Applications of Probe Capture Enrichment Next Generation Sequencing for Whole Mitochondrial Genome and 426 Nuclear SNPs for Forensically Challenging Samples

Shih, Shelly; Bose, Nikhil; Gonçalves, Anna Beatriz R; Erlich, Henry A.; Calloway, Cassandra

doi:10.3390/genes9010049

Cited by 44 publications

(24 citation statements)

References 60 publications

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“…It may be expected that with the current fastpace developments in targeted MPS technologies, technical solutions to simultaneously genotype thousands of SNPs with high accuracy and sensitivity from DNA with low quality and quantity, thereby fulfilling requirements of forensic DNA analysis, may become available in the future, which will boost the genomic prediction of human complex appearance phenotypes including adult height and more. A promising technological development is targeted capture sequencing [36] which is widely used for whole exome sequencing [37] in genetic epidemiology studies and has been introduced to the field of ancient DNA for analysing hundreds of thousands of SNPs [38] Targeted enrichment using probe capture has been introduced to forensic DNA analysis for whole mitogenome sequencing and sequencing of hundreds of SNPs [39] while forensic applications of targeted capture sequencing thousands of SNPs are pending as of yet.…”

Section: Discussionmentioning

confidence: 99%

Update on the predictability of tall stature from DNA markers in Europeans

Liu

Zhong

Jing

et al. 2019

Forensic Science International: Genetics

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Predicting adult height from DNA has important implications in forensic DNA phenotyping. In 2014, we introduced a prediction model consisting of 180 height-associated SNPs based on data from 10,361 Northwestern Europeans enriched with tall individuals (770 > 1.88 standard deviation), which yielded a mid-ranged accuracy (AUC = 0.75 for binary prediction of tall stature and R 2 = 0.12 for quantitative prediction of adult height). Here, we provide an update on DNA-based height predictability considering an enlarged list of subsequentlypublished height-associated SNPs using data from the same set of 10,361 Europeans. A prediction model based on the full set of 689 SNPs showed an improved accuracy relative to previous models for both tall stature (AUC = 0.79) and quantitative height (R 2 = 0.21). A feature selection analysis revealed a subset of 412 most informative SNPs while the corresponding prediction model retained most of the accuracy (AUC = 0.76 and R 2 = 0.19) achieved with the full model. Over all, our study empirically exemplifies that the accuracy for predicting human appearance phenotypes with very complex underlying genetic architectures, such as adult height, can be improved by increasing the number of phenotype-associated DNA variants. Our work also demonstrates that a careful sub-selection allows for a considerable reduction of the number of DNA predictors that achieve similar prediction accuracy as provided by the full set. This is forensically relevant due to restrictions in the number of SNPs simultaneously analyzable with forensically suitable DNA technologies in the current days of targeted massively parallel sequencing in forensic genetics.

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Section: Discussionmentioning

confidence: 99%

Update on the predictability of tall stature from DNA markers in Europeans

Liu

Zhong

Jing

et al. 2019

Forensic Science International: Genetics

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“…As a result, nuclear DNA which may be used for genetic fingerprinting is usually not detected in the hair shaft (Bender & Schneider, 2006). However, the application of next generation sequencing for the analysis of mitochondrial DNA, short tandem repeats, and single nucleotide polymorphisms has also demonstrated a great promise for forensically challenging samples (Shih et al, 2018). On the other hand, the potential of distinguishing individual hair donors based on their hair shaft proteins has also been highlighted (Wu et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Potential use of human hair shaft keratin peptide signatures to distinguish gender and ethnicity

Nasir

Hiji

Jayapalan

et al. 2020

PeerJ

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Background. Most human hairs collected at old crime scenes do not contain nuclear DNA and are therefore of less value for forensic investigations. In the present study, hair shaft proteins were extracted from 40 healthy subjects between the ages of 21 to 40 years and profiled using gel electrophoresis-based proteomics to determine if they can be used to distinguish gender and ethnicity. Methods. Extraction of the human hair shaft proteins was performed using a newly developed alkaline solubilisation method. The extracts were profiled by 2-dimensional electrophoresis and resolved protein spots were identified by mass spectrometry and queried against the human hair database. The study was then followed-up by immunoblotting of the identified hair shaft keratin of interest using commercially available antibodies. Results. Separation of the human hair shaft proteins by 2-dimensional electrophoresis generated improved and highly resolved profiles. Comparing the hair shaft protein profiles of 10 female with 10 male subjects and their identification by mass spectrometry and query of the human hair database showed significant altered abundance of truncated/processed type-II keratin peptides K81 (two spots), K83 (one spot) and K86 (three spots). The 2-dimensional electrophoresis profiling of 30 hair shaft samples taken from women of similar age range but from three distinctive ethnic subpopulations in Malaysia further showed significant altered abundance of one type-I and four type-II truncated/processed keratin peptides including K33b, K81, K83 and K86 (2 spots) between at least two of the ethnic groups. When a followed-up immunoblotting experiment was performed to detect the relative expression of the K86 peptides using commercialised antibodies, similar trends of expression were obtained. The present data, when taken together, demonstrated the potential use of keratin peptide signatures of the human hair shaft to distinguish gender and ethnicity although this needs to be further substantiated in a larger scale study.How to cite this article Mohamed Nasir N, Hiji J, Jayapalan JJ, Hashim OH. 2020. Potential use of human hair shaft keratin peptide signatures to distinguish gender and ethnicity. PeerJ 8:e8248 http://doi.org/10.7717/peerj.8248 Smith TA, Parry DAD. 2007. Sequence analyses of Type I and Type II chains in human hair and epithelial keratin intermediate filaments: promiscuous obligate heterodimers, Type II template for molecule formation and a rationale for heterodirner formation. Journal of Structural Biology MJ. 2000. A modified silver staining protocol for visualization of proteins compatible with matrix-assisted laser desorption/ionization and electrospray ionization-mass spectrometry. Electrophoresis 21:3666-3672.

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“…Hybridization capture targeting the mitochondrial genome and small (~1200) SNP sets for identity testing has been successfully applied to forensic casework, including degraded and chemically treated samples (16)(17)(18)(19). Yet due to the time and cost involved in hybridization capture, this method is not widely used in forensic casework, which can largely be solved using routine short tandem repeat (STR) typing or SNP arrays for genetic genealogy.…”

Section: Introductionmentioning

confidence: 99%

Extended kinship analysis of historical remains using SNP capture

Gorden¹,

Greytak

Sturk-Andreaggi

et al. 2020

Preprint

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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 ∼25,000 (25K) and ∼95,000 (95K) autosomal 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, with captured DNA having mean insert sizes ranging from 32-170 bp across the 14 samples. SNP comparison with DNA from known family references was performed in the Parabon Fχ Forensic Analysis Platform, which utilizes a likelihood approach for kinship prediction that was optimized for low-coverage sequencing data with DNA damage. The 25K and 95K panels produced 15,000 and 42,000 SNPs on average, respectively allowing for accurate kinship prediction in 17 and 19 of the 21 pairwise comparisons. Whole genome sequencing was not able to produce sufficient SNP data for accurate kinship prediction, demonstrating that hybridization capture is necessary for historical samples. This study provides the groundwork for the expansion of research involving compromised samples to include SNP hybridization capture.Author SummaryOur study evaluates ancient DNA techniques involving SNP capture and Next-Generation Sequencing for use in forensic identification. We utilized bone samples from 14 sets of previously identified historical remains aged 70 years postmortem for low-coverage SNP genotyping and extended kinship analysis. We performed whole genome sequencing and hybridization capture with two SNP panels, one targeting ∼25,000 SNPs and the other targeting ∼95,000 SNPs, to assess SNP recovery and accuracy in kinship estimation. A genotype likelihood approach was utilized for SNP profiling of degraded DNA characterized by cytosine deamination typical of ancient and historical specimens. Family reference samples from known relatives up to 4th degree were genotyped using a SNP microarray. We then utilized the Parabon Fχ Forensic Analysis Platform to perform pairwise comparisons of all bone and reference samples for kinship prediction. The results showed that both capture panels facilitated accurate kinship prediction in more than 80% of the tested relationships without producing false positive matches (or adventitious hits), which were commonly observed in the whole genome sequencing comparisons. We demonstrate that SNP capture can be an effective method for genotyping of historical remains for distant kinship analysis with known relatives, which will support humanitarian efforts and forensic identification.

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Applications of Probe Capture Enrichment Next Generation Sequencing for Whole Mitochondrial Genome and 426 Nuclear SNPs for Forensically Challenging Samples

Cited by 44 publications

References 60 publications

Update on the predictability of tall stature from DNA markers in Europeans

Update on the predictability of tall stature from DNA markers in Europeans

Potential use of human hair shaft keratin peptide signatures to distinguish gender and ethnicity

Extended kinship analysis of historical remains using SNP capture

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