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Sturk-Andreaggi, K., Parson, W., Allen, M. & Marshall, C. (2020). Impact of the sequencing method on the detection and interpretation of mitochondrial DNA length heteroplasmy. Forensic Science International: Genetics, 44, Article ID 102205.
Öppna denna publikation i ny flik eller fönster >>Impact of the sequencing method on the detection and interpretation of mitochondrial DNA length heteroplasmy
2020 (Engelska)Ingår i: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 44, artikel-id 102205Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Advancements in sequencing technologies allow for rapid and efficient analysis of mitochondrial DNA (mtDNA) in forensic laboratories, which is particularly beneficial for specimens with limited nuclear DNA. Next generation sequencing (NGS) offers higher throughput and sensitivity over traditional Sanger-type sequencing (STS) as well as the ability to quantitatively analyze the data. Changes in sample preparation, sequencing method and analysis required for NGS may alter the mtDNA haplotypes compared to previously generated STS data. Thus, the present study aimed to characterize the impact of different sequencing workflows on the detection and interpretation of length heteroplasmy (LHP), a particularly complicated aspect of mtDNA analysis. Whole mtDNA genome (mitogenome) data were generated for 16 high-quality samples using well-established Illumina and Ion methods, and the NGS data were compared to previously-generated STS mtDNA control region data. Although the mitogenome haplotypes were concordant with the exception of length and low-level variants ( < 30 % variant frequency), LHP in the hypervariable segment (HVS) polycytosine regions (C-tracts) differed across sequencing methods. Consistent with previous studies, LHP in HVS1 was observed in samples with nine or more consecutive cytosines (Cs) and eight Cs in the HVS2 region in the STS data. The Illumina data produced a similar pattern of LHP as the STS data, whereas the Ion data were noticeably different. More complex LHP (i.e. more length molecules) was observed in the Ion data, as length variation occurred in multiple homopolymer stretches within the targeted HVS regions. Further, the STS dominant or major molecule (MM) differed from the Ion MM in 11 (37 %) of the 30 regions evaluated and six instances (20 %) in Illumina data. This is of particular interest, as the MM is used by many forensic laboratories to report the HVS C-tract in the mtDNA haplotype. In general, the STS MMs were longer than the Illumina MMs, while the Ion MMs were the shortest. The higher rate of homopolymer indels in Ion data likely contributed to these differences. Supplemental analysis with alternative approaches demonstrated that the LHP pattern may also be altered by the bioinformatic tool and workflow used for data interpretation. The broader application of NGS in forensic laboratories will undoubtedly result in the use of varying sample preparation and sequencing methods. Based on these findings, minor LHP differences are expected across sequencing workflows, and it will be important that C-tract indels continue to be ignored for forensic queries and comparisons.

Ort, förlag, år, upplaga, sidor
ELSEVIER IRELAND LTD, 2020
Nyckelord
Mitochondrial DNA, Next generation sequencing, Length heteroplasmy
Nationell ämneskategori
Genetik
Identifikatorer
urn:nbn:se:uu:diva-402651 (URN)10.1016/j.fsigen.2019.102205 (DOI)000504051100018 ()31783338 (PubMedID)
Tillgänglig från: 2020-01-20 Skapad: 2020-01-20 Senast uppdaterad: 2020-01-20Bibliografiskt granskad
Bus, M. M., Lembring, M., Kjellstrom, A., Strobl, C., Zimmermann, B., Parson, W. & Allen, M. (2019). Mitochondrial DNA analysis of a Viking age mass grave in Sweden. Forensic Science International: Genetics, 42, 268-274
Öppna denna publikation i ny flik eller fönster >>Mitochondrial DNA analysis of a Viking age mass grave in Sweden
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2019 (Engelska)Ingår i: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 42, s. 268-274Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

In 1998, a Viking Age mass grave was discovered and excavated at St. Laurence's churchyard in Sigtuna, Sweden. The excavated bones underwent osteoarchaeological analysis and were assigned to at least 19 individuals. Eleven skeletons showed sharp force trauma from bladed weapons. Mass graves are an unusual finding from this time period, making the burial context extraordinary. To investigate a possible maternal kinship among the individuals, bones and teeth from the skeletal remains were selected for mitochondrial DNA (mtDNA) analysis. Sanger sequencing of short stretches of the hypervariable segments I and II (HVS-I and HVS-II) was performed. A subset of the samples was also analysed by massively parallel sequencing analysis (MPS) of the entire mtDNA genome using the Precision ID mtDNA Whole Genome Panel. A total of 15 unique and three shared mtDNA profiles were obtained. Based on a combination of genetic and archaeological data, we conclude that a minimum of 20 individuals was buried in the mass grave. The majority of the individuals were not maternally related. However, two possible pairs of siblings or mother-child relationships were identified. All individuals were assigned to West Eurasian haplogroups, with a predominance of haplogroup H. Although the remains showed an advanced level of DNA degradation, the combined use of Sanger sequencing and MPS with the Precision ID mtDNA Whole Genome Panel revealed at least partial mtDNA data for all samples.

Nyckelord
Human identification, Sanger sequencing, Massively parallel sequencing, Mitogenome, Bone samples, Degradation
Nationell ämneskategori
Arkeologi Genetik
Identifikatorer
urn:nbn:se:uu:diva-394251 (URN)10.1016/j.fsigen.2019.06.002 (DOI)000483955000038 ()31442669 (PubMedID)
Tillgänglig från: 2019-10-11 Skapad: 2019-10-11 Senast uppdaterad: 2019-10-11Bibliografiskt granskad
Strobl, C., Eduardoff, M., Bus, M. M., Allen, M. & Parson, W. (2018). Evaluation of the precision ID whole MtDNA genome panel for forensic analyses. Forensic Science International: Genetics, 35, 21-25
Öppna denna publikation i ny flik eller fönster >>Evaluation of the precision ID whole MtDNA genome panel for forensic analyses
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2018 (Engelska)Ingår i: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 35, s. 21-25Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Mitochondrial DNA (mtDNA) amplification and Massively Parallel Sequencing (MPS) using an early access version of the Precision ID Whole MtDNA Genome Panel (Thermo Fisher Scientific) and the Ion Personal Genome Machine (PGM) were evaluated using 15 forensically relevant samples. Samples were selected to represent typical forensic specimens for mtDNA analysis including hairs, hair shafts, swabs and ancient solid tissue samples (bones and teeth) that were stored in the freezer for up to several years after having been typed with conventional Sanger-type Sequencing and Capillary Electrophoresis. The MPS haplotypes confirmed the earlier results in all samples and provided additional sequence information that improved discrimination power and haplogroup estimation. The results raised the appetite for further experiments to validate and apply the new technology in forensic practice.

Nyckelord
Mitochondrial DNA, Mitogenome, Massively parallel sequencing, Next generation sequencing, Degraded DNA, Mini-amplicon, Primer tiling, Forensic genetics
Nationell ämneskategori
Rättsmedicin Medicinsk genetik
Identifikatorer
urn:nbn:se:uu:diva-358367 (URN)10.1016/j.fsigen.2018.03.013 (DOI)000434806300008 ()29626805 (PubMedID)
Tillgänglig från: 2018-08-31 Skapad: 2018-08-31 Senast uppdaterad: 2018-08-31Bibliografiskt granskad
Vanek, D., Budowle, B., Dubska-Votrubova, J., Ambers, A., Frolik, J., Pospisek, M., . . . Zander, J. (2017). Results of a collaborative study on DNA identification of aged bone samples. Croatian Medical Journal, 58(3), 203-213
Öppna denna publikation i ny flik eller fönster >>Results of a collaborative study on DNA identification of aged bone samples
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2017 (Engelska)Ingår i: Croatian Medical Journal, ISSN 0353-9504, E-ISSN 1332-8166, Vol. 58, nr 3, s. 203-213Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Aim: A collaborative exercise with several institutes was organized by the Forensic DNA Service (FDNAS) and the Institute of the Legal Medicine, 2nd Faculty of Medicine, Charles University in Prague, Czech Republic, with the aim to test performance of different laboratories carrying out DNA analysis of relatively old bone samples.

Methods: Eighteen laboratories participating in the collaborative exercise were asked to perform DNA typing of two samples of bone powder. Two bone samples provided by the National Museum and the Institute of Archaelogy in Prague, Czech Republic, came from archeological excavations and were estimated to be approximately 150 and 400 years old. The methods of genetic characterization including autosomal, gonosomal, and mitochondrial markers was selected solely at the discretion of the participating laboratory.

Results: Although the participating laboratories used different extraction and amplification strategies, concordant results were obtained from the relatively intact 150 years old bone sample. Typing was more problematic with the analysis of the 400 years old bone sample due to poorer quality.

Conclusion: The laboratories performing identification DNA analysis of bone and teeth samples should regularly test their ability to correctly perform DNA-based identification on bone samples containing degraded DNA and potential inhibitors and demonstrate that risk of contamination is minimized.

Ort, förlag, år, upplaga, sidor
MEDICINSKA NAKLADA, 2017
Nationell ämneskategori
Medicin och hälsovetenskap
Identifikatorer
urn:nbn:se:uu:diva-330753 (URN)10.3325/cmj.2017.58.203 (DOI)000404561800002 ()28613037 (PubMedID)
Tillgänglig från: 2017-10-03 Skapad: 2017-10-03 Senast uppdaterad: 2017-10-03Bibliografiskt granskad
Bus, M. M., Nilsson, M. & Allen, M. (2016). Analysis of Mitochondrial DNA from a Burned, Ninhydrin-Treated Paper Towel. Journal of Forensic Sciences, 61(3), 828-832
Öppna denna publikation i ny flik eller fönster >>Analysis of Mitochondrial DNA from a Burned, Ninhydrin-Treated Paper Towel
2016 (Engelska)Ingår i: Journal of Forensic Sciences, ISSN 0022-1198, E-ISSN 1556-4029, Vol. 61, nr 3, s. 828-832Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Contact-based evidence is likely to have limited quantities of DNA and may yield mixed profiles due to preexisting or contaminating DNA. In a recent arson investigation, a paper towel was collected and used as circumstantial evidence. The paper towel was partially burned and was likely set on fire with flammable liquid. As part of the investigation, the paper towel was treated with ninhydrin to visualize fingerprint evidence. Initial DNA analysis of two swabs was negative for short tandem repeat (STR) markers and revealed a mixture of mitochondrial DNA (mtDNA). Analysis of 13 additional cuttings yielded four more mixed profiles, but also two samples with a common single-source profile. The single-source mtDNA profile matched that of the primary suspect in the case. Thus, even if initial mtDNA analysis yields a mixed profile, a sampling strategy involving multiple locations can improve the chance of obtaining valuable single-source mtDNA profiles from compromised evidence in criminal casework.

Nyckelord
forensic science, DNA typing, mixed mtDNA profile, mitochondrial DNA, ninhydrin, trace DNA, paper towel
Nationell ämneskategori
Rättsmedicin
Identifikatorer
urn:nbn:se:uu:diva-297334 (URN)10.1111/1556-4029.13054 (DOI)000375076000036 ()
Forskningsfinansiär
VINNOVA
Tillgänglig från: 2016-06-23 Skapad: 2016-06-22 Senast uppdaterad: 2017-11-28Bibliografiskt granskad
Bus, M. M., Karas, O. & Allen, M. (2016). Multiplex pyrosequencing of InDel markers for forensic DNA analysis. Electrophoresis, 37(23-24), 3039-3045
Öppna denna publikation i ny flik eller fönster >>Multiplex pyrosequencing of InDel markers for forensic DNA analysis
2016 (Engelska)Ingår i: Electrophoresis, ISSN 0173-0835, E-ISSN 1522-2683, Vol. 37, nr 23-24, s. 3039-3045Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

The capillary electrophoresis (CE) technology is commonly used for fragment length separation of markers in forensic DNA analysis. In this study, pyrosequencing technology was used as an alternative and rapid tool for the analysis of biallelic InDel (insertion/deletion) markers for individual identification. The DNA typing is based on a subset of the InDel markers that are included in the Investigator (R) DIPplex Kit, which are sequenced in a multiplex pyrosequencing analysis. To facilitate the analysis of degraded DNA, the polymerase chain reaction (PCR) fragments were kept short in the primer design. Samples from individuals of Swedish origin were genotyped using the pyrosequencing strategy and analysis of the Investigator (R) DIPplex markers with CE. A comparison between the pyrosequencing and CE data revealed concordant results demonstrating a robust and correct genotyping by pyrosequencing. Using optimal marker combination and a directed dispensation strategy, five markers could be multiplexed and analyzed simultaneously. In this proof-of-principle study, we demonstrate that multiplex InDel pyrosequencing analysis is possible. However, further studies on degraded samples, lower DNA quantities, and mixtures will be required to fully optimize InDel analysis by pyrosequencing for forensic applications. Overall, although CE analysis is implemented in most forensic laboratories, multiplex InDel pyrosequencing offers a cost-effective alternative for some applications.

Nyckelord
InDels, DIPplex, Forensic genetics, Multiplex, Pyrosequencing
Nationell ämneskategori
Biokemi och molekylärbiologi
Identifikatorer
urn:nbn:se:uu:diva-316141 (URN)10.1002/elps.201600255 (DOI)000392421400001 ()27763658 (PubMedID)
Tillgänglig från: 2017-03-03 Skapad: 2017-03-03 Senast uppdaterad: 2017-11-29Bibliografiskt granskad
Ranasinghe, R., Tennekoon, K. H., Karunanayake, E. H., Lembring, M. & Allen, M. (2015). A study of genetic polymorphisms in mitochondrial DNA hypervariable regions I and II of the five major ethnic groups and Vedda population in Sri Lanka. Legal Medicine, 17(6), 539-546
Öppna denna publikation i ny flik eller fönster >>A study of genetic polymorphisms in mitochondrial DNA hypervariable regions I and II of the five major ethnic groups and Vedda population in Sri Lanka
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2015 (Engelska)Ingår i: Legal Medicine, ISSN 1344-6223, E-ISSN 1873-4162, Vol. 17, nr 6, s. 539-546Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Diversity of the hypervariable regions (HV) I and II of the mitochondrial genome was studied in maternally unrelated Sri Lankans (N-202) from six ethnic groups (i.e.: Sinhalese, Sri Lankan Tamil, Muslim, Malay, Indian Tamil and Vedda). DNA was extracted from blood and buccal swabs and HVI and HVII regions were PCR amplified and sequenced. Resulting sequences were aligned and edited between 16024-16365 and 73-340 regions and compared with revised Cambridge reference sequences (rCRS). One hundred and thirty-five unique haplotypes and 22 shared haplotypes were observed. A total of 145 polymorphic sites and 158 polymorphisms were observed. Hypervariable region I showed a higher polymorphic variation than hypervariable region II. Nucleotide diversities were quite low and similar for all ethnicities apart from a slightly higher value for Indian Tamils and a much lower value for the Vedda population compared to the other groups. When the total population was considered South Asian (Indian) haplogroups were predominant, but there were differences in the distribution of phylo-geographical haplogroups between ethnic groups. Sinhalese, Sri Lankan Tamil and Vedda populations had a considerable presence of West Eurasian haplogroups. About 2/3rd of the Vedda population comprised of macro-haplogroup N or its subclades R and U, whereas macro-haplogroup M was predominant in all other populations. The Vedda population clustered separately from other groups and Sri Lankan Tamils showed a closer genetic affiliation to Sinhalese than to Indian Tamils. Thus this study provides useful information for forensic analysis and anthropological studies of Sri Lankans.

Nyckelord
Mitochondrial DNA, Control region, HV region I, MV region II, Haplotype, Sri Lanka
Nationell ämneskategori
Medicinsk genetik
Identifikatorer
urn:nbn:se:uu:diva-274347 (URN)10.1016/j.legalmed.2015.05.007 (DOI)000366444600021 ()26065620 (PubMedID)
Forskningsfinansiär
Sida - Styrelsen för internationellt utvecklingssamarbete
Tillgänglig från: 2016-01-21 Skapad: 2016-01-21 Senast uppdaterad: 2018-01-10
Bus, M. M., Edlund, H. & Allen, M. (2015). Forensic Analysis of Mitochondrial and Autosomal Markers Using Pyrosequencing®.. Methods in Molecular Biology, 1315, 379-396
Öppna denna publikation i ny flik eller fönster >>Forensic Analysis of Mitochondrial and Autosomal Markers Using Pyrosequencing®.
2015 (Engelska)Ingår i: Methods in Molecular Biology, ISSN 1064-3745, E-ISSN 1940-6029, Vol. 1315, s. 379-396Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Forensic casework analyses often face challenges, such as limited genetic material with or without fragmentation and damage. To compensate for low amounts and degradation, shorter amplicons are often applied in the analysis. Also, a change of markers might be necessary using mitochondrial instead of autosomal markers. In addition, forensic research often involves analysis of large number of samples for marker evaluation and population-database compilation. Therefore, a flexible, robust but also rapid method for the detection of variation is highly useful. Pyrosequencing(®) is a rapid, reliable, easy-to-use method for sequence analysis. The method is well suited for rapid forensic analysis of a few targets or analysis of a single target in many samples. It allows sequencing of very short amplicons, which facilitates analysis of degraded DNA. Here we present the use of Pyrosequencing, a robust method for sensitive forensic analysis of mitochondrial DNA, autosomal STRs, and Y-chromosome STRs and SNPs.

Nationell ämneskategori
Naturvetenskap
Identifikatorer
urn:nbn:se:uu:diva-285274 (URN)10.1007/978-1-4939-2715-9_26 (DOI)26103912 (PubMedID)
Tillgänglig från: 2016-04-19 Skapad: 2016-04-19 Senast uppdaterad: 2017-05-04Bibliografiskt granskad
Isaksson, J., Allen, M., Nilsson, K. W. & Lindblad, F. (2015). Polymorphisms in the FK506 binding protein 5 gene are associated with attention deficit hyperactivity disorder and diurnal cortisol levels. Acta Paediatrica, 104(9), 910-915
Öppna denna publikation i ny flik eller fönster >>Polymorphisms in the FK506 binding protein 5 gene are associated with attention deficit hyperactivity disorder and diurnal cortisol levels
2015 (Engelska)Ingår i: Acta Paediatrica, ISSN 0803-5253, E-ISSN 1651-2227, Vol. 104, nr 9, s. 910-915Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

AIM: Previous studies have shown an association between childhood attention deficit hyperactivity disorder (ADHD) and a down-regulated hypothalamus-pituitary-adrenal axis (HPA-axis) with low diurnal cortisol levels. Given the role of the FK506 binding protein 5 (FKBP5) as an important regulator of the negative feedback system of the HPA-axis, we set out to investigate possible associations between single nucleotide polymorphisms (SNPs) in FKBP5 in relation to ADHD and diurnal cortisol levels.

METHODS: Children with ADHD (n=81) and healthy comparisons (n=88) collected saliva four times during a regular school day for radioimmunoassay analysis of cortisol and for genotyping of five SNPs in FKBP5 (rs9296158, rs1360780, rs9470080, rs7748266 and rs9394309).

RESULTS: We found associations between SNP genotypes and ADHD as well as between genotypes and diurnal cortisol levels. One of these SNPs, rs9470080, was significantly associated with both ADHD and lower cortisol levels.

CONCLUSION: This study contributes to previous findings on a down-regulated HPA-axis in children with ADHD by demonstrating an association between ADHD, lower cortisol levels and SNPs of the FKBP5-gene. The relevance of these findings for the development and shaping of ADHD symptoms need to be approached in larger samples, preferably also taking stress reactivity into consideration.

Nationell ämneskategori
Psykiatri Pediatrik
Identifikatorer
urn:nbn:se:uu:diva-255893 (URN)10.1111/apa.13056 (DOI)000359786100021 ()26032970 (PubMedID)
Tillgänglig från: 2015-06-18 Skapad: 2015-06-18 Senast uppdaterad: 2017-12-04
Bus, M. & Allen, M. (2014). Collecting and Preserving Biological Samples from Challenging Environments for DNA Analysis. Biopreservation and Biobanking, 12(1), 17-22
Öppna denna publikation i ny flik eller fönster >>Collecting and Preserving Biological Samples from Challenging Environments for DNA Analysis
2014 (Engelska)Ingår i: Biopreservation and Biobanking, ISSN 1947-5535, E-ISSN 1947-5543, Vol. 12, nr 1, s. 17-22Artikel i tidskrift (Refereegranskat) Published
Nationell ämneskategori
Medicin och hälsovetenskap
Identifikatorer
urn:nbn:se:uu:diva-220793 (URN)000331461200004 ()
Tillgänglig från: 2014-03-21 Skapad: 2014-03-20 Senast uppdaterad: 2017-12-05
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