghent, Ghent University, Ghent, Belgium
| | - Willy Lissens
- 1] Center for Medical Genetics, UZ Brussel, Vrije Universiteit Brussel (VUB), Brussels, Belgium [2] Research Group Reproduction and Genetics, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Arnaud Vanlander
- Department of Pediatrics, Division of Neurology and Metabolism, University Hospital Ghent, Ghent University, Ghent, Belgium
| | - Boel De Paepe
- Department of Pediatrics, Division of Neurology and Metabolism, University Hospital Ghent, Ghent University, Ghent, Belgium
| | - An Jonckheere
- Department of Pediatric Neurology, UZ Brussel, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Katrien Stouffs
- 1] Center for Medical Genetics, UZ Brussel, Vrije Universiteit Brussel (VUB), Brussels, Belgium [2] Research Group Reproduction and Genetics, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Linda De Meirleir
- 1] Research Group Reproduction and Genetics, Vrije Universiteit Brussel (VUB), Brussels, Belgium [2] Department of Pediatric Neurology, UZ Brussel, Vrije Universiteit Brussel (VUB), Brussels, Belgium
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Abstract
BRAF represents one of the most frequently mutated protein kinase genes in human tumours. The mutation is commonly tested in pathology practice. BRAF mutation is seen in melanoma, papillary thyroid carcinoma (including papillary thyroid carcinoma arising from ovarian teratoma), ovarian serous tumours, colorectal carcinoma, gliomas, hepatobiliary carcinomas and hairy cell leukaemia. In these cancers, various genetic aberrations of the BRAF proto-oncogene, such as different point mutations and chromosomal rearrangements, have been reported. The most common mutation, BRAF V600E, can be detected by DNA sequencing and immunohistochemistry on formalin fixed, paraffin embedded tumour tissue. Detection of BRAF V600E mutation has the potential for clinical use as a diagnostic and prognostic marker. In addition, a great deal of research effort has been spent in strategies inhibiting its activity. Indeed, recent clinical trials involving BRAF selective inhibitors exhibited promising response rates in metastatic melanoma patients. Clinical trials are underway for other cancers. However, cutaneous side effects of treatment have been reported and therapeutic response to cancer is short-lived due to the emergence of several resistance mechanisms. In this review, we give an update on the clinical pathological relevance of BRAF mutation in cancer. It is hoped that the review will enhance the direction of future research and assist in more effective use of the knowledge of BRAF mutation in clinical practice.
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15
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Mitochondrial DNA analysis of Swedish population samples. Int J Legal Med 2013; 127:1097-9. [DOI: 10.1007/s00414-013-0908-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 08/27/2013] [Indexed: 10/26/2022]
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16
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Mass spectrometric base composition profiling: Implications for forensic mtDNA databasing. Forensic Sci Int Genet 2013; 7:587-592. [PMID: 24054029 PMCID: PMC3820008 DOI: 10.1016/j.fsigen.2013.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 05/09/2013] [Accepted: 05/19/2013] [Indexed: 11/24/2022]
Abstract
In forensic genetics mitochondrial DNA (mtDNA) is usually analyzed by direct Sanger-type sequencing (STS). This method is known to be laborious and sometimes prone to human error. Alternative methods have been proposed that lead to faster results. Among these are methods that involve mass-spectrometry resulting in base composition profiles that are, by definition, less informative than the full nucleotide sequence. Here, we applied a highly automated electrospray ionization mass spectrometry (ESI-MS) system (PLEX-ID) to an mtDNA population study to compare its performance with respect to throughput and concordance to STS. We found that the loss of information power was relatively low compared to the gain in speed and analytical standardization. The detection of point and length heteroplasmy turned out to be roughly comparable between the technologies with some individual differences related to the processes. We confirm that ESI-MS provides a valuable platform for analyzing mtDNA variation that can also be applied in the forensic context.
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Diagnosis of mitochondrial disorders applying massive pyrosequencing. Mol Biol Rep 2012; 39:6655-60. [PMID: 22302390 DOI: 10.1007/s11033-012-1471-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 01/23/2012] [Indexed: 10/14/2022]
Abstract
Mitochondrial disorders are a frequent cause of neurological disability affecting children and adults. Traditionally, molecular diagnosis of mitochondrial diseases was mostly accomplished by the use of Sanger sequencing and PCR-RFLP. However, there are particular drawbacks associated with the use of these methods. Recent multidisciplinary advances have led to new sequencing methods that may overcome these limitations. Our goal was to explore the use of a next generation sequencing platform in the molecular diagnosis of mitochondrial diseases reporting our findings in adult patients that present with a clinical-pathological diagnosis of a mitochondrial encephalomyopathy. Complete genomic sequences of mitochondrial DNA were obtained by 454 massive pyrosequencing from blood samples. The analysis of these sequences allowed us to identify two diagnostic pathogenic mutations and 74 homoplasmic polymorphisms, useful for obtaining high-resolution mitochondrial haplogroups. In summary, molecular diagnosis of mitochondrial disorders could be efficiently done from readily accessible samples, such as blood, with the use of a new sequencing platform.
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