| 1. |
- Andreaggi, Kimberly, et al.
(författare)
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Complete Mitochondrial DNA Genome Variation in the Swedish Population
- 2023
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Ingår i: Genes. - : MDPI. - 2073-4425. ; 14:11, s. 1989-1989
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Tidskriftsartikel (refereegranskat)abstract
- The development of complete mitochondrial genome (mitogenome) reference data for inclusion in publicly available population databases is currently underway, and the generation of more high-quality mitogenomes will only enhance the statistical power of this forensically useful locus. To characterize mitogenome variation in Sweden, the mitochondrial DNA (mtDNA) reads from the SweGen whole genome sequencing (WGS) dataset were analyzed. To overcome the interference from low-frequency nuclear mtDNA segments (NUMTs), a 10% variant frequency threshold was applied for the analysis. In total, 934 forensic-quality mitogenome haplotypes were characterized. Almost 45% of the SweGen haplotypes belonged to haplogroup H. Nearly all mitogenome haplotypes (99.1%) were assigned to European haplogroups, which was expected based on previous mtDNA studies of the Swedish population. There were signature northern Swedish and Finnish haplogroups observed in the dataset (e.g., U5b1, W1a), consistent with the nuclear DNA analyses of the SweGen data. The complete mitogenome analysis resulted in high haplotype diversity (0.9996) with a random match probability of 0.15%. Overall, the SweGen mitogenomes provide a large mtDNA reference dataset for the Swedish population and also contribute to the effort to estimate global mitogenome haplotype frequencies.
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| 2. |
- Cavagnino, Courtney, et al.
(författare)
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Unearthing who and Y at Harewood Cemetery and inference of George Washington's Y-chromosomal haplotype
- 2024
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Ingår i: iScience. - : CELL PRESS. - 2589-0042. ; 27:4
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Tidskriftsartikel (refereegranskat)abstract
- An excavation conducted at Harewood Cemetery to identify the unmarked grave of Samuel Washington resulted in the discovery of burials presumably belonging to George Washington's paternal grandnephews and their mother, Lucy Payne. To confirm their identities this study examined Y -chromosomal, mitochondrial, and autosomal DNA from the burials and a living Washington descendant. The burial's Y-STR profile was compared to FamilyTreeDNA's database, which resulted in a one-step difference from the living descendant and an exact match to another Washington. A more complete Y-STR and Y -SNP profile from the descendant was inferred to be the Washington Y profile. Kinship comparisons performed in relation to the descendant, who is a 4 th and 5 th degree relative of the putative individuals, resulted in >37,000 overlapping autosomal SNPs and strong statistical support with likelihood ratios exceeding one billion. This study highlights the benefits of a multi -marker approach for kinship prediction and DNA -assisted identification of historical remains.
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| 3. |
- Gorden, Erin M., et al.
(författare)
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Capture enrichment and massively parallel sequencing for human identification
- 2021
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Ingår i: Forensic Science International. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 53
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Forskningsöversikt (refereegranskat)abstract
- In the past decade, hybridization capture has gained attention within the forensic field for its possible use in human identification. One of the primary benefits to capture enrichment is its applicability to degraded DNA fragments that, due to their reduced size, are not amenable to traditional PCR enrichment techniques. Hybridization capture is typically introduced after genomic library preparation of extracted DNA templates for the subsequent enrichment of mitochondrial DNA or single nucleotide polymorphisms within the nuclear genome. The enriched molecules are then subjected to massively parallel sequencing (MPS) for sensitive and highthroughput DNA sequence generation. Bioinformatic analysis of capture product removes PCR duplicates that were introduced during the laboratory workflow in order to characterize the original DNA template molecules. In the case of aged and degraded skeletal remains, the fraction of endogenous human DNA may be very low; therefore low-coverage sequence analysis may be required. This review contains an overview of current capture methodologies and the primary literature on hybridization capture as evaluated for forensic applications.
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| 4. |
- Gorden, Erin M., et al.
(författare)
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Extended kinship analysis of historical remains using SNP capture
- 2022
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Ingår i: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 57
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Tidskriftsartikel (refereegranskat)abstract
- DNA-assisted identification of historical remains requires the genetic analysis of highly degraded DNA, along with a comparison to DNA from known relatives. This can be achieved by targeting single nucleotide polymorphisms (SNPs) using a hybridization capture and next-generation sequencing approach suitable for degraded skeletal samples. In the present study, two SNP capture panels were designed to target similar to 25,000 (25 K) and similar to 95,000 (95 K) nuclear SNPs, respectively, to enable distant kinship estimation (up to 4th degree relatives). Low-coverage SNP data were successfully recovered from 14 skeletal elements 75 years postmortem using an Illumina MiSeq benchtop sequencer. All samples contained degraded DNA but were of varying quality with mean fragment lengths ranging from 32 bp to 170 bp across the 14 samples. SNP comparison with DNA from known family references was performed in the Parabon Fx Forensic Analysis Platform, which utilizes a likelihood approach for kinship prediction that was optimized for low-coverage sequencing data with cytosine deamination. The 25 K panel produced 15,000 SNPs on average, which allowed for accurate kinship prediction with strong statistical support in 16 of the 21 pairwise comparisons. The 95 K panel increased the average SNPs to 42,000 and resulted in an additional accurate kinship prediction with strong statistical support (17 of 21 pairwise comparisons). This study demonstrates that SNP capture combined with massively parallel sequencing on a benchtop platform can yield sufficient SNP recovery from compromised samples, enabling accurate, extended kinship predictions.
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| 5. |
- Marshall, Charla, et al.
(författare)
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Mitochondrial DNA haplogrouping to assist with the identification of unknown service members from the World War II Battle of Tarawa
- 2020
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Ingår i: Forensic Science International. - : ELSEVIER IRELAND LTD. - 1872-4973 .- 1878-0326. ; 47
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Tidskriftsartikel (refereegranskat)abstract
- The World War II Battle of Tarawa, 1943, was a devastating conflict that resulted in losses of more than 1100 American and 4690 Japanese troops. The United States government aims to identify and repatriate the remains of all missing American service members through the Defense Prisoner of War/Missing in Action (POW/MIA) Accounting Agency (DPAA) and its partners such as the Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL). Remains associated with the Battle of Tarawa have been recovered from field excavations conducted by History Flight, a DPAA strategic partner, as well as from the National Memorial Cemetery of the Pacific (NMCP) in Hawaii where unknowns have been disinterred for identification. DNA testing at the AFMES-AFDIL has produced mitochondrial DNA (mtDNA) sequences from 1027 case samples to date. Haplogroup assignments indicate that more than one third (36.2 %) of field-collected samples are likely of Asian maternal ancestry. Therefore the field collections from the Tarawa battlefield comprise the remains of American service members but also those of foreign nationals from Asia. The mtDNA of the NMCP unknowns is similar in ancestry proportion to the family reference sample distribution. The DPAA uses the ancestry information gleaned from mtDNA sequence data in conjunction with anthropological evidence to make foreign national determinations. In this way, mtDNA haplogrouping is used to sort the commingled and fragmentary remains recovered from Tarawa between Americans and foreign nationals, which are then repatriated to their country of origin.
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| 6. |
- Marshall, Charla, et al.
(författare)
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Pathogenic Variant Filtering for Mitochondrial Genome Haplotype Reporting
- 2020
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Ingår i: Genes. - : MDPI. - 2073-4425. ; 11:10
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Tidskriftsartikel (refereegranskat)abstract
- Given the enhanced discriminatory power of the mitochondrial DNA (mtDNA) genome (mitogenome) over the commonly sequenced control region (CR) portion, the scientific merit of mitogenome sequencing is generally accepted. However, many laboratories remain beholden to CR sequencing due to privacy policies and legal requirements restricting the use of disease information or coding region (codR) information. In this report, we present an approach to obviate the reporting of sensitive codR data in forensic haplotypes. We consulted the MitoMap database to identify 92 mtDNA codR variants with confirmed pathogenicity. We determined the frequencies of these pathogenic variants in literature-quality and forensic-quality databases to be very low, at 1.2% and 0.36%, respectively. The observed effect of pathogenic variant filtering on random match statistics in 2488 forensic-quality mitogenome haplotypes from four populations was nil. We propose that pathogenic variant filtering should be incorporated into variant calling algorithms for mitogenome haplotype reporting to maximize the discriminatory power of the locus while minimizing the reveal of sensitive genetic information.
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| 7. |
- Sturk-Andreaggi, Kimberly, et al.
(författare)
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Impact of the sequencing method on the detection and interpretation of mitochondrial DNA length heteroplasmy
- 2020
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Ingår i: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 44
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 8. |
- Sturk-Andreaggi, Kimberly, 1981-, et al.
(författare)
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Mitochondrial DNA genome variation in the Swedish population
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The development of mitochondrial genome (mitogenome) reference data for inclusion in publicly-available population databases is currently underway, and the more high-quality mitogenomes that can be generated will only enhance the statistical power of this forensically-useful locus. In order to promote mitogenome testing in Sweden, the mitochondrial DNA (mtDNA) data from the SweGen whole genome sequencing (WGS) dataset were analysed. To avoid the interference from nuclear mtDNA segments (NUMTs), a 10% frequency threshold was applied for the population analyses. In total, 934 forensic-quality mitogenome haplotypes were produced. Despite the elevated frequency threshold, 31 NUMT variants were observed in 13 lower coverage haplotypes. However, NUMT interference was minimal and localized to two hotspot regions, substantially reducing the analysis burden required at lower frequency thresholds. Almost 45% of the SweGen haplotypes belonged to haplogroup H and nearly all mitogenome haplotypes (99.1%) assigned to European haplogroups, which was expected based on previous mtDNA studies of the Swedish population. There were characteristic northern Swedish (i.e., Saami) and Finnish haplogroups observe in the dataset, consistent with the nuclear DNA analyses of the SweGen data. The analysis of the complete mitogenome resulted in high haplotype diversity (0.9996) with a random match probability of 0.15%. Overall, the mitogenomes generated from the SweGen WGS data provide a mitogenome reference database for Sweden as well as contribute to the global effort to increase the availability of mitogenome reference data.
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| 9. |
- Sturk-Andreaggi, Kimberly, et al.
(författare)
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The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies : Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes
- 2022
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Ingår i: International Journal of Molecular Sciences. - : MDPI AG. - 1661-6596 .- 1422-0067. ; 23:4
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing (WGS) data present a readily available resource for mitochondrial genome (mitogenome) haplotypes that can be utilized for genetics research including population studies. However, the reconstruction of the mitogenome is complicated by nuclear mitochondrial DNA (mtDNA) segments (NUMTs) that co-align with the mtDNA sequences and mimic authentic heteroplasmy. Two minimum variant detection thresholds, 5% and 10%, were assessed for the ability to produce authentic mitogenome haplotypes from a previously generated WGS dataset. Variants associated with NUMTs were detected in the mtDNA alignments for 91 of 917 (~8%) Swedish samples when the 5% frequency threshold was applied. The 413 observed NUMT variants were predominantly detected in two regions (nps 12,612–13,105 and 16,390–16,527), which were consistent with previously documented NUMTs. The number of NUMT variants was reduced by ~97% (400) using a 10% frequency threshold. Furthermore, the 5% frequency data were inconsistent with a platinum-quality mitogenome dataset with respect to observed heteroplasmy. These analyses illustrate that a 10% variant detection threshold may be necessary to ensure the generation of reliable mitogenome haplotypes from WGS data resources.
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| 10. |
- Sturk-Andreaggi, Kimberly, 1981-, et al.
(författare)
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Tools and considerations for mitochondrial haplogroup assignment
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Phylogenetic information can be used to infer maternal biogeographic ancestry and provide a valuable quality control (QC) check of mitochondrial DNA (mtDNA) data, identifying errors in the data such as artificial recombination and phantom mutations. Additionally, the phylogeny guides mtDNA nomenclature, which is crucial for forensic searches. This study compared three haplogrouping tools and their ability to provide proper guidance based on the predicted phylogeny. The Mitochondrial Haplogrouper tool of the AFDIL-QIAGEN mtDNA Expert (AQME), a plug-in for the CLC Genomics Workbench, and the web-based tools HaploGrep2 and EMPOP were included in the evaluation. Haplogroups were determined for 92 diverse mtDNA haplotypes by the three tools based on four regions: the entire mitochondrial genome (mitogenome), control region (CR), hypervariable segment 1 and 2 (HVS1-2) regions, and HVS1 only. There were only two differences (out of 92) between all three tools when using the mitogenome, and in these instances the haplogroups were less precise by one or two nodes. Haplogroup assignments for the CR and HVS1-2 were similar; though less precise haplogroups resulted for these HVS1-2 haplotypes compared to the CR due to haplogroup-diagnostic mutations outside the queried region. As an important QC aspect, the comparison between the haplogroup predictions of authentic and artificial haplotypes showed that it is possible to identify recombinant mitogenome haplotypes from two large (~8500-bp) amplicons, but the differentiation is more difficult with HVS1-2 “artificial” haplotypes. Overall, the tools performed similarly, but EMPOP’s SAM2 produced more precise haplogroup predictions than AQME and HaploGrep2 across all haplogroups and regions. An important consideration when using any haplogrouping tool is that the haplogroup identified is only a prediction, particularly when based on smaller regions. All three tools provided valuable phylogenetic information to enable QC of mtDNA data, but critical review of the predicted haplogroup may be required for certain applications.
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